Roberta L. Millstein

The neutral and nearly neutral theories of molecular evolution are sometimes characterized as theories about drift alone, where drift is described solely as an outcome, rather than a process. We argue, however, that both selection and drift, as causal processes, are integral parts of both theories. However, the nearly neutral theory explicitly recognizes alleles and/or molecular substitutions that, while engaging in weakly selected causal processes, exhibit outcomes thought to be characteristic of random drift. A narrow focus on outcomes obscures the significant role of weakly selected causal processes in the nearly neutral theory.

Evolutionary theory (ET) is teeming with probabilities. Probabilities exist at all levels: the level of mutation, the level of microevolution, and the level of macroevolution. This uncontroversial claim raises a number of contentious issues. For example, is the evolutionary process (as opposed to the theory) indeterministic, or is it deterministic? Philosophers of biology have taken different sides on this issue. Millstein (1997) has argued that we are not currently able answer this question, and that even scientific realists ought to remain agnostic concerning the determinism or indeterminism of evolutionary processes. If this argument is correct, it suggests that, whatever we take probabilities in ET to be, they must be consistent with either determinism or indeterminism. This raises some interesting philosophical questions: How should we understand the probabilities used in ET? In other words, what is meant by saying that a certain evolutionary change is more or less probable? Which interpretation of probability is the most appropriate for ET? I argue that the probabilities used in ET are objective in a realist sense, if not in an indeterministic sense. Furthermore, there are a number of interpretations of probability that are objective and would be consistent with ET under determinism or indeterminism. However, I argue that evolutionary probabilities are best understood as propensities of population-level kinds.

When philosophers of physics explore the nature of chance, they usually look to quantum mechanics. When philosophers of biology explore the nature of chance, they usually look to microevolutionary phenomena, such as mutation or random drift. What has been largely overlooked is the role of chance in macroevolution. The stochastic models of paleobiology employ conceptions of chance that are similar to those at the microevolutionary level, yet different from the conceptions of chance often associated with quantum mechanics and Laplacean determinism.

Alexander Rosenberg (1994) claims that the omniscient viewpoint of the evolutionary process would have no need for the concept of random drift. However, his argument fails to take into account all of the processes which are considered to be instances of random drift. A consideration of these processes shows that random drift is not eliminable even given a position of omniscience. Furthermore, Rosenberg must take these processes into account in order to support his claims that evolution is deterministic and that evolutionary biology is an instrumental science.

The four case studies on chance in evolution provide a rich source for further philosophical analysis. Among the issues raised are the following: Are there different conceptions of chance at work, or is there a common underlying conception? How can a given concept of chance be distinguished from other chance concepts and from nonchance concepts? How can the occurrence of a given chance process be distinguished empirically from nonchance processes or other chance processes? What role does chance play in evolutionary theory? I argue that in order to answer these questions, a careful distinction between process and outcome must be made; however, the purpose of this essay is not to answer these questions definitively, but rather to elaborate on them and to provide a starting point for further discussion

Recent discussions in the philosophy of biology have brought into question some fundamental assumptions regarding evolutionary processes, natural selection in particular. Some authors argue that natural selection is nothing but a population-level, statistical consequence of lower-level events (Matthen and Ariew [2002]; Walsh et al. [2002]). On this view, natural selection itself does not involve forces. Other authors reject this purely statistical, population-level account for an individual-level, causal account of natural selection (Bouchard and Rosenberg [2004]). I argue that each of these positions is right in one way, but wrong in another; natural selection indeed takes place at the level of populations, but it is a causal process nonetheless.

This paper explores whether natural selection, a putative evolutionary mechanism, and a main one at that, can be characterized on either of the two dominant conceptions of mechanism, due to Glennan and the team of Machamer, Darden, and Craver, that constitute the “new mechanistic philosophy.” The results of the analysis are that neither of the dominant conceptions of mechanism adequately captures natural selection. Nevertheless, the new mechanistic philosophy possesses the resources for an understanding of natural selection under the rubric.

The latter half of the twentieth century has been marked by debates in evolutionary biology over the relative significance of natural selection and random drift: the so-called “neutralist/selectionist” debates. Yet John Beatty has argued that it is difficult, if not impossible, to distinguish the concept of random drift from the concept of natural selection, a claim that has been accepted by many philosophers of biology. If this claim is correct, then the neutralist/selectionist debates seem at best futile, and at worst, meaningless. I reexamine the issues that Beatty raises, and argue that random drift and natural selection, conceived as processes, can be distinguished from one another.

In Darwin’s Sacred Cause, Adrian Desmond and James Moore contend that “Darwin would put his utmost into sexual selection because the subject intrigued him, no doubt, but also for a deeper reason: the theory vindicated his lifelong commitment to human brotherhood”. Without questioning Desmond and Moore’s evidence, I will raise some puzzles for their view. I will show that attention to the structure of Darwin’s arguments in the Descent of Man shows that they are far from straightforward. As Desmond and Moore note, Darwin seems to have intended sexual selection in non-human animals to serve as evidence for sexual selection in humans. However, Darwin’s account of sexual selection in humans was different from the canonical cases that Darwin described at great length. If explaining the origin of human races was the main reason for introducing sexual selection, and if sexual selection was a key piece of Darwin’s anti-slavery arguments, then it is puzzling why Darwin would have spent so much time discussing cases that did not really support his argument for the origin of human races, and it is also puzzling that his argument for the origin of human races would be so poor.

Sex and sensibility: The role of social selection Content Type Journal Article DOI 10.1007/s11016-010-9464-6 Authors Erika L. Milam, Department of History, University of Maryland, 2115 Francis Scott Key Hall, College Park, MD 20742, USA Roberta L. Millstein, Department of Philosophy, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA Angela Potochnik, Department of Philosophy, University of Cincinnati, P.O. Box 210374, Cincinnati, OH 45221, USA Joan E. Roughgarden, Department of Biology, Stanford University, Stanford, CA 94305-5020, USA Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796.

Biologists and philosophers have been extremely pessimistic about the possibility of demonstrating random drift in nature, particularly when it comes to distinguishing random drift from natural selection. However, examination of a historical case-Maxime Lamotte's study of natural populations of the land snail, Cepaea nemoralis in the 1950s - shows that while some pessimism is warranted, it has been overstated. Indeed, by describing a unique signature for drift and showing that this signature obtained in the populations under study, Lamotte was able to make a good case for a significant role for drift. It may be difficult to disentangle the causes of drift and selection acting in a population, but it is not impossible

Recently, much philosophical discussion has centered on the best way to characterize the concepts of random drift and natural selection, and, in particular, whether selection and drift can be conceptually distinguished (Beatty, 1984; Brandon, 2005; Hodge, 1983, 1987; Millstein, 2002, 2005; Pfeifer, 2005; Shanahan, 1992; Stephens, 2004). These authors all contend, to a greater or lesser degree, that their concepts make sense of biological practice. So it should be instructive to see how the concepts of drift and selection were distinguished by the disputants in a high-profile debate; debates such as these often force biologists to take a more philosophical turn, discussing the concepts at issue in greater detail than usual. Moreover, it is important to consider a debate where the disputants are actually trying to apply the models of population genetics to natural populations; only then can their proper interpretations become fully apparent. (Indeed, I contend that some of the philosophical confusion has arisen because authors have considered only the models themselves, and not the phenomena that the models are attempting to represent). A prime candidate for just such a case study is what Provine (1986) has termed “The Great Snail Debate,” that is, the debates over the highly polymorphic land snails Cepaea nemoralis and C. hortensis in the 1950s and early 1960s. These studies represent one of the best, if not the best, of the early attempts to demonstrate drift in natural populations.

The status of population genetics has become hotly debated among biologists and philosophers of biology. Many seem to view population genetics as relatively unchanged since the Modern Synthesis and have argued that subjects such as development were left out of the Synthesis. Some have called for an extended evolutionary synthesis or for recognizing the insignificance of population genetics. Yet others such as Michael Lynch have defended population genetics, declaring "nothing in evolution makes sense except in the light of population genetics" (a twist on Dobzhansky's famous slogan that "nothing in biology makes sense except in the light of evolution"). Missing from this discussion is the use of population genetics to shed light on ecology and vice versa, beginning in the 1940s and continuing until the present day. I highlight some of that history through an overview of traditions such as ecological genetics and population biology, followed by a slightly more in-depth look at a contemporary study of the endangered California Tiger Salamander. I argue that population genetics is a powerful and useful tool that continues to be used and modified, even if it isn't required for all evolutionary explanations or doesn't incorporate all the causal factors of evolution.

Biologists and philosophers have offered differing concepts of biological race. That is, they have offered different candidates for what a biological correlate of race might be; for example, races might be subspecies, clades, lineages, ecotypes, or genetic clusters. One thing that is striking about each of these proposals is that they all depend on a concept of population. Indeed, some authors have explicitly characterized races in terms of populations. However, including the concept of population into concepts of race raises three puzzles, all having to do with time. In this paper, I extend the causal interactionist population concept (CIPC) by introducing some simple assumptions about how to understand populations through time. These assumptions help to shed light on the three puzzles, and in the process show that if we want to understand races in terms of populations, we will need to revise our concept(s) of race.

Biologists studying ecology and evolution use the term “population” in many different ways. Yet little philosophical analysis of the concept has been done, either by biologists or philosophers, in contrast to the voluminous literature on the concept of “species.” This is in spite of the fact that “population” is arguably a far more central concept in ecological and evolutionary studies than “species” is. The fact that such a central concept has been employed in so many different ways is potentially problematic for the reason that inconsistent usages (especially when the usage has not been made explicit) might lead to false controversies in which disputants are simply talking past one another. However, the inconsistent usages are not the only, or even the most important reason to examine the concept. If any set of organisms is legitimately called a “population,” selection and drift processes become purely arbitrary, too. Moreover, key ecological variables, such as abundance and distribution, depend on a nonarbitrary way of identifying populations. I sketch the beginnings of a population concept, drawing inspiration from the Ghiselin-Hull individuality thesis, and show why some alternative approaches are nonstarters.

Many philosophers have become familiar with Leopold’s land ethic through the writings of J. Baird Callicott, who claims that Leopold bases his land ethic on a ‘protosociobiological’ argument that Darwin gives in the Descent of Man. On this view, which has become the canonical interpretation, Leopold’s land ethic is based on extending our moral sentiments to ecosystems. I argue that the evidence weighs in favor of an alternative interpretation of Leopold; his reference to Darwin does not refer to the Descent, but rather to the Origin of Species, where Darwin discusses the interdependencies between organisms in the struggle for existence.

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.

Recently, a number of philosophers of biology have endorsed views about random drift that, we will argue, rest on an implicit assumption that the meaning of concepts such as drift can be understood through an examination of the mathematical models in which drift appears. They also seem to implicitly assume that ontological questions about the causality of terms appearing in the models can be gleaned from the models alone. We will question these general assumptions by showing how the same equation — the simple 2 = p2 + 2pq + q2 — can be given radically different interpretations, one of which is a physical, causal process and one of which is not. This shows that mathematical models on their own yield neither interpretations nor ontological conclusions. Instead, we argue that these issues can only be resolved by considering the phenomena that the models were originally designed to represent and the phenomena to which the models are currently applied. When one does take those factors into account, starting with the motivation for Sewall Wright’s and R.A. Fisher’s early drift models and ending with contemporary applications, a very different picture of the concept of drift emerges. On this view, drift is a term for a set of physical processes, namely, indiscriminate sampling processes

This paper aims to illustrate one of the primary goals of the philosophy of biology⎯namely, the examination of central concepts in biological theory and practice⎯through an analysis of the concepts of population and metapopulation in evolutionary biology and ecology. I will first provide a brief background for my analysis, followed by a characterization of my proposed concepts: the causal interactionist concepts of population and metapopulation. I will then illustrate how the concepts apply to six cases that differ in their population structure; this analysis will also serve to flesh out and defend the concepts a bit more. Finally, I will respond to some possible questions that my analysis may have raised and then conclude briefly.

Aldo Leopold's land ethic has been extremely influential among people working in conservation biology, environmental ethics, and related fields. Others have abandoned the land ethic for purportedly being outdated or ethically untenable. Yet, both acceptance of the land ethic and rejection of the land ethic are often based on misunderstandings of Leopold's original meaning – misunderstandings that have become so entrenched as to have the status of myths. This essay seeks to identify and then debunk six myths that have grown up around the land ethic. These myths include misunderstandings about how we should understand key terms like “stability” and “biotic community” as well as the scope and main message of the land ethic. Properly understanding Leopold's original meaning, a meaning derived from ideas he developed after a lifetime of scientific theorizing and hands-on practical knowledge, prevents hasty rejection and provides a sounder basis for conservation policy.

Population genetics attempts to measure the influence of the causes of evolution, viz., mutation, migration, natural selection, and random genetic drift, by understanding the way those causes change the genetics of populations. But how does it accomplish this goal? After a short introduction, we begin in section (2) with a brief historical outline of the origins of population genetics. In section (3), we sketch the model theoretic structure of population genetics, providing the flavor of the ways in which population genetics theory might be understood as incorporating causes. In sections (4) and (5) we discuss two specific problems concerning the relationship between population genetics and evolutionary causes, viz., the problem of conceptually distinguishing natural selection from random genetic drift, and the problem of interpreting fitness. In section (6), we briefly discuss the methodology and key epistemological problems faced by population geneticists in uncovering the causes of evolution. Section (7) of the essay contains concluding remarks.

The controversy over genetically modified [GM] organisms is often framed in terms of possible hazards for human health. Articles in a previous volume of this *Encyclopedia* give a general overview of GM crops [@Mulvaney2014] and specifically examine human health [@Nordgard2014] and labeling [@Bruton2014] issues surrounding GM organisms. This article explores several other aspects of the controversy: environmental concerns, political and legal disputes, and the aim of "feeding the world" and promoting food security. Rather than discussing abstract, hypothetical GM organisms, this article explores the consequences of the GM organisms that have actually been deployed in the particular contexts that they have been deployed, on the belief that there is little point in discussing GM organisms in an idealized or context-independent way.

Aldo Leopold’s Land Ethic, an extremely influential view in environmental ethics and conservation biology, is committed to the claim that interdependence between humans, other species, and abiotic entities plays a central role in our ethical responsibilities. Thus, a robust understanding of “interdependence” is necessary for evaluating the viability of the Land Ethic and related views, including ecological ones. I characterize and defend a Leopoldian concept of “interdependence,” arguing that it ought to include both negative and positive causal relations. I also show that strength and type of interdependence can vary with time, space, and context.

This volume addresses fundamental issues in the philosophy of science in the context of two most intriguing fields: biology and economics. Written by authorities and experts in the philosophy of biology and economics, Mechanism and Causality in Biology and Economics provides a structured study of the concepts of mechanism and causality in these disciplines and draws careful juxtapositions between philosophical apparatus and scientific practice. By exploring the issues that are most salient to the contemporary philosophies of biology and economics and by presenting comparative analyses, the book serves as a platform not only for gaining mutual understanding between scientists and philosophers of the life sciences and those of the social sciences, but also for sharing interdisciplinary research that combines both philosophical concepts in both fields. The book begins by defining the concepts of mechanism and causality in biology and economics, respectively. The second and third parts investigate philosophical perspectives of various causal and mechanistic issues in scientific practice in the two fields. These two sections include chapters on causal issues in the theory of evolution; experiments and scientific discovery; representation of causal relations and mechanism by models in economics. The concluding section presents interdisciplinary studies of various topics concerning extrapolation of life sciences and social sciences, including chapters on the philosophical investigation of conjoining biological and economic analyses with, respectively, demography, medicine and sociology.

Recent work on the heat-shock protein Hsp90 by Rutherford and Lindquist (1998) has been included among the pieces of evidence taken to show the essential role of developmental processes in evolution; Hsp90 acts as a buffer against phenotypic variation, allowing genotypic variation to build. When the buffering capacity of Hsp90 is altered (e.g., in nature, by mutation or environmental stress), the genetic variation is "revealed," manifesting itself as phenotypic variation. This phenomenon raises questions about the genetic variation before and after what I will call a "revelation event": Is it neutral, nearly neutral, or non-neutral (i.e., strongly deleterious or strongly advantageous)? Moreover, what kinds of evolutionary processes do we take to be at work? Rutherford and Lindquist (1998) focus on the implications of non-neutral variation and selection. Later work by Queitsch, Sangster, and Lindquist (2002) and Sangster, Lindquist, and Queitsch (2004) raises the possibility that Hsp90 buffering may play the role that was played by drift in Sewall Wright's shifting balance model, permitting transition from one adaptive peak to another. However, Ohta (2002) suggests that much of this variation may be nearly neutral, which in turn, would imply a strong role for drift as well as selection. The primary goal of this paper is to illuminate the alternative scenarios and the processes operating in each. At the end, I raise the possibility of a synthesis between evo-devo and nearly neutral evolution.

As a number of biologists and philosophers have emphasized, ‘chance’ has multiple meanings in evolutionary biology. Seven have been identified. I will argue that there is a unified concept of chance underlying these seven, which I call the UCC (Unified Chance Concept). I will argue that each is characterized by which causes are consid- ered, ignored, or prohibited. Thus, chance in evolutionary biology can only be under- stood through understanding the causes at work. The UCC aids in comparing the different concepts and allows us to characterize our concepts of chance in probabilistic terms, i.e. provides a way to translate between ‘chance’ and ‘probability’.

The “land community” (or “biotic community”) that features centrally in Aldo Leopold’s Land Ethic has typically been equated with the concept of “ecosystem.” Moreover, some have challenged this central Leopoldean concept given the multitude of meanings of the term “ecosystem” and the changes the term has undergone since Leopold’s time (see, e.g., Shrader-Frechette 1996). Even one of Leopold’s primary defenders, J. Baird Callicott, asserts that there are difficulties in identifying the boundaries of ecosystems and suggests that we recognize that their boundaries are determined by scientific questions ecologists pose (Callicott 2013). I argue that we need to rethink Leopold’s concept of land community in the following ways. First, we should recognize that Leopold’s views are not identical to those of his contemporaries (e.g., Clements, Elton), although they resemble those of some subsequent ecologists, including some of our contemporaries (e.g., O’Neill 2001, Post et al. 2007, Hastings and Gross 2012). Second, the land community concept does not map cleanly onto the concept of “ecosystem”; it also incorporates elements of the “community” concept in community ecology by emphasizing the interactions between organisms and not just the matter/energy flow of the ecosystem concept. Third, the boundary question can be illuminated by considering some of the recent literature on the nature of biological individuals (in particular, Odenbaugh 2007; Hamilton, Smith, and Haber 2009; Millstein 2009), focusing on concentrations of causal relations as determinative of the boundaries of the land community qua individual. There are challenges to be worked out, particularly when the interactions of community members do not map cleanly onto matter/energy flows, but I argue that these challenges can be resolved. The result is a defensible land community concept that is ontologically robust enough to be a locus of moral obligation while being consistent with contemporary ecological theory and practice.

Recently, philosophers of biology have debated the status of the evolutionary process: is it deterministic or indeterministic? I argue that there is insufficient reason to favor one side of the debate over the other, and that a more philosophically defensible position argues neither for the determinacy nor for the indeterminacy of the evolutionary process. In other words, I maintain that the appropriate stand to take towards the question of the determinism of the evolutionary process is agnosticism. I then suggest that an examination of the phenomenon of developmental noise might yield a solution to the problem.