The philosophy of biology, like all of Western philosophy, began with the ancient Greeks. Although Plato (c. 428-c. 348 BC) was little interested in the subject, his student Aristotle (384-322), who for a time was a practicing biologist, had much to say about it. From a historical perspective, his most important contributions were his observations that biological organisms can be arranged in a hierarchy based on their structural complexity — an idea that later became the basis of the Great Chain of Being {?} — and that organisms of different species nevertheless display certain systematic similarities, now understood to be indicative of a common evolutionary ancestry (see homology) . More significant philosophically was Aristotle’s view of causation, and particularly his identification of the notion of final causality, or causality with reference to some purpose, function, or goal (see teleology) . Although it is not clear whether Aristotle thought of final causality as pertaining only to the domain of the living, it is certainly true that he considered it essential for understanding or explaining the nature of biological organisms. One cannot fully understand why the human eye or heart has the structure it does without taking into account the function the organ performs.

The notion of final causality was taken for granted by most philosophers from the Hellenistic age through the end of the Middle Ages. Indeed, philosophers and theologians in the medieval and early modern periods adopted it as the basis of an argument for the existence of God — the teleological argument, also known as the argument from design, which was developed in sophisticated ways in the 19th and 20th centuries (see intelligent design) . During the scientific revolution of the 17th century, however, final causes came to be regarded as unnecessary and useless in scientific explanation; the new mechanistic philosophy had no need for them. The English philosopher and scientist Francis Bacon (1561-1626) likened them to the Vestal Virgins — decorative but sterile.

Despite these criticisms, the notion of final causality persisted in biology, leading many philosophers to think that, in this respect at least, the biological sciences would never be the same as the physical sciences. Some, like the German Enlightenment philosopher Immanuel Kant (1724-1804), regarded biology’s reliance on final causality as an indication of its inherent inferiority to sciences like physics. Others, like the British historian and philosopher of science William Whewell (1794-1864), took it as demonstrating simply that different sciences are different and thus that a form of explanation that is appropriate in one field might not be appropriate in another.

In the late 19th century, the question of the supposed {?} inherent differences between the biological and the physical sciences took on new importance. Reaching back to the ideas of Aristotle, but also relying on more-recent theories promoted by the Count de Buffon (1707-88) and others, several philosophers and biologists began to argue that living organisms are distinguished from inert matter by their possession of a “life force” that animates them and propels their evolution into higher forms. The notion of an entelechy — a term used by Aristotle and adopted by the German biologist Hans Driesch (1867-1941) — or élan vital — introduced by the French philosopher Henri Bergson (1859-1941) — was widely accepted and became popular even outside academic circles. Ultimately, however, it fell out of favour, because it proved to have little {how little?} direct scientific application. The difficulty was not that life force was not observable in the world (at least indirectly) but that it did not lead to new predictions or facilitate unified explanations of phenomena formerly thought to be unrelated, as all truly important scientific concepts do.

The decline of vitalism, as the resort to such forces came to be known, had two important results. Some philosophers tried to find a way of preserving the autonomy of the biological sciences {?} without resort to special forces or entities. Such theories, referred to as “holism” or “ organicism,” attracted the attention of the British philosophers Alfred North Whitehead (1861-1947) and Samuel Alexander (1859-1938), who thought that the very order or structure of organisms distinguished them from nonliving things. Others turned to early 20th-century advances in logic and mathematics in an attempt to transform biology into something parallel to, if not actually a part of, the physical sciences. The most enthusiastic proponent of this approach, the British biologist and logician Joseph Woodger (1894-1981), attempted to formalize the principles of biology — to derive them by deduction from a limited number of basic axioms and primitive terms — using the logical apparatus of the Principia Mathematica (1910-13) by Whitehead and Bertrand Russell (1872-1970).

In the first half of the 20th century Anglo-American philosophy (analytic philosophy) was dominated by a school of scientific empiricism known as logical positivism. Its leading figures — Rudolf Carnap (1891-1970), Carl Hempel (1905-97), Ernest Nagel (1901-85), R.B. Braithwaite (1900-90), and Karl Popper (1902-94) — argued that genuine scientific theories, such as Newtonian astronomy, are hypothetico-deductive, with theoretical entities occupying the initial hypotheses and natural laws the ultimate deductions or theorems. For the most part these philosophers were not particularly interested in the biological sciences. Their general assumption was that, insofar as biology is like physics, it is good science, and insofar as it is not like physics, it ought to be. The best one can say of modern biology, in their view, is that it is immature; the worst one can say is that it is simply second-rate.

This uncharitable perspective was soon undermined, however, by at least three important developments. First, in the 1960s the biological sciences became philosophically much more complex and interesting, as the stunning breakthroughs in molecular biology of the previous decade — particularly the discovery in 1953 of the nature of the DNA molecule — were starting to bear fruit. For example, one could now study variation between or within populations quantitatively, rather than simply by estimation or guesswork. {?} At the same time, there were major new developments and discoveries in the theory of evolution,especially as it applied to the study of social behaviour. It was therefore no longer possible for philosophers to dismiss biology as an inferior science merely because it did not resemble physics.

Second, the conception of science advocated by logical positivists came under attack. Drawing on the work of the philosopher and historian of science Thomas Kuhn (1922-96), critics argued that the picture of scientific theories as structurally uniform and logically self-contained was ahistorical and unrealistic. Accordingly, as philosophers broadened their appreciation of scientific-theory construction in the real world, they became increasingly interested in biology as an example of a science that did not fit the old logical-positivist paradigm.

Third, in the early 1960s the history of science began to emerge as a distinct academic discipline. Its rapid growth attracted the attention of philosophers of science and helped to strengthen the new consensus among them that an appreciation of the history of science is necessary for a proper philosophical understanding of the nature of science and scientific theorizing. Significant new work by historians of science on the development of evolutionary theory was taken up by philosophers for use in the explication of the nature of science as it exists through time.

In this newly receptive intellectual climate, research in the philosophy of biology proceeded rapidly, and the influence and prestige of the discipline grew apace. New professional organizations and journals were established, and the area soon became one of the most vital and thriving disciplines within philosophy. Although the philosophy of biology is still marked by a concentration on evolutionary theory as opposed to other subjects in the life sciences, this may simply reflect the fact that evolution is an especially interesting and fertile topic for philosophical analysis.

Without doubt, the chief event in the history of evolutionary theory was the publication in 1859 of On the Origin of Species, by Charles Darwin (1809-82). Arguing for the truth of evolutionary theory may be conceived as involving three tasks: namely, establishing the fact of evolution—showing that it is reasonable to accept a naturalistic, or law-bound, developmental account of life’s origins; identifying, for various different species, the particular path, or phylogeny, through which each evolved; and ascertaining a cause or mechanism of evolutionary change. In On the Origin of Species, Darwin accomplished the first and the third of these tasks (he seemed, in this and subsequent works, not to be much interested in the second). His proposal for the mechanism of evolutionary change was natural selection, popularly known as “ survival of the fittest. ” Selection comes about through random and naturally occurring variation in the physical features of organisms and through the ongoing competition within and between species for limited supplies of food and space. Variations that tend to benefit an individual (or a species) in the struggle for existence are preserved and passed on (“selected”), because the individuals (or species) that have them tend to survive.

The notion of natural selection was controversial in Darwin’s time, and it remains so today. The major early objection was that the term is inappropriate: if Darwin’s basic point is that evolutionary change takes place naturally, without divine intervention, why should he use a term that implies a conscious choice or decision on the part of an intelligent being? Darwin’s response was that the term natural selection is simply a metaphor, no different in kind from the metaphors used in every other branch of science. Some contemporary critics, however, have objected that, even treated as a metaphor, “natural selection” is misleading. One form of this objection comes from philosophers who dislike the use of any metaphor in science—because, they allege, metaphorical description in some sense conceals what is objectively there—while another comes from philosophers who merely dislike the use of this particular metaphor.

The Darwinian response to the first form of the objection is that metaphors in science are useful and appropriate because of their heuristic role. In the case of “natural selection,” the metaphor points toward, and leads one to ask questions about, features that have adaptive value—that increase the chances that the individual (or species) will survive; in particular it draws attention to how the adaptive value of the feature lies in the particular function it performs.

The second form of the objection is that the metaphor inclines one to see function and purpose where none in fact exist. The Darwinian response in this case is to acknowledge that there are indeed examples in nature of features that have no function or of features that are not optimally adapted to serve the function they apparently have. Nevertheless, it is not a necessary assumption of evolutionary theory that every feature of every organism is adapted to some purpose, much less optimally adapted. As an investigative strategy, however, the assumption of function and purpose is useful, because it can help one to discover adaptive features that are subtle or complex or for some other reason easy to overlook. As Kuhn insisted, the benefit of good intellectual paradigms is that they encourage one to keep working to solve puzzles even when no solution is in sight. The best strategy, therefore, is to assume the existence of function and purpose until one is finally forced to conclude that none exists. It is a bigger intellectual sin to give up looking too early than to continue looking too long.

Although the theory of evolution by natural selection was first published by Darwin, it was first proposed by Darwin’s colleague, the British naturalist Alfred Russel Wallace (1823-1913). At Wallace’s urging, later editions of On the Origin of Species used a term coined by Herbert Spencer (1820-1903), survival of the fittest, in place of natural selection. This substitution, unfortunately, led to countless (and continuing) debates about whether the thesis of natural selection is a substantive claim about the real world or simply a tautology (a statement, such as “All bachelors are unmarried,” that is true by virtue of its form or the meaning of its terms). If the thesis of natural selection is equivalent to the claim that those that survive are the fittest, and if the fittest are identified as those that survive, then the thesis of natural selection is equivalent to the claim that those that survive are those that survive—true indeed, but hardly an observation worthy of science.

Defenders of Darwin have issued two main responses to this charge. The first, which is more technically philosophical, is that, if one favours the semantic view of theories, then all theories are made of models that are in themselves a priori—that is, not as such claims about the real world but rather idealized pictures of it. To fault selection claims on these grounds is therefore unfair, because, in a sense, all scientific claims start in this way. It is only when one begins to apply models, seeing if they are true of reality, that empirical claims come into play. There is no reason why this should be less true of selection claims than of any other scientific claims. One could claim that camouflage is an important adaptation, but it is another matter actually to claim (and then to show) that dark animals against a dark background do better than animals of another colour.

The second response to the tautology objection, which is more robustly scientific, is that no Darwinian has ever claimed that the fittest always survive; there are far too many random events in the world for such a claim to be true. However fit an organism may be, it can always be struck down by lightning or disease or any kind of accident. Or it may simply fail to find a mate, ensuring that whatever adaptive feature it possesses will not be passed on to its progeny. Indeed, work by the American population geneticist Sewall Wright (1889-1989) has shown that, in small populations, the less fit might be more successful than the more fit, even to the extent of replacing the more fit entirely, owing to random but relatively significant changes in the gene pool, a phenomenon known as genetic drift.

What the thesis of natural selection, or survival of the fittest, really claims, according to Darwinians, is not that the fittest always survive but that, on average, the more fit (or the fittest) are more successful in survival and reproduction than the less fit (or unfit). Another way of putting this is to say that the fit have a greater propensity toward successful survival and reproduction than the less fit.

Undoubtedly part of the problem with the thesis of natural selection is that it seems to rely on an inductive generalization regarding the regularity of nature (see induction) . Natural selection can serve as a mechanism of evolutionary change, in other words, only on the assumption that a feature that has adaptive value to an individual in a given environment—and is consequently passed on—also will have value to other individuals in similar environments. This assumption is apparently one of the reasons why philosophers who are skeptical of inductive reasoning—as was Popper—tend not to feel truly comfortable with the thesis of natural selection. Setting aside the general problem of induction, however, one may ask whether the particular assumption on which the thesis of natural selection relies is rationally justified. Some philosophers and scientists, such as the evolutionary biologist Richard Dawkins, think not only that it is justified but that a much stronger claim also is warranted: namely, that wherever life occurs—on this planet or any other—natural selection will occur and will act as the main force of evolutionary change. In Dawkins’s view, natural selection is a natural law.

Other philosophers and scientists, however, are doubtful that there can be any laws in biology, even assuming there are laws in other areas of science. Although they do not reject inductive inference per se, they believe that generalizations in biology must be hedged with so many qualifications that they cannot have the necessary force one thinks of as characteristic of genuine natural laws. (For example, the initially plausible generalization that all mammals give birth to live young must be qualified to take into account the platypus. ) An intermediate position is taken by those who recognize the existence of laws in biology but deny that natural selection itself is such a law. Darwin certainly thought of natural selection as a law, very much like Newton’s law of gravitational attraction; indeed, he believed that selection is a force that applies to all organisms, just as gravity is a force that applies to all physical objects. Critics, however, point out that there does not seem to be any single phenomenon that could be identified as a “force” of selection. If one were to look for such a force, all one would actually see are individual organisms living and reproducing and dying. At best, therefore, selection is a kind of shorthand for a host of other processes, which themselves may or may not be governed by natural laws.

In response, defenders of selection charge that these critics are unduly reductionistic. In many other areas of science, they argue, it is permissible to talk of certain phenomena as if they were discrete entities, even though the terms involved are really nothing more than convenient ways of referring, at a certain level of generality, to complex patterns of objects or events. If one were to look for the pressure of a gas, for example, all one would actually see are individual molecules colliding with each other and with the walls of their container. But no one would conclude from this that there is no such thing as pressure. Likewise, the fact that there is nothing to see beyond individual organisms living and reproducing and dying does not show that there is no such thing as selection.

Darwin held that natural selection operates at the level of the individual. Adaptive features are acquired by and passed on to individual organisms, not groups or species, and they benefit individual organisms directly and groups or species only incidentally. One type of case, however, did cause him worry: in nests of social insects, there are always some members (the sterile workers) who devote their lives entirely to the well-being of others. How could a feature for self-sacrifice be explained, if adaptive features are by definition beneficial to the individual rather than to the group? Eventually Darwin decided that the nest as a whole could be treated as a kind of superorganism, with the individual members as parts; hence the individual benefiting from adaptation is the nest rather than any particular insect.

Wallace differed from Darwin on this question, arguing that selection sometimes operates at the level of groups and hence that there can be adaptive features that benefit the group at the expense of the individual. When two groups come into conflict, members of each group will develop features that help them to benefit other group members at their own expense (i.e., they become altruists). When one group succeeds and the other fails, the features for altruism developed in that group are selected and passed on. For the most part Darwin resisted this kind of thinking, though he made a limited exception for one kind of human behaviour, allowing that morality, or ethics, could be the result of group selection rather than individual selection. But even in this case he was inclined to think that benefits at the level of individuals might actually be more important, since some kinds of altruistic behaviour (such as grooming) tend to be reciprocated.

Several evolutionary theorists after Darwin took for granted that group selection is real and indeed quite important, especially in the evolution of social behaviour. Konrad Lorenz (1903-89), the founder of modern ethology, and his followers made this assumption the basis of their theorizing. A minority of more-conservative Darwinians, meanwhile—notably Ronald Aylmer Fisher (1890-1962) and J.B.S. Haldane (1892-1964)—resisted such arguments. In the 1960s, the issue came to a fore, and for a while group selection was dismissed entirely. Some theorists, notably the American evolutionary biologist George C. Williams, argued that individual interests would always outweigh group interests, since genes associated with selfish behaviour would inevitably spread at the expense of genes associated with altruism. Other researchers showed how apparent examples of group selection could be explained in individualistic terms. Most notably, the British evolutionary biologist W.D. Hamilton (1936-2000) showed how social behaviour in insects can be explained as a form of “kin selection” beneficial to individual interests. In related work, Hamilton’s colleague John Maynard Smith (1920-2004) employed the insights of game theory to explain much social interaction from the perspective of individual selection.

Throughout these debates, however, no one denied the possibility or even the actuality of group selection—the issue was rather its extent and importance. Fisher, for example, always supposed that reproduction through sex must be explained in such a fashion. (Sexual reproduction benefits the group because it enables valuable features to spread rapidly, but it generally benefits the individual mother little or not at all.) In the 1970s, the group-selection perspective enjoyed a resurgence, as new models were devised to show that many situations formerly understood solely in terms of individual interests could be explained in terms of group interests as well. The American entomologist Edward O. Wilson, later recognized as one of the founders of sociobiology, argued that ants of the genus Pheidole are so dependent upon one another for survival that Darwin’s original suggestion about them was correct: the nest is a superorganism, an individual in its own right. Others argued that only a group-selection perspective is capable of explaining certain kinds of behaviour, especially human moral behaviour. This was the position of the American biologist David S. Wilson (no relation to Edward O. Wilson) and the American philosopher Elliott Sober.

In some respects the participants in these debates have been talking past each other. Should a pair of organisms competing for food or space be regarded as two individuals struggling against each other or as a group exhibiting internal conflict? Depending on the perspective one takes, such situations can be seen as examples of either individual or group selection. A somewhat more significant issue arose when some evolutionary theorists in the early 1970s began to argue that the level at which selection truly takes place is that of the gene. The “ genic selection” approach was initially rejected by many as excessively reductionistic. This hostility was partly based on misunderstanding, which is now largely removed thanks to the efforts of some scholars to clarify what genic selection can mean. What it cannot mean—or, at least, what it can only rarely mean—is that genes compete against each other directly. Only organisms engage in direct competition. Genes can play only the indirect role of encoding and transmitting the adaptive features that organisms need to compete successfully. Genic selection therefore amounts to a kind of counting, or ledger keeping, insofar as it results in a record of the relative successes and failures of different kinds of genes. In contrast, “ organismic selection,” as it may be called, refers to the successes and failures at the level of the organism. Both genic and organismic selection are instances of individual selection, but the former refers to the “replicators”—the carriers of heredity—and the latter to the “vehicles”—the entities in which the replicators are packaged.

Could there be levels of selection even higher than the group? Could there be “ species selection”? This was the view of the American paleontologist Stephen Jay Gould (1941-2002), who argued that selection at the level of species is very important in macro- evolution—i.e., the evolution of organisms over very long periods of time (millions of years). It is important to understand that Gould’s thesis was not simply that there are cases in which the members of a successful species possess a feature that the members of a failed species do not and that possession of the feature makes the difference between success and failure. Rather, he claimed that species can produce emergent features—features that belong to the species as a whole rather than to individual members—and that these features themselves can be selected for.

One example of such a feature is reproductive isolation, a relation between two or more groups of organisms that obtains when they cannot interbreed (e.g., human beings and all other primates). Gould argued that reproductive isolation could have important evolutionary consequences, insofar as it delimits the range of features (adaptive or otherwise) that members of a given species may acquire. Suppose the members of one species are more likely to wander around the area in which they live than are members of another species. The first species could be more prone to break up and speciate than the second species. This in turn might led to greater variation overall in the descendants of the first species than in the descendants of the second, and so forth. Critics responded that, even if this is possibly so, the ultimate variation seems not to have come about because it was useful to anyone but rather as an accidental by-product of the speciation process—a by-product of wandering. To this Gould replied that perhaps species selection does not in itself promote adaptation at any level, even the highest. Naturally, to conventional Darwinians this was so unsatisfactory a response that they were inclined to withhold the term “selection” to the whole process, whether or not it could be said to exist and to be significant.

One of the oldest objections to the thesis of natural selection is that it is untestable. Even some of Darwin’s early supporters, such as the British biologist T.H. Huxley (1825-95), expressed doubts on this score. A modern form of the objection was raised in the early 1960s by the British historian of science Martin Rudwick, who claimed that the thesis is uncomfortably asymmetrical. Although it can be tested positively, since features found to have adaptive value count in its favour, it cannot really be tested negatively, since features found not to have adaptive value tend to be dismissed as not fully understood or as indicative of the need for further work. Too often and too easily, according to the objection, supporters of natural selection simply claim that, in the fullness of time, apparent counterexamples will actually prove to support their thesis, or at least not to undermine it.

Naturally enough, this objection attracted the sympathetic attention of Popper, who had proposed a principle of “ falsifiability” as a test of whether a given hypothesis is genuinely empirical (and therefore scientific). According to Popper, it is the mark of a pseudoscience that its hypotheses are not open to falsification by any conceivable test. He concluded on this basis that evolutionary theory is not a genuine science but merely a “metaphysical research programme.”

Supporters of natural selection responded, with some justification, that it is simply not true that no counterevidence is possible. They acknowledged that some features are obviously not adaptive in some respects: in human beings, for example, walking upright causes chronic pain in the lower back, and the size of the infant’s head relative to that of the birth canal causes great pain for females giving birth.

Nevertheless, the fact is that evolutionary theorists must often be content with less than fully convincing evidence when attempting to establish what the adaptive value—if any—of a particular feature may be. Ideally, investigations of this sort would trace phylogenies and check genetic data to establish certain preliminary adaptive hypotheses, then test the hypotheses in nature and in laboratory experiments. In many cases, however, only a few avenues of testing will be available to researchers. Studies of dinosaurs, for example, cannot rely to any significant extent upon genetic evidence, and the scope for experiment is likewise very limited and necessarily indirect. A defect that is liable to appear in any investigation in which the physical evidence available is limited to the structure of the feature in question—perhaps in the form of fossilized bones—is the circular use of structural evidence to establish a particular adaptive hypothesis that one has already decided is plausible; other possible adaptations, just as consistent with the limited evidence available, are ignored. Although in these cases a certain amount of inference in reverse—in which one begins with a hypothesis that seems plausible and sees whether the evidence supports it—is legitimate and even necessary, some critics, including the American morphologist George Lauder, have contended that the pitfalls of such reasoning have been insufficiently appreciated by evolutionary theorists.

Various methods have been employed to improve the soundness of tests used to evaluate adaptive hypotheses. The “ comparative method, ” which involves considering evidence drawn from a wide range of similar organisms, was used in a study of the relatively large size of the testicles of chimpanzees as compared to those of gorillas. The adaptive hypothesis was that, given that the average female chimpanzee has several male sexual partners, a large sperm production, and therefore large testicles, would be an adaptive advantage for an individual male competing with other males to reproduce. The hypothesis was tested by comparing the sexual habits of chimpanzees with those of gorillas and other primates: if testicle size was not correlated with the average number of male sexual partners in the right way, the hypothesis would be disproved. In fact, however, the study found that the hypothesis was well supported by the evidence.

A much more controversial method is the use of so-called “ optimality models. ” The researcher begins by assuming that natural selection works optimally, in the sense that the feature (or set of features) eventually selected represents the best adaptation for performing the function in question. For any given function, then, the researcher checks to see whether the feature (or set of features) is indeed the best adaptation possible. If it is, then “optimal adaptation” is partially confirmed; if it is not, then either optimal adaptation is partially disconfirmed, or the function being performed has been misunderstood, or the background assumptions are faulty.

Not surprisingly, some critics have objected that optimality models are just another example of the near-circular reasoning that has characterized evolutionary theorizing from the beginning. Whether this is true or not, of course, depends on what one takes the studies involving optimality models to prove. John Maynard Smith, for one, denies that they constitute proof of optimal adaptation per se. Rather, optimal adaptation is assumed as something like a heuristic, and the researcher then goes on to try to uncover particular adaptations at work in particular situations. This way of proceeding does not preclude the possibility that particular adaptive hypotheses will turn out to be false. Other researchers, however, argue that the use of optimality models does constitute a test of optimal adaptation; hence, the presence of disconfirming evidence must be taken as proof that optimal adaptation is incorrect.

As most researchers use them, however, optimality models seem to be neither purely heuristic nor purely empirical. They are used as something like a background assumption, but their details are open to revision if they prove inconsistent with empirical evidence. Thus their careful use does not constitute circular reasoning but a kind of feedback, in which one makes adjustments in the premises of the argument as new evidence warrants, the revised premises then indicating the kind of additional evidence one needs to look for. This kind of reasoning is complicated and difficult, but it is not fallacious.

A major topic in many fields of philosophy, but especially in the philosophy of science, is reductionism. There are at least three distinct kinds of reductionism: ontological, methodological, and theoretical. Ontological reductionism is the metaphysical doctrine that entities of a certain kind are in reality collections or combinations of entities of a simpler or more basic kind. The pre-Socratic doctrine that the physical world is ultimately composed of different combinations of a few basic elements—e.g., earth, air, fire, and water—is an example of ontological reductionism. Methodological reductionism is the closely related view that the behaviour of entities of a certain kind can be explained in terms of the behaviour or properties of entities of another (usually physically smaller) kind. Finally, theoretical reductionism is the view in the philosophy of science that the entities and laws posited in older scientific theories can be logically derived from newer scientific theories, which are therefore in some sense more basic.

Since the decline of vitalism, which posited a special nonmaterial life force, ontological reductionism has been nearly universally accepted by philosophers and scientists, though a small number have advocated some form of mind-body dualism, among them Karl Popper and the Australian physiologist and Nobel laureate John Eccles (1903-97). Methodological reductionism also has been universally accepted since the scientific revolution of the 17th century, and in the 20th century its triumphs were outstanding, particularly in molecular biology.

The logical positivists of the 20th century advocated a thorough-going form of theoretical reductionism according to which entire fields of physical science are reducible, in principle, to other fields, in particular to physics. The classic example of theoretical reduction was understood to be the derivation of Newtonian mechanics from Einstein’s theories of special and general relativity. The relationship between the classic theory of genetics proposed by Gregor Mendel (1822-84) and modern molecular genetics also seemed to be a paradigmatic case of theoretical reduction. In the older theory, laws of segregation and independent assortment, among others, were used to explain macroscopic physical characteristics like size, shape, and colour. These laws were derived from the laws of the newer theory, which governed the formation of genes and chromosomes from molecules of DNA and RNA, by means of “bridge principles” that identified entities in the older theory with entities (or combinations of entities) in the newer one, in particular the Mendelian unit of heredity with certain kinds of DNA molecule. By being reduced in this way, Mendelian genetics was not replaced by molecular genetics but rather absorbed by it.

In the 1960s, the reductionist program of the logical positivists came under attack by Thomas Kuhn and his followers, who argued that, in the history of science, the adoption of new “paradigms,” or scientific worldviews, generally results in the complete replacement rather than the reduction of older theories. Kuhn specifically denied that Newtonian mechanics had been reduced by relativity. Philosophers of biology, meanwhile, advanced similar criticisms of the purported reduction of Mendelian genetics by molecular genetics. It was pointed out, for example, that in many respects the newer theory simply contradicted the older one and that, for various reasons, the Mendelian gene could not be identified with the DNA molecule. (One reason was that Mendel’s gene was supposed to be indivisible, whereas the DNA molecule can be broken at any point along its length, and in fact molecular genetics assumes that such breaking takes place.) Some defenders of reductionism responded to this criticism by claiming that the actual object of reduction is not the older theory of historical fact but a hypothetical theory that takes into account the newer theory’s strengths—something the Hungarian-born British philosopher Imré Lakatos (1922-74) called a “rational reconstruction.”

Philosophical criticism of genetic reductionism persisted, however, culminating in the 1980s in a devastating critique by the Australian philosopher Philip Kitcher, who denied the possibility, in practice and in principle, of any theoretical reduction of the sort envisioned by the logical positivists. In particular, no scientific theory is formalized as a hypothetico-deductive system as the positivists had contended, and there are no genuine “bridge principles” linking entities of older theories to entities of newer ones. The reality is that bits and pieces of newer theories are used to explain, extend, correct, or supplement bits and pieces of older ones. Modern genetics, he pointed out, uses molecular concepts but also original Mendelian ones; for example, molecular concepts are used to explain, not to replace, the Mendelian notion of mutation. The straightfoward logical derivation of older theories from newer ones is simply a misconception.

Reductionism continues to be defended by some philosophers, however. Kitcher’s former student Kenneth Waters, for example, argues that the notion of reduction can be a source of valuable insight into the relationships between successive scientific theories. Moreover, critics of reductionism, he contends, have focused on the wrong theories. Although strict Mendelian genetics is not easily reduced by the early molecular genetics of the 1950s, the much richer classical theory of the gene, as developed by the American Nobel laureate Thomas Hunt Morgan (1866-1945) and others in the 1910s, comes close to being reducible by the sophisticated molecular genetics of recent decades; the connections between the latter two theories are smoothly derivative in a way that would have pleased the logical positivists. The ideal of a complete reduction of one science by another is out of reach, but reduction on a smaller scale is possible in many instances.

At least part of this controversy arises from the contrasting visions of descriptivists and prescriptivists in the philosophy of science. No one on either side of the debate would deny that theoretical reduction in a pure form has never occurred and never will. On the other hand, the ideal of theoretical reduction can be a useful perspective from which to view the development of scientific theories over time, yielding insights into their origins and relationships that might otherwise not be apparent. Many philosophers and scientists find this perspective attractive and satisfying, even as they acknowledge that it fails to describe scientific theories as they really are.

Evolutionary biology is faced with two major explanatory problems: form and function. How is it possible to account for the forms of organisms and their parts and in particular for the structural similarities between organisms? How is it possible to account for the ways in which the forms of organisms and their parts seem to be adapted to certain functions? These topics are much older than evolutionary theory itself, having preoccupied Aristotle and all subsequent biologists. The French zoologist Georges Cuvier (1769-1832), regarded as the father of modern comparative anatomy, believed that function is more basic than form; form emerges as a consequence of function. His great rival, Étienne Geoffroy Saint-Hilaire (1772-1844), was enthused by form and downplayed function. Darwin, of course, was always more interested in function, and his thesis of natural selection was explicitly directed at the problem of explaining functional adaptation. Although he was certainly not unaware of the problem of form—what he called the “unity of type”—like Cuvier he thought that form was a consequence of function and not something requiring explanation in its own right.

One of the traditional tools for studying form is embryology, since early stages of embryonic development can reveal aspects of form, as well as structural relationships with other organisms, that later growth conceals. As a scientist Darwin was in fact interested in embryology, though it did not figure prominently in the argument for evolution presented in On the Origin of Species. Subsequent researchers were much more concerned with form and particularly with embryology as a means of identifying phylogenetic histories and relationships. But with the incorporation of Mendelian and then molecular genetics into the theory of evolution starting in the early 20th century, resulting in what has come to be known as the “synthetic theory,” function again became preeminent, and interest in form and embryology declined.

In recent years the pendulum has begun to swing once again in the other direction. There is now a vital and flourishing school of evolutionary development, often referred to as “ evo-devo,” and along with it a resurgence of interest in form over function. Many researchers in evo-devo argue that nature imposes certain general constraints on the ways in which organisms may develop, and therefore natural selection, the means by which function determines form, does not have a free hand. The history of evolutionary development reflects these limitations.

There are various levels at which constraints might operate, of course, and at certain levels the existence of constraints of one kind or another is not disputed. No one would deny, for example, that natural selection must be constrained by the laws of physics and chemistry. Since the volume (and hence weight) of an animal increases by the cube of its length, it is physically impossible for an elephant to be as agile as a cat, no matter how great an adaptive advantage such agility might provide. It is also universally agreed that selection is necessarily constrained by the laws of genetics.

The more contentious cases arise in connection with apparent constraints on more specific kinds of functional adaptation. In a celebrated article with Richard Lewontin, Gould argued that structural constraints on the adaptation of certain features inevitably result in functionally insignificant by-products, which he compared to the spandrels in medieval churches—the roughly triangular areas above and on either side of an arch. Biological spandrels, such as the pseudo-penis of the female hyena, are the necessary result of certain adaptations but serve no useful purpose themselves. Once in the population, however, they persist and are passed on, often becoming nearly universal patterns or archetypes, what Gould referred to as Baupläne (German: “body plans”).

According to Gould, other constraints operating at the molecular level represent deeply rooted similarities between animals that themselves may be as distant from each other as human beings and fruit flies. Humans have in common with fruit flies certain sequences of DNA, known as “homeoboxes,” that control the development and growth of bodily parts—determining, for example, where limbs will grow in the embryo. The fact that homeoboxes apparently operate independently of selection (since they have persisted unchanged for hundreds of millions of years) indicates that, to an important extent, form is independent of function.

These arguments have been rejected by more-traditional Darwinists, such as John Maynard Smith and George C. Williams. It is not surprising, they insist, that many features of organisms have no obvious function, and in any case one must not assume too quickly that any apparent Bauplän is completely nonfunctional. Even if it has no function now, it may have had one in the past. A classic example of a supposedly nonadaptive Bauplän is the four-limbedness of vertebrates. Why do humans have four limbs rather than six, like insects? Maynard Smith and Williams agree that four-limbedness serves no purpose now. But when vertebrates were aquatic creatures, two limbs fore and two limbs hind was of great value for moving upward and downward in water. The same point applies at the molecular level. If homeoboxes did not work as well as they do, selection would soon have begun tampering with them. The fact that something does not change does not mean that it is not functional or that it is immune to selective pressure. Indeed, there is evidence that, in some cases and as the need arises, even the most basic and most long-lived of molecular strands can change quite rapidly, in evolutionary terms.

As noted above, Aristotle provided a metaphysical justification of teleological language in biology by introducing the notion of final causality, in which reference to what will exist in the future is used to explain what exists or is occurring now. The great Christian philosophers of late antiquity and the Middle Ages, especially Augustine (354-430) and Thomas Aquinas (c. 1224-74), took the existence of final causality in the natural world to be indicative of its design by God. The eye serves the end of sight because God, in his infinite wisdom, understood that animals, human beings especially, would be better off with sight than without it. This perspective was commonplace among all educated people—not only philosophers, theologians, and scientists—until the middle of the 19th century and the publication of Darwin’s On the Origin of Species. Although Darwin himself was not an atheist (he was probably sympathetic to deism, believing in an impersonal god who created the world but did not intervene in it), he did wish to remove religion and theology from biology. One might expect, therefore, that the dissemination and acceptance of the theory of evolution would have had the effect of removing teleological language from the biological sciences. But in fact the opposite occurred: one can ask just as sensibly of a Darwinian as of a Thomist what end the eye serves.

In the first half of the 20th century many philosophers and scientists, convinced that teleological explanations were inherently unscientific, made attempts to eliminate the notion of teleology from the biological sciences, or at least to interpret references to it in scientifically more acceptable terms. After World War II, intrigued by the example of weapons, such as torpedoes, that could be programmed to track their targets, some logical positivists suggested that teleology as it applies to biological systems is simply a matter of being “directively organized,” or “goal-directed,” in roughly the same way as a torpedo. (It is important to note that this sense of goal-directedness means not just being directed toward a goal but also having the capacity to respond appropriately to potentially disruptive change.) Biological organisms, according to this view, are natural goal-directed objects. But this fact is not really very remarkable or mysterious, since all it means is that organisms are natural examples of a system of a certain well-known kind.

However, as pointed out by the embryologist C.H. Waddington (1905-75), the biological notion of teleology seems not to be fully captured by this comparison, since the “adaptability” implied by goal-directedness is not the same as the “adaptation” or “adaptedness” evident in nature. The eye is not able to respond to change in the same way, or to the same extent, as a target-seeking torpedo; still, the structure of the eye is adapted to the end of sight. Adaptedness in this sense seems to be possible only as a result of natural selection, and the goal-directedness of the torpedo has nothing to do with that. Despite such difficulties, philosophers in the 1960s and ’70s continued to pursue interpretations of biological teleology that were essentially unrelated to selection. Two of the most important such efforts were the “ capacity” approach and the “ etiological” approach, developed by the American philosophers Robert Cummins and Larry Wright, respectively.

According to Cummins, a teleological system can be understood as one that has the capacity to do certain things, such as generate electricity or maintain body temperature (or ultimately life). The parts of the system can be thought of as being functional or purposeful in the sense that they contribute toward, or enable, the achievement of the system’s capacity or capacities. Although many scientists have agreed that Cummins has correctly described the main task of morphology—to identify the individual functions or purposes of the parts of biological systems—his view does not seem to explicate teleology in the biological sense, since it does not treat purposefulness as adaptedness, as something that results from a process of selection. (It should be noted that Cummins probably would not regard this point as a criticism, since he considers his analysis to be aimed at a somewhat more general notion of teleology.)

The etiological approach, though developed in the 1970s, was in fact precisely the same as the view propounded by Kant in his Critique of Judgment (1790). In this case, teleology amounts to the existence of causal relations in which the effect explains or is responsible for the cause. The serrated edge of a knife causes the bread to be cut, and at the same time the cutting of the bread is the reason for the fact that the edge of the knife is serrated. The eye produces vision, and at the same time vision is the reason for the existence of the eye. In the latter case, vision explains the existence of the eye because organisms with vision—through eyes or proto-eyes—do better in the struggle for survival than organisms without it; hence vision enables the creation of newer generations of organisms with eyes or proto-eyes.

There is one other important component of the etiological approach. In a causal relation that is truly purposeful, the effect must be in some sense good or desired. A storm may cause a lake to fill, and in some sense the filling of the lake may be responsible for the storm (through the evaporation of the water it contains), but one would not want to say that the purpose of the storm is to fill the lake. As Plato noted in his dialogue the Phaedo, purpose is appropriate only in cases in which the end is good.

The etiological approach interprets the teleological language of biology in much the same way Kant did—i.e., as essentially metaphorical. The existence of a kind of purposefulness in the eye does not license one to talk of the eye’s designer, as the purposefulness of a serrated edge allows one to talk of the designer of a knife. (Kant rejected the teleological argument for the existence of God, also known as the argument from design.) But it does allow one to talk of the eye as if it were, like the knife, the result of design. Teleological language, understood metaphorically, is therefore appropriate to describe parts of biological organisms that characteristically seem as if they were designed with the good of the organism in mind, though they were not actually designed at all.

Although it is possible to make sense of teleological language in biology, some philosophers still think that the science would be better off without it. Most, however, believe that attempting to eliminate it altogether would be going too far. In part their caution is influenced by recent philosophy of science, which has emphasized the important role that language, and particularly metaphor, has played in the construction and interpretation of scientific theories. In addition, there is a widespread view in the philosophy of language and the philosophy of mind that human thinking is essentially and inevitably metaphorical. Most importantly, however, many philosophers and scientists continue to emphasize the important heuristic role that the notion of teleology plays in biological theorizing. By treating biological organisms teleologically, one can discover a great deal about them that otherwise would be hidden from view. If no one had asked what purpose the plates of the Stegosaurus serve, no one would have discovered that they do indeed regulate the animal’s body temperature. And here lies the fundamental difference between the biological and the physical sciences: the former, but not the latter, studies things in nature that appear to be designed. This is not a sign of the inferiority of biology, however, but only a consequence of the way the world is. Biology and physics are different, and so are men and women. The French have a phrase to celebrate this fact.

One of the oldest problems in philosophy is that of universals. The world seems to be broken up into different kinds of things. But what are these kinds, assuming they are distinct from the things that belong to them? Historically, some philosophers, known as realists, have held that kinds are real, whether they inhere in the individuals to which they belong (as Aristotle argued) or are independent of physical reality altogether (as Plato argued; see form) . Other philosophers, known as nonrealists but often referred to as nominalists, after the medieval school (nominalism) , held that there is nothing in reality over and above particular things. Terms for universals, therefore, are just names. Neither position, in its pure form, seems entirely satisfactory: if universals are real, where are they, and how does one know they exist? If they are just names, without any connection to reality, how do people know how to apply them, and why, nevertheless, do people apply them in the same way?

In the 18th century the philosophical debate regarding universals began to be informed by advances in the biological sciences, particularly the European discovery of huge numbers of new plant and animal species in voyages of exploration and colonization to other parts of the world. At first, from a purely scientific perspective, the new natural kinds indicated the need for a system of classification capable of making sense of the great diversity of living things, a system duly supplied by the great Swedish taxonomist Carolus Linnaeus (1707-78). In the early 19th century Jean Baptiste Lamarck (1744-1829) proposed a system that featured the separate classification of vertebrates and invertebrates. Cuvier went farther, arguing for four divisions, or embranchements, in the animal world: vertebrates, mollusks, articulates (arthropods), and radiates (animals with radial symmetry). All agreed, however, that there is one unit of classification that seems more fundamental or real than any other: the species. If species are real features of nature and not merely artefacts of human classifiers, then the question arises how they came into being. The only possible naturalistic answer—that they evolved over millions of years from more-primitive forms—leads immediately to a severe difficulty: how is it possible to define the species to which a given animal belongs in such a way that it does not include every evolutionary ancestor the animal had but at the same time is not arbitrary? At what point in the animal’s evolutionary history does the species begin? This is the “ species problem, ” and it is clearly as much philosophical as it is scientific.

The problem in fact involves two closely related issues: (1) how the notion of a species is to be defined, and (2) how species are supposedly more fundamental or real than other taxonomic categories. The most straightforward definition of species relies on morphology and related features: a species is a group of organisms with certain common features, such as hairlessness, bipedalism, and rationality. Whatever features the definition of a particular species may include, however, there will always be animals that seem to belong to the species but that lack one or more of the features in question. Children and the severely retarded, for example, lack rationality, but they are undeniably human. One possible solution, which has roots in the work of the French botanist Michel Adanson (1727-1806) and was advocated by William Whewell in the 19th century, is to define species in terms of a group of features, a certain number of which is sufficient for membership but no one of which is necessary.

Another definition, advocated in the 18th century by Buffon, emphasizes reproduction. A species is a group of organisms whose members interbreed and are reproductively isolated from all other organisms. This view was widely accepted in the first half of the 20th century, owing to the work of the founders of the synthetic theory of evolution (see above Form and function) , especially the Ukrainian-born American geneticist Theodosius Dobzhansky (1900-75) and the German-born American biologist Ernst Mayr (1904-2005). However, it encounters difficulties with asexual organisms and with individual animals that happen to be celibate. Although it is possible to expand the definition to take into account the breeding partners an animal might have in certain circumstances, the philosophical complications entailed by this departure are formidable. The definition also has trouble with certain real-world examples, such as spatial distributions of related populations known as “rings of races.” In these cases, any two populations that abut each other in the ring are able to interbreed, but the populations that constitute the endpoints of the ring cannot—even though they, too, abut each other. Does the ring constitute one species or two? The same problem arises with respect to time: since each generation of a given population is capable of interbreeding with members of the generation that immediately preceded it, the two generations belong to the same species. If one were to trace the historical chain of generations backward, however, at some point one would arrive at what seems to be a different species. Even if one were reluctant to count very distant generations as different species, there would still be the obvious problem that such generations, in all likelihood, would not be able to interbreed.

The second issue, what makes the notion of a species fundamental, has elicited several proposals. One popular view is that species are not groups but individuals, rather like super-organisms. The particular organisms identified as their “members” should really be thought of as their “parts.” Another suggestion relies on what William Whewell called a “ consilience of inductions. ” It makes a virtue of the plurality of definitions of species, arguing that the fact that they all coincide indicates that they are not arbitrary; what they pick out must be real.

Neither of these proposals, however, has been universally accepted. Regarding species as super-organisms, it is not clear that they have the kind of internal organization necessary to be an individual. Also, the idea seems to have some paradoxical consequences. When an individual organism dies, for example, it is gone forever. Although one could imagine reconstructing it in some way, at best the result would be a duplicate, not the original organism itself. But can the same be said of a species? The Stegosaurus is extinct, but if a clone of a stegosaur were made from a fossilized sample of DNA, the species itself, not merely a duplicate of the species, would be created. Moreover, it is not clear how the notion of a scientific law applies to species conceived as individuals. On a more conventional understanding of species, one can talk of various scientific laws that apply to them, such as the law that species that break apart frequently into geographically isolated groups are more likely to speciate, or evolve into new species. But no scientific law applies only to a single individual. If the species Homo sapiens is an individual, therefore, no law applies to it. It follows that social science, which is concerned only with human beings, is impossible.

Regarding the pluralist view, critics have pointed out that in fact the various definitions of species do not coincide very well. Consider, for example, the well-known phenomenon of sibling species, in which two or more morphologically very similar groups of organisms are nevertheless completely reproductively isolated (i.e., incapable of interbreeding). Is one to say that such species are not real?

The fact that no current proposal is without serious difficulties has prompted some researchers to wonder whether the species problem is even solvable. This, in turn, raises the question of whether it is worth solving. Not a few critics have pointed out that it concerns only a very small subsection of the world’s living organisms—the animals. Many plants have much looser reproductive barriers than animals do. And scientists who study microorganisms have pointed out that regularities regarding reproduction of macroorganisms often have little or no applicability in the world of the very small. Perhaps, therefore, philosophers of biology might occupy their thoughts and labours more profitably elsewhere.

The modern method of classifying organisms was devised by Swedish biologist Carl von Linné, better known by his Latin name Carolus Linnaeus (1707-78). He proposed a system of nested sets, with all organisms belonging to ever-more general sets, or “taxa,” at ever-higher levels, or “categories,” the higher-level sets including the members of several lower-level sets. There are seven basic categories, and each organism therefore belongs to at least seven taxa. At the highest category, kingdom, the wolf belongs to the taxon Animalia. At lower and more specific categories and taxa, it belongs to the phylum Chordata, the class Mammalia, the order Carnivora, the family Canidae, the genus Canis, and the species Canis lupus (or C. lupus).

The advantage of a system like this is that a great deal of information can be packed into it. The classification of the wolf, for example, indicates that it has a backbone (Chordata), that it suckles its young (Mammalia), and that it is a meat eater (Carnviroa). What it seems to omit is any explanation of why the various organisms are similar to or different from each other. Although the classification of dogs (C. familiaris) and wolves (C. lupus) shows that they are very much alike—they belong to the same genus and all higher categories—it is not obvious why this should be so. Although many researchers, starting with Linnaeus himself, speculated on this question, it was the triumph of Darwin to give the full answer: namely, dogs and wolves are similar because they have similar ancestral histories. Their histories are more similar to each other than either is to the history of any other mammalian species, such as Homo sapiens (human beings), which in turn is closer to the history of other chordate species, such as Passer domesticus (house sparrows). Thus, generally speaking, the taxa of the Linnaean system represent species of organisms whose histories are similar; and the more specific the taxon, the more similar the histories.

During the years immediately following the publication of On the Origin of Species, there was intense speculation about ancestral histories, though with little reference to natural selection. Indeed, the mechanism of selection was considered to be in some respects an obstacle to understanding ancestry, since relatively recent adaptations could conceal commonalities of long standing. In contrast, there was much discussion of the alleged connections between paleontology and embryology, including the notorious and often very inaccurate biogenetic law proposed by the German zoologist Ernst Haeckel (1834-1919): ontogeny (the embryonic development of an individual) recapitulates phylogeny (the evolutionary history of a taxonomic group). With the development of the synthetic theory of evolution in the early 20th century, classification and phylogeny-tracing ceased to be pursued for their own sake, but the theoretical and philosophical underpinnings of classification, known as systematics, became a topic of great interest.

The second half of the 20th century was marked by a debate between three main schools. In the first, traditional evolutionary taxonomy, classification was intended to represent a maximum of evolutionary information. Generally this required that groupings be “monophyletic,” or based solely on shared evolutionary history, though exceptions could occur and were allowed. Crocodiles, for example, are evolutionarily closer to birds than to lizards, but they were classified with lizards rather than birds on the basic of physical and ecological similarity. (Groups with such mixed ancestry are called “paraphyletic.”) Obviously, the determination of exceptions could be quite subjective, and the practitioners of this school were open in calling taxonomy as much an art as a science.

The second school was numerical, or phenetic, taxonomy. Here, in the name of objectivity, one simply counted common characters without respect to ancestry, and divisions were made on the basis of totals: the more characters in common, the closer the classification. The shared history of crocodiles and birds was simply irrelevant. Unfortunately, it soon appeared that objectivity is not quite so easily obtained. Apart from the fact that information that biologists might find important—like ecological overlap—was ignored, the very notion of similarity required subjective decisions, and the same was even more true of the idea of a “character.” Is the fact that humans share four limbs with the horses to be taken as one character or four? Since shared ancestry was irrelevant to this approach, it was not clear why it should classify the extinct genus Eohippus (dawn horse), which had five digits, with the living genus Equus, which has only one. Why not with human beings, who also have five digits? The use of computers in the tabulation of common characters was and remains very important, but the need for a systematic theory behind the taxonomy was apparent.

The third school, which has come to dominate contemporary systematics, is based on work by the German zoologist Willi Hennig (1913-76). Known as phylogenetic taxonomy, or cladism, this approach infers shared ancestry on the basis of uniquely shared historical (or derived) characteristics, called “ synapomorphies. ” Suppose, for example, that there is an original species marked by character A, and from this three species eventually evolve. The original species first breaks into two successor groups, in one of which A evolves into the character a; this successor group then breaks into two daughter groups, both of which have a. The other original successor group retains A throughout, with no further division. In this case, a is a synapomorphy, since the two species with a evolved from an ancestral species that had a uniquely. Therefore, the possessors of a must be classified more closely to each other than to the third species. Crocodiles and birds are classified together, before they can be jointly linked to lizards.

Both the theory and the practice of cladism raise a number of important philosophical issues (indeed, scientists explicitly turn to philosophy more frequently in this field than in any other in biology). At the practical level, how does one identify synapomorphies? Who is to say what is an original ancestral character and what a derived character? Traditional methods require one to turn to paleontology and embryology, and although there are difficulties with these approaches, - because of the incomplete record can one be sure that one can truly say that something is derived? - they are both still used. Why does one classify Australopithecus africanus with Homo sapiens rather than with Gorilla gorilla—even though the brain sizes of the second and third are closer to each other than to the brain size of the first? Because the first and second share characters that evolved uniquely to them and not to gorillas. The fossil known as Lucy, Australopithecus afarensis, shows that walking upright is a newly evolved trait, a synapomorphy, that is shared uniquely by Australopithecus and Homo sapiens.

A more general method of identifying synapomorphies is the comparative method, in which one compares organisms against an outgroup, which is known to be related to the organisms—but not as closely to them as they are to each other. If the outgroup has character A, and, among three related species, two have character B and only one A, then B is a synapomorphy for the two species, and the species with A is less closely related.

Clearly, however, a number of assumptions are being relied upon here, and critics have made much of them. How can one know that the outgroup is in fact closely, but not too closely, related? Is there not an element of circularity at play here? The response to this charge is generally that there is indeed circularity, but it is not vicious. One assumes something is a suitable outgroup and works with it, over many characters. If consistency obtains, then one continues. If contradictions start to appear (e.g., the supposed synapomorphies do not clearly delimit the species one is trying to classify), then one revises the assumptions about the outgroup.

Another criticism is that it is not clear how one knows that a shared character, in this case B, is indeed a synapomorphy. It could be that the feature independently evolved after the two species split—in traditional terminology, it is a “homoplasy” rather than a “homology”—in which case the assumption that B is indicative of ancestry would clearly be false. Cladists usually respond to this charge by appealing to simplicity. It is simpler to assume that shared characters tell of shared ancestry rather than that there was independent evolution to the same ends. They also have turned in force to the views of Karl Popper, who explained the theoretical virtue of simplicity in terms of falsifiability: all genuine scientific theories are falsifiable, and the simpler a theory is (other things equal), the more readily it can be falsified.

Another apparent problem with cladism is that it seems incapable of capturing certain kinds of evolutionary relationships. First, if there is change within a group without speciation—a direct evolution of Homo habilis to Homo erectus, for example — then it would not be recorded in a cladistic analysis. Second, if a group splits into three daughter groups at the same time, this too would not be recorded, because the system works in a binary fashion, assuming that all change produces two and only two daughter groups.

Some cladists have gone so far as to turn Hennig’s theory on its head, arguing that cladistic analysis as such is not evolutionary at all. It simply reveals patterns, which in themselves do not represent trees of life. Although this “transformed” (or “pattern”) cladism has been much criticized (not least because it seems to support creationism, inasmuch as it makes no claims about the causes of the nature and distribution of organisms), in fact is it very much in the tradition of the phylogeny tracers of the early 20th century. Although those researchers were in fact all evolutionists (as are all transformed cladists), their techniques, as historians have pointed out, were developed in the first part of the 19th century by German taxonomists, most of whom entirely rejected evolutionary principles. The point is that a theory of systematics may not in methodology be particularly evolutionary, but this is not to say that its understanding or interpretation is not evolutionary through-and-through.

Modern discussion of the structure of evolutionary theory was started by the American philosopher Morton O. Beckner (1928-2001), who argued that there are many more or less independent branches—including population genetics, paleontology, biogeography, systematics, anatomy, and embryology—which nevertheless are loosely bound together in a “net,” the conclusions of one branch serving as premises or insights in another. Assuming a hypothetico-deductive conception of theories and appealing also to Darwin’s intentions, the British philosopher Michael Ruse in the early 1970s claimed that evolutionary theory is in fact like a “fan,” with population genetics—the study of genetic variation and selection at the population level—at the top and the other branches spreading out below. The other branches are joined to each other primarily through their connection to population genetics, though they also borrow and adapt conclusions, premises, and insights from each other. Population genetics, in other words, is part of the ultimate causal theory of all branches of evolutionary inquiry, which are thus brought together in a united whole.

The kind of picture offered by Ruse has been challenged in two ways. The first questions the primacy of population genetics. Ruse himself allowed that in fact the formulators of the synthetic theory of evolution used population genetics in a very casual and non-formal way to achieve their ends. As an ornithologist and systematicist, Ernst Mayr, in his Systematics and the Origin of Species (1942), hardly thought of his work as deducible from the principles of genetics.

The second challenge has been advanced by paleontologists, notably Stephen Jay Gould (1941-2002), who argue that population genetics is useful—indeed, all-important—for understanding relatively small-scale or short-term evolutionary changes but that it is incapable of yielding insight into large-scale or long-term ones, such as the Cambrian explosion. One must turn to paleontology in its own right to explain these changes, which might well involve extinctions brought about by extraterrestrial forces (e.g., comets) or new kinds of selection operating only at levels higher than the individual organism (see above Levels of selection) . Gould, together with fellow paleontologist Niles Eldredge, developed the theory of “ punctuated equilibrium, ” according to which evolution occurs in relatively brief periods of significant and rapid change followed by long periods of relative stability, or “stasis.” Such a view could never have been inferred from studies of small-scale or short-term evolutionary changes; the long-term perspective taken by paleontology is necessary. For Gould, therefore, Beckner’s net metaphor would be closer to the truth.

A separate challenge to the fan metaphor was directed at the hypothetico-deductive conception of scientific theories. Supporters of the “ semantic” conception argue that scientific theories are rarely, if ever, hypothetico-deductive throughout, and that in any case the universal laws presupposed by the hypothetico-deductive model are usually lacking. Especially in biology, any attempt to formulate generalities with anything like the necessity required of natural laws seems doomed to failure—there are always exceptions. Hence, rather than thinking of evolutionary theory as one unified structure grounded in major inductive generalizations, one should think of it (as one should think of all scientific theories) as being a cluster of models, formulated independently of experience and then applied to particular situations. The models are linked because they frequently use the same premises, but there is no formal requirement that this be so. Science—evolutionary theory in particular—is less grand system building and more like motor mechanics. There are certain general ideas usually applicable in any situation, but, in the details and in getting things to work, one finds particular solutions to particular problems. Perhaps then the net metaphor, if not quite as Beckner conceived it, is a better picture of evolutionary theorizing than the fan metaphor. Perhaps an even better metaphor would be a mechanic’s handbook, which would lay out basic strategies but demand unique solutions to unique problems.

Darwin always understood that an animal’s behaviour is as much a part of its repertoire in the struggle for existence as any of its physical adaptations. Indeed, he was particularly interested in social behaviour, because in certain respects it seemed to contradict his conception of the struggle as taking place between, and for the sole benefit of, individuals. As noted above, he was inclined to think that nests of social insects should be regarded as superorganisms rather than as groups of individuals engaged in cooperative or (at times) self-sacrificing, or altruistic, behaviour.

In the century after the publication of On the Origin of Species the biological study of behaviour was slow to develop. In part this was because behaviour in itself is much more difficult to record and measure than physical characteristics. Experiment also is particularly difficult, for it is notoriously true that animals change their behaviours in artificial conditions. Another factor that hampered the study of behaviour was the rise of the social sciences in the early 20th century. Because these disciplines were overwhelmingly oriented toward behaviourism, which by and large restricted itself to the overt and observable, the biological and particularly evolutionary influences on behaviour tended to be discounted even before investigation was begun.

An important dissenting tradition was represented by the European practitioners of ethology, who insisted from the 1920s that behaviour must be studied in a biological context. The development in the 1960s of evolutionary explanations of social behaviour in individualistic terms (see above Levels of selection) led to increased interest in social behaviour among evolutionary theorists and eventually to the emergence of a separate field devoted to its study, sociobiology, as well as to the growth of allied subdisciplines within psychology and philosophy. The basic ideas of the movement were formulated in Sociobiology: The New Synthesis (1975), by Edward O. Wilson, and popularized in The Selfish Gene (1976), by the British biologist Richard Dawkins.

These works, Wilson’s in particular, were highly controversial, mainly (though not exclusively) because the theories they propounded applied to humans. Having surveyed social behaviour in the animal world from the most primitive forms up to primates, Wilson argued that Homo sapiens is part of the evolutionary world in its behaviour and culture. Although he did allow that experience can have effects, the legacy of the genes, he argued, is much more important. In male-female relationships, in parent-child interactions, in morality, in religion, in warfare, in language, and in much else, biology matters crucially.

Many philosophers and social scientists, notably Philip Kitcher, Richard Lewontin, and Stephen Jay Gould, rejected the new sociobiology with scorn. The claims of the sociobiologists were either false or unfalsifiable. Many of their conjectures had no more scientific substance than Rudyard Kipling’s Just So Stories for children, such as How the Camel Got His Hump and How the Leopard Got His Spots. Indeed, their presumed genetic and evolutionary explanations of a wide variety of human behaviour and culture served in the end as justifications of the social status quo, with all its ills, including racism, sexism, homophobia, materialism, violence, and war. The title of Kitcher’s critique of sociobiology, Vaulting Ambition, is an indication of the attitude that he and others took to the new science.

Although there was some truth to these criticisms, sociobiologists since the 1970s have made concerted efforts to address them. In cases where the complaint had to do with falsifiability or testability, newly developed techniques of genetic testing have proved immensely helpful. Many sociobiological claims, for example, concern the behaviour of parents. One would expect that, in populations in which males compete for females and (as in the case of birds) also contribute toward the care of the young, the efforts of males in that regard would be tied to reproductive access and success. (In other words, a male who fathered four offspring would be expected to work twice as hard in caring for them as a male who fathered only two offspring.) Unfortunately, it was difficult, if not impossible, to verify paternity in studies of animal populations until the advent of genetic testing in the 1990s. Since then, sociobiological hypotheses regarding parenthood have been able to meet the standard of falsifiability insisted on by Karl Popper and others, and in many cases they have turned out to be well-founded.

Regarding social and ethical criticisms, sociobiologists by and large have had no significant social agendas, and most have been horrified at the misuse that has sometimes been made of their work. They stress with the critics that differences between the human races, for example, are far less significant than similarities, and in any case whatever differences there may be do not in themselves demonstrate that any particular race is superior or inferior to any other. Similarly, in response to criticism by feminists, sociobiologists have argued that merely pointing out genetically-based differences between males and females is not in itself sexist. Indeed, one might argue that not to recognize such differences can be morally wrong. If boys and girls mature at different rates, then insisting that they all be taught in the same ways could be wrong for both sexes. Likewise, the hypothesis that something like sexual orientation is under the control of the genes (and that there is a pertinent evolutionary history underlying its various forms) could help to undermine the view among some social conservatives that homosexuals deserve blame for “choosing” an immoral lifestyle.

Moreover, it can be argued with some justice that “just so stories” in their own right are not necessarily a bad thing. In fact, as Karl Popper himself emphasized, one might say that they are exactly the sort of thing that science needs in abundance—bold conjectures. It is when they are simply assumed as true without verification that they become problematic.

In recent years, the sociobiological study of human beings has placed less emphasis on behaviour and more on the supposed mental faculties or properties on which behaviour is based. Such investigations, now generally referred to as “ evolutionary psychology, ” are still philosophically controversial, in part because it is notoriously difficult to specify the sense in which a mental property is innate and to determine which properties are innate and which are not. As discussed below, however, some philosophers have welcomed this development as providing a new conceptual resource with which to address basic issues in epistemology and ethics.

Because the evolutionary origins and development of the human brain must influence the nature, scope, and limits of the knowledge that human beings can acquire, it is natural to think that evolutionary theory should be relevant to epistemology, the philosophical study of knowledge. There are two major enterprises in the field known as “evolutionary epistemology”: one attempts to understand the growth of collective human knowledge by analogy with evolutionary processes in the natural world; the other attempts to identify aspects of human cognitive faculties with deep evolutionary roots and to explain their adaptive significance.

The first project is not essentially connected with evolutionary theory, though as a matter of historical fact those who have adopted it have claimed to be Darwinians. It was first promoted by Darwin’s self-styled “bulldog,” T.H. Huxley (1825-95). He argued that, just as the natural world is governed by the struggle for existence, resulting in the survival of the fittest, so the world of knowledge and culture is directed by a similar process. Taking science as a paradigm of knowledge (now a nearly universal assumption among evolutionary epistemologists), he suggested that ideas and theories struggle against each other for adoption by being critically evaluated; the fittest among them survive, as those that are judged best are eventually adopted.

In the 20th century the evolutionary model of knowledge production was bolstered by Karl Popper’s work in the philosophy of science. Popper argued that science—the best science, that is—confronts practical and conceptual problems by proposing daring and imaginative hypotheses, which are formulated in a “context of discovery” that is not wholly rational, involving social, psychological, and historical influences. These hypotheses are then pitted against each other in a process in which scientists attempt to show them false. This is the “context of justification,” which is purely rational. The hypotheses that remain are adopted, and they are accepted for as long as no falsifying evidence is uncovered.

Critics of this project have argued that it overlooks a major disanalogy between the natural world and the world of knowledge and culture: whereas the mutations that result in adaptation are random—not in the sense of being uncaused but in the sense of being produced without regard to need—there is nothing similarly random about the processes through which new theories and ideas are produced, notwithstanding Karl Popper’s belittling of the “context of discovery.” Moreover, once a new idea is in circulation, it can be acquired without the need of anything analogous to biological reproduction. In the theory of the British zoologist Richard Dawkins, such ideas, which he calls “ memes, ” are the cultural equivalent of genes.

The second major project in evolutionary epistemology assumes that the human mind, no less than human physical characteristics, has been formed by natural selection and therefore reflects adaptation to general features of the physical environment. Of course, no one would argue that every aspect of human thinking must serve an evolutionary purpose. But the basic ingredients of cognition—including fundamental principles of deductive and inductive logic and of mathematics, the conception of the physical world in terms of cause and effect, and much else—have great adaptive value, and consequently they have become innate features of the mind. As the American philosopher Willard Van Orman Quine (1908-2000) observed, those proto-humans who mastered inductive inference, enabling them to generalize appropriately from experience, survived and reproduced, and those who did not, did not. The innate human capacity for language use may also be viewed in these terms.

In evolutionary ethics, as in evolutionary epistemology, there are two major undertakings. The first concerns normative ethics, which investigates what actions are morally right or morally wrong; the second concerns metaethics, or theoretical ethics, which considers the nature, scope, and origins of moral concepts and theories.

The best known traditional form of evolutionary ethics is social Darwinism, though this view owes far more to Herbert Spencer than it does to Darwin himself. It begins with the assumption that in the natural world the struggle for existence is good, because it leads to the evolution of animals that are better adapted to their environments. From this premise it concludes that in the social world a similar struggle for existence should take place, for similar reasons. Some social Darwinists have thought that the social struggle also should be physical—taking the form of warfare, for example. More commonly, however, they assumed that the struggle should be economic, involving competition between individuals and private businesses in a legal environment of laissez faire. This was Spencer’s own position.

As might be expected, not all evolutionary theorists have agreed that natural selection implies the justice of laissez-faire capitalism. Alfred Russel Wallace (1823-1913), who advocated a group-selection analysis, believed in the justice of actions that promote the welfare of the state, even at the expense of the individual, especially in cases in which the individual is already well-favoured. The Russian theorist of anarchism Peter Kropotkin (1842-1921) argued that selection proceeds through cooperation within groups (“mutual aid”) rather than through struggle between individuals. In the 20th century, the British biologist Julian Huxley (1887-1975), the grandson of T.H. Huxley, thought that the future survival of humankind, especially as the number of humans increases dramatically, would require the application of science and the undertaking of large-scale public works, such as the Tennessee Valley Authority. More recently, Edward O. Wilson has argued that, because human beings have evolved in symbiotic relationship with the rest of the living world, the supreme moral imperative is biodiversity.

From a metaethical perspective, social Darwinism was famously criticized by the British philosopher G.E. Moore (1873-1958). Invoking a line of argument first mooted by the Scottish philosopher David Hume (1711-76), who pointed out the fallaciousness of reasoning from statements of fact to statements of moral obligation (from an “is” to an “ought”), Moore accused the social Darwinists of committing what he called the “ naturalistic fallacy, ” the mistake of attempting to infer nonnatural properties (being morally good or right) from natural ones (the fact and processes of evolution). Evolutionary ethicists, however, were generally unmoved by this criticism, for they simply disagreed that deriving moral from nonmoral properties is always fallacious. Their confidence lay in their commitment to progress, to the belief that the products of evolution increase in moral value as the evolutionary process proceeds—from the simple to the complex, from the monad to the man, to use the traditional phrase. Another avenue of criticism of social Darwinism, therefore, was to deny that evolution is progressive in this way. T.H. Huxley pursued this line of attack, arguing that humans are imperfect in many of their biological properties and that what is morally right often contradicts humans’ animal nature. In the late 20th century, Stephen Jay Gould made similar criticisms of attempts to derive moral precepts from the course of evolution.

The chief metaethical project in evolutionary ethics is that of understanding morality, or the moral impulse in human beings, as an evolutionary adaptation. For all the intraspecific violence that human beings commit, they are a remarkably social species, and sociality, or the capacity for cooperation, is surely adaptively valuable, even on the assumption that selection takes place solely on the level of the individual. Unlike the social insects, human beings have too variable an environment and too few offspring (requiring too much parental care) to be hard-wired for specific cooperative tasks. On the other hand, the kind of cooperative behaviour that has contributed to the survival of the species would be difficult and time-consuming to achieve through self-interested calculation by each individual. Hence, something like morality is necessary to provide a natural impulse among all individuals to cooperation and respect for the interests of others.

Although this perspective does not predict specific moral rules or values, it does suggest that some general concept of distributive justice (i.e., justice as fairness and equity) could have resulted from natural selection; this view, in fact, was endorsed by the American social and political philosopher John Rawls (1921-2002). It is important to note, however, that demonstrating the evolutionary origins of any aspect of human morality does not by itself establish that the aspect is rational or correct.

An important issue in metaethics—perhaps the most important issue of all—is expressed in the question, “Why should I be moral?” What, if anything, makes it rational for an individual to behave morally (by cooperating with others) rather than purely selfishly? The present perspective suggests that moral behaviour did have an adaptive value for individuals or groups (or both) at some stages of human evolutionary history. Again, however, this fact does not imply a satisfactory answer to the moral skeptic, who claims that morality has no rational foundation whatsoever; from the premise that morality is natural or even adaptive, it does not follow that it is rational. Nevertheless, evolutionary ethics can help to explain the persistence and near-universality of the belief that there is more to morality than mere opinion, emotion, or habit. Hume pointed out that morality would not work unless people thought of it as “real” in some sense. In the same vein, many evolutionary ethicists have argued that the belief that morality is real, though rationally unjustified, serves to make morality work; therefore, it is adaptive. In this sense, morality may be an illusion that human beings are biologically compelled to embrace.

One of the major developments in Anglo-American philosophy in the last three decades of the 20th century was a turn toward social issues in areas outside ethics and political philosophy, including the philosophy of biology. The logical positivists, with the notable exception of Karl Popper, did not think it appropriate for philosophers of science to engage in debate on social issues; this was the domain of preachers and politicians and the otherwise publicly committed. Today, in contrast, it is thought important—if not mandatory—for philosophers of science in general, and philosophers of biology in particular, to think beyond the strict limits of their discipline and to see what contributions they can make to issues of importance in the public domain.

One of the first attempts at this kind of public philosophizing by philosophers of biology occurred in response to the development in the 1970s of techniques of recombinant DNA (rDNA), which enabled, among other things, the insertion of genes from one or more species into host organisms of very different species. There was much concern that such experiments would lead to the fabrication of monsters. Others worried about the threats that could be posed to humankind and the environment by genetically mixed or modified organisms. Even worse was the possibility that the techniques could be used by despots to manufacture biological weapons cheaply and quickly.

It soon became evident, however, that much of this concern was the result of ignorance, even on the part of biologists. Epidemiologists, for example, demonstrated that the dangers that rDNA research could pose to human populations were much overblown. But there were still (and remain) issues of considerable interest. Echoing a traditional position in evolutionary ethics, opponents claimed that rDNA techniques must be unethical because they contravene the “wisdom of the genes.” Something that nature has wrought must be good and should not be lightly discarded or altered by human technology. But although there are obviously important thoughts included in this line of critique—if one does alter nature, then too often unexpected and unwanted results obtain—the simple appeal to nature or to evolution shows very little (as critics of social Darwinism have long maintained). To revert to the position of T.H. Huxley, often what should be done is exactly the opposite of what evolution has done. Sickle-cell anemia, for example, comes about as the result of a genetic, evolutionarily promoted defense against anemia. Is the attempt to cure sickle-cell anemia therefore morally wrong?

The 1990s were marked by increasing development and application of the techniques of molecular biology. The major scientific-technological undertaking of the decade was of course the Human Genome Project (HGP), which aimed to map the entire human genetic makeup; the initial sequencing of the genome was completed in 2000. The success of the HGP raised important social and ethical issues, particularly regarding the effects of prejudice. Suppose that the genes associated with an inherited disease—such as Huntington disease, which leads to insanity and early death—are identified. Should a healthy person who carries these genes be denied medical insurance? If not, should private, for-profit insurance companies be required to insure such people, or should the state assume the obligation?

Other issues have arisen in connection with cloning and stem cell research. Various religious and conservative groups take extreme objection to the manipulation of reproductive cells, whether for the end of producing new human beings (or other animals) or for the end of aiding already existing ones. The American bioethicist Leon Kass, for example, argues that any attempt to change or direct the natural reproductive processes is morally wrong, because it is an essential part of the human condition to accept whatever nature produces, however inconvenient or unpleasant it may be.

There are epistemological as well as ethical issues at stake here. How exactly should cloning be defined? Is it wrong (or not wrong) in itself, or only by virtue of its consequences? What about identical twins, who seem to be the result of natural cloning, without human aid? Should one think that, because they are not unique, they are in some sense less worthy as human beings? Or does environment and training make them, and any other clone, unique anyway?

It is often thought that differences in moral intuitions regarding these questions stem from the rivalry between the utilitarian and Kantian ethical traditions—the former judging actions in terms of their consequences, in particular the amount of happiness they tend to promote, the latter stressing good intentions and the importance of treating people as ends rather than as means. Conventionally, then, utilitarians are thought to favour cloning and stem-cell research, and Kantians are assumed to oppose it. The divisions are not quite this neat, however, since some utilitarians think that modern applications of molecular biology may do more harm than good, and some Kantians think that such applications are well motivated and treat the individuals they are designed to help as ends and not as means.

The introduction of genetically modified (GM) foods, chiefly plants, in the 1990s provoked a violent and complex debate involving agricultural and pharmaceutical corporations; scientists; environmental, consumer, and public-health organizations; and representatives of indigenous and farming communities in the developing world. Proponents, largely in the United States (where GM foods are widely used), argued that the use of crops that have been genetically modified to resist various pests or diseases can significantly increase harvests and decrease dependence on pesticides that are poisonous to human beings. Opponents contend that genetically modified plant species may create catastrophic changes in the ecosystems in which they are introduced or to which they may travel and that the long-term health effects of consuming GM foods are unknown. Also, if major firms in the West succeed in patenting such genetic modifications, the independence or self-sufficiency of farming communities in the developing world could be undermined. Consideration of many of these issues can be usefully informed by philosophical analysis. Indeed, some of the theoretical discussions covered in earlier sections of this article are directly relevant. How does one define an organism or a species? When is something that has been changed artificially no longer truly what it was? Is function most significant? If changing an adaptation of a species more important than changing simply a by-product—a “spandrel”?

There are also interesting and as-yet-little-discussed questions about balance and equilibrium in analyses of organisms in their native habitats. The ancient idea of a balance of nature has deep roots in Christian theology. But it has been transported—some would say with little change—into modern thinking about equilibrium in nature. Are these modern claims—for example, the well-known theorizing of Robert MacArthur and E.O. Wilson regarding the balancing effects of immigration, emigration, and extinction on islands—genuinely empirical assertions, or are they, as some critics claim, so vacuous as to be little more than tautologies?

Obviously, answers to questions such as these have important implications in areas far removed from purely theoretical aspects of the philosophy of biology. This application of the discipline to social and ethical issues of public concern should be acknowledged and welcomed. On the other hand, no one would attempt to justify the philosophy of biology solely on the basis of its practical application and relevance. In its own right, it is one of the most vibrant, innovative, and exciting fields of contemporary philosophy.

Die Philosophie der Biologie ist in vielen Fällen daran beteiligt, Forschungsfragen in der Biologie mit praktischer Bedeutung zu klären und zu lösen. Dabei geht es neben allgemeinen Probleme der Wissenschaftstheorie oft auch um eine Klärung der Standpunkte, Theorien und Begriffe innerhalb der Biologie, aber auch um Kontroversen über die gesellschaftlichen Auswirkungen biologischer Erkenntnisse und Technologien.

In der zweiten Hälfte des 20. Jahrhunderts erhielt die Philosophie der Biologie einen großen Bedeutungsschub, der mit der wissenschaftlich-technischen Entwicklung in der Biologie, aber auch in der Entwicklung der Gesellschaft begründet wird. Die Naturschutz­debatte und das Aufkommen der Diskussion um das richtige Verhältnis zur Ökologie lenkte die Aufmerksamkeit auf die Frage der anthropogenen Einflüsse auf das Naturgeschehen. Die Technisierung und Ökonomisierung der Biologie in der Biotechnologie und Gentechnologie fordert dagegen ethische, ontologische und epistemologische Antworten. Und zuletzt stellen die Ergebnisse der Neurobiologie neue Fragen nach einer technischen Anwendbarkeit und nach dem Menschenbild innerhalb der Biologie.

Philosophen, die sich mit biologischen Themen beschäftigen, sind oft auch selbst ausgebildete Biologen. Ebenso haben mehrere Biologen wie Ernst Mayr, Richard Dawkins und Michael Ghiselin bedeutende Beiträge zur Philosophie der Biologie geleistet. Seit 1985 erscheint die Zeitschrift „Biology und Philosophy“.

Die Philosophie der Biologie konzentrierte sich lange auf die Evolutionsbiologie und den Status der Organismen und vernachlässigte eher die physikalisch-chemisch orientierten Zweige der Biologie wie die Molekularbiologie. Andererseits bereichert die Philosophie der Biologie so auf vielfältige Weise weite Bereiche der Philosophie selbst. Wogegen die technisch und physikalisch-chemisch geprägten Disziplinen und ihre philosophische Reflexion in den meisten Fällen schon durch allgemeinere wissenschaftstheoretische Arbeiten abgedeckt sind. Konzepte und Bedingungen in der Biologie, die sich von allgemeinen wissenschaftstheoretischen Fragestellungen abheben, sind beispielsweise die Dualität von Phänotyp und Genotyp, das historische Element, die Einzigartigkeit und die vielfältige Organisation und Komplexität vieler Untersuchungsobjekte, aber auch der Begriff des Lebens selbst, die Teleologie (funktionale Zweckbestimmung) und die Natürliche Selektion.Nachdem die Physik und insbesondere die Mechanik jahrhundertelang die Modelle und Methoden der Wissenschaftstheorie geprägt haben, stellt sich nun die Frage, welchen Status die Biologie in der Philosophie der Wissenschaften hat. Diese Frage und die Antworten darauf betreffen alle Bereiche des Umgangs mit der Biologie und damit letztlich auch Fragen der Logik, Methodologie und der konkreten Forschungspraxis.

Die Philosophie der Biologie betreibt meistens die Reflexion biologischer Begriffe, Theorien und Methoden - also die Arbeit von Philosophen zum erfolgreichen Umgang mit Inhalten der biologischen Forschung. Umgekehrt sind über diese Beschäftigung auch viele Einflüsse auf allgemeinere Themen und Bereiche der Philosophie deutlich geworden. Die bekanntesten Beispiele sind die Evolutionäre Erkenntnistheorie für die Epistemologie, die Bioethik, aber auch ein wesentlicher Teil der aktuellen anthropologischen Themenfelder. Ebenso stellt die Biophilosophie mit ihren pluralistischen, ökologischen und historischen Ansätzen Herausforderungen an die Wissenschaftstheorie und das Ideal einer Einheitswissenschaft.

Als „Begründer“ der Philosophie der Biologie — und auch der Zoologie — gilt Aristoteles. Seine Philosophie prägte das westliche Denken über Organismen, ihrer Teile und ihrer Organisation bis in die Neuzeit. Ausgenommen von den „natürlichen Dingen“ sind bei Aristoteles die unbewegten Dinge, sie sind der Gegenstand der Theologie. Ebenso sind erschaffene Kunstwerke und irreguläre, also zufällige Ereignisse für Aristoteles nicht natürlich und somit kein Objekt seiner Physik. Organismen sind bei Aristoteles organisierte Körper, die einerseits in Organe differenziert, und andererseits durch ihre Funktionen verbunden sind. Die Form der Körper ist ihre Seele (s. a. Entelechie) und somit weder unabhängig noch untrennbar vom Körper. Funktionen der Seele sind beispielsweise essen, atmen, wachsen und schlafen. Mithilfe einer werthaltigen Hierarchie dieser Funktionen kann er eine „Stufenleiter der Natur“ (Scala Naturae) und somit eine Systematik über alle Lebewesen und darüber hinaus erstellen. Die Seele ist es auch, die für jedes Lebewesen einen Zweck bestimmt. Als Causa finalis (Finalursache) wirkt sie direkt in Richtung einer Selbstverwirklichung des Individuums. Aristoteles verankert damit das kosmologische teleologische Prinzip von Platon im konkreten Organismus und damit in der Natur. Ob man deshalb bei Aristoteles von „Teleologie“ sprechen kann, wird in der Philosophie der Biologie unterschiedlich beurteilt.

Das aristotelische Denken war weithin prägend für die abendländische Philosophie. Insbesondere das Prinzip der Finalursache wurde von den christlichen Theologen übernommen und zu einem Gottesbeweis ausgebaut. Erst mit dem mechanistischen Denken der frühen Neuzeit wurde der teleologische Ansatz verdrängt, da er der neu aufkommenden wissenschaftlichen Methode kaum zugänglich war. Eine weitere Abkehr von Aristoteles war die sehr einflussreiche dualistische Trennung in Körper und Geist von René Descartes. Alles was nicht (menschlicher) Geist war, war fortan „Körper“ und somit derselben wissenschaftlichen Methode zugänglich. Die Trennungen, die bei Aristoteles die Seelenfunktionen zwischen den Lebewesen und der nicht-lebenden Welt etabliert haben, wurden bedeutungslos. In der Folge des mechanistischen Denkens drehten sich viele Diskussionen um die Frage, wie die anscheinend offenkundige Andersartigkeit der Lebewesen doch noch erklärt werden könnte.

Ein aufmerksamer Beobachter der biologischen Forschung seiner Zeit war Immanuel Kant.Besonders interessierte ihn die Stellung des Menschen in der Natur, wodurch Modelle und Analogien aus der Biologie für seine Philosophie wichtiger waren als solche aus der Physik. Um die wissenschaftliche Erfahrung überhaupt erst zu ermöglichen, bedient sich Kant der „Zweckmäßigkeit“ als Ordnungs- und Strukturprinzip. Ähnlich wie Aristoteles definiert Kant die Zweckmäßigkeit als inneres Prinzip der Lebewesen selbst, nicht als konstitutives Element der Natur. Erst mit diesem Werkzeug schafft sich die Urteilskraft ein Ordnungsprinzip in der Biologie. Kant nimmt damit in seiner Philosophie selbst biologische Analogien und Modelle auf. Nicht zuletzt deshalb hatte er einen großen Einfluss auf die zeitgenössische Biologie.

Aber das Problem der Abgrenzung zwischen belebter und unbelebter Natur wurde weiterhin heftig diskutiert. Eine „Lebenskraft“ sollte die eigentliche Triebkraft der Höherentwicklung der Arten sein. Um die Jahrhundertwende zum 20. Jahrhundert waren die Ansätze von Hans Driesch (Entelechie), von Henri Bergson (Élan vital) oder Pierre Teilhard de Chardin (Omegapunkt) weit verbreitet und innerhalb und außerhalb der Wissenschaft populär. Weniger, weil man plötzlich keine zielgerichteten Prozesse mehr wahrnahm, sondern weil dieser Ansatz für die aktuelle wissenschaftliche Methode unfruchtbar war, wurde der Niedergang dieser vitalistischen Positionen eingeleitet. Der sogenannte Neovitalismus wurde durch die Arbeiten von Sven Hörstadius und John Runnström letztlich widerlegt. Für die Geschichte der Philosophie der Biologie liefert diese Episode allerdings eine Anschauung, wie allgemeine philosophische Konzeptionen in fachwissenschaftliche Forschungsprogramme übergehen und wie bedeutungsvoll eine klare Trennung in analytische Sätze der Wissenschaftstheorie und empirische Sätze der Biologie ist.

Nach dem beispiellosen Aufschwung der modernen Physik und dem Ende des Vitalismus in der Biologie wurde das Problem der Abgrenzung zur Frage nach den Unterschieden zwischen der Physik und der Biologie. Diskutiert wurden holistische und prozessphilosophische Ansätze. Alfred North Whitehead rückte die (Lebens-)Prozesse der Organismen in den Mittelpunkt seiner Metaphysik, wodurch die Elemente der Physik davon quasi abgeleitet werden. Dieser Organizismus hat in der Folge eher Schwierigkeiten, die Elemente der Physik zu rekonstruieren und entfaltet deshalb bis heute nur wenig konkrete Forschungsarbeit. Samuel Alexander versuchte auch kulturelle Werte in seinen Holismus zu integrieren, wodurch den Lebewesen und insbesondere dem Menschen eine zentrale Vermittlerrolle in den „Ebenen der Existenz“ zukommt. Richard Hönigswald, zugleich Mediziner und Philosoph, entwickelte in den 1920er Jahren im Rahmen seines realistischen Kritizismus eine Konzeption des Organischen als selbstregulierendem System, die mit den moderneren Ansätzen, etwa der evolutionären Erkenntnistheorie, vereinbar ist und auch Ansätze einer Kulturphilosophie aufweist.

Durchgesetzt hat sich aber die mechanistisch-naturalistische Auffassung. Joseph Henry Woodger (The Axiomatic Method in Biology, 1937) versuchte im Sinne des logischen Empirismus der Physikalisten seiner Zeit die Biologie axiomatisch zu rekonstruieren. Es blieb allerdings bei diesem einen Versuch, da die hypothetisch-deduktive Rekonstruktion nur schlecht auf die Disziplinen der Biologie anwendbar ist oder ganz abgelehnt wird. Das Interesse der Philosophie konzentrierte sich zu dieser Zeit auf die Physik und Psychologie. Zwei Entwicklungen in der Mitte des 20. Jahrhunderts, die Formulierung der Synthetischen Evolutionstheorie und die Entwicklungen in der Molekularbiologie, verhalfen dann auch der Philosophie der Biologie zu einem Aufschwung. Spätestens seit den 1970er Jahren hat sie sich als weitverzweigte und ernstzunehmende Teildisziplin der Philosophie etabliert und biologische Fragestellungen gehören heute zu den wichtigsten in der Philosophie.

Die zentrale Bedeutung der Evolutionstheorie für die moderne Biologie wurde schon häufig festgestellt. Unter ihrem Einfluss werden die unbelebte und insbesondere auch die belebte Natur als etwas Veränderliches betrachtet. Gegenüber den essentialistischen Konzepten, die jahrhundertelang das abendländische Denken beherrschten, ist dies ein radikaler Umbruch. {?} War bei Platon noch die überzeitliche „Idee“ das Wirkliche und die konkreten Formen das davon Abgeleitete, so sind im Kontext der biologischen Evolution die konkreten, zeitlichen und veränderlichen Objekte das Reale.

Die Anzahl der betrachteten Objektklassen ist in der Biologie im Verhältnis zu den Naturwissenschaften Physik und Chemie allerdings wesentlich höher. Während die Physik nur einige dutzend Objektklassen wie Sterne, Planeten und Atome kennt, gibt es in den verschiedenen Teildisziplinen der Biologie hunderte — wie Organe, Zellen und Arten. Zudem besitzen sie meist charakteristische Eigenschaften wie Heterogenität, Komplexität und Dynamik. Umso schwieriger ist die Bestimmung des ontologischen und biologischen Status der einzelnen Objektklassen. Es stellt sich auch die Frage, welches die elementaren Objekte im Sinne eines naturwissenschaftlichen Ansatzes sind. So war beispielsweise bei Rudolf Virchow die Zelle der „Elementarorganismus“ und seit der zweiten Hälfte des 20. Jahrhunderts liegt der Fokus auf dem Genom. Die überaus einflussreiche Formulierung eines ontologischen Dualismus bei René Descartes ermöglichte in der Folge auch eine methodologische Trennung in eine materielle und eine geistige Welt. In dieser Tradition erlebte die Physik einen bis dahin unvergleichlichen Aufschwung und die daran orientierte Wissenschaftstheorie ist auf einem materialistischen und naturalistischen Naturverständnis aufgebaut. Allerdings ist das daraus hervorgehende und heute noch vorherrschende Verständnis der Wissenschaftstheorie am sogenannten logischen Empirismus orientiert, der ontologische Fragestellungen unter den Verdacht fruchtloser Spekulation stellt und deshalb weitgehend ausklammert.

Auf der Suche nach grundlegenden Gesetzen und fundamentalen Strukturen versucht man die Eigenschaften und Merkmale aller Forschungsobjekte auf Gesetzmäßigkeiten dieser Strukturen zurückzuführen. Ein ontologischer Reduktionismus, also ein materialistischer Monismus wird heute allgemein akzeptiert. Bei der Betrachtung vieler biologischer Phänomene stößt aber eine Theorienreduktion auf ihre Grenzen, da in verschiedenen Fachbereichen der Biologie wie der Soziobiologie oder der Neurobiologie auch nicht-materielle Phänomene wie Wahrnehmungen, Bewusstsein und der Wille thematisiert werden. Es gibt zwar mehrere Ansätze aber noch keine überzeugenden Lösung für die Beschreibung und Erklärung von intentionalen und phänomenalen Zuständen. Ziel vieler Überlegungen ist ein Physikalismus, der keinen Reduktionismus impliziert, da sonst keine eigenständige biologischen Theorien möglich wären. Ein radikaler mechanistischer Physikalismus („alles ist Physik“) würde dagegen nicht nur die Abgrenzung der Biologie von der Physik unmöglich machen. Für einige Philosophen ist so ein Physikalismus schon allein deshalb unhaltbar, da er den Unterschied zwischen Leben und Tod leugnen würde. Ähnlich verhält es sich mit dem offensichtlichen Unterschied zwischen der unbelebten und belebten Natur. Dieser Gegensatz wurde dadurch entschärft, dass das vorherrschende Organismusmodell in der Biologie vom Maschinenmodell zum Programmmodell wechselte. Die aufkommende Kybernetik und nicht zuletzt die Entdeckung des genetischen Codes rückte funktionalistische Informationsmodelle in den Mittelpunkt. Der hochkomplexe Organismus kann aus dieser Sicht nur als Ganzes funktionieren. Das Nebeneinander von mentalen und materiellen Phänomenen wird heute vor allem anhand von emergenztheoretischen Positionen oder dem Konzept der Selbstorganisation diskutiert.

Die verwendeten Forschungsmethoden in den biologischen Teildisziplinen sind ebenso sehr umfangreich wie die untersuchten Objektklassen. Sie reichen von ingenieurwissenschaftlichen Methoden in der Biotechnologie, narrativen Methoden in den Neurowissenschaften und Einflüssen von historischen Wissenschaften in der Paläontologie bis hin zu bioethischen Fragestellungen. Erklärende Theorien in den Fachbereichen der Biologie haben eher den Charakter allgemeiner Regeln mit vielfältigen Ausnahmen und nur selten den Geltungsanspruch universeller Gesetze, wie sie beispielsweise in der Physik formuliert sind. Wichtigen Gütekriterien an wissenschaftlichen Theorien wie der Erklärungswert, die Prognosefähigkeit und Wiederholbarkeit sind in der Biologie Grenzen gesetzt.

Eine wichtige Fragestellung ist, ob sich Theorien in der Biologie auf physikalische (und chemische) Theorien reduzieren lassen. Der klassische Ansatz einer Theorienreduktion von Ernest Nagel (1961) geht den meisten Philosophen zu weit, da fundamentale Begriffe wie „Leben“ sich nicht reduzieren ließen. Meistens wird keine Notwendigkeit von zusätzlichen physikalisch-chemischen Theorien zur Erklärung und Unterstützung von biowissenschaftlichen Aussagen festgestellt. Beispielsweise bestreitet Philip Kitcher anhand der Gendefinition, dass sich der Genbegriff der klassischen Genetik auf den Genbegriff der Molekularbiologie zurückführen lässt und nennt dafür insbesondere drei Gründe: 1. Die klassische Genetik und die Molekulargenetik entsprechen nicht der Konzeption von Theorien, die Nagel verwendet. 2. Der Begriff „Gen“ aus der klassischen Genetik kann nicht in biochemischen Begriffen beschrieben werden. 3. Jede Ableitung einer Theorie wäre nicht-erklärend. Reduktionisten argumentieren hingegen, dass die Aufgabe, alle biologischen Theorien von physikalisch-chemischen abzuleiten, heute lediglich ein praktisches, aber kein prinzipielles Problem sei.

Dagegen ist eine „Konstitutive Reduktion“, also eine Übernahme der Theorien und Begriffe über die materielle Zusammensetzung von organischen und anorganischen Dingen, in der Biologie und Philosophie allgemein akzeptiert. Weiterhin sind Theorien in der Biologie in der Regel probabilistisch formuliert und beschreiben keinen strikten Determinismus wie in der klassischen Physik oder der Chemie. Es ist aber nicht darüber hinwegzusehen, dass probabilistische Theorien streng reduktionistisch sein können, wie das die Vererbungslehre Mendels zeigt. Sowohl diese, die ja einen Grundpfeiler der Synthese darstellt, als auch die synthetische Evolutionstheorie müssen als reduktionistisch eingestuft werden so lange letztere in der 2. Hälfte des 20. Jahrhunderts an einem strikten Genzentrismus festhielt, der das evolutionäre Geschehen weitgehend auf die Argumentationskette zufällige genetische Mutation — natürliche Selektion und Adaption in der Population zuschnitt. Erst langsam gelingt es der heutigen Evolutionstheorie, sich von engen Sichtweisen dieser Art zu befreien. Die heutige Evolutionstheorie behandelt weit mehr Evolutionsfaktoren als die Syntheses und sieht Evolution immer stärker in interdependenten Zusammenhängen. Diese Öffnung gibt Raum für komplexe Theoriemethoden. Dies wird unter anderen auch damit begründet, dass die betrachteten lebenden Systeme selbst sowie die Beziehungen zwischen ihnen, Prozessen der Natur hochkomplex, offen und individuell sind. So sind biologische Theorien meist mit der Offenheit für Ausnahmen formuliert und beanspruchen nur einen begrenzten Anwendungs- und Gültigkeitsbereich. Dem gegenüber stehen andere Gruppen, die auf der Grundlage erweiterter Vorschläge für die Rahmenbedingungen der Evolution unter Hinzunahme von Entwicklungsmechanismen (Evo-Devo), Umwelteinflüssen, Multilevel-Selektion, Nischenkonstruktion und großer Systemübergänge begonnen haben, das komplexere Szenario mit modernen Methoden zu erklären.

Alle Kennzeichen des Lebendigen, also des Untersuchungsgegenstandes der Biologie, treffen auch auf den Beobachter zu. Deshalb können alle Fragestellungen in der Biologie aus der anthropomorphen Innen- oder der technomorphen Außenperspektive angegangen werden. Von der Wahl der Perspektive hängt auch der Geltungsbereich einer Aussage ab. In einem weiteren Sinn ist jede biologische Forschung an historische, soziale, ökonomische, politische und anthropologische Bedingungen geknüpft. In einem kontextualistischen Ansatz werden Methoden und Erkenntnis der Biologie aus diesen Perspektiven beurteilt. Methodologische Forderungen sind ebenso Folge des Wunsches nach Kontrolle, Manipulation und Prognosen.

Der positivistische logische Empirismus konzentriert sich auf Theorien und Modelle, Beobachtungen und Abbildungen haben dagegen einen geringen Stellenwert. In der Biologie sind diese Methoden allerdings besonders wichtig. Von den handgezeichneten Illustrationen des Ernst Haeckel bis hin zu den aktuellen bildgebenden Verfahren der Neurowissenschaften ist die Rolle der Darstellung in der Biologie immer ein bedeutendes und teilweise kontroverses Thema der philosophischen Reflexion.

Obgleich seiner zentralen Bedeutung in der biologischen Forschung führte das Experiment in der wissenschaftstheoretischen Analyse lange Zeit ein Schattendasein. Es hat sich gezeigt, dass entgegen der üblichen Ansicht, dass Experimente bestehende Theorien testen, die meisten und fruchtbarsten Experimente selbst eine forschende Funktion haben (sogenannte explorative Experimente). Besonders im Kontext biologischer Forschung stellt sich das Experiment als ein künstlicher, manipulativer Eingriff in das Naturgeschehen dar. Die Natur wird dabei reduziert, separiert und in der Regel „apparativ vermittelt“ So sind beispielsweise mit dem Elektronenmikroskop technisch keine Vitalbeobachtungen (Beobachtungen an lebenden Strukturen) möglich. Eine idealisierte Kontrollsituation im biologischen Experiment ist nicht immer möglich. Dies gilt insbesondere in der Ökologie und in der Verhaltensforschung, aber auch in der Molekularbiologie.

Weitere spezielle Randbedingungen biologischer Forschungsgegenstände wie die Einzigartigkeit der Lebewesen, die Historizität der Evolution als Ganzes oder die Notwendigkeit von speziellen Umweltbedingungen für Modellorganismen, verursachen ebenso besondere Umstände und Einschränkungen biologischer Experimentalsysteme. Dasselbe gilt für Experimente an toten Objekten (In-vitro-Experimente) wie sie in verschiedenen Teilbereichen der Biologie üblich sind. Sie werfen die Frage auf, inwieweit sie Rückschlüsse auf lebende Systeme zulassen, aber auch ob sich die Experimentalbiologie tatsächlich mit der belebten Natur befasst.

Die wichtigsten Themen der Philosophie der Biologie kann man grob in drei Bereiche unterteilen. Die zentrale Rolle kommt der Analyse der Evolutionstheorie, ihrer Grundlagen, Aussagen und Folgen zu. Was sind Spezies, wie kann man sie wissenschaftlich definieren und wie klassifizieren und ordnen. Eine zweite Themengruppe dreht sich um die Reduktion oder das Verhältnis zwischen der Physik (und Chemie) und der Biologie. Hierzu gibt es viele technische und analytische Fragestellungen, die fließend in die dritte Problemgruppe übergehen: die Versuche, das Besondere an Lebewesen in der Natur zu umschreiben und an Kriterien festzumachen.

Leben wird in der naturwissenschaftlichen Biologie heute definiert als ein System von Eigenschaften. {?} So listet Georg Toepfer zwei Dutzend historische — und immerhin noch sechs seit 1980 gängige — Definitionen auf, die sich alle mehr oder weniger unterscheiden. Dabei sind die Begriffe Leben und Lebewesen keine biologischen, sondern ontologische Begriffe. {?} Für die Erkenntnisinteressen und Fragestellungen der Biologie sind beide Begriffe zudem irrelevant, falls man explizit darauf Bezug nehmen will, spricht man heute eher von „lebenden Systemen“.

Die Entdeckung der Entropie Mitte des 19. Jahrhunderts führte über ein Jahrhundert lang zur verbreiteten Überzeugung, dass die Ordnung des Lebendigen letztlich nicht mithilfe der Physik beschrieben und erklärt werden kann. Der Physiker Erwin Schrödinger beschrieb 1951 das Konzept der sogenannten „negativen Entropie“, heute auch Negentropie. Danach „ernähren“ sich Lebewesen quasi von negativer Entropie; wenn kontinuierlich Energie zugeführt wird, halten die Lebewesen ihren Zustand weit entfernt vom thermodynamischen Gleichgewicht aufrecht. Die Vorstellungen wurden später durch die Arbeiten von Ilya Prigogine, Isabelle Stengers und Manfred Eigen soweit ausgearbeitet, dass Entropie und Leben heute keinen konzeptionellen Gegensatz mehr darstellen und das Prinzip der Ordnung des Lebens auf einer sehr allgemeinen Ebene verstanden ist. Durch neuere Erkenntnisse über die Rolle von Viren und viren-ähnlichen RNA-Gruppen in der Evolution des Lebens und bei der Regulation nahezu aller zellulären Prozesse kommen zusätzlich zu physikalischen Bedingungen weitere Phänomene in den Blick. Hierzu gehören Gruppenverhalten, Kooperation und Koordination, Produktion völlig neuer genetischer Sequenzen und ihre Integration in bestehende Wirts-Genome.

Die heutige Synthetische Evolutionstheorie unterscheidet sich stark von den bekannten, mathematisch formulierten Theorien aus der Physik und Chemie. Der Versuch sie gemäß einem logischen Empirismus zu formulieren, birgt zudem einige Schwierigkeiten. Identifiziert man die „natürliche Selektion“ als grundlegendes Axiom, so fällt es schwer den Begriff der „Fitness“ daraus abzuleiten, da einerseits eine allgemeine Gesetzmäßigkeit sich nicht erkennen lässt, aber andererseits eine relative Definition trivial ist. Nichtsdestotrotz ist Fitness der wichtigste Parameter in der mathematisch modellierten Populationsbiologie. Der aktuelle Status in der Philosophie der Biologie zu diesem Problem ist die Auffassung, dass eine höhere Fitness lediglich die Disposition erhöht, lebensfähige Nachkommen hervorzubringen. Wenn man weiterhin die Vielzahl an Teilgebieten der Evolutionstheorie, wie die Paläontologie, vergleichende Anatomie oder Biogeographie, und die immense Anzahl an verschiedenen Befunden und Begriffen berücksichtigt, dann wird klar, dass eine axiomatische (Re)konstruktion im Sinne des logischen Empirismus für die Evolutionstheorie nicht möglich ist. Insofern bleibt der erkenntnistheoretische Status der Evolutionstheorie in der Philosophie der Biologie unklar.

Der Wert einer wissenschaftlichen Theorie kann anhand von mehreren Kriterien angegeben werden. Zunächst kann man in praktischen und theoretischen Wert unterscheiden. Der praktische Wert einer Theorie besteht einerseits in der Möglichkeit Voraussagen zu treffen. Für die Evolutionstheorie wird allgemein angenommen, dass sie Vorhersagen nicht oder kaum zulässt. Gründe dafür sind die Zufälligkeit der Ereignisse hinsichtlich ihrer Bedeutung, Einzigartigkeit der beteiligten Individuen, Komplexität der betrachteten Systeme und das Auftreten von sogenannter Emergenz – also bekannte Systeme entwickeln spontan neue und unvorhersehbare Eigenschaften.

Auch der Nutzen der Evolutionstheorie wird unterschiedlich dargestellt. Der praktische Nutzen einer wissenschaftlichen Theorie kann eingeteilt werden in die Fähigkeit, Prognosen zu erstellen und ihre technische Anwendbarkeit. Bei der darwinschen Evolutionstheorie wird nun angezweifelt, dass sie korrekte Prognosen ermöglicht. Dem wird aber entgegengehalten, dass zumindest Retrodiktionen, also Erklärungen vergangener Entwicklungen, möglich sind und in begrenzten Einzelfällen sogar korrekte Vorhersagen abgeleitet wurden. Hervorgehoben wird aber eher der intellektuelle Nutzen der Evolutionstheorie. Die Evolutionstheorie macht keine Allaussagen. Durch die Vielzahl möglicher Evolutionsfaktoren und ihren zufälligen Charakter, ist die darwinsche Evolutionstheorie auch keine deterministische Theorie. Es existiert auch keine einzige kanonische Form der Evolutionstheorie, auf die sich alle Biologen gleichermaßen beziehen. Die Bedeutung der Evolutionstheorie liegt vor allem in ihrer Rolle für das neuzeitliche wissenschaftliche Weltbild.

Die Evolutionäre Entwicklungsbiologie (Evo-Devo) hat mehrere Probleme der synthetischen Evolutionstheorie aufgegriffen und deutlich gemacht. So ist zunächst das Konzept der natürlichen Auslese auf erwachsene Organismen und ihre genetische Konstitution ausgerichtet. Diese beiden Komponenten – erwachsene Individuen und Gene – sollen im Zusammenspiel mit natürlicher Selektion und Adaptation jeden evolutionären Wandel erklären.

Aber in der Individualentwicklung führen Gene nur unter bestimmten Bedingungen zu der Ausprägung eines Merkmals des Phänotyps oder sie sind nicht mehr als Initiationsfaktoren für den phänotypischen Wandel, ohne diesen hinreichend darstellen zu können. Alle “vermittelnden” Bedingungen werden vorausgesetzt. Weiterhin besitzen bei den meisten mehrzelligen Lebewesen alle Zellen die gleichen Gene, sie können sich aber völlig verschieden entwickeln. Die klassische Vererbungslehre kann die Vererbung der Entwicklungsfaktoren nicht erklären. Es scheint, dass die Genexpression und ihre Bedingungen für die Evolution wichtiger sind als die Gene selbst. Auch erkennt Evo-Devo Autonomie von Zellen und Zellstrukturen, die zu Selbstorganisation befähigt. In einem solchen Umfeld können geringfügige genetische oder Umwelt-Anstöße das System Entwicklung mithilfe von Schwellenwerteffekten und vermittels dessen hoher Integrationsfähigkeit zu größeren Variationen verhelfen. Mit den Worten von Gerd B. Müller: Kleine Störungen (Mutationen, Umweltfaktoren) können auf einer höheren Ebene (embryonale Entwicklung) große, jedoch integrierte Wirkung (Variation) zeigen. Die Betrachtung der Individualentwicklung führt also dazu, das Gen als fundamentale Einheit der Information und Evolution abzulehnen. Evolution wird innerhalb von Evo-Devo als Variation und Replikation von ganzen Lebenszyklen begriffen. Die Gene sind dabei nur ein Element von vielen.

Manfred Laubichler analysiert die methodologischen und epistemologischen Unterschiede zwischen der Evolutionsbiologie und der Entwicklungsbiologie und findet neben verschiedenen Evidenzstandards und Forschungsmethodologien auch unterschiedliche Kausalitätsvorstellungen. So sucht die Evolutionsbiologie nach ultimaten Ursachen, also nach den Vorteilen von Anpassungen und der Plausibilität von Selektionen, während die Entwicklungsbiologie unmittelbare proximate Ursachen verfolgt, die sich in der Ontogenese zeigen.

Der Anspruch von Evo-Devo in der Evolutionstheorie geht noch weiter: Die Synthese wird in ihrer populationstheoretischen Ausprägung als eher "statistisch deskriptiv" gesehen, während mit der Erkenntnis evolutionärer Entwicklungsmechanismen eine mehr und mehr "kausal mechanistische Argumentation" greift.

Welche Bedeutung der evolutionären Entwicklungsbiologie insgesamt zukommt, wird in der Philosophie der Biologie und in der Evolutionsbiologie selbst kontrovers diskutiert. Die Positionen reichen von Ablehnung der Dominanz der synthetischen Evolutionstheorie, der Suche nach einer Theorieerweiterung oder Theorieergänzung bis hin zu Ersetzung durch eine "entwicklungsbasierte" Evolutionstheorie. Klar ist nur, dass ein rein statischer, genzentrierter Ansatz zur Erklärung der Evolution mit der Entwicklungsbiologie nicht in Einklang gebracht werden kann.

Die Begründer der Evolutionstheorie, Charles Darwin und Alfred Russel Wallace, waren sich in der Frage, wo die natürliche Selektion ansetzt, nicht einig. Während Darwin das Individuum als die einzige Einheit der Selektion ansah, argumentierte Wallace, dass Selektion auch auf der Ebene der Gruppen stattfinde. Danach wurde nahezu 100 Jahre eine Gruppenselektion in der Biologie für möglich gehalten, mit der Entwicklung der Molekulargenetik in den 1960er Jahren kamen neue Argumente dazu. Da sich nur das Individuum direkt aus den Genen entwickelt, wurde das nicht nur als Argument für die Selektion des einzelnen Organismus gewertet, sondern die Gene selbst wurden als Ebene der Selektion vorgeschlagen. In der Folge war das Thema in der Philosophie der Biologie eines der wichtigsten und wurde vielfach diskutiert. Dabei zeigte sich, dass die „Genselektion“ viele Beispiele in der Natur nicht hinreichend erklären konnte. Insbesondere versagt sie bei der Erklärung von systematischen Fluktuationen in der Häufigkeit von Genotypen. Ebenso müsste es eine eindeutige Kausalkette zwischen Genotyp und Phänotyp geben, damit ein Reproduktionserfolg direkt auf die Gene wirkt. Elisabeth Anne Lloyd schlug 1988 vor, die Kriterien für mögliche Selektionseinheiten genauer zu fassen. Demnach muss eine Einheit direkt mit ihrer Umwelt interagieren. Die meisten Wissenschaftler kamen daraufhin zu der Überzeugung, dass eine Genselektion unhaltbar sei.

Anfang des zwanzigsten Jahrhunderts wurde in der Evolutionsbiologie verstärkt die Frage diskutiert, ob es altruistisches Verhalten zwischen nicht-verwandten Individuen im Tierreich gibt und wie dessen Existenz mithilfe der Evolutionstheorie erklärt werden könnte. Darwin selbst brachte zwar schon die sogenannte Gruppenselektion ins Spiel, aber seine klassische Lehre der natürlichen Selektion kennt nur das Individuum als Reproduktionseinheit. Mit der Entwicklung der Molekulargenetik in den 1960er Jahren wurden auch die Gene als die Einheiten der Selektion identifiziert. Wie von George C. Williams 1966 vorgeschlagen, „benutzen“ die Gene Chromosomen, Zellstrukturen und den gesamten Organismus zur erfolgreichen Reproduktion. Das Individuum ist somit nur die äußere Erscheinung, die eigentlichen Subjekte der Selektion sind die Gene. Erst von da an begann eine systematische Beschäftigung mit dieser Frage in der Biophilosophie. So stellten Stephen J. Gould (1980) und Robert Brandom (1984) fest, dass Gene nach außen nicht „sichtbar“ sind und vom Organismus quasi „verdeckt“ werden. David Hull (1981) wollte daraufhin zunächst klären, ob die Trägereinheiten der Selektion lediglich als Replikatoren gedacht werden können oder mit ihrer Umwelt um den reproduktiven Erfolg kausal interagieren müssen. Im zweiten Fall würden Gene als Träger kaum in Frage kommen.

Elliott Sober benutzte das Beispiel einer dominant-rezessiven Vererbung, um zu zeigen, dass Gene nicht kausal an der natürlichen Selektion beteiligt sein können. Im Gegenzug stellt er die Theorie einer pluralistischen und hierarchischen Sicht der Selektion auf, die bis heute die vorherrschende ist. Demnach gibt es mehrere „Ebenen der Selektion“, und die Interaktion mit der Umwelt findet auf verschiedenen Ebenen statt. Es wird aber weiterhin kontrovers diskutiert, wie sich diese „Ebenen der Selektion“ gegenseitig beeinflussen und ob sie zumindest teilweise aufeinander reduzierbar sind. (Sober, 2003). Mit der Aufkommen der Evolutionären Entwicklungsbiologie hat sich zudem die Auffassung durchgesetzt, dass die sichtbaren Erscheinungen der Organismen (Phänotyp, manifest traits) nicht nur das Produkt der Gene sind, sondern sich aus dem Zusammenspiel der DNA, weiteren Molekülen und Zellstrukturen, sowie den Umwelteinflüssen entwickeln.

Die Frage des ontologischen und epistemologischen Status von Spezies wird in der Philosophie der Biologie häufig diskutiert. Die Vorstellung, dass es eindeutig getrennte Arten gibt, wird in der Biologie meistens unhinterfragt vorausgesetzt. Bei näherem Hinsehen sind aber alle Versuche einer eindeutigen Trennung mit verschiedenen Schwierigkeiten verbunden. Zunächst muss man klären, ob Arten oder alle Taxa als mathematische oder geometrische Klasse angesehen werden können. Folgen davon wären unter anderem, dass die Objekte abstrakte, eindeutige Eigenschaften haben müssen und dass Klassen über ihre Objekte definiert werden. Die Vorstellung statischer Klassen widerspricht jedoch dem Evolutionsgedanken der veränderlichen Arten. Mit dem Konzept der Familienähnlichkeit hat Ludwig Wittgenstein dagegen eine Möglichkeit formuliert, wie man durch unscharfe – und damit realistischere – Eigenschaftsdefinitionen ebenso klassifizieren kann.

Ernst Mayr definierte Arten als eine Anhäufung von Populationen oder Reproduktionsgemeinschaften. Eine biologische Art ist demnach die Summe ihrer konkreten Varianten und kein „Idealtyp“ oder Mittelwert. Anstelle von deskriptiven Merkmalen dient das Konzept der Herkunfts- und Existenzbedingungen zur Unterscheidung. Diese Definition stößt aber an Grenzen, wenn man beispielsweise Lebewesen betrachtet, die sich asexuell fortpflanzen, oder wenn man ausgestorbene Organismen klassifizieren will. Mayrs Definition der Arten als Reproduktionsgemeinschaften war dennoch ein großer Erfolg und setzte sich in der Biologie weitgehend durch. Ebenso wichtig in der Evolutionsbiologie ist eine Einteilung der Spezies durch ihre Abstammungsverwandtschaft (s. Phylogenese). Heute wird in der biologischen Praxis die Bestimmung von Spezies anhand von morphologischen Eigenschaften ergänzt durch die Betrachtung ihrer Abstammungsgeschichte (abgebildet durch homologe Gene und DNA-Sequenzen).

1974 überraschte der Biologe Michael Ghiselin mit dem Vorschlag, das abstrakte, essentialistische und mathematische Klassenkonzept durch ein raumzeitliches Individuum zu ersetzen. Spezies sind demnach eher wie Organismen mit einem individuellen Lebenszyklus und konkreten Beziehungen in ihrer Abstammung und Lebensgemeinschaft zu betrachten. Der Nachteil dieser Konzeption ist allerdings, dass die Anwendung mathematischer und insbesondere numerischer Verfahren zur Bestimmung der Spezies („numerical taxonomy“) aus dieser Sicht zweifelhaft ist. Zudem ist es unmöglich, dass Arten nach dem Aussterben erneut auftreten. Die Debatte um die Verwendung von Konzepten und Kriterien zur Klassifikation wird häufig auch unter den Begriffen „Artdefinition“ und „Speziesproblem“ mit wechselnden Schwerpunkten geführt und hält bis heute an.

Lebewesen sind bei Aristoteles wie alles andere auch durch Materie und Form bestimmt. Die „Form der Organismen“ ist dabei die Gliederung in Organe. Form und Wesen der Organismen entsprechen der Seele, wodurch der Unterschied zwischen Belebtem und Unbelebten über das Beseelte und Nicht-Beseelte bestimmt wird. Die Seele nutzt den Körper wie ein Werkzeug. Diese funktionale Werkzeuganalogie bezieht sich sowohl auf einzelne Organe als auch auf den Körper als Ganzes.

René Descartes vollzog im 17. Jahrhundert eine radikale Wende, indem er der Materie selbst das Vermögen aktiver Tätigkeit zusprach. Ihr gegenüber setzte er den menschlichen, denkenden Geist; das Konzept der Seele als formgebendes, aktives Prinzip verschwand fast völlig. Leben wird bei Descartes zum Automatismus des Materiellen und die Maschinenanalogie zum vorherrschenden Organismusmodell. Seither werden Organismusmodelle in den biologischen Wissenschaften generell von technomorphen Metaphern dominiert. Heutige Versuche, die Maschinenanalogie zu einer Maschinentheorie zu erweitern, haben sich nicht durchgesetzt, da Lebewesen alle Maschinenmetaphern mit ihren Fähigkeiten sprengen. Um die Homogenität, Regularität, Selbstähnlichkeit und Ordnung der Lebewesen auszudrücken, wurde im 19. Jahrhundert auch das Kristallmodell im Zuge der Zelltheorie durch Theodor Schwann und Matthias Jacob Schleiden populär. Im Gegensatz zum Maschinenmodell evoziert es keine Vorstellung eines geplanten, teleologischen Handelns, da es auf einen anorganischen Kontext hinweist. Theodor Schwann verwendete die Kristallanalogie für die Zellbildung, war sich aber immer der Grenzen des Modells bewusst. In dieser Zusammenstellung darf man nicht vergessen, dass der Begriff „Organismus“ selbst ein „Organismusbegriff“ ist. Eingeführt wurde er Anfang des 18. Jahrhunderts von Georg Ernst Stahl in dem Bestreben wieder mehr auf die besondere Stellung des Lebendigen in einer zunehmend mechanisierten Welt hinzuweisen.

Um Organismen und Populationen in heutigen wissenschaftlichen Theorien zu beschreiben, benötigt die Biologie formalisierte Modelle. Ausgehend von einer naturwissenschaftlichen Modellbildung werden Organismen als physikalisch-chemische Systeme beschrieben. Da aber sowohl die Physik als auch die Chemie die Eigenschaft der Lebendigkeit der Organismen nicht abbilden, gilt ein rein mechanistischer Ansatz als unhaltbar. Einen weiteren Ansatz in der Modellbildung findet sich in der sogenannten Konstruktions-Morphologie. Organismen werden dabei als mechanische Energiewandler betrachtet. Neben physiologischen Aspekten werden auch die Struktur und Form der Organismen, besonders aber ihre Funktionsweise anhand von Analogien zur Hydraulik beschrieben. Konstruktionsmorphologische Modelle haben sich in der Forschungspraxis schon häufiger bewährt.

Mit Erwin Schrödingers Buch „Was ist Leben?“ („What ist life?“, 1944) fand die Idee der Information Eingang in die Biologie. Träger dieser Information ist demnach der genetische Code. Seitdem überwiegen Analogien aus der Computer- und Informationstechnologie. Beispiele sind die Translation, Transkription und der Begriff der „genetischen Information“ selbst.

Ebenso wie Organismusmodelle der biologischen Forschung Ansatzpunkte für Fragestellungen und Theorien liefern, sind Modellorganismen zentral für die experimentelle Forschung. Die Hoffnung dabei ist, allgemeine Aussagen über Funktionen, Spezies oder gar das Leben selbst anhand von einer sehr begrenzten Auswahl an Forschungsobjekten zu finden. Inwieweit so eine Extrapolation gerechtfertigt ist, ist je nach Einzelfall umstritten. Dabei spiegelt die Verwendung eines bestimmten Modellorganismus immer auch die Forschungssituation wider. So wäre es Gregor Mendel nicht möglich gewesen, seine Vererbungsregeln mit Pferden, Schildkröten oder vielen anderen Arten experimentell abzuleiten. Ähnliches gilt auch für die Fruchtfliege Drosophila melanogaster und ihre Bedeutung für die Genetik und neuerdings auch für die Entwicklungsbiologie. Modellorganismen in Forschungslaboren besitzen als Teil von Experimentalsystemen aber noch weitere Besonderheiten. So muss immer ein Aufwand betrieben werden, um die Lebensbedingungen der Organismen herzustellen und zu erhalten. Die Experimentalsituation ist also unabwendbar kontrolliert und manipuliert.

Neben der Frage nach dem Wie gibt es in der Biologie immer auch das Interesse an der die Frage nach dem Warum. Beispielsweise kann man fragen, wie ein menschlicher Daumen funktioniert, aber auch warum er überhaupt existiert und welchem Zweck er dient. Überzeugende Funktionszuschreibungen erklären also nicht nur die Funktion, sondern auch die Existenz des Funktionsträgers selbst. Während entweder finalistische (auf ein Ziel oder Zweck bezogen), außerweltliche Kräfte oder eine immanente Zielgerichtetheit spekulativ die Fragen nach dem Zweck beantworten, konnten die Fragen nach der konkreten Funktion von Organen und anderen Dingen mit fortschreitender experimenteller Technik teilweise besser beantwortet werden. Gleichzeitig bleibt es unüberwindbar schwierig, Funktionen phänotypischer Merkmale zu erklären, die einem Zweck in der Vergangenheit dienen mochten, der heute nicht mehr gegeben ist. Dennoch ist das Merkmal vorhanden. Mit der Entwicklung der Evolutionstheorie und insbesondere mit der Theorie der natürlichen Selektion, erhoffte man sich auch die Erklärung von Zweckfragen mithilfe eines mechanistischen und naturalistischen Ansatzes. So wurde der Begriff der Teleonomie in die philosophische Diskussion eingeführt, um Adaptionen als kausale, zusammenhängende Folgen natürlicher Selektion zu erklären. Das zielgerichtete, formgebende Prinzip ist dabei ein Teil eines biologischen Programms. Der Zweckmäßigkeit richtet sich letztlich immer nach der Erhaltung der Art oder des Individuums. Mithilfe der natürlichen Selektion wird dies dann Teil des biologischen Programms.

Diese Erklärungen müssen sich aber vielfältiger Kritik stellen. Zum einen wird dieser Definition vorgeworfen, sie sei zirkulär, weil sie die Möglichkeit missachte, dass es auch Programme geben kann, die nicht zielgerichtet sind. Zum anderen ist Selektion nur auf die Vergangenheit gerichtet, sie "plant" nicht in die Zukunft. Carl Gustav Hempel stellte dazu 1965 fest, dass die funktionale Wirkung eines Merkmals immer erst für die Zukunft selektiert wird. Damit werde die historische Evolution von den Funktionen getrennt. Weiterhin wurde angeführt, dass selektionstheoretische Ansätze nicht für eine Zweckbestimmung verantwortlich sein können, da – auch nur hypothetisch – unselektierte Dinge dieselben Zwecke erfüllen können. Andererseits könne es auch Eigenschaften eines Organismus wie Organfehlleistungen geben, die nicht als Funktion bezeichnet werden, aber trotzdem genetisch fixiert sind.

Teleonomische Erklärungen leugnen keinesfalls die Zweckmäßigkeit von Dingen, sondern stellen sie als Folge natürlicher Prozesse dar. Solange also der Begriff Teleologie lediglich beschreibend verwendet wird, gibt es für einige Philosophen keinen Grund, einen anderen zu benutzen. So sind eine teleologische Sprache und teleologische Methoden, trotz aller Kritik, immer noch Teil der Biologie. Insbesondere in der Paläontologie gibt es viele Beispiele, wo heuristische teleologische Ansätze in der Forschung eine große Bedeutung haben. Als einzig gültige Form der Teleologie in der Biologie wird eine intentionalistische Interpretation als lediglich symbolische Repräsentation einer Zwecksetzung und somit als Ursache einer Handlung angesehen.

Der Genbegriff ist für die Molekularbiologie auf der einen und für die klassische Genetik, biologische Evolutionstheorie und Populationsgenetik auf der anderen Seite völlig verschieden definiert. Im Kontext der klassischen Genetik dient der Genbegriff als formale Einheit, mit dessen Hilfe Merkmalsveränderungen in Folgegenerationen allgemein abgebildet werden können. Weiterhin wesentlich für die Vorstellungen über Gene war die Trennung in Keimbahn und "Körpersubstanz" durch August Weismann und die begriffliche Trennung zwischen Genotyp und Phänotyp. In der Molekularbiologie werden Gene dagegen als eine physikalisch-chemische Substanz als Teil der Desoxyribonukleinsäure (DNA) betrachtet, die zugleich Trägereinheit einer „genetischen Information“ ist. Dadurch wurden sowohl die Stabilität und die Veränderlichkeit der Gene als auch ihre Reproduktionsfähigkeit plausibel. Diese Spannweite möglicher fragmentarischer Bestimmung des Gens lässt je nach verwendetem Experimentalsystem in den jeweiligen biologischen Teildisziplinen auch heute noch eine Vielzahl an Definitionen zu. So gibt es in der Biophysik, Biochemie, Molekulargenetik, Evolutionsbiologie und Entwicklungsgenetik unterschiedliche, aber zueinander nicht inkonsistente Definitionen.

Der Anreiz, eine Disziplinen-übergreifende und allgemeine Definition für ein Gen zu finden, war nie sehr groß. Heute lassen sich zwei Ansätze unterscheiden. Einer versucht, das Gen anhand von statischen, räumlichen und strukturellen Bedingungen als Teil der DNA zu fassen, der andere Ansatz bestimmt ein Gen mit Hilfe der Funktionalität der Ergebnisse (z. B. Proteine) als Vererbungseinheit oder funktionale Einheit. Es sieht allerdings so aus, dass neuere Erkenntnisse mit anderen Modellorganismen eine weitere Vereinfachung und Konsensfindung eher unwahrscheinlich machen.

Für Godfrey-Smith (2000b, 2003) ist der Begriff der genetischen Information durch die Rolle der Gene in der Ontogenese gerechtfertigt. Dem gegenüber sind sie für andere Autoren, Philosophen und Biologen lediglich Metaphern ohne ernst zu nehmenden theoretischen Beitrag. Das Bild der genetischen Information könne danach nicht im Sinne einer mathematischen Informationstheorie verstanden werden. Zwei Sequenzen von Basenpaaren in der DNS können den gleichen mathematischen Informationsgehalt haben, sich aber erheblich in ihrer „genetischen Information“ unterscheiden. So wird zwar die Quantität und Codierung betrachtet, die Bedeutung und Funktion der genetischen Information aber konsequent ausgeblendet.

Seit Aristoteles haben immer wieder Erkenntnisse, Methoden und Theorien aus der Lehre von den Lebewesen den Weg in die Philosophie gefunden. So vermittelt der Evolutionsbegriff einen zentralen historischen Zusammenhang für alle Erfahrungswissenschaften (s. a. Chemische Evolution, Soziokulturelle Evolution). Die Anwendung der Evolutionstheorie auf die Frage des Erkenntnisprozesses selbst führte zur Etablierung der sogenannten Evolutionären Erkenntnistheorie. Danach sind die Grundlagen der Möglichkeit des Erkennens durch die stammesgeschichtliche Entwicklung (des Menschen) entstanden und können auf diese Weise beschrieben, analysiert und bewertet werden. Diese Interpretation berührt viele philosophische Themen wie die Frage nach der Erkennbarkeit der Realität und die Frage nach der Güte und dem Wert einer Erkenntnis, die auf diese Weise vollständig determiniert ist. Evolutionärer Erfolg hat nach der evolutionären Erkenntnistheorie einen direkten Zusammenhang mit der Wahrheit im Sinne einer Korrespondenztheorie, sowie Auswirkungen auf die Wissenschaftsgeschichte, Didaktik und Anthropologie.

Es gibt ebenso Versuche, die biologische Evolutionstheorie auf die Ethik und die Ästhetik anzuwenden. Beide Ansätze sind allerdings sehr umstritten.

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Philosophers of biology examine the practices, theories, and concepts of biologists with a view toward better understanding biology as a scientific discipline (or group of scientific fields). Scientific ideas are philosophically analyzed and their consequences are explored. Philosophers of biology have also explored how our understanding of biology relates to epistemology, ethics, aesthetics, and metaphysics and whether progress in biology should compel modern societies to rethink traditional values concerning all aspects of human life. It is sometimes difficult to separate the philosophy of biology from theoretical biology.

• "What is a biological species?"
• "What is natural selection, and how does it operate in nature?"
• "How should we distinguish disease states from non-disease states?"

• "What is life?"
• "What makes humans uniquely human?"
• "What is the basis of moral thinking?"
• "How is rationality possible, given our biological origins?"
• "Is evolution compatible with Christianity or other religious systems?"

Increasingly, ideas drawn from philosophical ontology and logic are being used by biologists in the domain of bioinformatics. Ontologies such as the Gene Ontology are being used to annotate the results of biological experiments in a variety of model organisms in order to create logically tractable bodies of data available for reasoning and search. The Gene Ontology itself is a species-neutral graph-theoretical representation of biological types joined together by formally defined relations.

Philosophy of biology today has become a visible, well-organized discipline — with its own journals, conferences, and professional organizations. The largest of the latter is the International Society for the History, Philosophy, and Social Studies of Biology (ISHPSSB).

A prominent question in the philosophy of biology is whether or not there can be distinct biological laws in the way there are distinct physical laws.

Scientific reductionism is the view that higher-level biological processes reduce to physical and chemical processes. For example, the biological process of respiration is explained as a biochemical process involving oxygen and carbon dioxide. Some philosophers of biology have attempted to answer the question of whether all biological processes reduce to physical or chemical ones. On the reductionist view, there would be no distinctly biological laws.

Holism is the view that emphasizes higher-level processes, phenomena at a larger level that occur due to the pattern of interactions between the elements of a system over time. For example, to explain why one species of finch survives a drought while others die out, the holistic method looks at the entire ecosystem. Reducing an ecosystem to its parts in this case would be less effective at explaining overall behavior (in this case, the decrease in biodiversity). As individual organisms must be understood in the context of their ecosystems, holists argue, so must lower-level biological processes be understood in the broader context of the living organism in which they take part. Proponents of this view cite our growing understanding of the multidirectional and multilayered nature of gene modulation (including epigenetic changes) as an area where a reductionist view is inadequate for full explanatory power. (See also Holism in science.)

All processes in organisms obey physical laws, but some argue that the difference between inanimate and biological processes is that the organisation of biological properties is subject to control by coded information. This has led some biologists and philosophers (for example, Ernst Mayr and David Hull) to return to the strictly philosophical reflections of Charles Darwin to resolve some of the problems which confronted them when they tried to employ a philosophy of science derived from classical physics. The positivist approach used in physics emphasised a strict determinism (as opposed to high probability) and led to the discovery of universally applicable laws, testable in the course of experiment. It was difficult for biology, beyond a basic microbiological level, to use this approach. Standard philosophy of science {?} seemed to leave out a lot of what characterised living organisms — namely, a historical component in the form of an inherited genotype.

Philosophers of biology have also examined the notion of “teleology.” Some have argued that scientists have had no need for a notion of cosmic teleology that can explain and predict evolution, since one was provided by Darwin. But teleological explanations relating to purpose or function have remained useful in biology, for example, in explaining the structural configuration of macromolecules and the study of co-operation in social systems. By clarifying and restricting the use of the term “teleology” to describe and explain systems controlled strictly by genetic programmes or other physical systems, teleological questions can be framed and investigated while remaining committed to the physical nature of all underlying organic processes. While some philosophers claim that the ideas of Charles Darwin ended the last remainders of teleology in biology, the matter continues to be debated. Debates in these areas of philosophy of biology turn on how one views reductionism more generally.

Sharon Street claims that contemporary evolutionary biological theory creates what she calls a “Darwinian Dilemma” for realists. She argues that this is because it is unlikely that our evaluative judgements about morality are tracking anything true about the world. Rather, she says, it is likely that moral judgements and intuitions that promote our reproductive fitness were selected for, and there is no reason to think “true” moral intuitions would be selected for as well. She notes that a moral intuition most people share, that someone being a close family member is a prima facie good reason to help them, happens to an intuition likely to increase reproductive fitness, while a moral intuition almost no one has, that someone being a close family member is a reason not to help them, is likely to decrease reproductive fitness.

David Copp responded to Street by arguing that realists can avoid this so-called dilemma by accepting what he calls a “quasi-tracking” position. Copp explains that what he means by quasi tracking is that it is likely that moral positions in a given society would have evolved to be at least somewhat close to the truth. He justifies this by appealing to the claim that the purpose of morality is to allow a society to meet certain basic needs, such as social stability, and a society with a successful moral codes would be better at doing this.

While the overwhelming majority of English-speaking scholars operating under the banner of "philosophy of biology" work within the Anglo-American tradition of analytical philosophy, there is a stream of philosophic work in continental philosophy which seeks to deal with issues deriving from biological science. The communication difficulties involved between these two traditions are well known, not helped by differences in language. Gerhard Vollmer is often thought of as a bridge but, despite his education and residence in Germany, he largely works in the Anglo-American tradition, particularly pragmatism, and is famous for his development of Konrad Lorenz's and Willard Van Orman Quine's idea of evolutionary epistemology. On the other hand, one scholar who has attempted to give a more continental account of the philosophy of biology is Hans Jonas. His "The Phenomenon of Life" (New York, 1966) sets out boldly to offer an "existential interpretation of biological facts", starting with the organism's response to stimulus and ending with man confronting the Universe, and drawing upon a detailed reading of phenomenology. This is unlikely to have much influence on mainstream philosophy of biology, but indicates, as does Vollmer's work, the current powerful influence of biological thought on philosophy. Another account is given by the late Virginia Tech philosopher Marjorie Grene.

Philosophy of biology was historically associated very closely with theoretical evolutionary biology, however more recently there have been more diverse movements within philosophy of biology including movements to examine for instance molecular biology.

Research in biology continues to be less guided by theory than it is in other sciences. This is especially the case where the availability of high throughput screening techniques for the different "-omics" fields such as genomics, whose complexity makes them predominantly data-driven. Such data-intensive scientific discovery is by some considered to be the fourth paradigm, after empiricism, theory and computer simulation. Others reject the idea that data driven research is about to replace theory. As Krakauer et al. put it: "machine learning is a powerful means of preprocessing data in preparation for mechanistic theory building, but should not be considered the final goal of a scientific inquiry." In regard to cancer biology, Raspe et al. state: "A better understanding of tumor biology is fundamental for extracting the relevant information from any high throughput data." The journal Science chose cancer immunotherapy as the breakthrough of 2013. According to their explanation a lesson to be learned from the successes of cancer immunotherapy is that they emerged from decoding of basic biology.

Theory in biology is to some extent less strictly formalized than in physics. Besides 1) classic mathematical-analytical theory, as in physics, there is 2) statistics-based, 3) computer simulation and 4) conceptual/verbal analysis. Dougherty and Bittner argue that for biology to progress as a science, it has to move to more rigorous mathematical modeling, or otherwise risk to be "empty talk".

In tumor biology research, the characterization of cellular signaling processes has largely focused on identifying the function of individual genes and proteins. Janes showed however the context-dependent nature of signaling driving cell decisions demonstrating the need for a more system based approach. The lack of attention for context dependency in preclinical research is also illustrated by the observation that preclinical testing rarely includes predictive biomarkers that, when advanced to clinical trials, will help to distinguish those patients who are likely to benefit from a drug.

Le vivant se caractérise par sa sensibilité et son activité autonome. Celles-ci proviennent de la dynamique interne propre au métabolisme: l'être vivant est un corps qui forme lui-même sa propre substance à partir de celle qu’il puise dans le milieu. De ce phénomène d'assimilation, découlent tous les autres phénomènes propres au vivant: la régénération et le renouvellement de leurs tissus, la reproduction et le développement de l’organisme et enfin évoluent au cours du temps par acquisition d’organes diversifiés et de facultés plus éminentes. Les êtres vivants maintiennent, préservent et même enrichissent leur organisation. à l'échelle des espèces, le vivant ne cesse de se complexifier depuis 3,5 milliards d'années.

Le problème pour la philosophie de la biologie est alors de savoir si, en raison de ses particularités, la vie est quelque chose de fondamentalement différent de la matière inanimée ou non. Il y a trois positions fondamentales à ce sujet :

• Le vitalisme estime que la vie est le produit d'une force vitale, semblable à la force de gravitation universelle mais spécifique aux seuls êtres vivants. Le vitalisme est à l'origine d'inspiration matérialiste: il cherche à comprendre les êtres vivants en tant que phénomènes physiques à une époque où les moyens d'investigation scientifiques ne permettent pas de comprendre les ressorts physico-chimiques de la vie. Ce n'est qu' à partir du xixe siècle qu'il s'orientera vers des conceptions idéalistes, psychiques ou encore mystiques de la vie.
• Le mécanisme estime que l'être vivant n'est rien d'autre qu'une forme particulière de la matière, il s'apparenterait à une machine très complexe qu'il suffirait de démonter et d'analyser en détail pour certainement en percer le secret dans quelque temps. On retrouve cette thèse dans la conception créationniste de la vie comme créée par Dieu (cf. la théologie naturelle de William Paley). Charles Darwin, avec le mécanisme de la sélection naturelle, arrachera cette conception de l'être vivant comme machine de la théologie et la fera entrer dans le giron de la science.
• L'organiscisme estime que l'être vivant est le produit d'une organisation particulière de la matière. Ce nom a été donné par Ludwig von Bertalanffy dans les années 1930, mais en fait cette conception est plus ancienne. C'est notamment celle que Lamarck développe dans la théorie sur l'être vivant dans sa Philosophie zoologique (1809).

Charles Darwin publie L'Origine des espèces en 1859. Darwin essaie d'expliquer l'adaptation des êtres vivants à leurs conditions d'existence par des facteurs purement mécaniques.

à chaque nouvelle génération, les descendants présentent toujours des petites variations par rapport à leurs parents. L'espèce reste la même, mais il y a des variations individuelles, dues au hasard. Parmi ces variations, la plus grande partie ne représente ni avantage ni inconvénient particulier dans la lutte pour la vie (on les désigne comme neutres), mais un certain nombre d'entre elles constituent un handicap (on les appelles des mutations délétères), d'autres un avantage pour la survie et la procréation (mutations avantageuses). Sur toutes ces variations s'exerce la pression de la sélection naturelle. Le milieu ambiant laisse vivre les variations neutres, il élimine peu à peu les variations défavorables, et il favorise le développement des variations favorables. Tout cela n'a rien d'intentionnel.

Le mécanisme de l'évolution se ramène donc à deux facteurs essentiels :

• des variations ou mutations individuelles ;
• la pression de la sélection naturelle.

Pour concevoir sa théorie, Darwin s’est inspiré du travail des éleveurs. Ceux-ci opèrent une sélection artificielle au sein de leur cheptel pour l'«améliorer» (selon certains critères) au fil des générations: ils ne permettent qu' à leurs «meilleur(e)s» plantes ou animaux de se reproduire. Puis, parmi les spécimens de la nouvelle génération, ils sélectionnent ceux qui leur conviennent pour leur permettre de se reproduire. Cela, de génération en génération, jusqu' à ce qu'une nouvelle race ou variété se dessine. C'est ainsi par exemple que sont apparues les vaches laitières ou les carottes telles que nous les connaissons actuellement. La nature fait de même, à ceci près que c'est une sélection sans sélectionneur (Richard Dawkins parle métaphoriquement d'un «horloger aveugle»).

Plusieurs biologistes et philosophes ont tenté de mettre en évidence le noyau structurel de la théorie de l'évolution par sélection naturelle. à la suite d'un texte célèbre de Richard C. Lewontin, on affirme souvent qu'il y a évolution par sélection naturelle dès lors que trois conditions sont réunies : variation, hérédité, réplication différentielle. Une autre manière de comprendre le processus de l'évolution par sélection naturelle est celle du philosophe David Hull, qui propose de distinguer entre «réplicateur» et «interacteur». Récemment, Peter Godfrey-Smith est revenu sur les différentes manières de résumer en une « recette » le processus évolutionnaire.

L'examen critique du concept de gène, pour mettre en évidence ses différentes significations, sinon sa définitive caducité a été un chantier important de la discipline. Cette critique prend place dans le cadre général de l'ébranlement actuel du paradigme génétique, où résultats scientifiques aussi bien que réflexions philosophiques tendent à remettre très fortement en question le génocentrisme et le déterminisme génétique qui a largement imprégné la démarche scientifique pendant une grande partie du xxe siècle.

Une des victoires notables des philosophes de la biologie (notamment S. Oyama et P. Griffiths dans leur controverse avec John Maynard Smith), est d'avoir réussi à persuader les scientifiques que si l'on tient à parler d'information en biologie (ce qui, pour certains auteurs, est fort peu recommandé), alors il n'y a aucune raison de cantonner cette notion au discours sur l'ADN, mais qu'elle doit être employée à propos de tous les facteurs développementaux, en application rigoureuse de la théorie de l'information.

La philosophie de l'immunologie s'est avant tout construite comme une réflexion critique sur les notions de "soi" et de "non-soi", centrales en immunologie. L'élaboration de la théorie du soi et du non-soi fut un processus long et complexe, dont l'une des origines est la pensée de Metchnikoff. Néanmoins, l'immunologiste qui été le principal artisan de cette théorie est l'Australien Frank Macfarlane Burnet (1899-1985). Selon la théorie du soi et du non-soi, l'organisme ne déclenche pas de réponse immunitaire contre ses propres constituants ("soi") et déclenche une réponse immunitaire contre toute entité étrangère ("non-soi").

Plusieurs problèmes se posent concernant cette théorie et cette conceptualisation :

1. Un problème historique : de quelle manière les concepts de "soi" et de "non-soi" ont-ils été empruntés au vocabulaire de la philosophie et de la psychologie? Conservent-ils la trace de ces origines dans leur usage immunologique?
2. Un problème métaphysique : l'immunologie peut-elle éclairer le problème métaphysique de l'identité des êtres, et tout particulièrement le problème de l'identité biologique, classique au moins depuis Aristote?
3. Un problème théorique: la théorie du soi et du non-soi est-elle encore adéquate aujourd'hui?

D'autres enjeux émergent actuellement en philosophie de l'immunologie, notamment dans son articulation avec la biologie de l'évolution. Par exemple, plusieurs auteurs impliqués dans le débat sur les transitions évolutionnaires utilisent le système immunitaire comme un exemple paradigmatique de processus par lequel un individu évolutionnaire se constitue en réprimant la réplication d'entités de niveau inférieur. Face au manque de preuves expérimentales indiscutables, on ne peut que souhaiter la collaboration active d'immunologistes et de philosophes sur cette question.