The philosophy of molecular biology was, for a time, entirely preoccupied with reduction and reductionism: primarily the reduction of classical genetics to molecular genetics (Kitcher 1984, Waters 1994, Sarkar 1998), but also and more recently the reduction of complex organismal phenotypes to genes (Rosenberg 1997, Sarkar 1998). While these remain of substantial interest, some new areas of interest have also emerged, including philosophical attention to molecular mechanisms (Machamer, Craver, and Darden 2000, Darden and Tabery 2005) and mathematical models (Keller 2002, Sarkar 2005). In-depth focus on the intricate details of the science is increasingly commonplace (e.g., Schaffner 2000, Burian 2004, Sarkar 2005). Molecular biology has also proved to be of philosophical interest not only for its own sake, but also in the service of molecular explanations of evolution (e.g., Burian 2004), disease (e.g., Kitcher 1996), and behavior (e.g., Schaffner 2000), inter alia.

Accelerating developments in molecular biology since 1953 have strongly encouraged the advocacy of reductionism by a number of important biologists, including Crick, Monod, and E. O. Wilson, and strong opposition by equally prominent biologists, especially Lewontin, along with most philosophers of biology.

Reductionism is a metaphysical thesis, a claim about explanations, and a research program. The metaphysical thesis that reductionists advance (and antireductionists accept) is physicalism, the thesis that all facts, including the biological facts, are fixed by the physical and chemical facts; there are no nonphysical events, states, or processes, and so biological events, states, and processes are “nothing but” physical ones. This metaphysical thesis is one reductionists share with antireductionists. The reductionist argues that the metaphysical thesis has consequences for biological explanations: they need to be completed, corrected, made more precise, or otherwise deepened by more fundamental explanations in molecular biology. The antireductionist denies this inference, arguing that nonmolecular biological explanations are adequate and need no macromolecular correction, completion, or grounding. The research program that reductionists claim follows from the conclusion about explanations can be framed as the methodological moral that biologists should seek such macromolecular explanations.

Most of the issues found in traditional philosophy of science are recapitulated in the philosophy of neurobiology. In particular, philosophers of neurobiology worry about what counts as appropriate empirical justification for a theoretical claim, how to determine which level of organization is the correct one for a scientific explanation, what explanations should look like, whether all explanations will or should reduce to some primitives, and how what we learn about the mind/brain should affect larger social, economic, and political decisions.

In addition, philosophers of neurobiology concern themselves with some traditional aspects of philosophy of mind, including worrying how it is a brain can represent, if it does, and how and whether this representation ties to other notions of representation in cognitive science and beyond. It is difficult to focus on only one of these concerns to the exclusion of the rest. Most likely, as we come to understand some particular aspect of the practice of neurobiology, we will also understand others as well. In what follows, I discuss these areas of concern as they differ from traditional arguments. This discussion therefore should be laid on top of and be seen to complement the very rich literature in traditional philosophy of science and philosophy of mind.

INTRODUCTION

During the last three decades, biodiversity conservation has emerged as a central focus of environmental concern in many regions of the world (Sarkar 2005). As a result, large-scale efforts are being devoted to devising systematic protocols for conservation, sometimes involving computational efforts unprecedented in ecology (Margules and Pressey 2000). These efforts presume that a sufficiently precise concept of biodiversity is at hand. Some philosophical attention has also been focused on elaborating an adequate normative basis for conservation. These attempted normative justifications for biodiversity conservation also depend on what is meant by biodiversity. Yet, “biodiversity” remains a contested term.

The term “biodiversity” was first used in 1986 as a contraction for “biological diversity” by Walter G. Rosen while planning for a (U.S.) National Forum on Biodiversity (Takacs 1996). Subsequently, temporarily mutated as “BioDiversity,” it was used as the title for the proceedings from that meeting (Wilson 1988). No attempt was made to define the term precisely, even as its use spread - the chronology in Table 21.1 includes the most salient episodes. Conservation biology also emerged as a distinct interdisciplinary research area during the 1980s with its central aim the protection of biodiversity (Takacs 1996, Sarkar 2002, 2005).

INTRODUCTION

Population genetics is a subfield of evolutionary biology that aims to represent mathematically the changes in the genetic variation of populations (specifically, sexually reproducing populations with Mendelian heredity) over time. The mathematical models of population genetics provide a theoretical basis for experimental studies of laboratory populations and studies of natural populations. Our primary focus in this essay is on population genetics theory itself, rather than its applications, although towards the end of the essay we give some discussion of the latter.

Population genetics attempts to measure the influence of the causes of evolution, namely, mutation, migration, natural selection, and random genetic drift, by understanding the way those causes change the genetics of populations. But how does it accomplish this goal? We begin in Section 2 with a brief historical outline of the origins of population genetics. In Section 3, we sketch the model theoretic structure of population genetics, providing the flavor of the ways in which population genetics theory might be understood as incorporating causes. In Sections 4 and 5 we discuss two specific problems concerning the relationship between population genetics and evolutionary causes, namely, the problem of conceptually distinguishing natural selection from random genetic drift, and the problem of interpreting fitness. In Section 6, we briefly discuss the methodology and key epistemological problems faced by population geneticists in uncovering the causes of evolution. Section 7 of the essay contains concluding remarks.

The historian Raphael Falk has described the gene as a 'concept in tension' (Falk 2000) - an idea pulled this way and that by the differing demands of different kinds of biological work. Several authors have suggested that in the light of contemporary molecular biology 'gene' is no more than a handy term that acquires a precise meaning only in some specific scientific context in which it is used. Hence the best way to answer the question 'What is a gene?', and the only way to provide a truly philosophical answer to that question is to outline the diversity of conceptions of the gene and the reasons for this diversity. In this essay we draw on the extensive literature in the history of biology to explain how the concept has changed over time in response to the changing demands of the biosciences. In this section we have drawn primarily on the work of Raphael Falk (1986, 1991, 1995, 2000, 2001, 2005, in press), Michael Dietrich (2000a, 2000b), Robert Olby (1974, 1985), Petter Portin (1993), and Michael Morange (1998). When our historical claims are commonplaces that can be found in several of these sources we do not cite specific works in their support. We have also chosen not to explain basic genetic terminology, as this would have occupied much of the chapter. More specialized terms are explained when they cannot be avoided. In the final part of the essay we outline some of the conceptions of the gene current today. The seeds of change are implicit in many of those current conceptions and the future of the gene concept appears set to be at as turbulent as its past.

I distinguish between Platonic and Aristotelian teleologies. I detail William Paley's Platonic teleological argument for the existence of God from natural design and offer Darwin's theory of natural selection as an antiteleological response. But, since Aristotle's teleology is distinct from Plato's teleology I ask to what extent is Darwin's theory anti-Aristotelian.

Teleology in biology is making headline news in the United States. Conservative Christians are utilizing a teleological argument for the existence of a supremely intelligent designer to justify legislation calling for the teaching of “intelligent design” (ID) in public schools. Teleological arguments of one form or another have been around since antiquity. The contemporary argument from intelligent design varies little from William Paley's argument written in 1802. Both argue that nature exhibits too much complexity to be explained by “mindless” natural forces alone.

What is so remarkable about complex designs? Compare a watch with a stone. According to Paley, watches are complex and stones are not because a watch's functioning depends on its precise arrangement; a stone's does not. Michael Behe, a contemporary advocate of intelligent design, labels the sort of complexity “irreducible complexity”: if you remove any part, the whole structure ceases to function (Behe 1996). The bacterial flagellum, Behe argues, is irreducibly complex. It acts as a tiny propeller spinning at more than 20,000 revolutions per minute.

INTRODUCTION: MECHANISMS AND MODELS

Biologists often seek to discover mechanisms. Knowledge of biological mechanisms is valuable because descriptions of them often play the roles attributed to general scientific theories. They provide explanations of puzzling phenomena. They enable biologists to make predictions. They aid the design of experiments. They may explain domains of wide scope. They may make possible medical or biotechnological interventions for practical purposes. Especially in molecular biology, theories consist of sets of mechanism schemas, such as those for DNA replication and protein synthesis.

Biologists use many types of models to represent and discover mechanisms: diagrammatic models, physical scale models, analogue models, model organisms, in vitro experimental systems, mathematical models, computer graphic and simulation models. Models represent and substitute for the thing modeled, while being easier to understand, manipulate, or study. Choice of an appropriate model depends on the problem to be solved using it. In medicine, animal models are often used when the goal is to understand disease mechanisms in humans. Molecular biologists use bacteria and viruses as models for mechanisms with domains of very wide scope, such as DNA replication.

INTRODUCTION

The historical, conceptual, and cultural interplay between biology and religion involves a complex and philosophically fascinating set of relationships. Certainly the simple view that religion has uniformly been a hindrance to biological research is an unfair caricature. Religion has sometimes had a positive effect, often indirectly stimulating or even directly encouraging scientific research of the biological world. Similarly, biology has had a profound effect on religion, sometimes offering challenges that require believers to reassess basic theological assumptions. Scholars have examined both directions of influence, finding both expected and unexpected connections (e.g., Cantor 2005, Rolston 1999, Russell, Stoeger, and Ayala 1999). This chapter will give a necessarily selective account of some of the mutual influences between biology and religion. Its major purpose will be to highlight a deep pattern underlying their interplay, namely, the pervasive effect of the religious idea of the divinely created normativity of nature.

How this pattern is exemplified in multiple ways in the ongoing creationist controversy will be a recurring example, but we will also examine how it may be seen in a wide range of issues from questions about what it means to be human; to religious warnings against “playing God”; to views about gender roles and sexual morality, environmentalism, personhood, and the status of the fetus; and ultimately to metaphysics and the question of ultimate priority in creation. We begin by looking at biological evolution, a critical topic that intertwines with many of these other cases.

Evolutionary developmental biology is an emerging new research area that explores the links between two fundamental processes of life: development of individual organisms (ontogeny) and evolutionary transformation in the course of the history of life (phylogeny). For some of its more ardent proponents evolutionary developmental biology, or evo-devo for short, represents a new paradigm that completes the “Modern Synthesis” of the 1930s and 1940s, while others, often those with a more astute sense of the history of biology, have emphasized the long-standing connections between these two areas of study. But all agree that evo-devo offers some of the most promising theoretical perspectives in evolutionary biology at the beginning of the twenty-first century (see for example Amundson 2005, Carroll 2005, Carroll et al. 2005, Hall 1998, Kirschner and Gerhart 2005, Laubichler 2005, Müller 2005, Wagner et al. 2000). In this essay I will first sketch the emergence of present day evolutionary developmental biology during the last decades of the twentieth century followed by a brief overview of the central questions and research programs of evo-devo. I will conclude with a discussion of the one problem - the issue of how to explain evolutionary innovations and novelties - that has the most profound implications for the philosophy of biology.

The theory of evolution by natural selection is, perhaps, the crowning intellectual achievement of the biological sciences. There is, however, considerable debate about which entity or entities are selected and what it is that fits them for that role. In this chapter I aim to clarify what is at issue in these debates by identifying several distinct, though often confused, concerns and then identifying how the debates on what constitute the units of selection depend to a significant degree on which of these different questions a thinker regards as central. Chief among these distinctions are replicators versus interactors as well as who benefits from a process of evolution by selection, that is, who benefits in the long run from a selection process and who gets the benefit of possessing adaptations that result from a selection process. Because Richard Dawkins is the primary source of several of the confusions addressed in this essay, I treat his work at some length.

INTRODUCTION

For more than twenty-five years, certain participants in the ‘‘units of selection’’ debates have argued that more than one issue is at stake. Richard Dawkins (1978, 1982a), for example, introduced ‘‘replicator’’ and ‘‘vehicle’’ to stand for different roles in the evolutionary process. He proceeded to argue that the units of selection debates should not be about vehicles, as they had formerly, but about replicators. David Hull (1980) in his influential article ‘‘Individuality and Selection’’ suggested that Dawkins’s ‘‘replicator’’ subsumes two quite distinct functional roles and broke them up into ‘‘replicator’’ and ‘‘interactor.’’ Robert Brandon (1982), arguing that the force of Hull’s distinction had been underappreciated, analyzed the units of selection controversies further, claiming that the question about interactors should more accurately be called the ‘‘levels of selection’’ debate to distinguish it from the dispute about replicators, which he allowed to keep the ‘‘units of debate’’ title.

INTRODUCTION

The concept of information has acquired a strikingly prominent role in contemporary biology. This trend is especially marked within genetics, but it has also become important in other areas, such as evolutionary theory and developmental biology, especially where these fields border on genetics. The most distinctive biological role for informational concepts, and the one that has generated the most discussion, is in the description of the relations between genes and the various structures and processes that genes play a role in causing. For many biologists, the causal role of genes should be understood in terms of their carrying information about their various products. That information might require the cooperation of various environmental factors before it can be “expressed,” but the same can be said of other kinds of message.

An initial response might be to think that this mode of description is entirely anchored in a set of well-established facts about the role of DNA and RNA within protein synthesis, summarized in the familiar chart representing the “genetic code,” mapping DNA base triplets to amino acids. However, informational enthusiasm in biology predates even a rudimentary understanding of these mechanisms (Schrodinger 1944). And more importantly, current applications of informational concepts extend far beyond anything that can receive an obvious justification in terms of the familiar facts about the specification of protein molecules by DNA.

A SUMMARY OF THE ARGUMENT

Human biology faces three great research frontiers: ontogenetic decoding, the brain-mind puzzle, and the ape-to-human transformation. By ontogenetic decoding, or the egg-to-adult transformation, I refer to the problem of how the unidimensional genetic information encoded in the DNA of a single cell becomes transformed into a four-dimensional being, the individual that grows, matures, and dies. Cancer, disease, and aging are epiphenomena of ontogenetic decoding. By the brain-mind puzzle I refer to the interdependent questions of (1) how the physicochemical signals that reach our sense organs become transformed into perceptions, feelings, ideas, critical arguments, aesthetic emotions, and ethical values; and (2) how, out of this diversity of experiences, there emerges a unitary reality, the mind or self. Free will and language, social and political institutions, technology and art, are all epiphenomena of the human mind. By the ape-to-human transformation I refer to the mystery of how a particular ape lineage became a hominid lineage, from which emerged, over only a few million years, humans able to think and love, to develop complex societies and subject to ethical, aesthetic and other values. The human genome differs little from the chimp genome.

MINIMALIST MODELS OF MACROEVOLUTION

Palaeobiology is our main source of direct evidence about the history of life. But while that history is fascinating in itself, palaeobiology's most distinctive contribution to evolutionary theory is the insight it provides on the importance of scale. Palaeobiologists see the results of evolutionary processes summed over huge sweeps of space and time. As a consequence of that window on the effects of deep time and vast space, we have a chance to see whether the palaeobiological record enables us to identify evolutionary mechanisms that are invisible to contemporary microevolutionary studies with their local spatial, temporal, and taxonomic scales. Palaeobiology, in other words, is the discipline of choice for probing the relationship macroevolutionary patterns and microevolutionary processes.

This chapter will be organised around an important framing idea: that of a “minimalist model” of this relationship. I shall discuss minimalism in detail shortly, but as a rough first approximation, according to minimalism, macroevolutionary patterns are direct reflections of microevolutionary change in local populations; they are reflections of changes of the kind we can observe, measure, and manipulate. For example, Michael Benton (forthcoming) discusses models of global species richness that depend on scaling up in space and time equilibrium models of local ecological communities.

INTRODUCTION: UNDEAD DOGMAS OF EMPIRICISM

The philosophy of biology has matured quite a bit over the last two decades. Back in 1988, Ruse noted a conspicuous dearth of work on ecology. But by 1999, Sterelny and Griffiths devoted an entire chapter to it in their introduction to the philosophy of biology. There is still plenty of room, and reason, for more philosophical attention to a science so vital for understanding and addressing environmental concerns. But at least several people now make philosophy of ecology their academic specialty.

In the following I shall very briefly survey recent developments in both ecology and the philosophy thereof. One important aspect of the developments within ecology is an expansion to larger spatiotemporal scales of investigation. This wider focus has often, though not always, resulted in a shift in perspective, from viewing ecological entities as closed systems to treating them as open systems. I will take a closer look at three examples of scale expansion and tease out some of their implications for environmental policy, on one hand, and still-common reductionist philosophies of science, on the other. Finally, I will consider the philosophical implications of the search for mechanisms, when the open nature of the systems under study is acknowledged.

INTRODUCTION

Game theory is now a standard tool for explaining puzzling and counterintuitive behavior. But in spite of the fact that game theory was developed to investigate rational and economic behavior of modern humans, it has found equally valuable application in biology. For example, it has often been observed that when fights break out between members of the same species, the antagonists often display restraint by not inflicting serious injury on each other during the fight. To take another example, individual guppies will sometimes go out of their way to swim beside a larger fish that may turn out to be a predator (Dugatkin and Alfieri 1991a, b). And chimpanzees will often raise an alarm to the rest of their group when they spot a dangerous predator, in spite of the fact that an individual who does so will attract the attention of the predator.

These behaviors should be puzzling to anyone who thinks of evolution as 'nature red in tooth and claw'. However, they can all be explained in a very satisfying way by applying simple game-theoretic analyses. The purpose of this chapter is to illustrate enough game theory to show how it may be applied to the task of explaining such puzzling behavior. Although the range of such behaviors is extremely large, and the range of available game-theoretic techniques is equally large, I shall focus on game-theoretic explanations of one particular kind of behavior - namely, altruism.