Massimo Pigliucci

Is integrative biology a good idea, or even possible? There has been much interest lately in the unifica- tion of biology and the integration of traditionally separate disciplines such as molecular and develop- mental biology on one hand, and ecology and evolutionary biology on the other. In this paper I ask if and under what circumstances such integration of efforts actually makes sense. I develop by example an analogy with Aristotle’s famous four “causes” that one can investigate concerning any object or phenomenon: material (what something is made of), formal (what distinguishes that particular object from others), efficient (how was the object made) and final (why was the object made). The example is provided by ongoing research on different aspects of flowering time in the model system Arabidop- sis, a small weed belonging to the mustard family. I show that understanding how flowering time is controlled is an epistemologically different sort of question from why and how it evolved, and that the two research agendas can be pursued largely independently of each other. Toward the end, I propose that the real goal of integrative biology is to understand the boundary layers between levels of biologi- cal analysis, something to which modern philosophy of science can contribute significantly.

The theory of evolution, which provides the conceptual framework for all modern research in organismal biology and informs research in molecular bi- ology, has gone through several stages of expansion and refinement. Darwin and Wallace (1858) of course proposed the original idea, centering on the twin concepts of natural selection and common descent. Shortly thereafter, Wallace and August Weismann worked toward the complete elimination of any Lamarckian vestiges from the theory, leaning in particular on Weismann’s (1893) concept of the separation of soma and germ, resulting in what is some- times referred to as “neo-Darwinism”.

We attempt to improve the understanding of the notion of agene being `for a phenotypic trait or traits. Considering theimplicit functional ascription of one thing being `for another,we submit a more restrictive version of `gene for talk.Accordingly, genes are only to be thought of as being forphenotypic traits when good evidence is available that thepresence or prevalence of the gene in a population is the resultof natural selection on that particular trait, and that theassociation between that trait and the gene in question isdemonstrably causal. It is therefore necessary to gatherstatistical, biochemical, historical, as well as ecologicalinformation before properly claiming that a gene is for aphenotypic trait. Instead of hampering practical use of the `genefor talk, our approach aims at stimulating much needed researchinto the functional ecology and comparative evolutionary biologyof gene action.

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

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their func- tionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adapta- tions, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an oppor- tunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would sug- gest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to imple- ment novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engi- neering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engi- neering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms.

It is an unfortunate fact of academic life that there is a sharp divide between science and philosophy, with scientists often being openly dismissive of philosophy, and philosophers being equally contemptuous of the naivete ́ of scientists when it comes to the philosophical underpinnings of their own discipline. In this paper I explore the possibility of reducing the distance between the two sides by introducing science students to some interesting philosophical aspects of research in evolutionary biology, using biological theories of the origin of religion as an example. I show that philosophy is both a discipline in its own right as well as one that has interesting implications for the understanding and practice of science. While the goal is certainly not to turn science students into philoso- phers, the idea is that both disciplines cannot but benefit from a mutual dialogue that starts as soon as possible, in the classroom.

The so-called ‘‘species problem’’ has plagued evolution- ary biology since before Darwin’s publication of the aptly titled Origin of Species. Many biologists think the problem is just a matter of semantics; others complain that it will not be solved until we have more empirical data. Yet, we don’t seem to be able to escape discussing it and teaching seminars about it. In this paper, I briefly examine the main themes of the biological and philosophical liter- atures on the species problem, focusing on identifying common threads as well as relevant differences. I then argue two fundamental points. First, the species problem is not primarily an empirical one, but it is rather fraught with philosophical questions that require—but cannot be settled by—empirical evidence. Second, the (dis-)solution lies in explicitly adopting Wittgenstein’s idea of ‘‘family resemblance’’ or cluster concepts, and to consider spe- cies as an example of such concepts. This solution has several attractive features, including bringing together apparently diverging themes of discussion among bio- logists and philosophers. The current proposal is con- ceptually independent (though not incompatible) with the pluralist approach to the species problem advocated by Mishler, Donoghue, Kitcher and Dupre ́, which implies that distinct aspects of the species question need to be emphasized depending on the goals of the researcher. From the biological literature, the concept of species that most closely matches the philosophical discussion pre- sented here is Templeton’s cohesion idea.

Making Sense of Evolution explores contemporary evolutionary biology, focusing on the elements of theories—selection, adaptation, and species—that are complex and open to multiple possible interpretations, many of which are incompatible with one another and with other accepted practices in the discipline. Particular experimental methods, for example, may demand one understanding of “selection,” while the application of the same concept to another area of evolutionary biology could necessitate a very different definition.

During the last two decades the role of quantitative genetics in evolutionary theory has expanded considerably. Quantitative genetic-based models addressing long term phenotypic evolution, evolution in multiple environments (phenotypic plasticity) and evolution of ontogenies (developmental trajectories) have been proposed. Yet, the mathematical foundations of quantitative genetics were laid with a very different set of problems in mind (mostly the prediction of short term responses to artificial selection), and at a time in which any details of the genetic machinery were virtually unknown. In this paper we discuss what a model is in population biology, and what kind of model we need in order to address the complexities of phenotypic evolution. We review the assumptions of quantitative genetics and its most recent accomplishments, together with the limitations that such assumptions impose on the modelling of some aspects of phenotypic evolution. We also discuss three alternative appr oaches to the theoretical description of evolutionary trajectories (nonlinear dynamics, complexity theory and optimization theory), and their respective advantages and limitations. We conclude by calling for a new theoretical synthesis, including quantitative genetics and not necessarily limited to the other approaches here discussed.

The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we still lack a theory of forms. The field began, in fact, as a theory of forms in Darwin’s days, and the major goal that an EES will aim for is a unification of our theories of genes and of forms. This may be achieved through an organic grafting of novel concepts onto the foundational structure of the MS, particularly evolvability, phenotypic plasticity, epigenetic inheritance, complexity theory, and the theory of evolution in highly dimensional adaptive landscapes.

Mayr’s proximate–ultimate distinction has received renewed interest in recent years. Here we discuss its role in arguments about the relevance of developmental to evolutionary biology. We show that two recent critiques of the proximate–ultimate distinction fail to explain why developmental processes in particular should be of interest to evolutionary biologists. We trace these failures to a common problem: both critiques take the proximate–ultimate distinction to neglect specific causal interactions in nature. We argue that this is implausible, and that the distinction should instead be understood in the context of explanatory abstractions in complete causal models of evolutionary change. Once the debate is reframed in this way, the proximate–ultimate distinction’s role in arguments against the theoretical significance of evo-devo is seen to rely on a generally implicit premise: that the variation produced by development is abundant, small and undirected. We show that a “lean version” of the proximate–ultimate distinction can be maintained even when this isotropy assumption does not hold. Finally, we connect these considerations to biological practice. We show that the investigation of developmental constraints in evolutionary transitions has long relied on a methodology which foregrounds the explanatory role of developmental processes. It is, however, entirely compatible with the lean version of the proximate–ultimate distinction

Evolutionary theory is undergoing an intense period of discussion and reevaluation. This, contrary to the misleading claims of creationists and other pseudoscientists, is no harbinger of a crisis but rather the opposite: the field is expanding dramatically in terms of both empirical discoveries and new ideas. In this essay I briefly trace the conceptual history of evolutionary theory from Darwinism to neo-Darwinism, and from the Modern Synthesis to what I refer to as the Extended Synthesis, a more inclusive conceptual framework containing among others evo–devo, an expanded theory of heredity, elements of complexity theory, ideas about evolvability, and a reevaluation of levels of selection. I argue that evolutionary biology has never seen a paradigm shift, in the philosophical sense of the term, except when it moved from natural theology to empirical science in the middle of the 19th century. The Extended Synthesis, accordingly, is an expansion of the Modern Synthesis of the 1930s and 1940s, and one that—like its predecessor—will probably take decades to complete.

Why do irrational beliefs adopt the trappings of science, to become what is known as “pseudoscience”? Here, we develop and extend an epidemiological framework to map the factors that explain the form and the popularity of irrational beliefs in scientific garb. These factors include the exploitation of epistemic vigilance, the misunderstanding of the authority of science, the use of the honorific title of “science” as an explicit argument for belief, and the phenomenon of epistemic negligence. We conclude by integrating the various factors in an epidemiological framework and thus provide a comprehensive cultural evolutionary account of science mimicry.

The scientific status of evolutionary theory seems to be more or less perennially under question. I am not referring here (just) to the silliness of young Earth creation- ism (Pigliucci 2002; Boudry and Braeckman 2010), or even of the barely more intel- lectually sophisticated so-called Intelligent Design theory (Recker 2010; Brigandt this volume), but rather to discussions among scientists and philosophers of science concerning the epistemic status of evolutionary theory (Sober 2010). As we shall see in what follows, this debate has a long history, dating all the way back to Darwin, and it is in great part rooted in the fundamental dichotomy between what French biologist and Nobel laureate Jacques Monod (1971) called chance and necessity—i.e., the inevitable and inextricable interplay of deterministic and stochastic mechanisms operating during the course of evolution.

Philosophical inquiries into morality are as old as philosophy, but it may turn out that morality itself is much, much older than that. At least, that is the main thesis of prima- tologist Frans De Waal, who in this short book based on his Tanner Lectures at Princeton, elaborates on what biologists have been hinting at since Darwin’s (1871) book The Descent of Man and Hamilton’s (1963) studies on the evolution of altruism: morality is yet another allegedly human characteristic that turns out to be built over evolutionary time by natural

Discussions about the biological bases of the concept of race in the human species seem to be never ending. One of the latest rounds is represented by a paper by Neven Sesardic, which attempts to build a strong scientific case for the existence of human races, based on genetic, morphometric and behavioral characteristics, as well as on a thorough critique of opposing positions. In this paper I show that Sesardic’s critique falls far short of the goal, and that his positive case is exceedingly thin. I do this through a combination of analysis of the actual scientific findings invoked by Sesardic and of some philosophical unpacking of his conceptual analysis, drawing on a dual professional background as an evolutionary biologist and a philosopher of science.

Twenty years have passed since Gould and Lewontin published their critique of ‘the adaptationist program’ – the tendency of some evolutionary biologists to assume, rather than demonstrate, the operation of natural selection. After the ‘Spandrels paper’, evolutionists were more careful about producing just-so stories based on selection, and paid more attention to a panoply of other processes. Then came reactions against the excesses of the anti-adaptationist movement, which ranged from a complete dismissal of Gould and Lewontin’s contribution to a positive call to overcome the problems. We now have an excellent opportunity for finally affirming a more balanced and pluralistic approach to the study of evolutionary biology.

Lewis et al. (2011) attempted to restore the reputation of Samuel George Morton, a 19th century physician who reported on the skull sizes of different folk-races. Whereas Gould (1978) claimed that Morton’s conclusions were invalid because they reflected unconscious bias, Lewis et al. alleged that Morton’s findings were, in fact, supported, and Gould’s analysis biased. We take strong exception to Lewis et al.’s thesis that Morton was “right.” We maintain that Gould was right to reject Morton’s analysis as inappropriate and misleading, but wrong to believe that a more appropriate analysis was available. Lewis et al. fail to recognize that there is, given the dataset available, no appropriate way to answer any of the plausibly interesting questions about the “populations” in question (which in many cases are not populations in any biologically meaningful sense). We challenge the premise shared by both Gould and Lewis et al. that Morton’s confused data can be used to draw any meaningful conclusions. This, we argue, reveals the importance of properly focusing on the questions asked, rather than more narrowly on the data gathered.

Ever since Socrates, philosophers have been in the business of asking ques- tions of the type “What is X?” The point has not always been to actually find out what X is, but rather to explore how we think about X, to bring up to the surface wrong ways of thinking about it, and hopefully in the process to achieve an increasingly better understanding of the matter at hand. In the early part of the twentieth century one of the most ambitious philosophers of sci- ence, Karl Popper, asked that very question in the specific case in which X = science. Popper termed this the “demarcation problem,” the quest for what distinguishes science from nonscience and pseudoscience (and, presumably, also the latter two from each other).