Authors & Works cited in this section (citations below):

Agarwal, Sumeet. “Systems approaches in understanding evolution and evolvability.
Bach, Kent. “Language, Logic, and Form.
Benton, Michael. “The Red Queen and the Court Jester: Species Diversity and the Role of Biotic
Bos, E.P. & B. Sundholm. “History of Logic: Medieval.
Braakman, Rogier & Eric Smith. “The compositional and evolutionary logic of metabolism.
Bush, Andrew & R. Bambach. “Paleoecologic Megatrends in Marine Metazoa.”
Butterfield, Nicholas. “Macroevolution and macroecology through deep time.
Butterfield, Nicholas. “Animals and the invention of the Phanerozoic Earth system.”
Butterfield, Nicholas. “Modes of pre-Ediacaran multicellularity
Calvin, Sarah & V. Jirsa. “Perspectives on the Dynamic Nature of Coupling in Human
Caporael, Linnda. “Evolution, Groups, and Scaffolded Minds.”
Caporael, Linnda, Griesemer & Wimsatt. “Developing Scaffolds: An Introduction.
Carey, James. 1989. Communication As Culture: Essays on Media and Society
Costantini, M. & Sinigaglia. “Grasping Affordance: A Window onto Social Cognition.”
Costantini, Marcello, et al. “Where does an object trigger an action?
Davies, Paul. “Directionality principles from cancer to cosmology.
Davies, Jamie. Life Unfolding: How the human body creates itself
Davies, Paul. The Cosmic Blueprint: New Discoveries in Nature’s Creative Ability
Donoghue, M. “Key innovations, convergence, and success: macroevolutionary lessons from
Dreyfus, Hubert. “Introductory Essay: The Mystery of the Background qua Background.
Dunne, Jennifer et al. “Compilation and Network Analyses of Cambrian Food Webs.
Enfield, N.J. “Elements of Formulation.”
Erwin, Douglas. “Macroevolution of ecosystem engineering, niche construction and diversity
Farnsworth, Keith et al. “Living Is Information Processing: From Molecules to Global Systems.
Froese, Tom, N. Virgo & T. Ikegami. “Motility at the Origin of Life: Its Characterization
Froese, Tom & T. Fuchs. “The extended body: a case study in the neurophenomenology
George, Rolf & J. Van Evra. “The Rise of Modern Logic.
Gerson, Elihu. “Some Problems of Analyzing Cultural Evolution.
Gianelli, Claudi, C. Scorolli & A. Borghi. “Acting in perspective: the role of body and language
Gilbert, Scott, Sapp & Tauber. “A Symbiotic View of Life: We Have Never Been Individuals.
Godfrey-Smith, Peter. “Darwinian Individuals.”
Goodwin, Charles. “Contextures of Action.”
Gregory, Brad. The Unintended Reformation: How a Religious Revolution Secularized Society
Griesemer, James. “Reproduction and the Scaffolded Development of Hybrids.
Herzog, M. & Koch. “Seeing properties of an invisible object: Feature inheritance and shine-
Huys, Raoul. “The Dynamical Organization of Limb Movements.
Iddo, Tavory et al. “The Reproduction of the Social: A Developmental System Approach
Ingalls, Brian & P. Iglesias. “A Primer on Control Engineering.”
Jamshidi, Neema & Palsson. “Metabolic Network Dynamics: Properties and Principles.
Krakauer, David. “The inferential evolution of biological complexity: forgetting nature by
Malafouris, Lambros. How Things Shape the Mind: A Theory of Material Engagement
Mangano, M. & Buatois. “Decoupling of body-plan diversification and ecological structuring
Martijn, Joran & Ettema. “From archaeon to eukaryote: the evolutionary dark ages of
McNeely, Ian & Wolverton. Reinventing Knowledge: From Alexandria to the Internet
Morin, Edgar. On Complexity.
Morin, Francois. A World without Wall Street?
Morris, Simon Conway. “Life: the final frontier for complexity?
Newman, Stuart. “Excitable Media in Medias Res: How Physics Scaffolds Metazoan
Nicholson, Daniel. “Organisms ≠ Machines.”
Nunes-Neto, Nei, Moreno & El-Hani. “Function in ecology: an organizational approach.
Pezzulo, Giovanni. “The ‘Interaction Engine’: A Common Pragmatic
Quental, Tiago & Marshall. “How the Red Queen Drives Terrestrial Mammals to Extinction.
Reynolds, John. “How Are the Features of Objects Integrated into Perceptual Wholes
Rosenberger, Alfred. “Fallback Foods, Preferred Foods, Adaptive Zones, and Primate Origins.
Rospars, Jean-Pierre. “Trends in the evolution of life, brains and intelligence.
Ruiz-Mirazo, Kepa & A. Moreno. “Autonomy in evolution: from minimal to complex life.
Seigel, Jerrold. The Idea of the Self: Thought and Experience in Western Europe since
Smith, Kenny & S. Kirby. “Cultural evolution: implications for understanding
Smith, Robin. “Ancient Greek Philosophical Logic.
Smith, Eric. “Emergent order in processes: the interplay of complexity, robustness,
Spicher, Antoine et al. “Interaction-Based Simulations for Integrative Spatial Systems Biology
Streeck, Juergen, C. Goodwin & C. LeBaron. “Embodied Interaction in the Material World:
Sussman, Robert. D. Rasmussen & P. Raven. “Rethinking Primate Origins Again.
Theiner, Georg. “Onwards and Upwards with the Extended Mind: From Individual to Collective
Tomasello, Michael. A Natural History of Human Thinking.
Trestman, Michael. “The Cambrian Explosion and the Origins of Embodied Cognition.”
Wilson, Robert A. Genes and the Agents of Life: The Individual in the Fragile Sciences
Wimsatt, William. “Entrenchment and Scaffolding: An Architecture for a Theory of Cultural
Yokoo, Makoto. Distributed Constraint Satisfaction Foundations of Cooperation in Multi

Citations collected in 2014 (works listed above):

“Our ability to adopt a reflective attitude toward our own words and gestures – to regard and scrutinize them as our own objectivations – must have evolved from our primary ability to manufacture – and then behold, probe, and modify – meaningful things. Just like artifacts, words and gestures are external objects brought into existence by human action.” Streeck, Juergen, C. Goodwin & C. LeBaron. 2011. “Embodied Interaction in the Material World: An Introduction.” Pp. 1-26. From Streeck, Juergen, C. Goodwin & C. LeBaron. Embodied Interaction: Language and Body in the Material World. Cambridge University Press. P. 6.


“Cognitive scientists who conceive cognition as embodied widely agree on the following points:...

“(d) the original function of any brain is to control motion – only mobile organisms have brains; other functions of the brain must have evolved from this primary ability;...
“(f) perception and motor control are not separate in the brain; perceiving another human being’s action means producing an internal (i.e., inhibited, simulated) version of that action (this is known as common coding of motor-control and perception).”
Streeck, Juergen, C. Goodwin & C. LeBaron. 2011. “Embodied Interaction in the Material World: An Introduction.” Pp. 1-26. From Streeck, Juergen, C. Goodwin & C. LeBaron. Embodied Interaction: Language and Body in the Material World. Cambridge University Press. P. 7.


“In any communication setting, our richly multimodal flux of impressions is given order by the directing of mutual attention, in ‘pulses’ marked off in the flow of space and time, yielding sequences of contingent social action. These pulses of mutually attended social actions are called moves, following Goffman. A move can be defined as a unit contribution of communicative behavior constituting a single complete pushing forward of an interactional sequence by making some relevant social action recognizable (e.g., requesting the salt, passing the salt, saying Thanks with a smile).” Enfield, N.J. 2011. “Elements of Formulation.” Pp. 59-66. From Streeck, Juergen, C. Goodwin & C. LeBaron. Embodied Interaction: Language and Body in the Material World. Cambridge University Press. P. 61. Reference is to Goffman, Erving. 1981. Forms of talk. University of Pennsylvania Press.


“A line of research in developmental psychology has identified the onset of the pointing gesture as a watershed moment in the development of human social cognitive and communicative capacities, both ontogenetically and phylogenetically. As a species of move, pointing is the prototype, both in the sense of original precursor and common denominator.” Enfield, N.J. 2011. “Elements of Formulation.” Pp. 59-66. From Streeck, Juergen, C. Goodwin & C. LeBaron. Embodied Interaction: Language and Body in the Material World. Cambridge University Press. P. 61.


“A semiotic dimension is any independently variable component of perceptible form. Multiple semiotic dimensions can vary independently within a single modality. ‘Gesture,’ for example, is not a single dimension in this sense, because gestures are constructed from multiple semiotic dimensions. For example, a hand movement may be definable in terms of a set of independently variable features, like speed, acceleration, placement, and movement in three spatial dimensions – pitch, yaw, roll – and more, any one of which may be varied to modulate the meaning of the whole.” Enfield, N.J. 2011. “Elements of Formulation.” Pp. 59-66. From Streeck, Juergen, C. Goodwin & C. LeBaron. Embodied Interaction: Language and Body in the Material World. Cambridge University Press. P. 61.


“Interpreters do not calculate the meaning of a composite utterance by literally tallying up the meanings of its components. Instead, the elements of a composite utterance are understood with reference to a single, global construal.” Enfield, N.J. 2011. “Elements of Formulation.” Pp. 59-66. From Streeck, Juergen, C. Goodwin & C. LeBaron. Embodied Interaction: Language and Body in the Material World. Cambridge University Press. P. 63.


“The challenge for an interpreter faced with a composite utterance is to recover the relevance of each constituent sign to a single object of that move as a unified sign-vehicle, this object being the move’s informative intention.” Enfield, N.J. 2011. “Elements of Formulation.” Pp. 59-66. From Streeck, Juergen, C. Goodwin & C. LeBaron. Embodied Interaction: Language and Body in the Material World. Cambridge University Press. P. 64.


“... the organization of action and sign use that occurs here [analysis of dispute in girls’ playing hopscotch] is cooperative. This does not mean that actors are seeking solidarity and harmony.... Instead, cooperation refers to the way in which subsequent (as well as simultaneous) action is built by performing systematic operations on the sign complexes made publicly available by others.” Goodwin, Charles. 2011. “Contextures of Action.” Pp. 182-93. From Streeck, Juergen, C. Goodwin & C. LeBaron. Embodied Interaction: Language and Body in the Material World. Cambridge University Press. P. 183.


“Both action and the sign complexes used to accomplish action emerge within interactively sustained contextual configurations that link both diverse signs and differently positioned participants into common courses of action, within a continuous process of progressive transformation.” Goodwin, Charles. 2011. “Contextures of Action.” Pp. 182-93. From Streeck, Juergen, C. Goodwin & C. LeBaron. Embodied Interaction: Language and Body in the Material World. Cambridge University Press. P. 182.


“To be a speaker is thus to occupy a particular position within a dynamically unfolding interactive field structured through public sign use.” Goodwin, Charles. 2011. “Contextures of Action.” Pp. 182-93. From Streeck, Juergen, C. Goodwin & C. LeBaron. Embodied Interaction: Language and Body in the Material World. Cambridge University Press. P. 184.


“Human children appear preadapted to guess the rules of syntax correctly, precisely because languages evolve so as to embody in their syntax the most frequently guessed patterns. The brain has coevolved with respect to language, but languages have done most of the adapting. Deacon, Terrence. 1997. P. 122. Quoted in Smith, Kenny & Simon Kirby. “Cultural evolution: implications for understanding the human language faculty and its evolution.” Philosophical Transactions of The Royal Society – Biological Sciences. 2008. 363, Pp. 3591-3603. P. 3594.


“How does cultural selection for learnability explain compositionality? As discussed above, languages are infinitely expressive (due to the combination of recursion and compositionality). However, such languages must be transmitted through a finite set of learning data. We call this mismatch between the size of the system to be transmitted and its medium of transmission the learning bottleneck. Compositionality provides an elegant solution to this problem: to learn a compositional system, a learner must master a finite set of words and rules for their combination, which can be learned from a finite set of data but can generate a far larger system. This fit between the form of language (it is compositional) and a property of the transmission medium (it is finite but the system passing through it is infinite) is suggestive, and computational models of the iterated learning process have repeatedly demonstrated that cultural evolution driven by cultural selection for learnability can account for this goodness of fit.” Smith, Kenny & Simon Kirby. “Cultural evolution: implications for understanding the human language faculty and its evolution.” Philosophical Transactions of The Royal Society – Biological Sciences. 2008. 363, Pp. 3591-3603. P. 3594.


“Compositionality can therefore be explained as a cultural adaptation by language to the problem of transmission through a learning bottleneck.” Smith, Kenny & Simon Kirby. “Cultural evolution: implications for understanding the human language faculty and its evolution.” Philosophical Transactions of The Royal Society – Biological Sciences. 2008. 363, Pp. 3591-3603. P. 3595.


“Nevertheless, we argue that the current focus on spatial encapsulation in the service of both self-maintenance and natural selection remains an impoverished view of the phenomenon of life. Because the consensus only takes the two disparate time scales of chemical reactions and evolutionary history into account, it has failed to consider the relevance of the intermediate time scales of behavior and development.” Froese, Tom, N. Virgo & T. Ikegami. 2014. “Motility at the Origin of Life: Its Characterization and a Model.” Artificial Life 20: 55-76. P. 56.


“On this view, heredity can be based on the chemical composition of the system itself, which serves as a ‘compositional genome’.... Indeed, simulation models have demonstrated that under some conditions the growth and division of membrane-bounded autocatalytic systems is sufficient for differential replicative success.” Froese, Tom, N. Virgo & T. Ikegami. 2014. “Motility at the Origin of Life: Its Characterization and a Model.” Artificial Life 20: 55-76. P. 58.


“For instance, it has been shown that metabolic self-production can easily lead to spontaneous movement as well as adaptive gradient-following (i.e., chemotaxis) in minimal models of protocells.” Froese, Tom, N. Virgo & T. Ikegami. 2014. “Motility at the Origin of Life: Its Characterization and a Model.” Artificial Life 20: 55-76. P. 61.


“The upshot is that, at least in evolutionary terms, it does not matter if compartmentless individuals are more prone to die from adverse changes in environmental conditions, as long as they are able to replicate quickly and move to different areas fast enough.” Froese, Tom, N. Virgo & T. Ikegami. 2014. “Motility at the Origin of Life: Its Characterization and a Model.” Artificial Life 20: 55-76. P. 62.


“For the purpose of this article we define the concept of behavior broadly as a process in the relational individual-environment domain.” Froese, Tom, N. Virgo & T. Ikegami. 2014. “Motility at the Origin of Life: Its Characterization and a Model.” Artificial Life 20: 55-76. P. 65.


“One important distinction in biology and psychology is between reactive behavior, namely behavior that is directly triggered by events in the environment, and what we call intrinsic behavior, namely behavior that is spontaneously performed by the individual.” Froese, Tom, N. Virgo & T. Ikegami. 2014. “Motility at the Origin of Life: Its Characterization and a Model.” Artificial Life 20: 55-76. P. 65.


“The spots [graphics of a computer model of a theoretical reaction-diffusion system] are capable of following chemical gradients that increase the concentration of their constituents, which is akin to bacterial chemotaxis, and they are also capable of avoiding chemical gradients that decrease the concentration of their constituents.” Froese, Tom, N. Virgo & T. Ikegami. 2014. “Motility at the Origin of Life: Its Characterization and a Model.” Artificial Life 20: 55-76. Pp. 65-6.


“This gives the secondary autocatalyst the appearance of being attached as a tail behind the primary spot [graphics of a computer model of a theoretical reaction-diffusion system where a waste product not only decays but inhibits the autocatalysis of the primary reaction]. The spot-tail system as a whole moves around spontaneously even in a homogeneous environment. In the sense that this self-motility depends on the internal constitution of the whole spot-tail system itself, we can characterize it as a form of intrinsic, non-reactive behavior.” Froese, Tom, N. Virgo & T. Ikegami. 2014. “Motility at the Origin of Life: Its Characterization and a Model.” Artificial Life 20: 55-76. Pp. 67-8.


“More specifically, although the tail is parasitic on the primary spot (since it contributes nothing to it metabolically), their jointly induced movements in the system-environment domain can be adaptive in some environments. For instance, with certain parameter settings of the simulation, the spot-tail systems can reproduce more rapidly than the spots without tails, and their movement also tends to make them colonize new areas more rapidly.” Froese, Tom, N. Virgo & T. Ikegami. 2014. “Motility at the Origin of Life: Its Characterization and a Model.” Artificial Life 20: 55-76. P. 68.


“The important point is that what may be viewed as detrimental on the metabolic time scale (i.e., a parasitic reaction) can induce novelty on the behavioral time scale (i.e., self-motility), which then turns out to be adaptive on the evolutionary time scale (i.e., faster replication and wider population distribution).” Froese, Tom, N. Virgo & T. Ikegami. 2014. “Motility at the Origin of Life: Its Characterization and a Model.” Artificial Life 20: 55-76. P. 69.


“Thus, there is an enormous amount of information present in the retinal input of which the observer is completely oblivious. This striking reduction in the amount of information from what is implicitly present in the retinal input reflects the limited capacity of some stage (or stages) of sensory processing, decision making, or behavioral control. Somewhere between stimulating the retinae and generating a behavioral response, vast amounts of information are filtered out of the visual stream.” Reynolds, John. 2006. “How Are the Features of Objects Integrated into Perceptual Wholes That Are Selected by Attention?” Pp. 406-22. From Van Hemmen, J. Leo & T.J. Sejnowski. 23 Problems in Systems Neuroscience. Oxford University Press. Pp. 406-7.


“These studies [Single unit recording studies in awake, behaving monkeys] have shown that when attention is directed to a location in space, this boosts the responses of neurons that are selective for the stimulus appearing at the attended location, while suppressing neurons that would otherwise respond to stimuli appearing at unattended locations.” Reynolds, John. 2006. “How Are the Features of Objects Integrated into Perceptual Wholes That Are Selected by Attention?” Pp. 406-22. From Van Hemmen, J. Leo & T.J. Sejnowski. 23 Problems in Systems Neuroscience. Oxford University Press. P. 407.


“In summary, single-unit recording studies in monkeys trained to perform attentionally demanding tasks show that competitive circuits in extrastriate cortex can be biased in favor of behaviorally relevant stimuli, enabling the neurons they activate to elicit a response while suppressing the responses of neurons that are activated by ignored stimuli.” Reynolds, John. 2006. “How Are the Features of Objects Integrated into Perceptual Wholes That Are Selected by Attention?” Pp. 406-22. From Van Hemmen, J. Leo & T.J. Sejnowski. 23 Problems in Systems Neuroscience. Oxford University Press. Pp. 412-3.


“In all these studies, competing stimuli appeared at separate locations, and this confounds selection of locations with selection of objects. The observed competitive interactions could therefore reflect either competitive interactions among locations or competition between coherent objects. However, psychophysical and functional imaging paradigms developed to distinguish between object-based and spatial attention show that attention can select out whole objects for processing, and that this suppresses processing of other objects.” Reynolds, John. 2006. “How Are the Features of Objects Integrated into Perceptual Wholes That Are Selected by Attention?” Pp. 406-22. From Van Hemmen, J. Leo & T.J. Sejnowski. 23 Problems in Systems Neuroscience. Oxford University Press. Pp. 413-4.


“Early psychcophysical studies showed that observers can attend to one stimulus while suppressing another, even when the two stimuli are superimposed and cannot therefore be selected by spatial attention alone.” Reynolds, John. 2006. “How Are the Features of Objects Integrated into Perceptual Wholes That Are Selected by Attention?” Pp. 406-22. From Van Hemmen, J. Leo & T.J. Sejnowski. 23 Problems in Systems Neuroscience. Oxford University Press. P. 414.


“Subsequent studies have found that when an observer makes a judgment about one feature of an object (e.g., its color) simultaneous judgments about other features of the same object (e.g., its orientation and motion) do not interfere with the first judgment. This suggests that when attention is directed to one feature of an object, all of the features that make up the object are automatically selected together.” Reynolds, John. 2006. “How Are the Features of Objects Integrated into Perceptual Wholes That Are Selected by Attention?” Pp. 406-22. From Van Hemmen, J. Leo & T.J. Sejnowski. 23 Problems in Systems Neuroscience. Oxford University Press. P. 414.


“Mounting psychophysical evidence shows that attention can and does select out coherent objects for processing. When attention is directed to one feature of an object, other features of the same object can be evaluated at no additional cost, but judgments of feature[s] of unattended objects are impaired. Discovering where objects are represented as coherent wholes that can be selected by attention for processing is a major open question now confronting systems neuroscience.” Reynolds, John. 2006. “How Are the Features of Objects Integrated into Perceptual Wholes That Are Selected by Attention?” Pp. 406-22. From Van Hemmen, J. Leo & T.J. Sejnowski. 23 Problems in Systems Neuroscience. Oxford University Press. P. 420.


“Of particular interest for my purposes here, the CE (Cambrian Explosion) marks the appearance of animals with complex, active bodies (CABs). This is a cluster of related properties including: (1) articulated and differentiated appendages; (2) many degrees of freedom of controlled motion; (3) distal senses (e.g., ‘true’ eyes); (4) anatomical capability for active, distal-sense-guided mobility (fins, legs, jet propulsion, etc.); and (5) anatomical capability for active object manipulation (e.g., chelipeds, hands, tentacles, mouth-parts with fine-motor control).” Trestman, Michael. 2013. “The Cambrian Explosion and the Origins of Embodied Cognition.” Biological Theory. 8:80-92. P. 81.


“Today, these characteristics can be found together in only three lineages out of the (approximately) 34 described phyla of animals: arthropods, chordates, and mollusks (especially and perhaps exclusively cephalopods, e.g., squid, octopi, and cuttlefish).” Trestman, Michael. 2013. “The Cambrian Explosion and the Origins of Embodied Cognition.” Biological Theory. 8:80-92. P. 81.


“Marshall argues that by increasing the number of needs that animals had to satisfy in order to survive in a more hostile environment, the advent of predation roughened the fitness landscape for animals in general, and hence drove the increases in diversity and disparity as various lineages evolved different means of exploiting new food sources and protecting themselves from the changing array of predatory threats.” Trestman, Michael. 2013. “The Cambrian Explosion and the Origins of Embodied Cognition.” Biological Theory. 8:80-92. P. 86. Reference is to Marshall, C.R. 2006. “Explaining the Cambrian ‘explosion’ of animals.” Annual Review Earth Planetary Science. 34:355-384.


“Vision in the relevant sense is largely a matter not of the eye per se, but of the brain’s ability to extract information from patterns in light, and to make use of that information for controlling behavior in more sophisticated ways.” Trestman, Michael. 2013. “The Cambrian Explosion and the Origins of Embodied Cognition.” Biological Theory. 8:80-92. P. 87.


“What may have been most important for the CE was the spatial information that animals could suddenly see. Space had always been there, unseen.” Trestman, Michael. 2013. “The Cambrian Explosion and the Origins of Embodied Cognition.” Biological Theory. 8:80-92. P. 87.


“The CE marks the appearance of animals that could perceive, cognize, and move intelligently in space.” Trestman, Michael. 2013. “The Cambrian Explosion and the Origins of Embodied Cognition.” Biological Theory. 8:80-92. P. 87.


“Associative learning enhances adaptability during the lifetime of an animal, allowing it to exploit new resources.” Trestman, Michael. 2013. “The Cambrian Explosion and the Origins of Embodied Cognition.” Biological Theory. 8:80-92. P. 88.


“Ginsburg and Jablonka argue that as oxygen levels increased through the Ediacarian, animals increased in size, longevity and activity level. The increases in size and activity level drove a centralization of the nervous system, in order to allow integration of sensory inputs and coordination of motor outputs between regions of the body, even as the increase in longevity put a premium on learning from past experience, as the probability of situations recurring during a lifetime increased. Associative learning emerged simultaneously in many lineages (due to shared features of developmental gene-regulatory networks and neural net architecture) as the constraints on body size, metabolism and longevity due to oxygen availability were relaxed. This opened the door for adaptive behavior in the realms of habitat selection, niche construction, predation and anti-predation, driving the CE.” Trestman, Michael. 2013. “The Cambrian Explosion and the Origins of Embodied Cognition.” Biological Theory. 8:80-92. P. 88. Reference is to Ginsburg, S. & E. Jablonka. 2010. “The evolution of associative learning: a factor in the Cambrian explosion.” Journal of Theoretical Biology. 266(1):11-20.


“Furthermore, it is plausible that neurohormonal stress evolved early in the CE with the complexification of bodies and nervous systems, as (1) animals first became capable of energetic, coordinated, whole-body behavioral responses to danger; and (2) the importance of predation as a selection increased radically.

“Ginsburg and Jablonka argue that early in the Cambrian, phylogenetic diversification may have been extremely rapid because physiological stress had evolved, but physiological stress management had not.” Trestman, Michael. 2013. “The Cambrian Explosion and the Origins of Embodied Cognition.” Biological Theory. 8:80-92. Pp. 88-9. Reference is to Ginsburg, S. & E. Jablonka. 2010. “The evolution of associative learning: a factor in the Cambrian explosion.” Journal of Theoretical Biology. 266(1):11-20.


“BCE [Basic Cognitive Embodiment] is a cognitive toolkit for pickup, tracking, and use (for control of behavior) of certain information from the environment. The defining properties of BCE are that it is (1) spatial, (2) object-oriented, and (3) agentive or action-oriented.

“BCE is an awareness of spatial properties such as (1a) orientation to body (relative to the body’s structural axes and axes of active motion), and also to the body’s trajectory through space and other action capacities; (1b) distances (relative to action capacities); (1c) trajectories, rates of travel, and other spatial propensities; (1d) occlusion, concealment (including partial).

“BCE is also the ability to perceive and cognize in a way that is object-oriented. Objects, in the relevant sense, are co-tracked clusters of associated properties including: (2a) nonspatial properties such as colors, scents, flavors, and pitches; (2b) affordances (opportunities for behavioral exploitation, relative to bodily capacities and needs); (2c) spatial properties...

“Moreover, BCE is an agentive or action-oriented bodily self-awareness, i.e., an awareness of the animal’s own capacities for moving through space and influencing objects around it, including: (3a) judging distances relative to one’s own capacity for movement; (3b) canceling out sensory change caused by one’s own movements in order to build stable perception of the world; (3c) judging the relevance of objects and situations in the environment relative to the body’s needs and capacities.” Trestman, Michael. 2013. “The Cambrian Explosion and the Origins of Embodied Cognition.” Biological Theory. 8:80-92. Pp. 89-90.


“In particular, this [BCE] drove up the adaptive value of: (1) body structures facilitating locomotion, such as legs for walking or crawling, and fins, legs, lobes, and general musculature for swimming; (2) body structures facilitating manipulation of objects, in particular in the context of food-handling, such as anterior limbs mouth parts, chelicerae and antennules; (3) fancy distal exteroceptors such as improved eyes, better hearing, etc.; (4) improved capacity for memory, i.e., for learned associations between properties of salient objects and contexts; (5) canalization of development of adaptive perception/action patterns.” Trestman, Michael. 2013. “The Cambrian Explosion and the Origins of Embodied Cognition.” Biological Theory. 8:80-92. P. 90.


“... a lineage of animals cannot evolve CABs without first acquiring BCE. Therefore, the chief constraint determining whether or not a lineage evolves complex, active bodies is cognitive, rather than essentially genetic or environmental.” Trestman, Michael. 2013. “The Cambrian Explosion and the Origins of Embodied Cognition.” Biological Theory. 8:80-92. P. 91.


“The integrated evolution of primate diet and positional behavior is consistent with a growing reliance on angiospserm products–not prey–as preferred and seasonal fallback foods, temporally and phylogenetically coordinated with evolutionary phases of the angiosperm adaptive radiation.” Rosenberger, Alfred. 2013. “Fallback Foods, Preferred Foods, Adaptive Zones, and Primate Origins.” American Journal of Primatology. 75:883-890. P. 883.


“The primate/angiosperm co-evolution hypothesis ... was by definition a prevalent, driving factor in primate evolution.” Rosenberger, Alfred. 2013. “Fallback Foods, Preferred Foods, Adaptive Zones, and Primate Origins.” American Journal of Primatology. 75:883-890. P. 883.


“It is now evident from in-depth, long-term field studies across all radiations that primate feeding strategies are strongly influenced by shortages.... The selective role of uncommon foods was introduced in morphology as the critical-function hypothesis: in the interaction between organism and environment, behaviors that involve more challenging biomechanical requirements govern the evolution of form.” Rosenberger, Alfred. 2013. “Fallback Foods, Preferred Foods, Adaptive Zones, and Primate Origins.” American Journal of Primatology. 75:883-890. P. 884.


“Food scarcity is a fact of primate life, as even tropical forests are cyclically influenced by climate and weather, bringing the evolutionary roles of PFs [preferred foods] and SFBFs [seasonal fallback foods] sharply into focus.” Rosenberger, Alfred. 2013. “Fallback Foods, Preferred Foods, Adaptive Zones, and Primate Origins.” American Journal of Primatology. 75:883-890. P. 884.


“Faced with seasonally depleted PFs, primates do not migrate, hibernate, or cache food to tide them over like many other mammals. They switch to SFBFs. New leaves, mature leaves and vegetable matter rank highest as SFBFs, followed by fruits and animals,...” Rosenberger, Alfred. 2013. “Fallback Foods, Preferred Foods, Adaptive Zones, and Primate Origins.” American Journal of Primatology. 75:883-890. P. 884.


“For primates, several parameters and synergistic attributes frame the analysis. (1) Primates are an arboreal tropical radiation and experience seasonal food scarcity. (2) Fruits constitute the basic PF diet and vegetation remains favored as SFBFs during periods of scarcity. (3) Primate dentitions are characteristically eutherian-primitive, retaining a heterodont pattern without dramatic modifications for harvesting or processing a narrow food class. () Primates are athletic, generalized locomotors with prehensile cheiridia and deploy an enormous behavioral repertoire to meet ever-changing substrate conditions. (5) Primate vision emphasizes a centralized binocular gaze and good close-range depth perception as opposed to a large field of view and monocular peripheral vision.” Rosenberger, Alfred. 2013. “Fallback Foods, Preferred Foods, Adaptive Zones, and Primate Origins.” American Journal of Primatology. 75:883-890. P. 885.


“The first appearances of euprimates in the early Eocene co-occur with a burst of Tertiary angiosperm biodiversity and innovation, including an increase in seed size and predominance of closed-canopy forests, thus forging the critical link between diet and locomotion anticipated by Osborn.” Rosenberger, Alfred. 2013. “Fallback Foods, Preferred Foods, Adaptive Zones, and Primate Origins.” American Journal of Primatology. 75:883-890. P. 886. Reference is to Osborn, H.F. 1902. “The law of adaptive radiation.” American Naturalist. 36:353-63.


“Moreover, dynamical systems theory, which is the standard mathematical framework of the natural sciences, has also been successfully applied in cognitive science, thus forming a convenient interdisciplinary bridge from which to explore the mind-body problem.” Froese, Tom & T. Fuchs. 2012. “The extended body: a case study in the neurophenomenology of social interaction.” Phenomenology and the Cognitive Sciences. 11:205-235. P. 211.


“The guiding hypothesis is that through our mutual interactions with others our living and lived bodies become inextricably intertwined in a dynamical whole, thus forming an ‘extended body’ by which we enact and encounter the world together.” Froese, Tom & T. Fuchs. 2012. “The extended body: a case study in the neurophenomenology of social interaction.” Phenomenology and the Cognitive Sciences. 11:205-235. P. 211.


“First, the phenomenon of the extended body may be described as a form of pre-reflective face-to-face interaction, or embodied communication, which is taking place on the basis of an implicit inter-bodily resonance.” Froese, Tom & T. Fuchs. 2012. “The extended body: a case study in the neurophenomenology of social interaction.” Phenomenology and the Cognitive Sciences. 11:205-235. P. 212.


“This [interactions where feelings in one partner giving expressions which give impressions to other partner] creates a circular interplay of expressions and reactions running in split seconds and constantly modifying each partner’s bodily state, in a process that becomes highly autonomous and is not directly controlled by the partners.” Froese, Tom & T. Fuchs. 2012. “The extended body: a case study in the neurophenomenology of social interaction.” Phenomenology and the Cognitive Sciences. 11:205-235. P. 213.


“From early childhood on, patterns of interaction are sedimented in the infant’s implicit or bodily memory, resulting in what may be called inter-bodily or ‘intercorporeal memory.’ This means a pre-reflective, practical knowledge of how to interact with others–e.g., how to share pleasure, elicit attention, avoid rejection, re-establish contact, etc.” Froese, Tom & T. Fuchs. 2012. “The extended body: a case study in the neurophenomenology of social interaction.” Phenomenology and the Cognitive Sciences. 11:205-235. P. 213.


“However, when the live video of the mother was replaced with a video playback of her previously recorded actions, the infants became distressed or removed from the interaction. These results, and those of follow-up studies indicate that 2-month-old infants are sensitive to so-called ‘social contingency’, i.e., each other’s mutual responsiveness during an ongoing interaction, and that this sensitivity plays a fundamental role in the unfolding of the interaction process.” Froese, Tom & T. Fuchs. 2012. “The extended body: a case study in the neurophenomenology of social interaction.” Phenomenology and the Cognitive Sciences. 11:205-235. Pp. 215-6. Reference is to experimental results by Nadel, J., I. Carchon, C. Kervella, D. Marcelli & D. Reserbat-Plantcy. 1999. “Expectancies for social contingency in 2-month-olds.” Developmental Science. 2(2): 164-173.


“The basic take-home message is: when we consider two or more interacting nonlinear dynamical systems (e.g., two agents) as a single, integrated system (e.g., an interaction process), we can observe novel systemic properties that cannot be reduced to the properties of the isolated components.” Froese, Tom & T. Fuchs. 2012. “The extended body: a case study in the neurophenomenology of social interaction.” Phenomenology and the Cognitive Sciences. 11:205-235. P. 216.


“The essential features of the ‘extended body’ have already been illustrated above. First, there must be at least two embodied agents in a shared environment, each with a capacity for producing expressions and receiving impressions. Second, the body of each agent must consist of distinguishable parts, which can mutually influence each other’s activity. This [is] a necessary condition for the possibility of intra-bodily resonance. Third, the agents must be able to interactively coordinate their behaviors such that a recursive interaction process can be established. This is a necessary condition for the possibility of inter-bodily resonance.” Froese, Tom & T. Fuchs. 2012. “The extended body: a case study in the neurophenomenology of social interaction.” Phenomenology and the Cognitive Sciences. 11:205-235. P. 217.


“Here [two agent computer simulation] we thus have a basic dynamical account of the extended body: the behavior of the agents gives rise to an interaction process, which in turn transforms the agents’ internal conditions of behavior generation, such that their behavior in fact becomes more suited to further sustain the interaction process, and so forth. Not only do the agents make use of each other’s responsive presence to bootstrap into a more flexible behavioral domain, this process itself is a self-organized outcome of the self-maintaining interaction process that has emerged from their mutually responsive behavior. The bodies of the two simulated agents have become intertwined into one extended body through the interaction process.

“Thus, in contrast to the claims of classical cognitive science, the model has demonstrated that behavioral sensitivity to social contingency in actual experimental situations does not in principle require complex cognitive modules based on inner representations or mental simulation routines. Instead, it is also possible that such social behavior is an interactive achievement based on the dynamical principles of bodily extension that we have analyzed. Moreover, given that the extended body is an emergent outcome that is distributed across two or more agents, it places less demands on the cognitive capacities of the individuals than the cognitivist account.” Froese, Tom & T. Fuchs. 2012. “The extended body: a case study in the neurophenomenology of social interaction.” Phenomenology and the Cognitive Sciences. 11:205-235. P. 223.


“If instead we use the terminology of a continuous dynamical system to describe time consciousness, then the past can be conceived more like a holistic reservoir, and the continuous modification and degradation of memory thereby becomes an intrinsic aspect of temporality.” Froese, Tom & T. Fuchs. 2012. “The extended body: a case study in the neurophenomenology of social interaction.” Phenomenology and the Cognitive Sciences. 11:205-235. P. 224.


“The reform in thinking is a key anthropological and historical problem. This implies a mental revolution of considerably greater proportions than the Copernican revolution. Never before in the history of humanity have the responsibilities of thinking weighed so crushingly on us.” Morin, Edgar. 2008. On Complexity. Hampton Press. Translated by Robin Postel. P. vii.


“For three centuries, science has been dominated by the Newtonian and thermodynamic paradigms, which present the universe as either a sterile machine, or in a state of degeneration and decay. Now there is the paradigm of the creative universe, which recognizes the progressive, innovative character of physical processes. The new paradigm emphasizes the collective, cooperative, and organizational aspects of nature; its perspective is synthetic and holistic rather than analytic and reductionistic.” Davies, Paul. 1989. The Cosmic Blueprint: New Discoveries in Nature’s Creative Ability to Order the Universe. Simon & Schuster. P. 2. Cited in Morin, Edgar. 2008. On Complexity. Hampton Press. Translated by Robin Postel. P. xxix.


“It is important to point out right away the difference of level between the organizationism that we think is necessary, and traditional organicism. Organicism is a syncretic, historic, confused, romantic concept. Its starting point is from an organism conceived as an organized, harmonious totality, even when it carries within it antagonism and death. From this starting point, organicism makes of the organism a model both of the macrocosm (the organicist concept of the universe) and of human society. Therefore, a whole sociological current in the last century wanted to find in society an analogue of the animal organism, by looking meticulously for equivalencies between biological and social life.

“Organizationism, on the other hand, seeks not to discover phenomenal analogies, but to find the common principles of organization, the principles of evolution of these principles, the characteristics of their diversification.” Morin, Edgar. 2008. On Complexity. Hampton Press. Translated by Robin Postel. P. 15.


“But driven from science, the subject takes its revenge in morals, metaphysics, and ideology. Ideologically, it is the fabric of humanism, the human religion considering that the subject reigns, or should reign, over a world of objects.” Morin, Edgar. 2008. On Complexity. Hampton Press. Translated by Robin Postel. P. 24.


“King of the universe, guest of the universe, the subject spreads out in the kingdom unoccupied by science.” Morin, Edgar. 2008. On Complexity. Hampton Press. Translated by Robin Postel. P. 24.


“The subject is the unknown because it is indeterminate, because it is a mirror, because it is foreign, because it is a totality. Therefore, in the science of the West, the subject is the all-nothing–nothing exists without it, but everything excludes it. It is the fabric of all truth, but at the same time it is nothing more than ‘noise’ and error next to the object.” Morin, Edgar. 2008. On Complexity. Hampton Press. Translated by Robin Postel. P. 25.


“We hypothesize that our earliest primate relatives were likely exploiting the products of co-evolving angiosperms, along with insects attracted to fruits and flowers, in the slender supports of the terminal branch milieu. This has been referred to as the primate/angiosperm co-evolution theory.” Sussman, Robert. D. Rasmussen & P. Raven. 2013. “Rethinking Primate Origins Again.” American Journal of Primatology. 75: 95-106. P. 95.


“The Paleocene-Eocene boundary was a period of rapid change involving notably the culmination of a warming trend and widespread tropical to subtropical conditions (the Early Eocene Climatic Optimum, ca. 56-48 Myr), when mean annual temperature increased by ca. 6̊ C over already very warm global conditions. This involved concurrent adaptive shifts in a number of plant and animal groups, including primates. These shifts seem to have begun earlier, before the temperature peak, at around 70 Ma (64-78 Ma), a time in which the angiosperm component of floras had increased from 0% to 80% (80-125 Ma); this is considered a key event for the diversification of birds and mammals.” Sussman, Robert. D. Rasmussen & P. Raven. 2013. “Rethinking Primate Origins Again.” American Journal of Primatology. 75: 95-106. P. 99.


“It cannot be understated that angiosperm products necessarily will have insects associated with them; from the point of view of an early primate foraging in terminal branches, angiosperm products, and insects are found conveniently together with great reliability.” Sussman, Robert. D. Rasmussen & P. Raven. 2013. “Rethinking Primate Origins Again.” American Journal of Primatology. 75: 95-106. P. 100.


“Gomez & Verdu combined phylogenetic, neontological, and paleontological data to show that a facultative mutualistic plant-animal interaction emerging from frugivory and seed dispersal contributed to the diversification of primates.” Sussman, Robert. D. Rasmussen & P. Raven. 2013. “Rethinking Primate Origins Again.” American Journal of Primatology. 75: 95-106. P. 101. Reference is to Gomez, J.M. & M. Verdu. 2012. “Mutualism with plants drives primate-diversification.” Syst Biol. 61: 567-577.


“Recently, Changizi & Shimojo and Changizi have proposed the “X-ray vision’ hypothesis for the evolution of primate visual adaptations. They propose that the degree of binocular convergence is selected to maximize how much of its environment a mammal can see. Using data from 319 species and 17 orders of mammals, they found that, in ‘noncluttered’ or ‘nonleafy’ environments, mammals can see the most of their surroundings with panoramic, laterally directed eyes. On the other hand, in cluttered environments such as dense forest canopy, mammals can see more of their environment when their eyes face forward, because binocularity has the power of ‘seeing through’ the leaf clutter.” Sussman, Robert. D. Rasmussen & P. Raven. 2013. “Rethinking Primate Origins Again.” American Journal of Primatology. 75: 95-106. P. 102. References: Changizi, M.A. & S. Shimojo. 2008. “‘X-ray vision’ and the evolution of forward-facing eyes.” J Theoretical Biol 254: 756-767. Changizi, M.A. 2009. The Vision Revolution. BenBella Books.


“Ferri, Campione, Dalla Volta, Gianelli and Gentilucci compared the kinematics of reaching, grasping and placing a piece of food into the mouth of another person or into a mouth-like aperture. Results showed that, while interacting with another person, a special kind of interaction with the object is activated (social affordance), which leads to an increase of accuracy during the movement execution (slowing down of both the reaching and placing movement).” Gianelli, Claudi, C. Scorolli & A. Borghi. 2013. “Acting in perspective: the role of body and language as social tools.” Psychological Research. 77: 40-52. P. 41. Reference is: Ferri, F, G. Campione, R. Dalla Volta, C. Gianelli & M. Gentilucci. 2011. “Social requests and social affordances: how they affect the kinematics of motor sequences during interactions between conspecifics.” PLoS ONE 6(1), e15855.


“Overall, these studies [of social affordances in interactive behavior] show that we respond to objects differently when we are on our own and when we interact with others.” Gianelli, Claudi, C. Scorolli & A. Borghi. 2013. “Acting in perspective: the role of body and language as social tools.” Psychological Research. 77: 40-52. P. 41.


“One key issue for embodied cognition is to understand how the way we interact with objects is influenced by the constraints given by our own physical body and by the physical and social context. Our results clearly showed that not only our body, the body of others and their position with respect to us and to objects, but also the social relationship with other people, influence actions. The pattern of results reveals that the reach-to-grasp kinematics is affected by the variables we identified (relative position, social relationship, speaker and pronoun) in a complex interplay.” Gianelli, Claudi, C. Scorolli & A. Borghi. 2013. “Acting in perspective: the role of body and language as social tools.” Psychological Research. 77: 40-52. P. 47.


“The interaction between social relationship and position suggests that maximal finger aperture occurred earlier with non-friends than with friends, probably because the agent interpreted the other as a potential competitor with respect to the object.” Gianelli, Claudi, C. Scorolli & A. Borghi. 2013. “Acting in perspective: the role of body and language as social tools.” Psychological Research. 77: 40-52. P. 47.


“The interaction between relative position and speaker in the latency of maximal fingers aperture revealed that the shortest latencies were obtained when the other was frontal-near to the agent, and spoke. This result, which is quite novel, suggests that the simple fact of speaking can be considered as a form of action; the action of speaking increases the visibility and the potential ‘danger’ of the other.” Gianelli, Claudi, C. Scorolli & A. Borghi. 2013. “Acting in perspective: the role of body and language as social tools.” Psychological Research. 77: 40-52. P. 48.


“Third, the idea that language is a way to act and to direct attention is further supported by the interaction we found between speaker and pronoun, characterizing the reaching phase. The interaction between speaker and pronoun in the %RT [reaching time respective to the overall movement which is defined as the maximum kinetic movement time including finger opening and reaching] reveals that, when the other was speaking, the percentage of movement time devoted to the reaching phase was shorter with the ‘I’ pronoun. Notice that, when the other used the ‘I’ pronoun, no action of the other followed. In spite of this, it seemed that participants predicted that the other wold interact with the object, and this speeded up their reaching responses.” Gianelli, Claudi, C. Scorolli & A. Borghi. 2013. “Acting in perspective: the role of body and language as social tools.” Psychological Research. 77: 40-52. P. 48.


“Our study questions the idea that affordances are only individual action opportunities. Rather, results suggest that responses to objects are influenced by the complex social and physical context in which they are embedded.” Gianelli, Claudi, C. Scorolli & A. Borghi. 2013. “Acting in perspective: the role of body and language as social tools.” Psychological Research. 77: 40-52. P. 48.


“According to embodied theories during language comprehension, the same perception, action and emotional systems are recruited, which are at play during interaction with objects and with others. Evidence has successfully demonstrated that concrete words, such as ‘telephone’, activate multimodal experiences with their referents,...” Gianelli, Claudi, C. Scorolli & A. Borghi. 2013. “Acting in perspective: the role of body and language as social tools.” Psychological Research. 77: 40-52. P. 48.


“A demonstration that words are tools even comes from evidence showing that words lead us to perceive objects as more close to us than they are in reality.” Gianelli, Claudi, C. Scorolli & A. Borghi. 2013. “Acting in perspective: the role of body and language as social tools.” Psychological Research. 77: 40-52. P. 49.


“Flavell, Green & Flavell distinguished between two levels of visuo-spatial perspective taking (VPT): the first concerns the comprehension of what lies within somebody else’s line of sight (in front of vs. behind, VPT-1), the second implies some form of mental rotation (e.g., aimed at determining that an object is on the right of another object from somebody else’s point of view, VPT-2). VPT-1 develops earlier, around 2 years of age, and is characteristic of primates as well; VPT-2, instead, is more complex, develops later and children with autistic spectrum disorder experience some difficulties with this kind of VPT.” Gianelli, Claudi, C. Scorolli & A. Borghi. 2013. “Acting in perspective: the role of body and language as social tools.” Psychological Research. 77: 40-52. P. 49. Reference is Flavell, J.H., F. Green & E. Flavell. 1986. “Development of knowledge about the appearance-reality distinction.” Monographs of the Society for Research in Child Development. 1(i-v), 1-87.


“Levinson has convincingly argued that a prelinguistic interaction engine constitutes the pragmatic foundation that supports language and produces its universals. In this view, the pragmatic functions include multiple abilities (communicative and extra-communicative) intention attribution, multimodal signaling (using gestures, facial expressions, etc.), mastery of the ‘give and take of interaction’, turn-taking, the use of functions such as denying, requesting, greeting, and ultimately the ability to engage in cooperative activities and to pursue common objectives. These interactional abilities do not derive from language but provide a foundation for it. Many other scholars, such as Wittgenstein, Austin, Grice, Leech, Barwise and Perry, Clark, Sperber and Wilson, Tomasello, and Bara, while having distinct perspectives, all have acknowledged the relations between language and action-based pragmatic competence.” Pezzulo, Giovanni. 2012. “The ‘Interaction Engine’: A Common Pragmatic Competence Across Linguistic and Nonlinguistic Interactions.” IEEE Transactions on Autonomous Mental Development. 4(2): 105-23. Pp. 105-6. Reference is to Levinson, S.C. 2006. “On the human interaction engine.” From Enfield, N. J. & S. Levinson, Eds. Roots of Human Sociality: Culture, Cognition and Interaction. Berg. Pp. 39-69.


“In particular, we emphasize the importance of joint action dynamics in communicative domains, linguistic and nonlinguistic.” Pezzulo, Giovanni. 2012. “The ‘Interaction Engine’: A Common Pragmatic Competence Across Linguistic and Nonlinguistic Interactions.” IEEE Transactions on Autonomous Mental Development. 4(2): 105-23. P. 106.


“In this sense, [that most interactions can be communicated verbally or non-verbally] Speech acts such as asking a question, requesting help, challenging somebody, or informing somebody can be considered as linguistically mediated versions of nonlinguistic behaviors that express the same communicative intentions in nonlinguistic interactions.” Pezzulo, Giovanni. 2012. “The ‘Interaction Engine’: A Common Pragmatic Competence Across Linguistic and Nonlinguistic Interactions.” IEEE Transactions on Autonomous Mental Development. 4(2): 105-23. P. 106.


“In sum, we hypothesize that during evolution, linguistic communication reused the neurocognitive mechanisms (such as intention recognition mechanisms, mechanisms for orienting social attention, pointing at objects) originally developed by nonlinguistic primates for conveying and recognizing nonverbal communicative intentions, and for achieving joint goals.” Pezzulo, Giovanni. 2012. “The ‘Interaction Engine’: A Common Pragmatic Competence Across Linguistic and Nonlinguistic Interactions.” IEEE Transactions on Autonomous Mental Development. 4(2): 105-23. P. 107.


“It is worth noting that our arguments on reuse [that during evolution linguistic competence developed on top of the sophisticated action and gesture system of nonlinguistic primates] apply at the evolutionary level only. If we focus on cognitive development, we observe that children codevelop the pragmatics of action and language.” Pezzulo, Giovanni. 2012. “The ‘Interaction Engine’: A Common Pragmatic Competence Across Linguistic and Nonlinguistic Interactions.” IEEE Transactions on Autonomous Mental Development. 4(2): 105-23. P. 107.


“From a computational viewpoint, affordances can be considered as enhancing the prior probability P(A) of certain actions in the mere presence of objects.” Pezzulo, Giovanni. 2012. “The ‘Interaction Engine’: A Common Pragmatic Competence Across Linguistic and Nonlinguistic Interactions.” IEEE Transactions on Autonomous Mental Development. 4(2): 105-23. P. 110.


“... the objective of performing communicative actions and speech acts is changing the observer’s cognitive (hidden) variables rather than its behavior.” Pezzulo, Giovanni. 2012. “The ‘Interaction Engine’: A Common Pragmatic Competence Across Linguistic and Nonlinguistic Interactions.” IEEE Transactions on Autonomous Mental Development. 4(2): 105-23. P. 112.


“Shared representations can be formed unintentionally or intentionally, and through at least three mechanisms: entrainment, motor simulation and signaling strategies.” Pezzulo, Giovanni. 2012. “The ‘Interaction Engine’: A Common Pragmatic Competence Across Linguistic and Nonlinguistic Interactions.” IEEE Transactions on Autonomous Mental Development. 4(2): 105-23. P. 113.


“... turns in dialogs achieve two objectives: first, they carry on the interactive process, and second, they give evidence about the speaker’s understanding of the content of the preceding interaction.” Pezzulo, Giovanni. 2012. “The ‘Interaction Engine’: A Common Pragmatic Competence Across Linguistic and Nonlinguistic Interactions.” IEEE Transactions on Autonomous Mental Development. 4(2): 105-23. P. 116.


“Levinson convincingly argues that certain aspects of verbal communication, such as the possibility to address many persons at once, favor the formation of larger groups and of more complex interactions than nonverbal communication.” Pezzulo, Giovanni. 2012. “The ‘Interaction Engine’: A Common Pragmatic Competence Across Linguistic and Nonlinguistic Interactions.” IEEE Transactions on Autonomous Mental Development. 4(2): 105-23. P. 120.


“We make the case that interaction strategies (and dynamics), rather than additional cognitive mechanisms, keep the computational problems of language processing within tractable boundaries.” Pezzulo, Giovanni. 2012. “The ‘Interaction Engine’: A Common Pragmatic Competence Across Linguistic and Nonlinguistic Interactions.” IEEE Transactions on Autonomous Mental Development. 4(2): 105-23. P. 120.


“Whereas in a machine the size, shape, and structure of the whole is invariably determined by that of its parts, in an organism the size, shape, and structure of the parts do not suffice to account for that of the whole given that the whole has a determining influence on its parts.” Nicholson, Daniel. 2013. “Organisms ≠ Machines.” Studies in History and Philosophy of Biological and Biomedical Sciences. 44: 669-678. P. 672.


“Following Bradie, we can distinguish theoretical heuristic and rhetorical functions for metaphors in science. Metaphors with a theoretical function are central to scientific understanding, as they provide the foundation for the conceptualization, representation, and explanation of the target phenomenon. Metaphors with a heuristic function constitute methodological tools that facilitate the empirical investigation of the target phenomenon. And metaphors with a rhetorical function are employed in scientific communication to inform and educate non-specialists about the target phenomenon.” Nicholson, Daniel. 2013. “Organisms ≠ Machines.” Studies in History and Philosophy of Biological and Biomedical Sciences. 44: 669-678. P. 674.


“An organism in the initial stages of development cannot be studied as an assemblage of machine subunits because in it all functions are still assumed by the organism as a whole....

“It is only with the progressive differentiation of the embryo that the originally unitary action of the organism becomes partitioned into a myriad of individual actions, and it is at this later developmental stage that local machine-like structures within the organism begin to emerge, thus rendering the MCO [machine conception of the organism] of increasing heuristic value.” Nicholson, Daniel. 2013. “Organisms ≠ Machines.” Studies in History and Philosophy of Biological and Biomedical Sciences. 44: 669-678. P. 675.


“Zeno’s arguments take a particular form: beginning with premises accepted by his opponent, they derive conclusions that the opponent must recognize as impossible. Aristotle says that in introducing this form of argument, Zeno was the originator of ‘dialectic’. The meaning of this word is contested by scholars, but we may note three features of Zeno’s argument: (1) it is directed at someone else; (2) it takes its start from premises accepted by that other party; (3) its goal is the refutation of a view of that other party. These three characteristics can serve as a rough definition of a dialectical argument.” Smith, Robin. 2002. “Ancient Greek Philosophical Logic.” Pp. 11-23. From Jacquette, Dale (Ed.). A Companion to Philosophical Logic. Blackwell. P. 12.


“These names, under which the discipline has been known, relate to different aspects of logic, or of how the subject should be seen. ‘Logic,’ thus, would be the study of (the use of words for making) reasoned claims, and ‘Analytics’ resolves reasoning into simpler parts in order to provide grounds. ‘Dialectics’ grounds reasoning in (eternal) relations between logical entities, whereas when logic is thought of as an organon, it serves as the tool for multiplying knowledge through the use of reasoning.

“The purely formal logic of today is regularly confined to theory of (logical) consequence between well-formed formulas (WFFs). An analogous position within medieval logic would cover only the topics dealt with in the Prior Analytics. Medieval logic, however, covers a much wider range: it comprises also topics from philosophy of language, for example the theories of signification and supposition (reference), epistemology, for example the theory of demonstration, and philosophy of science (methodology), for example the method of analysis and synthesis. Indeed, logic is sometimes divided into Formal logic versus Material logic, which correspond to Aristotle’s two Analytics, and cover, respectively, the theory of consequence and the theory of demonstrations (or proofs). Today’s logician is primarily a ‘dialectician’ who studies relations among logical entities, be they meaningful sentences, (abstract) propositions, or the well-formed formulae of a formal language. The medieval logician, on the other hand, was primarily concerned with the exercise of the faculties of the intellect. The use of reasoning as part of the (human) act of demonstration was his main concern.” Bos, E.P. & B. Sundholm. 2002. “History of Logic: Medieval.” Pp. 24-34. From Jacquette, Dale (Ed.). A Companion to Philosophical Logic. Blackwell. Pp. 24-5.


“In medieval logic there is a complete parallelism between thought and reality, between mind and world. The important idea of carrying out purely mechanical, ‘formal,’ proofs, irrespective of content, emerges only with Leibniz, and does not yet form part of the medieval tradition in logic.” Bos, E.P. & B. Sundholm. 2002. “History of Logic: Medieval.” Pp. 24-34. From Jacquette, Dale (Ed.). A Companion to Philosophical Logic. Blackwell. P. 26.


“The language studied by medieval logicians is a highly stylized, technical Latin, with rigid syntactic rules and clear meaning and in this it resembles, not our current metalinguistic predicate-calculus, but rather those interpreted formal languages that were used by Frege and others to inaugurate modern logic.” Bos, E.P. & B. Sundholm. 2002. “History of Logic: Medieval.” Pp. 24-34. From Jacquette, Dale (Ed.). A Companion to Philosophical Logic. Blackwell. P. 27.


“Another very interesting, late addition to medieval logic is the theory of obligations, which is concerned with the proper rules for disputation and questioning. Thus, for instance, if I have asserted a conjunctive proposition, I have incurred an obligation and might be held to be asserting each conjunct separately. This theory lies on the borderline between logic, semantics, and pragmatics, incorporating also elements of the theory of speech acts.” Bos, E.P. & B. Sundholm. 2002. “History of Logic: Medieval.” Pp. 24-34. From Jacquette, Dale (Ed.). A Companion to Philosophical Logic. Blackwell. P. 31.


“Gottfried Wilhelm Leibniz was the great exception to the logic bashing of the seventeenth and eighteenth centuries. He saw the general outline of what logic would much later become, but left only fragments of a ‘universal characteristic’ through which it would be become possible, he thought, to settle philosophical disputes through calculation.” George, Rolf & J. Van Evra. 2002. “The Rise of Modern Logic.” Pp. 35-48. From Jacquette, Dale (Ed.). A Companion to Philosophical Logic. Blackwell. P. 36.


“While claiming earlier that the logician must know the human soul and cannot proceed without psychology, he [Kant] now held that ‘pure logic derives nothing from psychology.’

“Kant made two widely accepted distinctions: (1) he contrasted ‘organon’ and ‘canon.’ An organon (Kant uses the word in the sense Bacon gave it in the Novum Organum) attempts to codify methods of discovery. But ‘logic serves as a critique of the understanding ... not for creation.’ He sensibly held that there is no universal method of discovery, which rather requires a grasp of the special science that is to be advanced. But since logic must be general, attending only to form and not to content, it can only be a canon, a method of evaluation. Methodological rules and theories of the origin and association of ideas, though intended as improvements of logic, are not even part of. (2) Kant further divided logic into theoretical and practical. The latter, important but derivative, dealt with honing the skill of reasoning and disputation, while logic proper is a theoretical inquiry.” George, Rolf & J. Van Evra. 2002. “The Rise of Modern Logic.” Pp. 35-48. From Jacquette, Dale (Ed.). A Companion to Philosophical Logic. Blackwell. P. 37.


“Peirce introduced the memorable division of arguments into deduction, induction, and hypothesis, the last also called abduction and, more recently, ‘inference to the best explanation.’ He illustrated them as follows, using the then common terms ‘Rule’ for the major premise, ‘Case’ for the minor, and ‘Result’ for the conclusion of a categorical syllogism:

“Deduction: Rule: All the beans in this bag are white.
Case: These beans are from this bag.
∴ Result: These beans are white.
“Induction: Rule: These beans are from this bag.
Case: These beans are white.
∴ Result: All the beans in this bag are white.
“Hypothesis: Rule: All the beans in this bag are white.
Case: These beans are white.
∴ Result: These beans are from this bag.”
George, Rolf & J. Van Evra. 2002. “The Rise of Modern Logic.” Pp. 35-48. From Jacquette, Dale (Ed.). A Companion to Philosophical Logic. Blackwell. P. 42.


“They [philosophers] have supposed as Russell did in the case of sentences containing definite descriptions, that grammatical form is often misleading as to logical form. From a linguistic point of view, however, logical form is a level of syntactic structure. The logical form of a sentence is a property of the sentence itself, not just of the proposition it expresses or of the formula used to symbolize it. From this perspective, it makes no sense to say that grammatical form is misleading as to logical form.

“If logical form is a property of sentences themselves and not merely of the propositions they express or of the formulas used to symbolize them, it must be a level of grammatical form. It is that level which provides the input to semantic interpretation, the output of which consists of interpreted logical forms. This is on the supposition that natural language semantics is compositional, and that the semantics of a sentence is a projection of its syntax. Anything short of that puts the notion of logical form in a different light.” Bach, Kent. 2002. “Language, Logic, and Form.” Pp. 51-72. From Jacquette, Dale (Ed.). A Companion to Philosophical Logic. Blackwell. P. 68.


“‘[I]n order to be able to assert a truth, the actual subject must in the first place have a world or be in the world, that is, sustain round about it a system of meanings whose reciprocities, relationships and involvements do not require to be made explicit in order to be exploited.’

“Indeed, as Homer already knew [as Odysseus counseled Telemakos not to ask questions about the background light as they hid the suitors’ weapons but to leave the background to the Olympians], these background involvements and reciprocities cannot be made explicit and continue to function. They are a field of forces, not an aggregate of isolable intentional states like Husserl’s sedimented validities.” Dreyfus, Hubert. 2012. “Introductory Essay: The Mystery of the Background qua Background.” Pp. 1-10. From Radman, Zdravko. Knowing without Thinking: Mind, Action, Cognition and the Phenomenon of the Background. Palgrave Macmillan. P. 7. Subquote is from Merleau-Ponty, M. 1962. Phenomenology of Perception. Translated by C. Smith. Routledge & Kegan Paul. P. 129.


“A constraint satisfaction problem is a general framework that can formalize various application problems in artificial intelligence.” Yokoo, Makoto. 2001. Distributed Constraint Satisfaction Foundations of Cooperation in Multi-agent Systems. Springer. P. 1.


“These algorithms [for solving constraint satisfaction problems] can be divided into two groups, i.e., search algorithms and consistency algorithms. Consistency algorithms are performed before applying search algorithms to reduce futile search efforts. Furthermore, search algorithms can be divided into two groups, i.e., systematic depth-first tree search algorithms called back-tracking and hill-climbing algorithms called iterative improvement.” Yokoo, Makoto. 2001. Distributed Constraint Satisfaction Foundations of Cooperation in Multi-agent Systems. Springer. Pp. 1-2.


“Therefore, a trial-and-error exploration of alternatives is inevitable for solving constraint satisfaction problems.” Yokoo, Makoto. 2001. Distributed Constraint Satisfaction Foundations of Cooperation in Multi-agent Systems. Springer. P. 2.


“A distributed constraint satisfaction problem is a constraint satisfaction problem in which the variables and constraints are distributed among automated agents. Finding a value assignment to variables that satisfies inter-agent constraints can be viewed as achieving coherence or consistency among agents.” Yokoo, Makoto. 2001. Distributed Constraint Satisfaction Foundations of Cooperation in Multi-agent Systems. Springer. P. 47.


“Post-Gibson attempts to highlight what affordances are have mainly emphasized the mutuality of organism and environment in defining them....

“Here, we refine the notion of affordance by providing empirical data showing that the affordance relation, at least in the case of a situated object, is based not only on the mutual appropriateness of its constituent relata (i.e., objectual features and individual’s motor abilities) but also on their spatial relationship.” Costantini, Marcello, E. Ambrosini, G. Tieri, C. Sinigaglia & G. Committeri. 2010. “Where does an object trigger an action? An investigation about affordances in space.” Exp Brain Res. 207:95-103. P. 101.


“The dynamicity of the structure of a biological system have been repeatedly emphasized, and several formalisms have been proposed to specify both the evolution of states and the evolution of the structure. Examples include: the concept of (hyper)-cycle introduced by Eigen and Schuster in the study of auto-catalytic networks, the notion of autopoietic systems formulated by Varela et al, Luisi, the variable structure system theory developed in control (Itkis 1976), or the concept of organization introduced by Fontana and Buss to formalize and study the emergence of self-maintained functional structures in a range of chemical reactions.

“We call such systems dynamical systems with a dynamical structure ....” Spicher, Antoine, O. Michel & J-L. Giavitto. 2011. “Interaction-Based Simulations for Integrative Spatial Systems Biology.” Pp. 195-232. From Dubitzky, W., J. Southgate & H. Fuss. Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology. Springer. P. 199.


“Over the last 25 years or so, the notion that (perceptual) motor behavior may be conceived of in terms of dynamical structures, such as limit cycles and fixed points, has become widely accepted.” Huys, Raoul. 2010. “The Dynamical Organization of Limb Movements.” Pp. 69-90. Huys, Raoul & V.K. Jirsa (Eds). Nonlinear Dynamics in Human Behavior. Springer. P. 69.


“The human motor apparatus, for instance, comprises more than 200 bones, 110 joints and over 600 muscles, each one of which either spans one, two or even three joints. While the degrees of freedom are already vast on the biomechanical level of description, their number becomes dazzling when going into neural space. Functional goal-directed behavior requires that a certain order arises in this multi-degree of freedom system. From a control-theoretical perspective, this poses a seemingly unsolvable problem. Bernstein’s gist was that during action these degrees of freedom are temporally organized into a functional unit, referred to as a synergy or coordinative structure, so that the (mechanical) degrees of freedom are effectively minimized.” Huys, Raoul. 2010. “The Dynamical Organization of Limb Movements.” Pp. 69-90. Huys, Raoul & V.K. Jirsa (Eds). Nonlinear Dynamics in Human Behavior. Springer. Pp. 70-1. Reference is to Bernstein, N. 1967. The coordination and regulation of movement. Pergamon Press.


“... the conceptualization of movement and control in terms of dynamical structures, in particular rhythmic movements in terms of nonlinear oscillators (i.e., limit cycles), became firmly established.” Huys, Raoul. 2010. “The Dynamical Organization of Limb Movements.” Pp. 69-90. Huys, Raoul & V.K. Jirsa (Eds). Nonlinear Dynamics in Human Behavior. Springer. P. 71.


“The properties of limit cycles are well established in dynamical systems theory. Fundamental, in that regard, is the notion that a limit cycle is an isolated closed trajectory (in phase or state space) and is stable (or attractive) if all neighboring trajectories approach it.” Huys, Raoul. 2010. “The Dynamical Organization of Limb Movements.” Pp. 69-90. Huys, Raoul & V.K. Jirsa (Eds). Nonlinear Dynamics in Human Behavior. Springer. P. 73.


“It is well known that movement accuracy and amplitude are inversely related to movement time. The most well-known formulation of this so-called speed-accuracy trade-off was formalized by Fitts. Accordingly, movement time MT equals a + b x ID, where a and b represent parameters to be experimentally determined, and ID - the index of difficulty, a measure reflecting task difficulty, relates to target distance D and width W according to ID = log2(2D/W).” Huys, Raoul. 2010. “The Dynamical Organization of Limb Movements.” Pp. 69-90. Huys, Raoul & V.K. Jirsa (Eds). Nonlinear Dynamics in Human Behavior. Springer. P. 76. Reference is to Fitts, P.M. 1954. “The information capacity of the human motor system in controlling the amplitude of movement.” Journal of Experimental Psychology. 47:381-391.


“As the task difficulty increases in a Fitts’ task, the movements not only become slower and slower but corrective sub-movements also start to occur during the final ‘homing-in’ phase. In addition, the time on the target (the dwell time) also increases. That is, the movements obtain discrete characteristics. During discrete movements, energy is totally dissipated when the oscillation is at its excursions, i.e., the ratio of the acceleration at its maximal absolute position and the maximal acceleration vanishes. In contrast, harmonic movements reveal total energy conservation and the ratio above equals one.” Huys, Raoul. 2010. “The Dynamical Organization of Limb Movements.” Pp. 69-90. Huys, Raoul & V.K. Jirsa (Eds). Nonlinear Dynamics in Human Behavior. Springer. P. 77. Reference is to Fitts, P.M. 1954. “The information capacity of the human motor system in controlling the amplitude of movement.” Journal of Experimental Psychology. 47:381-391.


“... there has been a longstanding debate in the literature on whether motor control is fundamentally discrete (in which case rhythmic movements are mere concatenations of discrete motion elements) or rhythmic (in which case discrete movements are merely aborted rhythmical movements) or whether both movements are controlled distinctly and cannot be reduced to each other.” Huys, Raoul. 2010. “The Dynamical Organization of Limb Movements.” Pp. 69-90. Huys, Raoul & V.K. Jirsa (Eds). Nonlinear Dynamics in Human Behavior. Springer. P. 78.


“For discrete movement initiation, the separatrix can be thought of as a threshold mechanism; only if the system is brought across, a movement will be executed.” Huys, Raoul. 2010. “The Dynamical Organization of Limb Movements.” Pp. 69-90. Huys, Raoul & V.K. Jirsa (Eds). Nonlinear Dynamics in Human Behavior. Springer. P. 81.


“... more recent approaches incorporating rhythmic and discrete movements have provided strong argument that both movements belong to classes that are not reducible to each other–or at least, it so appears.” Huys, Raoul. 2010. “The Dynamical Organization of Limb Movements.” Pp. 69-90. Huys, Raoul & V.K. Jirsa (Eds). Nonlinear Dynamics in Human Behavior. Springer. P. 85.


“To be sure, matter and radiation may have been in thermodynamic equilibrium at the outset, but the gravitational field of the universe was in fact very far from such a state.” Davies, Paul. 2013. “Directionality principles from cancer to cosmology.” Pp. 19-41. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 20.


“Matter and radiation might have started out in a maximum entropy state, but the gravitational field, being relatively smooth, was in a low-entropy state. Added together, the gravitational, matter and radiation entropies have always been rising. The departure of the latter two components from equilibrium since 380000 years [after the Big Bang] may be traced, more or less, to the clumping effects of gravitation. For example, the shrinkage of gas clouds heats the material, creating the type of thermal gradients and heat flow familiar from the Sun radiating into cold space. The thermodynamic disequilibrium which this represents is paid for by the growing disorder of the gravitational field, which becomes more and more inhomogeneous, representing a rise in gravitational entropy.” Davies, Paul. 2013. “Directionality principles from cancer to cosmology.” Pp. 19-41. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 22.


“With the appearance of planets with solid surfaces, the way lay open for the further enrichment of material forms, through crystallization and the formation of amorphous substances. The explosion in the size of the possibility space for physical forms was astronomical, because the number of ways of combining solid structures is super-exponential.” Davies, Paul. 2013. “Directionality principles from cancer to cosmology.” Pp. 19-41. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 27.


“... there is the phenomenon of evolutionary inherency, the observation that much that will be required for the emergence of a complex form has already evolved at a substantially earlier stage.” Morris, Simon Conway. 2013. “Life: the final frontier for complexity?” Pp. 135-161. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 135.


“The chemical regularities of life that are its most robust feature do not seem to depend on aspects of organization at the individual level or on individuality as a concept, in striking contrast to Mendelian/Darwinian evolutionary dynamics in which individuality is fundamental. In relation to large-scale innovations in chemistry, individuality appears as a heterogeneous and derived property that has emerged in several forms in living systems, and brought Mendelian/Darwinian dynamics into existence as only one source of order within a larger universe of Markovian stochastic processes.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” Pp. 191-223. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 192.


“Attempts to define life that descend from the Darwinian emphasis on replication and selection treat ‘life’ as a predicate or property of entities; because entities play a subordinate role in the phase transition paradigm, this traditional form of definition can no longer be regarded as fundamental. I argue that the nature of the living state cannot be conflated with the nature of individuality or with properties of individuals; a characterization of life in terms of its distinctive chemistry, for which the natural scale of aggregation is the biosphere as a whole, is a better foundation on which to unify many aspects of biological order.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” Pp. 191-223. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. Pp. 192-3.


“Equilibrium entropy characterizes the least-constrained distribution with a given content of matter, energy, volume, etc., ensuring that the Boltzmann limit on the decrease of entropy within sub-systems which are subject to more constraints than those at equilibrium, the equilibrium ensemble may be too permissive, rendering bounds derived from the equilibrium entropy loose and therefore uninformative.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” Pp. 191-223. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 202.


“We tend to think of natural selection in relation to adaptation, but a large background of normalizing selection is constantly at work preserving the fidelity of enzymes and their integration into simple metabolic networks. A full understanding of the stability of the biosphere will require us to explain how so many levels can be reinforced by their support of such distinctively biological, but otherwise universal, forms of order as core metabolism and also why so many levels seem to be required.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” Pp. 191-223. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 208.


“I now argue for a thermodynamic view of the emergence, organization, and robustness of life as a phenomenon in chemistry, and show that this conceptualization greatly reduces the salience of individuality and requires a re-interpretation of its meaning and its role.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” Pp. 191-223. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 208.


“Across biology within the twentieth century, however, both of these presumptions have been eroded. In development, ecology, epidemiology, and evolutionary dynamics, the identification of entities has become more ambiguous and the importance of organizational patterns that are not naturally characterized as entities has become more apparent.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” Pp. 191-223. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. Pp. 208-9.


“Instead, ecosystems emerge as the level of organization more closely associated with the universality of biochemistry than organisms. Indeed, the conservation of the network is often only visible at the level of the trophically complete ecosystem; the division and diversification in the use of particular pathway segments among species is extensive. Yet the paths of biosynthesis of most of the essential biomolecucles – even when they are interrupted by catabolic reversals or detour through salvage pathways, and even when they proceed through several species on the way to completion – are in toto highly conservative, and more so in the core than in the periphery of the network.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” Pp. 191-223. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 209.


“If individuality is thus secondary and emergent, and if the modularity of biochemistry and physiology in organisms does follow outlines prefigured in core metabolism, and if the ecosystem is the natural level of aggregation at which core metabolism displays universal pathways and motifs, then the universality of the network, which does not depend on species, seems to provide a prior constraint to the small functional variations that are created by the elaboration of species and ecological complexity.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” Pp. 191-223. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 210.


“The flux through core metabolism is to be interpreted as the order parameter of a non-equilibrium phase transition that occurred in geochemistry as the first stage (or stages) in the emergence of the biosphere. Because all metabolites flow through the core, the flux in the core is a function of all secondary fluxes, defined by the rules of chemical stoichiometry.... A derivation of higher-order structures as functional components in the system whose feedback maintains the core flux – showing that such motifs as molecular replication, cellular compartmentalization of metabolism, or the modularization of biological energy systems both contribute to maintaining the core flux and are maintained by it through selection – further refines the dependence of restrictions of biological form on the stable order parameter.” Smith, Eric. 2013. “Emergent order in processes: the interplay of complexity, robustness, correlation, and hierarchy in the biosphere.” Pp. 191-223. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 213.


“For our purposes, complexity will be a measure of inferential or predictive capacity: the ability for a population to store adaptive responses to a variety of states of the environment.” Krakauer, David. 2013. “The inferential evolution of biological complexity: forgetting nature by learning to nurture.” Pp. 224-45. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 231.


“The amount of information that is acquired for performing a preferred function is directly proportional to the loss of life. The ability to find an adaptive peak requires that all resources are channeled into a single genotype.” Krakauer, David. 2013. “The inferential evolution of biological complexity: forgetting nature by learning to nurture.” Pp. 224-45. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 232.


“It follows that the greater the number of possible states of the environment, the more variant genotypes there must be in order to match them. Prediction of the environment requires memory of the possible states of the environment in the population.” Krakauer, David. 2013. “The inferential evolution of biological complexity: forgetting nature by learning to nurture.” Pp. 224-45. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 232.


“We note that there can be no information in the genome that is not already present in the environment.” Krakauer, David. 2013. “The inferential evolution of biological complexity: forgetting nature by learning to nurture.” Pp. 224-45. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 233.


“When the states of the environment are sufficiently small, there is a corresponding minimal need to encode or ‘remember’ alternative genetic configurations. As these states grow, there is a benefit in remaining capable of tracking these states. But the number of states of the environment is not sufficient to explain simplicity and complexity. We also need to attend to the predictability of these states. Completely predictable states of the environment do not require conditional responses, only a fixed feature of the organism. Completely random states can not be predicted by definition, and are better off ignored. So increasing the number of regular but not fixed features of the environment is predicted to lead to an increase in the number of adaptive states of the organism. Contrariwise, reducing the number of regular states, or moving towards regimes of perfect predictability or randomness, lead to a reduction in the number of adaptive states of the organism.” Krakauer, David. 2013. “The inferential evolution of biological complexity: forgetting nature by learning to nurture.” Pp. 224-45. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 235.


“How might an organism that is driven to acquire and store more information to survive discover a means of overcoming the genetic constraints imposed by mutation and selection? I suggest that this can be achieved through the evolution of mechanisms that possess three key properties. These properties are observed both at the level of single cells, and large tissue systems such as brains.

“(1) Self-similar structure generated by minimal (or short) genetic regulatory networks [repeating a genetic pattern].

“(2) Modification of these structures within a single generation using suitable environmental cues [epigenesis].’

“(3) A property of arbitrary assignment of modifications to structures [semiotic or arbitrary inscription of an environmental condition].” Krakauer, David. 2013. “The inferential evolution of biological complexity: forgetting nature by learning to nurture.” Pp. 224-45. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. Pp. 236-7.


“The developmental encoding of the lungs, circulatory system, and brain all make use of the small footprint property of fractals.” Krakauer, David. 2013. “The inferential evolution of biological complexity: forgetting nature by learning to nurture.” Pp. 224-45. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 239.


“Complexity therefore increases on a ‘need to know’ basis, and does not follow an inexorable trend but a wavering pathway governed by the rate of information production by the environment, where the environment includes organisms and their products.” Krakauer, David. 2013. “The inferential evolution of biological complexity: forgetting nature by learning to nurture.” Pp. 224-45. From Lineweaver, Charles, P. Davies & M. Ruse (Eds). Complexity and the Arrow of Time. Cambridge University Press. P. 244.


“An attractor is a structure toward which all the trajectories in state space converge as time goes to infinity. Different kinds of attractors are known: a/ (stable or unstable) fixed point, b/ (stable or unstable) limit cycle when the system exhibits a periodic behavior and c/ strange attractors when the system displays a chaotic, unpredictable quasi-cyclical behavior.” Calvin, Sarah & V. Jirsa. 2010. “Perspectives on the Dynamic Nature of Coupling in Human Coordination.” Pp. 91-114. Huys, Raoul & V.K. Jirsa (Eds). Nonlinear Dynamics in Human Behavior. Springer. P. 92.


“The discrete movement [of human limbs] can be described in terms of fixed point dynamics, whereas the rhythmic movement can be described in terms of [a] limit cycle. These two topologically different structures cannot be reduced to each other and have consequently a different (intrinsic) dynamics.” Calvin, Sarah & V. Jirsa. 2010. “Perspectives on the Dynamic Nature of Coupling in Human Coordination.” Pp. 91-114. Huys, Raoul & V.K. Jirsa (Eds). Nonlinear Dynamics in Human Behavior. Springer. P. 101.


“To fill these gaps [in discrete vs. rhythmic movements for human limbs], a theoretical framework based on first principles was recently introduced in terms of phase flows. More precisely, these authors [Jirsa & Kelso] have recently proposed that mechanisms and processes responsible for movement generation, timing and motor coordination can be conceived as phase flows. Phase flows describe the rate of change in a system’s state space and govern the evolution of the system as a function of its current state. The fundamental aspect of phase flows is that they can be classified according to their flow topology. Any dynamic system with the same phase flow topology is [a] member of the same class and essentially describes the same system. Then, the phase flow topology is an unbiased general representation of ‘processes’ executed by a dynamical system within its phase space.” Calvin, Sarah & V. Jirsa. 2010. “Perspectives on the Dynamic Nature of Coupling in Human Coordination.” Pp. 91-114. Huys, Raoul & V.K. Jirsa (Eds). Nonlinear Dynamics in Human Behavior. Springer. P. 103. Reference is to Jirsa, V. & J. Kelso. 2005. “The excitator as a minimal model for the coordination dynamics of discrete and rhythmic movement generation.” Journal of Motor Behavior. 37:35-51.


“While community ecology is more focused on objects such as the identity, variety, distribution and interactions of organisms, ecosystem ecology puts more emphasis on the flow of matter and energy in the ecological systems.

“Function plays an integrative role here because the ascription of function to the biodiversity or to its components (such as the traits, populations, functional groups, etc.) aims at explaining the maintenance of ecosystem properties (nutrient cycling, primary productivity, etc.).” Nunes-Neto, Nei, A. Moreno & C. El-Hani. 2014. “Function in ecology: an organizational approach.” Biol Philosophy. 29:123-141. P. 125.


“For Mossio et al., a trait T has a function in the organization O of a system S if and only if:

C1: T contributes to the maintenance of the organization O of S;
C2: T is produced and maintained under some constraints exerted by O;
C3: S is organizationally differentiated.”
Nunes-Neto, Nei, A. Moreno & C. El-Hani. 2014. “Function in ecology: an organizational approach.” Biol Philosophy. 29:123-141. P. 127. Reference is to Mossio, M, C. Saborido & A. Moreno. 2009. “An organizational account of biological functions.” British Journal of Philosophy of Science. 60:813-841.


“The idea of closure express[es] that a sequence of processes forms a causal loop. And here it is important to distinguish between closure of processes and closure of constraints.

“Some purely physical or chemical systems are characterized by a closure of processes, where one process influences another in a circular way. For instance consider the hydrologic cycle in prebiotic Earth....”

Closure of constraints, however, is a specific mode of dependence between a set of constraints, in which a system that produces some of the constraints harnessing its underlying dynamics realizes closure. This means that not only the constrained processes form a causal loop, but that this loop is achieved because the constraints generated in the system influence each other so as to achieve closure. In formal terms, a set of constraints C realises closure if, for each constraint Ci belonging to C, (1), Ci depends directly on at least one other constraint of C (Ci is dependent) and (2) there is at least one other constraint Cj belonging to C which depends on Ci. For instance, a living cell is maintained because of the constraining action of constraints like enzymes and membranes, which harness chemical reactions inside the cell in a cyclic way. But, in turn, each of these constraints contributes to the generation (and re-generation) of the other constraints.” Nunes-Neto, Nei, A. Moreno & C. El-Hani. 2014. “Function in ecology: an organizational approach.” Biol Philosophy. 29:123-141. Pp. 128-9.


“An ecological function is a precise (differentiated) effect of a given constraining action on the flow of matter and energy (process) performed by a given item of biodiversity, in an ecosystem closure of constraints.” Nunes-Neto, Nei, A. Moreno & C. El-Hani. 2014. “Function in ecology: an organizational approach.” Biol Philosophy. 29:123-141. P. 131.


“To finish, we can summarize our organizational approach to ecological function as follows: the items of biodiversity, when acting as constraints on the biologically generated flow of matter, functionally modulate (channel) these rates in such a manner that a global self-maintaining (ecological) cycle is ensured. This harnessing action of the items of biodiversity can be treated as being analogical to the constraining action of enzymes in metabolism. As with the enzymes–which catalyze biochemical reactions in cell metabolism–the items of biodiversity harness the ecological transformations of nutrients, which otherwise would happen only at a very slow rate or would not occur at all.” Nunes-Neto, Nei, A. Moreno & C. El-Hani. 2014. “Function in ecology: an organizational approach.” Biol Philosophy. 29:123-141. P. 137.


“The chemistry of life is distinguished both by its high degree of order and by its essential dependence on a number of far-from-equilibrium reactions. While in some cases reactions may be treated as isolated subsystems with equilibrium approximations, such isolations are themselves cumulative deviations far from equilibrium, reflecting the system-level properties of life as a whole. The dynamical order of life’s chemistry is maintained by the non-equilibrium transfer of electrons through the biosphere. Free energy from potential differences between electron donors and acceptors can be derived from a variety of biogeochemical cycles, but within cells electron transfer is mediated by a small number of universal electron carriers which drive a limited array of organic reactions. Together these reactions make up metabolism, which governs the chemical dynamics both within organisms and across ecosystems. The universal and apparently conserved metabolic network transcends all known species diversification and evolutionary change, and distinguishes the biosphere within the major classes of planetary processes. We identify metabolism with the quite specific substrate architecture and hierarchical control flow of this network, which provide the most essential characterization of the chemical nature of the living state.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 2.


“Metabolism is the sub-space of organic chemistry over which life has gained catalytic control,...” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 2.


“In addition to the standard ecological distinction between autotrophy and heterotrophy, scientists working in the area of bioremediation, for example, have coined the term epimetabolome to refer to those compounds that due to their slow degradation are freely diffusible across microbial communities. Thus, the causes and roles of evolutionary changes, even though they arise within cellular lineages, may be only partly explained by organization at the cellular or species level. Other levels that must also be considered include the meta-metabolome of trophic ecosystems, and the links to geochemistry. The great biogeochemical cycles–of carbon, nitrogen, phosphorus, or many metals–combine physiological, ecological and even geochemical links such as mantle convection or continental weathering.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 3.


“An important additional empirical observation is that the deepest universal features of metabolism are reliably seen not at the individual, but at the ecosystem level. The single-organism metabolisms among members of complex ecosystems may vary extremely widely, because different organisms perform different segments of biosynthetic or degradative pathways, using trophic links (predation, parasitism, symbiosis, syntrophy, saprophyty) to obtain what they do not make. The aggregate, or net, pathways to which these individual metabolisms contribute, once assembled through their trophic links, mostly remain within standard networks as reflected in databases such as KEGG or UniProt.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 3.


“We can argue for the existence of a universal anabolic, autotrophic network that comprises the chemistry essential to life.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 3.


“A functioning metabolism is both a network of fluxes through substrate molecules, and a set of hierarchical relations in which some of the more complex structures control the kinetics of flows within the network. Within the substrate network, distinguishable subnetworks include the core network to synthesize CHO backbones, networks radiating from the core that incorporate N, S, P or metals, higher-order networks that assemble complex organics from ‘building blocks’, and still others that synthesize all forms of polymers from small organic monomers. Within the control hierarchy, the layers of cofactors, oligomer catalysts, and integrated cellular energetic and biosynthetic subsystems are qualitatively distinct.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 3.


“The foundation of autotrophy–and more generally the anchor that embeds the biosphere within geochemistry–is carbon-fixation, the transformation of CO₂ into small organic molecules. A recent study combining evidence from phylogeny and metabolic network reconstruction–an approach we refer to as ‘phylometabolic’ reconstruction–showed that all carbon fixation phenotypes may be related by an evolutionary tree with very high (nearly perfect) parsimony, and a novel but sensible phenotype at the root. The branches representing innovations in carbon fixation were found to trace the standard deep divergences of bacteria and archaea. More striking, this work showed that likely environmental drivers could be identified for most divergences, suggesting that deep evolution reflects first incursions into novel geochemical environments. The tight coupling of the reconstructed phylogeny to geochemical variety suggests that constraints from chemistry and energetics drove early evolution in predictable ways, leaving little need to invoke historical contingency.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. Pp. 3-4.


“As carriers of electrons or essential functional groups, cofactors regulate kinetic bottlenecks in metabolic networks....

“The structurally most elaborate cofactors tend to facilitate the chemically most complex reaction mechanisms. As a result, the distinction between presence and absence of these cofactors is effectively the absolute presence or absence of reaction mechanisms (a ‘topological’ network property), as contrasted with a finite rate adjustment. Thus, the appearance and diversification of families of biosynthetically related cofactors introduced functions which served as ‘keys’ to domains in organic chemistry, incorporating these within biochemistry. As a result we may often map biosynthetic pathway diversification of cofactors onto particular lineage divergences in the tree of life.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 4.


“Our main message is twofold: (1) that the structure of biosynthetic networks and their observed variation, even though the networks are elaborate, has a compact representation in terms of a small collection of rules for composition, and (2) that the same rules we abstract from composition have a natural interpretation as constraints on evolutionary dynamics, which as a generating process has produced the observed variants.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. Pp. 4-5.


“Metabolic networks within organisms are commonly characterized as having three classes of pathways: (1) catabolic pathways that break down organic food to provide chemical ‘building blocks’ or energy; (2) core pathways through which nearly all small metabolites pass during primary synthesis or ultimate breakdown, and (3) anabolic pathways that build up all complex chemicals from components originating in the core. The motif of three-stage pathways–catabolic, core, anabolic–between typical pairs of metabolites has been abstracted into a paradigm of ‘bowtie’ architecture for metabolism.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 5.


“Whole-organism metabolisms are conventionally divided into two classes–autotrophic and heterotrophic–according to the ways they combine anabolic and catabolic pathways. Autotrophs synthesize all required metabolites from inorganic precursors, and can function without catabolism, using only the core and anabolic pathways radiating from it.... Heterotrophs, in contrast, are organisms that must obtain organic inputs from their environments because they lack essential biosynthetic pathways. Autotrophy and heterotrophy are best understood as modes of metabolism, between which some individual species may switch depending on circumstances, and which may even be mixed at the level of sub-networks within a given organism.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 5.


“Autotrophic metabolism forms the lowest trophic level in the biosphere, fixing CO₂ into organic matter, while heterotrophic metabolism forms all subsequent levels, determining the structure of flows of organic compounds in trophic webs, and actively cycling carbon from biomass back to environmental CO₂.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 6.


“Exponential growth results from proportional self-amplification of metabolic and other networks that have an ‘autocatalytic’ topology. Network autocatalysis is a term used to describe a topological (stoichiometric) property of the substrate network of chemical reactions. In a catalytic network, one or more of the network intermediates is needed as a substrate to enable the pathway to connect to its inputs or to convert them to outputs, but the catalytic species is regenerated by the stage at which the pathway completes. Network-catalytic pathways must therefore incorporate feedback and comprise one or more loops with regard to the internally produced molecules. An autocatalytic network is a catalytic network augmented by further reactions that convert outputs to additional copies of the network catalyst, rendering the pathway self-amplifying.

“Molecular autocatalysis – the property that intermediates in a pathway serve as conventional molecular catalysts for other reactions in the pathway–may be understood as a restricted form of network autocatalysis in which the reaction to which some species is an essential input is the same reaction that regenerates that species....

“Therefore all observed persistent material flows in the biosphere can only be products of autocatalytic networks, though they may require hard-to-recognize feedback ranging from the level of cell metabolism to trophic ecology for full regeneration.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. Pp. 7-8.


“The Calvin-Benson-Bassham (CBB) cycle is responsible for most known carbon fixation in the biosphere.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 14.


“Almost all anabolic pathways in extant organisms originate in one of five intermediates in the TCA cycle–acetate (as acetyl-CoA), pyruvate, oxaloacetate, succinate (or succinyl-CoA) or alpha-ketoglutarate–which have been dubbed the ‘pillars of anabolism.’” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 16.


“Thus as few as four TCA intermediates provide the organic inputs to all anabolic pathways.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 17.


“... we may list the seven modules from which all known autotrophic carbon-fixation pathways are assembled: (1) direct one-carbon reduction on folates or related compounds, with or without the CODH/ACS terminal reaction of WL [Wood-Ljungdahl, linear pathway]; (2) the short-molecule rTCA are from acetyl-CoA to succinyl-CoA; (3) the long-molecule rTCA are from succinyl-CoA to citryl-CoA; (4) the gluconeogenic/reductive pentose-phosphate pathway, with or without the RubisCO reaction of CBB [Calvin-Benson-Bassham cycle]; (5) the 3HP arc from acetyl-CoA to succinyl-CoA; (6) the long-molecule 4HB pathway from cuccinyl-CoA to acetoacetyl-CoA; (7) the glyoxy late-shunt/mesaconate pathway to citramalate, which is the long-molecule loop in the 3HP bicycle....

“The essential invariance across the biosphere of the seven sub-networks listed above allows us to represent all carbon-fixation phenotypes in terms of the presence or absence, connectivity and direction of these basic modules.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 22.


“The small number of modules that contribute to carbon fixation, and the even smaller number of ‘gateway’ molecules that serve as interfaces between most of them, permit free recombination into many phenotypes satisfying the constraints of autotrophy. An important consequence of free recombination is that a constraint of overall autotrophy only enforces network completeness–the existence of some connection between gateway molecules. Because there exist multiple modules that can be used to satisfy these constraints, autotrophy alone therefore does not lock in dependences within networks over distances longer than the modules themselves.... Through these mechanisms modularity promotes innovation-sharing and rapid and reliable adaptation to environmental conditions, but reduces standing variation among individuals sharing a common environment.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 24.


“The constraints which jointly required the insertion of a linked WL/rTCA network at the root have led us to propose a kind of redundancy not found in extant fixation pathways. Either WL or rTCA alone is self-maintaining (in a modern organism) so a network that incorporates both is redundantly autocatalytic. This is an important and speculative departure from known phenotypes, but it can be argued to have conferred a selective advantage under the more primitive conditions of early cells, because the pathway topology itself possesses a form of inherent robustness. The redundant network topology of the root phenotype would have allowed it to better cope with both internal and external perturbation in an era when regulation and kinetic control were probably less sophisticated and refined than they are today. In that respect it is a more plausible phenotype for a universal ancestor than any modern network.

“The enhanced robustness of the joint network follows from the interaction of short-loop and long-loop autocatalysis. The threshold for autocatalysis in the rTCA loop, fragile against parasitic side reactions or unconstrained anabolism, is supported and given a recovery mode when fed by an independent supply of acetyl-CoA from WL. In turn, the production of a sufficient concentration of folates to support direct C1 reduction, fragile if the long biosynthetic pathway is unreliable, is augmented by additional carbon fixed in rTCA.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. Pp. 26-7.



“Chemical self-amplification, if it can be demonstrated experimentally, is the most plausible mechanism by which the biosphere can concentrate all energy flows and material cycles through a small, stable set of organic compounds.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 27.


“The rise of oxygen seems to have put an end to innovation in carbon fixation, and led to a florescence of innovation in carbon sharing. By ‘sharing’ we refer to general exchanges in which organic compounds are re-used without de novo synthesis: we do not intend only symbiotic associations.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 28.


“It is perhaps counterintuitive, but we believe consistent, that the phylometabolic tree is more tree-like in the earlier era of more extensive single-gene lateral transfers, and becomes less tree-like and more reticulated in the era of complex ecosystems enabled by oxygenic metabolisms, which may have come as much as 1.5 billion years later. For reticulation to appear in a tree of reconstructed metabolisms, it is necessary that variants which evolved independently–as we have argued under distinct selection pressures–be maintained in new environments where they can be brought into both contact and interdependence. The maintenance of standing variation is facilitated both by the evolution of more advanced mechanisms to integrate genomes and limit horizontal transfer and by the greater power density of oxygenic metabolisms.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. Pp. 28-9.


“Cofactors form a unique and essential class of components within biochemistry, both as individual molecules and as a distinctive level in the control over metabolism. In synthesis and structure they tend to be among the most complex of the metabolites, and unlike amino acids, nucleotides, sugars and lipids, they are not primary structural elements of the macromolecular components of cells. Instead, cofactors provide a limited but essential inventory of functions, which are used widely and in a variety of macromolecular contexts. As a result they often have the highest connectivity (forming topological ‘hubs’) within metabolic networks, and are required in conjunction with key inputs or enzymes to complete the most elaborate metabolisms.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 29.


“Structurally, many cofactors from a class in transition between the core metabolites and the oligomers.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 30.


“The polymerization exhibited within cofactors is distinguished from that of oligomers by its heterogeneity. Srinivasan and Morowitz have termed cofactors ‘chimeromers’, because they often include monomeric components from several molecule classes.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 30. Reference is to Srinivasan, V. & H. Morowitz. 2009. “Analysis of the intermediary metabolism of a reductive chemoautotroph.” Biol. Bull. 217: 222-32. PMID: 20040747.


“We may understand the border between small and large molecules, where most cofactors are found, as more fundamentally a border between the use of heterogeneous organic chemistry to encode biological information in covalent structures, and the transition to homogeneous phosphate chemistry, with information carried in sequences of higher-order non-covalent structures.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 31.


“Large oligomeric macromolecules are almost entirely synthesized using the dehydration potential of phosphates to link monomers drawn from the inventory of small core metabolites.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 31.


“Nearly half of enzymes require cofactors as coenzymes.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 31.


“The universal reactions of intermediary metabolism depend on only about 30 cofactors.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 31.


“Cofactors fill roles in network or molecular catalysis below the level of enzymes, but they share with all catalysts the property that they are not consumed by participating in reactions, and therefore are key loci of control over metabolism.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 31.


“For proto-metabolism, spontaneous abiotic side-reactions may be hazardous, if catalysts in the main fixation pathway do not sufficiently accelerate their reaction rates, creating a separation of timescales relative to the uncatalyzed background. Within the first cells, the same hazard is posed by secondary anabolism, as its reaction rates become enhanced by catalysts similar to those in the core. This fact was clearly noted already in Huber and Guenter. It may thus be that the optimizations in either branch of the carbon-fixation tree were not possible until rates of anabolism were sufficiently well-regulated to protect supplies of loop intermediates or essential cofactors. Therefore, while the root node is plausible as a pre-cellular or an early cellular form, either branch from it may have required the greater control afforded by quite refined cellular regulation of reaction rates. It is here that we envision a crucial role for feedback regulation at the genomic level as a support for the architectural stability of the underlying substrate network, prior even to its service in homeostasis in complex environments or in phenotypic plasticity.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 43. Reference is to Huber, C. & W. Guenter. 2000. “Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions.” Science. 276: 245-7.


“The idealized adaptive function of coding is to give maximum evolutionary plasticity to aspects of phenotype derived from protein sequence, uncoupled from constraints of underlying biosynthesis. The near-wholesale transition from organic chemistry to polymer chemistry around the C₂₀ scale suggests that this separation has been effectively maintained by evolution. Strong regularities which make the description of the genetic code compressible relative to a random code reflect failures of this separation which have transmitted selection pressure across levels, during either the emergence or maintenance of the code. These include base-substitution errors, whether from mutation or in the transcription and translation processes, but also apparently chemical relations between nucleobases and amino acids.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 44.


“We may ask, would a hybrid pathway out-compete alternatives chemically as a kinetic channel for carbon reduction by H₂ (or perhaps directly by reduced iron)? To this we argue that a feeder augmented by a loop outcompetes an unaided feeder on average by virtue of autocatalytic self-amplification. A loop with a feeder outcompetes a bare loop in the context of loss or fluctuations because of greater robustness and recovery (self-re-ignition).” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 46.


“We have argued that the fundamental problem of electron transfer in aqueous solution leads to a qualitative division between catalytically ‘hard’ and ‘easy’ chemistry, and that this division in one form or another has led to much of the architecture and long-term evolution of metabolism and the biosphere. Hard chemistry involves electron transfers whose intermediate states would be unstable or energetically inaccessible in water if not mediated by transition-metal centers in metal-ligand complexes and/or elaborate and structurally complex organic cofactors. Easy chemistry involves hydrogenations and hydrations, intramolecular redox reactions and a wide array of acid-base chemistry. Easy chemistry is promiscuously re-used and provides the internal reactions within modules of core metabolism. Hard chemistry defines the module boundaries and the key constraints on evolutionary innovation.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 46.


“On the foundation of core metabolism laid by carbon fixation, the remainder of biosynthesis is arranged as a fan of increasingly independent anabolic pathways. The unifying role of the core permits diverse anabolic pathways to independently reverse and become catabolic, and the combinatorics of possible reversals in communities of organisms determines the space of evolutionary possibilities for heterotrophic ecology.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 46.


“Only seven carbon fixation modules, mostly determined by distinctive, metal-dependent carboxylation reactions, cover all known phylogenetic diversity and provide the building blocks for both autotrophic and heterotrophic metabolic innovation.” Braakman, Rogier & Eric Smith. 2013. “The compositional and evolutionary logic of metabolism.” Physical Biology. 10:011001. Pp. 1-62. P. 46.

“Indeed, our findings forced us to refine the classical notion of affordance, by highlighting that, at least at the basic level, the affordance may depend on the spatial relationship between the features of the situation and all the actors who could be involved in that situation. In this regard, it is worth noting that the fact that more than one individual might be involved in the same situation implies not only the presence of more than one member on the agent side of the affordance relation but also (and above all) the reshaping of the nature and the range of the relation itself. What our experiments show is that the features of a situation may suggest a given action to us, or even demand it from us, either directly, when they fall within our own peripersonal space, thus resulting in their being ready to our own hands, or indirectly, when they fall within the peripersonal space of other individuals, thus resulting in their being ready both to their own hands and through them also to our own hands.

“Paradoxical as it may seem, the spatial dependence does not at all reduce the range of the affordance relation–if anything, it extends its applicability domain by means of a mirror mechanism which allows us to match the surrounding space of others with our own peripersonal space, thus mapping action potentialities of others onto our own motor repertoire. What is more, the fact that the affordance relation is not a private business of a single individual but relies on a mirror mechanism that allows one to share the space of his or her own action with others highlights that the investigation of affordance mandatorily involves dealing with the cognitive processes underlying basic social cognition.” Costantini, Marcello & C. Sinigaglia. 2011. “Grasping Affordance: A Window onto Social Cognition.” Pp. 431-460. From Seemann, Axel (Ed.) Joint Attention: New Developments in Psychology, Philosophy of Mind, and Social Neuroscience. MIT Press. Pp. 451-2.


“The first assumption [for modeling biological systems with ordinary differential equations], called the continuum hypothesis, allows us to measure species abundance as a continuously changing concentration rather than a discrete number of molecules. This is usually considered a valid assumption provided the number of molecules is not less than about 1,000....

“The second required assumption is that the reactants find one another immediately and equally, the so-called well-mixed assumption. This is valid provided that the time scale of the process under investigation is longer than the time scale of diffusion of its components.” Ingalls, Brian & P. Iglesias. 2010. “A Primer on Control Engineering.” Pp. 1-28. From Iglesias, Pablo & B. Ingalls. Control Theory and Systems Biology. MIT Press.


“Perhaps the most fundamental property of life is its ability to use energy and materials to maintain and reproduce itself, in turn providing energy and materials to support more life.” Dunne, Jennifer, R. Williams, N. Martinez, R. Wood & D. Erwin. 2008. “Compilation and Network Analyses of Cambrian Food Webs.” PLoS Biology. Vol. 6, 4: 693-708. e102. P. 693.


“However, recent advances in the field of phylogenomics have started to lend support for a model that places a cellular fusion event at the basis of the origin of eukaryotes (symbiogenesis), involving the merger of an as yet unknown archaeal lineage that most probably belongs to the recently proposed ‘TACK superphylum’ (comprising Thaumarchaeota, Aigarchaeota, Crenarchaeota and Korarchaeota) with an alphaproteobacterium (the protomitochondrion). Interestingly, an increasing number of so-called ESPs (eukaryotic signature proteins) is being discovered in recently sequenced archaeal genomes, indicating that the archaeal ancestor of the eukaryotic cell might have been more eukaryotic in nature than presumed previously, and might, for example, have comprised primitive phagocytotic capabilities. In the present paper, we review the evolutionary transition from archaeon to eukaryote, and propose a new model for the emergence of the eukaryotic cell, the ‘PhAT (phagocytosing archaeon theory)’, which explains the emergence of the cellular and genomic features of eukaryotes in the light of transiently complex phagocytosing archaeon.” Martijn, Joran & T. Ettema. 2013. “From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell.” Biological Society Transactions. 41: 451-7. P. 451.


“Despite the large number of mutually incompatible scenarios that have been proposed to explain its [eukaryote’s] origin, some consensus has been reached about the following points; first, the LECA (last eukaryotic common ancestor) most probably contained the mitochondrial progenitor derived from endosymiosis with an alphaproteobacterium and, secondly, eukaryotic genomes have a chimaeric nature: genes for information storage and processing are archaea-related, and genes for metabolic or ‘operational’ processes are mostly bacterial in nature (but not necessarily derived from the mitochondrial progenitor). Finally, a significant fraction of the eukaryotic genes encode proteins that are restricted to eukaryotes, the so-called ESPs (euarkaryotic signature proteins).” Martijn, Joran & T. Ettema. 2013. “From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell.” Biological Society Transactions. 41: 451-7. P. 451.


“Schematic step-wise overview of the crucial steps of the proposed PhAT, comprising the following stages: (1) A ‘garden variety’ archaeon, probably belonging to the recently proposed ‘TACK superphylum’ contains an actin-based cytoskeleton. (2) After losing its proteinacious cell wall, the archaeon evolves a more flexible actin-based cytoskeleton, which supported the formation of cellular protrusions. (3) The archaeon’s cytoskeleton matures into a primitive phagocytotic machinery, and the uptake and digestion of other prokaryotic cells exposes the archaeon to increasing amounts of ‘foreign’ genomic DNA. The resulting elevated rates of HGT [horizontal gene transfer] destabilize the archaeal host genome, which causes the genetic material to evolve at accelerated rates, forming the basis of the gene innovation processes. (4) A protective membrane boundary is formed to protect the genetic integrity of the host cell genome via invagination events, giving rise to a primitive karyotic cell type. The protective membrane structure restabilizes the host genome and restores the evolutionary rates. An ancient alphaproteobacterium is taken up, but not digested, and establishes an endosymbiotic interaction with the ‘parakaryotic’ host cell. Conceivably, the symbiotic interaction was already established before the ingestion of this protomitochondrial cell type. (5) The transition of the alphaproteobacterial endosymbiont into an energy producing mitochondrion forms the basis of the emergence of cellular complexity typical for eukaryotes. The surplus of energy facilitates the maturation of the nucleus and additional endomembrane systems and allows the host genome to expand. This relaxed genomic stringency further accelerates genomic innovations via gene duplication events, recombination of existing genes and gene genesis events. In addition, with energy production now taking place at the mitochondrial membranes rather than the outer membrane, the volume of the cell is no longer restricted to typical prokaryotic dimensions.” Martijn, Joran & T. Ettema. 2013. “From archaeon to eukaryote: the evolutionary dark ages of the eukaryotic cell.” Biological Society Transactions. 41: 451-7. P. 454.


“There are two ways of viewing evolution, through the spectacles of either the Red Queen or the Court Jester. The Red Queen model stems from Darwin, who viewed evolution as primarily a balance of biotic pressures, most notably competition, and it was characterized by the Red Queen’s statement to Alice in Through the Looking-Glass that ‘it takes all the running you can do, to keep in the same place.’ The Court Jester model is that evolution, speciation, and extinction rarely happen except in response to unpredictable changes in the physical environment, recalling the capricious behavior of the licensed fool of Medieval times.” Benton, Michael. 2009. “The Red Queen and the Court Jester: Species Diversity and the Role of Biotic and Abiotic Factors Through Time.” Science. Vol. 323. Pp. 728-32. P. 728.


“Life on land today may be as much as 25 times as diverse as life in the sea,...” Benton, Michael. 2009. “The Red Queen and the Court Jester: Species Diversity and the Role of Biotic and Abiotic Factors Through Time.” Science. Vol. 323. Pp. 728-32. P. 729.


“Species diversity may increase by the occupation of new ecospace. The number of occupied guilds, that is, broad ecological groupings of organisms with shared habits, has increased in several steps through time, from 20 in the early Paleozoic to 62 in post-Paleozoic marine faunas. Further, marine animals have shown several step increases in tiering, the ability to occupy and exploit different levels in the habitat. At times, burrowers have burrowed deeper, and reef-builders have built taller and more complex reefs. Analogous, if even more dramatic, expansions of ecospace have occurred on land, with numerous stepwise additions of new habitats, from the water-margin plants and arthropods of the early Paleozoic to the forests and upland habitats of the later Paleozoic when land animals first burrowed, climbed, and flew, through the introduction of herbivory, giant size, endothermy, and intelligence among vertebrates, and the great blossoming of flowering plants (with associated vast expansions in the diversity of plant-eating and social insects and modern vertebrates) during the Cretaceous Terrestrial Revolution.” Benton, Michael. 2009. “The Red Queen and the Court Jester: Species Diversity and the Role of Biotic and Abiotic Factors Through Time.” Science. Vol. 323. Pp. 728-32. P. 730.


“The other mode of species increase globally or regionally is by niche subdivision, or increasing specialization. This is hard to document because of the number of other factors that vary between ecosystems through time. However, mean species number in communities (alpha diversity) has increased through time in both marine and terrestrial systems, even though niche subdivision may be less important than occupation of new ecospace in increasing biodiversity.” Benton, Michael. 2009. “The Red Queen and the Court Jester: Species Diversity and the Role of Biotic and Abiotic Factors Through Time.” Science. Vol. 323. Pp. 728-32. P. 730.


“Increase in size has many other effects [than circulatory systems for oxygen, growth by differentiation of cell types] that have been revealed by allometric studies: larger organisms move faster, they have longer generation time and they live longer. These consequences are all significant as they favour animals that develop slowly, invest heavily in a small number of offspring (K-strategy), and rely on complex behaviours.” Rospars, Jean-Pierre. 2013. “Trends in the evolution of life, brains and intelligence.” International Journal of Astrobiology. 12(3): 186-207. P. 189.


“The pre-eminence of terrestrial over marine diversity dates from the mid-Cretaceous period (~110Ma). It is ultimately related to the low cost of mobility on land resulting from physical differences between air and water in density, viscosity, specific heat and diffusion coefficient of oxygen.” Rospars, Jean-Pierre. 2013. “Trends in the evolution of life, brains and intelligence.” International Journal of Astrobiology. 12(3): 186-207. P. 191.


“Most of the energy in nervous tissues serves to drive the sodium potassium pumps that maintain constant the concentration of sodium and potassium ions. The brain is an energetically very expensive organ that demands a large and continual supply of glucose and oxygen irrespective of whether the animal is awake or asleep, active or at rest.” Rospars, Jean-Pierre. 2013. “Trends in the evolution of life, brains and intelligence.” International Journal of Astrobiology. 12(3): 186-207. P. 197.


“When two or more such configurations [arrangements of molecular components or of particular matter in space] are brought into association, there is a combined arrangement, which if persistent, also instantiates information: that of both components plus that of their association.” Farnsworth, Keith, J. Nelson & C. Gershenson. 2013. “Living Is Information Processing: From Molecules to Global Systems.” Acta Biotheor. 61:203-222. P. 207.


[As contradiction] “Apparently, life alone creates life, but before it appeared for the first time, individually persistent (non-transitory) stages of ordering among collections of molecular components must have occurred.” Farnsworth, Keith, J. Nelson & C. Gershenson. 2013. “Living Is Information Processing: From Molecules to Global Systems.” Acta Biotheor. 61:203-222. P. 208.


“Sepkoski’s three-faunas analysis is the classic description of taxonomic turnover in the marine realm; these faunas are statistical groupings of taxonomic classes that have similar diversity histories in geological time. The Cambrian fauna diversified rapidly in the Cambrian but declined rapidly thereafter, whereas the Paleozoic fauna expanded during the Ordovician, was dominant throughout the Paleozoic, and suffered greatly in the end-Permian extinction. The Modern fauna was present at low diversity in the earlier Paleozoic, diversified more slowly than the other two faunas, weathered mass extinctions fairly well, and came to dominate the modern world.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review of Earth Planetary Science. 39:241-69. P. 246. Reference is to Sepkoski, J.J. 1981. “A factor analytic description of the Phanerozoic marine fossil record.” Paleobiology. 7:36-53.


“The advent of numerous consumers such as predators during the Cambrian Explosion marks the lengthening of marine food chains, and the increase in a variety of energy-intensive behaviors (e.g., swimming, burrowing, and crawling) likewise indicates increasing energy consumption by animals. Other feeding types such as deposit feeders and grazers became abundant for the first time as well.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 251.


“During the Cambrian Explosion, disturbance on the seafloor increased significantly. Ediacaran sediments display little or no bioturbation (the stirring and mixing of sediment by the burrowing activities of animals), but burrows such as the trace fossil Treptichnus pedum that have shallow vertical shafts penetrate Lower Cambrian sediments, and the depth and intensity of burrowing increased from there. As a result, microbially stabilized substrates were replaced by the unconsolidated, dynamic sedimentary substrates that characterized most of the rest of the Phanerozoic (the Cambrian Substrate Revolution).” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 251.


“At the same time that shell-crushing predators radiated in the Devonian and Carboniferous, shell morphologies that may have protected against crushing increased in many taxa.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 254.


“Infaunality increased in the late Paleozoic as well, as seen in the maximum depth of burrowing and the proportion of infaunal genera in the global biota.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 254.


“Several lines of evidence, such as the increase in high-energy predators, suggested to Bambach that the energetics of the marine biosphere might have increased from the early to the late Paleozoic. On this note, body size in many marine invertebrates continued to increase during the middle Paleozoic, which Novack-Gottshall attributed to increased energetics.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 254. References are: Bambach, R. 1999. “Energetics in the global marine fauna: a connection between terrestrial diversification and change in the marine biosphere.” Geobios. 32:131-44. Novack-Gottshall, 2008. “Ecosystem-wide body-size trends in Cambrian-Devonian marine invertebrate lineages.” Paleobiology. 34:210-28.


“In many locations around the world, stromatolites and other indicators of microbial growth proliferated after the Permian-Triassic extinction, suggesting that grazing and sediment disturbance by animals decreased dramatically to levels rarely seen since the Cambrian.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 257.


“Reclining animals, which lie unattached and immobile on the seafloor, were common in the Paleozoic (e.g., brachiopods) and in the Mesozoic (e.g., the oyster Exogyra). This lifestyle is virtually absent today–most animals are attached or have some method of reorienting if disturbed.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 258.


“Increases in high-energy taxa such as predators, burrowers, and other motile forms, as well as increases in body size, have led to suggestions that the energetics of the global marine biosphere increased at this time [Mesozoic]. Finnegan et al. tested this hypothesis using Mesozoic and Cenozoic assemblages of gastropods and estimated that energy use increased by at least 150% and perhaps more. Increased energy use by animals could be linked to increased nutrients from land, related to the spread of angiosperms; increased nutrients from submarine volcanism; and/or the radiation of several groups of phytoplankton (diatoms, calcareous nannoplankton, and dinoflagellates).” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 258. Reference is to Finnegan, S., C. McClain, M. Kosnik & J. Payne. 2011. “Escargot through time: an energetic comparison of marine gastropod assemblages before and after the Mesozoic Marine Revolution.” Paleobiology. In press.


“A suite of changes has swept marine metazoan ecosystems from the Neoproterozoic to the present, with increases in (a) predation, (b) motility, (c) infaunality, (d) biological disturbance, and (e) energy use. These parameters may not have changed constantly or in unison, but evidence shows a general tendency to increase. Mass extinctions temporarily impeded or reversed some of these trends (e.g., a reduction in bioturbation after the Permian extinction), but the trends resumed or even accelerated during recovery intervals.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. Pp. 258-9.


“... increased primary production or higher oxygen levels could permit more energetic ecosystems with greater proportions of motile and predatory animals. It is even possible that these trends were self-reinforcing, in that increases in planktonic and burrowing animals increased the recycling of nutrients, which allowed increased primary productivity.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 259.


“From the Paleozoic to the Cenozoic, there was an increase in the relative abundance of infaunal animals, motile and facultatively motile animals, and predators. Novack-Gottshall also found an increase in animals that use other animals and structures as microhabitats.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 259. Reference: Novack-Gottshall, P. 2007. “Using a theoretical ecospace to quantify the ecological diversity of Paleozoic and modern marine biotas.” Paleobiology. 33:273-94.


“A complex ecosystem is characterized by organisms that perform many functions and by numerous types of ecological interactions. In contrast, organisms in a simple ecosystem would fulfill fewer ecological roles and would interact in fewer ways.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 260.


“The biological landscape in the Paleozoic was relatively uniform–several ecological lifestyles dominated, and many ecological lifestyles were similar in many properties. By the Cenozoic, more lifestyles were relatively common, and these lifestyles were more disparate in their ecology. Thus, an animal in the modern oceans is likely to be involved in more diverse types of biotic interactions compared with one in the Paleozoic.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 260.


“The abilities to control movement and manipulate the environment are critical in coping with a wide range of difficulties, including predation and disturbance. The ability to control physiology has been equally important, for example, in the end-Permian extinction, animals that had greater physiological control over the precipitation of calcium carbonate fared better than those that did not. In fact, organisms whose bodies were well buffered against physiological (i.e., chemical) stress constituted approximately 30% of genera in the Paleozoic, and this percentage rose to almost 70% by the late Cenozoic. The ability to control the environment and one’s internal state has evidently given some organisms the flexibility to cope with adverse conditions and to evolve new ecological strategies.” Bush, Andrew & R. Bambach. 2011. “Paleoecologic Megatrends in Marine Metazoa.” Annual Review Earth Planetary Science. 39:241-69. P. 262.



“In a ritual definition, communication is linked to terms such as ‘sharing,’ ‘participation,’ ‘association,’ ‘fellowship,’ and ‘the possession of a common faith.’ This definition exploits the ancient identity and common roots of the terms ‘commonness,’ ‘communion,’ ‘community,’ and ‘communication.’ A ritual view of communication is directed not toward the extension of messages in space but toward the maintenance of society in time; not the act of imparting information but the representation of shared beliefs.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 18.


“... communication is a symbolic process whereby reality is produced, maintained, repaired, and transformed.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 23.


“I want to suggest, to play on the Gospel of St. John, that in the beginning was the word; words are not the names for things but, to steal a line from Kenneth Burke, things are the signs of words. Reality is not given, not humanly existent, independent of language and toward which language stands as a pale refraction. Rather, reality is brought into existence, is produced, by communication–by, in short, the construction, apprehension, and utilization of symbolic forms.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 25.


“Thought involves constructing a model of an environment and then running the model faster than the environment to see if nature can be coerced to perform as the model does.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 28.


“If one tries to examine society as a form of communication, one sees it as a process whereby reality is created, shared, modified, and preserved.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 33.


“But social life is more than power and trade (and it is more than therapy as well). As Williams has argued, it also includes the sharing of aesthetic experience, religious ideas, personal values and sentiments, and intellectual notions–a ritual order.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 34. Reference is to Williams, Raymond who wrote several books on communications and culture between 1958 and 1973.


“This is a modest goal [for cultural studies]: to understand the meanings that others have placed on experience, to build up a veridical record of what has been said at other times, in other places, and in other ways, to enlarge the human conversation by comprehending what others are saying. Though modest, the inability to engage in this conversation is the imperative failure of the modern social sciences. Not understanding their subjects–that unfortunate word–they do not converse with them so much as impose meanings on them. Social scientists have political theories and subjects have political ideologies; the behavior of social scientists is free and rationally informed, whereas their subjects are conditioned and ruled by habit and superstition–not good intellectual soil for a working democracy.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 62.


“The mind–the associative, cooperative mind–its extension in culture and realization in technique, is the most important means of production. The most important product of the mind is a produced and sustained reality.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 74.


“Finally, if reality is what we will to believe in support of our shared purposes, then it is proper to claim that reality is constituted by human action, particularly symbolic action and particularly associative action. Therefore, reality has no essence to be discovered but rather a character to be, within limits, constituted.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 81.


“... language–the fundamental medium of human life–is increasingly defined as an instrument for manipulating objects, not a device to establish the truth but to get others to believe what we want them to believe.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 83.


“Meaning in this view [a cultural studies view] is not representation but a constituting activity whereby humans interactively endow an elastic though resistant world with enough coherence and order to support their purposes. The agency by which they do this is certainly representation, but not representations simply of the world. It is the great power of symbols to portray that which they pretend to describe. That is, symbols have an ‘of’ and a ‘for’ side. It is this dual nature that allows us to produce the world by symbolic work and then take up residence in the world so produced.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 85.


“Communication is an ensemble of social practices into which ingress conceptions, forms of expression, and social relations. These practices constitute reality (or alternatively deny, transform, or merely celebrate it).... Each moment in the practice coactualizes conceptions of the real, forms of expression, and the social relations anticipated and realized in both.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 86.


“Reality is, above all, a scarce resource. Like any scarce resource it is there to be struggled over, allocated to various purposes and projects, endowed with given meanings and potentials, spent and conserved, rationalized and distributed.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 87.


“... conceptual vocabularies always contain a rhetoric of attitudes and a rhetoric of motives. There is no way to do intellectual work without adopting a language that simultaneously defines, describes, evaluates, and acts toward the phenomena in question.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 101.


“The supply of valued things in a society, including valued occupations, is strictly limited.... Preferred jobs are positional goods, as opposed to material goods,... and they are valued because they are in short supply.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. Pp. 102-3.


“When he [Durkheim] applied this analysis to modern societies, though my chronology is off here, he tried to show how capitalist societies depended for their very existence and stability on an inherited precapitalist society–the so-called precontractual elements of contract. Gesellschaft society, the society regulated by utility and contract, could not work without the integrative mechanisms of Gemeinschaft society: nonutilitarian values, beliefs, traditions, and so on. To the old slogan that money is to the West what kinship is to the rest he added that kinship performs a continuing integrative function in advanced societies. In a sense Durkheim inverts the relations of base and superstructure: the capitalist economy thrives on the root system of traditional society.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 109.


“During the Civil War and in the decades thereafter, the American dream of the mechanical sublime was decisively reversed. It became increasingly evident that America was not exempt from history or isolated from the European experience of industrialization. The war itself called into question the dream of a continental democracy. In its aftermath American cities were turned into industrial slums, class and racial warfare were everyday features of life, economic stability was continually interrupted by depression, and the countryside was scarred and ravaged by the railroads, coal and iron mining, and the devastation of forests.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. Pp. 120-1.


“For Innis uncovered the most vulnerable point in the rhetoric of the electrical sublime and disputed all those claims for electricity that McLuhan celebrated. Innis principally disputed the notion that electricity would replace centralization in economics and politics with decentralization, democracy, and a cultural revival. Innis placed the ‘tragedy of modern culture’ in America and Europe upon the intrinsic tendencies of both printing press and electronic media to reduce space and time to the service of a calculus of commercialism and expansionism.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. Pp. 133-4. Reference is to Harold Innis.


“Innis divided communication and social control into two major types. Space-binding media, such as print and electricity, were connected with expansion and control over territory and favored the establishment of commercialism, empire, and eventually technocracy. On the other hand, time-binding media, such as manuscript and human speech, favored relatively close communities, metaphysical speculation, and traditional authority.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 134. Referenc is to Harold Innis.


“Despite what Marshall McLuhan said concerning the effect of television on the senses, the impact of such communications media stems from a simple technological fact: each of the modern media has increased the capacity for controlling space. They do this by reducing signaling time (the gap between the time a message is sent and the time it is received) between persons and places.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 136.


“Following the War of 1812 the country embarked on a vigorous campaign for what were benignly called ‘internal improvements,’ the object of which, again benignly expressed, was an attempt to bind the nation together or connect the east with the west. In fact, what developed was the same pattern of communication of the colonial period but now with New York replacing London as the central element in the system.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 152.


“The point is that since 1800 we have lived with essentially a dominant eastern corridor of American communication that has created an effective monopoly of knowledge in news and entertainment. Concretely, today this means that a few national figures and themes are pretty much exclusively focused on politics and entertainment, that local issues are of interest only when they can be alchemized into national issues of concern in a few urban centers, and that the drama of news and entertainment must be made increasingly slick and abstract to appeal to national and, increasingly, international audiences.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 154.


“Seymour Mandelbaum’s Boss Tweed’s New York is a marvelous though often complacent study of the reorganization of New York City essentially on a metropole-hinterland model. My own studies suggest that same model of development holds true at the regional and county levels.

“The United States, then, at all levels of social structure pursued what I call a high communications policy, one aimed solely at spreading messages further in space and reducing the cost of transmission. That is what Innis meant by exploiting the spatial bias of modern communication. Communication was seen, in other words, solely in the envelope of space and power.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 155.


“In summary, as the United States pursued an almost exclusive policy of improving communication over long distance, as it saw communication as a form of power and transmission, the effective units of culture and social organization underwent a radical transformation. There was a progressive shift from local and regional units to national and international ones, though not without considerable struggle and conflict. Individuals were linked into larger units of social organization without the necessity of appealing to them through local and proximate structures. Communication within these local units became less critical for the operation of society and less relevant to the solution of personal problems. Finally, the growth of long-distance communication cultivated new structures in which thought occurred–national classes and professions; new things thought about–speed, space, movement, mobility; and new things to think with–increasingly abstract, analytic, and manipulative symbols.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 156.


“In his studies of paper Innis discovered the true Canadian double bind. The United States imported the raw material of printing from Canada under the doctrine of freedom of trade, a doctrine of Manchester economics that the United States selectively adapted to its interests. It then exported back into Canada the finished products fashioned from Canadian raw materials: newspapers, books, magazines, and, above all, advertising and defended its exports with the doctrine of freedom of information. Here was the Canadian dilemma: caught between the scissors of American demand for paper and American supplies of newspapers, magazines, and books, its independent existence in North American was threatened.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. Pp. 159-60.


“In one of the most quoted statements Innis characterized modern Western history as beginning with temporal organization and ending with spatial organization. It is the history of the evaporation of an oral and manuscript tradition and the concerns of community, morals, and metaphysics and their replacement by print and electronics supporting a bias toward space.

“Innis argued that changes in communication technology affected culture by altering the structure of interests (the things thought about) by changing the character of symbols (the things thought with), and by changing the nature of community (the arena in which thought developed).” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 160.


“Literacy produces instability and inconsistency because the written tradition is participated in so unevenly.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 164.


“In short, Innis believed that the unstated presupposition of democratic life was the existence of a public sphere, of an oral tradition, of a tradition of public discourse as a necessary counterweight to printing.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 165.


“The First Amendment, then, did not secure the permanence of public life; in fact it acted against it because it finally placed the weight of education on the written tradition. Modern media of communication, largely for commercial purposes, created a system of communication that was essentially private. Private reading and the reading audience replaced the reading public and the public of discussion and argument. The system of communication that actually evolved was grounded, therefore, not merely in a spatial bias but in a privatized one as well. It was privatization more than the Bill of Rights that led to the decline of censorship: ‘Decline in the practice of reading aloud led to a decline in the importance of censorship. The individual was taken over by the printing industry and his interest developed in material not suited to general conversation’. Under such conditions the public becomes a mere statistical artifact, public taste a measure of private opinion that has been both cultivated and objectified but not realized in discourse. With that the public sphere goes into eclipse.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 166. Subquote is from Innis, Harold. 1952. Changing Concepts of Time. University of Toronto Press. P. 10.


“Modern oracles, like their ancient counterparts, constitute a privileged class who monopolize new forms of knowledge and alternatively panic and enrapture large audiences as they portray new versions of the future. Moreover, modern scientific elites often occupy the same double role of oracles to the people and servants of the ruling class as did the astrologers of ancient civilization.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 173.


“These views [futuristic views such as embellished at world fairs] have potent political uses. The ideology of the future can serve as a form of ‘false consciousness,’ a deflection away from the substantial problems of the present, problems grounded in conflicts over wealth and status and the appropriate control of technology, toward a future in which these problems, by the very nature of the future, cannot exist.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. Pp. 179-80.


“In the new literature of the future, the salvation is not other-worldly but terrestrial revolution and its correlates in moral, social, and material betterment.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 180.


“Modern engineering is communication engineering, for its major preoccupation is not the economy of energy ‘but the accurate reproduction of a signal.’” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 190.


“The first communication revolution was the innovation of printing, which mechanized the production of information, extended literacy, and enlarged the domain of empire. The second revolution occurred over the last century with the marriage, through electricity, of the capacity to simultaneously produce and transmit messages–a process that extends from the telephone and telegraph to television. Now, this third communication revolution involves the linkage of machines for information storage and retrieval with the telephone, television, and computer, producing new systems of ‘broadband’ communication or ‘information utilities.’” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 190.


“The technology of the computer and the satellite has real effects, among them the capacity to simulate complex environments and to reduce, as I said at the outset, time to a picosecond and space to a universal point. But postmodernism too often merely evacuates the present into a landscape where the world is all surface, no depth, and the vulgar appears sublime.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 200.


“The most important fact about the telegraph is at once the most obvious and innocent: It permitted for the first time the effective separation of communication from transportation.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 203.


“If the same story were to be understood in the same way from Maine to California, language had to be flattened out and standardized. The telegraph, therefore, led to the disappearance of forms of speech and styles of journalism and story telling–the tall story, the hoax, much humor, irony, and satire–that depended on a more traditional use of the symbolic, a use I earlier called the fiduciary. The origins of objectivity may be sought, therefore, in the necessity of stretching language in space over the long lines of Western Union.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 210.


“Until the transatlantic cable, it was difficult to determine whether British colonial policy was being set in London or by colonial governors in the field–out of contact and out of control. It was the cable and telegraph, backed, of course, by sea power, that turned colonialism into imperialism: a system in which the center of an empire could dictate rather than merely respond to the margin.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 212.


“After the telegraph, commodity trading moved from trading between places to trading between times. The arbitrager trades Cincinnati for St. Louis; the futures trader sells August against October, this year against next.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 218.


“The telegraph removed markets from the particular context in which they were historically located and concentrated on them forces emanating from any place and any time. This was a redefinition from physical or geographic markets to spiritual ones. In a sense they were made more mysterious, they became everywhere markets and everytime markets and thus less apprehensible at the very moment they became more powerful.

“Second, not only were distant and amorphous forces brought to bear on markets, but the commodity was sundered from its representations; that is, the development of futures trading depended on the ability to trade or circulate negotiable instruments independently of the actual physical movement of goods. The representation of the commodity became the warehouse receipts from grain elevators along the railroad line. These instruments were then traded independently of any movement of the actual goods.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 220.


“In order to lend itself to futures trading, a product has to be mixed, standardized, diluted in order to be reduced to a specific, though abstract, grade.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 221.


“It [a futures market] required that information move independently of and faster than products. It required that prices be made uniform in space and that markets be decontextualized. It required, as well, that commodities be separated from the receipts that represent them and that commodities be reduced to uniform grades.” Carey, James. 1989. Communication As Culture: Essays on Media and Society. Routledge. P. 221.


“Despite its shortcomings, the pre-Ediacaran acritarch record preserves a modest diversity of forms that are sufficiently complex to diagnose as biologically distinct entities, and sufficiently common to yield long-term macroevolutionary trends. Almost universally, the emerging pattern is one of profound stasis, with the evolutionary turnover (taxonomic origination and extinction) of pre-Ediacaran acritarchs typically running one to two orders of magnitude more slowly than their early Cambrian counterparts, and disparity essentially static from the mid-Mesoproterozoic to the Ediacaran. Distinctively spinose Trachyhystrichosphaera, for example, ranges for some 400 myr without obvious morphological changes, while Tappania persists for at least 600 myr, Chuaria/Tawuia macrofossils for c. 1000 myr, and concentrically sculptured Valeria for over 1100 myr.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 44.


“Thus, the overarching pattern of pre-Ediacaran eukaryotes, including both taxonomically resolved and problematic forms, is one of minimal morphological diversity and profound evolutionary stasis. Apart from the Mesoproterozoic disappearance of macroscopic Grypania there is no compelling evidence of extinction among early eukaryotes, and only the most modest indications of innovation.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 44.


“All this changes with the onset of the Ediacaran, which begins with a major radiation of large, conspicuously ornamented acritarchs, the first measurable radiation in the whole of the fossil record. At the same time, the distinctive and hitherto extinction-proof acritarchs of the pre-Ediacaran disappear, never to return, documenting the first (more or less) measurable extinction event in the whole of the fossil record. Most significantly, this turnover of acritarch biotas is accompanied by an unprecedented, order-of-magnitude increase in evolutionary rates, such that all of these novel early Ediacaran acritarchs have disappeared within 50 myr of their arrival. With similar alacrity, the famously problematic macrofossils of the late Ediacaran appear, flourish and disappear in the course of the next 40 myr.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 44.


“The fact that most pre-Ediacaran fossils with a diagnosable morphology exhibit stasis on a 100- to 1000-myr time-scale (vs. the c. 10-myr-scale longevity of Ediacaran and younger forms) marks a fundamental break in macroevolutionary expression.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 45.

“Evolution, even macroevolution, is not simply a matter of ‘evolvability’; it is also a reflection of the external selective pressures that make it happen.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 45.


“In the Phanerozoic, at least, it is clear that organismal morphology is largely a product of coevolution, whereby novel characteristics in one biological compartment induce secondary novelty in others, giving rise to enhanced sensory and locomotory systems, ecological specialization and escalatory arms races. Indeed, it is this pervasive ‘biological environment’ that gives the Phanerozoic its dynamic character, with special explanation required only for those few lineages that fail to take part, e.g. ‘living fossils’.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 45


“Indeed, it was the unique ability of eumetazoans to extend coevolutionary ecology into multicellular/macroscopic morphospace, by way of animals preying on animals, that gave rise to Phanerozoic-type trophic structures, which in turn accounts for the vast majority of all documented diversity. Some three-quarters of described living species are animals, while most of the rest are readily recognized as the product of animal co-evolution.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 45.


“The only ecological rule that comes close to being general is the species-area relationship (SAR), whereby species diversity increases in proportion to the area studied following a constant power law. In the modern biosphere the SAR appears to hold for animals and plants at moderately high values, whereas the relationship for unicellular protists and bacteria is close to flat, a consequence of their small size and high dispersability. Indeed, Finlay and colleagues argued that organisms smaller than c. 1 mm have essentially no biogeography/provinciality. Combined with astronomical population sizes, global distribution is expected to result in reduced evolutionary turnover as both the opportunities for allopatric speciation and the likelihood of extinction become increasingly limited.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 46. Reference is to Finlay, B. 2002. “Global dispersal of free-living microbial eukaryote species.” Science. 296, 1061-3.


“The modern SAR [species-area relationship] is an emergent property of Phanerozoic-style species richness and evolutionary turnover which, in turn, is contingent upon the uniquely disruptive ecology of eumetazoans.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 47.


“Contrary to May’s linear stability models, most real ecosystems become more stable as species richness increases; thus, it is the unusually simple or simplified communities such as boreal forests and agricultural monocultures that are prone to invasion and/or catastrophic reorganization. Diversity is thought to contribute to stability in a variety of ways, most of which can be viewed as ecological ‘insurance’, e.g. ecological redundancy, negative covariance and/or ‘portfolio’ effects. In multitrophic structures, diversity increases ‘connectance’ and reduces the average strength of trophic interactions, thereby disbursing the impact of any perturbation.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 47. Reference is to May, R. 1973. Stability and complexity in model ecosystems. Princeton University Press. “Portfolio” mention is to Lehman, C. & D. Tilman. 2000. “Biodiversity, stability, and productivity in competitive communities.” American Naturalist. 156, 534-52.


“One of the important stabilizing effects in modern ecosystems relates to the availability of diverse life-history strategies among multicellular/macroscopic organisms and the emergent concept of ecological succession, i.e. the tendency of communities to become occupied by increasingly larger, longer-lived, ‘K-selected’ organisms that increasingly buffer and modify physical environment. But this is a peculiarly Phanerozoic (and transitionally Ediacaran) phenomenon. Pre-Ediacaran communities were essentially ‘instantaneous’ owing to the rapid life cycles and global distribution of their microbial, ‘r-selected’ constituents, the ultimate in environmental trackers. Unbuffered physical environments can of course be highly variable locally, but on a planetary scale these have not changed since the early Proterozoic rise in atmospheric oxygen. Without the contribution of coevolutionary ‘biological environments’, this combination of taxonomic ubiquity and physical continuity imparted a decidedly monotonous tone to pre-Ediacaran evolution.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 47.


“Extinction, particularly mass extinction, is essentially a phenomenon of the Phanerozoic biosphere, imposed by the eumetazoan forcing of organism size, ecological specialization, and corresponding reductions in population sizes and geographical range. Probably the greatest contribution of eumetazoans to extinction dynamics was the emergence of extended trophic hierarchies which, despite their inherent stability, are subject to system-wide collapse.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 47.


“The truly revolutionary impact [from the Cambrian introduction of metazoans], however, relates to the increased biomass spectrum accompanying the invention of multitrophic food webs. In the modern oceans, total standing biomass is invariant with respect to body size across all pelagic organisms from unicellular plankton to whales, owing to the simple size structuring of marine food webs (‘big fish eat little fish’) and the three-quarter allometric scaling of metabolic rate to body mass, i.e. there is just as much ‘whale’ as there is ‘cod’ as there is phytoplankton in the (undisturbed) modern ocean. With the body mass of pelagic organisms extending over 20 orders of magnitude, and predators typically four orders of magnitude larger than their prey, some 80 per cent of modern marine biomass is likely to be eumetazoan (not including heterotrophic/chemoautotrophic prokaryotes, but also not including the considerable biomass of benthic metazoans, which also exhibit an essentially flat biomass spectrum). Even more remarkably, all this animal biomass comes essentially free of charge. The addition of new trophic layers does not require any additional primary productivity; apart from a modest increase in biologically sequestered phosphorus and nitrogen, it is little more than a diversion of primary productivity through a series of incrementally larger, longer lived and more slowly metabolizing organisms.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 48.


“Organism size also correlates with organism age, such that a biosphere of large multicellular organisms gives rise to life-history trade-offs, allowing diversity to be partitioned in time as well as space. Notably, it is the extended age of larger organisms that multiplied standing biomass in the early Phanerozoic, in much the same way that trees did in terrestrial ecosystems (though aquatic ecosystems do not exhibit an equivalent biomass pyramid because of the rapid life cycles of primary producers and nested, size-structured food webs).” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 48.


“Eumetazoans can also be held accountable for a major shift in the source of marine primary productivity, from predominately cyanobacteria in the Proterozoic to predominately (eukaryotic) algae in the Phanerozoic. In a world devoid of grazers, phytoplankton are expected to evolve to minute size without morphological elaboration, playing strongly to the strengths of cyanobacteria. With the introduction of herbivorous mesozooplankton, however, the ability of eukaryotes to respond morphologically, by adding protective ornamentation and increasing size, gave them a unique selective advantage, and an unprecedented role in marine primary productivity.” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 48.


“Macroevolution as we know it is limited almost exclusively to the Phanerozoic, for the simple reason that it derives from the activities and emergent macroecological phenomena of Phanerozoic-like organisms, i.e. eumetazoans and the byproducts of eumetazoan coevolution. Unlike their pre-Ediacaran counterparts, Phanerozoic ecosystems are dominated by large, diverse, evolutionarily dynamic organisms that exhibit unique SARs [species-area relationships] (including biogeographical partitioning), unique modes of ecosystem (in)stability (including mass extinction) and unique distribution of biomass (including eukaryote-dominated primary productivity and long-lived, trophically nested, secondary productivity).” Butterfield, Nicholas. 2007. “Macroevolution and macroecology through deep time.” Palaeontology. Vol. 50, Part 1, pp. 41-55. P. 49.


“We analyzed the evolutionary dynamics of 19 Cenozoic terrestrial mammalian clades with rich fossil records that are now fully extinct or in diversity decline. We find their diversity loss was not just a consequence of ‘gamblers ruin’ but resulted from the evolutionary loss to the Red Queen, a failure to keep pace with a deteriorating environment.” Quental, Tiago & C. Marshall. 2013. “How the Red Queen Drives Terrestrial Mammals to Extinction.” Science. July 19. Vol. 341: 290-2. P. 290.


“When diversity increased, origination rates dropped and extinction rates increased. Thus, these mammalian clades exhibit the macroevolutionary equivalent of MacArthur and Wilson’s model for diversity change during island colonization. In both scenarios, the existence of diversity-dependent rates implies that each island (in MacArthur and Wilson’s model) or clade (in the macroevolutionary equivalent of their model) has an equilibrium diversity, the diversity at which the origination rate equals the extinction rate.” Quental, Tiago & C. Marshall. 2013. “How the Red Queen Drives Terrestrial Mammals to Extinction.” Science. July 19. Vol. 341: 290-2. Pp. 290-1. Reference is to MacArthur, R. & E.O. Wilson. 1967. The Theory of Island Biogeography. Princeton University Press.


“Third, we unexpectedly find that, during the decline phase, decreases in the per-genus origination rate are just as important as increases in the per-genus extinction rate in driving the observed diversity losses. In fact, on average the initial origination rate is of a similar magnitude to the final extinction rate, and the final origination rate is as low as the initial extinction rate.” Quental, Tiago & C. Marshall. 2013. “How the Red Queen Drives Terrestrial Mammals to Extinction.” Science. July 19. Vol. 341: 290-2. P. 291.


“Most discussions of clade extinction focus only on the processes and rates of extinction and seldom consider the possibility that diversity can also be lost because of a failure to replace extinct taxa. However, Bambach et al. showed that the loss in generic diversity in the end-Devonian and end-Triassic mass extinctions was primarily driven by a lack of origination. Similarly, Van Valen noted that the decline in generic diversity of perissodactyl mammals was largely due to a drop in origination rate. The causes of a failure to originate, the evolutionary sterility that we call the Entwives effect, are not understood and require more attention.” Quental, Tiago & C. Marshall. 2013. “How the Red Queen Drives Terrestrial Mammals to Extinction.” Science. July 19. Vol. 341: 290-2. P. 291. References: Bambach, R., A. Knoll & S. Wang. 2004. Paleobiology. 30: 522-4. Van Valen, L. 1973. Evolutionary Theory. 1: 1-30. “Entwives” is a reference to Tolkien’s Lord of the Rings where the Ents lost their wives.


“Last, on average the overall diversity trajectories were more influenced by changes in origination rate than by changes in extinction rate.” Quental, Tiago & C. Marshall. 2013. “How the Red Queen Drives Terrestrial Mammals to Extinction.” Science. July 19. Vol. 341: 290-2. P. 291.


“... selfish metabolism...” De Lorenzo, V. 2013. “From the selfish gene to selfish metabolism: revisiting the central dogma.” BioEssays 36: 226-35.


“Many biological and engineered systems are observed to have the property of modularity, i.e., they consist of distinct subunits which function largely independently of each other. In the context of networks, ‘modularity’ has been given a more formal mathematical definition by Newman and Girvan. Many real-world networks display some sort of modular organisation, as they can be partitioned into cohesive groups of nodes such that there is a relatively high ratio of internal (within-group) to external (between-group) link density (the number of links as a fraction of the number of possible links). Such sub-networks, known as communities, are often construed to correspond to distinct functional units. The Newman-Girvan technique attempts to partition a network into groups of nodes so as to maximise the number of links between nodes in the same group, whilst minimising links between nodes in different groups. For a given partition, it quantitatively defines modularity as essentially the excess of within-group links, relative to a comparable random network with no modular structure.” Agarwal, Sumeet. 2013. “Systems approaches in understanding evolution and evolvability.” Progress in Biophysics and Molecular Biology. 113: 369-74. P. 371. Reference is to Newman, M. & M. Girvan. “Finding and evaluating community structure in networks.” Phys. Rev. E 69, 026113.


“Kashtan and Alon used this measure of modularity [Newman and Girvan’s] to study whether, in their model systems of logic circuits and neural networks mentioned earlier, higher modularity would emerge under certain kinds of evolutionary selective pressures. They found that evolution under rapidly switching, modularly varying goals leads to networks with high modularity and pronounced motifs, whereas evolution under a single goal led to relatively nonmodular solutions with low motif frequencies.” Agarwal, Sumeet. 2013. “Systems approaches in understanding evolution and evolvability.” Progress in Biophysics and Molecular Biology. 113: 369-74. P. 371. Reference is to Kashtan, N. & U. Alon. 2005. “Spontaneous evolution of modularity and network motifs.” Proc. Natl. Acad. Sci. U.S.A. 102, 13773-13778.


“The term evolvability has been used so far in our discussion to mean the capacity of an organism to produce new variants and functionality and thus respond to environmental changes. Recent path-breaking work by Feldman, Valiant, and collaborators has sought to formalise a somewhat different notion of evolvability: what kinds of functionality can evolve at all, given reasonably constrained time and resources? This work places evolution with[in] the context of computational learning theory, viewing it as a form of learning from experience (across generations).” Agarwal, Sumeet. 2013. “Systems approaches in understanding evolution and evolvability.” Progress in Biophysics and Molecular Biology. 113: 369-74. P. 372. Reference is to Feldman, V. & L. Valiant. 2008. “The learning power of evolution.” Proceedings of COLT. Pp. 513-4.


“The mammalian visual system is organized in terms of a multitude of visual areas that operate in parallel. This raises the problem of feature integration.” Herzog, Michael & C. Koch. 2000. “Seeing properties of an invisible object: Feature inheritance and shine-through.” Proceedings of the National Academy of Sciences. Vol. 98. No. 7. Pp. 4271-5. P. 4271.


“Finally, our findings relate to illusory conjunctions and feature migration. As in these phenomena, features of one object are incorrectly bound to another. One crucial difference to illusory conjunctions is that the first stimulus (the vernier) need not be visible for feature binding to occur and that feature inheritance depends on the spatio-temporal layout of the grating.” Herzog, Michael & C. Koch. 2000. “Seeing properties of an invisible object: Feature inheritance and shine-through.” Proceedings of the National Academy of Sciences. Vol. 98. No. 7. Pp. 4271-5. P. 4275.


“Human thinking is individual improvisation enmeshed in a sociocultural matrix.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 1.


“One set of classic theorists has emphasized the role of culture and its artifacts in making possible certain types of individual thinking. [e.g., Hegel, Peirce, Vygotsky] ...

“The other set of classic theorists has focused on the fundamental processes of social coordination that make human culture and language possible in the first place. [e.g., Mead, Piaget, Wittgenstein]... These social infrastructure theorists, as we may call them, all share the belief that language and culture are only the ‘icing on the cake’ of humans’ ultrasocial ways of relating to the world cognitively.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. Pp. 1-2.


“Empircally, one new finding is the surprisingly sophisticated cognitive abilities of nonhuman primates, ...

“Another new set of findings concern prelinguistic (or just linguistic) human infants, who have yet to partake fully of the culture and language around them. These still fledgling human beings nevertheless operate with some cognitive processes that great apes do not, enabling them to engage with others socially in some ways that great apes cannot, for example, via joint attention and cooperative communication. The fact that these precultural and prelinguistic creatures are already cognitively unique provides empirical support for the social infrastructure theorists’ claim that important aspects of human thinking emanate not from culture and language per se but, rather, from some deeper and more primitive forms of uniquely human social engagement.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 2.


“... although many animals also make simple causal and intentional inferences about external events, only make simple causal and intentional inferences about external events, only humans make socially recursive and self-reflective inferences about others’ or their own intentional states. And, finally, although many animals monitor and evaluate their own actions with respect to instrumental success, only humans self-monitor and evaluate their own thinking with respect to the normative perspectives and standards (‘reasons’) of others or the group. These fundamentally social differences lead to an identifiably different type of thinking, what we may call, for the sake of brevity, objective-reflective-normative thinking.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 4.


“Although humans’ great ape ancestors were social beings, they lived mostly individualistic and competitive lives, and so their thinking was geared toward achieving individual goals. But early humans were at some point forced by ecological circumstances into more cooperative lifeways, and so their thinking became more directed toward figuring out ways to coordinate with others to achieve joint goals or even collective group goals. And this changed everything.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. Pp. 4-5.


“There were two key evolutionary steps. The first step, reflecting the focus of social infrastructure theorists such as Mead and Wittgenstein, involved the creation of a novel type of small-scale collaboration in human foraging. Participants in this collaborative foraging created socially shared joint goals and joint attention (common ground), which created the possibility of individual roles and perspectives within that ad hoc shared world or ‘form of life.’

“The second step, reflecting the focus of culture theorists such as Vygotsky and Bakhtin, came as human populations began growing in size and competing with one another. This competition meant that group life as a whole became one big collaborative activity, creating a much larger and more permanent shared world, that is to say, a culture.... In the context of cooperative argumentation in group decision making, linguistic conventions could be used to justify and make explicit one’s reasons for an assertion within the framework of the group’s norms of rationality. This meant that individuals now could reason ‘objectively’ from the group’s agent-neutral point of view (‘from nowhere’). Because the collaboration and communication at this point were conventional, institutional, and normative, we may refer to all of this as collective intentionality. When put to use in thinking, collective intentionality comprises not just symbolic and perspectival representations but conventional and ‘objective’ representations; not just recursive inferences but self-reflective and reasoned inferences; and not just second-personal self-monitoring but normative self-governance based on the culture’s norms of rationality.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. Pp. 5-6.


“We will refer to this flexible, individually self-regulated, cognitive way of doing things as individual intentionality. Within this self-regulation model of individual intentionality, we may then say that thinking occurs when an organism attempts, on some particular occasion, to solve a problem, and so to meet its goal not by behaving overtly but rather, by imagining what would happen if it tried different actions in a situation–or if different external forces entered the situation–before actually acting. This imagining is nothing more or less than the ‘off-line’ simulation of potential perceptual experiences.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 9.


“Processes of great ape cognition and thinking may be usefully divided into those concerning the physical world, structured by an understanding of physical causality, and those concerning the social world, structured by an understanding of agentive causality, or intentionality.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 15.


“When taken together, the conditional (if-then) and negation operations structure all of the most basic paradigms of human logical reasoning. The claim is thus that great apes can solve complex and novel physical problems by assimilating key aspects of the problem situation to already known cognitive models with causal structure and then use those models to simulate or make inferences about what has happened previously or what might happen next–employing both a kind of protoconditional and a kind of protonegation in both forward-facing and backward-facing paradigms. Our general conclusion is thus that since the great apes in these studies are using cognitive models containing general principles of causality, and they are also simulating or making inferences in various kinds of protological paradigms, with various kinds of self-monitoring along the way, what the great apes are doing in these studies is thinking.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. Pp. 19-20.


“On the level of action, recent studies of great apes have shown that they can (1) delay taking a smaller reward so as to get a larger reward later, (2) inhibit a previously successful response in favor of a new one demanded by a changed situation, (3) make themselves do something unpleasant for a desired reward at the end, (4) persist through failures, and (5) concentrate through distractions.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 24.


“Cognitive evolution does not proceed from simple associations of varying complexities to flexible, individually self-regulated intentional actions underlain by cognitive representations, inferences, and self-monitoring.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 26.


“Great apes are all about cognition for competition.

“Human beings, in contrast, are all about (or mostly about) cooperation.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 31.


“Early humans’ new form of collaborative activity was unique among primates because it was structured by joint goals and joint attention into a kind of second-personal joint intentionality of the moment, a ‘we’ intentionality with a particular other, within which each participant had an individual role and an individual perspective.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 33.


“In all, cooperation is simply a defining feature of human societies in a way that it is not for the societies of the other great apes.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 36.


“For you and me to form a joint goal (or joint intention) to pursue a stag together, (1) I must have the goal to capture the stag together with you; (2) you must have the goal to capture the stag together with me; and, critically, (3) we must have mutual knowledge, or common ground, that we both know each other’s goal.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 38.


“Thus, Graefenhain et al. had preschoolers explicitly agree to play a game with one adult, and then another adult attempted to lure them away to a more exciting game. Although two-year-old children mostly just bolted to the new game straightaway, from three years of age children paused before departing and ‘took leave,’ either verbally or by handing the adult the tool they had been using together. The children seemed to recognize that joint goals involve joint commitments, the breaking of which requires some kind of acknowledgment or even apology. No study of this type has ever been done with chimpanzees, but there are no published reports of one chimpanzee taking leave from, making excuses to, or apologizing to another for breaking a joint commitment.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 40. Reference is to Graefenhain, M, T. Behne, M. Carpenter & M. Tomasello. 2009. “Young children’s understanding of joint commitments.” Developmental Psychology. 45: 1430-43.


“These young children [preschoolers from one to three years old] coordinate a joint goal, commit themselves to that joint goal until all get their reward, expect others to be similarly committed to the joint goal, divide the common spoils of a collaboration equally, take leave when breaking a commitment, understand their own and the partner’s role in the joint activity, and even help the partner in her role when necessary.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 41.


“Humans are exceptional in creating categories such as pet, husband, pedestrian, referee, customer, guest, tenant, and so forth, what Markman and Stillwell call ‘role-based categories.’ They are relational not in the sense of comparing two physical entities but, rather, in assessing the relation between an entity and some larger event or process in which it plays a role.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 42. Reference is to Markman, A. & H. Stillwell. 2001. “Role-governed categories.” Journal of Experimental and Theoretical Artificial Intelligence. 13: 329-58.


“Just as collaborative activities have the dual-level structure of joint goal and individual roles, joint attentional activities have the dual-level structure of joint attention and individual perspectives.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 46.


“Other great apes [than humans] do not appear to engage in such social self-monitoring. Thus, when Engelmann et al. gave apes the opportunity to either share or steal food from a groupmate, their behavior was totally unaffected by the presence or absence of other group members observing the process. In contrast, in the same situations, young human children shared more with others and stole less from others when another child was watching.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. Pp. 46-7. Reference is to Engelmann, J., E. Herrmann & M. Tomasello. 2012. “Five-year olds, but not chimpanzees, attempt to manage their reputations.” PLoS ONE. 7(10), e48433.


“The second important consequence of this new cooperative way of communicating was that it created a new kind of inference, namely, a relevance inference. The recipient of a cooperative communicative act asks herself: given that we know together that he is trying to help me, why does he think that I will find the situation he is pointing out to me relevant to my concerns. Consider great apes. If a human points and looks at some food on the ground, apes will follow the pointing/looking to the food and so take it–no inferences required. But if food is hidden in one of two buckets (and the ape knows it is in only one of them) and a human then points to a bucket, apes are clueless. Apes follow the human’s [pointing and looking to the bucket, but then they do not make the seemingly straightforward inference that the human is directing their attention there because he thinks it is somehow relevant to their current search for the food. They do not make this relevance inference because it does not occur to them that the human is trying to inform them helpfully–since ape communication is always directive–and this means that they are totally uninterested in why the human is pointing to one of the boring buckets.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 52.


“In the object choice task, the communicator is not pointing to the bucket qua physical object or qua vessel for carrying water, but rather qua location: I am informing you that the reward is located in there. Cooperative pointing thus creates different conceptualizations or construals of things.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 57.


“And so if we believe that human thinking is intimately tied to communication–how we have come to conceptualize things for others–then the fact that we did this for some time in our history by pantomiming in space may go a long way toward explaining the inordinately important role of space in human cognition.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 65.


“And so when early humans began engaging in obligate collaborative foraging, they schematized a cognitive model of the dual-level collaborative structure comprising a joint goal with individual roles and joint attention with individual perspectives.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 69.


“The key point from the perspective of cognitive representation is that communicators were not tied to their own goals and perspectives, but rather they were considering alternative perspectives for another person, whose conative and epistemic states they could only imagine. For her part, the recipient, in order to make the abductive leap necessary to grasp the communicator’s communicative intention, had to then simulate his perspective on her perspective (at least). This transacting in perspectives meant that early human individuals did not just experience the world directly for themselves, in the manner of all apes but, in addition, at least in some aspects, experienced the exact same world viewed simultaneously from different social perspectives. This triangulating process inserted for the first time a small but powerful wedge between what we might now call the subjective and the objective.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 70.


“Modern humans became cultural beings by identifying with their specific cultural group and creating with groupmates various kinds of cultural conventions, norms, and institutions built not on personal but on cultural common ground. They thus became thoroughly group-minded individuals.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 80.


“The transformative process was conventionalization, which has both a coordinative component, as individuals implicitly ‘agree’ to do something in a consistent way (everyone wants to do it this way as long as everyone else does, too), and a transmitive component, as this way of doing things sets a precedent to be copied by others who want to coordinate as well. The result is what we may call cultural practices, in which individuals, in effect, coordinate with the entire cultural group via collectively known cultural conventions, norms, and institutions.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 81.


“But group-minded and linguistically competent modern humans had to be prepared to coordinate with anyone from the group, with some kind of generic other. This meant that modern human individuals came to imagine the world in order to manipulate it in thought via ‘objective’ representations (anyone’s perspective), reflective inferences connected by reasons (compelling to anyone), and normative self-governance so as to coordinate with the group’s (anyone’s) normative expectations.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 81.


“The proposal is thus that with increasing population sites and competition among humans, the members of human groups began to think of themselves and their groupmates (known and unknown, present and past) as participants in one big, interdependent, collaborative activity aimed at surviving and thriving in competition with other human groups. Group members were identified most readily by specific cultural practices, and so teaching and conformity to the group’s lifeways became a critical part of the process. These new forms of group mindedness led to what we may call the collectivization of human social life, as embodied in group-wide cultural conventions, norms, and institutions–which transformed, one more time, the way that humans think.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 84.


“Unlike the second-personal common ground that early human individuals created with one another as they engaged in collaborative activities, the common ground at this point is what Clark calls cultural common ground: things that we all in the group know that we all know even if we did not experience them together as individuals.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 85. Reference is to Clark, Herbert. Using Language. 1996. Cambridge University Press.


“This agent neutrality in application is nowhere more evident than in the fact that people apply social norms to themselves in acts of guilt and shame.... Guilt and shame thus demonstrate with special clarity that the judgment being made is not my personal feeling about things, but rather, it is the group’s–which is especially clear in the case of shame, in which I may not even agree with the group. Nevertheless, I, as the emissary of the group, am sanctioning myself.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 89.


“And, critically, reputational status is more than just a sum of many social evaluations; it is nothing less than a Searlian status function in which my public personal is a reified cultural product created by the collectivity,...” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 90.


“Early humans made overt the way they were perspectivizing situations for others, for example, by pointing out relevant situations with a gesture, but the recipient could easily misunderstand, or even feign misunderstanding, and that would be the end of it. But now, if a modern human uses a communicative convention such as a snake-danger gesture, the partner cannot claim not to know it or, under normal circumstances, not to comprehend it. Since we all know the convention in cultural common ground, it is explicit, and so one must respond.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 95.


“Powerful skills of imitation and conformity thus undermine iconicity in communication, as iconicity is not necessary in a group with cultural common ground about what gesture to use for communicating about certain situations conventionally. Communicative conventions can thus become ‘arbitrary.’” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 96.


“Individuals thus did not have to invent their own ways of conceptualizing things; they just had to learn those of others, which embodied, as it were, the entire collective intelligence of the entire cultural group over much historical time. Individuals thus ‘inherited’ myriad ways of conceptualizing and perspectivizing the world for others, which created the possibility of viewing one and the same situation or entity simultaneously under different construals as, for example, berry, fruit, food, or trading resource. The mode of construal was not due to reality, or even to the communicator’s goals, but rather to the communicator’s thinking about how best to construe a situation or entity so that a recipient would most effectively discern his communicative intention.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 96.


“Conventionalization, after a drift to the arbitrary, breeds abstractness.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 97.


“It is difficult to imagine how to indicate for others complex situations and events such as justice in pantomime, except for acting out a kind of full narrative, and this is true even for more concrete narrative events like a celebration or a funeral, for which one would also have to pantomime whole sequences. But with arbitrary signs one may simply designate these complex situations with a single sign. This means that, in essence, arbitrary signs open up the novel possibility of symbolizing aspects of the relational, thematic, or narrative organization of human cognition ...” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 97.


“Second, arbitrary communicative conventions come to form a kind of ‘system’ such that, precisely because of their arbitrariness, the referential range of one is constrained by the referential range of others in the same ‘semantic field’. It is thus in our cultural common ground that I am making a choice between certain conventional expressions that we both know together I have available to me.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 98. Second subquote is from Saussure, F. de. 1916. Cours de linguistique generale.


“... Croft argues that the linguistic items in an utterance gain their communicative functions not via their syntactic relations to other items but, rather, from the collaborative syntactic role they play in the utterance/construction as a whole. A linguistic construction may thus be seen, in a way, as a symbolic collaboration.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 101. Reference is to Croft, W. 2001. Radical construction grammar. Oxford University Press.


“The idea is that this independence of the propositional content from any particular ‘illocutionary force’ makes the propositional content into a kind of quasi-independent, fact-like entity, free of particular instantiations in particular linguistic utterances.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 102.


“In this case, the independence is not only from speaker motive but also from how speakers feel or think about them. This distinction between content and attitude is also foundational to the idea of some kind of timeless, objective, propositionally structured facts that are independent of how anyone thinks of feels about them and, therefore, also to the general idea of an independent, ‘objective’ reality.

“If we now combine all of the distinctions we have made–that is, those that the communicator actively controls (and for which he must choose from among alternatives)–we have the basic structure of a conventional linguistic utterance: the force-content distinction, within that the attitude-content distinction, and within that the topic-focus (subject-predicate) distinction, ...” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 103.


“Many lines of evidence suggest that the main function of reasoning is to convince others, for example, people’s tendency to look for supporting rather than disconfirming evidence (the confirmation bias). In this view, convincing others is good for individual fitness, and so humans evolved reasoning abilities not for getting at the truth but for convincing others of their views.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 110.


“Cooperative argumentation would thus have been the birthplace of ‘assertive’ speech acts. Assertions go beyond the informative speech acts from which they derive in that the asserter commits himself to the truth of a statement (i.e., I commit not just to honesty but to the objective truth of the statement)....” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 112.


“Modern humans thus ‘collectivized’ early humans’ ways of life, and so ‘objectified’ their cognitive models of the world.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 116.


“And so, if from a moral point of view, cooperation always entails some kind of effacing of one’s own interests in deference to those of others or the group, then, from a cognitive point of view, cooperative thinking always entails some kind of effacing of one’s own perspective in deference to the more ‘objective’ perspective of others or the group.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 122.


“In this formulation, ‘objectivity’ is the result of being able to think of things from ever wider perspectives and also recursively, as one embeds one’s perspective within another, more encompassing perspective. In the current view, more encompassing means simply from the perspective of an every wider, more transpersonally constituted generic individual or social group–the view from anyone.

“The monumental second step on the way to modern humans thus took the already cooperativized and perspectival thinking of early humans and collectivized and objectified it. Whereas early humans internalized and referenced the perspective of what Mead calls the ‘significant other’, modern humans internalized and referenced the perspective of the group as a whole, or any group member, Mead’s ‘generalized other.’” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. Pp. 122-3. Reference is to Mead, G. 1934. Mind, self, and society. University of Chicago Press.


“Language is the capstone of uniquely human cognition and thinking, not its foundation.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 127.


“The emergence of shared intentionality thus effected a restructuring, a transformation, a socialization, of all the processes involved in individual intentionality and thinking–an unusual, if not unprecedented, evolutionary event.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 132.


“Great apes collaborate–that is, actually work together–very little, and when they do, it is best characterized as what Tuomela calls ‘group behavior in I-mode,’....” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 136. Reference is to Tuomela, R. 2007. The philosophy of sociality: The shared point of view. Oxford University Press.


“Early human collaborative activities and cooperative communication–employing new forms of social coordination–led to new forms of human thinking without either culture or language.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 137.


“Modern humans faced some new social challenges due to increases in group sizes accompanied by competition among groups. For survival, modern human groups had to begin operating as relatively cohesive collaborative units, with various division-of-labor roles. This created the problem of how individuals could coordinate with in-group strangers, with whom they had no personal common ground. The solution was the conventionalization of cultural practices: everyone conformed to what everyone else was doing, and expected others to conform as well (and expected them to expect them to, etc.), which created a kind of cultural common ground that could be assumed of all members of the group (not not other groups). Modern humans’ ways of communicating were conventionalized in this same way as well, which meant that individuals operated in a cultural common ground comprising a kind of group perspective and with conventionalized linguistic items and constructions that could be used effectively with anyone in the group.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. Pp. 138-9.


“Each individual was also now practicing a kind of normative self-governance in which she, as emissary of the group to which she was a committed member, regulated her own actions and thoughts in terms of the group’s normative standards.” Tomasello, Michael. 2014. A Natural History of Human Thinking. Harvard University Press. P. 139.


“Since the time of Descartes and Locke (and less explicitly before, as we shall see), the basis of selfhood in Western culture has been sought primarily along or within three dimensions, ones that are familiar and should be easily recognizable to anyone. We will call them the bodily or material, the relational, and the reflective dimensions of the self. The first involves the physical, corporeal existence of individuals, the things about our nature that make us palpable creatures driven by needs, urges, and inclinations, and that give us particular constitutions or temperaments, making us for instance more or less energetic, lethargic, passionate, or apathetic. Our selves on this level, including whatever consciousness we have of them, are housed in our bodies, and are shaped by the body’s needs. The second, relational, dimension arises from social and cultural interaction, the common connections and involvements that give us collective identities and shared orientations and values, making us people able to use a specific language or idiom and marking us with its particular styles of description, categorization, and expression. In this perspective our selves are what our relations with society and with others shape or allow us to be. The third dimension, that of reflectivity, derives from the human capacity to make both the world and our own existence objects of our active regard, to turn a kind of mirror not only on phenomena in the world, including our own bodies and our social relations, but on our consciousness too, putting ourselves at a distance from our own being so as to examine, judge, and sometimes regulate or revise it. On this level the self is an active agent of its own realization, establishing order among its attitudes and beliefs, and giving direction to its actions.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. Pp. 5-6.


“The dimension or dimensions chosen and the ways they are understood are central in determining the character and implications of any given conception of the self. On such bases there arise selves generated from within their own being or ones fabricated from outside, selves whose main features are universal or specific to some time and place, selves that are stable or fluid, and selves that are more or less autonomous or dependent, self-governing or in thrall to some power or powers of whose existence they may or may not be aware.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 7.


“Underlying the many specific ways of picturing the self, there stands one broad alternative whose presence and importance only comes to light once the separability of the three dimensions is recognized. This is the difference between what we will call multi-dimensional and one-dimensional accounts of the self.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 7.


“Another way to say this [states in which the self is all and in which it is nothing] is that the two alternatives of no-self and all-self both posit dependence and independence as incompatible with each other. What images of self-existence as fully under the sway of powers outside it have in common with pictures of an ego that is unconditioned or absolute is denial that the mix of autonomy and dependency commonly found in ordinary life represents the genuine or authentic condition of personal existence.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 10.


“In creating these alternatives as conditions of the self, the three dimensions do not all play the same role. Where the self’s freedom or autonomy is at issue, the reflective dimension is the one that is most likely to be exalted or diminished. The reason lies in the special kind of self-determination it promises.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 10.


“That all these terms – self, subject, identity, person – alternately or simultaneously bear passive and active forms is a sign that our manner of being ourselves, of persisting as who we are, involved both the ways in which our selfhood is a matter of natural sameness, and the ways in which it must encompass the differences within ourselves that being human unavoidably occasions and contains.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 16.


“Reflectivity allows humans to address and in some degree deal with the tensions or conflicts between what biology demands and what social and cultural existence imposes or allows.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 17.


“Cultural systems are not spontaneously given to us as ordered spaces where action can be coherently undertaken and understood, we must each come to know the system by way of the mindful interactions in which we are caught up....

“Restated slightly, social action and social learning are mutually dependent, and both require that we be able to combine the often puzzling and discontinuous phenomena of the social world into stable, intelligible objects of understanding. Only beings capable of developing reflective judgment can find their way along the interacting threads of meaning cultures spin to support and contain their members.

“One way in which cultures acknowledge the autonomous subjectivity of individuals is by structuring social life around sets of prohibitions or taboos. Such rules always assume the possibility that individuals are capable of transgressing them; as Marcel Mauss observed, the very existence of taboos is a recognition that they can be violated.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. Pp. 22-3.


“What reflective independence creates instead is a split, sometimes perplexing and painful, between our actual being, with its persisting limitations, and our expanded consciousness. Louis Sass paints this split in more somber tones: ‘Each new perspective on oneself brings, along with the legitimate insights it may offer, new and perhaps even more tortuous possibilities of ignorance, self-alienation and self-deception.’ Reflectivity bears not just benefits, but sobering risks and dangers.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 29. Reference is to Sass, Louis. 2001. “Deep Disquietudes: Reflections on Wittgenstein as Antiphilosopher.” From Klagge, James, Ed. Wittgenstein: Biography and Philosophy.


“Such a complex self [a variety of identities or loyalties that a single person may absorb from a complex social or cultural situation] can be a healthy mode of individual existence if its multiplicity does not degenerate into debilitating fragmentation, just as the more single-minded alternative can be a sound one if it avoids obsessiveness or fanaticism. That each also has a pathological form, however, reminds us that when reflectivity falls out of balance with the other dimensions of the self it may become self-destructive. Certain diseases of the mind may even be regarded as maladies of excessive or insufficient reflectivity.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 30.


“... this connection between reflectivity and the temporality of the self was recognized by some of Kant’s successors in Germany, and it was in the same milieu that the dynamism of living forms, pushing them ever beyond their mode of existence at any given moment, was imagined as a parallel manifestation of the same inner spiritual power that drove the reflective ego to realize itself. The roots of this idea lay in Leibniz’s theory of monads, and more remotely in Aristotle’s notion of form, but the first person to theorize biological development specifically in reflective terms, envisioning the phases of a plant’s growth or the passage of an animal through stages of maturation as successive moments of self-positing on the analogy of the ego’s progressive self-realization, was the young Schelling in his Naturphilosophie. Later the notion was adopted in different ways by other thinkers. In this way nature was reconfigured so that worldly life became a medium in which reflective selfhood could effect its self-realization.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 33.


“The approach to this history developed here provides an alternative to some common ideas about the topic. From widely diverse perspectives, thinkers and writers argue that modernity introduced a particular kind of self into the world. Marxists, Heideggerians, neo-classical republicans, and communitarians all agree in their fashion that modern selfhood is characterized by claims to an abstract mode of individual self-sufficiency, one that negates the human inherence in some higher or more encompassing mode of being, and that exalts rational calculation over other more promising features of human nature.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 41.


“Martin Heidegger saw modern selfhood as exemplified in the Cartesian cogito, which made the individual human mind the source of certainty and the only bearer of subjectivity, thus relegating every other mode of existence to the subordinate realm of lifeless objecthood. This misguided self-assertiveness set the stage for modernity’s negative and linked outcomes – technological domination over nature with its attendant destructiveness, the rise of abstract state power with its crushing of communal life, and the loss of meaning in the anonymity of mass society.

“Writing from a revived classical republican perspective, the French philosopher Alain Renaut shares much of Heidegger’s diagnosis of modern life, but he assigns the blame more narrowly to the victory of a certain type of individualism, the kind that regards society as made up of separate human atoms whose unrestrained activities are expected to produce an automatic harmony, a notion he finds embodied in Adam Smith’s figure of the ‘invisible hand.’ Renaut locates the first model for such a world or unrestrained individuals in Leibniz’s image of a universe made up of self-sufficient monads, championing against it the republican subjectivity of Rousseau and Kant, with its understanding of freedom as the autonomy rational creatures achieve when they respect and obey the laws and limits they impose on themselves. In his view the opposition between these two modern modes of personhood is total; only the first bears blame for the inhumanity let loose in modern life.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 41.


“More generally, one can say that all these writers share and help to keep alive a common confusion. They rightly see that modern conditions require individuals themselves to participate in forming their selves, and that this need distinguishes modern situations from the typical earlier one in which the self or soul could be viewed as a substance and a kind of cosmic given. But they conflate this understanding with a claim that modern individuals typically look only to themselves in order to give consistency and stability to their existence, that ‘the modern self’ lives in isolation and separation from the world and others.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 43.


“We should therefore not be too quick to conclude that ancient thinking, even in its Aristotelian form, conceived the self as given, unquestioned, or free of inner tensions and divisions. Conflicts between active spirit and passive matter, between individuality and universality, surfaced in ancient consciousness as in modern, perhaps because they are inescapable features of human life. But these strains appeared differently, and more easily resolvable in classical theory because ancient culture gave access to a resource of which many moderns have deprived themselves, namely the belief that the world, like the self, is structured so as to fulfill intelligible moral ends.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 51.


“Ptolemy’s world-picture was worked out on the basis of Aristotelian physics. It set the earth at the center of the universe because Aristotle located the ‘natural place’ of heavy bodies there, whereas the ‘light’ elements of air and fire naturally sought out the higher regions. This hierarchical view of matter corresponded to the grading of souls, rising from vegetative and sensitive at the bottom to intellective at the top, and culminating in the purely intellectual being who was wholly spirit and that found its end fulfilled in the pure contemplation of forms, God. The Ptolemaic cosmos was thus at once a gradation of physical substances and a hierarchy of dignity. Whoever contemplated it passed stepwise up the ladder, moving from brute matter at the bottom to divine spirit at the top, by way of compound forms in the middle, in particular the mixture of matter and spirit that was humanity.... At its deepest level, the self existed in relation to this divine structure.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 52.


“Whether either Descartes or Leibniz evolved a modern view of the self is a slippery question, since the answer to it will depend on what sense of the umbrella term ‘modern’ we choose to rely on. But even if some kind of positive response is appropriate, we still need to pay close attention to the differences between their versions of modern selfhood and the one we will find in Locke.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 56.


“In The World the only knowledge that could satisfy him [Descartes] was knowledge of everything; when that aspiration collapsed, it was replaced by the cogito, where knowledge began with the sudden influx of self-certainty dispersing the nothingness threatened by doubt. But the pure reflective ego that now provided this ground of certitude was immediately confronted with a new threat of nothingness, in the gap between consciousness and the world that the cogito left in its wake, and which only the beneficent illumination of divine perfection could bridge. Such a recurring lurch from allness to nothingness and back again is the dialectic of pure reflectivity, alternately identifying itself with its objects and finding itself at a distance from everything that is not itself. Similar patterns would recur in other one-dimensional models of the self. Alongside them, however, modern selfhood would emerge in many other forms.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 74.


“Intellectually the starting-point for Locke’s approach to the self was his famous rejection of ‘innate ideas’ – his often-quoted description of the mind at the moment it comes into the world as a tabula rasa or blank slate, and his insistence on the importance of experience in forming thoughts, opinions, and attitudes. Locke’s empiricism was not a one-sided account of the mind as the product of circumstances and conditions, since it went along with an unquestioned conviction that humans were active users of reason.” Seigel, Jerrold. 2005. The Idea of the Self: Thought and Experience in Western Europe since the Seventeenth Century. Cambridge University Press. P. 88.


“The paradigm cases of simple reproducers are cells, especially bacterial cells.... If something can reproduce but does contain other things that can reproduce in this sense, then it is a collective reproducer. The paradigm here is a large animal such as a human. People reproduce, making more people, but our reproduction occurs via organized cell-level reproduction....

“There are also scaffolded reproducers. These are objects which get reproduced, as part of the reproduction of some larger unit (a simple reproducer), or that are made by some other object. They do not contain the machinery for their own reproduction; their reproduction is dependent on ‘scaffolding’ of some kind that is external to them. Paradigm cases of scaffolded reproducers are viruses, which induce cells to make more of the virus, and the chromosomes and genes within our cells. Genes in this analysis are understood as material objects handled with the same criteria used in the other cases.” Godfrey-Smith, Peter. 2013. “Darwinian Individuals.” Pp. 17-36. From Bouchard, Frederic & P. Huneman (Eds). From Groups to Individuals: Evolution and Emerging Individuality. MIT Press. P. 20.


“Organisms like humans, bee colonies, buffalo herds, and lichens all give rise to more of themselves. In a loose sense, it is reasonable to call of these cases of reproduction. But they are not all on a par, from an evolutionary point of view. It is possible to find features of collectives which distinguish the clear or paradigm cases of reproduction from the more marginal ones. Three features can be used to make this distinction. All come in degrees, I symbolize them with capital letters.

“The first is B, which stands for ‘bottleneck.’ A bottleneck is a narrowing that marks the divide between generations....

“The second parameter is symbolized with G, which stands for germ line. G measures the degree of reproductive specialization within a collective....

“The third parameter is I, which stands for ‘integration’ of the collective in an overall sense. This involves a general division of labor (aside from that in G), the mutual dependence of parts, and the maintenance of a boundary between a collective and what is outside it.” Godfrey-Smith, Peter. 2013. “Darwinian Individuals.” Pp. 17-36. From Bouchard, Frederic & P. Huneman (Eds). From Groups to Individuals: Evolution and Emerging Individuality. MIT Press. P. 21.


“In retrospect, dichotomous branching may have established the conditions for–or enabled–the evolution of increased size, of vascular tissue, and of many other downstream character changes.

“The same line of reasoning applies to the evolution in euphyllophytes of the differentiation between a main axis, or trunk portion of stem, and lateral branches–so-called overtopping or pseudomonopodial growth. This seemingly minor shift at the level of the shoot apical meristem appears to have enabled the evolution of the determinate lateral organs that we call leaves (or, more specifically, megaphyllous leaves, as distinct from so-called microphyllous leaves of lycophytes), and, in turn, the evolution of seeds and flowers.” Donoghue, Michael. 2005. “Key innovations, convergence, and success: macroevolutionary lessons from plant phylogeny.” Paleobiology. 31(2, Supplement): 77-93. Pp. 81-2.



“The written word, by contrast, is untrustworthy and corrupting because it is detached from the actions, honor, and character of whoever uttered it.” [In contrasting Socrates’ distrust of the written word with the Sophists’ faith in it.] McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 10.


“Aristotle was able to coopt his rivals by grounding his scholarship decisively in writing. He determined to synthesize positions represented by contending schools, his method being to group discrete doctrines and treat their differences and similarities with an aim to unraveling their apparent contradictions.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 12.


“Speech thrives on one-sided positions, so argument can go on indefinitely around the same questions; writing makes an inclusive, ecumenical approach both possible and desirable.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 13.


“Critical reading became ‘a source for further writing’ at Alexandria, spawning new genres like the commentary, the glossary, and the index. Erudition, eclecticism, and a penchant for system-building, still the vices and virtues of the scholarly mind, were the manifestations of the new scholarly style.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 21.


“Calligraphy [viz. Chinese] , an elegant art intended for learned cultivation, carried a prestige unimaginable to a Greek scholar dictating to a slave.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 25.


“... whereas Chinese libraries were founded to stem the decay of a vanishing and partly destroyed intellectual tradition in their own homeland, Hellenistic libraries developed to render an existing body of knowledge reliably reproducible and physically portable.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 29.


“This future-orientedness [of book publishing unlike the “devotional act of monastic writing”] departed just as surely from the concern for transmission and authority in classical Islamic, Sanskritic, and Confucian traditions. All of these always sought to build a ‘golden chain’ from the past to the present. Scholars in the Republic of Letters were building a bridge to the future.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 142.


“As we have seen, the letter, the book, and the museum together reformed many practices of the university, the monastery, and the library and opened up new vistas for scholars. The Republic of Letters founded its legitimacy on these new institutions, which complemented yet often radically extended the old ones. But midnight correspondents, isolated and persecuted book authors, and eccentric collectors piling up stuff in curiosity cabinets could make for a very lonely scholarly universe. One other Renaissance institution, the academy, came about to put people in the same room, whether to witness scientific demonstrations, hear a lecture on Petrarch, participate in an experimental work of music, or debate agricultural reform schemes.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. Pp. 149-50.


“In Ming China, scholars reaffirmed the authority of ancient texts as a basis for criticizing an imperial government vested with theoretically absolute power. In early modern Europe, scholars reached for the authority of gentlemen, princes, courts, and kings in order to validate new knowledge not sanctioned by ancient texts. In neither case could scholars have their cake and eat it too. Chinese gentlemen were as worldly, literate, and curious as their European counterparts, and with the Jesuits bringing European discoveries to them, and to the imperial court, they had ample opportunity to abandon themselves to the pursuit of new science. But they elected to remain faithful to the Confucian classics and thereby retain the political influence this granted them. By contrast, Europeans achieved unprecedented breatkthroughs in astronomy, physics, anatomy, and natural history but at the cost of abandoning politics and constructing an imaginary Republic of Letters that thrived in the midst of unprecedented violence and chaos.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. Pp. 158-9.


“While country lawyers reclined with encyclopedias and maidservants devoured cheap novels–reading a lot, but superficially–the scholarly devout attended to a precious body of texts ever more intensively.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 173.


“Indoctrination–the molding of character and conscience, the quintessentially Pietist gift to the life of the mind–remained its central pedagogical goal. Goettingen’s seminar pedagogy aimed to reshape the inner person, not to fashion cookie-cutter gentlemen by drilling them, as was customary, to ape Cicero or Pericles in their outward manners and speech. Instead the Goettingen classicists instilled in their students a deeply internalized sense of what it meant to think like an ancient pagan....

“Philology denotes the love of words, which at Goettingen became a love disciplined by communal attention to revered texts–the secular version of Pietist Bible study.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. Pp. 177-8.


“Pandits could always ‘revise’ them [sastras, or divine texts] by claiming divine inspiration to reveal the timeless spoken truths inadequately preserved in the hand-copied manuscripts. In order to couch such innovation in the authority of antiquity, clever pandits used their expertise in texts to bridge the distance between past and present, not accentuate it, as European philologists did. In critical areas like law, pandits’ considerable room for maneuver allowed regional variations and local customs to coexist with a vast mental universe everywhere governed by the primacy of the Sanskrit language. The panoply of sastras was part and parcel of India’s diversity.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 187.


“In reshaping our domestic environment, Pasteur’s science literally made the world into a laboratory.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 223.


“New physical spaces, most notably the public school, the factory floor, and the immigrant slum, formed from the dissolution of the premodern household. Novelty made each an open field for experimentation. The values governing each domain–democracy or hierarchy, solidarity or productivity, diversity of assimilation–were still in flux and under negotiation.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 229.


“In the past the man has been first; in the future the system must be first.” Taylor, Frederick. Quoted in McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 236.


“Mediators like Brand instilled the practice of computer networking with the same utopian values of togetherness associated with hippie communes, acid trips, and Grateful Dead concerts. Today’s information utopianism, born of a homegrown countercultural humanism to replace the discredited classical humanism of the Republic of Letters, is one of the most enduring legacies of the sixties, and one with deep roots in American history.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 268. Reference is to Stewart Brand of the Whole Earth Catalog.



“The laboratory is, after all, the only Western institution without a non-Western analog. It is also the only one whose benefits to all societies are tangibly demonstrable, and the only one able to travel across international borders largely unencumbered by culturally and linguistically specific canons of knowing.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 271.


“The widespread conflation of knowledge and information reflects what we no longer value about the ways that disciplines interpret texts and ideas, art and music, and other products of culture.” McNeely, Ian & L. Wolverton. 2008. Reinventing Knowledge: From Alexandria to the Internet. W.W. Norton. P. 272.


“Certainly, Darwin provided a new general framework to understand how complex organisms could be generated from simpler ones, but he did not provide a theory of organisms (neither of how they work, nor of how they can originate from physicochemical systems).” Ruiz-Mirazo, Kepa & A. Moreno. 2012. “Autonomy in evolution: from minimal to complex life.” Synthese. 185:21-52. P. 23.


“Any known living being cannot exist but in the context of a global network of similar systems.” Ruiz-Mirazo, Kepa & A. Moreno. 2012. “Autonomy in evolution: from minimal to complex life.” Synthese. 185:21-52. P. 26.


“If the essence of biological organization is conceived as a web of diverse interactions among rather than within current living systems (extending the idea of living system to molecular replicators, viruses, prions, organelles, parasites, etc.), it will not be possible to determine whether organisms should be taken as a basic starting point (i.e., as a highly integrated and cohesive type of organization that gets progressively complex) or just as some occasional result of an ongoing dynamics of loose cooperative relations among different kinds of biological entities.” Ruiz-Mirazo, Kepa & A. Moreno. 2012. “Autonomy in evolution: from minimal to complex life.” Synthese. 185:21-52. P. 26.


“... a process of open-ended evolution cannot occur except in the context of a population of autonomous systems. And, conversely, the unfolding of autonomous systems and their long-term maintenance depend on their insertion in an open-ended evolutionary route. So it is really the integration of these two main ideas, autonomy and open-ended evolution, that provides a complete, rich enough picture of the phenomenon of life.” Ruiz-Mirazo, Kepa & A. Moreno. 2012. “Autonomy in evolution: from minimal to complex life.” Synthese. 185:21-52. P. 27.


“Regardless of the chemical specificities, what is more significant for the purposes of the present article is to notice that, even in this minimal case (i) a variety of constraints (and work forms), of completely different nature, must come together and (ii) these constraints are not just internal but include the production, maintenance and modulation of boundary conditions. In other words, they involve some control (i.e., an asymmetric influence, exerted by the system) on the domain of interactions with the environment. These two features are central to understanding why autonomy, in this basic, chemical sense, already involves both a constitutive and interactive dimension, and may hold the key to naturalizing the ideas of function and agency, as we argue more extensively below.” Ruiz-Mirazo, Kepa & A. Moreno. 2012. “Autonomy in evolution: from minimal to complex life.” Synthese. 185:21-52. P. 30.


“It is quite problematic to naturalize biological functions in terms of natural selection, because it is not possible to resort to the mechanism of natural selection without assuming the previous existence of systems with some phenotypic-functional diversity.” Ruiz-Mirazo, Kepa & A. Moreno. 2012. “Autonomy in evolution: from minimal to complex life.” Synthese. 185:21-52. P. 31.


“In other words, there is a reciprocal dependence between what defines the ‘self’ (or the subject) and the actions derived from its existence, because it is not really possible to separate the system’s doing from its being.” Ruiz-Mirazo, Kepa & A. Moreno. 2012. “Autonomy in evolution: from minimal to complex life.” Synthese. 185:21-52. P. 34.


“‘In eukaryotes, transcription occurs in the nucleus and translation in the cytoplasm, a separation that opens a window of opportunity for the intron RNA to excise itself. Introns can thus be more easily tolerated in eukaryotes.’

“In other words, the decoupling between transcription and translation permitted a much higher level of genetic regulatory control, which, in turn, would be required to increase the organizational complexity and plasticity of the whole cell.” Ruiz-Mirazo, Kepa & A. Moreno. 2012. “Autonomy in evolution: from minimal to complex life.” Synthese. 185:21-52. P. 39. Subquote is from Mattick, J. 2004. “The hidden genetic program of complex organisms.” Scientific American. 291(4): 60-7. P. 63.


“In addition, from an evolutionary perspective, the emergence of multicellular organisms had to solve many conflicts. On the one hand, as Bonner remarks, multicellular organisms must solve two opposite selective pressures, since ‘natural selection is simultaneously pushing for a large stage in the life cycle that can compete for food and for a minute single-cell stage that is essential for sex reproduction. The result is that all multicellular organisms (...) have a unicellular stage and a larger stage of varying dimensions of their life cycle.’” Ruiz-Mirazo, Kepa & A. Moreno. 2012. “Autonomy in evolution: from minimal to complex life.” Synthese. 185:21-52. P. 42. Subquote is from Bonner, J. 2000. First signals: The evolution of multicellular development. Princeton University Press. P. 50.


“Starting from forms of collective associations where the constitutive, autonomous units are more integrated and cohesive than the collectivity, evolutionary transitions show the appearance of increasingly integrated systems, leading to new forms of autonomous agents. The organization of those agents, then, becomes much more complex, functionally diversified and cohesive than that of their constitutive units....

“But the consequences of the appearance of more complex forms of autonomy are even more important at the interactive level, as Hooker and other authors have emphasized. From that perspective autonomy is not merely the development of intrinsic, normative functions, but more importantly of new domains of interactive capacities.” Ruiz-Mirazo, Kepa & A. Moreno. 2012. “Autonomy in evolution: from minimal to complex life.” Synthese. 185:21-52. P. 45. Reference is to Hooker, C. 2009. “Interaction and bio-cognitive order.” Synthese. 166: 513-46.


“Therefore, we consider that reorganization processes are the basis of all major evolutionary transitions. Starting from ‘basic autonomy,’ which can be considered as a reorganization of natural ‘self-organization’ phenomena, all subsequent forms of autonomy derive from deep structural rearrangements of the way the system operates internally or in relation to its environment (or both)... In particular, we highlighted a rather general principle underneath those transitions, allowing for the open-ended reorganization of autonomous systems: the relative dynamic decoupling that distinct parts, modules or modes of operation in the system must show with regard to one another. As a result of many subsequent transitions, the decoupling between the last ‘upper-level’ or regulatory set of mechanisms and the underlying ‘lower-level’ dynamics can appear very strong (making understandable to a certain extent, a Cartesian type of dualistic view).” Ruiz-Mirazo, Kepa & A. Moreno. 2012. “Autonomy in evolution: from minimal to complex life.” Synthese. 185:21-52. Pp. 46-7.


“There is a flip side to this tie between life and agency. Life, like mind, does not simply belong to agents, but is more intimately woven into their fabric. Life and mind determine what it is to be an agent. Life and mind are, in some sense, inside individuals.” Wilson, Robert A. 2005. Genes and the Agents of Life: The Individual in the Fragile Sciences. Cambridge University Press. P. 4.


“Our place in the living world is not as central as it is in the domain of cognition, a point reflected in the diminished role that human agency has within the biological sciences relative to that in the cognitive sciences.” Wilson, Robert A. 2005. Genes and the Agents of Life: The Individual in the Fragile Sciences. Cambridge University Press. P. 6.


“I intend to characterize an agent in quite a general way: an agent is an individual entity that is a locus of causation or action. It is a source of differential action, a thing from which and through which causes operate....

“The notion of an agent is linked, but not identical, to that of a cause. Agents are individuals, and causes often are not.” Wilson, Robert A. 2005. Genes and the Agents of Life: The Individual in the Fragile Sciences. Cambridge University Press. Pp. 6-7.


“Without the right kind of history, wing-shaped structures are not, cannot be, adaptations for flight, no matter what else is true of them, any more than pieces of paper lacking the right kind of history can be dollar bills.” Wilson, Robert A. 2005. Genes and the Agents of Life: The Individual in the Fragile Sciences. Cambridge University Press. P. 28.


“A common expression of physicalism about the mind says that the mind is realized in the physical constituents of the body.... Realization is a relation of determination at a time in much the sense that causation is a relation of determination across times;...” Wilson, Robert A. 2005. Genes and the Agents of Life: The Individual in the Fragile Sciences. Cambridge University Press. P. 34.


“But not all properties have entity-bounded realizations. Some have what I call a wide realization. Wide realizations also involve the arrangement of physical entities, but they are not contained within the physical boundary of the individual who has the corresponding property.” Wilson, Robert A. 2005. Genes and the Agents of Life: The Individual in the Fragile Sciences. Cambridge University Press. P. 34.


“It has seemed to me for some time that when it comes to metaphysics, there is a deep philosophical and scientific bias in favor of the small and so against the not so small. In keeping with times of political correctness, I have referred to this form of discrimination as smallism.” Wilson, Robert A. 2005. Genes and the Agents of Life: The Individual in the Fragile Sciences. Cambridge University Press. P. 38.


“For example, consider William Bechtel and Robert Richardson’s fascinating study of strategies of localization in nineteenth- and twentieth-century neurophysiology and biochemistry, Discovering Complexity. Bechtel and Richardson analyze a range of examples from the history of the psychological and biological sciences with an eye to highlighting the role and nature of strategies of decomposition and localization. In their view, when strategies of ‘upward’ integration attempt to challenge the smallist orientations – by appealing, for example, to emergent, holistic, or whole-greater-than-the-sum properties – they must content themselves with offering a more accurate description of the phenomena to be explained rather than with providing an alternative explanation of the phenomena of interest. This limits the appeal of such views within the relevant scientific community.” Wilson, Robert A. 2005. Genes and the Agents of Life: The Individual in the Fragile Sciences. Cambridge University Press. Pp. 40-1.


“There are no security products without a speculative counterpart, since the one who sells such an insurance is making a risky bet against the future. And speculation is fed as much by a bubble forming as it is by fears of the bubble bursting.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 19.


“Thus ‘derivative’ products developed powerfully because they were based upon ‘underlying’ ones like interest rates, stock exchange quotations or even mortgage credits (like the well-known sub-primes in the United States). Worse, these products have enlarged their range of underlying products to include petroleum, raw materials and food.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 24.


“To sum up, therefore. The virulence of the monetary centre stems, from the beginning, from the double liberalization of the monetary markets–a liberalization of the exchange rates during the 1970s and of the interest rates at the beginning of the 80s. A financial industry in the coverage of risks developed in order to protect the real economy from these two shocks. Companies had to cover themselves against risks linked to variations in the exchange and interest rates. Swelling visibly during the 90s, this industry began to cover risks of all sorts with more and more sophisticated products, all of which were exchangeable on the financial markets.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 26.


“Between 1988 and 2008, the world liquid assets went from 8 to 19 per cent of the planet’s GDP. Briefly interrupted by the crisis, this elevation has again increased over the past year. It is fed by two springs; the accumulation of the currency reserves of the emergent countries, and the monetary measures taken by the central banks of the rich countries.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. Pp. 39-40.


“Demands for a financial yield fixed a priori effectively imply a transfer of massive risk onto the management of the business which then sees itself constrained to an obligation for results–to reach, according to the particular case, the 15 or even 25 per cent norm of financial profit....

“One, the mechanism of the stock options was a powerful means to encourage senior management to create value for shareholders....

“Two, there was the introduction, in management methods, of the criteria of the Economic Value Added ....

Three, the obligation for results can be attained by the technique of so-called capital ‘accretion’–reducing the number of shares of a company [by buying back stock] and thereby allowing, at the end of the exercise and for the same amount of profit, higher dividends to be assigned to the shareholders....

“Four, ... This increasing transparency [selling off divisions of a particular public company or “a reduction in the number of its activities”] gives institutional investors an essential power of a macrofinancial nature on the planetary level–that of managing the circulation of the flow of liquid assets and the economic values between the different businesses and activities of the entire world.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. Pp. 45-9.


“What is fundamentally new is the convergence between the logics of deregulation to which the world economy has today been introduced. This convergence has been felt in the strength of the shock wave whose full force has struck three intrinsically connected realms. One, the world of work, in which unacceptable inequalities have been carved out. Two, our planet, which is now experiencing irreversible shocks while being on the verge of a major energy crisis. And three, political action, which, outstripped by the extent of three problems and incapable of resolving them, has been pulverized by 40 years of neoliberal practices and thinking.

“This shock wave radiates from the playground of financial markets.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 54.


“The Capgemini and Merrill Lynch report on world wealth and its distribution was published in June 2008 and showed that 95,000 people have at their disposal a patrimony of 13.1 T$–more than a quarter of the whole wealth produced in the world in 2006.

“We are therefore in the presence of a privileged caste which appropriates a major part of the resources of 6.7 billion people. This caste constitutes a ‘new aristocracy’....” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. Pp. 60-1.


“But the most disastrous consequence for countries is the considerable amounts needed to service the debt, a veritable annual tribute that has to be paid to the financial sphere, to the large banks in particular.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. Pp. 65-6.


“... financial markets have ceased to be places for the financing of business, even though this is still their main function. The net issuing of shares has become effectively non-existent or negative in the majority of developed countries.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 73.


“Apart from the role of financing, which they have lost, stock market shares normally fulfil two other functions; the evaluation of companies by a comparison of the supply and demand of shares, and the possibility of bringing together companies by merger or acquisition, notably by the exchange of shares. But is the stock exchange really necessary for this? We doubt it.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 76.


“There is no denying that a confrontation between two orders of logics, one financial, the other political, has become inevitable.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 79.


“Countries were no longer required to finance their budgetary deficits by printing money [because of the “liberalization of interest rates” in the 1980s], or, in other words, through the monetary financing of public deficits but, on the contrary, through financing on the bond markets.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. Pp. 94-5.


“In a theoretical framework which has progressively ossified round concepts of market equilibrium, competition and stimulation, authorized empirical confrontations are limited only to econometric tests–to what can simply be measured and made to fit the equation.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 100.


“‘Economic science’ was revealed in the eyes of all to be pitifully incapable of offering a reading of the contemporary world in a way that would illuminate the real causes of the catastrophe. How can one believe then that this ‘science’ might still nourish, for example, a democratic debate about the scenarios offering a way out of the crisis?” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 101.


“To put in place a currency that is ‘common’, but not necessarily a single currency, in stages, would be the most effective way of reducing the financial sphere, fighting against speculation of all sorts and rediscover the fundamentals of economic life in society.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 126.


“Another argument in favour of the remaking of the international monetary system is of a theoretical nature and can be supported by Robert Mundell’s so-called law of the impossible trinity. He affirmed that an independent monetary policy on the internal level, the free movement of capital on the external level and a fixed exchange rate for one national currency in relation to others cannot be reconciled with one another. There is an incompatibility that makes it necessary to abandon one of the three elements set out above, namely autonomous monetary policy; freedom of capital movements; and fixed rates of exchange.

“An international currency means adopting fixed parities between the major currencies and abandoning either the freedom of capital movements or an autonomous monetary policy. It appears desirable to abandon the freedom of capital movements when one knows how potentially destabilizing the to-and-fro movement of international capital is to productive activity. It then means putting in place an autonomous monetary policy at the level of each country (or union of countries). This will amount to the government fixing interest rates, necessarily taking account of two contradictory imperatives. On the one hand, it will need to determine the general cost of financing long-term investments which will impel it to reduce the rise in interest rates. But, on the other, it will be necessary for it attract national savings by sufficiently remunerative interest rates, especially in order to finance public deficits.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 127.


“It is here that Keynes’ idea of the ‘bancor’ [as international currency] should be reconsidered.... A clearing house needs to be created to regulate exchanges between countries.... This system would make possible not only the establishment of the commercial surplus and deficit of each country and the operation of their regulations, but also stigmatize those imbalances in one direction or the other. Keynes’ proposition, therefore, would mean establishing a principle of symmetry between the rights of creditors (those with external surplus) and those of debtors (those with external deficit). The rights of the former are not superior to those of the latter....

“A country in surplus should either revalue its currency or boost its internal demand. For credits as for unpaid debts, countries would have to pay an interest rate. Each of them would then have a strong incentive not to provoke imbalances in their external exchanges.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. Pp. 129-30.


“This is why it is necessary to privilege anew and in an absolute way the use-value of goods which have a genuinely collective sense [public services] and not their exchange value.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 138.


“Traditionally, the domain of the social economy is of associations, mutual societies, cooperatives and foundations. But, with the globalization and financialization of the economy, this field has lost part of its benchmarks.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 148.


“This must be answered in a way that will not be a restructuring of capitalism but a pathway which branches off to offer a new vision. Such a new company may be called an ‘alternative partnership business’, whose objective will be the sharing of power and the negotiation of the results between the providers of funds, the directors and the workforce. The standard results after taxes could remunerate the past (those who provided funds), the present (the workforce and the directors) and the future (the investments). This sharing is justified by the risk taking of each of those involved.” Morin, Francois. 2013. A World without Wall Street? Seagull Books. Translated by Krzysztof Fijalkowski. P. 154.


“For a cell to remain in a stable state, the total set of active genes must include those that specify the proteins that bind to recognition sequences near those very genes, but must not include any proteins that will activate currently inactive genes. Unless these conditions are met, the proteins made by the set of genes active now will not sustain that set of genes–some genes may go off and others on, and a new set of proteins will be made, and so on. These changes will continue to take place until a self-sustaining state is reached.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 10-11.


“The level of organization represented by protein complexes takes us to a very important boundary. The assembly of proteins into their complexes relies on information that resides only within proteins, themselves (‘information’ being, in this case, synonymous with structure). It therefore belongs within the domain of chemistry and the result is always the same: reliable, reproducible, but inflexible. At larger scales, biological structures are more variable, their exact arrangements being adapted to circumstances. The overall shape of a cell, for example, is adapted to the space it must fill in a tissue. The arrangement of the connections it makes with neighbouring cells must similarly be adapted to the location of the cells that surround it. These larger-scale structures cannot, therefore, be determined solely by the information contained in the chemical structure of their molecular components: extra information is needed. This transition between internally determined structure and structure that is regulated by external information as well, takes us across a boundary from pure chemistry to the realm of biology.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 12-3.


“... [In the first cell divisions of an embryo] cleavage means that each generation consists of cells that each have half the volume of their immediate predecessors; soon the size of cells will reach a practical minimum and interludes of cell growth will be needed between divisions. Cell growth implies a need for nutrients and the requirement to do something about obtaining them. This, in turn, means that some cells need to specialize to bring food to the others. In many animal embryos, feeding is achieved by harvesting yolk laid down in an egg. In mammals, it involves bringing resources directly from the mother, but the general point holds true: at some point, cleavage must end and specialization must begin.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 28.



“Those [cells of an early human embryo] that find themselves with a free surface activate a set of previously inactive genes and become the embryo’s first specialized tissue, the trophectoderm. Cells with no free surface, on the other hand, hold those genes firmly ‘off’. This use of a simple physical cue (free surface) as something that can be interpreted as ‘information’ frees the embryo from any requirement to have a prior spatial plan.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 29.


“The mode of life of a human embryo is essentially parasitic, but this metaphor must not be taken too far. The embryo may be a parasite but, since tolerance of this parasitism is the only way that a woman can reproduce, it is essential to the survival of the species.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 31.


“Over evolutionary time, new species seem to have arisen mainly by changing the later parts of their development, not the earlier, and embryos look much more alike than the adults that develop from them.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 55.


“The trick of dividing a body into many segments, which are basically similar but carry certain specializations according to how far along the body they are is a feature of many types of animal. In primitive species such as earthworms, each segment is remarkably self-sufficient in physiological terms, having its own primitive lungs, kidneys, nervous system, etc. Some systems, such as the gut, run through all or most of the segments, and the nervous systems of each segment are connected so that the animal behaves as a coherent whole. Nevertheless, building much of the body by repeating a basic module probably confers a great advantage in being able to use the same genetic and cellular systems again and again. This economy will have made the evolution of animals of this scale much less unlikely than it would have been had every part of the body been radically different. It is in the most primitive animals, primitive both in the sense of simplicity and in the sense of early appearance in the fossil record, that segments are most similar to one another. During subsequent evolutionary history, there has been a gradual pattern of making particular segments more and more specialized for particular tasks, such as powering insect wings or walking. As segments have become more specialized, they have become more dependent on each other physiologically so that, instead of each segment having its own kidney, breathing apparatus, etc., they share centralized services.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 66.


“The longer a tissue that is to be patterned by a single concentration gradient is, the less steep the slope of that gradient will be compared to the size of any cell. The shallower the gradient, the less the difference in concentration between adjacent cells, and the harder it would be for cells to make accurate decisions that are meant to reflect their exact positions in an embryo. The gradient system that was adequate for imposing crude differences in cell behaviour in the short early embryo is simply not up to the task of imposing a succession of fine differences along the much larger body that now exists.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 69-70.


“The opposing gradients of retinoic acid (RA) from the head end of the body, including maturing somites, and of FGF from the tail end, define a narrow ‘permissive zone’ within which cells are capable of committing themselves to make a new somite.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 71.


“Four mechanisms that operate on the local, cell-scale level, then–production of retinoic acid, production of FGF, the somite clock [“self-repressing loops of the kind described above that are reliant on proteins being short-lived compared to transcriptional and translational delays involved in their production”], and the tailward growth of the embryo–integrate space and time in a way that lets cells decide whether or not to participate in making a new somite.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 74.


“It is striking that, during all of the 460 million years or so that jawed vertebrates have swum, walked, or flown this planet, the order of HOX genes along the clusters has never changed in any of these animals... The reason that the order of the HOX genes has been so conserved is that the order is linked fairly directly to the order in which different specializations of segments appear along the body....

“By this mechanism, the order of genes in the HOX clusters, which is a structure at the molecular scale, is translated into the order of HOX gene expression along the embryo, which has already reached the millimetre scale. This is one of a very few examples in which genetic structure relates directly to embryonic structure.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 77.


“All over the embryo, adjacent blocks of tissue use signals coming from each other to divide themselves up into different cell types, based on whether a cell is near to or far from the source of the signal. An immediate result of this process is the formation of new boundaries between the just-created cell types within the original block of tissue. If these cell types secrete different signalling proteins, the same trick can be used again to create ever more zones of different cell types. It is a powerful invention, and it is perhaps no surprise that around a fifth of the set of all human genes are devoted to producing proteins involved in some way with cell signalling.

“As well as allowing tissues to be subdivided almost without limit, the use of cell communication is an excellent mechanism for coping with errors in development.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 90.


“Building a body with hundreds of different cell types that have to interact with each other precisely would, though, be out of the question. In a system in which tissues rely on each other for signals, on the other hand, the formation of special cell types in each tissue is positioned automatically so that cells specialize appropriately close to the tissue whose signals are used to drive specialization, even if that tissue is itself a little out of position. The organization of the system therefore keeps adapting itself to circumstances, and errors do not accumulate but are instead corrected at each stage.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 90.


“The use of conversations, conducted in the language of proteins, to organize the subdivision of tissues has an interesting consequence for animal development. The range over which a protein will spread to give useable concentrations is fixed by the laws of biophysics and biochemistry, and for most proteins it is around a twentieth of a millimetre (= 50 microns). This means that a group of cells that is using this method to acquire a pattern tends to be around a twentieth of a millimetre long at the time that it acquires the pattern, whether we are talking of the spacing between dorsal and ventral parts of the neural tube, or between developing tooth roots, or developing hairs, or anything else. This has two consequences. One consequence is that not all of the embryo can acquire pattern at once. First the ‘coarse-scale’ patterning has to be done while the embryo is quite small then, as the parts that acquired their basic identity in this phase grow larger as the whole embryo grows larger they can be subdivided, and so on. This is one reason that human development cannot proceed by making a minuscule but complete baby in the first week and then just growing it: successive phases of patterning have to be separated by growth. First, the embryo is divided crudely into head and trunk then, when the head has grown, it is in turn patterned to specify one region as jaw (to take an example). Then, when the jaw has grown, it is in turn patterned to specify the positions of teeth, and so on.

“The second consequence is that, for any particular patterning event, such as specification of zones of the neural tube, an embryo has to be within a fairly restricted range of sizes. Thus, at this stage of this development, the embryos of a shrew, a human, and a blue whale are almost exactly the same size.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 90-1.


“Migrations at a cellular scale are every bit as astonishing as the great odysseys of birds and fish that have so long fascinated zoologists. Even more so given that, unlike birds, cells have to navigate accurately through an environment whose shape is changing all the time and they have to do so without the benefits of eyes, brains, or an opportunity to learn from their parents.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 92.


“The activation of filament-nucleating proteins and the inactivation of capping proteins at the membrane [of the forward side of a cell that is moving] create an asymmetrical environment that ensures that most new microfilaments grow towards the membrane and any growing the wrong way are quickly capped.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 95.


“This fixation [attachment to an exterior surface of a cell] is achieved by complexes of adhesion proteins that can attach the cell to the surface on which it is crawls.

“As well as providing the microfilaments at the leading edge with something against which to push, the adhesion complexes are important in allowing the bulk of the cell to follow the leading edge rather than being left behind. Away from the branched network found at the leading edge, actin filaments tend to form ‘cables’ of many parallel filaments cross-linked by a protein called myosin, which can ‘pull’ on the filaments and make the cables tense. These cables, similar to the cables that run between cell-cell junctions, are prevented from forming within the leading edge itself, because myosin is inactivated in that environment. Further into the cell, though, myosin is free to act and to organize actin into cables.... The adhesion complexes therefore carry two sets of forces: the network of leading edge actin filaments pushes off them to advance the front of the cell, and the thick cables running to the rest of the cell pull on them, to draw the rest of the cell forwards.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 95-6.


“Even though mechanics can account completely for guidance [of a cell’s direction of movement] in some cases, chemical signalling is very important in others. Some molecules on the surface are not used for adhesion, but are instead recognized by receptors in the cell membrane that activate signalling pathways inside the cell. Some receptors and pathways act to stimulate, locally, the activity of filament-nucleating proteins and therefore the local advance of the membrane.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 99.


“... there are many different types of adhesive complex, each of which adheres most strongly to a specific surface protein.... Different types of cells carry different combinations of adhesive complex.... This means that different cell types will make different decisions about direction, even when they are crossing the same set of surfaces.

“The stationary cells of the developing tissues of an embryo synthesize surface molecules such as Laminin and Fibronectin. Different types of cells secrete different combinations of molecules. This means that the different tissues of a developing animal appear, to a crawling cell, as a richly patterned landscape of more or less adhesive surfaces, some of which might also have chemical signalling molecules on them that are either attractive or repulsive. Different types of crawling cell will see this landscape in different ways, according to the adhesion complexes and receptors they carry, and what might be a highly attractive surface for one cell type may be completely repulsive to another.... In this way, different types of cell can follow different routes through the embryo.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 99.


“Making maturation depend on signals from the correct destination ensures that cells that have not found their destination continue to seek it rather than give up and mature in the wrong place.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 102.


“The maximum distance a typical mammalian cell in a solid tissue can be from a source of raw materials, and still obtain enough by random thermal diffusion, is a few tens of cell diameters (a few specialized cells, particularly in the skeleton and its associated tissues, tolerate greater distances).” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 107.


“There is an almost infinite variety of possible toxins that might have to be removed from blood, especially in an animal with a varied diet, so it is not feasible for the kidney to work by having specific export systems, each tailored for one specific waste. Instead, all small molecules, good and bad, are filtered out of the blood to a temporary holding area, then specific transport systems recover only the finite number of types of molecule that are still needed by the body.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 125-6.


“As the mesenchyme [clump of cells that will form the kidney] signals to the tube that branched out from the Wolffian duct, so the tube signals back to the mesenchyme. Its signals cause the previously loose-packed mesenchyme cells to make a dense cap around the tip of the branch. Within this cap, the mesenchyme cells make new proteins and they begin to multiply. As they do, they continue to make GDNF and other signalling molecules, and these cause the branch to keep growing and dividing into more branches, each of which will divide again, and so on. As the tips divide, each inherits some of the cap mesenchyme. The result of this is the development of a small ‘tree’ of tubes, each bearing its own cap of GDNF-ssecreting mesenchyme cells. The tree of tubes will form the urine collecting system of the kidney.

“A striking feature of this process is the inter-dependence of the branching tubes and the cells that cap them. In principle, one could imagine an alternative system in which each of these cell types would multiply of its own accord. In such a case, however, there would be a real risk of one cell type multiplying faster than the other, so that the ratio of the two tissues would become more and more unbalanced and there would either be a lot of uncapped tubes or a large lump of cap cells with nothing to cap. Even if the relative multiplication rates in this imagined organ were exactly right, there would still be the risk that the tubes would extend in directions that take them away from the bulk of the cap cells, again resulting in a dysfunctional organ. In the real kidney, the dependence of the tube for cap-derived signals and the dependence of the cap for tube-derived signals keep the development of these two tissues properly in step. Any cells of one type that stray too far from adequate population of cells of the other type will simply cease to multiply and will not create a problem. This inter-dependence between tissues is an important feature of the self-organization of the kidney and it is, unsurprisingly, seen in other organs as well. The identities of the signalling molecules are sometimes different, but the general principle remains the same.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 128-9.


“The development of the kidney, like all other internal organs, is therefore controlled to a very large extent by conversations between different cells, conversations conducted in the language of spreading signalling proteins. What each cell does, and importantly what signals it sends out, are controlled by the signals it receives. The system is therefore rife with inter-dependencies. This makes it very adaptable, both in terms of tolerance of error and in terms of being able to accommodate evolutionary change. If, for example, an evolutionary change in an animal makes it continue growing for longer, then extending the growing period of the kidney will automatically just add yet more branches to the collecting ducts and yet more nephrons and more blood vessel branches, with no need for any detailed changes to be made to the system. Major alterations in body size, and to a large extent shape, can therefore be accommodated by organs that organize themselves using internal conversations between their tissues.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 132.


“The limb, then, seems to control its internal patterning by gradients of signalling molecules, the gradients being arranged at right angles to one another so that they cover all three dimensions of space. In terms of geometry, these axes are independent of each other but in terms of biochemical activity they remain tightly and confusingly connected.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 143.


“The choice of sex is therefore a struggle between two latches. If SRY is present and can switch the FGF-SOX9 latch in time, male-development is self-sustaining and the WNT4 pathway, necessary for female development, is held firmly ‘off’. If SRY is not present or for any other reason fails to establish the FGF-SOX9 latch in time–about six hours in mice–then the WNT4 pathway becomes active, promotes female development, and holds any vestige of male development firmly ‘off’.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 149.


“The main problem faced by the developing nervous system is to arrange all of this ‘wiring’ so that neurons are connected properly to one another and, where applicable, to organs of sense (eyes, ears, nose, touch, temperature, etc.) or to organs of action (muscles, blood vessels, glands, etc.). Much of the work needed to achieve this is done by special structures found at the ends of growing axons–the growth cones.

“Growth cones consist mainly of the proteins that run the cell migration mechanisms ....” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 163-4.


“Different types of neuron make different adhesion complex proteins, and even one single type of neuron can produce different sets of adhesion complex proteins at different stages of its life. Each of these complexes sticks to a different partner molecule on an underlying surface, provided that the partner molecule is present. In this way, it is possible for different neurons to be faced with the same choice of surfaces but to make opposite decisions about where to grow.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 165.


“An example of the all-or-none type of response can be seen in a system that determines whether axons cross the midline of the spinal cord. Strong control of this is very important for a person to be able to move asymmetrically, for example to be able to hold a saucer still with the left hand while raising a teacup with the right. Raising the teacup involves voluntary contraction of the biceps muscle (and others). To the best of anyone’s knowledge, there is nothing intrinsically different between the molecules expressed by the biceps of the left arm and the right arm. Growth cones of motor neurons in the spinal cord that are destined to control biceps would not in themselves be able to tell the difference. If growth cones could wander freely across the midline of the spinal cord before exiting it to seek the muscles, many of the neurons that should control the right arm would control the left one too, and vice versa, so the arms could only move together. It is therefore very important that this cannot happen, and motor neurons on the right side of the spinal cord can reach only the right arm.... It is true the body can detect and correct for occasional errors, by the processes of refinement ..., but these will only work if most of the wiring goes to roughly the right place in the first instance.

“Whether or not a growth cone, say of the axons of an interneuron that passes signals from one spinal cord neuron to another, is allowed to cross the mid-line depends mainly on its reaction to contact with cells of the floor plate, the strip that runs along the ventral surface of the neural tube. Floor plate cells display on their surfaces a protein called SLIT. SLIT is detected by a receptor called ROBO, which is present in the growth cones of some neurons. When ROBO binds SLIT, it triggers signalling pathways inside the growth cone that block protrusion of the leading edge and also cause it to be pulled back actively. A part of the leading of a ROBO-carrying growth cone that blunders into contact with a cell expressing SLIT therefore collapses, blocking the advance of the axon in that direction.... If a growth cone does not possess ROBO, on the other hand, that growth cone is completely blind to the presence of SLIT and can cross the midline with impunity.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 165-6.


“Growth cones can change the set of proteins that they express at different stages of their lives. The axons that are supposed to cross the midline are an excellent example of this. On their way down to the midline, they possess receptor proteins that detect attractive signals that are released by midline cells and are therefore attracted there, and they express almost no ROBO and make proteins that dull the effect of ROBO signalling anyway, so they are able to cross the midline. As they are crossing, though, they are exposed to the high levels of Sonic Hedgehog that are made at the floor plate, and this causes them to become sensitive to ROBO after a small delay that is just long enough to allow them to complete their crossing. Their new sensitivity to ROBO means that the growth cones now find the midline repulsive: they therefore do not attempt to re-cross it but instead move away to travel on to their final targets.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 166.


“The axons of cells that are only supposed to connect on their own side of the central nervous system produce axons that must not cross the floor plate. The growth cones of these axons express ROBO and are repelled by contact with the floor plate. They therefore cannot cross the unwelcoming territory. Some of these neurons are sensitive both to the attractive signals that emanate from the floor plate and to the repulsive SLIT at the floorplate. Faced with the conflicting influences of attraction and repulsion, they stay as close as they can to the attractive signal, without being so close that repulsion becomes too strong. Like moths flying as close as they can to a flame without being burned, they maintain a constant distance from the floor plate as they grow parallel to it, along the length of the spinal cord. These connect different levels of the body to one another along the head-tail axis,....” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 167.


“An example of repulsion operating in a relative, rather than an all-or-none, way is seen in the way that the eye is wired to the brain.... The processing cells each send out an axon that travels directly into the brain. Many go to an area near the back of the head called the superior colliculus in mammals. The axons of the retinal ganglion cells all run parallel to each other as a thick cable–the optic nerve–but when they reach the superior colliculus they disperse and connect to it in a quite remarkable manner: the place to which each one connects to the colliculus depends, in a precise way, on each ganglion cell’s place on the retina. In effect, the exact layout of the ganglion cells on the retina is replicated on the colliculus so that it has a fully laid-out image, in electrical activity, of the optical image that is present at the back of the eye.

“Several mechanisms coopeate to create this mapping of retina to colliculus, and turn an initially rough mapping into a more precise one. One powerful mechanism is provided by the interaction of repulsive molecules carried by cells of the colliculus with receptors on the growth cone that, if they detect the repulsive molecule, encourage local collapse of the growth cone’s leading edge. The production of the repulsive molecule on the colliculus is not uniform. Instead, it is very strong in the part of the colliculus that should end up being connected to axons from the side of the eye nearest the nose, the ‘nasal side’. It becomes progressively weaker across the colliculus until it is very low in the part that should end up being connected to axons from the side of the eye that is nearest to the ear. The production of the receptor by the growth cones of retinal ganglion cells is also not uniform: the growth cones coming from the nasal side of the eye make very little, but the amount expressed rises steadily until the growth cones coming from the side of the eye nearest the ear express very large amounts.... By their competing to get away from the repulsive molecule, and competing harder the more sensitive they are, the growth cones therefore arrange themselves on the colliculus in the same spatial order that they left the retina.

“The mechanism described above orders growth cones according to their place along the horizontal, nose-ear axis of the eye. A very similar system that uses other pairs of repulsive molecules and receptors organizes the brow-cheek axis, so that the ‘wiring’ of the eye to the colliculus is a faithful two-dimensional map. For both axes, it is likely that there are still-undiscovered signalling systems, perhaps attractive ones as well as repulsive ones, that act with the repulsion-based mechanisms described above to refine the map. We are still in the very early stages of understanding all of this.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 167-170.


“As cells in the central nervous system develop, a combination of cues provided by neighbouring tissues and the proteins already present in the cells determine which of their genes will be switched on or off. Some of these genes specify the production of signalling molecules that act as cues for other neighbouring cells and can affect their gene expression. In this way, an initially simple and homogeneous system can organize itself to become very complicated and heterogeneous. Within the nervous system, there is the added complication that, once neurons start to send out growth cones and these growth cones use cues from surrounding cells to navigate and to lay out axons behind them, the axons themselves can act as cues that can either change gene expression in nearby cells or direct the migration of subsequent growth cones from other cells. Like the embryo as a whole, the developing nervous system is a self-creating landscape that adds complexity on complexity, and in which present geography depends on past history.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 173.


“This method of development, in which the response to one change becomes the stimulus for the next, is a powerful method of increasing complexity, but it entails serious risks. Where small differences made by one mechanism are amplified many-fold by the way that subsequent events build on that initial difference, there is little room for error, and the failure of one system early on can have disproportionately devastating effects later.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 173.


“It is estimated that more than half of the cells made by a foetus eliminate themselves from the body as part of entirely normal development. Because cells ‘choose’ to destroy themselves, the process is called ‘elective cell death’.

“One reason that cells may choose to die is that they form a tissue that is needed for construction of the body without actually being included in the final product. Tissues like this can be compared to the scaffolding that builders use to make an arched bridge, which is removed once the bridge is complete and self-supporting. The temporary kidneys ... are arguably examples of such tissues. In ‘lower’ animals, such as fish, this type of kidney remains in place and functions in the adult, but in adult mammals excretion is done by the ‘new’ type of kidney.... Like fish, mammals make their first blood cells and blood vessels in a complex of tissues that includes the primitive kidneys. Males also use parts of the drainage system of the temporary kidney for reproductive plumbing. Mammals therefore have to make the structure in embryonic life, even though their adult bodies have no need of it for its original purpose of excretion.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 177-8.


“Many developing tissues over-produce cells initially and then use signals from other tissues to determine how many, and which, should be kept.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 178.


“Painstaking biochemical analysis of the developing muscles has revealed that they produce very limited amounts of neural survival factors. Initially, motor neurons can survive without these but, as they mature, they become dependent on an adequate supply. Within the cells, a suicide-promoting pathway is already present, and it is only held off by signals from the survival factors. In the normal foetus, the arm muscles do not produce enough survival factors to keep all of the motor neurons alive, and only cells that have made the best connections to the muscles will receive enough. Other cells will have insufficient signal to hold the suicide pathway off and they eliminate themselves.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 180.


“The principle of cells competing for target-derived survival signals is by no means limited to the motor neurons of the spinal cord. It is also seen in the sensory system and in many areas deep within the brain itself. Importantly, it is also seen in non-neuronal organs. Indeed, it is so general that it has given rise to the ‘trophic hypothesis’; this postulates that all cells depend for their survival on limited quantities of survival factors released by other cells.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 180.


“The trophic hypothesis is useful to human development at both very short and very long timescales. At short timescales, it means that cells that have formed in the wrong place, or have wandered away from where they are meant to be, will be far from their intended interaction partners and will simply kill themselves. They will therefore not cause problems. At much longer timescales, it is one of the things that makes evolution of complex bodies possible. Consider two hypothetical animals, of the same body shape, one of which produces exactly the right number of motor neurons to serve its arm muscles in the first place, and the other of which over-produces them initially and then culls the excess, as we actually do. Now imagine that the environment of the animals changes, and a new ecological niche opens up that can be exploited by animals with strong arms: examples might be lifestyles that involve digging or that entail swinging through trees. For an animal of the first type to acquire larger but still functional arms, there would have to be two types of mutation brought together in the same individual, one that makes the arms larger and the other that makes the pool of motor neurons larger, by just the right amount. For an animal of the second type, though, just the mutation for larger arms would be enough, because the number of motor neurons that survive would adjust automatically for the new, larger source of survival factors.... Animals that use overproduction of cells followed by target-dependent survival are therefore better placed to win evolutionary races–to evolve faster and thus be the first to exploit new environments.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 181.


“The NMDAR receptors are therefore at the heart of Hebb’s system, because they are active only when the receiving cell is already active and the particular synapse is active (presence of glutamate), and they can alter the strength of the synaptic connection by making its AMPAR system more sensitive.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 188.


“As they make synaptic connections in the superior colliculus and in other areas of the brain, branches of the axons from a particular part of the eye will connect to a lot of correct cells, also connected to by their neighbours, but will also connect to a few wrong cells too. Left in this condition, the system would result in blurred vision that would not do justice to the capabilities of the eye. The wiring pattern is therefore refined, after birth when the eyes are open, by activity-dependent remodelling of connections. The mechanism for this is similar to Hebb’s, but this time not only the strength of synaptic connections by also their very survival depends on a synapse’s own firing coinciding with the firing of the receiving cell. If a synapse from an axon from, say, the top left of the eye connects to a neuron to which axons from other cells in the top left of the eye also connect, then it will be firing when they do, because all will be reporting the same events in the visual field. The combined action of all of these synapses will fire the receiving neuron, and all of these synaptic connections will be strengthened. As a receiving cell fires more often, it becomes less willing to support weak synapses whose firing never coincides with that of the receiving cell. A synapse whose own firing does not coincide with the firing of the receiving cell must be responding to different stimuli from the majority of synapses on the receiving cell, which means it must come from a different part of the eye or must be sensitive to some other aspect of the visual field: either way, it does not belong. By disengaging from such out-of-synch synapses, the receiving cell frees itself from inappropriate connections. The freed axon end can then try its luck connecting to a different cell, and repeat the process until it can settle on a neuron that is being stimulated by other synapses with the same firing pattern.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 189-90.


“Neurons that fire together, wire together.

“Hebbian learning to establish associations between different neural signals, and activity-dependent remodelling to hard-wire the associations, have obvious roles to play in improving the processing of sensory information and for promoting very basic types of learning, ....” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 191.


“In both cases [patients such as Toulouse-Lautrec whose bones grew abnormally short but where their other tissues remained proportional], the primary biochemical defect affects specifically the growth of the long bones of the limb. There is no direct effect on the growth of skin, muscle, nerves, blood vessels, etc., yet these tissues did not grow to make some floppy mass composed of a normal amount of these soft tissues, all centred on abnormally short bones. Rather, they all grow to be an appropriate size for the short leg. This illustrates a deep dichotomy in size control: some tissues of the body, like the bones in the rabbit experiment, regulate their own absolute size and may be considered ‘master’ determinants of body size, while other tissues pay attention, not to their absolute sizes, but rather to their sizes relative to the masters’. Tissues of this second type are in a sense ‘slaves’ when it comes to size control: their job is to keep up, but never to overshoot, the growth of the master tissues.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 198.


“There is, though, one type of signal that would report both relative size and shape very effectively at any time of life and for any body shape, however bizarre. That ‘signal’ is mechanical force....

“A mechanism that used excessive tension as a reporter of inadequate growth would have the merit of size-invariance: it would work just as well for a large tissue as for a small one. It would also have the merit of having to carry no expectation or knowledge of shape....

“There is strong evidence that mechanical tension is able to drive proliferation [of cells].” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 204.


“As tension and stretch might be used to tell a tissue that it is not growing quickly enough, compression and crowding might be used to tell cells that they have already proliferated quite enough and should cease. Many years ago, it was observed that when normal cells are placed on the bottom of a culture dish, they proliferate until they have covered the bottom of the dish and then stop. If some cells are then removed to create space, for example by wiping a sterile pencil eraser across the dish, the cells surrounding the gap proliferate again until the hole is filled, and then they stop again. This phenomenon, termed ‘contact inhibition’, provided an early hint that the proliferation of cells may be controlled by their own sense of crowding.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 205-6.


“Another way in which a slave tissue might sense the appropriateness of its size is to sense its own biochemical effect on the body, either directly or indirectly in conversation with other tissue types.... If one foetal spleen rudiment is grafted into a host whose own spleen has been removed, it grows to the size of a normal adult spleen. If multiple spleen rudiments are grafted into the same host, then each stops growing when the sum of their individual volumes has reached the size of an adult spleen.... The phenomenon is not universal, though. When approximately the same experiment was been done with the thymus, each rudiment grew to the size of a normal thymus, leaving the animal very over-endowed in that department.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 206.


“Recent research suggests that humans and their helpful bacteria have, over their long association, evolved ways of communicating with each other so that the two very different types of organism can operate as a single, integrated system.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 209.


“Each part of the gut creates a nurturing environment for precisely the type of bacteria that it needs.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 210.


“Animal cells in general, including those of humans, tend to decorate the proteins they secrete or place on their surfaces with chains of sugars. Within the chains, the sugars are linked to each other with strong chemical bonds and, unlike single molecules of sugar floating about freely in a glucose drink, for example, they cannot be used directly as food because the sugar-protein complex is far too large to pass through the uptake channels on the surface of a bacterial cell. The only way that a bacterium can get food from these sugar chains is by having an enzyme that can cut the bonds holding the chain together, and different enzymes are needed to liberate different types of sugar from the end of a chain. Bacteroides thetaiotamicron makes an enzyme that can liberate the sugar fucose from the ends of one of these chains. Before they receive the signal from Bacteroides thetaiotamcron, intestine cells do not place fucose residues at the ends of many of their chains but, once they receive the signal, they switch to add the fucose. Effectively, the bacterium is saying ‘feed me’ and the cell is obliging, and doing so in a way that will not feed other random organisms that may be present but that will not have the right enzyme to liberate fucose. Other parts of the gut express other types of linked sugars, probably in response to other signals from other symbiotic bacteria. In this way, each part of the gut might create a nurturing environment for the bacterial species it needs.

“The advantage to the gut of having Bacteroides thetaiotamicron is that it can process hard-to-digest components of food and liberate nutrients to be taken up by intestinal cells.... Yet other signals from Bacteroides thetaiotamicron induces tissue cells to secrete antibacterial molecules that are relatively harmless to this particular bacterium but are toxic to some unwanted and dangerous competitors such as Listeria. The symbiotic bacterium and the gut lining therefore look after each other, the body providing food and protection for the bacterium, the bacterium providing nutrients for the body, and their combined action discouraging colonization by less friendly species. This discouragement proceeds both by the system making antimicrobial molecules and by the Bacteroides thetaiotamicron simply taking up the space that would otherwise be available for unwanted species.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 210-1.


“There are three basic layers of defence. The first layer is essentially passive, and it has both physical and chemical components. The physical component consists of barriers to infection, such as tough layers of dead cells on the outside of the skin, frequently replaced, viscous mucus inside the nose, mouth, trachea, gut, urethra, and vagina, and even films of symbiotic bacteria that are impenetrable to pathogens. The chemical component consists of a variety of proteins that bind to and damage the cell walls of bacteria. These wall structures are unique to bacteria–animals cannot make them–so they form a useful target that can be attacked chemically without risking the health of tissue cells. Animals therefore make a variety of enzymes and pore-forming proteins that make lethal holes in bacterial walls. Some, including lysozyme and defensins, protect external surfaces such as the eyes....

“The second layer of defence is active and uses various types of migratory cells called phagocytes, literally ‘cells that eat’. There are several different types of phagocyte, but all have their origins in the bone marrow,.... They spread through the body in blood but can choose to leave blood vessels by pushing between the cells that line them. Once across the blood vessel wall, the cells enter the tissue spaces where they can settle or actively patrol, crawling through fine spaces. When they are crawling, phagocytes have much in common with the migratory cells of the embryo.... They make a leading edge, the extension of which is controlled by the activity of signalling pathways triggered by receptors on the cell surface. Phagocytes have receptors that are triggered by two broad classes of signal. One type of signal, of which there are numerous different examples, consists of bacterial cell walls and waste products that living bacteria cannot help releasing....

“Once there, the phagocytes secrete more signalling molecules, release a cocktail of highly toxic chemicals, and endeavour to engulf and destroy any bacteria they meet. The signalling molecules increase local blood flow and leakage of fluid from blood vessels, bringing more phagocytes as reinforcements. The toxic chemicals kill bacteria even without their having to be engulfed. They are so aggressive that they often inflict considerable damage to the ordinary human tissue as well. The result of all of this is a local build-up of redness and heat, from the increased blood flow, swelling from the fluid and accumulating cells, and pain from nerve endings suffering under the onslaught of a toxic cocktail: rubor, calor, tumor et dolor, the classic signs of inflammation .... In the middle of the inflammation may also be an area of whitish pus–essentially phagocytes, dead bacteria, and dead human tissue.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 212-4.


“Having a defensive system that relied completely on recognizing particular chemical signatures, such as bacterial wastes, would leave us completely open to attack from anything that did not make those signature chemicals.... This is where receptors that detect stressed and dead human tissue come in. Anywhere cells are being killed, a defensive response will be mounted. That is why even sterile burns are followed by painful inflammation. In the context of sudden tissue damage, the apparently excessive violence of excited phagocytes, whose toxins kill not just bacteria but even neighbouring human tissue as well, makes sense: even a micro-organism or virus that hides inside those cells and so could never be detected or tackled directly by the phagocyte, will be killed in the general melee....

“... requires an appreciation of the third layer of defence. This is something possessed only by vertebrate animals: the ability to learn from experience. It still uses the ancient weapons of complement–the soluble chemical-based defence–and phagocytes to kill invaders, and it is still controlled, ultimately, by signals from damaged or infected tissue. What it adds is a few more cells and, critically, a set of highly specific proteins that can direct phagocytes and complement very accurately and rapidly against an invader, provided that the system has enough time. Because of its ability to learn and adapt, this new layer is called the adaptive immune system.

“The adaptive immune system, consisting as it does of migratory cells in relatively brief contact with one another, has a physical structure very different from that other learning machine, the brain.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 214-5.


“Young T cells that have just finished the random gene rearrangement and have started to make their TCR live in the thymus, surrounded by cells that have many fragments of body protein on their surfaces.... The life of each T cell depends, at this stage, on its TCRs being stimulated, but only weakly. A TCR that reports absolutely no binding to anything is probably useless, and the cell that carries it kills itself. A TCR that reports weak, sporadic binding can clearly detect fragments of molecules, but not strongly. This is actually quite hopeful, because detecting a fragment of a normal body protein weakly means that the TCR at least works, and it may detect some unknown bacterial or viral protein fragment much better. These cells therefore live, mature, and enter the rest of the body. A TCR that reports strong binding while still in the thymus is almost certainly recognizing fragments of normal human material and either kills itself or enters a state that suppresses activity against those fragments in order to prevent the immune system acting against its own body.

“At the end of this process, the body will have populated itself with millions of T cells, all carrying different versions of the TCR, none of which react strongly to body components, but all of which have shown a very weak response to at least something. While out in the body, T cells have frequent contact with types of phagocyte that present them with little fragments of what they have engulfed, again on fragment-displaying proteins at the cell surface. If the phagocyte has come from a site of infection, there will be pieces of the microorganism amongst these fragments. For a given micro-organism, the TCRs of most T cells will not recognize anything but, occasionally, the phagocyte will happen to present its load to a T cell that does recognize it. This is what the T cell has been waiting for, and it becomes fully activated. It proliferates quickly to create a small army of daughter cells with the same TCR, and it secretes signalling molecules that recruit further T cells to the area. Some of these will recognize other fragments of the microbe and they too will become activated. A subset of these T cells will go on to kill tissue cells that display the same protein fragment, and are presumably therefore infected.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 217-8.


“T cells are not the only cells of the body to use random rearrangement of specific genes to produce a vast variety of receptors. A similar set of cells, B cells, use exactly the same trick of gene rearrangement to make B cell receptors, or BCRs. These are very similar to TCRs. Again, each individual B cell has just one unique variety of BCR. B cells patrol the body and, if they find any molecule that their BCR recognizes, they take it in and chop it up with enzymes. They then present its fragments on their surfaces, on a fragment-displaying protein, on the off-chance that they might meet a T cell that will recognize the complex. If they do, the T cell signals back to the B cell, causing it to multiply to make more B cells with the same BCR. Some daughters of the B cell become memory cells, in readiness for future battles against the same microorganism, while others start to secrete their BCR into the fluid around them. Secreted BCR is called antibody, and it can spread rapidly through tissues and bind to the molecule it recognizes, whether that molecule is floating about or still on the surface of the microbe or infected cell. Antibody recruits that ancient chemical defence, complement, and also phagocytes: it is thus a death warrant for any cell it binds.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 219.


“Very recently, it has been discovered that human gut cells that detect signals from symbiotic bacteria produce signals to the defensive systems that effectively say ‘nothing alarming is happening here’. The signals act on the phagocytes that specialize in presenting surface-bound fragments to T cells. These phagocytes can be in two states: in one state, they present the fragments along with signals that encourage T cells to commence an aggressive attack, while in the other state they accompany their presentation with signals that encourage the T cells to calm down and be tolerant. Unstressed gut cells in contact only with symbiotic bacteria secrete two proteins that instruct the phagocytes in their vicinity to enter the calming state. The phagocytes will still present molecules associated with bacteria, with part-digested food, etc., but they will promote tolerance rather than aggression. If, on the other hand, the gut lining cells are in contact with bacteria that damage them, they do not make these calming signals and make alarm signals instead. Under these circumstances, phagocytes present fragments to T cells along with strong activating signals, and a defence is quickly mounted. Again, the main controlling element of the defensive response is whether or not a tissue (including the immune cells therein) is suffering stress. What the dialogue between bacteria and gut lining adds to this is a positive message that nothing bad is happening.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 220-1.


“Development of the mind ... and development of the immune system described here are each critical developmental events that take place after birth. They have to, because both involve interaction of the new human with an unpredictable environment.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 222.


“Within cells, damaged proteins are replaced by new ones, and within tissues, damaged cells are replaced by new ones, but that is the limit of scale of replacement parts. Whole tissues and organs are not exchanged as complete units; instead, the existing organ is maintained continuously by very small-scale repairs from within. There are probably three main reasons for this. The first is that many organs arise, in embryonic and foetal life, from tissues that do not exist in the adult body.... The second reason is that many parts of the body subject to rapid wear and tear, such as the surface layers of the skin and the gut lining, last only a week or so before they have to be replaced, but it takes much more than a week to make these organs in foetal life. A complete organ new-for-old plan therefore could not keep up with demand. The third reason is the geometric and logistical difficulty of swapping new organ systems for old inside a crowded body. Maintenance therefore has to proceed by mechanisms that are quite distinct from embryonic development.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 226.


“For all of its simplicity, maintenance only by peer replacement would run into serious problems in a long-lived animal. Many cells exist in a hostile environment where they are exposed constantly to agents that damage them.... After a few generations of replacement of dead cells by proliferation of already damaged neighbours, there will be very little healthy tissue left.

“There are two ways that an animal might deal with this problem without abandoning the idea of peer replacement. One would be to have a very short life and to avoid any stressful environments; it is quite possible that many very small animals have taken exactly this course.... The other would be to invest heavily in damage control and repair mechanisms within cells. Such mechanisms do certainly exist: there is a set of enzymes and other proteins that can detect damage to DNA and repair it, membrane pumps exist that can expel small toxins from cells, and protein-destroying enzymes exist to make all cellular proteins short lived so that they are replaced rapidly with pristine ones.... The problem is that the cost of such an investment in cellular repair processes to protect every single cell to this level, as would be necessary in a peer-replacement system, might simply be more than the resources (food) that the animal can procure.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 227.


“A key feature of the problematic peer-replacement system is that all cells are equal and have to be protected equally, and therefore expensively. If an animal were instead to protect only a few of its cells, and to use only these to produce replacements for damaged ordinary cells, then it could economize considerably on its expenditure. If the highly protected cells could be located somewhere physically safer than an exposed surface, so much the better. Even better still, further savings in resources could be made if just a very few highly protected cells could make any of the cell types in the tissue. Such cells would lie effectively at the stem of a ‘family tree’ of the different cells types they can produce: cells that work this way are therefore called ‘stem cells’. Maintenance of a tissue by the activities of stem cells offers considerable advantages over the peer-replacement system and, while peer-replacement may be used for quick patches to small wounds, stem cell-based tissue regeneration seems to be the way that large animals, including mice and humans, keep their tissues going over months and years.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. Pp. 227-8.


“In mice, in which the cell biology of the intestines has been studied very carefully, most surface cells last only about five days;...” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 228.


“In the small intestine, the inner surface is covered in small finger-like columns called villi that stick up to form the general level of the surface. Villi are present even at birth. Shortly afterwards, the regions between the villi fold downwards to make narrow depressions, called crypts. The bottom of each crypt is formed of Paneth cells, which specialize in secreting proteins that kill bacteria. The walls of the crypt above the Paneth cells contain many mucus-secreting cells. Protected by its position from mechanical trauma, protected by mucus from chemical attack, and protected by defensins from bacterial attack, the crypt is a much less dangerous environment than the villi. Unsurprisingly it is deep in the crypts that intestinal stem cells reside.

“Somewhere, either between the Paneth cells right at the bottom of the crypt, or just above them, or possibly at both of these locations, the intestinal stem cells can be found. There they proliferate, about one every four days. The daughters of this proliferation make a decision between becoming a new stem cell or leaving the stem cell niche and starting to move up the crypt walls.... As they move, these cells continue to proliferate so that the daughter of a single stem cell division has become up to sixty-four individual cells over the course of about three days. During this process, different cells become committed to becoming different types of intestine cells; some will become absorptive cells, some mucus-producing cells, some Paneth cells and some will become rare, specialized cells that make hormones.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 229.


“The rates at which intestinal cells are lost will vary with the health and diet of the person concerned.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 230.


“The problem of controlling proliferation [of daughters of stem cells] therefore extends downwards to every level of the tree. It seems that it is solved by a relatively simple generic signalling mechanism that operates similarly for all of the cells, although different molecules are used for different cell types. Basically, each cell secretes molecules that inhibit the proliferation of the cell type below it in the family tree. If there are enough cells at a higher level, they will together make enough inhibitory signal that the cells below them are quiet. If the population at a higher level falls, because cells there are maturing and leaving the bone marrow, there will be less inhibitory signal and lower levels therefore proliferate more and their daughters replenish the level above them. This system extends downwards, level by level to the ultimate stem cells resident in the bone marrow, the HSC’s themselves.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 236.


“At every stage of development, protein-based machines detect signals from a cell’s environment, be these signals mechanical (tension, free surface) or biochemical (molecules from other tissues), and a combination of these signals and the existing internal state of each cell determines what it will do next. This rich communication between components is quite unlike conventional engineering, in which relays and transistors pay no attention to one another in the construction phase even if–as in a computer–they communicate extensively when the completed machine is switched on.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 248.


“... signalling between cells achieves two things: it increases complexity, and it corrects errors.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 248.


“Once a difference exists between cells within an embryo, cells can use detection of this difference to become a third cell type.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 248.


“... differences feed on differences: the embryo uses this effect to bootstrap itself from dull uniformity to exquisite internal diversity and organization.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 248.


“The presence of feedback loops gives the communication between cells the character of a true conversation, signals being answered by other signals coming back, directly or indirectly, so that the behaviours of cells are strongly inter-dependent.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 250.


“A striking feature of developmental mechanisms is the way they are nested, later ones including earlier ones to run fine-scaled events.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 251.


“The problem with the ‘Gene for X’ view is that it evokes the idea of a fixed plan, rather than a multi-layered nesting of mechanisms that organize the body by integrating their own signals and those from their environment.” Davies, Jamie. 2014. Life Unfolding: How the human body creates itself. Oxford University Press. P. 253.


“Therefore, [based on evidence from trace fossils, signs of movement left in sand and rock] animals displaying sophisticated feeding strategies involving strophotaxis (i.e. proclivity to make U-turns so that the animal turns around 180̊ at intervals), phobotaxis (i.e. tendency to avoid crossing its own and other trails) or thigmotaxis (i.e. propensity to keep close contact with a former segment of the trail) are not present in Ediacaran rocks.” Mangano, M. Gabriela & L. Buatois. 2014. “Decoupling of body-plan diversification and ecological structuring during the Ediacaran-Cambrian transition: evolutionary and geobiological feedbacks.” Proceedings of The Royal Society: B. Pp. 1-9. P. 3.


“Trace-fossil data strongly support a rapid increase of animal diversity in the Early Cambrian (i.e the Cambrian explosion scenario). However, our systematic analysis also points to the existence of a relatively short period of phylogenetic fuse [slower diversification] during the terminal Ediacaran and the Fortunian. By the end of the Fortunian, the diversification event evidenced by the appearance of complex architectural designs reflecting body-plan diversification and behavioural innovations was well under way. Therefore, the trace-fossil record indicates that the evolutionary radiation occurred earlier than suggested according to the classic Cambrian explosion scenario based on the appearance of the main phyla in the body-fossil record.” Mangano, M. Gabriela & L. Buatois. 2014. “Decoupling of body-plan diversification and ecological structuring during the Ediacaran-Cambrian transition: evolutionary and geobiological feedbacks.” Proceedings of The Royal Society: B. Pp. 1-9. P. 7.


“In contrast to the prevailing view that diversification of animals and infaunal colonization were roughly coincident during the Cambrian explosion, our study indicates that the presence of a wide array of metazoan behaviours preceded the establishment of a modern infaunal ecological structure (i.e. mixground ecology), indicating a decoupling of cladogenesis and the major shift in benthic ecology that typifies the Phanerozoic.” Mangano, M. Gabriela & L. Buatois. 2014. “Decoupling of body-plan diversification and ecological structuring during the Ediacaran-Cambrian transition: evolutionary and geobiological feedbacks.” Proceedings of The Royal Society: B. Pp. 1-9. P. 7.


“The first event [diversification in the Fortunian, late Ediacaran] involves the appearance of a wide repertoire of behavioural strategies reflecting the interactions of newly developed, distinctive body plans with the substrate. Most of these interactions were characterized by the reworking of fine-grained sediments by sediment bulldozers in diffusion-dominated benthic systems as typified by bioturbation in offshore deposits. This style of biogenic reworking was probably conducive to large-scale changes in both the sediment and the water column, including promotion of water fluxes at the sediment-water interface, average deepening of the redox discontinuity surface, release of nitrogen from the sediment, increase in the sediment-water flux of iron and manganese, and several-fold increase in seawater sulfate concentration. By being the primary determinant of oxygen concentration in the sediment, bioturbation may have also influenced the biomass of organisms, the expansion of aerobic bacteria, the rate of organic matter decomposition and the regeneration of nutrients vital for primary productivity, among other aspects.” Mangano, M. Gabriela & L. Buatois. 2014. “Decoupling of body-plan diversification and ecological structuring during the Ediacaran-Cambrian transition: evolutionary and geobiological feedbacks.” Proceedings of The Royal Society: B. Pp. 1-9. P. 7.


“The second event [Cambrian Stage 2 agronomic revolution or the establishment of a Phanerozoic-style ecology] marks a qualitative change in ecological structure, recording an increased complexity of the food route and trophic web, and a re-organization of the infaunal ecospace. The appearance of deep-tier suspension feeders is central to this second phase, revealing bioturbation in advection-dominated benthic systems. The establishment of suspension-feeding communities had a major impact in marine ecosystems, signalling the coupling between plankton productivity and the benthos. The key innovation introduced by filter-feeding mesozooplankton may have not only acted as the trigger of the evolution of large-size metazoans, but also played a role in the final turnover from matgrounds to mixgrounds. By repacking unicellular phytoplankton as nutrient-rich larger particles, zooplankton provides a more concentrated and exploitable resource for the benthos. Because suspension feeders move and process large amounts of material, they play a major role in nutrient cycling, including regeneration of nitrogen and phosphorus to the water column. The dramatic increase in bioturbation intensity and depth that occurred during the Cambrian Stage 2 resulted in higher irrigation levels, and was conducive to a further deepening of the redox discontinuity surface.” Mangano, M. Gabriela & L. Buatois. 2014. “Decoupling of body-plan diversification and ecological structuring during the Ediacaran-Cambrian transition: evolutionary and geobiological feedbacks.” Proceedings of The Royal Society: B. Pp. 1-9. P. 8.


“Late medieval Christianity was an institutionalized worldview, but one long and deeply marked by the gulf between the faith’s own prescriptions and many Christians’ actual practices, between its ideals and its realities. This comprised a first set of problems. How was the gap to be narrowed and shared human life to be made more genuinely Christian? Reformation leaders thought the root problem was doctrinal, and in seeking to fix it by turning to the Bible they unintentionally introduced multiple sorts of unwanted disagreement. This constituted a new set of problems, different from the first. What was true Christianity and how was it known? Doctrinal controversy was literally endless, and religio-political conflicts between Catholics and magisterial Protestants from the early sixteenth through the mid-seventeenth century were destructive and inconclusive. The undesired nonresolution of intra-Christian contention brought with it a third set of problems, related to the second. How was human life among frequently antagonistic Christians to be rendered stable and secure? The solution eventually adopted in all modern, liberal Western states was to privatize religion and to distinguish it from public life, ideologically as well as institutionally, through politically protected rights to individual religious freedom. Not subjective faith but objective reason, in science and modern philosophy, would be the basis for public life. But modern states continued to rely on citizens’ behaviors that depended on beliefs rooted in Christianity (such as individual rights) even as other cross-confessionally embraced behaviors (such as material acquisitiveness) were antithetical to its teachings. Within the liberal institutional framework of modern rights, secularization in recent decades has led to the proliferation of secular and religious truth claims along with related practices that constitute contemporary hyperpluralism. These contemporary realities present a set of problems that are an outgrowth of those of the Reformation era, but in radically altered intellectual, institutional, and material circumstances.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 21.


“Starting from the traditional position of the radical distinction between God and creation, Scotus asked what could be said about God strictly on the basis of reason or philosophy.... He predicated of God something that he thought God had to share with everything else in the same sense, simply by virtue of existing, namely being.... Insofar as God’s existence is considered in itself and in its most general sense, Scotus agreed that God’s being does not differ from that of everything else that exists. This is Scotus’s univocal conception of being–‘univocal’ because it is predicated in conceptually equivalent terms of everything that exists, including God. By contrast, Christian theologians who continued to hold the inherited view, before and after Scotus, denied that God belonged to the same order or type of existence as his creation.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. Pp. 36-7.


“In the early fourteenth century, Occam radicalized Scotus’s views on univocity and much else, rejecting more thoroughly Aquinas’s way of speaking about God, for whom ‘ana-logical’ had not meant comparable or proportional to creatures or creation. According to Aquinas, God in metaphysical terms was, incomprehensibly, esse–not a being but the sheer act of to-be, in which all creatures participated insofar as they existed and through which all creation was mysteriously sustained. In Occamist nominalism, by contrast, insofar as God existed, ‘God’ had to denote some thing, some discrete, real entity, an ens–however much that entity differs from everything else, ... At the outset of the sixteenth century, the dominant scholastic view of God was not esse but an ens–not the incomprehensible act of to-be, but a highest being among other beings.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 38.


“Bacon seems not to have held the notion widely attributed to him, namely that through experiments nature was actually to be tortured. Nevertheless, forcing nature out of its natural state is no more disinterested than declarations of nature as devoid of God’s presence are objective. But the first practice serves human ambitions, and the second clears the way.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 57.


“The secular academy is the domain of Weberian facts, not values–except, contradictorily, for the one hegemonic and supreme value that no judgments about competing truth claims pertaining to values or morality should or can be made. Which is itself, in fact, a normative claim that reflects certain values, despite diversionary disavowals to the contrary. And which, in fact, virtually no academics actually believe, unless they would be prepared not to give any ‘moral guidance’ or ‘moral advice’ if a student claimed to find nothing wrong with genocide, murder, torture, or rape.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. Pp. 81-2.


“Whereas Latitudinarians emphasized reason in vindicating the Bible as God’s word and in establishing basic biblical truths, spiritualists employed reason against the reliability of scripture itself. The more suspect the biblical text, they reasoned, the stronger the case for seeking the truth inwardly, through the Spirit speaking in the heart...

“The impotence of reason in resolving Protestant doctrinal disputes made it not the polar opposite of appeals to the Spirit, but rather its non-identical twin. Both augmented rather than ameliorated, complicated rather than clarified, the doctrinal pluralism they were intended to surmount.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. Pp. 106-7.


“... modern philosophy’s foundationalist aspirations, beginning with Descartes, emerged in an intellectual milieu pervaded by Pyrrhonism. Hence ‘first philosophy’ in the modern period, from Descartes through Edmund Husserl and arguably beyond, would be not metaphysics but epistemology. In a specifically epistemological context, the chief objective was to transcend skeptical doubt about the possibility of certainty regarding moral principles, human nature, metaphysics (including God), and the natural world. In the context of competing views about Christian truth, the aim was to secure a rational foundation for the domains of human life covered by Christianity, and so to provide a means of superseding intractable doctrinal controversies and destructive conflicts.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 113.


“Modern philosophy sought to provide what Protestantism could not, via reason rather than scripture.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 125.


“Historically and empirically, modern philosophy, like Protestantism, has produced and continues to yield an every-proliferating number of truth claims,... Sola ratio has not overcome the problem that stemmed from sola scriptura, but rather replicated it in a secular, rationalist register.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 126.


“The shift from neo-Marxist to Foucauldian ideas permits the migration of a rhetoric of resistance previously invested in anticapitalist class struggle, and the survival of a secular sense of purpose that it afforded. Properly politicized in the approved ways, scholarship can remain meaningful even if one studies obscure people who lived centuries ago, so long as it obeys the one-note analytical paradigm of power imposed and resisted. The recovery of the agency and discontented voices of the oppressed, by prefiguring the emancipatory narrative of modernity, can at least partially redeem the otherwise dismal premodern human past. In a worldview premised on individual autonomy as the teleological apotheosis of human history, locating the agency of resistance becomes a secular substitute for the salvation of scholars who reconstruct its redemptive exercise by their premodern subjects and thereby, through fashioning a suitably usable past, stand in vicarious solidarity with them.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 127.


“Whether in Western confessional, liberal, or totalitarian regimes, states control churches: whether they prescribe, permit, or proscribe religion, they do so entirely on their terms, exercising an institutional monopoly of power in the public sphere.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 130.


“As especially Augustine contended and so influentially theorized in The City of God in the early fifth century, the practice of Christian love in obedience to Jesus in a far from fully redeemed world would require as a moral responsibility the proper exercise of power, over oneself and over others, lest selfish sinfulness rush in and default wickedness be given free rein. To wash one’s hands of politics and refuse to exercise public power justly and virtuously was in effect to relinquish the ‘city of man’ to the frightening libido dominandi on which Augustine trained his unsparing analytical gaze.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 136.


“According to Luther, justification by faith through grace transformed human lives by obliterating the anxiety of consciences overwhelmed by their inevitable inability to follow Jesus’s commands, thus liberating them for the loving service to others that flowed from faith.... Luther thus interpreted Jesus’s dictum (‘Render unto Caesar...’) to mean that all human beings belonged to two entirely different kingdoms, each with discrete and respective jurisdiction over bodies and souls: ‘Secular government has laws that extend no further than the body, goods and whatever is external on earth. But God cannot and will not allow anyone but himself alone to rule over the soul.’...

“So although Luther sought to curtail tyrannical domination by either secular or ecclesiastical authorities over souls, in fact his solution implicitly theorized the control of human bodies and thus human beings by secular authorities.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. Pp. 147-8.


“The very success of confessional regimes, magisterial Protestant as well as Catholic, in suppressing radical Protestants between Muenster in 1535 and England in the 1640s kept the number of Protestant radicals small and their sociopolitical influence minimal.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 151.


“Always and only on the terms of sovereign secular rulers, churches in general would exert only as much public power and authority as they were permitted. In the confessionalizing sixteenth and seventeenth centuries, that was usually quite a lot. In the nineteenth and twentieth centuries, as nationalist and imperialist states not only controlled churches but also diverted to themselves the primary, deepest devotional allegiance and mandatory obedience of their citizens in what John Bossy called a ‘migration of the holy’ from church to state, it was usually much less....”

“Religiously motivated subjects might still risk rebellion against secular authorities .... Nowhere, however, did or could leaders in institutional churches dictate to secular sovereigns either the terms of the public exercise of power, or the terms of the relationship between secular and ecclesiastical authorities. Churches were entirely subordinate and dependent institutions....

“With the exception of the Papal States in central Italy before 1870 and some small Catholic ecclesiastical principalities before the Napoleonic era, never since the Reformation era has a church exercised sovereignty over a state.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. Pp. 153-4.


“It turned out that these concerted efforts at Christianization [‘More instruction, education, catechesis, preaching, exhortation, supervision, warnings, and focus’ by both Protestants and Catholics] would require the exercise of more consistent, surveillant, coercive power than had characterized medieval Christendom. As we shall see, this would have major, enduring consequences. Secular, lay authorities obliged, in what looked like a win-win scenario for them and the clergy. Not only would rulers discharge their God-given duties conscientiously; they would also get subjects who were more obedient, more disciplined, and less immoral.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 157.


“... the substantive similarities among American Christians from different churches with respect to public life rather than relative to their doctrinal disagreements were doing the work that early modern European confessional regimes had sought to achieve through frequently coercive, established churches, and which had resulted so catastrophically in persecution and had contributed to multiple wars.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 169.


“In Moralistic Therapeutic Deism, religion is conceived instrumentally, its central purpose being to make one ‘feel good and happy about oneself and one’s life.’ Hence one should believe whatever conduces to this end. God’s ‘job is to solve our problems and make people feel good,’ God being ‘something like a combination Divine Butler and Cosmic Therapist:...” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 171. The term “Moralistic Therapeutic Deism” is from Christian Smith as ‘the actual dominant religion among U.S. teenagers.’ Smith, Christian & M. Denton. 2005. Soul Searching: The Religious and Spiritual Lives of American Teenagers. Oxford University Press.


“The laws guarding this principle [homage to God only as the individual believes] meant that notwithstanding their social relationships in self-chosen communities of faith, the ideological scaffolding and political framework beneath the energetic, mostly Protestant churches and effervescent evangelization in the United States between the ratification of the Constitution and the Civil War was religion of the individual, by the individual, and for the individual. Thomas Paine understood one of the implications already in 1794: ‘My own mind is my own church.’ Tocqueville observed more broadly that ‘in most mental operations each American relies on individual effort and judgment. So, of all countries in the world, America is the one in which the precepts of Descartes are least studied and best followed.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 171.


“The privatization of religious belief and practice pioneered in the Dutch Republic and institutionalized in the United States rejected confessional Christianity as a publicly shared way of life.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 172.


“Controlling the churches by disestablishing them freed not only political institutions from churches but also established the institutional framework for the eventual liberation of society from religion.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 172.


“In Aristotelian (and Platonic) conceptions, ethics and politics are inseparable from one another and necessarily part of the same discourse, because the good for individual human beings as social, rational animals depends on the common good that they acknowledge, build, share, maintain, and police. Only in a community made possible by a shared common good can human beings realize as well their individual good. In political liberalism, by contrast, ethics and politics are distinguished–or put more precisely, the particular, substantive moral views that individuals happen to hold and are free to hold according to their preferences are distinguished from and subordinated to the universal, formal and foundational ethical imperatives of individual liberty and equality, with politics and laws arranged accordingly. From Locke through Mill to Rawls and his contemporary followers, this distinction and its political institutionalization is the heart of modern liberalism.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 183.


“However open-ended the pluralism that it permits, a modern ethics of rights requires that those whose rights it protects share certain values and commitments–certain goods–among their preferences. Otherwise the state would have to be crushingly oppressive in order to insure social stability. The more heterogeneous the preferred goods of flesh-and-blood human beings in democratic civil society, the more difficult does the achievement of a Rawlsian ‘overlapping consensus’ among those with different ‘comprehensive theories’–or simply preferred desires–become, and the more difficult is the task of the state in ensuring peace and civility, let alone something resembling a justice widely reckoned as legitimate by its citizens.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. Pp. 186-7.


“In medieval Christianity, not only politics but also economics was inseparable from ethics.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 233.


“Thus knowledge as such is distinct from morality and from concrete human relationships.... Conversely, any truth claims about reality that are dependent on the concrete circumstances, relationships, or experiences of individuals or groups, and thus are not independently accessible to or confirmable by others in different circumstances, cannot count as a source of knowledge about reality in general. Such claims can only serve as data for knowledge about such individuals or groups and their particular circumstances.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. Pp. 303-4.


“Against the intentions of anti-Roman reformers but as a result of their actions, the church became the churches.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 369.


“The late medieval Christianity that Protestant reformers sought to fix was not something called ‘religion,’ separate from the rest of life. It was an institutionalized worldview on which eternal life depended, with ramifications for all of human life lived in certain ways rather than others.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 370.


“A centrally important, paradoxical characteristic of modern liberalism is that it does not prescribe what citizens should believe, how they should live, or what they should care about, but it nonetheless depends for the social cohesion and political vitality of the regimes it informs on the voluntary acceptance of widely share beliefs, values, and priorities that motivate people’s actions.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 375.


“But the failure of modern philosophy to provide a convincing rational substitute for religion with respect to the Life Questions suggests that there is no reason to believe modern claims about the supersessionist triumph of secular reason over religion per se. On the contrary, the failure strongly implies that philosophical efforts to contrive a universal, self-sufficient, rational replacement for religion, for all their historical intelligibility and desirability in the context of early modern Christian doctrinal controversies, were self-deceived from the outset,...” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 383.


“The secularization of knowledge was a historically contingent process that derives from the religious disagreements of the Reformation era, even though it has been for a century or so an ideological imperialism masquerading as an intellectual inevitability.” Gregory, Brad. 2012. The Unintended Reformation: How a Religious Revolution Secularized Society. Harvard University Press. P. 386.


“All predators owe their existence to pre-existing prey, but prey diversity itself derives largely from predation; hence, the myriad morphological, chemical and behavioral adaptations for avoiding being eaten. Biomineralization and burrowing are coevolutionary by-products of life in a dangerous metazoan world, but they also underlie the rich biodiversity that evolved in their engineering wake.” Butterfield, Nicholas. 2011. “Animals and the invention of the Phanerozoic Earth system.” Trends in Ecology and Evolution. Pp. 81-7. P. 83.


“Astronomically large populations of microbes are effectively immune to the extinction and founder effects experienced by larger, less abundant, organisms. Microbes and microbial consortia do share certain ecological habits with their macroscopic counterparts, but are also fundamentally more limited in their capacity to exploit morphological and behavioral diversity, engineer environments and drive coevolutionary change.” Butterfield, Nicholas. 2011. “Animals and the invention of the Phanerozoic Earth system.” Trends in Ecology and Evolution. Pp. 81-7. P. 83.


“The Ediacaran appearance of gut-based multicellular heterotrophy opened up a new universe of evolutionary opportunity and macro-evolutionary dynamics. In less than 100 million years, the marine biosphere shifted from an exclusively microbial world to an alternate, more or less, stable state based on the pervasive influence of animals. Disparity, diversity, maximum body size, standing biomass and rates of evolutionary turnover all dramatically increased, whereas ecosystem stability was effectively reinvented.” Butterfield, Nicholas. 2011. “Animals and the invention of the Phanerozoic Earth system.” Trends in Ecology and Evolution. Pp. 81-7. P. 83.


“In the absence of relatively large-celled eukaryotic phytoplankton, a positive feedback loop of cyanobacteria-induced turbidity is likely to have excluded higher light-demand eukaryotic algae (both phytoplankton and benthic macrophytes) from all but the most oligotrophic or shallow-water marine settings, thereby inducing widespread oceanic stratification. Stratified, bacterially dominated oceans are a signature of the Proterozoic and have generally been viewed in terms of atmospheric oxygen availability. However, without the water-clearing abilities of suspension-feeding animals, there would have been no mechanism for tipping the system out of this condition, irrespective of ambient oxygen. It is simply the default structure of aquatic ecosystems in an exclusively microbial world.” Butterfield, Nicholas. 2011. “Animals and the invention of the Phanerozoic Earth system.” Trends in Ecology and Evolution. Pp. 81-7. Pp. 84-5.


“Indeed, the Ediacaran-Cambrian emergence of metazoans marks the tipping point between two alternative stable states of biospheric expression; on the one hand, an exclusively microbial world driven largely by physical circumstance and, on the other hand, a Phanerozoic world dominated by engineered biological environments.” Butterfield, Nicholas. 2011. “Animals and the invention of the Phanerozoic Earth system.” Trends in Ecology and Evolution. Pp. 81-7. P. 85.


“The Ediacaran and early Cambrian are marked by some of the most pronounced biogeochemical perturbations in Earth history, including unprecedented shifts in C and sulfur cycling, iron geochemistry, phosphate deposition and oceanic oxygenation. These data have conventionally been interpreted as marking the bottom-up arrival of environmental circumstances conducive to animal evolution, with particular emphasis on atmospheric oxygenation. What is missing from such hypotheses, however, is an appreciation of just how pervasive the role of animals has been in defining the modern Earth system. By facilitating and forcing the diversification of, for example, eukaryotic phytoplankton, large body size, bioturbation and biomineralization, early animals reinvented the chemical interchange between the biosphere and planet. In this light, the biogeochemical perturbations of the Ediacaran-Cambrian interval are more likely to be the top-down consequences of animal evolution than its bottom-up cause. Early animals did not simply fill up previously existing but unoccupied niche space; they created the space itself.” Butterfield, Nicholas. 2011. “Animals and the invention of the Phanerozoic Earth system.” Trends in Ecology and Evolution. Pp. 81-7. P. 85.


“There is a clear record of long-term changes in body size, biomass and behavior throughout the course of the Phanerozoic, all of which contributed to the ‘progressive’ emergence of the modern biosphere.” Butterfield, Nicholas. 2011. “Animals and the invention of the Phanerozoic Earth system.” Trends in Ecology and Evolution. Pp. 81-7. P. 85.


“It is worth recalling, however, that respiration rates of large organisms are fundamentally lower than those of their microscopic counterparts, and animals are as much a source as a sink for limiting nutrients. Thus, the sequestering of biomass into ever larger-bodied metazoans not only reduces per-unit oxygen consumption, but also enhances nutrient recycling, providing a basis for major increases in productivity, maximum body size and standing biomass without appeal to external subsidies. In other words, the incremental evolution of animals themselves is likely to have driven much of the long-term increase that characterizes the Phanerozoic record.” Butterfield, Nicholas. 2011. “Animals and the invention of the Phanerozoic Earth system.” Trends in Ecology and Evolution. Pp. 81-7. P. 85.


“... it is not always appreciated just how intimately plant diversity is linked to the antagonistic, mutualistic and/or engineering effects of coevolving animals. Without large terrestrial grazers, there would be no savannah grasslands, leading to fundamental differences in fire regimes, climate and ecosystem structure. Without animal pollinators, there would be no angiosperms, yielding a fundamentally less biologically buffered, Paleozoic-like, terrestrial environment.” Butterfield, Nicholas. 2011. “Animals and the invention of the Phanerozoic Earth system.” Trends in Ecology and Evolution. Pp. 81-7. P. 85.


“The critical threads through the conceptions of scaffolding we use are reproduction, repeated assembly, and entrenchment. Items that are reproduced and repeatedly assembled can become entrenched early in a system and are thereby available to serve as scaffolding for later items, as a platform or as a constraint.” Caporael, Linnda, J. Griesemer & W. Wimsatt. 2014. “Developing Scaffolds: An Introduction.” Pp. 1-20. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 2.


“It is commonly true that things occurring earlier in development have more chance to acquire downstream dependencies and thus to be more deeply entrenched.” Caporael, Linnda, J. Griesemer & W. Wimsatt. 2014. “Developing Scaffolds: An Introduction.” Pp. 1-20. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 2.


“Together, the reproduction, repeated assembly, and entrenchment of heterogeneous relations, parts, and processes provide an alternative, albeit complementary, to the neo-Darwinian population genetic basis for conceptualizing evolutionary change.” Caporael, Linnda, J. Griesemer & W. Wimsatt. 2014. “Developing Scaffolds: An Introduction.” Pp. 1-20. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 2.


“We have avoided following the conventional way of imagining biology as a foundation for cognition, which then serves as a foundation for culture, in hopes that alternative groupings would reveal more about the conceptual links around reproduction, repeated assemblies, entrenchments, and groups. We hope that readers will find that they have their own alternative and generative ways of grouping–a sign of the success of our endeavors.” Caporael, Linnda, J. Griesemer & W. Wimsatt. 2014. “Developing Scaffolds: An Introduction.” Pp. 1-20. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 3.


“Reproduction in general is the multiplication of entities with a material overlap of parts between parents and offspring, that is, where parts of parents become parts of offspring either directly or through chains of material continuity.... At least some parts that flow from parents to offspring must be organized as mechanisms of development.” Caporael, Linnda, J. Griesemer & W. Wimsatt. 2014. “Developing Scaffolds: An Introduction.” Pp. 1-20. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 10.


“More significantly, humans are obligately interdependent, unable to reproduce and survive to reproductive age without a group even–indeed more so–in a technological world. Ours is a group-living species, a product of the coevolution of genetic endowment, social structure, and culture. The gene’s-eye view addresses these issues awkwardly at best.” Caporael, Linnda, J. Griesemer & W. Wimsatt. 2014. “Developing Scaffolds: An Introduction.” Pp. 1-20. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 11.


“The core-configuration model is a narrative (and highly idealized) model about structural dynamics. The model posits that ecology and morphology have constrained humans to living in face-to-face groups for much of their prehistory and, until recently, their history. Consequently, groups have become a significant interface between individual and habitat....

“The model proposes four core configurations based on group size and ‘modal tasks’ that are plausibly continuous from human prehistory through the present and afford the coevolution of capacities that enable the recurrence of the task. For example, a dyad is a core configuration with a group size of two and modal tasks that include interaction with an infant. Core configurations scaffold certain capacities, such as finely tuned microcoordination (e.g., joint attention, rhythmic patterns, pointing) that develops in infant-caregiver engagements but can be seen in interactions with some artifacts that require ‘careful handling,’ as well. Other configurations are task groups (four to seven individuals), demes (twenty-five to fifty individuals), and macrodemes, which are collections of demes. These core configurations are generalizations from the foraging parties, bands, and macrobands of hunter-gatherers studied by anthropologists and the ‘demic structure of science.’ The overarching hypothesis is that unique aspects of human mental systems would have evolved in groups and should correspond to features of modal tasks characteristic of configurations, which in turn are grounded in the interrelations of body, tasks, ecology, and culture of evolving humans.” Caporael, Linnda, J. Griesemer & W. Wimsatt. 2014. “Developing Scaffolds: An Introduction.” Pp. 1-20. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 12.


“Two features predictable from generative entrenchment are particularly noteworthy. First, things that get relatively fixed in cultural systems tend both to play a larger generative role and to be protected from falsification or rejection in other ways. These are properties of systems we associate with norms, conventions, and standards.... Second, we tend to layer newer features on older ones (even if creativity and revolutionary change will occasionally upset applecarts) and to broaden the application of things we already have readily in hand. Thus (1) we will tend to accumulate contingencies of structure, behavior, procedures, technology, and symbolic culture, and (2) those that become quite common (possibly even standardized) may accumulate additional layers of contingent adaptations or tweakings of co-options by the same process. Repetitions of this cycle should generate a kind of fractal order of contingencies on multiple scales of generality and importance.” Caporael, Linnda, J. Griesemer & W. Wimsatt. 2014. “Developing Scaffolds: An Introduction.” Pp. 1-20. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 14.


“In all its senses, scaffolding refers to (1) facilitation of a process that would otherwise be more difficult or costly without it, which (2) tends to be temporary–an element of the maintenance, growth, development, or construction process that fades away, is removed, or becomes ‘invisible’ even if it becomes assimilated and remains structurally integral to the product. All kinds of scaffolding are relational: they connect, span, support, or interface disparate elements across different time and size scales; they provide usable developmental contexts and may serve only in some circumstances or for some actors and not for others.” Caporael, Linnda, J. Griesemer & W. Wimsatt. 2014. “Developing Scaffolds: An Introduction.” Pp. 1-20. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 14.


“Three categories are especially salient.

“Artifact scaffolding Artifacts can scaffold acts/actions/events when they make them possible, feasible, or easier than they otherwise would have been. Of course, to count as artifacts, objects must be made or taken as such by agents. No agency, no artifacts.

“Infrastructure scaffolding Some artifacts or artifact types have the character of infrastructure–objects that persist on a much longer time scale than typical artifact scaffolding interactions such that they can be commonly regarded as parts of the environment or ‘niche’ in which an action takes place.

“Developmental agent scaffolding Artifacts and infrastructure function as scaffolding when agents and their targets respond and cooperate in such a way that they in fact grow, differentiate, learn new skills, or acquire new capacities that would have been more difficult or impossible to acquire or do so with less cost or danger than they otherwise would have.” Caporael, Linnda, J. Griesemer & W. Wimsatt. 2014. “Developing Scaffolds: An Introduction.” Pp. 1-20. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 15.


“The empirical claim of the [core configuration] model is that an evolutionary/cultural history of living in face-to-face groups has shaped human bodies and minds, and that the repeated assembly of such group structures, whole or in part, scaffolds human development, cognition, and culture across generations, even in large-scale society.” Caporael, Linnda. 2014. “Evolution, Groups, and Scaffolded Minds.” Pp. 57-76. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 58.


“One particular and very powerful kind of entrenchment, ‘combinatorial entrenchment,’ in which a number of components are used as a constructional ‘alphabet’ to make a wide variety of adaptive devices or artifacts, is a powerful force for standardization, and has often engendered adaptive radiations, both in biology and culture.” Wimsatt, William. 2014. “Entrenchment and Scaffolding: An Architecture for a Theory of Cultural Change.” Pp. 77-105. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 77.


“At least five kinds of elements are necessary for a theory of cultural evolution and to account for the role of scaffolding in this articulated structure. These are divided into two main categories.

“First there are units of two types recognized in one form or another in all theories of cultural evolution:

“1. Meme-like things (MLTs) that are transmissible or copyable units....

“2. Biological individuals who develop, are socialized, and are trained and acquire skills over time ...

“3. Institutions Institutions are ideational elements like MLTs, but at a social/group level constituting or containing normative rules or frameworks that guide behavior:...

“4. Organizations or self-maintaining groups of individuals, self-organized for some purpose These are like individuals, but at a social/group level, ...

“5. Artifact structures or artifacts mediating short-term activities or processes or providing physical infrastructure maintained on transgenerational time scales providing ‘public goods.’” Wimsatt, William. 2014. “Entrenchment and Scaffolding: An Architecture for a Theory of Cultural Change.” Pp. 77-105. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. Pp. 78-80.


“Such groups may include professional associations, place of employment, political and governmental affiliations, from local to national, condominium association, religious congregation, various interest groups, each with its characteristic norms of behavior and modes of interaction. And their organization is presumably modulated by the core configurations of various sizes that we find natural.

“Many of these kinds of cultural elements are specifically designed to aid the construction or development of and promulgation of competencies and commitments among individuals and organizations. Griesemer and I call this scaffolding. Scaffolding refers to structure-like dynamical interactions with performing individuals that are means through which other structures or competencies are constructed or acquired by individuals or organizations. Material or ideational entities that accomplish this are scaffolds. Thus, chaperone molecules scaffold the right configuration for folding proteins, and the cell scaffolds gene replication and expression so fully that the cell is arguably the relevant reproductive unit rather than the gene or genome. So too the enculturated socialized human, whose agency is richly socially and culturally constructed and supported, is also scaffolded.

“We must distinguish agent scaffolding, artifact scaffolding, and infrastructural scaffolding, cross-classifying the foregoing types of elements:

“6a. Scaffolding for individuals Examples of scaffolding for individuals include family structure, schools, curricula, disciplines, professional societies, church, work organization, interest groups, governmental units, laws.

“6b. Scaffolding for organizations Examples of scaffolding for organizations include articles of incorporation, corporate law, manufacturers’ organizations, chambers of commerce, and distribution networks for manufactured parts in the business world.

“6c. Infrastructural scaffolding A particularly important kind of scaffolding, infrastructure, is so broadly applicable that it may be difficult to specify what particular individuals or organizations and what competencies it is designed for. Language is an obvious one, so obvious it is easily overlooked. Our technological civilization has many such systems: highway, sea, rail, and air networks, shopping centers, containerized shipping, distribution networks for gas, water, power, and telephone, warehouses and reservoirs, public transport, Internet, and waste removal. Since it facilitates so many diverse kinds of things, this kind of scaffolding is commonly very deeply entrenched.” Wimsatt, William. 2014. “Entrenchment and Scaffolding: An Architecture for a Theory of Cultural Change.” Pp. 77-105. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 81.


“Research over the past two decades has shown that with respect to the multicellular animals, the products of subsets of a common set of ancient genes–the ‘developmental toolkit’–which first evolved in single-celled ancestors, are employed for the generation of pattern and form at the embryonic stages of each phylum’s members. This toolkit contains transcription factors, which determine cell-type identity, as well as molecules involved in cell-cell interaction (e.g., adhesion and communication). The latter molecules function in the three-dimensional arrangement of cells to produce bodies and organs.

“However, the gene products constituting the ‘cell interaction toolkit’ do not act on their own to generate organismal form. More specifically, embryogenesis is not simply a matter of self-assembly of proteins and other molecules. Living tissues, including the primordial cell clusters that founded the first metazoan lineages, are physical materials, and many of their morphological states and transformations can be understood in terms of ‘generic’ properties they share with nonliving viscoelastic materials, particularly those (excitable media’) that store mechanical and chemical energy. We have proposed that the main role of the interaction toolkit is to mobilize physical forces and processes of the ‘middle scale’ (mesoscale: 100μm-10mm) relevant to the dimensions of multicellular aggregates.

“In conjunction with this hypothesis we have coined the term ‘dynamical patterning modules’ (DPMs) for the functional units composed of one or more interaction-toolkit molecules and the physical effect they mobilize.” Newman, Stuart. 2014. “Excitable Media in Medias Res: How Physics Scaffolds Metazoan Development and Evolution.” Pp. 109-123. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. Pp. 109-10.


“In this view, the physics of mesoscale materials provides a scaffold for the organization of animal form. This is distinct from the claim that animal embryos are merely mesoscale materials. Genetics also plays a decisive role; only the expression of certain genes permits cell clusters to mobilize particular physical forces on this scale.” Newman, Stuart. 2014. “Excitable Media in Medias Res: How Physics Scaffolds Metazoan Development and Evolution.” Pp. 109-123. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 110.


“Once multicellularity was achieved in proto-metazoans, the biological entities in question were no longer the internally highly structured parcels of matter surrounded by inextensible membranes that individual cells are. In a multicellular aggregate the cells assume the role of loosely associated and independently mobile subunits of what is, in a formal sense, a liquid droplet. Liquids exhibit surface tension, and if their subunits do not exhibit any marked anisotropy, their droplets will contain no internal spaces and be spherical by default (due to the principle of energy minimization). Similarly for an aggregate of cells: if its cellular subunits are uniform in their surface adhesive properties, any interior spaces will automatically become filled in and, if cell shape is relatively isotropic, the cluster’s shape will be a sphere. If, however, the individual cells become polarized in either surface composition or shape, energy minimization will drive such aggregates to become hollow or elongated.

“Another property liquid-like tissues have in common with nonliving liquids is the capacity to ‘phase separate’ when there are different subunits with different affinities for each other. Energy minimization, for example, leads to tissue multilayering if cells reliably differ (qualitatively or quantitatively) with respect to the expression of adhesion molecules.

“All cells potentially exhibit multistable dynamics due to the properties of their internal gene regulatory networks. The physical effect that enables a multicellular cluster to maintain a balance of different cell types is lateral inhibition, whereby a cell signals adjoining or nearby ones to assume a different state than its own. In addition, the secretion of mobile molecules (morphogens) transported by a diffusion or related processes, permits the multicellular aggregate to develop chemical gradients, making it different from one end to the other, an effect that promotes spatially dependent cell differentiation.

“Oscillation in internal chemical composition, a behavior potentially sustained at multiple biochemical levels by any cell, has the reciprocal effect since the oscillations spontaneously and inevitably come into synchrony at the multicellular level, generating long-range coordination of cell state, that is, morphogenetic fields. When synchronized oscillations or related circuitry (e.g. the reaction-diffusion mechanism ... or the local autoactivatory-lateral inhibitory mechanism ...) interacts with morphogen gradients, the result may be the periodic or quasi-periodic arrangement structures, such as the skeletal elements of the vertebrate backbone or the paired limbs.

“Lastly are extracellular matrices (ECMs), which can cause epithelial cell sheets to resist bending deformations and promote invagination, evagination, and branching morphogenesis, or turn liquid-like mesenchymal aggregates solid.” Newman, Stuart. 2014. “Excitable Media in Medias Res: How Physics Scaffolds Metazoan Development and Evolution.” Pp. 109-123. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. Pp. 112-3.


“Dynamical patterning modules, as we have seen, came into existence not by the evolution of new genes but by virtue of the capacity of the ancient gene products described above to mobilize mesoscale physical forces, processes, and effects when they came to operate in cell clusters. Significantly, all present-day embryos pass through an ontogenetic stage analogous to the phylogenetic stage of primitive cell clusters in which DPMs first appeared. Corresponding to (depending on the species), the morula, blastula, blastoderm, or inner cell mass, this ‘morphogenetic stage’, consists of dozens to scores of identically sized cells and is the end product of cleavage of the fertilized egg. It is also precisely the stage of development at which the embryo becomes a parcel of mesoscopic matter and all the DPMs characteristic of the embryo’s phylum are operative.” Newman, Stuart. 2014. “Excitable Media in Medias Res: How Physics Scaffolds Metazoan Development and Evolution.” Pp. 109-123. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 113.


“One important way that variability of form within the various phyla is manifested and implemented is by evolutionary alterations in egg size and shape, and most specifically, in the intra-egg patterning processes that occur prefertilization (i.e., during oogenesis) and postfertilization. Comparing the eggs of the different vertebrate classes–the huge, yolky bird egg, the microscopic eutherian mammal egg, the intermediate-sized egg of fish, amphibians, and nonavian reptiles–shows the lack of obvious mapping between egg morphology and body plan (which is similar in all these examples).” Newman, Stuart. 2014. “Excitable Media in Medias Res: How Physics Scaffolds Metazoan Development and Evolution.” Pp. 109-123. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 115.


“The passage of all of a taxonomic group’s (e.g., a phylum’s) embryos through a morphologically conserved intermediate stage of development before they go on to assume their subgroup-specific characteristics has been termed the embryonic hourglass.” Newman, Stuart. 2014. “Excitable Media in Medias Res: How Physics Scaffolds Metazoan Development and Evolution.” Pp. 109-123. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 118.


“The notion of mesoscale physics as a scaffold for the action of genes that mediate cell-cell interactions, that is, the DPM framework, accounts for both the origination and entrenchment of animal form over the course of evolution. In this perspective, the major morphological motifs of animal body plans arose early, by mechanisms that yielded outcomes that were simultaneously plastic and stereotypical.” Newman, Stuart. 2014. “Excitable Media in Medias Res: How Physics Scaffolds Metazoan Development and Evolution.” Pp. 109-123. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 119.


“To reorient the reigning paradigm, Hutchins has recently proposed the ‘hypothesis of enculturated cognition’ (HEnC) as an alternative to Clark’s largely individualistic vision of the extended mind.” Theiner, Georg. 2014. “Onwards and Upwards with the Extended Mind: From Individual to Collective Epistemic Action.” Pp. 191-208. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 191.


“Their [Clark & Chalmers’] reasoning is based on the premise–which has since become known as the parity principle–that ‘[I]f, as we confront some task, a part of the world functions as a process which, were it done in the head, we would have no hesitation of recognizing as part of the cognitive process, then that part of the world is (so we claim) part of the cognitive process.’” Theiner, Georg. 2014. “Onwards and Upwards with the Extended Mind: From Individual to Collective Epistemic Action.” Pp. 191-208. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 193. Subquote is from Clark, Andy & D. Chalmers. 1998. “The extended mind.” Analysis. 58:7-19. P. 8.


“The technophilic assimilation of people and artifacts under the ambit of highly accessible auxiliary equipment confirms the suspicion, previously raised by Sterelny, that ‘cognition for [Clark], remains paradigmatically a solitary vice, though one prosthetically enhanced by wideware.’” Theiner, Georg. 2014. “Onwards and Upwards with the Extended Mind: From Individual to Collective Epistemic Action.” Pp. 191-208. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 194. Reference is to Andy Clark. Subquote is from Sterelny, K. 2004. “Externalism, Epistemic Artefacts, and the Extended Mind.” Pp. 239-54. From Schantz, R. (Ed.) The Externalist Challenge. de Gruyter. P. 246.


“... Barnier et al. usefully distinguish among three ways in which the process of remembering–or any other cognitive activity–can be socially distributed. According to the triggering thesis, social phenomena can be a valuable source of input, trigger, or context eliciting individuals to engage in certain forms of psychological processes inside the head. For the bulk of research done in many areas of cognitive but also social psychology that tend to have a strongly individualistic bent, the triggering thesis succinctly summarizes a kind of standard view about the place of ‘the social’ in cognition. As an alternative to the rampant methodological individualism in mainstream psychology, Barnier et al. appropriate the so-called social manifestation thesis (SMT) that has been developed in a series of papers and books by Robert Wilson. The SMT asserts that at least some psychological processes can be manifested only insofar as the individual engaged in that process forms part of a social group of a certain kind....”

“Central to the SMT is the idea that individuals incorporate certain aspects of their social and cultural environment so deeply into their mental functioning that those aspects become constitutive features of cognition. Hence the SMT can be seen as advocating an ‘active’ form of social externalism, insofar as the individual-bound portion of a socially manifested cognitive process is not seen as metaphysically sufficient for the psychological phenomenon in question to occur.”

“Finally, Barnier et al. dub as the group mind thesis (GMT) the claim that groups themselves, over and above the individuals who compose those groups, can engage in psychological processes or have psychological abilities in their own right. The somewhat pretentious locution of a ‘group mind’ should be taken with a grain of salt.” Theiner, Georg. 2014. “Onwards and Upwards with the Extended Mind: From Individual to Collective Epistemic Action.” Pp. 191-208. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. Pp. 194-5. References: Barnier, A., J. Sutton, C. Harris & R. Wilson. 2008. “A conceptual and empirical framework for the social distribution of cognition: The case of memory.” Cognitive Systems Research. 9:33-51. Wilson, R. 2004. Boundaries of the Mind: The Individual in the Fragile Sciences: Cognition. Cambridge UP.


“... we can say that collective epistemic actions are actions that people perform to improve their cognitive performance as a group, or, alternatively, actions by which groups change the world in order to simplify their problem-solving tasks, or, as a final variant, actions that are performed by groups to unearth valuable information that is currently unavailable, hard to detect, or hard to compute.” Theiner, Georg. 2014. “Onwards and Upwards with the Extended Mind: From Individual to Collective Epistemic Action.” Pp. 191-208. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 197.


“Building on Clark and Chalmer’s original parity principle, the principle of social parity suggests that if, in confronting some cognitive task, the members of a group collaboratively interact in a process which, were it done in the head, would be accepted as a cognitive process, then that group (as a whole) is performing that cognitive process.” Theiner, Georg. 2014. “Onwards and Upwards with the Extended Mind: From Individual to Collective Epistemic Action.” Pp. 191-208. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 197. Reference is to Clark, Andy & D. Chalmers. 1998. “The extended mind.” Analysis. 58:7-19.


“Here, I want to mention four alternative conceptions of culture, each of which has a following among some researchers.... The alternatives are culture as an object of evaluative criticism; culture as systems of meaning, symbolization, and belief; culture as intergenerational transmission via learning; and culture as a system of conventions and institutions.” Gerson, Elihu. 2014. “Some Problems of Analyzing Cultural Evolution.” Pp. 265-81. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 267.


“The view that culture consists of transmission from individual to individual raises many difficulties for any analysis that seeks to understand institutions such as organized research or textbook publishing. These approaches may attempt to capture the effects of institutions via reference to ‘biases’ in transmission or ‘background’ factors, but this strategy simply begs the question of how we are to understand repeated assembly of coordinated practices and their scaffolding by excising the very phenomena which were to be explained.” Gerson, Elihu. 2014. “Some Problems of Analyzing Cultural Evolution.” Pp. 265-81. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 268.


“The fourth view of culture, and the one I shall adopt here, defines culture as a system of institutions made up of conventions. An institution is a collective capacity to carry out some task, ‘a collective enterprise carried on in a somewhat established and expected way.’” Gerson, Elihu. 2014. “Some Problems of Analyzing Cultural Evolution.” Pp. 265-81. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 268.


“The core idea in this view is that a culture is made up of a system of interdependent and interacting institutions. Institutions, in turn, are systems of related conventions. For example, it was conventional for Saturday night jazz bands in post-World War II Chicago to wear dark suits and ties, to know and be able to play a large number of ‘standard’ songs, to coordinate their playing through a series of routinized gestures, to allow for solos as part of the performance of songs, to receive payment in standardized ways, and so on.” Gerson, Elihu. 2014. “Some Problems of Analyzing Cultural Evolution.” Pp. 265-81. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 269.


“A convention then, is a collective capacity to conduct a certain kind of organized activity, to come together and make something happen reliably.” Gerson, Elihu. 2014. “Some Problems of Analyzing Cultural Evolution.” Pp. 265-81. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 269.


“The structure of an institution is the pattern of relationships among the conventions that make it up. Eating a meal, for example, involves many conventions about required and forbidden ingredients, how dishes are composed, the order in which they are eaten, the use of implements such as knives, chopsticks, napkins, bread, and so on. This pattern is almost entirely independent of the scope of the institution, which refers to the number of people who are capable of participating effectively in the institution.” Gerson, Elihu. 2014. “Some Problems of Analyzing Cultural Evolution.” Pp. 265-81. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 270.


“The idea that culture consists solely of transmission from individual to individual confounds the scope or range of an institution with the organization of the institution. An institution can change structure without changing its scope, and vice versa. These two different properties of institutions are not completely separable. For example, if the number of people who eat salad becomes small enough, then the institution will disappear.” Gerson, Elihu. 2014. “Some Problems of Analyzing Cultural Evolution.” Pp. 265-81. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 270.


“These individuals and organizations [particular people or families, clubs, etc.] are the material things which actually perform the activities, the parts of society whose operation realizes institutions. Organizations perform conventions and institutions just as jazz bands play music. Indeed, a jazz band playing a ‘standard’ song is neither more nor less than an organization conducting a convention.” Gerson, Elihu. 2014. “Some Problems of Analyzing Cultural Evolution.” Pp. 265-81. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 270.


“... institutions give order to the conduct of organizations, organizations give material substance to the conduct of institutions. Society is the repeated assembly of organizations in an institutionalized way; culture is the routinized manner in which organizations are assembled and conducted.” Gerson, Elihu. 2014. “Some Problems of Analyzing Cultural Evolution.” Pp. 265-81. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 271.


“Darwinian models are utterly lost in the face of modern industrial economies with relatively fluid systems of stratification. In these societies, many different interacting institutions form a complex reticulated system of dependencies. As a result, there are many alternative life courses available to individuals, and their social characteristics are only loosely determined. Developmental histories and environmental variation, not the intrinsic properties of individuals, are overwhelmingly important.” Gerson, Elihu. 2014. “Some Problems of Analyzing Cultural Evolution.” Pp. 265-81. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 275.


“In what sense are malnutrition or alcohol consumption, with their transgenerational deleterious effects, adaptive? Rather than trying to speak of adaptive cultural behaviors–an attempt that is prone to tautological reasoning and oblique moralizing–it seems that descriptions in terms of differential stabilization are more adequate and more informative. With processes such as urban poverty, it is developmental stabilization, not adaptability, that is the key issue.” Iddo, Tavory, S. Ginsburg & E. Jablonka. 2014. “The Reproduction of the Social: A Developmental System Approach.” Pp. 307-25. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. Pp. 310-1.


“A DST approach to cultural evolution suggests that the most useful unit of analysis is the dynamically reproducing sociocultural system under study, rather than any particular causal factor that contributes to the reproduction dynamics of such a state.” Iddo, Tavory, S. Ginsburg & E. Jablonka. 2014. “The Reproduction of the Social: A Developmental System Approach.” Pp. 307-25. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 321.


“The realization that the units of investigation set by classical evolutionary theory or its most obvious analogical extensions to cognition or culture cannto work for these domains, due to the extent and character of scaffolding interactions and hybridizations across kinds of materials and ideas, calls for new units of investigation.” Griesemer, James, L. Caporael & W. Wimsatt. 2014. Developing Scaffolds: An Epilogue.” Pp. 363-88. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 371.


“They [scaffolding authors Martinez, Allen, Gerson, Tavory, Ginsburg & Jablonka] seek a finer-grained, mechanistic account, in which the interplay of cognizing, developing system and scaffolding environment interact to produce the observed stability of inheritance patterns of cultural practices rather than simply a description of those patterns.” Griesemer, James, L. Caporael & W. Wimsatt. 2014. Developing Scaffolds: An Epilogue.” Pp. 363-88. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 378.


“We aimed to introduce scaffolding as theoretically significant for a broadened eco-evo-devo perspective that we expect to be far more generative than traditional neo-Darwinism and to offer new theoretical tools and ideas about units of investigation for culture and cognition.” Griesemer, James, L. Caporael & W. Wimsatt. 2014. Developing Scaffolds: An Epilogue.” Pp. 363-88. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 387.


“Material engagement is the synergistic process by which, out of brains, bodies, and things, mind emerges.” Malafouris, Lambros. 2013. How Things Shape the Mind: A Theory of Material Engagement. MIT Press. P. 17.


“Recent studies don’t simply show that gesture is tightly intertwined with speech in timing, meaning, and function; they suggest that gesturing reduces cognitive load and thus frees speakers’ cognitive resources to perform other tasks (e.g., memory tasks).” Malafouris, Lambros. 2013. How Things Shape the Mind: A Theory of Material Engagement. MIT Press. P. 60.


“Indeed, according to David Kirsh, spatial arrangements form an important part of the functional architecture of any distributed cognitive system in at least three important and correlated respects: by supporting choice, by supporting perception, and by supporting problem solving.” Malafouris, Lambros. 2013. How Things Shape the Mind: A Theory of Material Engagement. MIT Press. P. 72. Reference is to Kirsh, David. 1996. “Adapting the environment instead of oneself.” Adaptive Behavior. 4:415-452.


“Whereas mainstream externalism (or the idea of external symbolic storage) implies externalization of cognitive content, active externalism implies externalization of cognitive states and processes. For active externalism, marks made with a pen on paper are not an ongoing external record of the contents of mental states; they are an extension of those states. Cognition and action arise together, dialectically forming each other. There is a huge ontological distance between a mind able to externalize its contents to material structures and a mind whose states and processes aren’t limited by the skin.” Malafouris, Lambros. 2013. How Things Shape the Mind: A Theory of Material Engagement. MIT Press. P. 74.


“Contrary to my discussion of the linguistic sign, the meaning of the material sign is expressive. That means that the material sign, in most cases, does not stand for a concept but rather substantiates a concept. This is what in philosophy is called instantiation. The material sign instantiates rather than symbolizes. It brings forth the concept as a concrete exemplar and a substantiating instance.... Indeed, a material sign as an expressive sign does not refer to something existing separately from it, but is a constitutive part of what it expresses and which otherwise cannot be known. It operates on the principle of participation rather than that of symbolic equivalency.” Malafouris, Lambros. 2013. How Things Shape the Mind: A Theory of Material Engagement. MIT Press. P. 97.


“Reality, at least for Material Engagement theory, is neither post nor ante res; is is in res. Material signs are not simply message carriers in some pre-ordered social universe. Material signs are the actual physical forces that shape the social and cognitive universe.” Malafouris, Lambros. 2013. How Things Shape the Mind: A Theory of Material Engagement. MIT Press. P. 97.


“The structure of this emergent conceptual space [hybrid mental spaces of the conceptual integration or blending theory of Fauconnier] is identical to none of the contributing input spaces but is instead constructed according to a set of uniform structural and dynamic principles defined by Fauconnier as composition, completion, and elaboration.” Malafouris, Lambros. 2013. How Things Shape the Mind: A Theory of Material Engagement. MIT Press. P. 103. Reference is to Fauconnier, G. 1997. Mappings in Thought and Language. Cambridge UP.


“Hutchins’ argument, more specifically, is that often material structure is directly projected into the blended space in order to stabilize the conceptual blend. Hutchins calls this direct projection of material structure onto the blend ‘material anchoring.’” Malafouris, Lambros. 2013. How Things Shape the Mind: A Theory of Material Engagement. MIT Press. P. 104. Reference is to Hutchins, Edwin. 2005. “Material anchors for conceptual blends.” Journal of Pragmatics. 37:1555-77.


“... Clark introduces the term ‘surrogate material structures,’ referring to any kind of real-world structure, artifact, or material assemblage that is used to stand in for, or take the place of, some aspect of some target situation, thereby allowing human reason to reach out to that which is absent, distant, or otherwise unavailable. Clark points out two interesting and often unnoticed properties of many surrogate situations; the way they highlight important features by suppressing concrete detail and the way they relax temporal constraints on reasoning.” Malafouris, Lambros. 2013. How Things Shape the Mind: A Theory of Material Engagement. MIT Press. P. 104. Reference is Clark, A. 2010. “Material surrogacy and the supernatural: Reflections on the role of artefacts in ‘off-line’ cognition.” From Malafouris, L. & C. Renfrew (Eds). The Cognitive Life of Things: Recasting the Boundaries of the Mind. McDonald Institute for Archeological Research.


“Seen from the perspective of ‘active externalism,’ the Background becomes a part of the mind, or what might be called an extended intentional state. This implies that the objects and material structures that constitute this Background can be argued to project toward me as much as I project toward them. In other words,

‘The world is inseparable from the subject, but from a subject which is nothing but a project of the world, and the subject is inseparable from the world, but from a world which the subject itself projects.’

“In the case of ‘G-intentionality’ [Gestalt intentionality or ‘intention-in-action’] the line between human intention and material affordance becomes all the more difficult to draw. In fact, it might even be suggested that in certain cases human intentionality identifies with the physical affordance.” Malafouris, Lambros. 2013. How Things Shape the Mind: A Theory of Material Engagement. MIT Press. Pp. 142-3. Subquote is from Merleau-Ponty, M. 1962. Phenomenology of Perception. Routledge. P. 430.


“To this end [of recognizing “visual perception as a mode of probing the outside world rather than representing it”], an analogy may be useful: Whereas the toolmaker brings forth the possibility of a new form of tactile thinking, the image maker brings forth the possibility of a new form of visual thinking. As the liberation of the prehensile hand from the requirement of locomotion allowed it to become a privileged interface between the organism and its physical environment, so, it seems to me, the liberation of a sight from its ordinary experiential requirements, in the case of the Paleolithic image [where lines seem to follow the hand and the irregularities of the material rather than a representation goal], allowed the eye to gradually become the privileged interface of human perceiving.” Malafouris, Lambros. 2013. How Things Shape the Mind: A Theory of Material Engagement. MIT Press. Pp. 203-4.


“When are environments reliable enough to deliver developmental capacities in the form of nutrition (material, energy), scaffolding (physical interaction through hybrid states to facilitate development), and prosthetics (organized parts that enhance or substitute for developed ones, e.g., hermit crab houses, nest sites, knowledge recorded in books, scientific instruments that enhance perception), so that developing systems may forego making or managing those processes on their own?” Griesemer, James. 2014. “Reproduction and the Scaffolded Development of Hybrids.” Pp. 23-55. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 28.


“It would appear that a scaffold per se does not contribute material parts to the developing system, so it cannot count as food and does not count as a parent, but only counts as a facilitating or catalyzing part of the system’s environment. That view depends, however, on where we place the system-environment boundary and how we narrate the changes in the system over its life trajectory.” Griesemer, James. 2014. “Reproduction and the Scaffolded Development of Hybrids.” Pp. 23-55. From Caporael, Linnda, J. Griesemer & W. Wimsatt, Eds. Developing Scaffolds in Evolution, Culture, and Cognition. MIT Press. P. 30.


“Nor is multicellularity exclusively eukaryotic. Among Bacteria it has been extensively exploited by cyanobacteria, including a filmanentous clade capable of differentiating both N-fixing heterocysts and reproductive akinetes. It has also been adopted by numerous other lineages, including photosynthetic green non-sulfur bacteria, large sulfur-oxidizing proteobacteria, aggregating myxobacteria, magnetotactic bacteria, and a remarkably diverse range of actinobacteria. It is less common among Archaea, but certain methanogens do form ensheathed multicellular chains up to several hundred micrometers long.” Butterfield, Nicholas. 2009. “Modes of pre-Ediacaran multicellularity.” Precambrian Research. 173: 201-11. P. 202.


“The question, of course, is what exactly is meant by ‘multicellularity,’ and how the condition can be usefully recognized in the fossil record. For ‘higher’ organisms the inter-dependent division of labour between differentiated organs, tissues and/or cell-types provides a useful and widely accepted diagnostic criterion; however, this still leaves a significant grey zone represented by more cryptic levels of intercellular integration, as well as a disparate range of ‘colonies’ and facultatively filamentous unicells. At another level, microbial biofilm communities have sometimes been promoted as multicellular organisms on the grounds that they are capable of sophisticated cell signaling, collective production of extracellular matrix, and differential development including programmed cell death.” Butterfield, Nicholas. 2009. “Modes of pre-Ediacaran multicellularity.” Precambrian Research. 173: 201-11. P. 202.


“At its most basic level, the selective advantages of multicellularity lie in the buffering properties of increased size, which in turn offers a potential for increased cellular differentiation, functional specialization and emergent organismal/ecological complexity.” Butterfield, Nicholas. 2009. “Modes of pre-Ediacaran multicellularity.” Precambrian Research. 173: 201-11. P. 209.


“Large size and increased divisions of labour multiply the ways in which morphological differentiation confers selective advantage, but also entail increasingly complex developmental programming; hence the enormous range of organisms that have adopted simple colonial habits, relatively fewer instances of truly integrated, obligate multicellularity, and many fewer still that are distinguished by differentiated inter-dependent cell-types. Only two lineages – eumetazoans and embryophytes – have ever advanced to the next level, where whole populations of differentiated cells have acted collectively to form inter-dependent tissues and organs.” Butterfield, Nicholas. 2009. “Modes of pre-Ediacaran multicellularity.” Precambrian Research. 173: 201-11. P. 210.


“Ecosystem engineering: modifications to the environment by a species that affects resource availability for another species.... Niche construction: informed activities of organisms that influence the environment and affect the fitness of the population.” Erwin, Douglas. 2008. “Macroevolution of ecosystem engineering, niche construction and diversity.” Trends in Ecology and Evolution. Vol 23, No. 6. Pp. 304-10. P. 304.


“Rivalrous goods are those for which, if someone else uses the good, it degrades the ability of others to use the good. For example, there is a limit to how many can use a bicycle simultaneously.... The concept of excludability is subtly different because it relates to the ease with which a user can be excluded from using a good.... Romer’s crucial insight was to realize that economic growth ultimately depends on the generation of non-rivalrous, non-excludable goods because these goods produce economic spillover effects (positive feedback) that percolate across the economy. These goods have a greater impact on growth than other types of innovation.” Erwin, Douglas. 2008. “Macroevolution of ecosystem engineering, niche construction and diversity.” Trends in Ecology and Evolution. Vol 23, No. 6. Pp. 304-10. P. 308. Reference is to Romer, P. 1990. “Endogenous technological change.” Journal Political Economics. 98: S71-S102.


“There are three matrices that will be of interest in this chapter: the stoichiometric, gradient, and Jacobian matrices. The stoichiometric matrix is a mathematical representation of the ‘links and nodes’ of a network. The columns correspond to the links (or reactions) and the rows correspond to modes (or chemical species/metabolites). The gradient matrix represents the dependence of the links of the modes (in the linear regime). The Jacobian matrix is used to describe the overall dynamic relationships in the network; as will be seen however, this matrix can be composed from the stoichiometric and gradient matrices. The key point here is that the fundamental matrices of interest are the stoichiometric and gradient matrices, and these are in fact biological data matrices.” Jamshidi, Neema and B. Palsson. 2011. “Metabolic Network Dynamics: Properties and Principles.” Pp. 19-37. From Dubitzky, Werner, J. Southgate & H. Fuss (Eds). Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology. Springer Verlag. P. 23.


“A key feature of biological networks is the presence of many interactions that occur on a wide range of different time scales....

“One overall goal of dynamic analyses of networks is to simplify network structure and to determine which interactions are relevant at particular time scales of interest. This enables one to filter out interactions that are either too fast or too slow to be of interest and to also characterize the progressive pooling of metabolites across slower and slower time scales.” Jamshidi, Neema and B. Palsson. 2011. “Metabolic Network Dynamics: Properties and Principles.” Pp. 19-37. From Dubitzky, Werner, J. Southgate & H. Fuss (Eds). Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology. Springer Verlag. P. 25.


“Metagenomic sequencing has shown that each human gut has entered into a persistent partnership with over 150 species of bacteria, and that the human species maintains about 1000 major bacteria groups in our gut microbiome. The gene set contained by this symbiotic metagenome is about 150 times larger than that of the human eukaryotic genome. And this does not include the symbionts of human airways, skin, mouth, or reproductive orifices.” Gilbert, Scott, J. Sapp & A. Tauber. 2012. “A Symbiotic View of Life: We Have Never Been Individuals.” The Quarterly Review of Biology. Vol. 87, No. 4. Pp. 325-41.


“Neither humans, nor any other organism can be regarded as individuals by anatomical criteria. To capture this complexity, the term ‘holobiont’ has been introduced as the anatomical term that describes the integrated organism comprised of both host elements and persistent populations of symbionts.” Gilbert, Scott, J. Sapp & A. Tauber. 2012. “A Symbiotic View of Life: We Have Never Been Individuals.” The Quarterly Review of Biology. Vol. 87, No. 4. Pp. 327-8.


“The coevolution of mammals and their gut bacteria has in effect resulted in the ‘outsourcing’ of developmental signals from animal cells to microbial symbionts.” Gilbert, Scott, J. Sapp & A. Tauber. 2012. “A Symbiotic View of Life: We Have Never Been Individuals.” The Quarterly Review of Biology. Vol. 87, No. 4. P. 328.


“The immune system may be formulated as having two ‘limbs’: an outward-looking limb that defines the organism as that which is to be protected from foreign pathogens, and an inward-looking arm that looks for potential dangers arising from within the organism itself. This dualistic vision was the original conception of Metchnikoff at the end of the 19th century. He regarded immunity as a general physiology of inflammation, which included repair, surveillance for effete, dying, and cancer cells, as well as responsibility for the defense against invading pathogens. This larger, systemic understanding thus places defensive properties as only part of a continuous negotiation of numerous interactions between the organism and its biotic environment–both ‘internal’ and ‘external.’” Gilbert, Scott, J. Sapp & A. Tauber. 2012. “A Symbiotic View of Life: We Have Never Been Individuals.” The Quarterly Review of Biology. Vol. 87, No. 4. P. 332.


“To use an anthropomorphic analogy, the immune system is not merely the body’s ‘armed forces.’ It is also the ‘passport control’ that has evolved to recognize and welcome those organisms that help the body.” Gilbert, Scott, J. Sapp & A. Tauber. 2012. “A Symbiotic View of Life: We Have Never Been Individuals.” The Quarterly Review of Biology. Vol. 87, No. 4. P. 333.


“Thus, animals can no longer be considered individuals in any sense of classical biology: anatomical, developmental, physiological, immunological, genetic, or evolutionary. Our bodies must be understood as holobionts whose anatomical, physiological, immunological, and developmental functions evolved in shared relationships of different species.” Gilbert, Scott, J. Sapp & A. Tauber. 2012. “A Symbiotic View of Life: We Have Never Been Individuals.” The Quarterly Review of Biology. Vol. 87, No. 4. P. 334.