Online research in philosophy

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• Philosophy of Biology

I am an evolutionary biologist with a background in molecular evolution & evolutionary genetics. Philosophers who are interested in evolutionary mechanisms and causal explanations may be interested in my publications on the role of biases in the introduction of variation, which I view as a fundamental concept that (interestingly) is not part of neo-Darwinian thinking. This work includes theory (simulations and mathematics), empirical analysis (sequence divergence), and conceptual analysis. Some of the conceptual analysis shows that evolutionary biologists have been misled by the "forces" view of causation into reasoning incorrectly about the potential for mutation-biased evolution.

5 items found. Sort by: publication yearfirst authorviewingsaddition date Arlin Stoltzfus (forthcoming). Constructive Neutral Evolution: Exploring Evolutionary Theory's Curious Disconnect. Biology Direct. Constructive neutral evolution (CNE) suggests that neutral evolution may follow a stepwise path to extravagance. Whether or not CNE is common, the mere possibility raises provocative questions about causation: in classical neo-Darwinian thinking, selection is the sole source of creativity and direction, the only force that can cause trends or build complex features. However, much of contemporary evolutionary genetics departs from the conception of evolution underlying neo-Darwinism, resulting in a widening gap between what formal models allow, and what the prevailing (...) view of the causes of evolution suggests. In particular, a mutationist conception of evolution as a 2-step origin-fixation process has been a source of theoretical innovation for 40 years, appearing not only in the Neutral Theory, but also in recent breakthroughs in modeling adaptation (the "mutational landscape" model), and in practical software for sequence analysis. In this conception, mutation is not a source of raw materials, but an agent that introduces novelty, while selection is not an agent that shapes features, but a stochastic sieve. This view, which now lays claim to important theoretical, experimental, and practical results, demands our attention. CNE provides a way to explore its most significant implications about the role of variation in evolution. (shrink) Anti-Darwinist Approaches in Philosophy of Biology Evolution of Complexity in Philosophy of Biology Mechanisms of Evolution, Misc in Philosophy of Biology Process Structuralism in Philosophy of Biology Direct download (2 more)     My bibliography     Export citation   Arlin Stoltzfus & Lev Yampolsky (2009). Climbing Mount Probable: Mutation as a Cause of Non-Randomness in Evolution. Journal of Heredity 100 (5):637-647. The classic view of evolution as "shifting gene frequencies" in the Modern Synthesis literally means that evolution is the modulation of existing variation ("standing variation"), as opposed to a "new mutations" view of evolution as a 2-step process of mutational origin followed by acceptance-or-rejection (via selection and drift). The latter view has received renewed attention, yet its implications for evolutionary causation still are not widely understood. We review theoretical results showing that this conception of evolution allows for a role of (...) mutation as a cause of nonrandomness, a role that could be important but has been misconceived and associated misleadingly with neutral evolution. Specifically, biases in the introduction of variation, including mutational biases, may impose predictable biases on evolution, with no necessary dependence on neutrality. As an example of how important such effects may be, we present a new analysis partitioning the variance in mean rates of amino acid replacement during human-chimpanzee divergence to components of codon mutation and amino acid exchangeability. The results indicate that mutational effects are not merely important but account for most of the variance explained. The challenge that such results pose for comparative genomics is to address mutational effects as a necessary part of any analysis of causal factors. To meet this challenge requires developing knowledge of mutation as a biological process, understanding how mutation imposes propensities on evolution, and applying methods of analysis that incorporate mutational effects. (shrink) Anti-Darwinist Approaches, Misc in Philosophy of Biology Mechanisms of Evolution, Misc in Philosophy of Biology Process Structuralism in Philosophy of Biology Direct download     My bibliography     Export citation   Arlin Stoltzfus (2006). Mutationism and the Dual Causation of Evolutionary Change. Evolution and Development 8 (3):304-317. The rediscovery of Mendel's laws a century ago launched the science that William Bateson called "genetics," and led to a new view of evolution combining selection, particulate inheritance, and the newly characterized phenomenon of "mutation." This "mutationist" view clashed with the earlier view of Darwin, and the later "Modern Synthesis," by allowing discontinuity, and by recognizing mutation (or more properly, mutation-and-altered-development) as a source of creativity, direction, and initiative. By the mid-20th century, the opposing Modern Synthesis view was a prevailing (...) orthodoxy: under its influence, "evolution" was redefined as "shifting gene frequencies," that is, the sorting out of pre-existing variation without new mutations; and the notion that mutation-and-altered-development can exert a predictable influence on the course of evolutionary change was seen as heretical. Nevertheless, mutationist ideas re-surfaced: the notion of mutational determinants of directionality emerged in molecular evolution by 1962, followed in the 1980s by an interest among evolutionary developmental biologists in a shaping or creative role of developmental propensities of variation, and more recently, a recognition by theoretical evolutionary geneticists of the importance of discontinuity and of new mutations in adaptive dynamics. The synthetic challenge presented by these innovations is to integrate mutation-and-altered-development into a new understanding of the dual causation of evolutionary change--a broader and more predictive understanding that already can lay claim to important empirical and theoretical results--and to develop a research program appropriately emphasizing the emergence of variation as a cause of propensities of evolutionary change. (shrink) Anti-Darwinist Approaches, Misc in Philosophy of Biology Biological Sciences in Natural Sciences Evolution of Phenomena, Misc in Philosophy of Biology Mechanisms of Evolution, Misc in Philosophy of Biology Process Structuralism in Philosophy of Biology Direct download (2 more)     My bibliography     Export citation   Lev Yampolsky & Arlin Stoltzfus (2001). Bias in the Introduction of Variation as an Orienting Factor in Evolution. Evolution and Development 3 (2):73-83. According to New Synthesis doctrine, the direction of evolution is determined by selection and not by "internal causes" that act by way of propensities of variation. This doctrine rests on the theoretical claim that because mutation rates are small in comparison to selection coefficients, mutation is powerless to overcome opposing selection. Using a simple population-genetic model, this claim is shown to depend on assuming the prior availability of variation, so that mutation may act only as a "pressure" on the frequencies (...) of existing alleles, and not as the evolutionary process that introduces novelty. As shown here, mutational bias in the introduction of novelty can strongly influence the course of evolution, even when mutation rates are small in comparison to selection coefficients. Recognizing this mode of causation provides a distinct mechanistic basis for an "internalist" approach to determining the contribution of mutational and developmental factors to evolutionary phenomena such as homoplasy, parallelism, and directionality. (shrink) Biological Sciences in Natural Sciences Evolutionary Biology in Philosophy of Biology Direct download     My bibliography     Export citation   Arlin Stoltzfus (1999). On the Possibility of Constructive Neutral Evolution. Journal of Molecular Evolution 49 (2):169-181. The neutral theory often is presented as a theory of "noise" or silent changes at an isolated "molecular level", relevant to marking the steady pace of divergence, but not to the origin of biological structure, function, or complexity. Nevertheless, precisely these issues can be addressed in neutral models, such as those elaborated here in regard to scrambled ciliate genes, gRNA-mediated RNA editing, the transition from self-splicing to spliceosomal splicing, and the retention of duplicate genes. All of these are instances of (...) a more general scheme of "constructive neutral evolution" that invokes biased variation, epistatic interactions, and excess capacities to account for a complex series of steps giving rise to novel structures or operations. The directional and constructive outcomes of these models are not due to neutral allele fixations per se, but to these other factors. Neutral models of this type may help to clarify the poorly understood role of non-selective factors in evolutionary innovation and directionality. (shrink) Anti-Darwinist Approaches, Misc in Philosophy of Biology Exaptation in Philosophy of Biology Genetic Drift in Philosophy of Biology Mechanisms of Evolution, Misc in Philosophy of Biology Process Structuralism in Philosophy of Biology Direct download (2 more)     My bibliography     Export citation

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