While the notion of chance has been central in discussions over the probabilistic nature of natural selection and genetic drift, its role in the production of variants on which populational sampling takes place has received much less philosophical attention. This article discusses the concept of chance in evolution in the light of contemporary work in evo-devo. We distinguish different levels at which randomness and chance can be defined in this context, and argue that recent research on variability and evolvability demands (...) a causal understanding of variational probabilities under which development acquires a creative, rather than a constraining role in evolution. We then provide a propensity interpretation of variational probabilities that solves a conceptual confusion between causal properties, variational probabilities and extant variation present in the literature, and explore some metaphysical consequences that follow from our interpretation, specifically with regards to the nature of developmental types. 2.1Mutational randomness 2.2Morphological randomness 2.3Adaptive randomness3Variability and Phenotypic Probabilities 3.1The RNA model as a model for evo-devo4Evolvability and the Probability of Evolving5Variational Propensities in Evo-Devo 5.1Individuating variational propensities 5.2Developmental types6Conclusion. (shrink)

Mutations are often described as being “random with respect to fitness.” Here we show that the experiments used to establish randomness with respect to fitness are only capable of showing that mutations are random with respect to current external selection. Current debates about whether or not mutations are directed may be at least partially resolved by making use of this distinction. Additionally, this distinction has important mathematical, experimental, and inferential implications.

I argue that the propensity interpretation of fitness, properly understood, not only solves the explanatory circularity problem and the mismatch problem, but can also withstand the Pandora’s box full of problems that have been thrown at it. Fitness is the propensity (i.e., probabilistic ability, based on heritable physical traits) for organisms or types of organisms to survive and reproduce in particular environments and in particular populations for a specified number of generations; if greater than one generation, “reproduction” includes descendants of (...) descendants. Fitness values can be described in terms of distributions of propensities to produce varying number of offspring and can be modeled for any number of generations using computer simulations, thus providing both predictive power and a means for comparing the fitness of different phenotypes. Fitness is a causal concept, most notably at the population level, where fitness differences are causally responsible for differences in reproductive success. Relative fitness is ultimately what matters for natural selection. (shrink)

This paper argues, first, that biological evolution can be both random and divinely guided at the same time. Next it discusses the idea that the claim that evolution is unguided is not part of the science of evolution, and defends it against a number of objections.

Contingency-theorists have gestured to a series of phenomena such as random mutations or rare Armageddon-like events as that which accounts for evolutionary contingency. These phenomena constitute a class, which may be aptly called the ‘sources of contingency’. In this paper, I offer a probabilistic conception of what it is to be a source of contingency and then examine two major candidates: chance variation and genetic drift, both of which have historically been taken to be ‘chancy’ in a number of different (...) senses. However,contrathe gesturing of contingency-theorists, chance variation and genetic drift are not always strong sources of contingency, as they can be non-chancy in at least one sense that opposes evolutionary contingency. The probabilistic conception offered herein allows for sources of contingency to appropriately vary in strength. To this end, I import Shannon’sinformation entropyas a statistical measure for systematically assessing the strength of a source of contingency, which is part and parcel of identifying sources of contingency. In brief, the higher the entropy, the greater the strength. This is also empirically significant because molecular, mutational, and replicative studies often contain sufficient frequency or probability data to allow for entropies to be calculated. In this way, contingency-theorists can evaluate the strength of a source of contingency in real-world cases. Moreover, the probabilistic conception also makes conceptual room for the converse of sources of contingency: ‘sources of directionality’, which ought to be recognised, as they can interact with genuine sources of contingency in undermining evolutionary contingency. (shrink)

This paper argues, first, that biological evolution can be both random and divinely guided at the same time. Next it discusses the idea that the claim that evolution is unguided is not part of the science of evolution, and defends it against a number of objections.

By focussing on the logical relations between scientific theories and religious beliefs in his book Where the Conflict Really Lies, Alvin Plantinga overlooks the real conflict between science and religion. This conflict exists whenever religious believers endorse positive factual claims to truth concerning the supernatural. They thereby violate an important rule of scientific method and of common sense, according to which factual claims should be endorsed as true only if they result from validated epistemic methods or sources.

One hotly debated philosophical question in the analysis of evolutionary theory concerns whether or not evolution and the various factors which constitute it may profitably be considered as analogous to “forces” in the traditional, Newtonian sense. Several compelling arguments assert that the force picture is incoherent, due to the peculiar nature of genetic drift. I consider two of those arguments here – that drift lacks a predictable direction, and that drift is constitutive of evolutionary systems – and show that they (...) both fail to demonstrate that a view of genetic drift as a force is untenable. I go on to diagnose the reasons for the stubborn persistence of this problem, considering two open philosophical issues and offering some preliminary arguments in support of the force metaphor. (shrink)

Philosophers of biology have worked extensively on how we ought best to interpret the probabilities which arise throughout evolutionary theory. In spite of this substantial work, however, much of the debate has remained persistently intractable. I offer the example of Bayesian models of divergence time estimation as a case study in how we might bring further resources from the biological literature to bear on these debates. These models offer us an example in which a number of different sources of uncertainty (...) are combined to produce an estimate for a complex, unobservable quantity. These models have been carefully analyzed in recent biological work, which has determined the relationship between these sources of uncertainty, both quantitatively and qualitatively. I suggest here that this case shows us the limitations of univocal analyses of probability in evolution, as well as the simple dichotomy between “subjective” and “objective” probabilities, and I conclude by gesturing toward ways in which we might introduce more sophisticated interpretive taxonomies of probability as a path toward advancing debates on probability in the life sciences. (shrink)

Advocates of an ‘extended evolutionary synthesis’ have claimed that standard evolutionary theory fails to accommodate epigenetic inheritance. The opponents of the extended synthesis argue that the evidence for epigenetic inheritance causing adaptive evolution in nature is insufficient. We suggest that the ambiguity surrounding the conception of the gene represents a background semantic issue in the debate. Starting from Haig’s gene-selectionist framework and Griffiths and Neumann-Held’s notion of the evolutionary gene, we define senses of ‘gene’, ‘environment’, and ‘phenotype’ in a way (...) that makes them consistent with gene-centric evolutionary theory. We argue that the evolutionary gene, when being materialized, need not be restricted to nucleic acids but can encompass other heritable units such as epialleles. If the evolutionary gene is understood more broadly, and the notions of environment and phenotype are defined accordingly, current evolutionary theory does not require a major conceptual change in order to incorporate the mechanisms of epigenetic inheritance. _1_ Introduction _2_ The Gene-centric Evolutionary Theory and the ‘Evolutionary Gene’ _2.1_ The evolutionary gene _2.2_ Genes, phenotypes, and environments _3_ Epigenetic Inheritance and the Gene-Centred Framework _3.1_ Treating the gene as the sole heritable material? _3.2_ Epigenetics and phenotypic plasticity _4_ Conclusion. (shrink)

Although random mutation is central to models of evolutionary change, a lack of clarity remains regarding the conceptual possibilities for thinking about the nature and role of mutation in evolution. We distinguish several claims at the intersection of mutation, evolution, and directionality and then characterize a previously unrecognized category: complex conditioned mutation. Empirical evidence in support of this category suggests that the historically famous fluctuation test should be revisited, and new experiments should be undertaken with emerging experimental techniques to facilitate (...) detecting mutation rates within specific loci at an ultra‐high, individual base pair resolution. (shrink)

Here, we propose that the heterogeneity of mutational types in populations underpins alternative pathways of evolutionary adaptation. Point mutations, deletions, insertions, transpositions and duplications cause different biological effects and provide distinct adaptive possibilities. Experimental evidence for this notion comes from the mutational origins of adaptive radiations in large, clonal bacterial populations. Independent sympatric lineages with different phenotypes arise from distinct genetic events including gene duplication, different insertion sequence movements and several independent point mutations. The breadth of the mutational spectrum in (...) the ancestral population should be viewed as a form of bet‐hedging, reducing the risk of evolutionary dead ends and complementing the phenotypic and epigenetic heterogeneities that improve the survival capabilities of a population. Different mutational events arise from distinct cellular processes and are subject to separate environmental impacts, so the availability of any particular type of mutation may constrain or promote adaptive pathways in populations. (shrink)

Philosophy of immunology is a subfield of philosophy of biology dealing with ontological and epistemological issues related to the studies of the immune system. While speculative investigations and abstract analyses have always been part of immune theorizing, until recently philosophers have largely ignored immunology. Yet the implications for understanding the philosophical basis of organismal functions framed by immunity offer new perspectives on fundamental questions of biology and medicine. Developed in the context of history of medicine, theoretical biology, and medical anthropology, (...) philosophy of immunology differs from these related branches of study in its focus on traditional philosophical questions concerning identity, individuality, ecology, cognition, scientific methodology and theory construction. This broad agenda derives from immunology’s multifaceted research program that has developed from its initial clinical challenges of host defense, transplantation, autoimmunity, tumor immunology, and allergy. In addition to these well-established research areas, immunity is now understood to play a central role in other physiological functions, development, ecology, and evolutionary mechanics. Holding together these diverse domains of inquiry lie philosophical commitments oriented by organismal identity. In this regard, pertinent issues are raised concerning cognition (organization of immune perception and information processing), the character of individuality (framed by the ecological context of immune-mediated assimilation and rejection), and the dynamics of complex systems (understood as holistic systems biology). Indeed, immunology, in the context of cognitive science, evolutionary biology, environmental sciences, and development provides multi-focal perspectives for philosophy of science. (shrink)

Discussions of “chance” and related concepts are found throughout philosophical work on evolutionary theory. By drawing attention to three very commonly-recognized distinctions, I separate four independent concepts falling under the broad heading of “chance”: randomness, epistemic unpredictability, causal indeterminism, and probabilistic causal processes. Far from a merely semantic distinction, however, it is demonstrated that conflation of these obviously distinct notions has an important bearing on debates at the core of evolutionary theory, particularly the debate over the interpretation of fitness, natural (...) selection, and genetic drift. (shrink)