Biology & Philosophy

Addiction is almost universally held to be characterized by a loss of control over drug-seeking and consuming behavior. But the actions of addicts, even of those who seem to want to abstain from drugs, seem to be guided by reasons. In this paper, I argue that we can explain this fact, consistent with continuing to maintain that addiction involves a loss of control, by understanding addiction as involving an oscillation between conflicting judgments. I argue that the dysfunction of the mesolimbic dopamine system that typifies addictions causes the generation of a mismatch between the top-down model of the world that reflects the judgment that the addict ought to refrain from drugs, and bottom-up input caused by cues predictive of drug availability. This constitutes a powerful pressure toward revising the judgment and thereby attenuating the prediction error. But the new model is not stable, and shifts under the pressure of bottom-up inputs in different contexts; hence the oscillation of all-things-considered judgment. Evidence from social psychology is adduced, to suggest that a similar process may be involved in ordinary cases of weakness of will.

Both written and graphic accounts of history can be biased by the perspective of the historian. O'Hara (Biol Philos 7:135-160, 1992) has demonstrated that this also applies to evolutionary history and its historians, and identified four narrative devices that introduce anthropocentricisms into accounts of phylogeny. In the current paper, I identify a fifth such narrative device, viz. the left-right ordering of the taxa at the tips of cladograms. I define two measures that make it possible to quantify the degree of anthropocentricism of cladograms, the human attention score and human rightness score. I then carry out an analysis of the presence of the different distorting mechanisms in phylogenetic textbooks. I deliberately chose two textbooks that adopted a cladistic perspective, since their authors can be assumed to be more conscious about the aim of avoiding anthropocentricisms. Three of the narrative devices are thus absent from cladistic works. However, there is a weak tendency that the resolution of cladogram branches is biased in favour of Homo sapiens. Furthermore, the human perspective is clear and highly significant in the positioning of taxa along the left-right axis of cladograms. I discuss the reasons for and implications of these biased presentations.

The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth's biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called "omic" techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These 'omic methods have been used to describe the taxonomic structure of microbial communities in different environments and to discover new genes and enzymes of industrial and medical interest. However, microbial community structure varies in different spatial and temporal scales and none of the 'omic techniques are individually able to elucidate the complex aspects of microbial communities and ecosystems. In this article we highlight the importance of a spatiotemporal sampling design, together with a multilevel 'omic approach and a community analysis strategy (association networks and modeling) to examine and predict interacting microbial communities and their impact on the environment.

Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts from traditional ecology have been used to generate new insight into microbial communities, and novel system-level models developed to explain and predict microbial interactions. The process of moving from molecular inventories to functional understanding is complex and challenging, and never more so than when many thousands of dynamic interactions are the phenomena of interest. We outline the process of how epistemic transitions are made from producing catalogues of molecules to achieving functional and predictive insight, and show how those insights not only revolutionize what is known about biological systems but also about how to do biology itself. Examples will be drawn primarily from analyses of different human microbiota, which are the microbial consortia found in and on areas of the human body, and their associated microbiomes (the genes of those communities). Molecular knowledge of these microbiomes is transforming microbiological knowledge, as well as broader aspects of human biology, health and disease.

We are grateful to the commentators for taking the time to respond to our article. Too many interesting and important points have been raised for us to tackle them all in this response, and so in the below we have sought to draw out the major themes. These include problems with both the term 'ultimate causation' and the proximate-ultimate causation dichotomy more generally, clarification of the meaning of reciprocal causation, discussion of issues related to the nature of development and phenotypic plasticity and their roles in evolution, and consideration of the need for an extended evolutionary synthesis.

Several have argued that the aims of scientific research are not always independent of social and ethical values. Yet this is often assumed only to have implications for decisions about what is studied, or which research projects are funded, and not for methodological decisions or standards of evidence. Using the case of the recently developed HPV vaccines, we argue that the social aims of research can also play important roles in justifying decisions about (1) how research problems are defined in drug development, (2) evidentiary standards used in testing drug "success", and (3) clinical trial methodology. As a result, attending to the social aims at stake in particular research contexts will produce more rational methodological decisions as well as more socially relevant science.

Viruses are major drivers of global biogeochemistry and the etiological agents of many diseases. They are also the winners in the game of life: there are more viruses on the planet than cellular organisms and they encode most of the genetic diversity on the planet. In fact, it is reasonable to view life as a viral incubator. Nevertheless, most ecological and evolutionary theories were developed, and continue to be developed, without considering the virosphere. This means these theories need to be to reinterpreted in light of viral knowledge or we need to develop new theory from the viral point-of-view. Here we briefly introduce our viral planet and then address a major outstanding question in biology: why is most of life viral? A key insight is that during an infection cycle the original virus is completely broken down and only the associated information is passed on to the next generation. This is different for cellular organisms, which must pass on some physical part of themselves from generation to generation. Based on this premise, it is proposed that the thermodynamic consequences of physical information (e.g., Landauer's principle) are observed in natural viral populations. This link between physical and genetic information is then used to develop the Viral Information Hypothesis, which states that genetic information replicates itself to the detriment of system energy efficiency (i.e., is viral in nature). Finally, we show how viral information can be tested, and illustrate how this novel view can explain existing ecological and evolutionary theories from more fundamental principles.

Philosophers of evolutionary biology favor the so-called etiological concept of function according to which the function of a trait is its evolutionary purpose, defined as the effect for which that trait was favored by natural selection. We term this the selected effect (SE) analysis of function. An alternative account of function was introduced by Robert Cummins in a non-evolutionary and non-purposive context. Cummins''s account has received attention but little support from philosophers of biology. This paper will show that a similar non-purposive concept of function, which we term causal role (CR) function, is crucial to certain research programs in evolutionary biology, and that philosophical criticisms of Cummins''s concept are ineffective in this scientific context. Specifically, we demonstrate that CR functions are a vital and ineliminable part of research in comparative and functional anatomy, and that biological categories used by anatomists are not defined by the application of SE functional analysis. Causal role functions are non-historically defined, but may themselves be used in an historical analysis. Furthermore, we show that a philosophical insistence on the primary of SE functions places practicing biologists in an untenable position, as such functions can rarely be demonstrated (in contrast to CR functions). Biologists who study the form and function of organismal design recognize that it is virtually impossible to identify the past action of selection on any particular structure retrospectively, a requirement for recognizing SE functions.

In Molecular Models: Philosophical Papers on Molecular Biology, Sahotra Sarkar presents a historical and philosophical analysis of four important themes in philosophy of science that have been influenced by discoveries in molecular biology. These are: reduction, function, information and directed mutation. I argue that there is an important difference between the cases of function and information and the more complex case of scientific reduction. In the former cases it makes sense to taxonomise important variations in scientific and philosophical usage of the terms “function” and “information”. However, the variety of usage of “reduction” across scientific disciplines (and across philosophy of science) makes such taxonomy inappropriate. Sarkar presents reduction as a set of facts about the world that science has discovered, but the facts in question are remarkably disparate; variously semantic, epistemic and ontological. I argue that the more natural conclusion of Sarkar’s analysis is eliminativism about reduction as a scientific concept. KeywordsReduction-Function-Information-Eliminativism-Molecular

The philosophy of "pattern cladism" has been variously explained by reference to the work of Louis Agassiz. The present study analyzes Agassiz's attempt to combine an empirical approach to the study of nature with an idealistic philosophy. From this emerges the problem of empiricism and of the isomorphy between the order of nature and human thinking. The analysis of the writings of Louis Agassiz serves as the basis for discussion of the "reality" of natural groups as postulated by pattern cladists.

Almost all of the themes contained in E.O.Wilson's sociobiological writing on war and human aggression were prefigured in Anglo-American bio-social discourse, c. 1880–1919. Instinct theory – stemming from animal psychology and the genetics revolution – encouraged the belief that pugnacity had been programmed into the ancient part of the human brain as a result of evolutionary pressures dating from prehistory. War was seen to be instinct-driven, and genocidal fighting postulated as a eugenic force in early human evolution. War was explained in distinctly modern sociobiological terms as adaptive behaviour springing from territorial urges, crowding, competition for resources and reproductive advantage, ethnocentrism and pseudo-speciation.

To honour the memory of Sir Karl Popper, I put forward six elements of his philosophy which might be of particular interest to biologists and to philosophers of biology and which I think Popper would like them not to ignore, even if they disagree with him. They are: the primacy of problems; the criticizability of metaphysics (and thus the dubiousness of materialism); how downward causation might be real; how norms should matter to scientists; why dogmatism should be avoided; how genuine science is recognizable. I preface these six things with a brief discussion of Popper's early (but later recanted) mistakes concerning biology.

This paper analyzes the interaction between science, philosophy and politics (including ideology) in the early work of J. B. S. Haldane (from 1922 to 1937). This period is particularly important, not only because it is the period of Haldane's most significant biological work (both in biochemistry and genetics), but also because it is during this period that his philosophical and political views underwent their most significant transformation. His philosophical stance first changed from a radical organicism to a position far more compatible with mechanical materialism. The primary intellectual influence that was responsible for this shift was that of F. G. Hopkins. Later, Haldane came to accept Marxism and its official metaphysics, dialectical materialism, a move that let him accept the materialist conception of the world while still maintaining a resolute distance from mechanism. Throughout all these changes, what is most obvious is the influence of science on Haldane's philosophical views. An influence in the opposite direction is far less apparent.

Sewall Wright introduced the metaphor of evolution on “adaptive landscapes” in a pair of papers published in 1931 and 1932. The metaphor has been one of the most influential in modern evolutionary biology, although recent theoretical advancements show that it is deeply flawed and may have actually created research questions that are not, in fact, fecund. In this paper I examine in detail what Wright actually said in the 1932 paper, as well as what he thought of the matter at the very end of his career, in 1988. While the metaphor is flawed, some of the problems which Wright was attempting to address are still with us today, and are in the process of being reformulated as part of a forthcoming Extended Evolutionary Synthesis.

This symposium discusses J.-L. Dessalles's account of the evolution of language, which was presented in Why we Talk (OUP 2007). KeywordsEvolution of language-Costly signaling-Evolutionary game theory-Semantics-Pragmatics-Syntax

In this paper, I argue against John Beatty’s position in his paper “The Evolutionary Contingency Thesis” by counterexample. Beatty argues that there are no distinctly biological laws because the outcomes of the evolutionary processes are contingent. I argue that the heart of the Caspar–Klug theory of virus structure—that spherical virus capsids consist of 60T subunits (where T=k 2+hk+h 2 and h and k are integers)—is a distinctly biological law even if the existence of spherical viruses is evolutionarily contingent. KeywordsScientific laws-Laws of biology-Laws of design-Virology-Contingency-Degrees of necessity-Adaptationism-Biological design-Stephen Jay Gould

At the beginning of the 1950s most students of animal behavior in Britain saw the instinct concept developed by Konrad Lorenz in the 1930s as the central theoretical construct of the new ethology. In the mid 1950s J.B.S. Haldane made substantial efforts to undermine Lorenz''s status as the founder of the new discipline, challenging his priority on key ethological concepts. Haldane was also critical of Lorenz''s sharp distinction between instinctive and learnt behavior. This was inconsistent with Haldane''s account of the evolution of language, and, according to Haldane, inconsistent with elementary genetics. British attitudes to the instinct concept changed dramatically in the wake of Daniel S. Lehraman''s 1953 critique of Lorenz, and by the 1960s Lorenz drew a clear distinction between his own views and those of the English-speaking ethologists. The inconsistencies between Lorenz''s ideas and the trends in contemporary evolutionary genetics that are reflected in Haldane''s critiques may help to explain why the Lorenzian instinct concept was unable to maintain itself in Britian.

Foundationalist theories of justification for science were undermined by the theory-ladeness thesis, which has affinities with coherentist epistemologies. A challenge for defenders of coherentist theories of scientific justification is to specify coherence relations relevant to science and to show how these relations make the truth of their bearers likely. Coherence relations include characteristics that pick out better explanations in the implementation of abductive arguments. Empiricist philosophers have attacked abductive reasoning by claiming that explanatory virtues are pragmatic, having no implications regarding truth. However, empiricist's basic beliefs are subject to the same challenges facing abduction, both of which can be met by citing causally coherent etiologies, which are commonplace in biological explanations, and by demonstrating the relevance of causal coherence to truth.

This paper discusses the individuation of characters for the use asunits by geneticists at the beginning of the 20th century. Thediscussion involves the Presence and Absence Hypothesis as a case study. It issuggested that the gap between conceptual consideration and etiological factorsof individuating of characters is being handled by way of mutual adjustment.Confrontation of a suggested morphological unit character with experimentresults molded the final boundaries of it.

What is the best way to analyse abstraction in scientific modelling? I propose to focus on abstracting as an epistemic activity, which is achieved in different ways and for different purposes depending on the actual circumstances of modelling and the features of the models in question. This is in contrast to a more conventional use of the term ‘abstract’ as an attribute of models, which I characterise as black-boxing the ways in which abstraction is performed and to which epistemological advantage. I exemplify my claims through a detailed reconstruction of the practices involved in creating two types of models of the flowering plant Arabidopsis thaliana, currently the best-known model organism in plant biology. This leads me to distinguish between two types of abstraction processes: the ‘material abstracting’ required in the production of Arabidopsis specimens and the ‘intellectual abstracting’ characterising the elaboration of visual models of Arabidopsis genomics. Reflecting on the differences between these types of abstracting helps to pin down the epistemic skills and research commitments used by researchers to produce each model, thus clarifying how models are handled by researchers and with which epistemological implications.

Abstraction is seen as an active process which both enlightens and obscures. Abstractions are not true or false but relatively enlightening or obscuring according to the problem under study; different abstractions may grasp different aspects of a problem. Abstractions may be useless if they can answer questions only about themselves. A theoretical enterprise explores reality through acluster of abstractions that use different perspectives, temporal and horizontal scales, and assumes different givens.

In Can Abstractions be Causes, David Johnson defends the view that abstractions can have causal force. He offers as his own example of natural kinds ecological niches, arguing that the causal force of these niches in nature is akin to the force of Aristotelian final causes. He concludes that, rooted as it is in seventeenth century mechanism, the currently-accepted model of causality which recognises only efficient causes is inadequate to the needs of contemporary science. In Natural Kinds and Ecological Niches — Response to Johnson''s Paper, Melinda Hogan offers a critique of Johnson''s paper which, by begging the question in favor of the very sort of causality Johnson seeks to supplement, misses the epistemological implications of his idea. In this paper I will attempt to clarify and defend Johnson''s position, pointing out some of its implications for the epistemology of science in general.

The Empiricist or Lockean view says natural kinds do not exist objectively in nature but are practical categories reflecting use of words. The Modern, Ostensive view says they do exist, and one can refer to such a kind by ostention and recursion, assuming his designation of it is related causally to the kind itself. However, this leads to a problem: Kinds are abstract repeatables, and it seems impossible that abstractions could have causal force. In defence of the Modern view, I suggest we can think of kinds as — or as like — ecological niches existing in nature, which are causally effective by virtue of the fact that they predictively determine (some) properties of the things that happen to occupy them.

Karl Popper has been one of the few philosophers of sciences who has influenced scientists. I evaluate Popper's influence on our understanding of evolutionary theory from his earliest publications to the present. Popper concluded that three sorts of statements in evolutionary biology are not genuine laws of nature. I take him to be right on this score. Popper's later distinction between evolutionary theory as a metaphysical research program and as a scientific theory led more than one scientist to misunderstand his position on evolutionary theory as a scientific theory. In his later work Popper also introduced what he took to be improvements of evolutionary theory. Thus far these improvements have had almost no influence on evolutionary biology. I conclude by examining the influence of Popper on the reception of cladistic analysis.

The commentaries by Dennett, Sterelny, and Queller on Darwinian Populations and Natural Selection (DPNS) are so constructive that they make it possible to extend and improve the book’s framework in several ways. My replies will focus on points of disagreement, and I will pick a small number of themes and develop them in detail. The three replies below are mostly self-contained, except that all my comments about genes, discussed by all three critics, are in the reply to Queller. Agential views of evolution, discussed by Queller and Dennett, are addressed in my reply to Dennett. KeywordsEvolution–Genes–Symbiosis–Individuals

Contrary to widely held assumptions, an evolutionary metaethics need not be non-cognitivist. I define evolutionary metaethics as the claim that certain phenotypic traits expressing certain genes are both necessary and sufficient for explanation of all other phenotypic traits we consider morally significant. A review of the influential cognitivist Immanuel Kants metaethics shows that much of his ethical theory is independent of the anti-naturalist metaphysics of transcendental idealism which itself is incompatible with evolutionary metaethics. By matching those independent aspects to an evolutionary metaethics a cognitivist Kantian evolutionary metaethical theory is a possibility for researchers to consider.

Operational definitions of biological altruism in terms of actual fitness exchanges will not work because they include accidental acts as altruistic and exclude altruistic acts that have gone awry. I argue that the definition of biological altruism should contain an analogue of the role intention plays in psychological altruism. I consider two possibilities for this analogue, selected effect functions and the proximate causes and effects of behavior. I argue that the selected-effect function account will not work because it confuses the explanation of some altruistic behavior with the definition of all of it and the information needed to justify a selected effect account of function is too often inaccessible. Close attention to the proximate explanations of a behavior is all that is needed to determine if an act is biologically altruistic, returning biological altruism to descriptive ethology, where it belongs.

The claim that conceptual systems change is a platitude. That our conceptual systems are theory-laden is no less platitudinous. Given evolutionary theory, biologists are led to divide up the living world into genes, organisms, species, etc. in a particular way. No theory-neutral individuation of individuals or partitioning of these individuals into natural kinds is possible. Parallel observations should hold for philosophical theories about scientific theories. In this paper I summarize a theory of scientific change which I set out in considerable detail in a book that I shall publish in the near future. Just as few scientists were willing to entertain the view that species evolve in the absence of a mechanism capable of explaining this change, so philosophers should be just as reticent about accepting a parallel view of conceptual systems in science evolving in the absence of a mechanism to explain this evolution. In this paper I set out such a mechanism. One reason that this task has seemed so formidable in the past is that we have all construed conceptual systems inappropriately. If we are to understand the evolution of conceptual systems in science, we must interpret them as forming lineages related by descent. In my theory, the notion of a family resemblance is taken literally, not metaphorically. In my book, I set out data to show that the mechanism which I propose is actually operative. In this paper, such data is assumed.

Classification in eighteenth-century natural history was marked by a battle of systems. The Linnaean approach to classification was severely criticized by those naturalists who aspired to a truly natural system. But how to make oneself nature''s spokesman? In this article I seek to answer that question using the approach of the French anthropologist of science Bruno Latour in a discussion of the work of the French naturalists Buffon and Cuvier in the eighteenth and early nineteenth century. These naturalists followed very different strategies in creating and defending of what they believed to be a natural classification in zoology. Buffon failed, whereas Cuvier''s work appeared to be very successful. My argument will be that, to explain Buffon''s failure and Cuvier''s success, we should not focus on the epistemological or theoretical concerns and justifications of these naturalists, but on the concrete and heterogeneous means or tools through which animals were mobilized, stabilized and combined into ever more comprehensive systems of classification.

A naturalistic account of the strengths and limitations of cladistic practice is offered. The success of cladistics is claimed to be largely rooted in the parsimony-implementing congruence test. Cladists may use the congruence test to iteratively refine assessments of homology, and thereby increase the odds of reliable phylogenetic inference under parsimony. This explanation challenges alternative views which tend to ignore the effects of parsimony on the process of character individuation in systematics. In a related theme, the concept of homeostatic property cluster natural kinds is used to explain why cladistics is well suited to provide a traditional, verbal reference system for the evolutionary properties of species and clades. The advantages of more explicitly probabilistic approaches to phylogenetic inference appear to manifest themselves in situations where evolutionary homeostasis has for the most part broken down, and predictive classifications are no longer possible.

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.

In his critical notice, Rosenberg (1991) raises three objections to my evolutionary account of science: whether it is more than a week metaphor, the compatibility of my past objections to reduction and my current advocacy of viewing selection in terms of replication and interaction, and finally, the feasibility of identifying appropriate replicators and interactors in biological evolution, let alone conceptual evolution. I discuss each of these objections in turn.

The greatest challenge for Cultural Selection Theory lies is the paucity of evidence for structural mechanisms in cultural systems that are sufficient for adaptation by natural selection. In part, clarification is required with respect to the interaction between cultural systems and their purported selective environments. Edmonds et al. have argued that Cultural Selection Theory requires simple, conclusive, unambiguous case studies in order to meet this challenge. To that end, this paper examines the songs of the Rufous-collared Sparrow, which seem to exhibit cultural adaptations minimizing signal degradation relative to local environments. Specifically, the more forested the habitat, the more the tail end of the song resembles a whistle rather than a trill; yet, variation in song is uncorrelated with genetic variation. This paper explores the mechanisms responsible for these putative acoustic adaptations through a series of computer simulations. The main point of this research is not to test this model, but to demonstrate that models of this type have the resources to meet the in-principle objections that have been raised against Cultural Selection Theory. This research lends much-needed empirical support to Cultural Selection Theory by clarifying the nature of the interaction between culture and environment. It also contributes to evolutionary theory by clarifying the scope and limits of adaptation by natural selection. KeywordsBird song-Computer simulation-Cultural evolution-Cultural Selection Theory-Formal model-Meme-Natural selection

The Aristotle-Kant tradition requires that autonomous activity must originate within the self and points toward a new type of causation (different from natural efficient causation) associated with teleology. Notoriously, it has so far proven impossible to uncover a workable model of causation satisfying these requirements without an increasingly unsatisfying appeal to extra-physical elements tailor-made for the purpose. In this paper we first provide the essential reason why the standard linear model of efficient causation cannot support the required model of agency: its causal thread model of efficient causation cannot support the core requirement that an action is determined by, and thus an expression of, the agent’s nature. We then provide a model that corrects these deficiencies, constructed naturalistically from within contemporary biology, and argue that it provides an appropriate foundation for all the features of genuine agency. Further, we provide general characterisations of freedom and reason suitable to this bio-context (but that also capture the core classical conceptions) and show how this model reconciles them.

In a recent paper in this journal (Rottschaefer and Martinsen 1990) we have proposed a view of Darwinian evolutionary metaethics that we believe improves upon Michael Ruse's (e.g., Ruse 1986) proposals by claiming that there are evolutionary based objective moral values and that a Darwinian naturalistic account of the moral good in terms of human fitness can be given that avoids the naturalistic fallacy in both its definitional and derivational forms while providing genuine, even if limited, justifications for substantive ethical claims. Jonathan Barrett (this issue) has objected to our proposal contending that we cannot hold for the reality of supervenient moral properties without either falling foul of the naturalistic fallacy or suffering the consequences of postulating inexplicable moral properties. In reply, we show that Barrett's explicit arguments that we commit either the definitional or derivational form of the naturalistic fallacy fail and that his naturalistic intuitions that supervenience explanations of moral properties by nonmoral properties force us into what we call the explanatory form of the naturalistic fallacy also fail. Positively, his objections help us to clarify the nature of the naturalistic fallacy within an evolutionary based naturalistic ethics and to point out the proper role of both supervenience explanations and moral explanations in such an ethics.

Conventional wisdom has it that evolution makes a sham of morality, even if morality is an adaptation. I disagree. I argue that our best current adaptationist theory of meaning offers objective truth conditionsfor signaling systems of all sorts. The objectivity is, however, relative to species – specifically to the adaptive history of the signaling system in question. While evolution may not provide the kind of species independent objective standards that (e.g.) Kantians desire, this should be enough for the practical work of justifying our confidence in the objectivity of moral standards. If you believe morality is an adaptation, you should be a moral realist.

It is shown that complex adaptations are best modelled as discrete processes represented on directed weighted graphs. Such a representation captures the idea that problems of adaptation in evolutionary biology are problems in a discrete space, something that the conventional representations using continuous adaptive landscapes does not. Further, this representation allows the utilization of well-known algorithms for the computation of several biologically interesting results such as the accessibility of one allele from another by a specified number of point mutations, the accessibility of alleles at a local maximum of fitness, the accessibility of the allele with the globally maximum fitness, etc. A reduction of a model due to Kauffman and Levin to such a representation is explicitly carried out and it is shown how this reduction clarifies the biological questions that are of interest.

It is important to distinguish adaptation per se (adaptedness, or being adapted) from the more specific concept of adaptation for some function. Commonly used criteria for adaptation in either sense have limited applicability. There are, however, a number of widely applicable criteria for adaptation per se, such as several kinds of cost, low variation, the maintenance of integration, and the fitness distribution of mutations. Application of these criteria leads to the conclusion that adaptation is overwhelmingly prevalent for features of organisms. Neither the presence nor the absence of adaptation has a privileged status in inference. Effectively neutral evolution can occur on adaptive buttes while maintaining the same degree of adaptation, but it is likely to be relatively minor.