Phenotypic plasticity integrates the insights of ecological genetics, developmental biology, and evolutionary theory. Plasticity research asks foundational questions about how living organisms are capable of variation in their genetic makeup and in their responses to environmental factors. For instance, how do novel adaptive phenotypes originate? How do organisms detect and respond to stressful environments? What is the balance between genetic or natural constraints (such as gravity) and natural selection? The author begins by defining phenotypic plasticity and detailing its history, including (...) important experiments and methods of statistical and graphical analysis. He then provides extended examples of the molecular basis of plasticity, the plasticity of development, the ecology of plastic responses, and the role of costs and constraints in the evolution of plasticity. A brief epilogue looks at how plasticity studies shed light on the nature/nurture debate in the popular media. (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)

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)

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)

Introduction : science versus pseudoscience and the "demarcation problem" -- Hard science, soft science -- Almost science -- Pseudoscience -- Blame the media? -- Debates on science : the rise of think tanks and the decline of public intellectuals -- Science and politics : the case of global warming -- Science in the courtroom : the case against intelligent design -- From superstition to natural philosophy -- From natural philosophy to modern science -- The science wars I : do we (...) trust science too much? -- The science wars II : do we trust science too little? -- Who's your expert? -- Conclusion : so, what is science after all? (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)

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)

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)

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)

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: [email protected]. (shrink)

The term “scientism” is used in a variety of ways with both negative and positive connotations. I suggest that some of these uses are inappropriate, as they aim simply at dismissing without argument an approach that a particular author does not like. However, there are legitimate negative uses of the term, which I explore by way of an analogy with the term “pseudoscience.” I discuss these issues by way of a recent specific example provided by a controversy in the field (...) of bioethics concerning the value, or lack thereof, of homeopathy. I then frame the debate about scientism within the broader context of C.P. Snow’s famous essay on the “two cultures.”. (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)

‘‘Theoretical biology’’ is a surprisingly heter- ogeneous field, partly because it encompasses ‘‘doing the- ory’’ across disciplines as diverse as molecular biology, systematics, ecology, and evolutionary biology. Moreover, it is done in a stunning variety of different ways, using anything from formal analytical models to computer sim- ulations, from graphic representations to verbal arguments. In this essay I survey a number of aspects of what it means to do theoretical biology, and how they compare with the allegedly much more restricted (...) sense of theory in the physical sciences. I also tackle a recent trend toward the presentation of all-encompassing theories in the biological sciences, from general theories of ecology to a recent attempt to provide a conceptual framework for the entire set of biological disciplines. Finally, I discuss the roles played by philosophers of science in criticizing and shap- ing biological theorizing. (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)

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. (shrink)

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)

The relationship between ethics and science has been discussed within the framework of continuity versus discontinuity theories, each of which can take several forms. Continuity theorists claim that ethics is a science or at least that it has deep similarities with the modus operandi of science. Discontinuity theorists reject such equivalency, while at the same time many of them claim that ethics does deal with objective truths and universalizable statements, just not in the same sense as science does. I propose (...) here a third view of quasi-continuity (or, equivalently, quasi-discontinuity) that integrates ethics and science as equal partners toward the uncovering of new knowledge. In this third way, a program envisioned by William James but made practicable only by contemporary scientific advancement, science can and must inform ethics at a deep level, and ethical theory— while going beyond science—cannot do without it. In particular, I identify four areas of ethics-science collaboration: neurobiological research into the basis of moral judgment, comparative anthropol- ogy, comparative evolutionary biology of primates, and game-theo- retical modeling. I provide examples within each of these fields to show how they link to ethical theories (including prescriptive work) and questions. The essay concludes with a brief discussion of the light that a scientifically informed ethics can shed on some classical problems in moral theory, such as the relationships between rational- ity and selfishness, egoism and altruism, as well as the concept of social contract. A joint research program involving both philosophers and scientists is called for if we wish to move ethical theory into the twenty-first century. (shrink)

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)

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. (shrink)

The creation-evolution “controversy” has been with us for more than a century. Here I argue that merely teaching more science will probably not improve the situation; we need to understand the controversy as part of a broader problem with public acceptance of pseudoscience, and respond by teaching how science works as a method. Critical thinking is difficult to teach, but educators can rely on increasing evidence from neurobiology about how the brain learns, or fails to.

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)

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. (shrink)

A new voice in the nature-nurture debate can be heard at the interface between evolution and development. Phenotypic integration is a major growth area in research.

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)

Thought experiments are cheap and popular, but how do they work?

A humorous treatment of scientism within the context of the television series, The Big Bang Theory.

Phenotypic integration refers to the study of complex patterns of covariation among functionally related traits in a given organism. It has been investigated throughout the 20th century, but has only recently risen to the forefront of evolutionary ecological research. In this essay, I identify the reasons for this late flourishing of studies on integration, and discuss some of the major areas of current endeavour: the interplay of adaptation and constraints, the genetic and molecular bases of integration, the role of phenotypic (...) plasticity, macroevolutionary studies of integration, and statistical and conceptual issues in the study of the evolution of complex phenotypes. I then conclude with a brief discussion of what I see as the major future directions of research on phenotypic integration and how they relate to our more general quest for the understanding of phenotypic evolution within the neo-Darwinian framework. I suggest that studying integration provides a particularly stimulating and truly interdisciplinary convergence of researchers from fields as disparate as molecular genetics, developmental biology, evolutionary ecology, palaeontology and even philosophy of science. (shrink)

Public discussions of science are often marred by two pernicious phenomena: a widespread rejection of scientific findings (e.g., the reality of anthropogenic climate change, the conclusion that vaccines do not cause autism, or the validity of evolutionary theory), coupled with an equally common acceptance of pseudoscientific notions (e.g., homeopathy, psychic readings, telepathy, tall tales about alien abductions, and so forth). The typical reaction by scientists and science educators is to decry the sorry state of science literacy among the general public, (...) and to call for more science education as the answer to both problems. But the empirical evidence concerning the relationship between science literacy, rejection of science and acceptance of pseudoscience is mixed at best. In this chapter I argue that—while certainly important—efforts at increasing public knowledge of science (science education) need to be complemented by attention to common logical fallacies (philosophy), cognitive biases and dissonance (psychology), and the role of ideological commitments (sociology). Even this complex, multi-disciplinary approach to science education will likely only yield measurable results in the very long term. Meanwhile science remains, as Carl Sagan famously put it, a candle in the dark, delicate and in need of much nurturing. (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)

How to use a model organism to study phenotypic integration and constraints on evolution.

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.

A quick look at the concept of reflective equilibrium in philosophy.

Apparently, I’m a righteous son of a bitch, morally speaking. At least that’s the conclusion I would have to reach if I trusted the results of a morality test I took at the BBC website (bbc.co.uk/labuk/experiments/morality). The test was devised to collect data for a “new theory” that seeks to make sense of human morality in terms of a super-organism concept. Briefly, the idea is that “we, as individuals, behave as if we are part of a bigger ‘superorganism’ when we (...) are organised into large social groups, as in cities or societies. ... all moral actions are based on the fundamental need to ‘police’ society in order to keep the ‘superorganism’ functioning properly.”. (shrink)

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

An exploration of the relationship between secular humanism and politics, from a liberal perspective.