TABLE OF CONTENTS
1. Contingency, Chance, and Randomness in Ancient, Medieval, and Modern Biology - Grant Ramsey, Charles H. Pence
DOI: 10.7208/chicago/9780226401911.003.0001
[chance;contingency;teleology;intelligent design;natural selection;randomness]
This chapter summarizes a sequence of ways in which, from antiquity to the present, chance has been connected to, or in some cases dissociated from, two related concepts, contingency and randomness. Aristotle’s theory of generation steered a course between chance and necessity by affirming the contingency of reproductive chains without denying their reliability or their purposiveness. This fact supports recent scholarship debunking the idea that everyone before Darwin was a “typological essentialist.” Typological essentialism did exist, but only much later. It arose in the 17th and 18th century, when under the influence of modern physics necessity displaced contingency and chance was reduced to ignorance of deterministic causes. Darwin revived the contingency of reproductive lineages and the purposiveness of organic traits by innovatively inserting an element of chance between the origin of variation and its adaptive utility. His analysis has been amply confirmed by the discovery of random changes in DNA sequences. Randomness in this sense does not, however, make adaptation or evolution random. The subtle balance among chance, determinism, and purposiveness that is built into the idea of natural selection precludes that. (pages 1 - 12)
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2. Chance and Chances in Darwin’s Early Theorizing and in Darwinian Theory Today
DOI: 10.7208/chicago/9780226401911.003.0002
[chance;accident;probability;Charles Darwin;natural selection;genetic drift;fitness;force;statistics;causation]
Darwin’s theorising about adaptive changes in branching descents invoked the same old-fashioned concepts of chance (accident) and chances (probabilities) before and after he first formulated his theory of natural selection. He was a determinist and materialist and held the venerable ignorance view of chance in both bodily and mental processes. His theory of natural section did give new causal roles to chance and chances in the cooperation of inherited variation and natural selection. The causal concept of selection – as non-accidental, non-fortuitous differential reproduction of hereditary variants – links Darwin’s theorising to current controversies over selectionist and neutralist views. Focusing on this conceptual continuity can clarify also what is historically convincing and philosophically cogent in recent statisticalist and causalist takes on selection and fitness, and in persistent quests for a general, explanatory and non-tautologous principle of natural selection. (pages 41 - 75)
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University of Chicago Press
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3. Chance in the Modern Synthesis
DOI: 10.7208/chicago/9780226401911.003.0003
[modern synthesis;theoretical population genetics;mutation;genetic drift;chance;randomness;probability;contingency;founder effect;speciation]
The “modern synthesis” in evolutionary biology involved agreement upon a core theoretical framework in biology, the collection, integration and popular communication of a variety of different types of empirical data in support of evolution, and rhetorical and institutional transformations in the discipline. This chapter classifies the key senses of “chance” deployed by (selected) major synthesis authors, and discusses whether and why they regard chance as a more or less significant factor in evolution. As illustrated below, the sense of “chance” intended in any particular author’s work is often a matter of context: different authors mean different things by “chance,” and have different contrasts in mind. Nonetheless, we conclude that there is general agreement on core ways in which “chance” is understood, and core ways in which it’s agreed to play a causal role in evolution. Finally, we concur with Gould that there was a “hardening” of the synthesis, and document a pendulum shift from viewing chance as a relatively minor, to rather more significant, and then less significant causal factor in evolution over the course of the period spanning 1920-1950. (pages 76 - 102)
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4. Is it Providential, by Chance? Christian Objections to the Role of Chance in Darwinian Evolution
DOI: 10.7208/chicago/9780226401911.003.0004
[Charles Hodge;Cristoph Schönborn;providence;natural theology;argument from design;evolution;contingency]
One objection to Darwinian evolution that surfaced early, crosses Christian denominational lines, and continues to resurface even today, is that the role given to chance in the Darwinian telling of life’s history makes it impossible to give a complementary account of God’s purposive involvement in that history. Considering this objection as found early (in Presbyterian theologian, Charles Hodge) and late (in Roman Catholic theologian, Cristoph Schönborn) it can be shown, first, that the many emergences and reemergences of this objection derive in part from the multiple points within Christian theology at which the assertion of chance in natural processes complicates accounts of divine agency, and second, that the exclusive use of mechanistic metaphors for “design” further obstructs the requisite re-envisioning of divine providence. The essay concludes with a few comments on solving the problem that point toward premodern theologies of divine providential action, of the transparency or opacity of natural processes to such a providence, and scriptural ways of emplotting narratives that do not set divine purposive action and contingency in absolute competition. (pages 103 - 121)
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5. Does Darwinian Evolution Mean We Are Here by Chance?
DOI: 10.7208/chicago/9780226401911.003.0005
[Charles Darwin;evolution;natural selection;humankind;chance;arms race;ecological niche;randomness]
Before Charles Darwin published his Origin of Species in 1859, the automatic assumption of evolutionists was that the process leads upwards to humankind, the climax of history. Darwin’s mechanism of natural selection throws considerable doubt on this happy story, because it is relativistic and (with the coming of Mendelian genetics) the building blocks of evolution are chance, in the sense of not appearing according to need. The past 150 years have seen a series of attempts to show that humans must evolve, either because of or in the face of natural selection. Darwin himself, and following him in recent years Richards Dawkins, favored a kind of “arms race,” with adaptations improving as lines of organisms try to outrun competitors. He thought this would lead to intelligence. Another gambit involving selection, favored by paleontologists Stephen Jay Gould and Simon Conway Morris, suggests that there are ecological niches waiting to be occupied and that selection pushes organisms to find them. Culture is one such niche and if humans had not found it, another line of organisms would. A third strategy, non-Darwinian in the spirit of Herbert Spencer, argues that complexity and hence humankind just comes as part of natural chance happenings, randomly. (pages 122 - 142)
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University of Chicago Press
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6. The Reference Class Problem in Evolutionary Biology: Distinguishing Selection from Drift
DOI: 10.7208/chicago/9780226401911.003.0006
[genetic drift;evolutionary theory;physical probability;explanation;statistical explanation;problem of reference class;method of arbitrary functions;reference class]
Evolutionary biology distinguishes differences in survival and reproduction rates due to selection from those due to drift. The distinction is usually thought to be founded in probabilistic facts: a difference in outcomes that is due to selection is explained by differences in the probabilities relevant to survival; in drift, the probabilities are equal and the difference in lifespans is “a matter of chance”. In both cases, there is a difference in causal histories, but in drift, this differences make no contribution to the relevant probabilities. What is the rationale for ignoring these differences in a probabilistic description of evolutionary change? This is evolutionary biology’s version of philosophy of probability’s reference class problem. Skeptical answers beckon – perhaps it is something cultural or epistemological that decides what gets counted and what gets ignored. This paper uses the author’s recent work on biological probabilities (Strevens, Bigger than Chaos, 2003) and probabilistic explanation (Strevens, Depth, 2008) to argue for a more objectivist answer: the causal factors that are counted are those that make a difference to the frequencies of outcomes that determine evolutionary change. Causal factors are ignored, then, just when they are explanatorily irrelevant to the episode of evolution to be explained. (pages 145 - 175)
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7. Weak Randomness at the Origin of Biological Variation: The Case of Genetic Mutations
DOI: 10.7208/chicago/9780226401911.003.0007
[chance;randomness;stochasticity;mutation;mutational biases;biological variation;molecular level]
The concept of chance, when used to characterize genetic mutation, has often been analyzed and defined from the evolutionary point of view, i.e., looking at the relationship between mutation, selection, and adaptation. More precisely, chance mutation in this sense means that the mutation is not specifically provoked with a view to the adaptation of the organism concerned. However, genetic mutations, as other sources of biological variation (e.g., recombination), are said to be “chancy” or “random” events from the molecular point of view as well, and no philosophical analysis of this discourse has been developed until now. Which notion of chance is invoked in this context? The present chapter provides an answer to this question by introducing and defining two notions of randomness: “strong randomness” and “weak randomness”. On the basis of recent research advances on the mutational process and its biased character, I show that all genetic mutations are “weakly random” molecular events. I conclude the chapter by replying to three possible objections that might be raised against my view. (pages 176 - 195)
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University of Chicago Press
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8. Parallel Evolution: What Does It (Not) Tell Us and Why Is It (Still) Interesting?
DOI: 10.7208/chicago/9780226401911.003.0008
[mutationism;selectionism;convergent evolution;prediction;fitness landscapes;Fisher's geometric model;distribution of fitness effects;population genetic theory;experimental evolution]
Parallel evolution has been used as “proof” of a bewildering array of sometimes contradictory assertions: that Darwinism is wrong, that selection is all powerful, that the modern synthesis is incomplete, that chance matters, or that chance does not matter. Perhaps most importantly, parallel evolution is a source of fascination, as the evolution of a particular life form is seen as one of the least probable chains of events imaginable. Our stance is that both chance and history do matter in evolution. Beyond reasserting these well-known points, the central question is what parallel evolution (or the lack thereof) tells us about evolutionary processes. First, we argue that the topic of parallel evolution crystallizes a series of unsolved issues that have fueled recurrent debates throughout the history of evolutionary genetics. Second, we discuss the implications of parallel evolution at different biological levels. Third, we review the causes of genotypic and phenotypic parallel evolution. Fourth, we show how parallel evolution can be modeled and the additional insights brought by theory. We conclude with a series of questions for future work, and by stressing that using explicit phenotypic landscape models is a useful way to resolve controversies emerging from the observation of parallel evolution. (pages 196 - 220)
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9. Contingent Evolution: Not by Chance Alone
DOI: 10.7208/chicago/9780226401911.003.0009
[chance;path dependence;Long-Term Experimental Evolution;generative entrenchment;phylogenetic constraint;macroevolution;macroecology;Francois Jacob;LTEE]
This paper articulates a view of contingent evolution in terms of path dependence, a notion captured by the idea of dependence on past vagaries. As such, path dependence combines two forms of contingency: chance and (causal) dependence on more or less extended series of past events. The first part of the paper elaborates on the conceptual distinction between chance and path dependence, and analyzes how the Long-Term Evolutionary Experiment (LTEE) recently addressed the challenge of obtaining observational evidence permitting the distinction between chancy and path-dependent evolutionary processes. The second part of the paper explains why generative entrenchment and phylogenetic constraints are important sources of path dependence in macroevolution. (pages 223 - 243)
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10. History’s Windings in a Flask: Microbial Experiments into Evolutionary Contingency
DOI: 10.7208/chicago/9780226401911.003.0010
[historical contingency;evolution;experimental evolution;long-term evolution experiments;path dependence;evolutionary repeatability;microbiology;E. coli;LTEE]
Evolution is an inherently historical phenomenon that involves both deterministic and stochastic processes that play out in the context of historically continuous lineages existing in a world subject to sometimes sudden, capricious change. Stephen Jay Gould argued that these characteristics imparts a historicity to evolution that makes evolutionary outcomes profoundly sensitive to the through which they arise. Famously, Gould proposed that this historical contingency means that, were one to replay the “tape of life”, a very different biological world would result. This is, of course, a difficult thought experiment to instantiate on the global level Gould envisioned. However, replay experiments are possible on the small scale using laboratory populations of microbes. In recent decades, many researchers have used evolution experiments with microorganisms to empirically examine the role of historical contingency in evolution. These experiments have made substantial contributions to our understanding of the role of contingency in evolution, even if it is too early to make any final conclusions. Just as importantly, they have aided in better understanding exactly what historical contingency is. In this chapter I survey the designs, findings, and implications of microbial evolution experiments into evolutionary contingency. (pages 244 - 263)
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11. Rolling the Dice Twice: Evolving Reconstructed Ancient Proteins in Extant Organisms
DOI: 10.7208/chicago/9780226401911.003.0011
[synthetic biology;paleomolecular biochemistry;genetic engineering;evolutionary biochemistry;experimental evolution;elongation factor;molecular evolution;historical contingency]
Scientists have access to artifacts of evolutionary history, but they have limited ability to infer the exact events that produced today’s living world. An intriguing question to arise from this limitation is whether the evolutionary paths of organisms are dominated by controlled processes, or whether they are inherently random, subject to different outcomes if repeated. Two experimental approaches, ancestral sequence reconstruction and experimental evolution, can be used to recapitulate ancient adaptive pathways and provide insights into the mutational steps that constitute an organism’s genetic heritage. Ancestral sequence reconstruction follows a backwards-from-present-day strategy in which ancestral forms of a gene or protein are reconstructed and studied mechanistically. Experimental evolution, by contrast, follows a forward-from-present-day strategy in which microbial populations are evolved in the laboratory under defined conditions. Here I describe a novel hybrid of these two methods, in which synthetic components constructed from inferred ancestral gene or protein sequences are placed into the genomes of modern organisms that are then experimentally evolved. Through this system, we aim to establish the comparative study of ancient phenotypes as a novel, statistically rigorous methodology with which to explore the impacts of biophysics and chance in evolution within the scope of the Extended Synthesis. (pages 264 - 276)
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12. Wonderful Life Revisited: Chance and Contingency in the Ediacaran-Cambrian Radiation
DOI: 10.7208/chicago/9780226401911.003.0012
[Burgess Shale;Cambrian;Ediacaran;contingency;macroevolution]
In his 1989 book Wonderful Life, Stephen Jay Gould employed the fossils of the middle Cambrian Burgess Shale to argue for a pervasive role of contingency in the history of life. But Gould wrote at the advent of an explosion of research in the Ediacaran-Cambrian diversification of animals, before ‘tree-thinking’ had made great inroads into the reconstruction of phylogeny, and with just the first glimmer of data on the remarkable conservation of developmental genes across major animal clades. More than twenty years on, not only have views of the Burgess Shale fossils undergone considerable change, but the role of contingency has become more widely accepted among paleobiologists. Yet much of Gould’s argument that if one ‘played the tape again’ the outcome would differ is difficult to accept. In this contribution I review new views of the Ediacaran-Cambrian explosion relevant to the role of chance in evolution as an example of a larger tension between historicity and laws in evolution. (pages 277 - 298)
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