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. (shrink)

Recognition that biological systems are stabilized far from equilibrium by self-organizing, informed, autocatalytic cycles and structures that dissipate unusable energy and matter has led to recent attempts to reformulate evolutionary theory. We hold that such insights are consistent with the broad development of the Darwinian Tradition and with the concept of natural selection. Biological systems are selected that re not only more efficient than competitors but also enhance the integrity of the web of energetic relations in which they are embedded. (...) But the expansion of the informational phase space, upon which selection acts, is also guaranteed by the properties of open informational-energetic systems. This provides a directionality and irreversibility to evolutionary processes that are not reflected in current theory.For this thermodynamically-based program to progress, we believe that biological information should not be treated in isolation from energy flows, and that the ecological perspective must be given descriptive and explanatory primacy. Levels of the ecological hierarchy are relational parts of ecological systems in which there are stable, informed patterns of energy flow and entropic dissipation. Isomorphies between developmental patterns and ecological succession are revealing because they suggest that much of the encoded metabolic information in biological systems is internalized ecological information. The geneological hierarchy, to the extent that its information content reflects internalized ecological information, can therefore be redescribed as an ecological hierarchy. (shrink)

According to Aristotelian essentialism, the nature of an organism is constituted of a particular goal-directed disposition to produce an organism typical of its kind. This paper argues—against the prevailing orthodoxy—that essentialism of this sort is indispensable to evolutionary biology. The most powerful anti-essentialist arguments purport to show that the natures of organisms play no explanatory role in modern synthesis biology. I argue that recent evolutionary developmental biology provides compelling evidence to the contrary. Developmental biology shows that one must appeal to (...) the capacities of organisms to explain what makes adaptive evolution adaptive. Moreover, the specific capacities in question are precisely those that, according to Aristotle, constitute the nature of an organism. Essentialism 1.1 Aristotelian biological kinds Evolutionary anti-essentialism 2.1 Taxonomic anti-essentialism 2.2 Explanatory anti-essentialism Adaptation 3.1 Stability 3.2 Mutability 3.3 Phenotypic plasticity and adaptive evolution The natures of organisms Conclusion. (shrink)

An increasing number of biologists are expressing discontent with the prevailing theory of neo-Darwinism. In particular, the tendency of neo-Darwinians to adopt genetic determinism and atomistic notions of both genes and organisms is seen as grossly unfair to the body of developmental theory. One faction of dissenteers, the Process Structuralists, take their inspiration from the rational morphologists who preceded Darwin. These neo-rationalists argue that a mature biology must possess universal laws and that these generative laws should be sought within organismal (...) development. Such a rational biology will only be possible once the neo-Darwinian paradigm, with its reliance on inherently stochastic processes, is overthrown.To facilitate this revolution, process structuralism launches a broad attack on the theoritical adequacy of its opponent. It is charged that neo-Darwinism is untestable and therefore its hypotheses are nothing more than adaptive stories. Further, the lamentable tendencies toward genetic determinism and atomism by modern biologists is seen as the inescapable consequences of adopting the neo-Darwinian outlook. (shrink)

The aim of this paper is to outline a typologyof selection processes, and show that differentsub-categories have different explanatorypower. The basis of this typology of selectionprocesses is argued to be the difference ofreplication processes involved in them. Inorder to show this, I argue that: 1.Replication is necessary for selection and 2.Different types of replication lead todifferent types of selection. Finally, it isargued that this typology is philosophicallysignificant, since it contrasts cases ofselection (on the basis of the replicationprocesses involved in them) (...) whereby selectioncauses adaptation – and, therefore, can beused in explanations of the (real or apparent)teleology of Nature – and cases in whichselection lacks such explanatory power. (shrink)

In this paper I distinguish various ways in which empirical claims about evolutionary and ecological models can be supported by data. I describe three basic factors bearing on confirmation of empirical claims: fit of the model to data; independent testing of various aspects of the model, and variety of evident. A brief description of the kinds of confirmation is followed by examples of each kind, drawn from a range of evolutionary and ecological theories. I conclude that the greater complexity and (...) precision of my approach, as compared to, for instance, a Popperian approach, can facilitate detailed analysis and comparison of empirical claims. (shrink)

Embryonic development and ontogeny occupy whatis often depicted as the black box betweengenes – the genotype – and the features(structures, functions, behaviors) of organisms– the phenotype; the phenotype is not merelya one-to-one readout of the genotype. Thegenes home, context, and locus of operation isthe cell. Initially, in ontogeny, that cell isthe single-celled zygote. As developmentensues, multicellular assemblages of like cells(modules) progressively organized as germlayers, embryonic fields, anlage,condensations, or blastemata, enable genes toplay their roles in development and evolution.As modules, condensations are (...) fundamentaldevelopmental and selectable units ofmorphology (morphogenetic units) that mediateinteractions between genotype and phenotype viaevolutionary developmental mechanisms. In ahierarchy of emergent processes, gene networksand gene cascades (genetic modules) link thegenotype with morphogenetic units such ascondensations, while epigenetic processes suchas embryonic inductions, tissue interactionsand functional integration, link morphogeneticunits to the phenotype. To support theseconclusions I distinguish units of heredityfrom units of transmission and discussepigenetic inheritance by tracing the historyof relationship between embryology andevolution, especially the role(s) assigned tocells or to cellular components in generatingtheories of morphological change in evolution.The concept of cells as modular morphogeneticunits is modeled and illustrated using themammalian dentary bone. (shrink)

A consensus view appears to prevail among academics from diverse disciplines that biological races do not exist, at least in humans, and that race -concepts and race -objects are socially constructed. The consensus view has been challenged recently by Robin O. Andreasen's cladistic account of biological race. This paper argues that from a scientific viewpoint there are methodological, empirical, and conceptual problems with Andreasen's position, and that from a philosophical perspective Andreasen's adherence to rigid dichotomies between science and society, facts (...) and values, nature and culture, and the biological and the social needs to be relinquished. DNA forensics is just one field of research that reveals how race remains both idea and object for human population biologists, an indication that it is premature to accept the existence of a no- race consensus across the disciplines. DNA forensics research also demonstrates ways in which race is reified by scientists by the representation of what is cultural or social as natural or biological, and of what is dynamic, relative, and continuous as static, absolute, and discrete. The philosophical analysis of foundational concepts of human population biology such as population, race, and ethnic group is best served by foregoing traditional objectivist approaches for a critical stance that recognises the inextricability of the biological and the social. Introduction Consensus view: biological races do not exist Andreasen's defence of the biological reality of races as clades Biological permutations of race Conclusion. (shrink)

The encounter between the Darwinian theory of evolution and Mendelism could be resolved only when reductionist tools could be applied to the analysis of complex systems. The instrumental reductionist interpretation of the hereditary basis of continuously varying traits provided mathematical tools which eventually allowed the construction of the Modern Synthesis of the theory of evolution.When genotypic as well as environmental variance allow the isolation of parts of the system, it is possible to apply Mendelian reductionism, that is , to treat (...) the phenotypic trait as if ti causally determined by discrete genes for the trait. howeverm such a beanbag genetics approach obscures the system's eye-view. The concept of heritability, defined as the proportion of the total phenotypic variance due to (additive) hereditary variation, asserts that genetic elements have discrete effects; but by relating to the genotypic variance, it avoids the trap of reffering to genes for characters. (shrink)

Richard Lewontin's (1970) early work on the units of selection initiated the conceptual and theoretical investigations that have led to the hierarchical perspective on selection that has reached near consensus status today. This paper explores other aspects of his work, work on what he termed continuity and quasi-independence, that connect to contemporary explorations of modularity in development and evolution. I characterize such modules and argue that they are the true units of selection in that they are what evolution by natural (...) selection individuates, selects among, and transforms. (shrink)

We argue that a fashionable interpretation of the theory of natural selection as a claim exclusively about populations is mistaken. The interpretation rests on adopting an analysis of fitness as a probabilistic propensity which cannot be substantiated, draws parallels with thermodynamics which are without foundations, and fails to do justice to the fundamental distinction between drift and selection. This distinction requires a notion of fitness as a pairwise comparison between individuals taken two at a time, and so vitiates the interpretation (...) of the theory as one about populations exclusively. (shrink)

The greatest diversity of butterflies and their host plants occurs in tropical regions. Some groups of butterflies in the tropics exhibit monophagous feeding in the larval stage, exploiting only one family of plants; others are polyphagous, feeding on plants in two or more distinct families. The two major types of tropical habitats for butterflies, namely primary and secondary forests, offer very different evolutionary opportunities for the exploitation of plants as larval food. Butterflies are faced with the major logistical problem, as (...) are many other herbivorous insects, of depositing eggs on the correct plant for successful larval feeding. This paper, using the concepts of phenotype set and spatial patchiness of resources, attemps to make some predictions as to the optimal phenotypic systems for monophagous and polyphagous feeding in tropical butterflies, as related to the spatial patchiness of larval host plants in primary and secondary forests. In addition to the secondary compound chemistry of larval host plants as playing a role in the evolution of monophagy and polyphagy, the assumption is made that the spatial patchiness of host plants within and among different families also acts as a major factor in determining optimal ranges of phenotypes for different patterns of larval feeding. Owing to the high spatial patchiness of primary forest species of canopy trees and vines, it is predicted that butterflies exploiting these will be mostly polyphagous, whereas secondary forests having stable formations of fewer plant species and larger patches of these plants, will have mostly monophagous species. Forest understories may have both monophagous and polyphagous species, depending upon the layer of forest and the general type of understory (i.e. palmaceous or dicotyledonous). Field data on some groups of butterflies from tropical America support these predictions. Polyphagous butterflies are predicted to possess a genetic system of mixed morphs with a population being polymorphic as a whole; monophagous butterflies are predicted to have individuals all more or less similar genetically, and with a high amount of genic variation within individuals. Other forms of monophagy may evolve in species that are essentially monomorphic but with various mechanisms (physiological, developmental, behavioral) of phenotypic flexibility at the individual level. Although the environment is essentially coarse-grained for larvae since most are sedentary and polymorphism is an optimal adaptive strategy, the oviposition strategy of the adult must also be considered and some situations (i.e. forest canopy) have resources (host plants) distributed in a fine-grained fashion. Other forms of limited polyphagy may result from monomorphic genetic systems in which there is considerable phenotypic flexibility. (shrink)

Levins and Lewontin have contributed significantly to our philosophical understanding of the structures, processes, and purposes of biological mathematical theorizing and modeling. Here I explore their separate and joint pleas to avoid making abstract and ideal scientific models ontologically independent by confusing or conflating our scientific models and the world. I differentiate two views of theorizing and modeling, orthodox and dialectical, in order to examine Levins and Lewontin’s, among others, advocacy of the latter view. I compare the positions of these (...) two views with respect to four points regarding ontological assumptions: (1) the origin of ontological assumptions, (2) the relation of such assumptions to the formal models of the same theory, (3) their use in integrating and negotiating different formal models of distinct theories, and (4) their employment in explanatory activity. Dialectical is here used in both its Hegelian–Marxist sense of opposition and tension between alternative positions and in its Platonic sense of dialogue between advocates of distinct theories. I investigate three case studies, from Levins and Lewontin as well as from a recent paper of mine, that show the relevance and power of the dialectical understanding of theorizing and modeling. (shrink)

Richard Levins’ distinction between aggregate, composed and evolved systems acquires new significance as we recognize the importance of mechanistic explanation. Criteria for aggregativity provide limiting cases for absence of organization, so through their failure, can provide rich detectors for organizational properties. I explore the use of failures of aggregativity for the analysis of mechanistic systems in diverse contexts. Aggregativity appears theoretically desireable, but we are easily fooled. It may be exaggerated through approximation, conditions of derivation, and extrapolating from some conditions (...) of decomposition illegtimately to others. Evolved systems particularly may require analyses under alternative complementary decompositions. Exploring these conditions helps us to better understand the strengths and limits of reductionistic methods. (shrink)

We distinguish dynamical and statistical interpretations of evolutionary theory. We argue that only the statistical interpretation preserves the presumed relation between natural selection and drift. On these grounds we claim that the dynamical conception of evolutionary theory as a theory of forces is mistaken. Selection and drift are not forces. Nor do selection and drift explanations appeal to the (sub-population-level) causes of population level change. Instead they explain by appeal to the statistical structure of populations. We briefly discuss the implications (...) of the statistical interpretation of selection for various debates within the philosophy of biologythe `explananda of selection' debate and the `units of selection' debate. (shrink)

Sewall Wright's adaptive landscape is the most influential heuristic in evolutionary biology. Wright's biographer, Provine, criticized Wright's adaptive landscape, claiming that its heuristic value is dubious because of deep flaws. Ruse has defended Wright against Provine. Ruse claims Provine has not shown Wright's use of the landscape is flawed, and that, even if it were, it is heuristically valuable. I argue that both Provine's and Ruse's analyses of the adaptive landscape are defective and suggest a more adequate understanding of it.

The philosophical or metaphysical architecture of Darwin's theory of evolution by natural selection is analyzed and diflussed. It is argued that natural selection was for Darwin a paradigmatic case of a natural law of change — an exemplar of what Ghiselin (1969) has called selective retention laws. These selective retention laws lie at the basis of Darwin's revolutionary world view. In this essay special attention is paid to the consequences for Darwin's concept of species of his selective retention laws. Although (...) Darwin himself explicity supported a variety of nominalism, implicit in the theory of natural selection is a solution to the dispute between nominalism and realism. It is argued that, although implicit, this view plays a very important role in Darwin's theory of natural selection as the means for the origin of species. It is in the context of these selective retention laws and their philosophical implications that Darwin's method is appraised in the light of recent criticisms, and the conclusion drawn that he successfully treated some philosophical problems by approaching them through natural history. Following this an outline of natural selection theory is presented in which all these philosophical issues are highlighted. (shrink)

In a small handful of papers in theoretical population genetics, John Gillespie (2000a, 2000b, 2001) argues that a new stochastic process he calls "genetic draft" is evolutionarily more significant than genetic drift. This case study of chance in evolution explores Gillespie's proposed stochastic evolutionary force and sketches the implications of Gillespie's argument for philosophers' explorations of genetic drift.

If one investigates a process that has several causes but assumes that it has only one cause, one risks ruling out important causal factors. Three mechanisms account for this mistake: either the significance of the single cause under test is masked by noise contributed by the unsuspected and uncontrolled factors, or the process appears only when two or more causes interact, or the process appears when there are present any of a number of sufficient causes which are not mutally exclusive. (...) In ecology and evolutionary biology, experiments usually test single factor hypotheses, and many scientists apparently believe that hypotheses incorporating several factors are so much more difficult to test that to do so would not be practical. We discuss several areas in ecology and evolutionary biology in which the presupposition of simple causation has apparently impeded progress. We also examine a more mature field, the study of atherosclerosis, in which single factor studies did significantly delay progress towards understanding what now appears to be a multifactor process. The problem has three solutions: either factorial experiments, dynamic models that make quantitative predictions, response-surface methods, or all three. In choosing a definition for ‘cause’, we make a presupposition that profoundly influences subsequent observations and experimental designs. Alternative definitions of causation should be considered as contributing to potential cures for research problems. (shrink)

Like everyone with a scientific bent of mind, Dennett thinks our capacity for meaningful language and states of mind is the product of evolution (Dennett [1987, ch. VIII]). But unlike many of this bent, he sees virtue in viewing evolution itself from the intentional stance. From this stance, ?Mother Nature?, or the process of evolution by natural selection, bestows intentionality upon us, hence we are not Unmeant Meaners. Thus, our intentionality is extrinsic, and Dennett dismisses the theories of meaning of (...) Dretske, Fodor, Burge, Putnam, and Kripke on the grounds that each requires that our mental states, unlike those of artifacts, have meaning intrinsically. I argue that we are Unmeant Meaners, incidentally defending Dretske et al., though my goal is to test the explanatory virtue of the intentional stance as applied to the evolution of intentionality. (shrink)

Chance has been a focus of attention ever since the beginning of population genetics, but neutrality has not, as natural selection once appeared to be the only worthwhile issue. Neutral change became a major source of interest during the neutralist–selectionist debate, 1970–1980. It retained interest beyond this period for two reasons that contributed to its becoming foundational for evolutionary reasoning. On the one hand, neutral evolution was the first mathematical prediction to emerge from Mendelian inheritance: until then evolution by natural (...) selection was considered the alternative to the fixity of species; now it appears to be the alternative to continuous change. Second, neutral change generated a set of clear predictions on standing variation. These could be used as a reference for detecting more elusive alternative mechanisms of evolution including natural selection. In the wake of the transition from Mendelism to genomics, the combination of coalescent theory, DNA sequence variation, and numerical analysis made it possible to integrate contingent aspects of the history of species into a new null model, thus opening a new dimension in the concept of population that the Modern Synthesis formerly considered as a mere gene pool. (shrink)

This is the second of a two-part essay on the history of debates concerning the creativity of natural selection, from Darwin through the evolutionary synthesis and up to the present. In the first part, I focussed on the mid-late nineteenth century to the early twentieth, with special emphasis on early Darwinism and its critics, the self-styled “mutationists.” The second part focuses on the evolutionary synthesis and some of its critics, especially the “neutralists” and “neo-mutationists.” Like Stephen Gould, I consider the (...) creativity of natural selection to be a key component of what has traditionally counted as “Darwinism.” I argue that the creativity of natural selection is best understood in terms of selection initiating evolutionary change, and selection directing evolutionary change, for example by creating the variation that it subsequently acts upon. I consider the respects in which both of these claims sound non-Darwinian, even though they have long been understood by supporters and critics alike to be virtually constitutive of Darwinism. (shrink)

This paper extends previous arguments against the assumption that the study of variation at the molecular level was instigated with a view to solving an internal conflict between the balance and classical schools of population genetics. It does so by focusing on the intersection of basic research in protein chemistry and the molecular approach to disease with the enactment of global health campaigns during the Cold War period. The paper connects advances in research on protein structure and function as reflected (...) in Christian Anfinsen’s The molecular basis of evolution, with a political reading of Emilé Zuckerkandl and Linus Pauling’s identification of molecular disease and evolution. Beyond atomic fallout, these advances constituted a rationale for the promotion of genetic surveys of human populations in the Third World, in connection with international health programs. Light is shed not only on the experimental roots of the molecular challenge but on the broader geopolitical context where the rising role of biomedicine and public health had an impact on evolutionary biology. (shrink)

The term “genetic load” first emerged in a paper written in 1950 by the geneticist H. Muller. It is a mathematical model based on biological, social, political and ethical arguments describing the dramatic accumulation of disadvantageous mutations in human populations that will occur in modern societies if eugenic measures are not taken. The model describes how the combined actions of medical and social progress will supposedly impede natural selection and make genes of inferior quality likely to spread across populations – (...) a process which in fine loads their progress. Genetic load is based on optimal fitness and emerges from a “typological view” of evolution. This model of evolution had previously, however, been invalidated by Robert Wright and Theodosius Dobzhansky who, as early as 1946, showed that polymorphism was the rule in natural populations. The blooming and persistence of the concept of genetic load, after its theoretical basis had already expired, are a historical puzzle. This persistence reveals the intricacy of science and policy-making in eugenic matters. The Canguilhemian concept of ‘scientific ideology’ is used along with the concept of ‘immutable mobile’ and compared with the concept of ‘co-production’, to provide complementary perspectives on this complex phenomenon. (shrink)

A key issue in the philosophy of biology is evolutionary contingency, the degree to which evolutionary outcomes could have been different. Contingency is typically contrasted with evolutionary convergence, where different evolutionary pathways result in the same or similar outcomes. Convergences are given as evidence against the hypothesis that evolutionary outcomes are highly contingent. But the best available treatments of contingency do not, when read closely, produce the desired contrast with convergence. Rather, they produce a picture in which any degree of (...) contingency is compatible with any degree of convergence. This is because convergence is the repeated production of a given outcome from different starting points, and contingency has been defined without reference to the size of the space of possible outcomes. In small spaces of possibilities, the production of repeated outcomes is almost assured. This paper presents a definition of contingency which includes this modal dimension in a way that does not reduce it to the binary notion of contingency found in standard modal logic. The result is a conception of contingency which properly contrasts with convergence, given some domain of possibilities and a measure defined over it. We should therefore not ask whether evolution is contingent or convergent simpliciter, but rather about the degree to which it is contingent or convergent in various domains, as measured in various ways. (shrink)

This paper gives a detailed narrative of a controversial empirical research in postwar population genetics, the analysis of the cytological polymorphisms of an Australian grasshopper, Moraba scurra. This research intertwined key technical developments in three research areas during the 1950s and 1960s: it involved Dobzhansky’s empirical research program on cytological polymorphisms, the mathematical theory of natural selection in two-locus systems, and the building of reliable estimates of natural selection in the wild. In the mid-1950s the cytologist Michael White discovered an (...) interesting case of epistasis in populations of Moraba scurra. These observations received a wide diffusion when theoretical population geneticist Richard Lewontin represented White’s data on adaptive topographies. These topographies connected the information on the genetic structure of these grasshopper populations with the formal framework of theoretical population genetics. As such, they appeared at the time as the most successful application of two-locus models of natural selection to an empirical study system. However, this connection generated paradoxical results: in the landscapes, all grasshopper populations were located on a ridge while they were expected to reach a peak. This puzzling result fueled years of research and triggered a controversy attracting contributors from Australia, the United States and the United Kingdom. While the original problem seemed, at first, purely empirical, the subsequent controversy affected the main mathematical tools used in the study of two-gene systems under natural selection. Adaptive topographies and their underlying mathematical structure, Wright’s mean fitness equations, were submitted to close scrutiny. Suspicion eventually shifted to the statistical machinery used in data analysis, reflecting the crucial role of statistical inference in applied population genetics. In the 1950s and 1960s, population geneticists were not simply in search for new generalizations about the evolutionary process and for new evidence about genetic variation: struggling against statistical artifacts, they were searching for reliable tests and descriptors to analyze their data. (shrink)

The aim of this article is to discuss and develop the diagnose of the Hardy-Weinberg law made by van Fraassen (1987, p. 110), according to which: 1) that law cannot be considered a law used as an axiom for the classical population genetics as a whole, since it is an equilibrium-law that holds only under certain special conditions; 2) it just determines a subclass of models; 3) its generalization shades off into logical vacuity; and 4) more complex variants of the (...) law can be deduced for more realistic assumptions. The discussion and development of such a diagnose will be carried out with the notions of another semantic conceptions of theories, related to that of van Fraassen, namely, the structuralist view of theories, and a rational reconstruction of classical population genetics made within the framework of such a metatheory, also presented in this paper. (shrink)

Philosophers of science increasingly believe that much of science is concerned with understanding the mechanisms responsible for the production of natural phenomena. An adequate understanding of scientific research requires an account of how scientists develop and test models of mechanisms. This paper offers a general account of the nature of mechanical models, discussing the representational relationship that holds between mechanisms and their models as well as the techniques that can be used to test and refine such models. The analysis is (...) supported by study of two competing models of a mechanism of speech perception. (shrink)

The allegedly alternative theories of Phyletic Gradualism and Punctuated Equilibria are examined as regards the nature of their differences. The explanatory value of both models is determined by establishing their actual connection with reality. It is concluded that they are to be considered complementary rather than mutually exclusive at all levels of infraspecific, specific, and supraspecific evolution. So, in order to be described comprehensively, the pathways of evolution require at least two distinct models, each based on a discrete range of (...) real phenomena. [Phyletic Gradualism; Punctuated Equilibria; evolutionary theories; divergence models; additive speciation; microevolution; macroevolution; anagenesis.]. (shrink)

In a recent paper, Sahotra Sarkar compares the Standard Dynamical interpretation of natural selection with the Information-Theoretic interpretation from Steven A. Frank. I address Sarkar’s three arguments against Frank’s interpretation. I show that Sarkar’s major argument that a key component of Frank’s account “does not have any natural biological interpretation” is premised on a contradiction stemming from a mathematical error. Consequently, Sarkar’s major argument is unsound. I also address Sarkar’s claim that a central equation in Frank’s interpretation is dynamically insufficient (...) and his claim that Frank’s interpretation uses nonintuitive parameters to simply rewrite familiar results. (shrink)

Since the late 1990s, the characterization of complete DNA sequences for a large and taxonomically diverse set of species has continued to gain in speed and accuracy. Sequence analyses have indicated a strikingly baroque structure for most eukaryotic genomes, with multiple repeats of DNA sequences and with very little of the DNA specifying proteins. Much of the DNA in these genomes has no known function. These results have generated strong interest in the factors that govern the evolution of genome architecture. (...) While adaptationist ‘just so’ stories have been offered, recent theoretical analyses based on mathematical population genetics strongly suggest that non-adaptive processes dominate genome architecture evolution. This article critically synthesizes and develops these arguments, explicating a core argument along with several variants. It provides a critical assessment of the evidence that supports these arguments’ premises. It also analyses adaptationist responses to these arguments and notes potential problems with the core argument. These theoretical analyses continue the molecular reinterpretation of evolution initiated by the neutral theory in 1968. The article ends by noting that some of these arguments can also be extended to evolution at higher levels of organization which raises questions about adaptationism in general. This remains a puzzle because there is probably little reason to doubt that many organismic features are genuine adaptations. 1 Introduction2 Preliminaries: Senses of Adaptationism3 Genome Architecture3.1 Surprises of early eukaryotic genetics3.2 Genome structure, post-20014 The Case against Adaptationism4.1 Just so stories versus population genetics4.2 The core argument4.3 Three variants of the core argument4.4 Examples: Non-adaptive features of the genome5 Adaptationist Responses6 Concluding Remarks. (shrink)

What are biological species? Aristotelians and Lockeans agree that they are natural kinds; but, evolutionary theory shows that neither traditional philosophical approach is truly adequate. Recently, Michael Ghiselin and David Hull have argued that species are individuals. This claim is shown to be against the spirit of much modern biology. It is concluded that species are natural kinds of a sort, and that any 'objectivity' they possess comes from their being at the focus of a consilience of inductions.