The theoretical heuristic of assuming distinct alleles (or genotypes) for alternative phenotypes is the foundation of the paradigm of evolutionary explanation we call the Modern Synthesis. In modeling the evolution of sociality, the heuristic has been to set altruism and selfishness as alternative phenotypes under distinct genotypes, which has been dubbed the “phenotypic gambit.” The prevalence of the altruistic genotype that is of lower evolutionary fitness relative to the alternative genotype for non-altruistic behavior in populations is the basis (...) of the “paradox of altruism.” I show in this article that the assumption of contrasting genotypes for altruism and selfishness in our “phenotypic gambit” is inconsistent with the empirical data when viewed in the light of today’s post-Mendelian understanding of gene expression. I demonstrate that however nuanced and sophisticated the models may have become today, they are still rooted in that fundamentally problematic assumption. I then offer a genetic conception of altruism that best fits the field data. (shrink)

In this article we analyse the role that artificial intelligence (AI) could play, and is playing, to combat global climate change. We identify two crucial opportunities that AI offers in this domain: it can help improve and expand current understanding of climate change and it contribute to combating the climate crisis effectively. However, the development of AI also raises two sets of problems when considering climate change: the possible exacerbation of social and ethical challenges already associated with AI, and the (...) contribution to climate change of the greenhouse gases emitted by training data and computation-intensive AI systems. We assess the carbon footprint of AI research, and the factors that influence AI’s greenhouse gas (GHG) emissions in this domain. We find that the carbon footprint of AI research may be significant and highlight the need for more evidence concerning the trade-off between the GHG emissions generated by AI research and the energy and resource efficiency gains that AI can offer. In light of our analysis, we argue that leveraging the opportunities offered by AI for global climate change whilst limiting its risks is a gambit which requires responsive, evidence-based and effective governance to become a winning strategy. We conclude by identifying the European Union as being especially well-placed to play a leading role in this policy response and provide 13 recommendations that are designed to identify and harness the opportunities of AI for combating climate change, while reducing its impact on the environment. (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)

Philosophical arguments usually are and nearly always should be abductive. Across many areas, philosophers are starting to recognize that often the best we can do in theorizing some phenomena is put forward our best overall account of it, warts and all. This is especially true in esoteric areas like logic, aesthetics, mathematics, and morality where the data to be explained is often based in our stubborn intuitions. -/- While this methodological shift is welcome, it's not without problems. Abductive arguments involve (...) significant theoretical resources which themselves can be part of what's being disputed. This means that we will sometimes find otherwise good arguments which suggest their own grounds are problematic. In particular, sometimes revising our beliefs on the basis of such an argument can undermine the very justification we used in that argument. -/- This feature, which I'll call self-effacingness, occurs most dramatically in arguments against our standing views on the esoteric subject matters mentioned above: logic, mathematics, aesthetics, and morality. This is because these subject matters all play a role in how we reason abductively. This isn't an idle fact; we can resist some challenges to our standing beliefs about these subject matters exactly because the challenges are self-effacing. The self-effacing character of certain arguments is thus both a benefit and limitation of the abductive turn and deserves serious attention. I aim to give it the attention it deserves. (shrink)

An exploration of the nexus between ecology, evolutionary biology and molecular biology, via the concept of phenotypic plasticity.

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)

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)

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)

I examine the central atheistic argument of Richard Dawkins’s book The God Delusion (“Dawkins’s Gambit”) and illustrate its failure. I further show that Dawkins’s Gambit is a fragment of a more comprehensive critique of theism found in David Hume’s Dialogues Concerning Natural Religion. Among the failings of Dawkins’s Gambit is that it is directed against a version of the God Hypothesis that few traditional monotheists hold. Hume’s critique is more challenging in that it targets versions of the (...) God Hypothesis that are central to traditional monotheism. Theists and atheists should put away The God Delusion and pick up Hume’s Dialogues. (shrink)

After summarizing the essential details of Anil Gupta’s account of perceptual justification in his book _Empiricism and Experience_, I argue for three claims: (1) Gupta’s proposal is closer to rationalism than advertised; (2) there is a major lacuna in Gupta’s account of how convergence in light of experience yields absolute entitlements to form beliefs; and (3) Gupta has not adequately explained how ordinary courses of experience can lead to convergence on a commonsense view of the world.

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)

Developmental plasticity as the nexus between genetics and ecology.

A phenome occurs through the many pathways of the complex net of interaction between the phenome and its environment; therefore researching and understanding how it arises requires investigation into many possible causes that are in constant interaction with each other. The most comprehensive investigations in biology are the ones in which many biologists from different sub-areas—evolutionary biology, developmental biology, molecular biology, physiology, genetics, epigenetics, ecology—have collaborated. Still, biologists do not always need to collaborate or look for the most comprehensive explanations. (...) A more standard investigation in biology occurs within a single subarea, and uses well-defined experiments with very specific conditions. This paper is about causation and related explanation in plant phenome research and its relevance to Aristotle’s Theory of Four Causes. I argue that there are causes which resemble Aristotle’s formal, material, and efficient causes in phenotype explanation and occurrence; but causes which resemble Aristotle’s final causes occur in phenotype explanation only, not in the occurrence. (shrink)

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

Psychiatry has witnessed a new wave of approaches to clinical phenotyping and the study of psychopathology, including the National Institute of Mental Health’s Research Domain Criteria, clinical staging, network approaches, the Hierarchical Taxonomy of Psychopathology, and the general psychopathology factor, as well as a revival of interest in phenomenological psychopathology. The question naturally emerges as to what the relationship between these new approaches is – are they mutually exclusive, competing approaches, or can they be integrated in some way and used (...) to enrich each other? In this opinion piece, we propose a possible integration between clinical staging and phenomenological psychopathology. Domains identified in phenomenological psychopathology, such as selfhood, embodiment, affectivity, etc., can be overlaid on clinical stages in order to enrich and deepen the phenotypes captured in clinical staging (‘high resolution’ clinical phenotypes). This approach may be useful both ideographically and nomothetically, in that it could complement diagnosis, enrich clinical formulation, and inform treatment of individual patients, as well as help guide aetiological, prediction, and treatment research. The overlaying of phenomenological domains on clinical stages may require that these domains are reformulated in dimensional rather than categorial terms. This integrative project requires assessment tools, some of which are already available, that are sensitive and thorough enough to pick up on the range of relevant psychopathology. The proposed approach offers opportunities for mutual enrichment: clinical staging may be enriched by introducing greater depth to phenotypes; phenomenological psychopathology may be enriched by introducing stages of severity and disorder progression to phenomenological analysis. (shrink)

A response to Via about the existence (or not) and role of plasticity genes in evolution.

Background: One of the all-time questions in evolutionary biology regards the evolution of organismal shapes, and in particular why certain forms appear repeatedly in the history of life, others only seldom and still others not at all. Recent research in this field has deployed the conceptual framework of constraints and natural selection as measured by quantitative genetic methods. Scope: In this paper I argue that quantitative genetics can by necessity only provide us with useful statistical sum- maries that may lead (...) researchers to formulate testable causal hypotheses, but that any inferential attempt beyond this is unreasonable. Instead, I suggest that thinking in terms of coordinates in phenotypic spaces, and approaching the problem using a variety of empirical methods (seeking a consilience of evidence), is more likely to lead to solid inferences regarding the causal basis of the historical patterns that make up most of the data available on phenotypic evolution. (shrink)

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

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

Digital phenotyping will potentially enable earlier detection and prediction of mental illness by monitoring human interaction with and through digital devices. Notwithstanding its promises, it is certain that a person’s digital phenotype will at times be at odds with their first-person testimony of their psychological states. In this paper, we argue that there are features of digital phenotyping in the context of psychiatry which have the potential to exacerbate the tendency to dismiss patients’ testimony and treatment preferences, which can be (...) instances of epistemic injustice. We first explain what epistemic injustice is, and why it is argued to be an extensive problem in health and disability settings. We then explain why epistemic injustice is more likely to apply with even greater force in psychiatric contexts, and especially where digital phenotyping may be involved. Finally, we offer some tentative suggestions of how epistemic injustice can be minimised in digital psychiatry. (shrink)

Invasion biologists often suggest that phenotypic plasticity plays an important role in successful plant invasions. Assuming that plasticity enhances ecological niche breadth and therefore confers a fitness advantage, recent studies have posed two main hypotheses: (1) invasive species are more plastic than non-invasive or native ones; (2) populations in the introduced range of an invasive species have evolved greater plasticity than populations in the native range. These two hypotheses largely reflect the disparate interests of ecologists and evolutionary biologists. Because (...) these sciences are typically interested in different temporal and spatial scales, we describe what is required to assess phenotypic plasticity at different levels. We explore the inevitable tradeoffs of experiments conducted at the genotype vs. species level, outline components of experimental design required to identify plasticity at different levels, and review some examples from the recent literature. Moreover, we suggest that a successful invader may benefit from plasticity as either (1) a Jack-of-all-trades, better able to maintain fitness in unfavourable environments; (2) a Master-of-some, better able to increase fitness in favourable environments; or (3) a Jack-and-master that combines some level of both abilities. This new framework can be applied when testing both ecological or evolutionary oriented hypotheses, and therefore promises to bridge the gap between the two perspectives. (shrink)

After introducing the new field of cultural evolution, we review a growing body of empirical evidence suggesting that culture shapes what people attend to, perceive and remember as well as how they think, feel and reason. Focusing on perception, spatial navigation, mentalizing, thinking styles, reasoning (epistemic norms) and language, we discuss not only important variation in these domains, but emphasize that most researchers (including philosophers) and research participants are psychologically peculiar within a global and historical context. This rising tide of (...) evidence recommends caution in relying on one’s intuitions or even in generalizing from reliable psychological findings to the species, Homo sapiens. Our evolutionary approach suggests that humans have evolved a suite of reliably developing cognitive abilities that adapt our minds, information-processing abilities and emotions ontogenetically to the diverse culturally-constructed worlds we confront. (shrink)

How we ought to diagnose, categorise and respond to spectrum disabilities such as autism and Attention Deficit/Hyperactivity Disorder (ADHD) is a topic of lively debate. The heterogeneity associated with ADHD and autism is described as falling on various continua of behavioural, neural, and genetic difference. These continua are varyingly described either as extending into the general population, or as being continua within a given disorder demarcation. Moreover, the interrelationships of these continua are likewise often vague and subject to diverse interpretations. (...) -/- In this paper, I explore geneticists' and self-advocates’ perspectives concerning autism and ADHD as continua. These diagnoses are overwhelmingly analysed as falling on a continuum or continua of underlying traits, which supports the notion of “the neurodiversity spectrum”, i.e., a broader swath of human neural and behavioural diversity on which some concentrations of different functioning are diagnosed. I offer a taxonomy of conceptions of the genetic, phenotypic, and endophenotypic dimensionality within and beyond these diagnostic categories, and suggest that the spectrum of neurodiversity is characteristically endophenotypic. (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)

Noting minimal philosophical attention to the shift of the meanings of “genotype” and “phenotype,” and their distinction, as well as to the variety of meanings that have co-existed over the last hundred years, this note invites readers to join in exploring the implications of shifts that have been left unexamined.

Metaphors play a crucial role in both science in particular and human discourse in gen- eral. Plato’s story of the cave—about people shackled to a wall and incapable of perceiv- ing the world as it really is—has stimulated thinking about epistemology and the nature of reality for more than two millennia. But metaphors can also be misleading: being too taken with Plato’s story has cost philosophers endless discussions about how to access the world “as it is,” until Kant showed us (...) that it is just not going to happen, ever. (shrink)

Mehlman and Li offer a framework for approaching the bioethical issues raised by the military use of genomics that is compellingly grounded in both the contemporary civilian and military ethics of medical research, arguing that military commanders must be bound by the two principles of paternal- ism and proportionality. I agree fully. But I argue here that this is a much higher bar than we may fully realize. Just as the principle of proportionality relies upon a thorough assessment of harms (...) caused and military advantage gained, the use of genomic research, on Mehlman and Li’s view, will require an accurate understanding of the connection between genotypes and phenotypes – accurate enough to ameliorate the risk undertaken by our armed forces in being subject to such research. Recent conceptual work in evolutionary theory and the philosophy of biology, however, renders it doubtful that such knowledge is forthcoming. The complexity of the relationship between genotypic factors and realized traits (the so-called ‘G→P map’) makes the estimation of potential military advantage, as well as potential harm to our troops, incredibly challenging. Such fundamental conceptual challenges call into question our ability to ever satisfactorily satisfy the demands of a sufficiently rigorous ethical standard. (shrink)

The concept of reaction norms plays a crucial role in connecting molecular and evolutionary biology.

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 transformational pace of modern education, healthcare, business management systems, etc., requires new approaches for prompt and reliable personality assessment. Phenotypology is one of such theories and it claims of the discovered interconnections of a person’s psychological and psychophysical characteristics on the basis of individual features of his/her phenotype. The article aim is to present some validation results for the Phenotypology hypotheses as a possible tool for personality assessment. In order to verify connections between phenotypic treats and individual behavior, (...) we conducted the study when respondents were differentiated according to some anthropometric (facial) peculiarities and characterological features. The results were quantified and analyzed using the mathematical-statistical linear regression. The research output contains the rationale for the conclusion that there are no statistically significant correlations between some phenotypic body features and such individual psychological characteristics as aggressiveness, impetuosity, pedantry, passivity, etc. In particular, the validity of using of appropriate phenotypologic representations to predict the examined character traits was studied. The obtained results disproved the possibility to use directly the phenotypic approach for reliable characterological profiling. Though, the study outcome is tentative due to some limitations on generality. It is necessary to continue verification of the Phenotypology hypotheses with a broader experimental sample with the inclusion of various ethnic and racial groups’ representatives. However, until then, based on actual findings, the practical application of the Phenotypology statements is doubtful, at least for the purposes of character diagnosis and personality assessment. (shrink)

In this article, we examine in detail the New Atheists' most serious argument for the conclusion that God does not exist, namely, Richard Dawkins's Ultimate 747 Gambit. Dawkins relies upon a strong explanatory principle involving simplicity. We systematically inspect the various kinds of simplicity that Dawkins may invoke. Finding his crucial premises false on any common conception of simplicity, we conclude that Dawkins has not given good reason to think God does not exist.

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

In this chapter, Logan Paul Gage examines the only real attempt to disprove God’s existence by a New Atheist: Richard Dawkins’s “Ultimate 747 Gambit.” Central to Dawkins’s argument is the claim that God is more complex than what he is invoked to explain. Gage evaluates this claim using the main extant notions of simplicity in the literature. Gage concludes that on no reading does this claim survive scrutiny. Along the way, Dawkins claims that there are no good positive arguments (...) for God’s existence. Gage attempts to show that Dawkins’s argument depends upon distinctively philosophical assumptions that do not appear to withstand scrutiny. (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)

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)

Many have argued that there is no reason why natural selection should cause directional increases in measures such as body size or complexity across evolutionary history as a whole. In this paper I argue that this conclusion does not hold for selection for adaptations to environmental variability, and that, given the inevitability of environmental variability, trends in adaptations to variability are an expected feature of evolution by natural selection. As a concrete instance of this causal structure, I outline how this (...) may be applied to a trend in phenotypic plasticity. (shrink)

I argue that the Conceptual Ethics and Conceptual Engineering framework, in its pragmatist version as recently defended by Thomasson, provides a means of articulating and defending the conventionalist interpretation of projects of conceptual extension (e.g. the extended mind, the extended phenotype) in biology and psychology. This promises to be illuminating in both directions: it helps to make sense of, and provides an explicit methodology for, pragmatic conceptual extension in science, while offering further evidence for the value and fruitfulness of the (...) Conceptual Ethics/Engineering framework itself, in particular with respect to conceptual change within science, which has thus-far received little attention in the literature on Conceptual Ethics/Engineering. (shrink)

In the fall of 1990 I had just began my doc- toral studies at the University of Connecticut. Freshly arrived from Italy, I came to the United States to work with Carl Schlichting on something to do with phenotypic plastic- ity. I spent most of that semester discussing with other graduate students what I thought was a momentous paper by Mary Jane West- Eberhard (1989) in the Annual Review of Ecol- ogy and Systematics. That paper, entitled Phe- notypic Plasticity (...) and the Origins of Diversity, was a (quite lengthy) forerunner of the (also quite bulky) book I am reviewing now. Like the paper, this volume has the potential to be momentous in the development of our ideas on phenotypic evolution. (shrink)

Moral debunking arguments are meant to show that, by realist lights, moral beliefs are not explained by moral facts, which in turn is meant to show that they lack some significant counterfactual connection to the moral facts (e.g., safety, sensitivity, reliability). The dominant, “minimalist” response to the arguments—sometimes defended under the heading of “third-factors” or “pre-established harmonies”—involves affirming that moral beliefs enjoy the relevant counterfactual connection while granting that these beliefs are not explained by the moral facts. We show that (...) the minimalist gambit rests on a controversial thesis about epistemic priority: that explanatory concessions derive their epistemic import from what they reveal about counterfactual connections. We then challenge this epistemic priority thesis, which undermines the minimalist response to debunking arguments (in ethics and elsewhere). (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)

In “Accepting Moral Responsibility for the Actions of Autonomous Weapons Systems—a Moral Gambit” (2022), Mariarosaria Taddeo and Alexander Blanchard answer one of the most vexing issues in current ethics of technology: how to close the so-called “responsibility gap”? Their solution is to require that autonomous weapons systems (AWSs) may only be used if there is some human being who accepts the ex ante responsibility for those actions of the AWS that could not have been predicted or intended (in such (...) cases, the human being takes what the authors call the “moral gambit”). The authors then propose several institutional safeguards to implement in order to ensure that the moral gambit is taken in a fair and just way. This paper explores this suggestion in the context of the institutional settings within which AWSs are most likely to be deployed. It raises some concerns as to the feasibility of Taddeo and Blanchard’s proposal, in light of the recent empirical work on the incentive structures likely to exist within militaries. It then presents a potential problem that may arise in case the accountability mechanisms are successfully implemented. (shrink)

This chapter examines the status of inference to the best explanation in naturalistic metaphysics. The methodology of inference to the best explanation in metaphysics is studied from the perspective of contemporary views on scientific explanation and explanatory inferences in the history and philosophy of science. This reveals serious shortcomings in prevalent attempts to vindicate metaphysical "explanationism" by reference to similarities between science and naturalistic metaphysics. This critique is brought out by considering a common gambit of methodological unity: (1) Both (...) metaphysics and science employ inference to the best explanation. (2) One has no reason to think that if explanationism is truth-conducive in science, it is not so in metaphysics. (3) One has a positive reason to think that if explanationism is truth-conducive in science, it is also so in metaphysics. (shrink)

A discussion of plasticity genes and the genetic architecture of gene-environment interactions.

Darwinian evolutionary theory has two key terms, variations and biological selection, which finally lead to survival of the fittest variant. With the rise of molecular genetics, variations were explained as results of error replications out of the genetic master templates. For more than half a century, it has been accepted that new genetic information is mostly derived from random error-based events. But the error replication narrative has problems explaining the sudden emergence of new species, new phenotypic traits, and genome (...) innovations as a sudden single event. Meanwhile, it is recognized that errors cannot explain the evolution of genetic information, genetic novelty, and complexity. Now, empirical evidence establishes the crucial role of non-random genetic content editors, such as viruses, diversity generating retroelements, and other RNA networks, to produce new genetic information, complex regulatory control, inheritance vectors, genetic identity, immunity, new sequence space, evolution of complex organisms, and evolutionary transitions. (shrink)

Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants (...) during stress. Coopted by lymphocytes, the ancient mutagenic processing systems retained their diversification functions instilling the adaptive immune cells with enhanced evolvability and defensive capacity to resist infection and damage. As reviewed here, the ubiquity and conserved character of specialized variation-generating mechanisms from bacteria to lymphocytes highlight the importance of these mechanisms for evolution of life in general. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

I’m often asked why, as a philosopher of science, I study archaeology. Philosophy is so abstract and intellectual, and archaeology is such an earth-bound, data-driven enterprise, what could the connection possibly be? This puzzlement takes a number of different forms. In one memorable exchange in the late 1970s when I was visiting Oxford as a graduate student an elderly don, having inquired politely about my research interests, tartly observed that archaeology isn’t a science, so I couldn’t possibly be writing a (...) dissertation in philosophy of science on archaeology. At job interviews a few years later a standard opening gambit was to ask: “so what’s philosophical about the work you do on archaeology” or, more querulously, “what could possibly be of philosophical interest in archaeology”? And from archaeologists, weary of the “theory wars” that raged through 1980s and 1990s, the standard question was, “What’s the point?! Better to step away from the wrangling about philosophical ‘isms’ and get on with the empirical work that needs doing.”. (shrink)

The field of the philosophy of biology is flourishing in its aim to evaluate and rethink the view inherited from the previous century ---the Modern Synthesis. Different research areas and theories have come to the fore in the last decades in order to account for different biological phenomena that, in the first instance, fall beyond the explanatory scope of the Modern Synthesis. This thesis is anchored and motivated by this revolt in the philosophy of biology. -/- The central target in (...) this context is the possibility of naturalizing teleology, a classical nightmare for the history of biology itself. This requires, principally, understanding the causes of teleological explanations without assuming an unfashioned backward causation of sorts. As the riddles of teleological explanations are about their temporal dimension, I analyze different temporal scales of biological processes: evolutionary, developmental, and physiological. -/- The first one is the one defended in the context of the Modern Synthesis. As expected, one of the aims of this thesis is to evaluate the adequacy of an evolutionary account of teleological explanation. The scrutiny is negative. Evolutionary explanations in the context of the Modern Synthesis lack the necessary causal roots to naturalize teleology. Concerning the physiological scale, a long tradition pushed up by Kant and the organicist movement in the 20th century allows us to better understand how teleological explanations can be naturalized in physiological process. The key notions in this temporal scale are self-organization and the recursive, looped character of physiological process. While the physiological scale may be suitably accounted by contemporaries views, such as Autonomous Systems Theory, different central teleological phenomena remain unexplained from a purely physiological perspective. In particular, different issues concerning the (adaptive) construction of organism ---such as plasticity, robustness, variation, novelty, inheritance--- deserve an ontogenetic analysis. -/- The principal aim of this thesis is to provide a theory of teleological development that falls beyond the Modern Synthesis' framework and is prompted by different insights from the history of biology. I call it Agential Teleosemantics. It rests on two central pillars. First, that developmental processes, beyond any gene-centered stance, can be understood in informational terms; i.e. developmental processes are about the interaction of developmental resources conveying biological information. The second ingredient is agentivity, namely the idea that development is regulated by an agentive system according to the adaptiveness of the phenotypic outcomes produced. The role of agency in Agential Teleosemantic is equivalent to the role of genes in the Modern Synthesis: it is responsible for explaining the order and the adaptive complexity in the living realm. -/- The second target of this thesis regards the possibility of naturalizing intentional explanations in cognitive science. The central project involved in such an aim is known as teleosemantics. Classical teleosemantics however is etiological: it explains the teleofunctions of representational systems in terms of evolutionary processes. The different disputes in the contemporary philosophy of biology provide two insights to analyze teleosemantics in cognitive science. First, the challenges against the Modern Synthesis must be extended to the evolutionary approach of etiological teleosemantics. Second, as Agential Teleosemantics suggests an alternative source for teleofunctions ---ontogeny, I offer an attempt to integrate Agential Teleosemantics into cognitive science in order to provide an alternative teleosemantic project to understand intentional explanations in cognitive science. (shrink)

Darwinism presents a paradox. It discredits the notion that one’s life has any intrinsic meaning, yet it predicts that we are designed by Darwinian natural selection to generally insist that it must—and so necessarily designed to misunderstand and doubt Darwinism. The implications of this paradox are explored here, including the question of where then does the Darwinist find meaning in life? The main source, it is proposed, is from cognitive domains for meaning inherited from sentient ancestors—domains that reveal our evolved (...) human nature as the fool that it is: given to distractions and delusions of many kinds, designed by natural selection primarily for one essential purpose—to allay our instinctual fear of failed legacy, rooted in our uniquely human awareness that we are not immortal. Darwinism, however, also teaches that genuine legacy is a fate enjoyed only by individual genes. Accordingly, as argued here, those genes with the grandest legacy—and hence rampant within us—are of two types: “legacy-drive” genes delude us into thinking that the legacy can be individually and personally ours; and “leisure-drive” genes distract us from the agonizing truth that it can never be. The most rudimental delusion of legacy is the perception of offspring as vehicles for memetic legacy—the transmission of resident memes from one’s mind to the minds and behaviors of offspring— thus also ensuring genetic legacy: the transmission of resident genes, including importantly, genes inherited from ancestors that influence both legacy and leisure drives. Today, legacyand leisure-drive genes reveal their phenotypes across a wide range of human affairs, and together with the phenotypes of survival- and sex-drive genes, they provide a foundation for a novel view of the Darwinian roots of cultural evolution. (shrink)