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.