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)

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)

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)

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)

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 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)

In the contemporary philosophy of set theory, discussion of new axioms that purport to resolve independence necessitates an explanation of how they come to be justified. Ordinarily, justification is divided into two broad kinds: intrinsic justification relates to how `intuitively plausible' an axiom is, whereas extrinsic justification supports an axiom by identifying certain `desirable' consequences. This paper puts pressure on how this distinction is formulated and construed. In particular, we argue that the distinction as often presented is neither well-demarcated nor (...) sufficiently precise. Instead, we suggest that the process of justification in set theory should not be thought of as neatly divisible in this way, but should rather be understood as a conceptually indivisible notion linked to the goal of explanation. (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)

The paper investigates the role played by pre-scientific experience in the philosophy of Josiah Royce and Edmund Husserl. Such a notion, generally associated with Husserl’s conception of the life-world (Lebenswelt) in the Crisis of European Sciences and Transcendental Phenomenology (1936), finds an equivalent and historical antecedent in Royce’s distinction between a world of description and a world of appreciation. The final goal is to show how, despite their different philosophical frameworks, Royce and Husserl agree on the idea that, through the (...) rejection of the world given through mere perception (Lebenswelt/world of appreciation), European sciences have somehow failed their task of universality. As it will be shown, this idea is also due to methodological affinities among the two thinkers. The experience of interconnectedness among individual minds, while precluded in the mere scientific explanation of the world, it becomes possible through the enactment of the Lebenswelt or, as in Royce’s case, through a return to the experience of the world of appreciation. (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)

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)

Provided that traditional jus ad bellum principles are fulfilled, military humanitarian intervention to stop large scale violations of human rights (such as genocide, crimes against humanity or war crimes) is widely regarded as morally permissible. In cases of “supreme humanitarian emergency”, not only are the victims morally permitted to rebel, but other states are also permitted to militarily intervene. Things are different if the human rights violations in question fall short of supreme humanitarian emergency. Because of the importance of respecting (...) political self-determination, in cases of “ordinary oppression”, we normally think that rebellion might be permissible, but not military humanitarian intervention. Thus, according to the received view, the conditions for the permissibility of intervention coincide with the conditions for the permissibility of revolution in cases of supreme humanitarian emergency, but not in cases of ordinary oppression. In cases of ordinary oppression there is an asymmetry between the conditions for the permissibility of revolution and intervention (call this the Asymmetry View). Should we accept the Asymmetry View? I answer this question by outlining an account of political self-determination and by illustrating the complex role that this notion should play in discussing the morality of revolution and intervention. (shrink)

Just war theory is currently dominated by two positions. According to the orthodox view, provided that jus in bello principles are respected, combatants have an equal right to fight, regardless of the justice of the cause pursued by their state. According to “revisionists” whenever combatants lack reasons to believe that the war they are ordered to fight is just, their duty is to disobey. I argue that when members of a legitimate state acting in good faith are ordered to fight, (...) they acquire a pro-tanto obligation to obey which does not depend for its validity on the justice of the cause being pursued. However, when the war is unjust, this obligation may be overridden, under certain conditions, by the obligation not to contribute to the unjustified killing of innocents. This is because the pro-tanto force of the duty to obey the law is best understood in terms of “presumptive”, rather than “exclusionary” reasons for action. This approach captures the insights of both the orthodox and the revisionist view, while avoiding the problems that afflict each of them. (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)

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)

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)

The study of phenotypic plasticity has progressed significantly over the past few decades. We have moved from variation for plasticity being considered as a nuisance in evolutionary studies to it being the primary target of investigations that use an array of methods, including quantitative and molecular genetics, as well as of several approaches that model the evolution of plastic responses. Here, I consider some of the major aspects of research on phenotypic plasticity, assessing where progress has been made and where (...) additional effort is required. I suggest that some areas of research, such the study of the quantitative genetic underpinning of plasticity, have been either settled in broad outline or superseded by new approaches and questions. Other issues, such as the costs of plasticity are currently at the forefront of research in this field, and are likely to be areas of major future development. (shrink)

In this commentary, we discuss the nature of reversible and irreversible questions, that is, questions that may enable one to identify the nature of the source of their answers. We then introduce GPT-3, a third-generation, autoregressive language model that uses deep learning to produce human-like texts, and use the previous distinction to analyse it. We expand the analysis to present three tests based on mathematical, semantic, and ethical questions and show that GPT-3 is not designed to pass any of them. (...) This is a reminder that GPT-3 does not do what it is not supposed to do, and that any interpretation of GPT-3 as the beginning of the emergence of a general form of artificial intelligence is merely uninformed science fiction. We conclude by outlining some of the significant consequences of the industrialisation of automatic and cheap production of good, semantic artefacts. (shrink)

Cabanis’ enucleation of the notion of instinct in his Rapports du physique et du moral de l’homme articulates through a critique of the use of this notion by Étienne Bonnot de Condillac, who would not have recognised the founding role of physiology in human perceptive and intellectual activity. An analysis of Cabanis’ criticism to Condillac and an investigation of the meaning attributed to the notion of instinct by both philosophers allow to individuate in this notion the expression of two different (...) types of materialism. The different position of Cabanis and Condillac on this notion, in fact, reflects the divergence on a series of notions – e.g. reflexion, sensitivity, habitus – which can be traced back to the different aims of their investigations. In addition to highlighting this basic divergence, this paper aims to bring out – especially referring to Condillac’s Logique – some points of contact, of which Cabanis seems not to have considered, concerning the conception of the human body as ‘organisation physique’. (shrink)

In the 17th century the dissemination of philosophical ideas relied also on the critical summaries and reviews published by the journals. The focus of this paper is the reactions of two of these journals – the Journal de Trévoux, edited by the Jesuits of the Parisian Collège Louis Le Grand, and the Journal des Sçavans – to Condillac’s works. The Jesuit journal, under the direction of pére Berthier – probably himself the author of the reviews – had a precise plan (...) in presenting Condillac’s philosophy as an anti-empiricist and anti-materialist doctrine, sometime giving a misrepresentation of the author’s thought, which is also criticized on some points. The decision of the Journal de Trévoux to review the main works of Condillac is anyway worthy of attention, and probably betrays a certain interest toward the more up to date philosophical enquiry. The Journal des Sçavans was on the other hand more faithful in presenting Condillac’s works. (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)

How does our language relate to reality? This is a question that is especially pertinent in set theory, where we seem to talk of large infinite entities. Based on an analogy with the use of models in the natural sciences, we argue for a threefold correspondence between our language, models, and reality. We argue that so conceived, the existence of models can be underwritten by a weak notion of existence, where weak existence is to be understood as existing in virtue (...) of language. (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)

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 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)

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)

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.

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.

The idea of genetic assimilation, that environmentally induced phenotypes may become genetically fixed and no longer require the original environmental stimulus, has had varied success through time in evolutionary biology research. Proposed by Waddington in the 1940s, it became an area of active empirical research mostly thanks to the efforts of its inventor and his collaborators. It was then attacked as of minor importance during the ‘‘hardening’’ of the neo-Darwinian synthesis and was relegated to a secondary role for decades. Recently, (...) several papers have appeared, mostly independently of each other, to explore the likelihood of genetic assimilation as a biological phenomenon and its potential importance to our understanding of evolution. In this article we briefly trace the history of the concept and then discuss theoretical models that have newly employed genetic assimilation in a variety of contexts. We propose a typical scenario of evolution of genetic assimilation via an intermediate stage of phenotypic plasticity and present potential examples of the same. We also discuss a conceptual map of current and future lines of research aimed at exploring the actual relevance of genetic assimilation for evolutionary biology. (shrink)

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.

As short a time ago as 1992, political scientist Francis Fukuyama was optimistically (and wrongly, as it turned out) predicting “the end of history”, a stable future where liberal democracies would be the norm throughout the world, leading to lasting peace and economic prosperity. A few years later we have Eric Li, who equally gingerly predicts (for example in the pages of Foreign Affairs magazine) a “post-democratic” future, beginning with the success of China. Oh boy.

Research in ecology and evolutionary biology (evo-eco) often tries to emulate the “hard” sciences such as physics and chemistry, but to many of its practitioners feels more like the “soft” sciences of psychology and sociology. I argue that this schizophrenic attitude is the result of lack of appreciation of the full consequences of the peculiarity of the evo-eco sciences as lying in between a-historical disciplines such as physics and completely historical ones as like paleontology. Furthermore, evo-eco researchers have gotten stuck (...) on mathematically appealing but philosophi- cally simplistic concepts such as null hypotheses and p-values defined according to the frequentist approach in statistics, with the consequence of having been unable to fully embrace the complexity and subtlety of the problems with which ecologists and evolutionary biologists deal with. I review and discuss some literature in ecology, philosophy of science and psychology to show that a more critical methodological attitude can be liberating for the evo-eco scientist and can lead to a more fecund and enjoyable practice of ecology and evolutionary biology. With this aim, I briefly cover concepts such as the method of multiple hypotheses, Bayesian analysis, and strong inference. (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)

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)

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)

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)

Concerning how to educate science educators about the nature of science, in the context of the creationism debates.

Il lavoro di tesi analizza il problema cristologico nella filosofia di Spinoza alla luce delle riletture contemporanee sul tema, attraversando questioni di argomento etico, pedagogico e religioso. Viene condotto dall'autore un meticoloso lavoro di analisi relativo alle occorrenze testuali delle espressioni riferite a Cristo e ai Cristiani nell'intera produzione spinoziana. Sebbene il tema cristologico non sia affrontato quasi mai in modo esplicito dal filosofo olandese, il lavoro di tesi mostra quanto diffusi siano tali riferimenti e come possa essere interessante rileggere (...) Spinoza proprio a partire dalla sua profonda ammirazione nei confronti della figura più affascinante della storia dell'Occidente. (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)

What is the purpose of philosophy of science? Here are some answers.

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

Spinoza’s philosophy could be understood as a tireless research of the truth. Nevertheless it can’t be interpreted as a path that leads only the wise to the salvation. The effort to reach the bliss, freedom, the true knowledge of the mind, has to belong to all humanity. So the role of the philosopher must be to encourage men to seek the truth, to love it through the union with God above all else. This is the soteriological fabric of the early (...) works of Spinoza. It will lead to the exaltation of the homo liber and of the Spirit of Christ as the way of salvation in his mature works. Nature’s knowledge will be the lifeblood in the context of the research for the universal salvation of individuals as a happy community. (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)

On the status of hypotheses in science, and why scientists would be better off asking questions.