Philosophy of Biology PDF

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Philosophy of Biology

Philosophy of biology is the branch of philosophy of science that deals with biological knowledge. It can be practiced not only by philosophers, but also by scientists who reflect on their own work. The distinctive mark of philosophy of biology is the effort to achieve generalizations about biology, up to various degrees. For instance, philosophy of biology makes biology relevant to classic issues in philosophy of science such as causation and explanation, chance, progress, history, and reductionism. It also works to characterize how knowledge is acquired and modified in different areas of biology, and sometimes to clarify the criteria that demarcate science from non-science.

Philosophy also performs constructive criticism of biology. For example, it has an important role in analyzing cases of “naturalization”—when science becomes able to study issues that traditionally were the exclusive domain of philosophy. The life sciences and their objects are changing and growing exponentially. A challenge for philosophy of biology is thus to keep the pace, not only with new knowledge modifying long-standing ideas (for example, the “Tree of Life”), but also with new scientific practices and unprecedented kinds of data. Accordingly, philosophy of biology is constantly provoked in shifting its own methods and attention.

In some cases, philosophy of biology can aid the life sciences to reach their goals, by means of conceptual analysis, linguistic analysis, and epistemological analysis.

Hybridizations and intersections between scientific fields are particularly conducive to philosophical considerations. Contemporary examples are

‘EvoDevo’ (the recent integration between development and evolution) and ‘cultural evolution’ (an approach to cultural change inspired by evolutionary biology). Theses and analyses of philosophy of biology are often entwined with history of biology and with the history of evolution.

Finally, philosophy of biology can elaborate messages and general views out of biology, and has a crucial role in caring for how science is publicly interrogated and communicated.

1. Introduction

According to several reconstructions of the history of philosophy of biology, the field emerged gradually in the 1960s with a first generation of self-identified philosophers of biology, especially Morton Beckner, David Lee Hull, Marjorie Grene, Kenneth Schaffner, Michael Ruse, and William C. Wimsatt. As an explanation for such branching of philosophy of science, some philosophers put forth the decline of logical positivism in the 1960s and 1970s. For others, logical positivism did not actually decline, and anyway it had never suppressed philosophy of biology (Callebaut 1993). At times, the ‘official’ chronology gets questioned. For Byron (2007), proper philosophy of biology was already there in early philosophy of science, since the 1930s, as shown by a bibliometrical analysis. The most quoted philosopher in this article is David Lee Hull (1935-2010). He is a noncontroversially important figure in the founding generation of philosophers of biology. His meta-reflective papers “What

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philosophy of biology is not” (1969) and “Recent philosophy of biology”

(2002) are particularly useful.

Philosophy of biology turned into a professional subdiscipline since the mid-1970s, with a ‘second generation’ of philosophers, the most cited being Ronald Amundson, John Beatty, Robert N. Brandon, Richard Burian, Lindley Darden, David J. Depew, John Dupré, James R. Griesemer, Philip Kitcher, Elisabeth A. Lloyd, Alexander Rosenberg, Elliott Sober, and Bruce H. Weber. Some of them were experienced philosophers who progressively shifted to biological issues. The first journal partially devoted to philosophy of biology – History and Philosophy of the Life Sciences – began to be published in 1979, and in the mid-1980s the discipline was fully established. Specialized journals flourished. In the early 2000s, a growing number of scholars, institutions, and journals specialized in philosophy of biology, and the discipline gained more and more room in scientific books, journals, and conferences (see the resources at the end of the article).

As we shall see, philosophy of biology provides accounts of biological knowledge, asking: how are explanation, causation, evidence and other epistemological primitives elaborated in the explanations that are typical of biology, such as natural selection, genetic drift, and homology? Does biology differ from other sciences? How? And how do we understand the epistemological diversity across different branches of the biological sciences? Philosophy of biology also considers whether biology may contribute to redefine classical demarcations of science from other forms of knowledge and human creation.

Philosophy of biology can be seen as a possible aid for scientific advancement in the life sciences. Contributions of philosophers were widely appreciated by scientists, for example, in the areas of classification, taxonomy, and related activities, and in the abstract formulation of natural selection in the development of biology after Darwin. Scientists themselves may reflect philosophically on their own field of research, justifying and correcting their practices, or denouncing biases and transformations in their own community. Concepts, such as

‘adaptation’ or ‘species,’ are underlain by complex, inferential structures that can be revealed and sometimes criticized by philosophical analysis.

Multiple and conflicting meanings may be uncovered and systematized to help the progress of science and to develop more general messages.

Phenomena studied by biology make this science particularly sensible and interesting for philosophy. Humans are organisms, and quite a few fields of biology have potential or direct implications for our self- understanding. Interesting philosophical debates have stemmed, for example, since the 1970s from the provocative proposal of a

‘sociobiological synthesis’; such synthesis claims to provide evolutionary explanations for human prosocial (and anti-social) behaviors that were traditionally covered by ethics. Philosophy overcame mere self-defensive attitudes, and its important role lied in epistemological analysis and in deep reflections on the limits and conditions of naturalization, which may

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be understood as the transition of a problem into the domain of empirical science. Neurobiology offers a particularly fertile ground for reflections about how human phenomena can be related to, or even explained by, biology. And how should a philosophical field like moral philosophy take biology into account? (For more on the topic of the naturalization of morality, for example, see ethics.)

Philosophy of biology may study and support the interaction among different life sciences, as in the case of evolutionary developmental biology, where workers claim to be reuniting genetics and evolution with embryology, recomposing a historical divide in biology. How do different research traditions integrate or replace each other? This question illuminates classic issues such as progress and scientific change with new light. Philosophy of biology also monitors the natural hybridization of biology with extra-biological fields, such as cultural transmission, and enriches the debate among scientists where extreme positions often pop out: does biology offer more rigorous methods to replace the failing methods of the social sciences? Are we facing, instead, a case of mutual inspiration? Or methodological integration? Which reciprocal prejudices are well-grounded? And how can they be overcome for fruitful scientific collaborations?

Philosophy of biology also has a mandatory critical role towards biology.

For example, it can unveil the progressionist, anthropomorphic, and anthropocentric biases that affect scientists as human beings who live immersed in a society and in a cultural environment. Critical attention must be particularly high when scientific classifications of humans (for example, through measures such as IQ or ethnicity) may lead to justify and increase social discrimination, segregation or oppression.

Philosophy of biology may also develop ways of thinking up from biological research, providing an inspiring and readable encompassing view of the living world that will hardly be found in any standard, scientific publication. Furthermore, philosophy of biology is called upon to work on the interface between science and society, contributing to both the common misunderstandings and the best strategies for citizens to become conscious and informed, as they are called to decide what kind of research and intervention will be allowed or actively pursued by society.

It is hard for philosophy of biology to keep pace with the fast development of biological knowledge. But the effort of following the moving frontier of knowledge allows philosophy of biology to study the fall of influential ideas, such as the universal Tree of Life, and the rise of new scientific practices, such as intensive computer modeling.

Philosophy also has the unsettling opportunity to constantly rethink its own approach, avoiding drifting too far away from scientific practice so as to become detached. In this dynamic, philosophy of biology is also well integrated with history of science, so that it is often hard to distinguish between the two. An analysis of the relationship between molecular

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biology and Mendelian genetics, for example, is intertwined with the historical account of the birth and early development of molecular biology in the 1980s. In turn, the philosophical framing of genetics and developmental biology as either ontology-based disciplines or research styles transforms radically the way in which the history of the two fields is told.

Philosophy of biology belongs to philosophy, therefore, no fixed procedure or protocol constrains its research (what is philosophy?).

Philosophy of biology consists in free and critical — although rigorous and informed — thought on biological knowledge as the latter develops through time. However, as a mature and recognized field with its own interconnected practicing community, philosophy of biology seems to feature some methodological principles:

 Philosophy of biology is supposed to be scientifically informed and up-to-date, capturing how recent research modifies

established knowledge and creates new scientific practices. In turn, these novelties transform philosophy’s problems and approaches, especially in the current explosive growth of biology.

 Philosophy and biology are not always clearly distinct.

Scientific work can routinely require, for

example, conceptual or epistemological On the other hand, philosophy can turn out to be effective in setting up scientific research projects. However, philosophy can be characterized by its leaning towards generalities about biology, namely general philosophical problems, general characterizations of fields and approaches within biology, or conceptualizations of biology as a whole or even of science as a whole.

 Philosophy of biology should try to be understandable and possibly useful to biologists. Its tools — conceptual

analysis, epistemology, traditions of thinking and debates — should be put to use for improving scientific research.

 Biologists can do philosophy of biology. This happens, for example, when they become interested in general features of biology and try to contribute with principles derived from their work or when they think about the inferential patterns

employed by themselves and their colleagues. Also, scientists can do philosophy and speak to philosophy when particular objects of philosophical study, such as human morality, get naturalized (see below).

 Philosophy of biology cares for working across disciplinary contexts. For example, it studies novel contacts between previously separated fields, develops general views of the living world from some aspect of the life sciences, or reveals complex connections between science and the socio-cultural context in which it is carried out. It also takes advantage of its knowledge for monitoring and assisting how science is

publicly communicated and interrogated.

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 Philosophy of biology is increasingly seen as one piece with history of biology, since philosophical and historical theses are mutually necessary, and their results reverberate reciprocally.

These six methodological principles are usually tacit, but sometimes they are made explicit by philosophers of biology, who may also disagree on some of them. The principles will be presented here by means of exemplar studies. Any set of examples is anyhow partial and biased, since philosophy of biology is a huge field full of fascinating topics, growing exponentially along with biology. For a more complete picture, the interested reader will have to navigate the resources listed at the end of the article, such as philosophy of biology journals or programs of conferences such as the biennial meetings of the International Society for the History, Philosophy, and Social Studies of Biology, the main reference society of the field. A number of textbooks in philosophy of biology are available, often in the form of anthologies. A list of all these resources is provided at the end for further reading.

Given the vastness of the philosophy of biology literature, this article can only indicate some of the main topics and the richness of discussions. The examples in this article are mainly focused on evolutionary biology.

Evolutionists such as Ernst Mayr (1904-2005) and Stephen Jay Gould (1942-2002), two of the most influential authors, are extensively treated in this article though they are not universally representative. The predominance of evolution can be justified not only by the author’s specialization, but also by the fact that—as many philosophers of biology have critically stressed in recent times—evolutionary theory has long been the main target of philosophy of biology. Only in the last few decades has this situation changed radically (Müller-Wille 2007, Pradeu 2009). Philosophy of biology is already tackling an enormous range of topics in the most disparate fields, from biomedicine to community ecology, from neurobiology to microbiology and microbial ecology, and from chemistry and biochemistry to exobiology. To look for some specific area, the interested reader is, once again, encouraged to venture into the journals and online resources.

2. General Issues in Philosophy of Biology

Philosophers of science (though not always under this fairly recent name) have reflected for centuries on explanation, causation, correlation, chance, and many other general topics concerning science or knowledge in general. Important philosophers contributed to concepts like reduction vs. multiple realizability, and provided theories of explanation that describe what a scientific explanation is. During the second half of the 20th century, philosophy of science adopted a pluralistic strategy, considering the diversity of scientific disciplines and methods and striving to understand their differences along with their common aspects. With this pluralization, the complex task remained of finding a satisfying description of science as an endeavor which—unitary or not—is distinct from other forms of knowledge.

The study of living beings offers a universe of occasions for philosophy of science to advance the reflection. For instance, explanations by natural

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selection and by drift (see below, 2.a) can be seen as instances of causal explanations that nonetheless bring about new reflections and conceptual puzzles on the classic issues of causation, randomness, and ontology of processes. Homology explanations, another typical feature of biology, explain the properties or the variability of a biological character by citing the ancestral character or organ, and the causal factors that historically modify the descendants of that ancestral organ. In trying to account for biological sciences, philosophy of biology may take concepts from philosophy of science, such as causal explanation or reduction, and find new putative cases of them in the life sciences or locate failures of reduction in biology. Other times, philosophy of biology may need to tailor new concepts to accommodate biology. In fact, some kinds of explanation seem peculiar to biology or to historical sciences. While chasing the peculiarities of biology, philosophy of biology also has some general research goals among its aims:

1. Often, philosophy of biology scours biology in search of new insights on general philosophical problems about science, such as the “problem of induction,” or the realism vs.

instrumentalism dichotomy. Additionally, new general problems arise from the particular forms

that explanation, causation, or reduction take in biology.

2. Sometimes philosophy of biology seeks general

characterizations of particular fields, practices, or ways of thinking within the life sciences Other times, the goal seems to be a general picture of biology, especially by contrast to other sciences, such as classical mechanics.

Sometimes philosophy of biology suggests general views of science, descriptions and characterizations of science with all the complexity, differentiation, and plurality that it exhibits in the contemporary world.

In fact, the classical task of a demarcation of true science from other forms of knowledge has lost importance under the effect of philosophy of

‘special’ sciences like biology (Fodor 1974).

a. General Problems in Philosophy of Science, as Seen in Biology

Natural selection is a major biological explanation for the features of organisms. Inherited traits, originated by cumulative retention of random variation, are there because of the positive contribution they have brought to their bearers in past generations, in terms of survival and reproduction. Yet, the explanatory structure of natural selection is very complex, and implies a reflection on concepts like causality and randomness. In a classic book, Sober (1984) pointed out that only a few of the traits that get selected are in fact explanatory, specifically those traits that are selected for. Other traits are free riders that are somehow correlated with traits that are selected for and thus are preserved in the population without actively contributing to fitness. Thus, there is selection of such free rider traits that are not causally relevant to survival and reproduction. Hearts are positively selected; heartthrob is also selected, but not selected for; efficiency in pumping blood is selected for;

the existence of heartthrob is thus explained by natural selection, but

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heartthrob is not explanatory per se; it undergoes selection of, not selection for. The idea of free riders on selection was already considered by Darwin, but philosophers of biology spelled out its consequences for the explanatory structure of natural selection. Causal relationships are the core of some theories of explanation. Sober proposed rethinking the idea of causality in light of evolutionary biology, and this is an example of how classic philosophical categories can be modified in their application to biology: “We must show that by considering evolutionary theory, old problems can be transformed and new problems brought into being. It remains to be seen, I think, how radically the philosophy of science will be reinterpreted” (Sober 1984: 7; see Matthen and Ariew 2009, Ramsey 2013).

Randomness and chance are very important in biology. Natural selection is not random: “it requires randomness as its ‘input’…but the ‘output’ of natural selection is decidedly nonrandom, the differential survival and reproduction of the variants that are better adapted” (Rosenberg and McShea 2008: 21). Philosophers worked, for example, on the meaning of

“random mutation,” a concept considered essential to Darwinism as opposed to Lamarckism (Merlin 2010). Random does not necessarily mean lacking deterministic causes. Rather, random mutation points to the fact that the usefulness of a trait in the environment where it appears is not among the causes of its appearance. The source of variation is thus more properly contingent with respect to fitness. An interesting line of reasoning and evidence points out that “evolutionary divergence is sometimes due to differences in the order of appearance of chance variations, and not to differences in the direction of selection” (Beatty 2010: 39).

Genetic drift is the predictable change of the frequencies of traits that are not under selection. The absence of selection makes the dynamic depend only on the reproduction mechanism, and although the fate of individual traits is not predictable, the overall landscape of frequencies is. Genetic drift has long been known in formal models, studied in the field, and used for evolutionary reconstruction: it is not only necessary, but also causally relevant to evolution. Yet, a lively philosophical debate exists on the ontology of drift and selection (Millstein 2002; Walsh et al.

2002). A major disagreement concerns the epistemic status of mathematical models: granted that drift is a necessary feature of mathematical models, what can be legitimately inferred about the existence of a process in the world to be called drift? A statistical interpretation sees both drift and selection as mathematical features of aggregates of individuals (Walsh 2007, Matthen 2009, 2010). Another point of view considers them as causal physical processes (Millstein 2006, Millstein and Skipper 2009). The notion of evidence as a way of choosing between alternative explanatory hypotheses, selection versus drift, for example, is another object of philosophical study. Some philosophers think scientists are more qualified to evaluate and weigh evidence (Hull 1969: 169). Others point out that it is up to philosophy to probe the explanatory limits—current and constitutional—of biology (Rosenberg and McShea 2008: 2). One fortunate approach to such a task is the technical account of evidence based on Bayesianism (Sober 2008).

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Bayes’ theorem belongs to the mathematics of probability theory. It is based on prior probability, the probability of a particular statement before the observation, and posterior probability, the probability of the statement in the light of the observation. Bayes’ theorem is used by some schools of philosophers of biology in explicating various issues connected with evidence and confirmation.

Homology explanations explain the properties or the variability of a biological character, the form of a wing or the range of different wing shapes across different groups of organisms, for example, by citing the ancestral character or organ, and the modification factors that affect the descendants of that ancestral organ. Like many modes of explanation in biology, homology explanations are historical (see also 3.a). Philosopher Ereshefsky (2012) compares homology explanations with analogy explanations, which instead explain a character by citing the contribution of that character to a function. Ereshefsky points out that homology explanations are more detailed and offer a better account of observed differences. Homology explanations can be also turned into strong historical explanations, as opposed to weak ones that only cite the ancestral, initial condition. This happens, for example, when detailed molecular studies of the development of the target character enlighten precise events, such as gene duplications, that must have been crucial along the historical path. The study of genetic and developmental pathways also gives access to hierarchical disconnect which, for Ereshefsky, relates homology explanations to classical topics of philosophy of science: multiple realizability and reductionism.

Hierarchical disconnect happens when “a homologue at one level of biological organization is caused by non-homologous developmental factors at lower levels of organization” (p. 385). Along the historical path, for example, a morphological structure can remain stable while its underlying developmental modules change (Griffiths and Brigandt 2007).

For Ereshefsky, this is a biological example of multiple realizability, that is the fact that one level of organization cannot be reduced to a kind at a lower level. This in turn, for Ereshefsky, counters ideas by Alex Rosenberg about reductionism in biology (Rosenberg 2006). For Rosenberg—Ereshefsky says—the history of homologous characters should be reducible to the history of their physical substrata, but Ereshefsky says hierarchical disconnect shows decoupled histories and multiple realizability.

b. A General Picture of Biology

In characterizing ways of thinking and kinds of explanations and evidence, philosophy of biology formulates generalizations about biology.

These generalizations become particularly encompassing when philosophy of biology tries to characterize biology explicitly and comprehensively as distinct from other sciences. Biology is generally considered a ‘special science’—a term inherited from logical positivist philosophy of science that doesn’t preclude, in the long run, a reduction to physics (Fodor 1974, Rosenberg and McShea 2008). Among the most noticed and studied features of biology there is the apparent absence of scientific laws, whose blueprint, so to speak, are physical laws

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(but see Waters 1998). Many have been the endeavors of describing biology as a science without relying on laws, but also without relegating it as a mere collection and description of singular events where exceptions are the law.

For Ernst Mayr (1982, 2004), biology is based on concepts or principles, which are more flexible than laws: biology is a unique science by virtue of concepts that allow for biological explanation, including inheritance, program, population, variation, emergence, organism, individual, species, selection, fitness, and so on. Biology is also characterized by population thinking, introduced by Darwin, which differentiates biology from mechanics or chemistry whose thinking is, for Mayr, essentialist or typological (for more on this see 4.a.i).

For paleontologist Niles Eldredge biology is based on patterns. Patterns are law-like regularities, consisting of repeated schemes of events. This notion characterizes biology as a historical science, while reducing the gap that, in other views, separates biology from other natural sciences like physics. The pattern of inclusive hierarchical similarity in the biological world was seen by Linnaeus and captured in his binomial nomenclature. Darwin saw more patterns, for example in the geographical distribution of species and varieties. He then discovered a subset of the grand complex of repeated events, or regular processes, that give rise to biodiversity on Earth—the pattern of evolution. Mendel caught some patterns as well, in his observations of inheritance. Patterns have a double nature, ontological and epistemological: “Patterns in the natural world are extremely important.… They pose both the questions and the answers that scientists formulate as they seek to describe the world…. Science is a search for resonance between mind and natural pattern as we try to answer these questions” (Eldredge 1999: 4-5).

Other scholars think of biology as a science of mechanisms. A growing philosophical movement called “the New Mechanism” (Machamer et al.

2000) use the concept to revise classic ideas like causation, discovery, and explanation. In this view, biologists aim to discover and represent mechanisms with their schemas, sketches, and theoretical models. The characterization of natural selection as a mechanism, for instance, has been proposed, but is yet to be resolved (Skipper and Millstein 2005).

Model-based accounts have acquired particular importance in philosophy of biology (Schaffner 1993, 1998). The semantic view of scientific theories in the 1980s (see 2.c) was a first ambitious endeavor to characterize biology as a model-based science. Downes (1992) pointed out the limits of the semantic view in its original formulation, but proposed that philosophers of biology keep some of its central claims, among which are the centrality of various kinds of models in biology and their promise of accounting for all scientific theorizing.

At a lower degree of generality, philosophy of biology offers a proliferation of ideas about how schools of scientists, fields, or approaches perform fundamental activities of science like explaining, describing, understanding, or predicting. Some included the aforementioned and conceptually challenging explanations like natural selection, drift and historical homology explanations. Others include the practices of ecological modeling and model organisms, (6.b) particular

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inferential patterns such as adaptationism (4.a.ii), and the difference between geneticists and developmental biologists (7). These are all typicalities, or modest generalizations, of sub-parts of biology. Population genetics is a thoroughly studied field from this point of view. By studying population genetics, philosophers have raised wide-ranging topics of reflection, such as the degree of idealization of models and experiments (Plutynski 2005, Morrison 2006). The concept of the possible has played a role in accounting for how biological idealizations can be explanatory: if biological models cannot predict or demonstrate necessity, they can at least restrict the field of what is possible, yielding so-called “how possibly” answers or explanations. For Rosenberg and McShea (2008) it is a “usual scientific” strategy that “scientists try to characterize a range of possible causes of evolution, and then to determine which of these possibilities actually obtained. The actual is first understood by first embedding it in the possible” (p. 13).

Even the tightest case studies usually produce generalizations to a certain degree. Grote and O’Malley (2011), for example, claim that their historical reconstruction of research on microbial rhodopsins

offers a novel perspective on the history of the molecular life sciences…, sheds light on the dynamic connections between basic and applied science, and hypothesis-driven and data-driven approaches [and]

provides a rich example of how science works over longer time periods, especially with regard to the transfer of materials, methods and concepts between different research fields. (Grote and O’Malley 2011, p. 1082)

Sometimes generalizations come in negative form. Case studies are counted as evidence that science may not have features that are commonly thought as necessary requirements. Grote and O’Malley (cit.) propose their case against those philosophical descriptions that interpret scientific advancement in terms of general, overarching, and unifying theories. They observe that “productive interactions between different fields of science occur not only through the adaptation of theories, concepts, or models, but very much at the level of materials or experimental systems” (p. 1094, emphasis added).

c. A General Picture of Science

What is science in and of itself? How does it differ from other forms of knowledge? These two sides of the coin were a major motivating question for philosophy of science since its very beginning. Philosophers of biology sometimes take the methodological lessons they learn from biology and tentatively postulate their broader applicability to science (see Griesemer in section 7). However, a general view of science is often far from the explicit goals of philosophy of biology. There are historical reasons for this. In a paper on general philosophy of science, Psillos (2012) traces the problem back to Aristotle, through landmark thinkers like Immanuel Kant and Pierre Duhem, to the Modern era. The problem of demarcation was surely central in logical empiricism, but in the 1970s the idea was spread that “individual sciences are not similar enough to be lumped together under the mould of a grand unified scheme of how science works”

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(Psillos, cit.: 100). After 1950s—and certainly in the early 1980s, when philosophy of biology became an academic field—there was a consensus on the basic fact that science employs a variety of methods. Indeed, biology, together with other sciences like the human and the social sciences, had shaken the Modern idea of the scientific method.

Nevertheless, some important works have been moved by the need of finding new descriptions of science that would fit biology better than received ones, in order to legitimately include biology among the natural sciences. Political and intellectual movements, such as Intelligent Design, contribute to urging philosophy of biology to tackle the demarcation of science: their strategy includes casting doubts on the scientific status of official biological sciences and presenting alternative, religiously inspired views as scientific theories (Sober 2007, Boudry et al. 2010). The creationist movement is present in the philosophers’ mental map worldwide since at least 1981, when philosopher of biology Michael Ruse was a key witness for the plaintiff in the trial McLean vs. Arkansas, a challenge to the state law permitting the teaching of creation science in the Arkansas school system. The federal judge ruled that the state law was unconstitutional. A significant part of the written opinion (see http://www.talkorigins.org/faqs/mclean-v-arkansas.html) was devoted to philosophical considerations on the epistemological characteristics of science (Claramonte Sanz 2011). Intelligent Design is a new form of scientific creationism, characterized by the wedge strategy, or public insistence on supposed flaws in the established biological sciences combined with supposed scientific demonstrations of an Intelligent Designer of the Universe. While there are different positions about whether philosophers and scientists should directly appear in public debates with creationists, Intelligent Design undoubtedly engages philosophers of biology in reflecting upon possible distinctions within science (between hypotheses, theories, and models, for example), between science and pseudo-science, and between science and religious beliefs. With their competence, philosophers can help scientists in what sociologist Thomas F. Gieryn termed “boundary work” (1999). The need of working on demarcation can also stimulate critical revisions of the patterns of scientific explanation in biology. In a book on evidence, Elliott Sober (2008) stated in a provocatively:

If the only thing that evolutionary biologists do is go around saying

‘that’s due to natural selection’ when they examine the complex and useful traits that organisms have, they are engaged in the same sterile game that creationists play when they declare ‘that’s due to intelligent design’. Assumptions about natural selection of course can be invented that allow the hypothesis of natural selection to fit what we observe. But that is not good enough: the question is whether there is independent evidence for those auxiliary propositions. (Sober 2008, p. 189)

The semantic view of scientific theories is an example of a general account of science that was put to work in justifying evolutionary biology as a model-based science, in face of the inveterate poor fit of

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the received view based on syntactic theories and universal laws (Lloyd 1983, 1984, 1988). Under the semantic view, models constitute the core of scientific work; theories are to be seen as combinations of families of models plus hypotheses about the empirical scope of those models. This framework contrasts with the received view which described theories as sets of sentences—including laws—about the world. In the semantic view, laws are conceived in a new way: from universal empirical claims about the world, they become specifications of models, embedded in them. An important argument for philosophers of biology in the 1980s was that the semantic view was not developed ad hoc for evolutionary theory: it had already been successful in describing Newtonian mechanics, equilibrium thermodynamics, and quantum mechanics. However, it was also said, these sciences fitted the received view as well. The semantic view was very demanding in terms of formalization, so it worked only for a very limited area of biology Not all scientific work consists in model building, so the semantic view is hardly considered an exhaustive view of science, and things work so differently for different kinds of models (for example, mathematical vs. non-mathematical) that the existence of a unitary view was questioned (Downes 1992). But new versions of the semantic view continue to be the topic of papers and debates in philosophy of biology.

d. Generalization as a Possible Distinctive Feature of Philosophy with Respect to Biology

As we have seen, philosophy of biology formulates various degrees of generalizations about biology. These generalizations may concern biology as a whole or some subfield of biology. Even in close-distance case studies, where generalization seems far from the goals, it can be shown that generalizations are made (2.b). Philosophy is a generalizing activity.

This feature of philosophy may be a way to approach a tricky issue, namely the distinction between biology and philosophy of biology.

Intuitively, philosophy is different from science. The methods of philosophy are based, for example, on logical differences and implications (Hull 1969: 162) or on thought experiments (Rosenberg and McShea 2008: 6), while the methods of science are based on empirical phenomena. But this distinction is not as clear-cut as it might seem.

Scientists also use thought experiments. Einstein famously used them for developing both special relativity and general relativity, and Darwin worked intensely with thought experiments—to mention only two representative cases. Conceptual, foundational, and linguistic analyses are an integral part of scientific research too. This means that scientists autonomously do philosophy in their day-to-day work. Indeed, professional biologists, as thinkers, could and should shift from their own main activity to more philosophical ones whenever needed. The other way around, philosophers of biology usually want to contribute to the advancement of science. In a sense, they want to be part of science.

Furthermore, the methods of philosophy are constantly evolving, stimulated by advancements in biology, so that it is not rare now to find philosophical studies that include mathematical analysis, computer

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simulations, or even empirical research. The science-philosophy distinction is thus very blurred. Given this situation, is there any possible demarcation between philosophy and biology?

David Hull (2002) characterized philosophy of biology as meta-science:

Knowing some science can be of great assistance to philosophers of science, but philosophers of science as philosophers of science do not do science…. For example, the equation F = ma is part of science, in particular physics. The claim that F = ma is a law of nature is part of the domain of philosophy of science. To the extent that science and philosophy can be distinguished in practice, scientists tell us what the world is like, and philosophers of science tell us what science is like.

(Hull 2002, p. 117)

One interpretation of philosophy of science as meta-science, which seems faithful to Hull’s idea, is that philosophy of biology seeks generalizations about biology.

The idea of philosophy of biology as generalization about biology has descriptive advantages, but it would be contested by some philosophers.

In fact, no idea in the literature about the specificity of philosophy remains uncontroversial. When it comes to ambiguous science-philosophy cases, philosophers debate the right way of doing philosophy. They are much clearer in saying what it means to be a scientist than they are in saying what it means to be a philosopher.

In a view of philosophy as meta-science, the mark of philosophy is the leaning towards generalizations about science. This is not a yes/no requirement; it comes in degrees. Sometimes, for instance, works in biology make generalizations about biology (see Mayr and Gould’s examples below). These works sometimes become philosophical while other times they remain scientific because they generalize only to a degree which is functional to the scientific activity. This continuity accounts for the demarcation uncertainties that are going to persist in the field.

3. Philosophy Flanking Biology

As is demonstrated in other parts of this article, philosophy can take a theme and develop it with great autonomy from science or adopt a critical focus on science and on the complex relationship between science and society. According to many authors, however, there is also potential for philosophy to actively and directly contribute to the advancement of life sciences. While it is commonly accepted that biologists can undertake philosophy of biology, it is more controversial whether philosophers can do biology in a proper sense. But biologists have generally been a receptive community. In 2002, David Hull had written:

Philosophers are attempting to join with biologists to improve our understanding of…biological phenomena. As such, they run the risk of being considered by biologists to be ‘intruders’. In point of fact,

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biologists have been amazingly receptive to philosophers who have turned their hand to philosophy of biology with a significant emphasis on

“biology.” (Hull 2002: 124)

When philosophers are close to scientific practice and current problems, they see how they can help science in advancing towards its aims, either by criticizing existing ideas and practices or by proposing revised ones.

In Hull’s line of thought, philosophers are encouraged to devote time and effort to work with biologists, or to formulate problems in ways that are interesting and understandable to biologists. Philosophical treatments that are too extensive, stereotypical, or posed in a way that is not relevant to biologists, or those with an excess of philosophical formalization that prevents access to scientists, should be avoided:

“Formalization may be an excellent way of working out problems in the philosophy of science. It is not a very good way of communicating the results” (Hull 1969: 178).

Philosophers try to help biologists to better frame their questions, for example by “uncovering presuppositions and making them explicit”

(Sober 1984), by analyzing conceptual foundations (Pigliucci and Kaplan 2006), or by pursuing the detection, analysis, and sometimes solution of theoretical and methodological problems. A great deal of the philosophy of biology consists in working on scientific language to clarify the meaning of concepts such as life, purpose, progress, complexity, genetic program, adaptation, and so on (Rosenberg and McShea 2008: 4). Since these concepts frame the scientific questions, philosophy of biology can

“clarify, broaden or narrow the domain of theories, uncovering ‘pseudo- questions’” (Rosenberg and McShea, cit.: 6). Critical analysis and conceptual clarification are particularly valued tasks, and conceptual clarity is seen as a necessary virtue of philosophy of biology. One mode of work consists in looking, together with biologists, at concepts or mathematical models and their interpretations. This line of work is exemplified hereafter (3.a, 3.b): two traditional areas where philosophy has contributed by casting some light are the connections among biological enterprises like taxonomy, classification, and systematics (3.a), and the abstract descriptions of natural selection (3.b).

a. Clarifying Taxonomy, Classification, Systematics, Phylogeny, Homology

In biology, taxonomy consists in the recognition of natural groups, that is the taxa (singular: taxon). Classification deals with the categories and ranks to be assigned to taxa (for example, species, genus, family). Systematics is, by definition, a systematic study of the living world in search for order, or, in other words, the search for the relationships among taxa. And phylogeny is the reconstruction of the temporal scheme of common descent and relatedness among taxa. In fact, despite these gross characterizations, the four activities are intertwined and depend on each other. Their distinctions, definitions, and relationships are a traditional matter of reflection for philosophy of biology (Wilkins and Ebach 2011).

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In the 1960s, philosophers, perhaps thanks to the heritage of the Western philosophical tradition, proved to be particularly ready and equipped for helping scientists understand their own various ways of finding order in the living world. According to Hull (1969), one of the important early contributions of philosophy of biology to logical clarity was the taxon- category distinction, the distinction between “individuals, classes, and classes of classes” (p. 171). Philosophers were able to contribute, for Hull, once they accepted to arrange their formalisms to communicate with biologists. Hull himself (1976) long argued for species having the ontological status of evolutionary individuals unlike taxa in other categories. Hull relied on the Biological Species Concept (BSC) that defines species as reproductive communities. In accordance with the BSC, whereas a taxon is determined by a set of shared characteristics, the species-rank of the taxon—its membership in the species category—is determined by actual evolutionary relationships, in particular by interbreeding habits. With a similar line of reasoning, Hull defended the idea of species as historical individuals, as opposed to classes or types.

Species, perhaps, are leaving the limelight of philosophical reflection as a consequence of the body of discoveries about the fluidity of their boundaries, the heterogeneity of their phenomenology, and the rarity of canonic biological species across the biological world. But the debate on individuality was complex and lively, and is still partly open today (Wilkins 2011).

In early years, philosophy of biology demonstrated its value also by analyzing the entanglement among biological hypotheses—explicit and implicit—in different domains. For example, philosophers refuted the idea of taxonomy as a theory-free activity, prior to functional attributions and to evolutionary hypotheses. Character recognition does bring into play theoretical considerations: the definition of “kidney,” for instance, presupposes physiological knowledge of kidney function, and/or hypotheses on the evolutionary derivation of kidneys. The acceptance of evolutionary theory in all fields of biology, completed during the first half of the 20th century, triggered hot debates on its relevance to taxonomy, systematics, and classification (Hull 1970): does taxonomy have to reflect evolution? And in what sense? Could adaptation by natural selection be a criterion for systematics, or is pure common descent the candidate?

Philosophers took part in trying to clarify these issues.

The network of assumptions and hypotheses of biology is an enduring object of study for philosophy. There is a certain consensus on the fact that phylogeny should constrain systematics; that is, systematics should reflect phylogeny as much as possible. Many authors even equate the two tasks altogether: “Practitioners of systematics study the historical pattern of evolution among groups of living things, i.e., phylogeny”

(Haber 2008). Yet, taxonomy, classification, systematics, and phylogeny are unequally performed by different professionals upon significantly uneven living and fossil taxa, and there are many conflicting needs and goals. Species concepts in paleontology are by force very different from those that fit neontology (Wilkins 2011), an issue that yields differently organized classifications (Wilkins & Ebach 2013). Even among biologists who study currently living organisms, the ideas on how to integrate

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taxonomy and classification with systematics and phylogeny vary much across specialists at all degrees of specialization—for example,entomologists, botanists, and mammalogists. Furthermore, a classification of domestic animals or plants is likely to incorporate much morphological, physiological, and ecological information beyond phylogenetic relationships if it is to be of any practical use to the knowledge communities that are involved in rearing. And when it comes to decide what information is relevant to identify endangered species (or other units) that should be the object of conservation biology, different ideas —and ethical stances are on the table (Casetta and Marques da Silva 2015).

Philosophy of biology can make or support concrete proposals about how to integrate and refine the various ways of ordering the living world.

Philosopher Marc Ereshefsky (1997), for example, has been arguing for systems of nomenclature that are alternative to the Linnean hierarchy (species-genera-Orders etc.). The reason for this position is that all scientific changes that have been happening after Linnaeus’ century—

Darwinism, neo-Darwinism, cladistics and new methods in systematics—

have turned the hierarchy into an obstacle rather than an aid to taxonomical work.

A specific challenge for philosophy of biology isphylogenetic trees, which are ever revisable hypotheses corroborated to varying degrees. Epistemological and methodological discussions concern the ways of building, interpreting, testing, and revising trees, as well as of relating them to other domains of knowledge such as taxonomy or adaptation. “So what can biologists meaningfully say about phylogeny?”

philosopher Matt Haber asks (2008).

Broadly, two different issues have been at the center of recent systematics debates: given epistemic limitations, whether any inference of phylogeny may justifiably be drawn; and given an affirmative answer, what methods ought biologists use to justifiably infer phylogenies, and what are the limits of these inferences? (Haber 2008, p. 231)

Competing and sometimes conflicting methods have been developed to make phylogenetic inference more exact, manageable, or informative. In this domain, methodological differences raised heated conflicts among scientists. The parsimony principle was questioned in its legitimacy and importance. The principle states that the most economic hypothesis has to be more true (Sober 1988). More generally, trees have been examined for their theory-ladenness, that is, their sensitivity to background theoretical assumptions. Other contentious matters were the acceptability of different kinds of data ( genetic vs. morphological, for example), and the limits of the domain of phylogenetic inference. Some workers maintain that methods in phylogenetics should be able to detect homologies (see also 2.a) with certainty, discerning them from analogies.

Many others argue under different conceptions that homology detection should rely on large amounts of data, mathematical models of evolution, and probability. Supporters of cladistics reject probability and likelihood for being an unstable ground on which to draw evolutionary trees. They

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put more confidence in the cladist practictioner’s ability to recognize derivation between characters (Hull 1970, Haber 2008). Meanwhile, the great majority of phylogenetic trees are built by relying on huge sets of genetic sequences and a few morphological characters by means of more and more cost-effective computer programs (this is an example of novel computer-based scientific techniques posing new philosophical problems, see more below). “Total evidence” methods (Sober 2008) address the challenge of building phylogenetic trees by integrating all the available evidence—morphological, geological, ecological, and fossil.

The question of homology is a last example of philosophical enquiry into entangled theoretical backgrounds and hypotheses: “when are two instances of a character to be considered instances of the same character and in what sense?” (Hull 1969: 174). Griffiths and Brigandt (2007) recognize different concepts of homology. The taxic approach to homology—the best known in systematics and philosophy—uses points of resemblances between organisms (shared character states) to diagnose their evolutionary relationships. The transformational approach focuses on the different states in which the same character can exist and be transformed by evolution. A third approach to homology has emerged in conjunction with findings of evolutionary developmental biology (EvoDevo): homology at the phenotypic level is potentially decoupled from homology of developmental processes and homology at the level of the genome (a phenomenon called hierarchical disconnect, see also 2.a).

The level of depth thus becomes a necessary specification for homology.

Griffiths and Brigandt (cit.) see the different concepts of homology as not only compatible but strongly complementary, and trigger a series of reflections on their relationships.

b. Formulating Natural Selection

Charles Darwin (1859) conceived natural selection as the mechanism of change, splitting, and divergence of lineages. Natural selection is thus the most essential notion of evolutionary theory. Darwin’s formulation of natural selection, substantiated by many empirical studies, was essentially verbal. After Darwin, definitions of natural selection underwent diversification as well as progressive refinement.

Mathematical models of natural selection, created in the 20th century, made the process more precise, as population genetics introduced technical terms such as fitness and selection pressures (Haldane 1924), and established different formulas to quantify natural selection and to measure its intensity and effects. But population genetics and mathematics didn’t exhaust the task of formulating natural selection in a theoretical and general way, and philosophers of biology eventually became very actively involved. A classical abstraction of natural selection was elaborated by Richard Lewontin (1970). It was based on variation, fitness, and heritability. Today philosophers acknowledge the value of that account, but they also criticize it as, at once, too simple and too demanding (Godfrey-Smith 2009), ascribing it to a category of recipe descriptions that list the supposedly few and simple ingredients of natural selection. David Hull and Richard Dawkins, for example,

independently introduced the original distinction

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between replicator and interactor, or vehicle. A replicator is anything that passes its structure on largely intact, while an interactor is a cohesive unit whose action in the environment makes a difference in the replication of the replicators it carries. Richard Dawkins (1976), interpreting the work of William Hamilton and George C. Williams (1966), famously took the basic idea of kin selection and developed it into the gene’s eye view, a general view of evolution where selection in the long run is seen as operating basically on genes and organisms are seen as their vehicles. Kin selection (Maynard-Smith 1964) is based on shared inheritance among relatives. Social donor traits are expected to spread in the population if they increase the fitness of the donor’s close relatives, which are likely bearers of the same traits. Inclusive fitness (Hamilton 1963, 1964) is the fitness of a trait deriving from the bearer’s survival and reproduction plus survival and reproduction of relatives (proportionally to the amount of genetic sharing). Dawkins’s “selfish gene” metaphor, based on these mathematical findings, was welcomed by many biologists as a clarifying device in their day-to-day work. Its effects in the public perception of science are a different story that will be addressed later in the article. Some philosophers of biology got involved in the metaphor, either to develop it (for example, Dennett 1995) or, more often, to criticize it (see Oyama 1998). Several philosophers tried to find other ways of characterizing natural selection. We have already mentioned Sober’s (1984) work on this problem (2.a). Sober (1983) also described evolutionary theory as a theory of forces and population genetics as a theory of “equilibrium models.” Abstract accounts of natural selection and its enabling conditions flourished again with the turn of the 21st century. For Okasha (2006), a replicators-interactors account is too demanding and narrow, imposing unnecessary requirements for natural selection to occur. For Godfrey-Smith (2009), the concept of a population is the crucial one: some features of a population render it “paradigmatically Darwinian”, making natural selection happen. One motivating idea of such descriptions is their potential use for evaluating the operation of natural selection among units at different levels and in different domains (Rosenberg and McShea 2008). We will see below the example of the domain of culture: what kind of selection, if any, is plausible in the cultural domain?

Darwin thought natural selection happened chiefly among individuals:

the individual organism was the unit of selection. But late Darwin introduced “group selection” for explaining some traits of humans and social insects (Darwin 1971). Groups were foreshadowed as a larger unit of selection, and group selection seemed to be the explanation for traits that jeopardize individual interest, such as cooperation and abnegation.

In the 1960s, evolutionary modeling showed that group selection required repeated isolation, mixture, and re-isolation, namely conditions too narrow to be found in nature with any significant frequency (Maynard-Smith 1964). Group selection was disavowed; traits would not evolve simply because they are good for a group, they have to be selectively advantageous in inter-individual competition from their inception. In the 1970s, some philosophers of biology participated in a movement along with evolutionary biologists and social scientists to try

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and develop group selection into a scientifically respectable concept (Wilson 1975). In the meantime, kin selection had emerged as a potential alternative explanation for group-beneficial, unselfish traits, leading many scientists to conclude that group selection may be apparent and re- described as kin selection if group members are relatives. Philosophers got directly involved in the debate, sometimes working directly with biologists. In 1984, Elliott Sober, citing Williams (1966) among others, talked about the “mirage” of group fitness, seen as a mere statistical summation of individual fitnesses: “Selection works for the good of the organism; a consequence may be that some groups are better than others. However, it does not follow that selection works for the good of the group” (Sober 1984: 2). In many cases, the individual-based hypothesis is simpler than the group-level characterization, so the principle of parsimony would recommend not adding explanatory mechanisms. However, more in general, “Group, kin, and individual selection need to be disentangled, their difference made clear” (Sober 1984: 4). In fact, conceptual difficulties and fallacies in the units of selection framework were the attractor for philosophers to this debate.

Sober changed his mind about group selection through a more careful conceptual analysis and by joining the work of biologist D.S. Wilson (Sober and Wilson 1998). Most philosophers now think that unselfish traits may be explained or made plausible by some combination of trait- level selection, organismal selection, and group selection in a weak sense, together with a multiplication of hierarchies of evolutionary entities and an “extended taxonomy of fitness” that contemplates co- opted by-products and functional shifts (Pievani 2011).

Beyond gene, individual, and group selection, some authors have also attempted to recognize higher levels, such as family selection, species selection, and clade selection, although authoritative biologists such as Ernst Mayr contested this idea: “in no case are these entities as such the object of selection. Selection in these cases always takes place at the level of individuals” (Mayr 1997). Today, for many biologists, the question of what unit is the “true” fundamental unit of selection has been satisfactorily settled—there are several—but there are now new theoretical and empirical questions. Given that multiple levels of vehicles exist, how does natural selection affect selection at lower or higher levels, and how are higher-level vehicles created by lower-level selection (Keller 1999)? The explanatory scope of multi-level selection, as philosophers have often emphasized, is challenged by the major evolutionary transitions in the history of life (Maynard Smith and Szathmáry 1995). Philosophers tend to describe a major transition in evolution as a phase of emergence of a new level—with new units—of selection. The new level contrasts or suppresses selection at the lower level, a process baptized “de-Darwinization” by Godfrey-Smith (2009).

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