Saturday, December 8, 2012


I would like to thank Ivan Gomez.


     Teleology as applied to the study of biological evolution has a history going back to Plato  and Aristotle. Plato attempted to ground final causes into those necessary ends which were the  good based on the whim of an external agency (9; sec. 99), whereas Aristotle grounded his  account as a type of formative force intrinsic to natural forms (10; pp. 639-643). He [Aristotle]  also presents four causes in his Physics. One of them, the efficient cause, is the principle which,  as I will show, begins with the primitive entropic relation between the original components  which have been implicated in the origin of life. The final ends assigned to biological structures  constituting organisms have become part of a linguistic game given by the statement S: “the structure X is for the function Y” (5; line 1). I use the term biological structure to mean those components which we can view under the microscope that seem to constitute organic life when cultured – morphological structures. Indeed, this view has served well in the fields of Medicine and Microbiology (e.g. “Genes are for the encoding of proteins”). However, it has failed to provide an account for the phenomena underlying the unity of living organisms due to its inability to achieve a complete model encompassing the plurality of functions which biological structures are capable of expressing within the constraints of this Universe’s physics, the world which we can observe around us. Consider the case of a mousetrap. We would say that its function – the natural purpose that comes from its structure – is to catch mice. What is not considered is that nothing would stop me from using it as a tie-clip, either. This example elucidates what is meant by the plurality of functions that the organism is capable of expressing, whether it is the components making it up or the whole organism interacting with the environment. 

     Mechanistic theories that explain highly organized systems as having a list of structures working towards natural purposes cannot be explained without reference to immanent teleology  (6; pp. 22). When a mechanism or otherwise linear pathway is proposed for the function of an organism, the classical teleology would ascribe this generally as S. S can further be extended in a chain of causation going backwards and forward in time and space. The structure X, initiating function Y which enacts on structure Y’ and so on, is the backbone of such mechanisms or bauplan/wiring diagrams for organisms, tracing the chain from the birth of the living system to its destruction. From the DNA/RNA come proteins, functional units which are used for building blocks involved in a hierarchy of structures going from the single cell up to entire organs, which compose the organism. Mind you, this only applies for the case of organisms which transfer a genetic component to an offspring generation. In the cause-and-effect scheme, we can determine the life history of an organism using such mechanisms, and whether we ascribe the final cause of a biological individual to perpetuate selfish replicators, or to pursue God as a result of having conscious minds, there is still a question which remains of what moved that first cause. The ultra-reductionist analysis which has been applied to biological individuals has, in effect, asserted that life has some vital force in an attempt to better understand it. However, that there is a greater abundance of the data regarding the physical components making up an organism (and always growing) does not lead us to a holistic understanding of the phenomena that leads to novelty within organisms; that principle which gives life autonomy-without-purpose and causes the structures underlying organisms to transmute into novelty, giving rise to new lineages. 

     Contrast this account of teleology with the Principia Cybernetica*. The linguistic states  that we formulate to study the natural purposes of the living recursively interact with and continually transform/perturb the system under consideration (18). Maturana and Varela say that once an observer actually applies the statement S to their system, the observation made under S will transform subsequent claims made about that system in the future. It is upon this definition that first-order cybernetics bases itself upon. From the point of view of humans, we can see that since Darwin came up with his theory, the natural philosophers that came to follow him operated upon the organisms they studied with the domain of knowledge that Darwin himself interacted in. The idea itself subsequently became absorbed in that recursive process to go on and change what we understood about teleology in the context of life and continues to iterate as modern scientists attempt to apply the theory to lower and lower levels of resolution. As Dennett said, Darwinian evolution has become a universal acid (24), and it is a matter of course that this recursive path it has set us upon will continue to assign meaning to the structures which we study. What S suggests as the generic feature of this teleology is insufficient under the cybernetic view because what we observe as humans will fail to refer to the set of components which are not denoted by structure X but may actually be for a function Y. Although this may sound like solipsism on the surface, I direct the reader towards the instrumentation problem. The structure called “gene” is for the encoding of functional proteins in sexually reproducing life-forms, but in the 19th century the equipment was not available to actually map this structure and establish the gene as a sufficient cause for that clockwork. This failure in reference occurs today with our linear pathways paradigm, particularly in Medicine where advances in Systems Biology are showing associations connections between components that were thought to be completely unrelated before, but are somehow implicated in disease (23). An example of this is the association between the kidney and brain. 

     However, despite how operationally useful this view of “applying S” may be, there is a paradoxical situation (3) faced by the notion of intrinsic natural purposes. We may only apprehend the natural purposes in nature in terms of a “reciprocal domination” between the parts and the whole of an organism. The poverty of statements such as S lies in the detail that once a final cause has been identified for the parts (and sum-of-parts), then we have in essence already recognized the efficient cause to be inseparable from the final. In essence, the developmental program that we recognize as the intrinsic teleology to interacting agents is precisely that which we want to prove. Van de Vijver states it beautifully by stating that we are “inverting cause and effect in such a way that future events could determine that which happened in an anterior time” (pp. 147). Beginning with that which you set out to prove or otherwise purport is “the end” for a living system is akin to supposing the conclusion of an experiment as its very hypothesis. 

     Now that it has been shown that organisms have neither immanence nor intrinsic natural purpose based on the interplay between their parts and wholes, I will instead focus on what is meant by teleonomy. I stress first that living systems are without purpose entirely. From a first-order cybernetics point of view, it is my purpose to view such systems from the outside as an observer and integrate teleonomy as a descriptive term for the domain of observations made in the empirical study of the relations underlying the components we can currently handle under the constraints of our technology. Under this framework, there is an end for the living system, and it occurs at the level of the biological individual maintaining itself through its organization (1; pp. 67), although this is unique from the intrinsic purpose which underlies animistic accounts of mechanicism. I consider such an individual to be that which has task closure, which will be expanded on in a later segment. The distinction of observing from the outside versus developing a system within the bounds of say, second-order cybernetics, is the difference of whether we include the observer-community as part of the closure. As was mentioned, it is the case with humans that as we continue observations within a domain of knowledge, we will continue down that research program. By assuming this externalist stance, I seek to extend the current scientific theories we have regarding the study of biological evolution to a generalized view of tackling these largely metaphysical questions regarding where novelty has its origins and how a plurality across biological structures finds itself co-evolving with the external world without purpose. 

     To address these questions, I introduce entropy. The term entropy has usages within thermodynamics and information theory (7, 13, 15, 17, 19). With respect to being a thermodynamic property, it is the physical quantity which, as it increases over time, determines the ability of life to work and subsequently create useable structures for maintaining its existence (17). In the cell, when the entropy outweighs its capacitive abilities to continue splitting, programmed cell death will occur. With respect to a single living organism, composed of many cells, as this quantity increases over time, order will collapse into ever-increasing disorder as the organism dissipates into other forms of useable energy in the Universe. On the other side, the entropy of information theory (Shannonian) represents a mathematical term for measuring uncertainty (7). This term measures the statistical mechanics of discrete outcomes (15) for a system. One may measure the Shannonian entropy of a coin toss and obtain a solution to how likely it will be to make predictions about its outcome in the future. As the number of coin tosses increases in time, the total entropy begins to increase, implying the unpredictable nature of the outcome as information is lost. Denbigh claims that both of these contexts in which the word is used is independent of man’s presence and thus fully objective on the basis of the persistence of the Universe (pp. 115) and the creativity it manifested pre-human history. Not only is entropy scientifically objective, but the thermodynamic and statistical mechanical forms is also interchangeable within the framework I wish to propose. The basis upon which I consider entropy to be scientifically objective does not necessitate its material existence, however. Rather, it is used here as an abstraction for what appears to be an external phenomena to our observer-community; that as time goes forward, complexity and the irreversibility of the reactions underlying the physico-chemical equations behind life’s self-maintaining processes become greater. It is much easier to reverse the formation of sodium hydroxide than it is to reverse an adult human male back into a fetus. The distinction between reversible and irreversible reactions based on a synthesized view of entropy also allows us to reconsider what is life as it moves from minimal life-forms to incredibly complex ones. 

     Now that we have a working definition of entropy, I will demonstrate why biological life definitely has a finite initial point. Imagine a machine with a series of knobs on it. This machine (call it B) is controlled by another (A), which works towards optimizing the knobs in the precise positions required for B to begin tinkering with the next machine in the sequence, C. However, if such knobs exist on all the machines in this sequence, then either there is an infinite number of such machines or there was a prime agency which started tinkering with the first machine. In the case of life, if we are to assume the Big Bang occurred 3.5 billion years ago, then organic life cannot be in an infinite state of such machines extending back since time is finite under this theory. In evolutionary time, we know that life on earth did not begin 3.5 billion years ago, as it took an even longer time for the formation of planets even capable of sustaining life. This issue does not even begin to account for the other forms of life which have unfolded asexually or non-genetically. As Brillouin points out, “life is playing upon all these exceptional conditions on the fringe of the second principle of thermodynamics” (pp. 566). Any “prime mover” we know of is residual of how life emerged, although addressing the origin of life cannot give us the “why”. I do not wish to understand the conditions before the seed was planted, only how it lead to the world’s state of affairs as they are today. 

     On first-order cybernetics, there have been attempts in the field of theoretical biology to provide an account of organization in living systems using autopoiesis (self-creation) and metabolic-repair (M, R) systems (11). The emergence of rudimentary life-forms has been characterized by the following formula F: (in)organic chemistry => prebiotic metabolism => RNA world => proteins => DNA (13; pp. 1735). The transition between (in)organic chemistry to prebiotic metabolism is particularly important, because the presence of a metabolic cycle is early evidence of rudimentary, self-replicating structures (19) capable of converting useable energy into work (and subsequently, entropy). The earliest work cycles could only have been made possible by what is called task closure. Closure is defined mathematically as a function, or a reference to a function, which has a reference table to all the free variables within the function. To better explain this, consider the term self-referentiality. The clearest example of this is Ouroburos; the world-snake which is forever consuming itself. Self-referentiality in reality is not so extreme, but considers the case of one object, or node, which contains such a pointer back to itself (i.e. the pointer for Ouroburos is his mouth referring back to his tail). When two nodes in concert point to each other, the set over both becomes closed. Experimental and computational evidence has made it quite clear that the existences of such sets are certainly plausible. In the case of that transition between in(organic) chemistry to prebiotic metabolism, metabolic closure based on the Krebs cycle has been proposed as the network underlying minimal life (11). Such reactions are notably reversible, and chemoautotrophs which are living today are capable of this metabolism, which would imply that this lineage has existed from its minimal predecessors. Ashkenazy et al discovered a nine-peptide autocatalytic set capable of achieving closure over a task space which involves the catalysis of all reactions within that set by its very own members out of those nine peptides (21). Others have shown that components such as stem cells can commit to specific lineages based on a rule-based discrete transition at the level of transcriptome-wide noise (2). At what point do these phenomena converge? 

     Apply the metaphor of machines optimizing one another in sequence to an origin of life scenario on early earth. The scientific literature lends ear to notions such as a primordial soup (a mixture of organic and inorganic components within the open system of the first oceans. Suppose that these first oceans are a finitely bounded, but open, thermal bath (i.e. early earth was “very hot”). Given enough [evolutionary] time (Bywater says it is ~0.3 Gya; pp. 167) the probability of at least one of the organic or inorganic components to collide with one another becomes very high. It is from this collision, similar to the particle collision which unfolded the Universe from the Big Bang that the first primitive relations began, as well as the unfolding of prebiotic, informational components which could self-replicate the very primitive relations implied by that initial contact. Whichever component was first to manifest itself as a “classical” biological structure – the cell membrane, DNA, RNA, cytoplasm – is inconsequential. This is what is meant by component-independence. Instead, if we focus on the primitive relation that emerged from the task closure from minimal life as the efficient cause for biological life to begin on earth, the cybernetic-teleonomic account of life becomes a matter of the change through time of that relation, as implied by the micro-states which it takes, as opposed to a final meaning that is intrinsic to morphological structures. It is on this basis that I pretend to claim Shannonian micro-states perpetuate spontaneous creativity through the production of negative entropy. If the primitive relations underlying the first forms of autonomy and rudimentary life are irreversible, then the living system is guaranteed to also persist and replicate on the basis of entropy in the thermodynamic sense as well (a necessary principle of the second law). 

     To visualize, suppose that two particles collide in a thermal bath, representing the initial conditions of early earth. Under the collision, the particles form a complex X, which is denoted by the symbol *. The symbol represents the first node (the root) of what is called a binary tree, where successive self-replications of * gives rise to two more, and those two nodes replicate two more nodes and so on. In a sequence, the number of nodes increases in a geometric series on each level, which begins as {1, 2, 4, 8, 16…}. Level n = 0 is defined as the root node. It is at this level that the total information entropy is 1, which represents a finite, yet undetermined, amount of free energy available to convert into useful work within that closure (19). I call this variable ΔI  which is the change in information entropy from level n to n + k, where k > 0. In this manner, as the binary tree grows to an indefinite level, the production of negative entropy increases, and the living system loses meaningful micro-states as the information required to maintain the unity begins to experience a loss of integrity. It is at this point that the entropy underlying the relation between the components can no longer undergo self-maintenance and self- renewal, resulting in biological death. When a unique micro-state denoted by ΔI comes about by the behaviour of cells on a continuous space-time plane in two-dimensions, I hypothesize that it is sufficient to be able to trace the emergence of conditions such as cancer. What is especially elegant about tracing such changes through a binary tree is that its growth can be denoted by a logarithmic function, where the logarithm of n (the number of nodes) is actually ΔI  As ΔI goes closer to 0, one would expect to observe features such as a loss in genomic stability and a greater number of say, copy-number variations. In the case of n = 0, ΔI = log2 (0) which is 1; intuitively, at the point of origin for an organism, the amount of meaningful information available to its cells to proliferate is 100%. As its cells continue to divide, ΔI becomes smaller and the predictability of what micro-state the cell will take on will continue to grow smaller as well, a result of Shannonian information theory. Within this descriptive domain, the unpredictability of how biological structures, such as the cell membrane, will behave becomes less clear than the statement S which I have originally explained. Evidence from cell signaling studies have shown us that when stem cells move away from their “natural purposes”, the communication between individual cells loses its integrity and as cells within the same tissue are unable to pass messages on to one another, they split into distinct cell populations. As far as a biological program goes, if such a structure as the entire group of cells is for the function of “normal proliferation” leading to non-cancerous tissue, it will inevitably fail as the integrity of the relations between them begins to collapse. At the level of resolution of evolution acting on entire species and sets of individuals constituting a lineage, we can determine their paths insofar as the most probabilistic directions they can take under the constraints imposing themselves on the very micro-states that define those relations, which itself is a recursive process. This does not mean that “the best” structures are selected for based on the solution of an optimization problem, given by the computer gestalt model of evolution (12). 

     Such autocatalytic sets capable of achieving task closure and performing work (13, 14) are Kantian wholes, where the whole exists for and by the mean of the parts, and the parts for and by the means of the whole (22; pp. 1381). In the context of evolution, the likeliest Kantian wholes to continue to survive in biological evolution were those with the highest probability distribution of obtaining a micro-state x at time t, or the least set of entropy capable of self-maintaining the living functions by means of available, meaningful information within the system. The meaning, behaviours, and even the perceived goal-directedness towards a final cause for organisms are derived from the ways the Kantian wholes assert their autonomy. As rudimentary autocatalytic sets begin to tend towards multicellularity and increase in the total available degrees of freedom (16), the requirement of the living system to develop control systems also begin to manifest themselves. Examples of these are microRNA noise modulators which attenuate DNA coding strands to increase expression levels and the transcription/translation process which is akin to an assembly line for producing functional units (protein). By implementing first-order cybernetics with entropy, I am essentially attributing the intrinsic purposelessness of biological components to their self-referentiality. At the resolution of the Kantian whole, entropy underlies that self-referential pointer of the task closure, and from this foundation of entropy change as an inherently meaningless phenomena (does energy have goals?), I conclude that the only meaning we can assign to the living system is that which emerges from the constraints which a micro-state imposes between components. 

     However, there are some shortcomings with respect to this view. The first lies with the term entropy itself. I have used it here as a mathematical description – an abstraction – of what seems to happen during the life history of individuals and to account for the origins of novelty. However, even von Neumann, when discussing the matter with Shannon, suggested the term entropy over information or uncertainty for the mere fact that in its thermodynamics context, no one actually knows (and still do not) what entropy actually is as a physical entity in this Universe (7; pp. 113). If I claim that my intention is to nevertheless apply the formalism to biological evolution, and then try to resolve the dynamics of individuals under them, then I have already failed to account for the apparent process of inscribing meanings as an observer embedded within that domain of discourse. Even within the bounds of a second-order cybernetics, where I consider myself as an observer as an input within the feedback loops that underlie living systems, we still cannot say with full confidence that such laws as applied to the thermodynamics and linguistics used to describe those systems – and the subsequent perturbations made by recursive process between the observer (myself) and the individual – apply. Largely this is due to the unresolved gap between the quantum and classical worlds at which evolution enacts upon the biosphere. Furthermore, considering entropy as a primitive relation has been considered by some scientists to be a vital force or perhaps even the res extensa that Descartes describes. However, as I have also recognized, applying this principle of self-referentiality on the level of Kantian wholes does not imply a meaningful substance is where biological individuals derive purposes and intentions from. In the continuous arrow of time, notions of agency, intentionality and meaning – particularly in regards to humans – could be indicative of the discrete transitions under which local compartments (15) emerge given the unique state of entropy flow within that whole. For an example of such a transition, consider the decoupling of the neural tube from the fetus, which gives rise to the brain (6). The development of the brain as such and it becoming an autonomous entity may give rise to inscribed meanings which also lock onto notions of intentions and immanence, but could also be illusions based on the recursions which arise from that “mind” being embedded in the so-called external world. I have derived this line of reasoning as an operational matter constrained within the bounds of the cybernetic-teleonomic account. This cannot be stressed enough, as the self-creating and autonomous nature of the individual exists independently of such first-order cybernetic accounts with which we operate upon them with. To know the inherent purposelessness of life is to understand the mind of God. 


1. Varela, F. (1979) “Principles of Biological Autonomy.” New York: Elsevier North Holland, Inc. 
2. Pina, C., Fugazza, C., Tipping, A.J., Brown, J., Soneji, S., Teles, J., Peterson, C., Enver, T. 
(2012) “Inferring rules of lineage commitment in hematopoiesis.” Nat Cell Bio, 14(3): 287-94. 
3. Van de Vijver, G. (2006) “Kant and the Intuitions of Self-Organization.” Self-Organization and 
Emergence in Life Sciences, 143-161. 
4. Weber, A., Varela, F. (2002) “Life after Kant: Natural purposes and the autopoietic foundations 
of biological individuality.” Phenomenology and the Cognitive Sciences, 1: 97-125. 
5. Cummins, R. “Neo-Teleology.” Philosophy of Biology (Part V: 12) in Rosenberg and Arp. 
6. Ruiz-Mirazo, K., Moreno, A. (2011) “Autonomy in evolution: from minimal to complex life.” 
Synthese, 185: 21-52. 
7. Denbigh, K. (1981) “How subjective is entropy?” in Maxwell’s Demon: Entropy Information 
Computing, Princeton Series in Physics. 
8. Brillouin, L. (1949) “Life, Thermodynamics, and Cybernetics.” in Maxwell’s Demon: Entropy 
Information Computing, Princeton Series in Physics. 
9. Plato. “Phaedo 99.” Retrieved from 
10. Aristotle. “The Organon and Other Works: Physics.” Retrived from 
11. Letelier, JC., Marin, G., Mpodozis, J. (2003) “Autopoietic and (M, R) Systems.” J Theor Biol, 
2(21): 261-272. 
12. Dawkins, R. (1986) “The Blind Watchmaker: The Weasel Program.” Oxford University Press. 
13. Hordijk, W., Hein, J., Steel, M. (2010) “Autocatalytic Sets and the Origin of Life.” Entropy, 12: 
14. Monaco, RR., de Montozon, FR. (2012) “Self-Organization, Autocatalysis and Models of the 
Origin of Life.” Working draft: NASA Ames Research Center and University for College London. 
15. Bennett, CH. (1986) “On the Nature and Origin of Complexity in Discrete, Homogenous, 
Locally-Interacting Systems.” Foundations of Physics, 16(6): 585-592. 
16. Furusawa, C., Kaneko, K. (2000) “Origin of complexity in multicellular organisms.” Phys Rev 
Lett, 84: 6130-6133. 
17. Lloyd, S. (1988) “Black Holes, Demons and the Loss of Coherence: How complex systems get 
information, and what they do with it.” The Rockefeller University PhD Thesis. 
18. Maturana, HR., Varela, F. (1980) “Autopoiesis and Cognition: The Realization of the Living.” D. 
Riedel Publishing Company. 
19. England, JL. (2012) “Statistical Physics of Self-Replication.” Working draft: MIT Physics 
Laboratory. SUBMITTED. 
20. Bywater, RP. (2012) “On dating stages in prebiotic chemical evolution.” Naturwissenschaften, 3: 
21. Zadon, Z, Samiappan, M., Wagner, N., Ashkenasy, N., Ashkenasy, G. (2012) “Peptide Based 
Computation: Switches, Gates, and Simple Arithmetic.” Biomol Info Proc: From Logic Sys to 
Sensors and Actuators, pp. 9-32. 
22. Longo, G., Montevil, M., Kauffman, SA. (2012) “No entailing laws, but enablement in the 
evolution of the biosphere.”, Proceedings of the fourth international conference on Genetic and 
Evolutionary Computation Conference Companion (GECCO Companion ’12), Terence Soule 
(Ed.). ACM, New York, NR, USA, 1379-1392. 
23. Huang, S. (2011) “Systems biology of stem cells: three useful perspectives to help overcome the 
paradigm of linear pathways.” Philos Trans R Soc Lond B Biol Sci, 366(1575): 2247-59. 
24. Dennett, D. (1995) “Darwin’s Dangerous Idea: Evolution and the Meanings of Life.” ISBN: 0-

*I derive subsequent orders of cybernetics from this definition as a result of the recursion indicated by the 


     The transient emergence from lower-level assemblies (genes, cells) to individuals like us assumes that the ensembles of such assemblies function as a hierarchy of forms which leads to the whole. This view is, prima facie, a reductionist one, which would lead us to believe that the living system first embodies the sum-of-its-parts and the evolutionary forces subsuming these parts act on more than one level of resolution. The distinction that Godfrey-Smith has made between an organism and a Darwinian individual seeks to go past the living system as a sum-of-parts towards clarifying the phenomena of selection acting upon collectives, whether very small or very large. In this respect, a “dynamic linking” of organisms and Darwinian individuals becomes context-dependent upon the scale of interaction at which evolution unfolds.

     I extend the binary distinction and dance between the two and place them within the context of a Kantian whole, where the parts exist for and by the means of the whole, and the whole for and by the means of the parts (2). The Kantian whole itself is the phenomena of biological evolution, where biological species falling under the organism/Darwinian individual dualism are characterized by the observation of the interactions between material objects in our reduction-materialist domain of knowledge. The emergence of novelty in the physical world by those things we cannot see or touch, but may be real in its pressure upon this Kantian whole is manifested in the actual Universe (i.e. accessible by our senses), although somehow immaterial as well and still enacting upon the biological evolution of species. Homo sapiens devise an ever-increasing number of virtual realities; whether in silico, our social structures, and civilizations and the subsequent memes developed within them. Subsequently, these virtual realities also allow us to dominate and manipulate the land around us – and perhaps it is the bacteria! The superstructure which consists of all the domains within the web of evolution takes into account these types of non-material realities, and the scales of resolution at which we operate upon is that context-dependence which the organism/Darwinian individual dualism recognizes as far as being under one law binding all of them together. Other examples of this are the dance of honey bees
and mating rituals between peacocks that could have mathematically well-defined dynamics, but go beyond the interaction of the inner-machinations of individual members of that organism set. For the peacocks to mate, they would have to lock eyes, and the eyes are connected to the brain, which “processes” the photons perceived as images. However, recently the link between photons and colour has not been so clear*, and the brain is not an information processor as given by the computational theory of mind (7). Even the dynamic linking the quantum effects as applied to the photon do not necessarily entail or integrate with the physics at the level of a protein encoded by sexual mating signals in the genome, although specific mechanisms do link components such as electrons with pathways, as in the case of electron chain transport in the plant. This is what is meant by the whole being greater than the sum-of-parts. The mixtures of these virtual realities, the interactions that emerge from the materialization of lineages in time, constitute the web of evolution which I have recognized as a Kantian whole. Darwinian individuals and organisms co-create instances in which they interact as observers and being observed as well, manifesting their own domain of knowledge upon the world around them through their behaviour at all the scales of existence we have recognized. The success of an idea, a creature, a kind – and the exchange between these classes – in maintaining their own existence, is that selection pressure which ensures the continued existence of the Kantian whole as well. This process also includes destruction if it has to; the destruction of stars, self-sacrificing ants, suicide, warfare and the like.

     When implementing a biological theory such as classical Darwinian selection, these considerations must be taken into mind as well. Although Godfrey-Smith’s model does well to classify the distinction between the non-mating mule as an organism and sexually reproducing mammals, he does not consider the Darwinian legacy that organisms may leave behind. In this sense, the boundary he purports fails, since the conditions of the niche in which the unique Darwinian individuals perpetuate their coil to an offspring generation is influenced by such Darwinian legacies. There is evidence (4, 5), for example, that the food tastes of a human father are epigenetically imprinted into his daughter through a methyl-tag. The legacy of a mule is the methyl-tag which encodes for a father’s taste in food, which passes onto his daughter, who later goes on to become a mule breeder. In a sense, this could be kin selection; the mule has ensured the success of his species, albeit non-sexually, nor even asexually in the sense of a yeast budding. If that epigenetic mark is embedded within the mule that would go onto the daughter, but the mule was merely an organism acting as vehicle to that mark (the Darwinian individual), then whence came the residuum of the mule enacting itself as a replicator (6) upon the world around it despite its status as a eunuch? To place the distinction of organism/Darwinian individual under the enablement of Kantian wholes avoids this dangerous reduction-materialist game and allows us to focus on the generation and implications of useful results in analyzing nonconventional phenomena in the biosphere otherwise not riddled onto the biologist.


1. Godfrey-Smith, P. (2011) “The Evolution of the Individual.” The Lakatos Award
Lecture, LSE.
2. Weber, A., Varela, F. (2002) “Life after Kant: Natural purposes and the autopoietic
foundations of biological individuality.” Phenomenology and the Cognitive Sciences, 1:
3. Dennett, DD. (1993) “Review of F. Varela, E. Thompson and E. Rosch, the Embodied
Mind.” American Journal of Psychology, 106: 121-6.
4. Landecker, H. (2011) “Food as exposure: Nutritional epigenetics and the new
metabolism.” Biosocieties, 6: 167-194.
5. Muhlhausler, S., Ong, Z. (2011) “The Fetal Origins of Obesity: Early Origins of Altered
Food Intake.” Endocrine, Metabolic & Immune Disorders, 11(3): 189-197.
6. Dawkins, R. (1990). “The Selfish Gene.” ISBN-13: 978-0192860927. Pp. 15.
7. Horst, S. (2005). “The Computational Theory of Mind.” The Stanford Encyclopedia of

*“The same is true of the color of objects: they have indeed coevolved with the color-vision systems of the organisms that
perceive them, but, except on an evolutionary time scale, they are in the main imperturbable by organisms' perceptual activity.
Once we have this metaphysical point duly corrected and secured, does it play much of a role in ongoing cognitivist research?”

Tuesday, December 4, 2012


       Taxonomy as an ontological question (2) falls under the purview of what is meant by a definite description.  On the basis of Frege’s analysis, we are told that a singular common noun is a referring expression (4; Sinn), and I use this notion to ground taxonomy within a pluralist context. Questions concerning life, particularly the taxa we devise for it, necessarily refer to those components which we can observe. When the biologist splits reptiles and birds as separate classes, she is referring to a list of features extracted from observations made about those individuals within them. In evolutionary biology, such a list will generate a number of splittings depending on the algorithm used. For example, algorithm A may place alligators and chickens into a closely-related clade, whereas algorithm B would recognize alligators as being distinctly separated from Aves within the taxonomy. As well, the organization and collection of data is instrumentation-dependent, which subsequently “co-evolves” with the observer community and vice versa. From this phenomena stems plurality. The referent components analyzed and subsequently categorized are in a dynamical flux on the basis of evolving methods for collecting novel features in the specimen under study. What was previously invisible to the senses will become “real” in the future. For example, Darwin could create taxonomies without knowing genetic sequences, although the supposed “transforming principle” underlying evolution did not refer in this case. Darwin could simply not see DNA with his eyes, a direct result of unavailable instrumentation. The beauty of Frege’s analysis is that it allows for gappy propositions (5), and I suppose that the referents collected for each individual take the object position of the gap within Frege’s calculus.  I will contrast this allowance with Russell’s method to show why gappy propositions are vehicles for pluralism and potentially high-dimensional spaces.

In Russell’s view, particularly the On Denoting period, singular common nouns cannot be referring expressions because they are merely symbols which quantify objects in space and time; our observable, “actual world”. If statements of this quantified form are computable, then we cannot implement it within taxonomy without sacrificing the transforming nature of life in the program’s output. To say that a symbol quantifies an object in the actual world is to select a finite subset of characters and assigning it the value of a string, which is a referential data type for denoting alphabetical expressions. Consider the following sentence:
(1)  The present King of France is bald

First recognize that “the present King of France” (a string denoted by X) has some unique properties as a definite description. It is temporally restricted to the present time. Using tuple notation, an object X has some monadic property/universal Y (denoted as “is bald”; the universal is the state of being bald) at time t, which can be read as A = <<X, t>, Y>. On the case of what is meant by present, view the following set B = {...,<<X, t – 1>, Y>,< <X, t>, Y>, <<X, t + 1>, Y>,...}. B informs us of a fatalist state of affairs, where the dot notation denotes the object X for all time-points in the history of our universe of discourse far in the past and the future, and is subsequently true for all time. When discussing what is meant by the present, it is precisely the behaviour/property Y of X at that time-point which is not t - 1 and t + 1. The implication of this view is that when we are discussing X, we have one, already presupposed its existence; and two, the arrow of time can be constrained to single points in a continuous life history. However, t “right now” and t in “the future” (t + 1) are both denoting expressions for what is already the present. The king of France may have been bald when he was alive (eg. t - 1), but certainly his “monadic status” in the world has since passed. B taken as a set would fall under having a truth value of false. Furthermore, time flows forward, and to make a statement about an object at t + 1 is to say that we will definitely know the dynamics of the object in all future flows of time as well; Y is not necessarily universal across all time, and certainly not when Y is with respect to biological evolution. Unfortunately for Russell, it seems that truth is not as static as he would like in this context, his purports on linguistic rules are too tight for generating dynamic taxonomies for biological entities in this instance and leaves no room for the imagination when considering the instrumentation problem.

On the other hand, the consideration of a “gap” within a proposition about a species acts as a placeholder which may be presupposed to be those adjacent possible (3) properties that emerge from available resources in the future. We cannot know the morphology and functions biological structures will take in the future, but the development of techniques such as genetic stochastic modeling allows us to account for theoretical properties and derived traits from current information extracted from the species being classified. In the scheme of devising an effective ontology for discerning “useful” taxonomies from ones that have no utility, using incomplete, gappy propositions allows the [in silico] experimentalist to consider higher dimensions in which they capture the level of resolution being studied in the set of species being classified. For example, the set  C = {...<X, t - 1>, Y0, Y1, Y2...>>, <Z, t>, Y0, Y2, Y5...>>, <   , t + 1>, Y0, Y2, Y3...>>,...} contains gaps in the object position of future elements and now recognizes an existential difference between an object X and Z versus an undetermined adjacent structure in the future falling under a suspected list of properties. If the presupposition of such empty structures fail to generate references within our model, the list is rejected for a better optimization and we may derive a stronger taxonomy for our species set with a more effective predictive power.

1. Russell, B. "On Denoting." Mind 14 (1905): 479-493.
2. Ereshefsky, M.  “Species, Taxonomy, and Systematics.”  In Rosenberg and Arp.
3. Kauffman, SA. “Investigations.” Oxford University Press (2002): 22.
4.  Frege, G. “. Über Sinn und Bedeutung.” Zeitschrift für Philosophie und philosophische Kritik, (1892): 25-50.
5. Everett, G. “Empty Names and ‘Gappy’ Propositions’.” Philosophical Studies: An International Journal for Philosophy in the Analytic Tradition, 116(1), (2003): 1-36.

Saturday, November 24, 2012


Selected poetry. 1 March 2010; 22:24


None brightens, though all shine
Riddle of the gap
Your silence, oh so divine
All gone.. no map

Fury is the silent killer
Coming to you when you sleep
Kindness, the dirge of hypocrisy
Only causing the masses to weep

Your ways are changed, yet they are not
Secular negation, contradiction complete
Yet coincidence, but a shadow of an illusion
All wolves ultimately compete

Are you a wolf?


Selected poetry. 5 March 2010; 22:45


Blue renegade
Ejected energy

Waste of time
Down the drain

No more fight
I say to you..

Good night.

Thursday, November 22, 2012


If it is unclear what is meant by closure, it is defined clearly by this example. Consider two elements or objects and assign one the symbol "*" and the other the symbol "~". When there is an interaction between * and ~, we call it a walk. When there is a walk from * to ~ and a walk from ~ to *, the set is called closed. Closed sets like these have been called auto-catalytic and have been implicated as being sources of order for the origin of life, with RNA as a classical example of such a closed system.


     There can be no doubt that the term species denotes a set composed of organisms which can interbreed with one another, thus perpetuating an evolving spatiotemporal principle to a new generation, of which is composed a new set of unique individuals, operating and maintaining novel processes in their life-history. Largely, this firmness of belief stems from the operational usages of the term “species” in evolutionary biology. The existence of algorithms, such as hierarchical clustering, which can split populations of individuals into taxa, implies a real, although abstract, way of distinguishing finite attributes across a list of objects. Generally, hierarchical clustering, also called numerical taxonomy, is the process of producing groups of objects which share statistically meaningful pair-wise relationships among a list of chosen attributes for each object (2). The taxa that are generated by such a process can be as multi-dimensional as one would like, although the clustering of individuals into apparent classes should occur regardless of the system you are focusing on. As an example, clustering by genes would produce the same splitting as a clustering by phenotypic characteristics such as “wing length” and “head circumference” as measured in a group of some birds, although an observer could actually take both systems (the genetic and phenotypic) into account as variables assigned to their objects of study. I reject the notion that the entire set of such individuals is actually a natural kind in the sense that gold is a natural kind, as this multi-dimensional space in biological life is constantly evolving through time. Indeed, if one were to collect information about individual objects composing the class of all objects falling under “gold”, you may find over time that such a list of characteristics are also changing. The difference, perhaps, is that the method of clustering you choose to classify objects such as gold versus biological life produces a significant difference in variance. The change over thousands versus millions of years in gold apparently does not exhibit the novelty that biological life does at those time-scales.

     Certainly, when you recognize that this method of clustering can take into consideration many levels of resolution, it must be recognized that the splitting of a feature-space into taxa will occur at many levels of resolution as well. Where do we distinguish applying the word species merely to a study involving the clustering of cells within an individual into groups as opposed to comparing actual biological individuals against one another? Once again, I would pretend to claim that this becomes operational matter. If it is experimentally useful to analyze the internal machinations of an individual and then assign observable clusters produced by them the name of “species”, then the observer is certainly entitled to do so. However, this must be distinguished from the act of how we consider a species in the domain of evolutionary biology; without that distinction, we would have no basis for considering when Homo sapiens diverged from its ancestral forms. Indeed, this notion we recognize as speciation is a benchmark of evolutionary theory. The other alternative is unifying these multiple resolutions by doing the following. If a biological individual is composed of cells, and natural selection posits that the fittest forms of life pass their spatiotemporal principle to a new generation, then the taxa of cells which continue to proliferate from a cluster x are the fittest for that individual. This cluster will continue to proliferate until such a time when the individual dies. Down to the resolution of the individual cell, the makeup that composes that cell from its original point of origin for the ontogeny of that organism from birth also uniquely proliferates insofar as being the informational element that initiates and survived from the moment of conception. Applying natural selection to the scale of unique components such as nucleic acids and proteins should also show us that only the fittest of them will continue to grow, whereas ones which contribute to those processes running counter to self-renewal would be discarded. We can continue an analysis in this fashion at all scales of resolution and organize the top clusters which have survived into the present into the nodes of what is called Eigen’s hypercycle (1). Such a hypercycle is organizationally closed, which means that all components are involved in a self-renewing process working towards maintaining the existence of the individual. The interaction also creates a closure between the individuals of the set called “species” which they are involved in, and this interaction is the ability of interbreeding at the level of resolution for a group of organisms. The hypercycle which survives is that closure between individuals in a set that manage to exist in the future, as well. In evolutionary time, once an observer in the future can note sufficient variance between these unique cycles at time-point X1 and X2, she may also recognize enough noticeable differences, whether from genetic analysis or the fossil record, that speciation has occurred. This type of analysis and recognition of apparently unique classes is something uncharacteristic of a natural kind and rejects the notion of an essential force underlying individuals or groups of them. Another particularly beautiful result of such a method also places the species problem as an ontological one. In the world of biology, ontological solutions in the questions of life have certainly allowed the scientists to at least deal with the deluge of data and biological information generated in the laboratory.


1. Eigen, M., and P. Schuster. 1978. “Part A: Emergence of the Hypercycle.” Naturwissenschaften 65:7–41.

2. Press, WH; Teukolsky, SA; Vetterling, WT; Flannery, BP (2007). "Section 16.4. Hierarchical Clustering by Phylogenetic Trees". Numerical Recipes: The Art of Scientific Computing (3rd ed.). New York: Cambridge University Press.

Thursday, November 8, 2012


     There is a particularly profound claim that Hull makes concerning organisms, which is that genes control the ontogeny of an organism.  Although it is largely uncontroversial that Mendelian genetics shows us that some spatiotemporal principle is passed down from the parental generation to its offspring, I will address the view that genes are actually the principle underlying the ontogeny of a developmental system. Ontogeny, otherwise called morphogenesis, seeks to address how a member of a species actually comes to acquire its shape. If genes are considered to be a set of a string of DNA, then the ontogeny of an organism is implied by the unfolding of that DNA into a functional unit (protein), which subsequently informs the components of that organism precisely how a system within it will develop. A classic example of these phenomena is presented in embryogenesis, where the compartmentalization of segments such as the mesoderm is correlated with the activation of a gene circuit or particular concert of genes which encodes for that portion of the embryo.  Aside from whether or not correlation does imply causation, the developmental systems view, as posited by characters such as Griffiths (1), directly contradicts genes as the causal factor for ontogenesis. As Hull apparently points out, the “unrestricted generalization” (2) of the scientific law underlying that of the gene ought to be reducible to the domain of physics and chemistry.

     However, if an organism is an individual and genes are substituent, individual parts constituting the whole, then it should be the case that if genes are a necessary condition for the unfolding of such an ontogenic program, that all members across the spectrum of a species should fall under the same characteristics and/or phenotype. We can compare this to an example of a cue ball breaking a group of billiard balls; the entailing laws underlying the mechanics of the cue ball making contact with the preliminary grouping ought to produce the precisely same result in each instance. Clearly, this is not the case – a Pool player will tell you that not two breaks are the same. When analyzing the situation of ontogenesis, we can also see that from the realm of cellular biology up to that of the whole, functioning organism that no two members are precisely the same, either. One need only to look at n-number of Homo sapiens to see there is an endless diversity in – say – the ideas we generate about the apparent external world around us.

     To address this, I claim that genes are not autonomous entities. By this, I mean that they cannot be individuals simply for the reason that they rely on the existence of the cell membrane. When one says that genes are not autonomous is to say that the dynamics underlying the conception of a distinctly unique member of a species transcend the boundaries of a naïve unfolding of some program which gives rise to the living unity of the organism. Although I do not pretend to claim that genes as entities denoted by DNA are actually passed down from parents to offspring, to say that some set of physico-chemical equations imply some structure of an organism coming to be discounts an entirely counter-intuitive nature of genic evolution. Consider the case of a red blood cell. It is quite common knowledge that the red blood cell is un-nucleated, which means that DNA will not be present within that biological structure. As a result, neither will genes (I suppose that DNA encodes genes). However, what we do observe is that the factor giving rise to red blood cells is passed down (parents and their children both have blood). It seems that the genic selectionists have some explaining to do with respect to this type of gene-independent ontogenesis. Although considering genes as individuals may be categorically useful, it certainly does not give us a complete account of the strange phenomena such as that presented by the red blood cell.


1. Griffiths, PE. Gray, RD. (1994). Developmental Systems Theory and Evolutionary Explanation. J Phil. 91(6): 277-304.

2. Hull, DL. (1978). A Matter of Individuality. Phil Sci. 45(3): 335-360.

Tuesday, November 6, 2012


A Primer on Formal Logic: Part I of 'Analytic Philosophy' 

REVISED: 22 January 2012, 19 FEBRUARY 2012 


Keywords: Frege, Russell, Wittgenstein, Analytic, Logic

I begin this series with a primer on the essential rules of formal logic. These rules are presented in the form of what are called "truth tables", forumlated by Ludwig Wittgenstein in the 20th century. The notion of truth tables arguably originated with Frege, who first defined what it means for a statement to fall under what he called 'The True' and 'The False' ("Begriffsschrift", 1879) As this series unfolds, contributions made to the fields of formal logic and analytic philosophy by Frege and Russell will be included. If this blog can ever profess to be written by 'Philosophers with hammers', then indeed formal logic is the hammer with which our positions are tempered with.

A word of caution.. just because an argument is logical does not make it 
reasonable. For example, consider:

 (1) If the sun is square, then my cat has claws.

The above sentence (1) can be denoted in the material form:

 (2) The sun is square => my cat has claws.

Where "=>" means 'implies' (see Material Implication table below). In this case, it is FALSE that the sun is square, but it is TRUE that a cat has claws. HOWEVER, by definition of the material implication, the entire statement is actually TRUE. It is clear that that (1) is actually completely unreasonable, but by the formal rules is logically sound. In this manner, it is important to understand first that formal logic is a tool to assist us in dissecting and formulating arguments. That said, the ART of formulating a reasonable and logically sound argument is up to the individual in their chosen mode of discourse. 

Use these tools wisely. 

^ = 'AND', Logical Conjunction
v = 'OR', Logical Disjunction
x = 'XOR', Exclusive Disjunction
~ = 'NOT', Negation, Logical Complement

T or 1 = TRUE
F or 0 = FALSE

In computer science speak, T is denoted as 1, and F is denoted as 0. The reasons for this are underlied by the binary (logarithm with a base of 2) logic circuits which innervate hardware/software interfaces, where any logical expression can be represented by a series of binary "logic gates".

Using these symbols, we can begin to analyze very simple to complex

Truth Tables (A and B are objects, sentences)

Logical Conjunction

A ^ B
T   T   T
T   F   F
F   T   F
F   F   T

Logical Disjunction

A v B
T   T   T
T   F   T
F   T   T
F   F   F

Exclusive Disjunction (AKA xor; the exclusive 'or')


T   T   F
F   F   F
T   F   T
F   T   T

Material Implication

A => B
T    T  T
F    T  T  (Vacuous truth)
T    F  F
F    F  F

Biconditional Logical Connective (IFF, If and only if)

T   T   T
T   F   F
F   T   F
F   F   T

Thursday, November 1, 2012


My previous post introduced concepts such as contingency and attraction. With this small essay I seek to open up some brick roads to matters of time and evolution, although you should really take a look at the articles I reference if you want to see how the "masters" do it.


Written for Philosophy of Biology (PHIL565 at the University of Calgary)
Professor: Marc Ereshefsky <>

     Let us begin with Reichenbach’s common-cause principle. The principle states that simultaneous correlated events must have prior common causes (1). Specifically, for events x and y, when the probability of x and y occurring together is greater than the probability of x and y occurring independently of each other, there exists a “common-cause” z where it is true that: Pr(x/z) > Pr(x/~z), Pr(y/z > Pr(y/~z), Pr(x&y/z) = Pr(x/z) × Pr(y/z) and Pr(x&y/~z) = Pr(x/~x) × Pr(y/~z), where the symbol “Pr” denotes the probability of an event. It is upon this principle that, as Cleland argues (3), narratives about the distant past are generated. I will demonstrate that such narratives generated by the principle are insufficient for explaining why the states of affairs of the present are the way they are.

     Under a physics worldview we ought to be able to observe the world around us and write a story about the dynamics of that system. When this story has been written, observers use those tools to make claims about events in the past. For example, that volcanoes erupt today and have an underlying model to explain their behaviour lends weight to the fact that perhaps volcanoes occurred in the past as well and share similar behaviour. However, in the history of time, there are some problems with the notion of extending such a worldview to the past. First, an observer cannot know the entire phase-space of the system that they are studying – this is a particularly difficult when you attempt to travel back in time. Second, since the phase space of a system is not prestatable, the asymmetry of overdetermination is rendered useless since it is never guaranteed that an observer can derive the common-cause because some set of effects occur. Now, keeping this in mind, suppose that there are no entailing laws, but enablement, for the evolution of the biosphere (2). By enablement, I mean that in an historical network, life emerges out of a web where the changing conditions of space and time “lock into” a moment such that novelty may arise, although not necessarily. That the conditions for something to materialize exist does not guarantee it will actually happen. For example, if a hostage is taken and a hero has a villain in a clear line of sights down their rifle, the hero is not guaranteed to take the shot – evolution could work the same way. Under this pretext, as the biosphere bubbles forth, the laws which are created over time to account for observable phenomena exist at the level of the phase-space. In turn, this phase-space has and will continue to evolve as the staggering diversity of variables, forms and niches are enabled in the biosphere. Since the physical phase-space is ever-evolving, any method we devise to generate our historical narrative will become contingent upon the axioms derived from those observations (à la Gödel’s incompleteness theorem). What I am not trying to say is that the world is unobservable or that an entailing laws worldview is entirely useless, but that the layer at which we generate narratives is grounded in the symmetries of such an axiomatic method, where the predictive power of the mathematical form our narrative takes is not restrained within the confines of a material reality. A mathematical form in this context becomes an operational description based on symbols, but will not actually inform us about what the specific components of events in the past are. Since these components are unknowable as ultimate ends to the effects leading to the present state of affairs, any historical narrative created as a result of our observation is rendered a correlation as opposed to having any one explanation as an overdetermining cause (e.g.; meteor impact versus pandemic in the extinction of dinosaurs).

     With respect to this notion of symmetry, Longo and Montévil assert that objects in the physical world continually transform and renew their symmetries (called symmetry change) (4) which give rise to the variance seen at all scales of existence, lending an ear to concepts such as fractal geometry. Mathematically, as symmetries change over time, the object passes over a continuous landscape and enters into and breaks critical points, which could actually give rise to processes such as biological evolution itself under some conditions-N when given enough time (tending towards infinity). In the context of historical narratives, the breaking of critical points over time represents instances where a set of objects observed in the present may allow us to observe how a state of affairs came to be today, but since the domain of discourse used to study that phenomena depends on the state variables of the present, we ought not have confidence that the entailing laws of today necessarily constrain the symmetry of that object in the past. When applied to the common-cause principle, a “screener” cause z is a selection of the one of many such objects. Choosing just one is not only inadequate, but it provides no account for the self-similarity seen through time in the patterns of organization implied by the renewal and projection of objects whose symmetries evolve at such critical points.


1. Reichenbach, H. (1956). “The Direction of Time”, Berkeley, University of Los Angeles Press.

2. Longo, G., Montévil, M., Kauffman, SA. (2012). “No entailing laws, but enablement in the evolution of the biosphere”, Proceedings of the fourteenth international conference on Genetic and evolutionary computation conference companion (GECCO Companion '12), Terence Soule (Ed.). ACM, New York, NY, USA, 1379-1392. DOI=10.1145/2330784.2330946

3. Cleland, CE. (2011). “Prediction and Explanation in Historical Natural Science”, Brit. J. Phil. Sci., 62: 551-582.

4. Longo, G., Montévil, M. (2012). “From physics to biology by extending criticality and symmetry breakings”, Prog. Biophys. Mol. Biol., 106(2): 340-347.

Wednesday, October 31, 2012


Perhaps a disclaimer is in order. I do not pretend to necessarily agree with the notion of attraction used in the context of cell biology. However, the metaphor used by Waddington does seem to be of use in this question of contingency to account for the ever-prevailing theme in this war of life: variety.

Written for Philosophy of Biology (PHIL565 at the University of Calgary)
Professor: Marc Ereshefsky <>

     Beatty discusses and attempts to reconcile two views of contingency in historicity in evolutionary biology generated by Gould, namely its unpredictability and causal-dependent structures. What Beatty seeks to do is reconcile these structures by claiming that they are complementary to one another and will give us a complete picture of historical contingency when applied to natural selection. I will assess the unpredictability structure of contingency and why, counter to at least Gould’s ignorance on the matter with respect to random drift, that unpredictability does represent a stochastic effect, and evolutionary outcomes are part of an historical network where gene frequencies can be used as a marker for assessing multiple pathways of evolution.

     Contingency is the notion that an event X may lead to event Y in an arrow of time, but that the event Y is not certain to occur. In the unpredictability case, Gould presents a thought experiment about a “tape of life”, where replaying such a tape could actually lead to novel evolutionary pathways as opposed to replaying it in the precisely same sequence leading up to the same structures (2). This view of contingency shares parallels to two concepts. Namely, Waddington’s epigenetic landscape (3) and the arrow of time (4). The epigenetic landscape is compared to a marble rolling down the hill, where, despite dropping the marble from the same starting position in each instance, it will actually take on a new path to reach the basin of the landscape. Once the marble is in motion, time represents an arrow – a direction – in which evolution will direct itself. Instances of Newtonian physics would actually tell us that the process of such a marble rolling down the hill is quite deterministic, that an equation of force would generate a distinct result for what path the object would take once in motion. However, although it is clearly seen that new paths will be generated, the result is still the same based on the initial condition: a timely attraction to the bottom of the landscape.

     The tape of life also experiences such an end, at the bottom of the basin where it can continue to play no longer. Keeping this in mind, I move onto Travisano et al.’s microevolutionary experiment. Focusing on random drift as a marker, we see that the experiment actually generates profiles of gene frequencies acquiring independent and distinct stable-states after x generations (x > 0) from a single initial condition (genetic homogeneity). Stochastic processes comes into play at the level of resolution of a concert of genes, where a series of experiments in parallel actually shows those factors such as mutation and the frequency of change for mutations  lead to divergence. There are two intriguing effects of this divergence: (i) homogenous genotypes and experimental conditions can lead a living system to novelty even within the same system (genetically identical E. coli, in this instance) and (ii) genes as bodies in motion do not conform to fixed net results during evolution at the level of point mutations.

     Although I do concede that multiple stable states could actually mean that the dynamics are the “same” in the Newtonian sense, what is actually seen is that individual members of a genetically identical population will definitely exhibit signs of non-genetic and phenotypic heterogeneity (1). As Beatty does point out, this is clearly by definition a sign of stochasticity in nature. However, I will take it a stretch further to say that historical constraints impose themselves on the epigenetic landscape in the movement of time by physically creating restrictions on which “direction” a structure can actually find its niche in and ultimately carve out a novel lineage. Clearly, using the marble metaphor, the marble will not move back up the hill – however, it can go “backwards” in time if we consider contingency as a type of enablement for all possible structures (although, not worlds). This gives us evidence for why vestigial structures may re-appear in nature, called atavism, even though these structures may be considered “obsolete” or entirely primitive in the past. By saying that a marble can go backwards in time is not to say it will actually move backwards in a predestined sequence, only that the stochastic processes which weigh into evolution go above the level of resolution of the gene by carving out a distinct set of behaviours for that marble in each experiment. As was pointed out earlier, the bottom of the hill is still the ultimate resting point for all life (death), although this perspective sought to address how stochasticity can actually manifest itself independent of genes.

1. Huang, S. (2011) “Systems biology of stem cells: three useful perspectives to help
overcome the paradigm of linear pathways,” Philosophical Transactions of the Royal
Society B, 366, 2247-2259.

2. Beatty, J. (2006) “Replaying Life’s Tape,” The Journal of Philosophy, 103, 336-362.

3. Goldberg, DA., Allis, CD., Bernstein, E. (2007) “Epigenetics: A Landscape Takes
Shape,” Cell, 128, 635-638.

4. Wang, J., Xu, L., Huang, S. (2010) “The potential landscape of genetic circuits imposes
the arrow of time in stem cell differentiation,” Biophysical Society, 99(1), 29-39.

Friday, September 14, 2012


Einstein is typically (wrongly) claimed to a proponent of the mixture between science and religion. In reality, Einstein was very much a "pantheistic atheist" in the sense that he viewed "God" as nature -- but not a divinity, not even in a deistic sense.

Princeton, 3. 1. 1954

Dear Mr Gutkind,

Inspired by Brouwer’s repeated suggestion, I read a great deal in your book, and thank you very much for lending it to me ... With regard to the factual attitude to life and to the human community we have a great deal in common. Your personal ideal with its striving for freedom from ego-oriented desires, for making life beautiful and noble, with an emphasis on the purely human element ... unites us as having an “American Attitude.”

Still, without Brouwer’s suggestion I would never have gotten myself to engage intensively with your book because it is written in a language inaccessible to me. The word God is for me nothing more than the expression and product of human weakness, the Bible a collection of honorable, but still purely primitive, legends which are nevertheless pretty childish. No interpretation no matter how subtle can (for me) change this. ... For me the Jewish religion like all other religions is an incarnation of the most childish superstition. And the Jewish people to whom I gladly belong ... have no different quality for me than all other people. As far as my experience goes, they are also no better than other human groups, although they are protected from the worst cancers by a lack of power. Otherwise I cannot see anything “chosen” about them.

In general I find it painful that you claim a privileged position and try to defend it by two walls of pride, an external one as a man and an internal one as a Jew. As a man you claim, so to speak, a dispensation from causality otherwise accepted, as a Jew of monotheism. But a limited causality is no longer a causality at all, as our wonderful Spinoza recognized with all incision...

Now that I have quite openly stated our differences in intellectual convictions it is still clear to me that we are quite close to each other in essential things, i.e. in our evaluation of human behavior ... I think that we would understand each other quite well if we talked about concrete things.

With friendly thanks and best wishes,


A. Einstein