Biological research on race has often been seen as motivated by or lending credence to underlying racist attitudes; in part for this reason, recently philosophers and biologists have gone through great pains to essentially deny the existence of biological human races. We argue that human races, in the biological sense of local populations adapted to particular environments, do in fact exist; such races are best understood through the common ecological concept of ecotypes. However, human ecotypic races do not in general (...) correspond with 'folk' racial categories, largely because many similar ecotypes have multiple independent origins. Consequently, while human natural races exist, they have little or nothing in common with 'folk' races. (shrink)

This paper outlines a critique of the use of the genetic variance–covariance matrix (G), one of the central concepts in the modern study of natural selection and evolution. Specifically, I argue that for both conceptual and empirical reasons, studies of G cannot be used to elucidate so-called constraints on natural selection, nor can they be employed to detect or to measure past selection in natural populations – contrary to what assumed by most practicing biologists. I suggest that the search for (...) a general solution to the difficult problem of identifying causal structures given observed correlation’s has led evolutionary quantitative geneticists to substitute statistical modeling for the more difficult, but much more valuable, job of teasing apart the many possible causes underlying the action of natural selection. Hence, the entire evolutionary quantitative genetics research program may be in need of a fundamental reconsideration of its goals and how they correspond to the array of mathematical and experimental techniques normally employed by its practitioners. (shrink)

Will the scientific quest ever end? Will it be with a bang or with a whisper?

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. (shrink)

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. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Why Gaia?Massimo Pigliucci (bio)The Gaia Hypothesis: Science on a Pagan Planet, Michael Ruse, Chicago: University of Chicago Press, 2013. 272 pages.“The Gaia Hypothesis: Science on a Pagan Planet tells a story that comes out of the 1960s, a story that reflects all of the beliefs and enthusiasms and tensions of that decade.” So begins Michael Ruse’s fascinating, if at times puzzling, exploration of James Lovelock’s famous idea (...) that our planet is, in a serious scientific sense, a living organism with a tendency of taking care of (her)self. But why tell this particular story, especially considering that Gaia hardly makes an appearance in today’s scientific or philosophical publications, and doesn’t even seem quite that popular with the lay public as it used to be? Because, as Ruse tells us near the end of the book, at the onset of chapter seven: “the paradox that set us on our path [is] why the scientific community reacted so negatively to the Gaia hypothesis, whereas the public reaction was so positive.”As it turns out, there is a good answer to that conundrum, one that Ruse himself lays out clearly in the last chapter of the book, and which makes the reader wonder why this should count a paradox at all. But we will get there in due time. First, the basics: the so-called Gaia hypothesis is the brainchild of iconoclastic inventor-turned-independent-scientist James Lovelock, who later got significant help in elaborating (and promoting) his ideas from another iconoclast, biologist Lynn Margulis. By the time you get to the end of Ruse’s engaging book, however, you won’t have gained a particularly good understanding of what the hypothesis actually consists. But that’s not Ruse’s fault, it is Lovelock’s (and Margulis’). At times it sounds like the entirely uncontroversial claim that the Earth’s [End Page 117] biosphere is a somewhat homeostatic system—i.e., a biophysical system that is resistant to major changes, at the least within a certain range (the planet’s atmosphere, after all, did change dramatically early on, increasing its oxygen content as a result of the evolution of photosynthetic organisms—the anaerobic life forms that had up to that point been dominant did not appreciate the novelty). At other times the claim is downright preposterous: the Earth literally is a living organism (according to Lovelock) (Chapter 7),1 a finding that allegedly puts in question the whole Darwinian view of biological evolution (according to Margulis) (Chapter 7), a position that can only be characterized as nonsense on stilts. At yet other moments, Gaia is presented as just a metaphor to help us wrap our minds around the complexities (and homeostatic properties) of the world’s ecosystems (Chapter 8). It is this never-ending oscillation between the trivial and the bizarre that has led the majority of scientists to write off Gaia, to the chagrin of Lovelock, Margulis, and a large number of New Age tree huggers from the 1960s.Indeed, the scientific reaction to Gaia was swift and ranging from the condescending to the unforgiving. Evolutionary biologist John Maynard Smith—never one to mince words—called it “an evil religion” (Chapter 2). Another evolutionary biologist, Stephen Jay Gould (whose own disagreements with Maynard Smith became legendary) said that “Gaia strikes me as a metaphor, not a mechanism” (Chapter 2). Ecologist Robert May, who eventually became president of the Royal Society, called Lovelock “a holy fool” (Chapter 2). The highly respected theoretical biologist W.D. Hamilton said that in order for the hypothesis to work, it would require “treaties between Neptune and Zeus, a Gaian Interpol, conventions about bills of lading for chemical transport by air and water, and so on” (Chapter 7). Finally, Richard Dawkins accused Lovelock of committing the fallacy of “the BBC theorem,” assuming (or wishfully thinking) that the world is a harmonious place, just like in naive BBC nature documentaries (Chapter 2).You get the gist: pretty much from the beginning, and with very few exceptions, the scientific establishment rejected Gaia on the grounds that it is not a scientific hypothesis at all, and that its main tenets actually go against pretty... (shrink)

The “demarcation problem,” the issue of how to separate science from pseu- doscience, has been around since fall 1919—at least according to Karl Pop- per’s (1957) recollection of when he first started thinking about it. In Popper’s mind, the demarcation problem was intimately linked with one of the most vexing issues in philosophy of science, David Hume’s problem of induction (Vickers 2010) and, in particular, Hume’s contention that induction cannot be logically justified by appealing to the fact that “it works,” (...) as that in itself is an inductive argument, thereby potentially plunging the philosopher straight into the abyss of a viciously circular argument. (shrink)

Recent debates between proponents of the modern evolutionary synthesis (the standard model in evolutionary biology) and those of a possible extended synthesis are a good example of the fascinating tangle among empirical, theoretical, and conceptual or philosophical matters that is the practice of evolutionary biology. In this essay, we briefly discuss two case studies from this debate, highlighting the relevance of philosophical thinking to evolutionary biologists in the hope of spurring further constructive cross-pollination between the two fields.

The concept of burden of proof is used in a wide range of discourses, from philosophy to law, science, skepticism, and even in everyday reasoning. This paper provides an analysis of the proper deployment of burden of proof, focusing in particular on skeptical discussions of pseudoscience and the paranormal, where burden of proof assignments are most poignant and relatively clear-cut. We argue that burden of proof is often misapplied or used as a mere rhetorical gambit, with little appreciation of the (...) underlying principles. The paper elaborates on an important distinction between evidential and prudential varieties of burdens of proof, which is cashed out in terms of Bayesian probabilities and error management theory. Finally, we explore the relationship between burden of proof and several (alleged) informal logical fallacies. This allows us to get a firmer grip on the concept and its applications in different domains, and also to clear up some confusions with regard to when exactly some fallacies (ad hominem, ad ignorantiam, and petitio principii) may or may not occur. (shrink)

The so-called “New Atheism” is a relatively well-defined, very recent, still unfold- ing cultural phenomenon with import for public understanding of both science and philosophy. Arguably, the opening salvo of the New Atheists was The End of Faith by Sam Harris, published in 2004, followed in rapid succession by a number of other titles penned by Harris himself, Richard Dawkins, Daniel Dennett, Victor Stenger, and Christopher Hitchens.

Intelligent Design proponents want to distinguish themselves from creationists. But the distinction appears to be without a difference.

Discussions about the biological bases (or lack thereof) 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 philo- sophical unpacking of his conceptual analysis, drawing on a dual professional background as an evolu- tionary biologist and a philosopher of science. (shrink)

A new conceptual essay introducing one of the classics of the evolutionary biological literature.

Are science and religion compatible when it comes to understanding cosmology (the origin of the universe), biology (the origin of life and of the human species), ethics, and the human mind (minds, brains, souls, and free will)? Do science and religion occupy non-overlapping magisteria? Is Intelligent Design a scientific theory? How do the various faith traditions view the relationship between science and religion? What, if any, are the limits of scientific explanation? What are the most important open questions, problems, or (...) challenges confronting the relationship between science and religion, and what are the prospects for progress? These and other questions are explored in Science and Religion: 5 Questions--a collection of thirty-three interviews based on 5 questions presented to some of the world's most influential and prominent philosophers, scientists, theologians, apologists, and atheists. Contributions by Simon Blackburn, Susan Blackmore, Sean Carroll, William Lane Craig, William Dembski, Daniel C. Dennett, George F.R. Ellis, Owen Flanagan, Owen Gingerich, Rebecca Newberger Goldstein, John F. Haught, Muzaffar Iqbal, Lawrence Krauss, Colin McGinn, Alister McGrath, Mary Midgley, Seyyed Hossein Nasr, Timothy O'Connor, Massimo Pigliucci, John Polkinghorne, James Randi, Alex Rosenberg, Michael Ruse, Robert John Russell, John Searle, Michael Shermer, Victor J. Stenger, Robert Thurman, Michael Tooley, Charles Townes, Peter van Inwagen, Keith Ward, Rabbi David Wolpe. (shrink)

A counter analysis of David Chalmers' claims about the possibility of mind uploading within the context of the Singularity event.

The term ‘naturalism’ has a long and complex history in modern philosophy. W.V.O. Quine famously advocated what has come to be known as a ‘naturalistic turn’ for philosophy as a discipline, meaning that philosophical thought should become continuous with the natural sciences – even claiming that epistemology (theory of knowledge) is nothing but applied psychology.

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. (shrink)

Back in 1942, C.H. Waddington proposed a new mechanism of evolutionary change, which he termed “genetic assimilation”.1,2 The idea was that certain environmental or genetic factors can disrupt the normally canalized (i.e., stable) course of development of living organisms. This disruption may then generate phenotypic variation that could allow a population to persist in a novel or stressful environment until new mutations would eventually let natural selection fix (“assimilate”) the advantageous phenotypic variants.

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. (shrink)

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). (shrink)

A few field notes from the philosophy of science meeting in Vancouver.

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. (shrink)

The concepts of reaction norms and phenotypic plasticity help us better understand what a biological trait is.

On the cultural roots, philosophical issues and science education of various blends of creationism.

Evolutionary theory has evolved over time, but has there ever been a paradigm shift in evolutionary biology?

Philosophy has been a public endeavor since its origins in ancient Greece, India, and China. However, recent years have seen the development of a new type of public philosophy conducted by both academics and non- professionals. The new public philosophy manifests itself in a range of modalities, from the publication of magazines and books for the general public to a variety of initiatives that exploit the power and flexibility of social networks and new media. In this paper we examine the (...) phenomenon of public philosophy in its several facets, and investigate whether and in what sense it is itself a mix of philosophical practice and teaching. We conclude with a number of suggestions to academic colleagues on why and how to foster further growth of public philosophy for the benefit of society at large and of the discipline itself. (shrink)

In recent years, biologists have increasingly been asking whether the ability to evolve — the evolvability — of biological systems, itself evolves, and whether this phenomenon is the result of natural selection or a by-product of other evolutionary processes. The concept of evolvability, and the increasing theoretical and empirical literature that refers to it, may constitute one of several pillars on which an extended evolutionary synthesis will take shape during the next few years, although much work remains to be done (...) on how evolvability comes about. (shrink)

What makes humans different from other animals, what humans are entitled to do to other species, whether time travel is possible, what limits should be placed on science and technology, the morality and practicality of genetic engineering—these are just some of the philosophical problems raised by Planet of the Apes. Planet of the Apes and Philosophy looks at all the deeper issues involved in the Planet of the Apes stories. It covers the entire franchise, from Pierre Boulle’s 1963 novel Monkey (...) Planet to the successful 2012 reboot Rise of the Planet of the Apes. The chapters reflect diverse points of view, philosophical, religious, and scientific. The ethical relations of humans with animals are explored in several chapters, with entertaining and incisive observations on animal intelligence, animal rights, and human-animal interaction. Genetic engineering is changing humans, animals, and plants, raising new questions about the morality of such interventions. The scientific recognition that humans and chimps share 99 percent of their genes makes a future in which non-human animals acquire greater importance a distinct possibility. Planet of the Apes is the most resonant of all scientific apocalypse myths. (shrink)

The articles in this issue reflect the results of the 25th Altenberg Workshop in Theoretical Biology on ‘‘The Meaning of ‘Theory’ in Biology’’ held at the Konrad Lorenz Institute for Evolution and Cognition Research, Altenberg, Austria, 30 June–3 July, 2011.

Whenever we try to make an inventory of humankind’s store of knowledge, we stumble into an ongoing battle between what CP Snow called ‘the two cultures’. On one side are the humanities, on the other are the sciences (natural and physical), with social science and philosophy caught somewhere in the middle. This is more than a turf dispute among academics. It strikes at the core of what we mean by human knowledge.

Science has always strived for objectivity, for a ‘‘view from nowhere’’ that is not marred by ideology or personal preferences. That is a lofty ideal toward which perhaps it makes sense to strive, but it is hardly the reality. This collection of thirteen essays assembled by Denis R. Alexander and Ronald L. Numbers ought to give much pause to scientists and the public at large, though historians, sociologists and philosophers of science will hardly be surprised by the material covered here.

When I was fifteen, I was having serious doubts about the existence of a supernatural entity benevolently looking over me, and—perhaps even more disturbingly—about the possibility of an afterlife in which I would again see my friends and relatives and exist happily ever after. It was at that point that I started reading the writings of Bertrand Russell,1,2 one of the most controversial philosophers and political activists of the Twentieth century.

A critical examination of the dispute about the existence and significance of "plasticity genes.".

Few metaphors in biology are more enduring than the idea of Adaptive Landscapes, originally proposed by Sewall Wright (1932) as a way to visually present to an audience of typically non- mathematically savvy biologists his ideas about the relative role of natural selection and genetic drift in the course of evolution. The metaphor, how- ever, was born troubled, not the least reason for which is the fact that Wright presented different diagrams in his original paper that simply can- not refer (...) to the same concept and are therefore hard to reconcile with each other (Pigliucci 2008). For instance, in some usages, the landscape’s non- fitness axes represent combinations of individual genotypes (which cannot sensibly be aligned on a linear axis, and accordingly were drawn by Wright as polyhedrons of increasing dimensionality). In other usages, however, the points on the diagram represent allele or genotypic frequencies, and so are actually populations, not individuals (and these can indeed be coherently represented along continuous axes). (shrink)

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”. (shrink)

Stoicism is an ancient Greco-Roman practical philosophy focused on the ethics of everyday living. It is a eudaemonistic (i.e., emphasizing one’s flourishing) approach to life, as well as a type of virtue ethics (i.e., concerned with the practice of virtues as central to one’s existence). This paper summarizes the basic tenets of Stoicism and discusses how it tackles the issues of death and suicide. It presents a number of exercises that modern Stoics practice in order to prepare for death (one’s (...) own, or those of relatives and friends). It argues that modern Stoicism is a viable personal philosophy. (shrink)

Genes are often described by biologists using metaphors derived from computa- tional science: they are thought of as carriers of information, as being the equivalent of ‘‘blueprints’’ for the construction of organisms. Likewise, cells are often characterized as ‘‘factories’’ and organisms themselves become analogous to machines. Accordingly, when the human genome project was initially announced, the promise was that we would soon know how a human being is made, just as we know how to make airplanes and buildings. Impor- tantly, (...) modern proponents of Intelligent Design, the latest version of creationism, have exploited biologists’ use of the language of information and blueprints to make their spurious case, based on pseudoscientific concepts such as ‘‘irreducible complexity’’ and on flawed analogies between living cells and mechanical factories. However, the living organ- ism = machine analogy was criticized already by David Hume in his Dialogues Concerning Natural Religion. In line with Hume’s criticism, over the past several years a more nuanced and accurate understanding of what genes are and how they operate has emerged, ironically in part from the work of computational scientists who take biology, and in particular developmental biology, more seriously than some biologists seem to do. In this article we connect Hume’s original criticism of the living organism = machine analogy with the modern ID movement, and illustrate how the use of misleading and outdated metaphors in science can play into the hands of pseudoscientists. Thus, we argue that dropping the blueprint and similar metaphors will improve both the science of biology and its understanding by the general public. (shrink)

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. (shrink)

The idea of phenotypic novelty appears throughout the evolutionary literature. Novelties have been defined so broadly as to make the term meaningless and so narrowly as to apply only to a limited number of spectacular structures. Here I examine some of the available definitions of phenotypic novelty and argue that the modern synthesis is ill equipped at explaining novelties. I then discuss three frameworks that may help biologists get a better insight of how novelties arise during evolution but warn that (...) these frameworks should be considered in addition to, and not as potential substitutes of, the modern synthesis. †To contact the author, please write to: Departments of Ecology and Evolution and Philosophy, Stony Brook University, Stony Brook, NY 11794; e‐mail: pigliucci@platofootnote.org. (shrink)

In addition to considerable debate in the recent evolutionary literature about the limits of the Modern Synthesis of the 1930s and 1940s, there has also been theoretical and empirical interest in a variety of new and not so new concepts such as phenotypic plasticity, genetic assimilation and phenotypic accommodation. Here we consider examples of the arguments and counter- arguments that have shaped this discussion. We suggest that much of the controversy hinges on several misunderstandings, including unwarranted fears of a general (...) attempt at overthrowing the Modern Synthesis paradigm, and some fundamental conceptual confusion about the proper roles of phenotypic plasticity and natural selection within evolutionary theory. (shrink)

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. (shrink)

Evolutionary biology is a field currently animated by much discussion concerning its conceptual foundations. On the one hand, we have supporters of a classical view of evolutionary theory, whose backbone is provided by population genetics and the so-called Modern Synthesis (MS). On the other hand, a number of researchers are calling for an Extended Synthe- sis (ES) that takes seriously both the limitations of the MS (such as its inability to incorporate developmental biology) and recent empirical and theoretical research on (...) issues such as evolvability, modularity, and self-organization. In this article, I engage in an in-depth commentary of an influential paper by population geneticist Michael Lynch, which I take to be the best defense of the MS-population genetics position published so far. I show why I think that Lynch’s arguments are wanting and propose a modification of evolutionary theory that retains but greatly expands on population genetics. (shrink)

Why Jerry Fodor and Massimo Piattelli-Palmarini are wrong about Darwin and evolution.

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. (shrink)

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. (shrink)

In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch’s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened (...) the need for a different conceptual treat- ment of how phenotypes are produced. Old-fashioned metaphors like genetic blueprint and genetic programme are not only woefully inadequate but positively misleading about the nature of G!P, and are being replaced by an algorithmic approach emerging from the study of a variety of actual G!P maps. These include RNA folding, protein function and the study of evolvable soft- ware. Some generalities are emerging from these disparate fields of analysis, and I suggest that the concept of ‘developmental encoding’ (as opposed to the classical one of genetic encoding) provides a promising computational–theoretical underpinning to coherently integrate ideas on evolvability, modularity and robustness and foster a fruitful framing of the G!P mapping problem. (shrink)

The philosophical study of consciousness is chock full of thought experiments: John Searle’s Chinese Room, David Chalmers’ Philosophical Zombies, Frank Jackson’s Mary’s Room, and Thomas Nagel’s ‘What is it like to be a bat?’ among others. Many of these experiments and the endless discussions that follow them are predicated on what Chalmers famously referred as the ‘hard’ problem of consciousness: for him, it is ‘easy’ to figure out how the brain is capable of perception, information integration, attention, reporting on mental (...) states, etc, even though this is far from being accomplished at the moment. What is ‘hard’, claims the man of the p-zombies, is to account for phenomenal experience, or what philosophers usually call ‘qualia’: the ‘what is it like’, first-person quality of consciousness. (shrink)

The term pseudoscience refers to a highly heterogeneous set of practices, beliefs, and claims sharing the property of appearing to be scientific when in fact they contradict either scientific findings or the methods by which science proceeds. Classic examples of pseudoscience include astrology, parapsychology, and ufology; more recent entries are the denial of a causal link between the HIV virus and AIDS or the claim that vaccines cause autism. To distinguish between science and pseudoscience is part of what the philosopher (...) Karl Popper referred to as the demarcation problem, a project that has been dismissed by another philosopher, Larry Laudan, but that keeps gathering much interest in philosophers, scientists, educators, and policymakers. This entry provides the basics of the debate about demarcation, as well as a brief discussion of why it is of vital importance not just intellectually but for society at large. (shrink)

Science and philosophy have a very long history, dating back at least to the 16th and 17th centuries, when the first scientist-philosophers, such as Bacon, Galilei, and Newton, were beginning the process of turning natural philosophy into science. Contemporary relationships between the two fields are still to some extent marked by the distrust that maintains the divide between the so-called “two cultures.” An increasing number of philosophers, however, are making conceptual contributions to sciences ranging from quantum mechanics to evolutionary biology, (...) and a few scientists are conducting research relevant to classically philosophical fields of inquiry, such as consciousness and moral decision-making. This article will introduce readers to the borderlands between science and philosophy, beginning with a brief description of what philosophy of science is about, and including a discussion of how the two disciplines can fruitfully interact not only at the level of scholarship, but also when it comes to controversies surrounding public understanding of science. (shrink)