Evolutionary Biology

Researchers often pursue proof of concept research, but criteria for evaluating such research remain poorly specified. This article proposes a general framework for proof of concept research that k...

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory (...) of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin.We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question. (shrink)

In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such ‘eukaryotes first’ (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier ‘progenotic’ period or RNAworld. Bacteria and Archaea thus must have lost these complex features secondarily, through (...) ‘streamlining’. If the canonical three-domain tree in which Archaea and Eukarya are sisters is accepted, EF entails that Bacteria and Archaea are convergently prokaryotic.We ask what this means and how it might be tested. (shrink)

Stephen Jay Gould argued that replaying the ‘tape of life’ would result in radically different evolutionary outcomes. Recently, biologists and philosophers of science have paid increasing attention to the theoretical importance of convergent evolution—the independent origination of similar biological forms and functions—which many interpret as evidence against Gould’s thesis. In this paper, we examine the evidentiary relevance of convergent evolution for the radical contingency debate. We show that under the right conditions, episodes of convergent evolution can constitute valid natural experiments (...) that support inferences regarding the deep counterfactual stability of macroevolutionary outcomes. However, we argue that proponents of convergence have problematically lumped causally heterogeneous phenomena into a single evidentiary basket, in effect treating all convergent events as if they are of equivalent theoretical import. As a result, the ‘critique from convergent evolution’ fails to engage with key claims of the radical contingency thesis. To remedy this, we develop ways to break down the heterogeneous set of convergent events based on the nature of the generalizations they support. Adopting this more nuanced approach to convergent evolution allows us to differentiate iterated evolutionary outcomes that are probably common among alternative evolutionary histories and subject to law-like generalizations, from those that do little to undermine and may even support, the Gouldian view of life. (shrink)

This essay explores the relation between nature and culture and analyses it from the perspective of contemporary evolutionary theory. Both animals and humans are conceived of as attaining both natural and cultural features that interact with each other on a number of levels of varying complexity: nature as cultural, nature as influenced by culture, culture as natural, and culture as influenced by nature. “Nature as cultural” is meant to express a decoupling of behavioral/phenotypic changes of an organism from its genetic (...) determination. “Nature as influenced by culture” is the idea of niche construction, wherein such decoupled changes can causally feedback to genetic reality, thereby influencing the evolutionary features of downstream species. “Culture as natural” portrays how cultural structures of humans and animals persist through the generations, accumulate incurred changes, and evolve in analogous ways to biological natural selection. “Culture as influenced by nature” is the notion that the cultural/linguistic capacities of animals and humans have evolutionarily emerged from precultural history. All this is meant to evaluate the viability of constructing a nature/culture divide. The conclusion is made that the divide seems arbitrary within and between human and animal life when considering how the differences between the natural and cultural dynamics of humans and animals are modelled as differences of degree, not kind. A potential approach in using the concept of consciousness to recontextualize a nature/culture divide in terms of the possession of consciousness is proposed at the end. (shrink)

Most philosophical discussions of disagreement have used idealized disagreements to draw conclusions about the nature of disagreement. I closely examine an actual, non-idealized disagreement in dinosaur paleobiology and show that it can not only teach us about the features of some of our real world disagreements, but can help us to argue for the possibility of reasonable real world disagreement.

Alvin Plantinga has famously argued that the naturalist who accepts evolutionary theory has a defeater for all of her beliefs, including her belief in naturalism and evolution. Hence, he says, naturalism, when conjoined with evolution, is self defeating and cannot be rationally accepted. This is known as the evolutionary argument against naturalism (EAAN). However, Tyler Wunder (Religious Studies 51:391– 399, 2015) has recently shown that if the EAAN is framed in terms of objective probability and theism is assumed to be (...) non-contingent, then either theism is necessarily false or the EAAN is unsound. Neither option is attractive to the proponent of the EAAN. Perry Hendricks (Religious Studies 1–5, 2018) has responded to Wunder’s criticism, showing that the EAAN can be salvaged and, indeed, strengthened, by framing it in terms not of naturalism (N), but of a proposition that is entailed by N that is also consistent with theism. We will show that once Hendricks’ solution to Wunder’s objection is accepted, a puzzle ensues: if the EAAN provides the naturalist with a defeater for all of her beliefs, then an extension of it appears to provide God with a defeater for all of his beliefs. After bringing out this puzzle, we suggest several ways in which the proponent of the EAAN might solve it, but also show some potential weaknesses in these purported solutions. Whether the solutions to the puzzle that we consider ultimately succeed is unclear to us. (Translation: the authors disagree. One author thinks that the solutions (or,at least, some of them) that we consider do solve the puzzle while the other author does not.) However, it is clear to us that this is an issue that proponents of the EAAN need to address. (shrink)

CONTENT 1. Misconceptions of Darwin's Theory of Evolution 2. Darwinism against Essentialism and the Concept of Species 3. Function and Biological Explanation 4. The Gene 목차 1. 다윈의 진화론에 대한 오해들 2. 본질주의에 대한 진화론의 반대와 종(Species)의 개념 3. 기능(function)과 생명과학적 설명 4. 유전자 맺음말.

In this work I propose a theory of evolution as a process of unfolding. This theory is based on four logically concatenated principles. The principle of evolutionary order establishes that the more complex cannot be generated from the simpler. The principle of origin establishes that there must be a maximum complexity that originates the others by logical deduction. Finally, the principle of unfolding and the principle of actualization guarantee the development of the evolutionary process from the simplest to the most (...) complex. These logical principles determine the existence of a virtual ideological matrix that contains the sequence of the preformed and folded morphogenetic fields. In this manner, the evolutionary process consists of the sequential unfolding and actualization of these fields, which is motorized by a process of teleologization carried out by the opening consciousness of the forms included in the fields of the ideological matrix. This theory leads to a radical change of perspective regarding the materialist worldview, and places life at the center of the evolutionary process as an activity carried out by a consciousness that seeks to fulfill a purpose by actualizing its own potentialities. (shrink)

Contemporary biological research has suggested that some host–microbiome multispecies systems (referred to as “holobionts”) can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the (...) species-level (genomic adaptations). In this paper, we cover this gap by investigating the nature of hologenomic adaptations. By drawing on the case of the evolution of sanguivory diet in vampire bats, we argue that a trait constitutes a hologenomic adaptation when its evolution can only be explained if the holobiont is considered the biological individual that manifests this adaptation, while the bacterial taxa that bear the trait are only opportunistic beneficiaries of it. We then use the philosophical notions of emergence and inter-identity to explain the nature of this form of individuality and argue why it is special of holobionts. Overall, our paper illustrates how the use of philosophical concepts can illuminate scientific discussions, in the trend of what has recently been called metaphysics of biology. (shrink)

There is a widespread belief that for their own safety and for the protection of wildlife, cats should be permanently kept indoors. Against this view, I argue that cat guardians have a duty to provide their feline companions with outdoor access. The argument is based on a sophisticated hedonistic account of animal well-being that acknowledges that the performance of species-normal ethological behavior is especially pleasurable. Territorial behavior, which requires outdoor access, is a feline-normal ethological behavior, so when a cat is (...) permanently confined to the indoors, her ability to flourish is impaired. Since cat guardians have a duty not to impair the well-being of their cats, the impairment of cat flourishing via confinement signifies a moral failing. Although some cats assume significant risks and sometimes kill wild animals when roaming outdoors, these important considerations do not imply that all cats should be deprived of the opportunity to access the outdoors. Indeed, they do not, by themselves, imply that any cat should be permanently kept indoors. (shrink)

In this article, I advance a novel hypothesis on the evolution of hominin bipedalism. I begin by arguing extensively for how the transition to bipedalism must have been problematic for hominins during the Neogene. Due to this and the fact that no other primate has made the unusual switch to bipedalism, it seems likely that the selection pressure towards bipedalism was unusually strong. With this in mind, I briefly lay out some of the most promising hypotheses on the evolutionary origin (...) of hominin bipedalism and show how most, if not all, fail in the face of the need for an unusually strong selection pressure. For example, some hypotheses maintain that hominins became bipedal so they could use their hands for carrying infants, food, or other valuable objects. But extant apes are able to carry objects in one of their front limbs (while walking with the other three), and thus it does not seem plausible that our hominin ancestors went through the troublesome transition to bipedalism just so they could carry objects a little more efficiently. After I show that past hypotheses are wanting in the face of this challenge, I argue that there is only one selection pressure powerful enough to instigate a strange and problematic evolutionary adaptation like bipedalism, and that is sexual selection. Specifically, from the fact that bipedal locomotion is an important strategy for intimidating others and ascending the dominance hierarchy in extant apes, I argue that for no particular selective reason bipedal locomotion became a signal for high fitness (much as a large and intricate tail became a signal for high fitness for peahens), and this led to the trait being continuously reinforced in spite of all its deleterious fitness consequences. (shrink)

This is an epistemologically-driven history of the concept of evolution. Starting from its inception, this work will follow the development of this pregnant concept. However, in contradistinction to previous attempts, the objective will not be the identification of the different meanings it adopted through history, but conversely, it will let the concept to be unfolded, to be explicated and to express its own inner potentialities. The underlying thesis of the present work is, therefore, that the path that leads to the (...) development of the concept of evolution is the path that studies the possibilities of the evolution of concepts, and that the historical reconstruction of its conceptual trajectory will shed light into potential and unexploited possibilities. This methodology will provide useful tools and resources for future developments of the concept. For example, it will define the concept of transmutation as a different conceptual trajectory deviating from the one corresponding to evolution, at the onset of the 19th century. Moreover, epigenesis will not be the opposing concept to evolution, but only to simultaneous and instantaneous generation. It will demonstrate that every important system of epigenesis drew upon some kind of formative power to explain development. More importantly, it will show that the problem of preformation cannot be overlooked, and that some kind of virtual preformation must be considered in order to address the problems of generation and development. (shrink)

Philippe Huneman has recently questioned the widespread application of mechanistic models of scientific explanation based on the existence of structural explanations, i.e. explanations that account for the phenomenon to be explained in virtue of the mathematical properties of the system where the phenomenon obtains, rather than in terms of the mechanisms that causally produce the phenomenon. Structural explanations are very diverse, including cases like explanations in terms of bowtie structures, in terms of the topological properties of the system, or in (...) terms of equilibrium. The role of mathematics in bowtie structured systems and in topologically constrained systems has recently been examined in different papers. However, the specific role that mathematical properties play in equilibrium explanations requires further examination, as different authors defend different interpretations, some of them closer to the new-mechanistic approach than to the structural model advocated by Huneman. In this paper, we cover this gap by investigating the explanatory role that mathematics play in Blaser and Kirschner’s nested equilibrium model of the stability of persistent long-term human-microbe associations. We argue that their model is explanatory because: i) it provides a mathematical structure in the form of a set of differential equations that together satisfy an ESS; ii) that the nested nature of the ESSs makes the explanation of host-microbe persistent associations robust to any perturbation; iii) that this is so because the properties of the ESS directly mirror the properties of the biological system in a non-causal way. The combination of these three theses make equilibrium explanations look more similar to structural explanations than to causal-mechanistic explanation. (shrink)

This article critically examines one of the most prevalent metaphors in modern biology, namely the machine conception of the organism (MCO). Although the fundamental differences between organisms and machines make the MCO an inadequate metaphor for conceptualizing living systems, many biologists and philosophers continue to draw upon the MCO or tacitly accept it as the standard model of the organism. This paper analyses the specific difficulties that arise when the MCO is invoked in the study of development and evolution. In (...) developmental biology the MCO underlies a logically incoherent model of ontogeny, the genetic program, which serves to legitimate three problematic theses about development: genetic animism, neo-preformationism, and developmental computability. In evolutionary biology the MCO is responsible for grounding unwarranted theoretical appeals to the concept of design as well as to the interpretation of natural selection as an engineer, which promote a distorted understanding of the process and products of evolutionary change. Overall, it is argued that, despite its heuristic value, the MCO today is impeding rather than enabling further progress in our comprehension of living systems. (shrink)

Evolutionary theory coheres with its neighboring theories, such as the theory of plate tectonics, molecular biology, electromagnetic theory, and the germ theory of disease. These neighboring theories were previously unconceived, but they were later conceived, and then they cohered with evolutionary theory. Since evolutionary theory has been strengthened by its several neighboring theories that were previously unconceived, it will be strengthened by infinitely many hitherto unconceived neighboring theories. This argument for evolutionary theory echoes the problem of unconceived alternatives. Ironically, however, (...) the former recommends that we take the realist attitude toward evolutionary theory, while the latter recommends that we take the antirealist attitude toward it. (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.

We review some of the main implications of the free-energy principle (FEP) for the study of the self-organization of living systems – and how the FEP can help us to understand (and model) biotic self-organization across the many temporal and spatial scales over which life exists. In order to maintain its integrity as a bounded system, any biological system - from single cells to complex organisms and societies - has to limit the disorder or dispersion (i.e., the long-run entropy) of (...) its constituent states. We review how this can be achieved by living systems that minimize their variational free energy. Variational free energy is an information theoretic construct, originally introduced into theoretical neuroscience and biology to explain perception, action, and learning. It has since been extended to explain the evolution, development, form, and function of entire organisms, providing a principled model of biotic self-organization and autopoiesis. It has provided insights into biological systems across spatiotemporal scales, ranging from microscales (e.g., sub- and multicellular dynamics), to intermediate scales (e.g., groups of interacting animals and culture), through to macroscale phenomena (the evolution of entire species). A crucial corollary of the FEP is that an organism just is (i.e., embodies or entails) an implicit model of its environment. As such, organisms come to embody causal relationships of their ecological niche, which, in turn, is influenced by their resulting behaviors. Crucially, free-energy minimization can be shown to be equivalent to the maximization of Bayesian model evidence. This allows us to cast natural selection in terms of Bayesian model selection, providing a robust theoretical account of how organisms come to match or accommodate the spatiotemporal complexity of their surrounding niche. In line with the theme of this volume; namely, biological complexity and self-organization, this chapter will examine a variational approach to self-organization across multiple dynamical scales. (shrink)

Big History provides a unique opportunity to consider the development of the Universe as a single process. Within Big History studies one can distinguish some common evolutionary laws and principles. However, it is very important to recognize that there are many more such integrating principles, laws, mecha-nisms and patterns of evolution at all its levels than it is usually supposed. In the meantime, we can find the common traits in development, functioning, and interaction of apparently rather different processes and phenomena (...) of Big History. Of special importance is the point that many principles, patterns, regularities, and rules of evolution, which we tend to find relevant only for the biological and social levels of evolution, may be also applied to the cosmic phase of evolution. The present article attempts (within such a framework for the first time in the Big History framework) at combining Big History potential with the potential of Evolutionary Studies. It does not only analyze the history of the Cosmos. It studies similarities between evolutionary laws, principles, and mechanisms at various levels and phases of Big History. Such an approach opens up some new perspectives for our understanding of evolution and Big History, their driving forces, vectors, and trends; it creates a consolidated field for interdisciplinary research. (shrink)

This Ph.D. thesis provides a pilosophical account of the structure of the evolutionary synthesis of the 1930s and 40s. The first, more historical part analyses how classical genetics came to be integrated into evolutionary thinking, highlighting in particular the importance of chromosomal mapping of Drosophila strains collected in the wild by Dobzansky, but also the work of Goldschmidt, Sumners, Timofeeff-Ressovsky and others. The second, more philosophical part attempts to answer the question wherein the unity of the synthesis consisted. I argue (...) that it exemplifies a weak of form of explanatory unification. (shrink)

The book A critical overview of biological functions is a short monograph by J. Garson, which provides a survey of the views on biological functions in the analytic tradition of philosophy. The notion of function is ubiquitous in biology and all of its subfields. Behind the notion of biological functions lurks the shadow of final causes. Overcoming this shadow is a challenge that has stimulated many philosophers and the literature on this topic is very rich. In the analytic tradition, researchers (...) focus on providing naturalized accounts of functions. To do so, the main difficulty is to provide accounts of functions that exclude the use of final causes. The outcome of this collective work is a diversity of accounts of functions. Some of these accounts are fairly recent while others have been proposed several decades ago and are the object of many discussions. (shrink)

In this paper I defend a teleological explanation of normativity, i. e., I argue that what an organism is supposed to do is determined by its etiological function. In particular, I present a teleological account of the normativity that arises in learning processes, and I defend it from some objections.

In this paper I take evolutionary biology as an example to reflect on the role of philosophy and on the transformations that philosophy is constantly stimulated to do in its own approach when dealing with science. I consider that some intellectual movements within evolutionary biology (more specifically, the various calls for 'synthesis') express metascientific views, i.e., claims about 'what it is to do research' in evolutionary biology at different times. In the construction of metascientific views I see a fundamental role (...) to be played by philosophy, and, at the same time, a need to complement the philosophical methods with many more methods coming from other sciences. What leads philosophy out of itself is its own attention to scientific practice. My humble methodological suggestions are, at this stage, only meant to help us imagine metascientific views that are built with a more scientific, interdisciplinary approach, in order to attenuate partiality, subjectivity and impressionism in describing the scientific community. And yet, we should not be naïve and imbued with the myth of 'datadriven' research, especially in this field: other complex issues about metascientific views call for a serious, constant philosophical reflection on scientific practice. (shrink)

Evolutionary developmental biology represents a paradigm shift in the understanding of the ontogenesis and evolutionary progression of the denizens of the natural world. Given the empirical successes of the evo-devo framework, and its now widespread acceptance, a timely and important task for the philosophy of biology is to critically discern the ontological commitments of that framework and assess whether and to what extent our current metaphysical models are able to accommodate them. In this paper, I argue that one particular model (...) is a natural fit: an ontology of dispositional properties coherently and adequately captures the crucial casual-cum-explanatory role that the fundamental elements of evo-devo play within that framework. (shrink)

Among philosophical analyses of Darwin’s Origin, a standard view says the theory presented there had no concrete observational consequences against which it might be checked. I challenge this idea with a new analysis of Darwin’s principal geographical distribution observations and how they connect to his common ancestry hypothesis.

The biological sciences have always proven a fertile ground for philosophical analysis, one from which has grown a rich tradition stemming from Aristotle and flowering with Darwin. And although contemporary philosophy is increasingly becoming conceptually entwined with the study of the empirical sciences with the data of the latter now being regularly utilised in the establishment and defence of the frameworks of the former, a practice especially prominent in the philosophy of physics, the development of that tradition hasn’t received the (...) wider attention it so thoroughly deserves. This review will briefly introduce some recent significant topics of debate within the philosophy of biology, focusing on those whose metaphysical themes (in everything from composition to causation) are likely to be of wide-reaching, cross-disciplinary interest. (shrink)

If asked to explain why the Golds’ treatment of other colors in Red Rising is wrong, it is tempting to say something like “they are all human beings, and it is wrong to treat humans in this way!” In this essay, I’ll argue that this simple answer is considerably complicated by the fact that the different colors might not be members of the same biological species, and it is in fact unclear whether any of them are the same species as (...) current humans. Explaining why exactly this is so will lead us to an exploration the long-running debate in biology and philosophy over what exactly it means for two organisms to be “members of the same species.” I’ll begin by discussing the biological essentialism of Aristotle and his followers, who held that an individual organism’s species was determined by essence. One can easily imagine that the Golds might find this attractive, since it would suggest that their “superior” mental and physical capacities made them a different (and probably “higher”) species of humanity than the other colors. Unfortunately for Aristotle, this turns out to be inconsistent with Charles Darwin’s account of evolution by natural selection. This development has led many modern biologists and philosophers of biology to conceptualize species not as an abstract “form” that serves to classify organisms, but rather as a concrete collection of organisms relatively close to each other in space and time. In contrast to biological essentialism, this view of “species as concrete individual” might seem to support the Reds’ claim to the “same species” as the Gold, since they are both part of the same overarching society. Next, I’ll consider how we might tell where one species “ends” and another one “begins.” As it turns out, biologists have many ways of answering his question, each of which makes different judgments about the species of Red Rising’s characters. So, for example, the “Biological Species Concept” bases judgements about species membership on the ability to produce fertile offspring. This concept is far from perfect, however, for reasons that Red Rising makes clear: it doesn’t deal clearly with cases where reproduction is possible but very difficult (a Red and a Gold having a child) or for organisms that do not reproduce sexually (such as Pinks). I’ll then explore a few prominent alternatives to BSC, including both genetically and ecologically based species concepts, and consider their consequences for the society of Red Rising. I’ll conclude by advocating for a “pluralism” about species membership, and will suggest that the people of Red Rising (as well as in the real world) should beware of basing arguments for moral or political equality on the all-too-slippery notion of “shared humanity.” Instead, they should focus on the qualities that make the lives of the individuals (regardless of their species) worth caring about, such as their shared desires to avoid suffering and to lead fulfilling, meaningful lives. (shrink)

A book review of R. Paul Thompson's "A Remarkable Journey: The Story of Evolution.

In his recent book Warranted Christian Belief, Alvin Plantinga argues that the defender of naturalistic evolution is faced with adefeater for his position: as products of naturalistic evolution, we have no way of knowing if our cognitive faculties are in fact reliably aimed at the truth. This defeater is successfully avoided by the theist in that, given theism, we can be reasonably secure that out cognitive faculties are indeed reliable. I argue that Plantinga’s argument is ultimately based on a faulty (...) comparison, that he is comparing naturalistic evolution generally to one particular model of theism. In light of this analysis, the two models either stand or fall together with respect to the defeater that Plantinga offers. (shrink)

The nature of learning processes as well as evolutionary considerations suggest that aesthetic judgement is of central importance in the formation of custom. Learning and extrapolation rely on evaluations of non-instrumental features like simplicity, analogy, straightforwardness, and clarity. Further, learning is particularly effective if it is driven by an active desire to uncover new regularities, rather than merely gathering information in a passive way.From an evolutionary perspective, learning has evolved as an adaptation to fast and transitory environmental changes which cannot (...) be effectively traced by the slow and long-term evolutionary processes which take place on the genetic level. The evolutionary raison d’être of learning is to enable the individual to incessantly search for upcoming new regularities, and to act appropriately on them. As learning depends on aesthetic judgement, the evolutionary selection for learning implies an evolutionary molding of an aesthetic sense, and a preference for patterns and patterned action which ultimately leads to the formation of custom and social learning. The paper presents, thus, an evolutionary underpinning for the behavioral tendencies underlying my theory of custom. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Saturated free fatty acids-induced hepatocyte lipoapoptosis plays a pivotal role in non-alcoholic steatohepatitis. Theactivation of endoplasmic reticulum (ER) stress isinvolved in hepatocyte lipoapoptosis induced by thesaturated free fatty acidpalmitate (PA). However, the underlying mechanismsof the role of ER stress in hepatocyte lipoapoptosis remain largely unclear.In this study, we showed that PA and tunicamycin (Tun), a classic ER stress inducer, resulted in differential activation of ERstress pathways. Our data revealed that PA inducedchronic and persistent ER stress response, but Tuninduced acute and (...) transientER stress response. (shrink)

Any theory of confirmation must answer the following question: what is the purpose of its conception of confirmation for scientific inquiry? In this article, we argue that no Bayesian conception of confirmation can be used for its primary intended purpose, which we take to be making a claim about how worthy of belief various hypotheses are. Then we consider a different use to which Bayesian confirmation might be put, namely, determining the epistemic value of experimental outcomes, and thus to decide (...) which experiments to carry out. Interestingly, Bayesian confirmation theorists rule out that confirmation be used for this purpose. We conclude that Bayesian confirmation is a means with no end. 1 Introduction2 Bayesian Confirmation Theory3 Bayesian Confirmation and Belief4 Confirmation and the Value of Experiments5 Conclusion. (shrink)

After its review of the Human Fertilization and Embryology Act of 1990, the Department of Health concluded that the British Parliament ought to outlaw sex selection for any but the most serious of medical reasons. This paper reviews the most frequently expressed objections to social sex selection and concludes that there is simply no moral justification for prohibiting parents from using sex selection technology to balance their families.

This paper argues that scientific realism commits us to a metaphysical determination relation between the mathematical entities that are indispensible to scientific explanation and the modal structure of the empirical phenomena those entities explain. The argument presupposes that scientific realism commits us to the indispensability argument. The viewpresented here is that the indispensability of mathematics commits us not only to the existence of mathematical structures and entities but to a metaphysical determination relation between those entities and the modal structure of (...) the physical world. The no-miracles argument is the primary motivation for scientific realism. It is a presupposition of this argument that unobservable entities are explanatory only when they determine the empirical phenomena they explain. I argue that mathematical entities should also be seen as explanatory only when they determine the empirical facts they explain, namely, the modal structure of the physical world. Thus, scientific realism commits us to a metaphysical determination relation between mathematics and physical modality that has not been previously recognized. The requirement to account for the metaphysical dependence of modal physical structure on mathematics limits the class of acceptable solutions to the applicability problem that are available to the scientific realist. (shrink)

partial review of Thomas Nagel’s book, Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False is used to articulate some systems-theoretic ideas about the challenge of understanding subjective experience. The article accepts Nagel’s view that reductionist materialism fails as an approach to this challenge, but argues that seeking an explanation of mind based on emergence is more plausible than seeking one based on pan-psychism, which Nagel favors. However, the article proposes something similar to Nagel’s neutral (...) monism by positing a hierarchy of information processes that spans the domains of matter, life, and mind. As depicted in this hierarchy, subjective experience is emergent, but also continuous with informational phenomena at lower levels. (shrink)

Elimination controversies are ubiquitous in philosophy and the human sciences. For example, it has been suggested that human races, hysteria, intelligence, mental disorder, propositional attitudes such as beliefs and desires, the self, and the super-ego should be eliminated from the list of respectable entities in the human sciences. I argue that eliminativist proposals are often presented in the framework of an oversimplified “phlogiston model” and suggest an alternative account that describes ontological elimination on a gradual scale between criticism of empirical (...) assumptions and conceptual choices. (shrink)

Debates about the underdetermination of theory by data often turn on specific examples. Cases invoked often enough become familiar, even well worn. Since Helen Longino’s discussion of the case, the connection between prenatal hormone levels and gender-linked childhood behaviour has become one of these stock examples. However, as I argue here, the case is not genuinely underdetermined. We can easily imagine a possible experiment to decide the question. The fact that we would not perform this experiment is a moral, rather (...) than epistemic, point. Finally, I suggest that the ”underdetermination’ of the case may be inessential for Longino to establish her central claim about it. (shrink)

We present a dynamic model of the evolution of communication in a Lewis signaling game while systematically varying the degree of common interest between sender and receiver. We show that the level of common interest between sender and receiver is strongly predictive of the amount of information transferred between them. We also discuss a set of rare but interesting cases in which common interest is almost entirely absent, yet substantial information transfer persists in a *cheap talk* regime, and offer a (...) diagnosis of how this may arise. -/- . (shrink)

Review of Peter Godfrey-Smith's Philosophy of Biology.

I propose a distinct type of robustness, which I suggest can support a confirmatory role in scientific reasoning, contrary to the usual philosophical claims. In model robustness, repeated production of the empirically successful model prediction or retrodiction against a background of independentlysupported and varying model constructions, within a group of models containing a shared causal factor, may suggest how confident we can be in the causal factor and predictions/retrodictions, especially once supported by a variety of evidence framework. I present climate (...) models of greenhouse gas global warming of the 20th Century as an example, and emphasize climate scientists’ discussions of robust models and causal aspects. The account is intended as applicable to a broad array of sciences that use complex modeling techniques. (shrink)

Peter Singer argues that we’re obligated to donate our entire expendable income to aid organizations. One premiss of his argument is "If it is in your power to prevent something bad from happening, without sacrificing anything nearly as important, it is wrong not to do so." Singer defends this by noting that commonsense morality requires us to save a child we find drowning in a shallow pond. I argue that Singer’s Drowning Child thought experiment doesn’t justify this premiss. I offer (...) my own Drowning Children thought experiment, which should reveal that commonsense morality entails that premiss two is actually false. (shrink)

Causal accounts of scientific explanation are currently broadly accepted (though not universally so). My first task in this paper is to show that, even for a causal approach to explanation, significant features of explanatory practice are not determined by settling how causal facts bear on the phenomenon to be explained. I then develop a broadly causal approach to explanation that accounts for the additional features that I argue an explanation should have. This approach to explanation makes sense of several aspects (...) of actual explanatory practice, including the widespread use of equilibrium explanations, the formulation of distinct explanations for a single event, and the tight relationship between explanations of events and explanations of causal regularities. (shrink)

Two popular, yet highly controversial concepts of non-human agency from two different fields of knowledge are compared in this essay: the theory of the Selfish Gene, introduced into neo-Darwinian evolutionary biology by Richard Dawkins, and Actor-Network Theory, as brought forward in Science & Technology Studies by Bruno Latour. It is argued that the two theories, despite all apparent differences, share key motifs and motivations when they try to forward knowledge in their respective fields by adopting a vocabulary that aims at (...) metaphorical redescriptions of the origins of intentionality – in both senses: as purposefulness of action and as meaning. (shrink)

This article discusses the reasons why illusory contours are likely to result from adaptive perceptual mechanisms that have evolved across species to promote behavioral success.

The following considers the role of historical fidelity in habitat reconstruction efforts. To what extent should habitat reconstruction be guided by the goal of recreating some past state of a damaged ecosystem? I consider Sarkar’s “replacement argument,” which holds that, in most habitat reconstruction efforts, there is little justification for appealing to historical fidelity. I argue that Sarkar does not provide adequate grounds for deprecating historical fidelity relative to other natural values such as biodiversity or wild nature.