I investigate how theoretical assumptions, pertinent to different perspectives and operative during the modeling process, are central in determining how nature is actually taken to be. I explore two different models by Michael Turelli and Steve Frank of the evolution of parasite-mediated cytoplasmic incompatility, guided, respectively, by Fisherian and Wrightian perspectives. Since the two models can be shown to be commensurable both with respect to mathematics and data, I argue that the differences between them in the (1) mathematical presentation of (...) the models, (2) explanations, and (3) objectified ontologies stem neither from differences in mathematical method nor the employed data, but from differences in the theoretical assumptions, especially regarding ontology, already present in the respective perspectives. I use my "set up, mathematically manipulate, explain, and objectify" (SMEO) account of the modeling process to track the model-mediated imposition of theoretical assumptions. I conclude with a discussion of the general implications of my analysis of these models for the controversy between Fisherian and Wrightian perspectives. (shrink)

The organizational account of biological functions interprets functions as contributions of a trait to the maintenance of the organization that, in turn, maintains the trait. As has been recently argued, however, the account seems unable to provide a unified grounding for both intra- and cross-generation functions, since the latter do not contribute to the maintenance of the same organization which produces them. To face this ‘ontological problem’, a splitting account has been proposed, according to which the two kinds of functions (...) require distinct organizational definitions. In this article, we propose a solution for the ontological problem, by arguing that intra- and cross-generation functions can be said to contribute in the same way to the maintenance of the biological organization, characterized in terms of organizational self-maintenance. As a consequence, we suggest maintaining a unified organizational account of biological functions. (shrink)

I argue that recent advances in developmental biology demonstrate the inadequacy of suborganismal mechanism. The category of the organism, construed as a ’natural purpose’ should play an ineliminable role in explaining ontogenetic development and adaptive evolution. According to Kant the natural purposiveness of organisms cannot be demonstrated to be an objective principle in nature, nor can purposiveness figure in genuine explain. I attempt to argue, by appeal to recent work on self-organization, that the purposiveness of organisms is a natural phenomenon (...) and, by appeal to the apparatus of invariance explanation, that biological purposiveness provides genuine, ineliminable biological explanations. (edited). (shrink)

In this paper, we develop an organizational account that defines biological functions as causal relations subject to closure in living systems, interpreted as the most typical example of organizationally closed and differentiated self-maintaining systems. We argue that this account adequately grounds the teleological and normative dimensions of functions in the current organization of a system, insofar as it provides an explanation for the existence of the function bearer and, at the same time, identifies in a non-arbitrary way the norms that (...) functions are supposed to obey. Accordingly, we suggest that the organizational account combines the etiological and dispositional perspectives in an integrated theoretical framework. IntroductionDispositional ApproachesEtiological TheoriesBiological Self-maintenance Closure, teleology, and normativityOrganizational differentiationFunctions C1: Contributing to the maintenance of the organization C2: Producing the functional trait Implications and Objections Functional versus useful Dysfunctions, side effects, and accidental contributionsProper functions and selected effectsReproductionRelation with other ‘unitarian’ approachesConclusions. (shrink)

Debate about adaptationism in biology continues, in part because within “the” problem of assessing adaptationism, three distinct problems are mixed together. The three problems concern the assessment of three distinct adaptationist positions, each of which asserts the central importance of adaptation and natural selection to the study of evolution, but conceives this importance in a different way. As there are three kinds of adaptationism, there are three distinct "anti-adaptationist" positions as well. Or putting it more formally, there are three different (...) dimensions here, and strongly adaptationist views, strongly anti-adaptationist views, and moderate views are possible for each dimension. (shrink)

I defend the view that many biological categories are defined by homology against a series of arguments designed to show that all biological categories are defined, at least in part, by selected function. I show that categories of homology are `abnormality inclusive'—something often alleged to be unique to selected function categories. I show that classifications by selected function are logically dependent on classifications by homology, but not vice-versa. Finally, I reject the view that biologists must use considerations of selected function (...) to abstract away from variation and pathology to form a canonical description of a class of biological systems. (shrink)

In this paper I defend an etiological theory of biological functions (according to which the proper function of a trait is the effect for which it was selected by natural selection) against three objections which have been influential. I argue, contrary to Millikan, that it is wrong to base our defense of the theory on a rejection of conceptual analysis, for conceptual analysis does have an important role in philosophy of science. I also argue that biology requires a normative notion (...) of a "proper function", and that a normative notion is not ahistorical. (shrink)

I consider some hitherto unexplored examples of teleological language in the sciences. In explicating these examples, I aim to show (a) that such language is not the sole preserve of the biological sciences, and (b) that not all such talk is reducible to the ascription of functions. In chemistry and biochemistry, scientists explaining molecular rearrangements and protein folding talk informally of molecules rearranging “in order to” maximize stability. Evolutionary biologists, meanwhile, often speak of traits evolving “in order to” optimize some (...) fitness-relevant variable. I argue that in all three contexts such locutions are best interpreted as shorthands for more detailed explanations which, were we to spell them out in full, would show that the relevant process would robustly converge towards the same end-point despite variation in initial conditions. This suggests that, in biology, such talk presupposes a substantial form of adaptationism. The upshot is that such shorthands may be more applicable in the physical sciences than the biological. (shrink)

Kant’s analysis of the concept of natural purpose in the Critique of judgment captured several features of organisms that he argued warranted making them the objects of a special field of study, in need of a special regulative teleological principle. By showing that organisms have to be conceived as self-organizing wholes, epigenetically built according to the idea of a whole that we must presuppose, Kant accounted for three features of organisms conflated in the biological sciences of the period: adaptation, functionality (...) and conservation of forms..Kant’s unitary concept of natural purpose was subsequently split in two directions: first by Cuvier’s comparative anatomy, that would draw on the idea of adaptative functions as a regulative principle for understanding in reconstituting and classifying organisms; and then by Goethe’s and Geoffroy’s morphology, a science of the general transformations of living forms. However, such general transformations in nature, objects of an alleged ‘archaeology of nature’, were thought impossible by Kant in the §80 of the Critique of judgment. Goethe made this ‘adventure of reason’ possible by changing the sense of ‘explanation’: scientific explanation was shifted from the investigation of the mechanical processes of generation of individual organisms to the unveiling of some ideal transformations of types instantiated by those organisms. (shrink)

The notion that natural selection is a process of fitness maximization gets a bad press in population genetics, yet in other areas of biology the view that organisms behave as if attempting to maximize their fitness remains widespread. Here I critically appraise the prospects for reconciliation. I first distinguish four varieties of fitness maximization. I then examine two recent developments that may appear to vindicate at least one of these varieties. The first is the ‘new’ interpretation of Fisher's fundamental theorem (...) of natural selection, on which the theorem is exactly true for any evolving population that satisfies some minimal assumptions. The second is the Formal Darwinism project, which forges links between gene frequency change and optimal strategy choice. In both cases, I argue that the results fail to establish a biologically significant maximization principle. I conclude that it may be a mistake to look for universal maximization principles justified by theory alone. A more promising approach may be to find maximization principles that apply conditionally and to show that the conditions were satisfied in the evolution of particular traits. (shrink)

Recently philosophers of science have begun to pay more attention to the use of highly idealized mathematical models in scientific theorizing. An important example of this kind of highly idealized modeling is the widespread use of optimality models within evolutionary biology. One way to understand the explanations provided by these models is as a censored causal explanation: an explanation that omits certain causal factors in order to focus on a modular subset of the causal processes that led to the explanandum. (...) In this paper, I first argue that the censored causal model approach fails to establish a permanent explanatory role for optimality models in biology and mischaracterizes the explanatory virtues of biological optimality modeling. In addition, I argue that many biological optimality explanations cannot be characterized as censored causal explanations. In response, I propose an alternative approach that analyzes optimality models’ reliance on synchronically representing a system’s constraints and tradeoffs as well as their employment of various kinds of idealization in order to provide equilibrium explanations. (shrink)

The etiological approach to ‘proper functions’ in biology can be strengthened by relating it to Robert Cummins' general treatment of function ascription. The proper functions of a biological trait are the functions it is assigned in a Cummins-style functional explanation of the fitness of ancestors. These functions figure in selective explanations of the trait. It is also argued that some recent etiological theories include inaccurate accounts of selective explanation in biology. Finally, a generalization of the notion of selective explanation allows (...) an analysis of the proper functions of human artifacts. (shrink)

Biological functions are dispositions or effects a trait has which explain the recent maintenance of the trait under natural selection. This is the "modern history" approach to functions. The approach is historical because to ascribe a function is to make a claim about the past, but the relevant past is the recent past; modern history rather than ancient.

I distinguish two senses in which organisms are mechanically inexplicable for Kant. Mechanical inexplicability in the first sense is shared with artefacts, and consists in their exhibiting regularities irreducible to the regularities of matter. Mechanical inexplicability in the second sense is peculiar to organisms, consisting in the reciprocal causal dependence of an organism's parts. This distinction corresponds to two strands of thought in Aristotle, one supporting a teleological conception of organisms, the other supporting a conception of organisms as natural. Recognizing (...) this distinction helps us to see how a teleological conception of organisms is compatible with recent advances in biology. (shrink)

According to a prominent view of evolutionary theory, natural selection and the processes of development compete for explanatory relevance. Natural selection theory explains the evolution of biological form insofar as it is adaptive. Development is relevant to the explanation of form only insofar as it constrains the adaptation-promoting effects of selection. I argue that this view of evolutionary theory is erroneous. I outline an alternative, according to which natural selection explains adaptive evolution by appeal to the statistical structure of populations, (...) and development explains the causes of adaptive evolution at the level of individuals. Only together can a statistical theory of selection and a mechanical theory of development explain why populations of organisms comprise individuals that are adapted to their conditions of existence. (shrink)

One central tenet of the Modern Evolutionary Synthesis , and the consensus view among biologists until now, is that all genetic mutations occur by “chance” or at “random” with respect to adaptation. However, the discovery of some molecular mechanisms enhancing mutation rate in response to environmental conditions has given rise to discussions among biologists, historians and philosophers of biology about the “chance” vs “directed” character of mutations . In fact, some argue that mutations due to a particular kind of mutator (...) mechanisms challenge the Modern Synthesis because they are produced when and where needed by the organisms concerned. This paper provides a defense of the Modern Synthesis’ consensus view about the chance nature of all genetic mutations by reacting to Jablonka and Lamb’s analysis of genetic mutations and the explicit Lamarckian flavor of their arguments. I argue that biologists can continue to talk about chance mutations according to what I call and define as the notion of “evolutionary chance,” which I claim is the Modern Synthesis’ consensus view and a reformulation of Darwin’s most influential idea of “chance” variation. Advances in molecular genetics are therefore significant but not revolutionary with respect to the Modern Synthesis’ paradigm. (shrink)

Kant’s analysis of the concept of natural purpose in the Critique of judgment captured several features of organisms that he argued warranted making them the objects of a special field of study, in need of a special regulative teleological principle. By showing that organisms have to be conceived as self-organizing wholes, epigenetically built according to the idea of a whole that we must presuppose, Kant accounted for three features of organisms conflated in the biological sciences of the period: adaptation, functionality (...) and conservation of forms..Kant’s unitary concept of natural purpose was subsequently split in two directions: first by Cuvier’s comparative anatomy, that would draw on the idea of adaptative functions as a regulative principle for understanding in reconstituting and classifying organisms; and then by Goethe’s and Geoffroy’s morphology, a science of the general transformations of living forms. However, such general transformations in nature, objects of an alleged ‘archaeology of nature’, were thought impossible by Kant in the §80 of the Critique of judgment. Goethe made this ‘adventure of reason’ possible by changing the sense of ‘explanation’: scientific explanation was shifted from the investigation of the mechanical processes of generation of individual organisms to the unveiling of some ideal transformations of types instantiated by those organisms. (shrink)

This paper is a commentary on the focal article by Grafen and on earlier papers of his on which many of the results of this focal paper depend. Thus it is in effect a commentary on the “formal Darwinian project”, the focus of this sequence of papers. Several problems with this sequence are raised and discussed. The first of these concerns fitness maximization. It is often claimed in these papers that natural selection leads to a maximization of fitness and that (...) this view is claimed in Fisher’s “fundamental theorem of natural selection”. These claims are refuted, and various incorrect statements about the meaning and interpretation of the fundamental theorem of natural selection, in this sequence and in other papers by other authors, are discussed. Next, much of the work in this sequence rests on the first Price equation. In the deterministic (infinite population) case this equation is no more than the standard classical equation relating to changes in gene frequencies. In the stochastic case the equation gives the change in gene frequencies as the sum of two terms (the second of which vanishes in the deterministic case). These two terms are of essentially equal importance in the situation considered in the focal article, yet one of Grafen’s results ignores the second term in the stochastic analysis. This is associated with a wavering between deterministic and stochastic analyses and the use of the Price fitness concept and the classical fitness concept. These comments cast doubts on Grafen’s optimization theory. (shrink)

The broader context for the formal darwinism project established by two of the commentators, in terms of reconciling the Modern Synthesis with Darwinian arguments over design and in terms of links to other types of selection and design, is discussed and welcomed. Some overselling of the project is admitted, in particular of whether it claims to consider all organic design. One important fundamental question raised in two commentaries is flagged but not answered of whether design is rightly represented by an (...) optimisation program, and another from one commentary of whether the coreplicon dissolves in the face of multi-generational imprinting. Calls for the project to be extended to design at levels above and below the individual are considered sympathetically, but judged impractical at the high level of abstraction of the project. All claims of substantive technical error are emphatically rejected. Close technical readings are welcomed that, among other things, represent the project as 'axiomatizing fitness'. The prospects for the project are set out in the light of this highly varied set of commentaries. (shrink)