Debate about legal and policy reform has been haunted by a pernicious confusion about human nature, the idea that it is a set of rigid dispositions, today generally conceived as genetic, that is manifested the same way in all circumstances. Opponents of egalitarian alternatives argue that we cannot depart far from the status quo because human nature stands in the way. Advocates of such reforms too often deny the existence of human nature because, sharing this conception, they think it would (...) prevent changes they deem desirable. Both views rest on deep errors about what it is to have a nature and how genetics works. Human nature, like the nature of anything else, is a set of potentials to behave certain ways in given environments, not a nonsocial genetic something that inevitably produces the same result in any environment. To say that existing inequalities, are due to our genes, inalterable because heritable, ignores that genetic propensities may be differently manifested in different environments. Heritability has meaning only relative to an environment and a population and implies nothing about inevitability. A better sort of inegalitarian argument is that a proposed reform, given our nature, would be too costly even if possible. However, this sort of argument is too rarely supported by evidence and generally ignores the costs of existing inequalities. But egalitarians err in supposing that, if behavior is unconstrained by biology, the status quo is easily alterable. The environment may be extremely hard to change. Legal and policy debate should adopt a correct understanding of human nature as a set of propensities and ask of any proposed reform agreed to be otherwise desirable what and how alterable are its causes, genetic, environmental, or more accurately both. (shrink)

Synthetic biologists aim to generate biological organisms according to rational design principles. Their work may have many beneficial applications, but it also raises potentially serious ethical concerns. In this article, we consider what attention the discipline demands from bioethicists. We argue that the most important issue for ethicists to examine is the risk that knowledge from synthetic biology will be misused, for example, in biological terrorism or warfare. To adequately address this concern, bioethics will need to broaden its scope, (...) contemplating not just the means by which scientific knowledge is produced, but also what kinds of knowledge should be sought and disseminated. (shrink)

Human nature has always been a foundational issue for philosophy. What does it mean to have a human nature? Is the concept the relic of a bygone age? What is the use of such a concept? What are the epistemic and ontological commitments people make when they use the concept? In What’s Left of Human Nature? Maria Kronfeldner offers a philosophical account of human nature that defends the concept against contemporary criticism. In particular, she takes on challenges related to social (...) misuse of the concept that dehumanizes those regarded as lacking human nature (the dehumanization challenge); the conflict between Darwinian thinking and essentialist concepts of human nature (the Darwinian challenge); and the consensus that evolution, heredity, and ontogenetic development results from nurture and nature. After answering each of these challenges, Kronfeldner presents a revisionist account of human nature that minimizes dehumanization and does not fall back on outdated biological ideas. Her account is post-essentialist because it eliminates the concept of an essence of being human; pluralist in that it argues that there are different things in the world that correspond to three different post-essentialist concepts of human nature; and interactive because it understands nature and nurture as interacting at the developmental, epigenetic, and evolutionary levels. On the basis of this, she introduces a dialectical concept of an ever-changing and “looping” human nature. Finally, noting the essentially contested character of the concept and the ambiguity and redundancy of the terminology, she wonders if we should simply eliminate the term “human nature” altogether. (shrink)

DARWIN’s (1859, 1871) discoveries have profound ethical implications that continue to be misrepresented and/or ignored. In contrast to socialdarwinistic misuses of his theory, Darwin was a great humanitarian who paved the way for an integrated scientific and ethical world view. As an ethical doctrine, socialdarwinism is long dead ever since its defeat by E. G. Moore although the socialdarwinistic thought is a hard-die in the biological community. The accusations of sociobiology for being socialdarwinistic are unfounded and stem from the moralistic (...) fallacy that is, a false assumption that morality is good by definition. Both social and developmental psychology demonstrate that the moral agency is a motivational device for executing reciprocity that remains at the core of any morality across all studied societies and throughout the ontogeny of moral judgment. The level of true universalizing ethical reflection (KOHLBERG’s postconvential stages or GIBBS’s existential phase) is achieved by a small minority of humans, thus showing that Homo sapiens is a moral but not an ethical animal. While the origin of reciprocity has been perfectly explained by sociobiology, the evolutionary assembly of affective and cognitive elements that make up the moral agency is being successfully studied by the social/personality/developmental psychology as extended to non-human primates. As DARWIN (1871) expected, the key innovation for the evolution of moral agency was the emergence of empathy that evolved independently at least three times: in elephants, dolphins and primates. Empathy has a motivational power of its own; it is also necessary for moral agency that requires two cognitive abilities: reflective self-consciousness and understanding of causality; the two make possible the attribution of responsibility. All these requirements are met by the chimpanzees whose moral agency operates in dyads. In contrast, the human moral agency allows for a third party intervention that opens up vast opportunities for ideologies, especially religions, to use and misuse the moral agency to enforce a reciprocation that may be harmful to both individuals and the entire group. Also, the moral agency is known to enforce enhanced intragroup cohesion and loyalty in response to conflict and war, which suggests that the two prima facie opposed human universals, morality and warfare, may have coevolved. The most important ethical consequence that follows from the increasing understanding of the primate moral agency is that every received morality is ethically flawed, none can be taken as a paragon of goodness, and each needs corrections by science-informed ethics. In fact, Darwin pioneered the integration of science and ethics, an approach that has come to be appreciated only recently under the heading of consilience. (shrink)

Since Gintis is a senior economist and I have read some of his previous books with interest, I was expecting some more insights into behavior. Sadly he makes the dead hands of group selection and phenomenology into the centerpieces of his theories of behavior, and this largely invalidates the work. Worse, since he shows such bad judgement here, it calls into question all his previous work. The attempt to resurrect group selection by his friends at Harvard, Nowak and Wilson, a (...) few years ago was one of the major scandals in biology in the last decade, and I have recounted the sad story in my article ‘Altruism, Jesus and the End of the World—how the Templeton Foundation bought a Harvard Professorship and attacked Evolution, Rationality and Civilization -- A review of E.O. Wilson 'The Social Conquest of Earth' (2012) and Nowak and Highfield ‘SuperCooperators’ (2012).’ Unlike Nowak, Gintis does not seem to be motivated by religious fanaticism, but by the strong desire to generate an alternative to the grim realities of human nature, made easy by the (near universal) lack of understanding of basic human biology and blank slateism of behavioral scientists, other academics, and the general public. -/- Gintis rightly attacks (as he has many times before) economists, sociologists and other behavioral scientists for not having a coherent framework to describe behavior. Of course the framework needed to understand behavior is an evolutionary one. Unfortunately he fails to provide one himself (according to his many critics and I concur), and the attempt to graft the rotten corpse of group selection onto whatever economic and psychological theories he has generated in his decades of work, merely invalidates his entire project. Although Gintis makes a valiant effort to understand and explain the genetics, like Wilson and Nowak, he is far from an expert, and like them, the math just blinds him to the biological impossibilities and of course this is the norm in science. As Wittgenstein famously noted on the first page of Culture and Value “There is no religious denomination in which the misuse of metaphysical expressions has been responsible for so much sin as it has in mathematics.” -/- It has always been crystal clear that a gene that causes behavior which decreases its own frequency cannot persist, but this is the core of the notion of group selection. Furthermore, it has been well known and often demonstrated that group selection just reduces to inclusive fitness (kin selection), which, as Dawkins has noted, is just another name for evolution by natural selection. Like Wilson, Gintis has worked in this arena for about 50 years and still has not grasped it, but after the scandal broke, it took me only 3 days to find, read and understand the most relevant professional work, as detailed in my article. It is mind boggling to realize that Gintis and Wilson were unable to accomplish this in nearly half a century. -/- I discuss the errors of group selection and phenomenology that are the norm in academia as special cases of the near universal failure to understand human nature that are destroying America and the world. -/- Those who wish to read all my articles please consult the ebook here Philosophy, Human Nature and the Collapse of Civilization -- Articles and Reviews 2006-2016 by Michael Starks 662p (2016) -/- All of my papers and books have now been published in revised versions both in ebooks and in printed books. -/- Talking Monkeys: Philosophy, Psychology, Science, Religion and Politics on a Doomed Planet - Articles and Reviews 2006-2017 (2017) https://www.amazon.com/dp/B071HVC7YP. -/- The Logical Structure of Philosophy, Psychology, Mind and Language in Ludwig Wittgenstein and John Searle--Articles and Reviews 2006-2016 (2017) https://www.amazon.com/dp/B071P1RP1B. -/- Suicidal Utopian Delusions in the 21st century: Philosophy, Human Nature and the Collapse of Civilization - Articles and Reviews 2006-2017 (2017) https://www.amazon.com/dp/B0711R5LGX -/- . (shrink)

One big question in biology is what life is, but another is how life divides into living things. This is the problem of biological individuality. Proposed statements of the problem have been vague and incomplete. And proposed theories of biological individuality are not detailed enough to solve the problem even if they are correct. The root of these troubles is that their authors have not recognized the metaphysical claims presupposed in their statement of the problem. Making these claims explicit (...) will enable us to see better what the problem is and what form a solution to it would need to have. (shrink)

This collection of essays explores the metaphysical thesis that the living world is not made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organised as an interdependent hierarchy of processes, which are stabilised and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, (...) which have tended to use Alfred North Whitehead’s panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be found in the empirical findings of science. Biology provides compelling reasons for thinking that the living realm is fundamentally dynamic, and that the existence of things is always conditional on the existence of processes. The phenomenon of life cries out for theories that prioritise processes over things, and it suggests that the central explanandum of biology is not change but rather stability, or more precisely, stability attained through constant change. This edited volume brings together philosophers of science and metaphysicians interested in exploring the consequences of a processual philosophy of biology. The contributors draw on an extremely wide range of biological case studies, and employ a process perspective to cast new light on a number of traditional philosophical problems, such as identity, persistence, and individuality. (shrink)

This chapter argues that scientific and philosophical progress in our understanding of the living world requires that we abandon a metaphysics of things in favour of one centred on processes. We identify three main empirical motivations for adopting a process ontology in biology: metabolic turnover, life cycles, and ecological interdependence. We show how taking a processual stance in the philosophy of biology enables us to ground existing critiques of essentialism, reductionism, and mechanicism, all of which have traditionally been (...) associated with substance ontology. We illustrate the consequences of embracing an ontology of processes in biology by considering some of its implications for physiology, genetics, evolution, and medicine. And we attempt to locate the subsequent chapters of the book in relation to the position we defend. (shrink)

Since Gintis is a senior economist and I have read some of his previous books with interest, I was expecting some more insights into behavior. Sadly, he makes the dead hands of group selection and phenomenology into the centerpieces of his theories of behavior, and this largely invalidates the work. Worse, since he shows such bad judgement here, it calls into question all his previous work. The attempt to resurrect group selection by his friends at Harvard, Nowak and Wilson, a (...) few years ago was one of the major scandals in biology in the last decade, and I have recounted the sad story in my article ‘Altruism, Jesus and the End of the World—how the Templeton Foundation bought a Harvard Professorship and attacked Evolution, Rationality and Civilization -- A review of E.O. Wilson 'The Social Conquest of Earth' (2012) and Nowak and Highfield ‘SuperCooperators’ (2012).’ Unlike Nowak, Gintis does not seem to be motivated by religious fanaticism, but by the strong desire to generate an alternative to the grim realities of human nature, made easy by the (near universal) lack of understanding of basic human biology and blank slateism of behavioral scientists, other academics, and the general public. -/- Gintis rightly attacks (as he has many times before) economists, sociologists and other behavioral scientists for not having a coherent framework to describe behavior. Of course, the framework needed to understand behavior is an evolutionary one. Unfortunately, he fails to provide one himself (according to his many critics and I concur), and the attempt to graft the rotten corpse of group selection onto whatever economic and psychological theories he has generated in his decades of work, merely invalidates his entire project. -/- Although Gintis makes a valiant effort to understand and explain the genetics, like Wilson and Nowak, he is far from an expert, and like them, the math just blinds him to the biological impossibilities and of course this is the norm in science. As Wittgenstein famously noted on the first page of Culture and Value “There is no religious denomination in which the misuse of metaphysical expressions has been responsible for so much sin as it has in mathematics.” -/- It has always been crystal clear that a gene that causes behavior which decreases its own frequency cannot persist, but this is the core of the notion of group selection. Furthermore, it has been well known and often demonstrated that group selection just reduces to inclusive fitness (kin selection), which, as Dawkins has noted, is just another name for evolution by natural selection. Like Wilson, Gintis has worked in this arena for about 50 years and still has not grasped it, but after the scandal broke, it took me only 3 days to find, read and understand the most relevant professional work, as detailed in my article. It is mind boggling to realize that Gintis and Wilson were unable to accomplish this in nearly half a century. -/- I discuss the errors of group selection and phenomenology that are the norm in academia as special cases of the near universal failure to understand human nature that are destroying America and the world. -/- Those wishing a comprehensive up to date framework for human behavior from the modern two systems view may consult my book ‘The Logical Structure of Philosophy, Psychology, Mind and Language in Ludwig Wittgenstein and John Searle’ 2nd ed (2019). Those interested in more of my writings may see ‘Talking Monkeys--Philosophy, Psychology, Science, Religion and Politics on a Doomed Planet--Articles and Reviews 2006-2019 3rd ed (2019), The Logical Structure of Human Behavior (2019), and Suicidal Utopian Delusions in the 21st Century 4th ed (2019) . (shrink)

Purpose Prescription stimulant use as “cognitive enhancers” has been described among undergraduate college students. However, the use of prescription stimulants among future health care professionals is not well characterized. This study was designed to determine the prevalence of prescription stimulant misuse among students at an academic health sciences center. -/- Method Electronic surveys were e-mailed to 621 medical, pharmacy, and respiratory therapy students at East Tennessee State University for four consecutive weeks in fall 2011. Completing the survey was voluntary (...) and anonymous. Surveys asked about reasons for, frequency of, and side effects of nonprescription misuse of prescription stimulants. Given the sensitive material, an opportunity to win one of ten $50 gift cards was used as an incentive. -/- Results Three hundred seventy-two (59.9%) students completed the survey from three disciplines (47.6% medical, 70.5% pharmacy, and 57.6% respiratory therapy). Overall, 11.3% of responders admitted to misusing prescription stimulants. There was more misuse by respiratory therapy students, although this was not statistically significant (10.9% medicine, 9.7% pharmacy, 26.3% respiratory therapy; P = .087). Reasons for prescription stimulant misuse included to enhance alertness/ energy (65.9%), to improve academic performance (56.7%), to experiment (18.2%), and to use recreationally/get high (4.5%). -/- Conclusions Prescription stimulant misuse was prevalent among participating students, but further research is needed to describe prevalence among future health care workers more generally. The implications and consequences of such misuse require further study across professions with emphasis on investigating issues of academic dishonesty (e.g., “cognitive enhancement”), educational quality, and patient safety or health care quality. (shrink)

The use of counterfactuals for considerations of algorithmic fairness and explainability is gaining prominence within the machine learning community and industry. This paper argues for more caution with the use of counterfactuals when the facts to be considered are social categories such as race or gender. We review a broad body of papers from philosophy and social sciences on social ontology and the semantics of counterfactuals, and we conclude that the counterfactual approach in machine learning fairness and social explainability can (...) require an incoherent theory of what social categories are. Our findings suggest that most often the social categories may not admit counterfactual manipulation, and hence may not appropriately satisfy the demands for evaluating the truth or falsity of counterfactuals. This is important because the wide- spread use of counterfactuals in machine learning can lead to misleading results when applied in high-stakes domains. Accordingly, we argue that even though counterfactuals play an essential part in some causal inferences, their use for questions of algorithmic fairness and social explanations can create more problems than they resolve. Our positive result is a set of tenets about using counterfactuals for fairness and explanations in machine learning. (shrink)

Teleological Theories of mental representation are probably the most promising naturalistic accounts of intentionality. However, it is widely known that these theories suffer from a major objection: the Indeterminacy Problem. The most common reply to this problem employs the Target of Selection Argument, which is based on Sober’s distinction between selection for and selection of . Unfortunately, some years ago the Target of Selection Argument came into serious attack in a famous paper by Goode and Griffiths. Since then, the question (...) of the validity of the Target of Selection Argument in the context of the Indeterminacy Problem has remained largely untouched. In this essay, I argue that both the Target of Selection Argument and Goode and Griffiths’ criticisms to it misuse Sober’s analysis in important respects. (shrink)

Review of: "Biology as a postmodern science: Universals, historicity, and context".

Biological theory demands a clear organism concept, but at present biologists cannot agree on one. They know that counting particular units, and not counting others, allows them to generate explanatory and predictive descriptions of evolutionary processes. Yet they lack a unified theory telling them which units to count. In this paper, I offer a novel account of biological individuality, which reconciles conflicting definitions of ‘organism’ by interpreting them as describing alternative realisers of a common functional role, and then defines individual (...) organisms as essentially possessing some mechanisms that play this role. (shrink)

Biological individuality is a notoriously thorny topic for biologists and philosophers of biology. In this paper we argue that biological individuality presents multiple, interconnected questions for biologists and philosophers that together form a problem agenda. Using a case study of an interdisciplinary research group in ecology, behavioral and evolutionary biology, we claim that a debate on biological individuality that seeks to account for diverse practices in the biological sciences should be broadened to include and give prominence to questions (...) about uniqueness and temporality. We show that broadening the problem agenda of biological individuality draws attention to underrecognized philosophical issues and discussions and thereby organizes and enriches the existing debate. (shrink)

Aristotle is a political scientist and a student of biology. Political science, in his view, is concerned with the human good and thus it includes the study of ethics. He approaches many subjects from the perspective of both political science and biology: the virtues, the function of humans, and the political nature of humans. In light of the overlap between the two disciplines, I look at whether or not Aristotle’s views in biology influence or explain some of (...) his theses in political science. I show that we should not seek a unified answer to this question, for the relationship between the two disciplines varies depending on the topic. In some cases, e.g. the nature of the human function, the biological background is likely to be endorsed as one of the presuppositions of the ethical enquiry. In other cases, e.g. the study of social hierarchies, even though the ethical works and the biological works come to similar conclusions, it is hard to establish that the biological approach is intended to provide support to the ethico-political approach. In conclusion, I show that Aristotle’s political science and his biology are in conflict at least in two important cases: his account of justice towards non-human animals and his exhortation to contemplate. (shrink)

While many different mechanisms contribute to the generation of spatial order in biological development, the formation of morphogenetic fields which in turn direct cell responses giving rise to pattern and form are of major importance and essential for embryogenesis and regeneration. Most likely the fields represent concentration patterns of substances produced by molecular kinetics. Short range autocatalytic activation in conjunction with longer range “lateral” inhibition or depletion effects is capable of generating such patterns (Gierer and Meinhardt, 1972). Non-linear reactions are (...) required, and mathematical criteria were derived to design molecular models capable of pattern generation. The classical embryological feature of proportion regulation can be incorporated into the models. The conditions are mathematically necessary for the simplest two-factor case, and are likely to be a fair approximation in multi-component systems in which activation and inhibition are systems parameters subsuming the action of several agents. Gradients, symmetric and periodic patterns, in one or two dimensions, stable or pulsing in time, can be generated on this basis. Our basic concept of autocatalysis in conjunction with lateral inhibition accounts for self-regulatory biological features, including the reproducible formation of structures from near-uniform initial conditions as required by the logic of the generation cycle. Real tissue form, for instance that of budding Hydra, may often be traced back to local curvature arising within an initially relatively flat cell sheet, the position of evagination being determined by morphogenetic fields. Shell theory developed for architecture may also be applied to such biological processes. (shrink)

Change is the fundamental idea of evolution. Explaining the extraordinary biological change we see written in the history of genomes and fossil beds is the primary occupation of the evolutionary biologist. Yet it is a surprising fact that for the majority of evolutionary research, we have rarely studied how evolution typically unfolds in nature, in changing ecological environments, over space and time. While ecology played a major role in the eventual acceptance of the population genetic viewpoint of evolution in the (...) synthetic era (circa 1918-1956), it held a lesser role in the development of evolutionary theory until the 1980s, when we began to systematically study the evolutionary dynamics of natural populations in space and time. As a result, early evolutionary theory was initially constructed in an abstract vacuum that was unrepresentative of evolution in nature. The subtle synthesis between ecology with evolutionary biology (eco-evo synthesis) over the past 40 years has progressed our knowledge of natural selection dynamics as they are found in nature, thus revealing how natural selection varies in strength, direction, form, and, more surprisingly, level of biological organization. Natural selection can no longer be reduced to lower levels of biological organization (i.e., individuals, selfish genes) over shorter timescales but should be expanded to include adaptation at higher levels and over longer timescales. Long-term and/or emergent evolutionary phenomena, such as multilevel selection or evolvability, have thus become tenable concepts within an evolutionary biology that embraces ecology and spatiotemporal change. Evolutionary biology is currently suspended at an intermediate stage of scientific progress that calls for the organization of all the recent knowledge revealed by the eco-evo synthesis into a coherent and unified theoretical framework. This is where philosophers of biology can be of particular use, acting as a bridge between the subdisciplines of biology and inventing new theoretical strategies to organize and accommodate the recent knowledge. Philosophers have recommended transitioning away from outdated philosophies that were originally derived from physics within the philosophical zeitgeist of logical positivism (i.e., monism, reductionism, and monocausation) and toward a distinct philosophy of biology that can capture the natural complexity of multifaceted biological systems within diverse ecosystems—one that embraces the emerging philosophies of pluralism, emergence, and multicausality. Therefore, I see recent advances in ecology, evolutionary biology, and the philosophy of biology as laying the groundwork for another major biological synthesis, what I refer to as the Second Synthesis because, in many respects, it is analogous to the aims and outcomes of the first major biological synthesis (but is notably distinct from the inorganic and contrived progressive movement known as the extended evolutionary synthesis). With the general development of a distinctive philosophy of science, biology has rightfully emerged as an autonomous science. Thus, while the first synthesis legitimized biology, the Second Synthesis autonomized biology and afforded biology its own philosophy, allowing biology to finally realize its full scientific potential. (shrink)

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

In the first part of this article we survey general similarities and differences between biological and social macroevolution. In the second (and main) part, we consider a concrete mathematical model capable of describing important features of both biological and social macroevolution. In mathematical models of historical macrodynamics, a hyperbolic pattern of world population growth arises from non-linear, second-order positive feedback between demographic growth and technological development. Based on diverse paleontological data and an analogy with macrosociological models, we suggest that the (...) hyperbolic character of biodiversity growth can be similarly accounted for by non-linear, second-order positive feedback between diversity growth and the complexity of community structure. We discuss how such positive feedback mechanisms can be modelled mathematically. (shrink)

The type-level abstraction is a formal way to represent molecular structures in biological practice. Graphical representations of molecular structures of biological objects are also used to identify functional processes of things. This paper will reveal that category theory is a formal mathematical language not only to visualize molecular structures of biological objects as type-level abstraction formally but also to understand how to infer biological functions from the molecular structures of biological objects. Category theory is a toolkit to understand biological knowledge (...) at the type-level formally, not individual token-level, as well as typical heuristic strategies in molecular biology. (shrink)

Research in infection biology aims to understand the complex nature of host–pathogen interactions. While this knowledge facilitates strategies for preventing and treating diseases, it can also be intentionally misused to cause harm. Such dual-use risk is potentially high for highly pathogenic microbes such as Risk Group-3 (RG3) bacteria and RG4 viruses, which could be used in bioterrorism attacks. However, other pathogens such as influenza virus (IV) and enterohemorrhagic Escherichia coli (EHEC), usually classified as RG2 pathogens, also demonstrate high dual-use (...) risk. As the currently approved therapeutics against these pathogens are not satisfactorily effective, previous outbreaks of these pathogens caused enormous public fear, media attention and economic burden. In this interdisciplinary review, we summarize the current perspectives of dual-use research on IV and EHEC, and further highlight the dual-use risk associated with evolutionary experiments with these infectious pathogens. We support the need to carry out experiments pertaining to pathogen evolution, including to gain predictive insights on their evolutionary trajectories, which cannot be otherwise achieved with stand-alone theoretical models and epidemiological data. However, we also advocate for increased awareness and assessment strategies to better quantify the risks-versus-benefits associated with such evolutionary experiments. In addition to building public trust in dual-use research, we propose that these approaches can be extended to other pathogens currently classified as low risk, but bearing high dual-use potential, given the particular pressing nature of their rapid evolutionary potential. (shrink)

Over the last decades, network-based approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While these approaches continue to grow very rapidly, some of their conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organisational and descriptive levels of networks can be applied universally across biological sciences. To this end, this highly interdisciplinary theme issue focuses on the (...) definition, motivation and application of key concepts in biological network science, such as explanatory power of distinctively network explanations, network levels, and network hierarchies. (shrink)

Statistics play a critical role in biological and clinical research. To promote logically consistent representation and classification of statistical entities, we have developed the Ontology of Biological and Clinical Statistics (OBCS). OBCS extends the Ontology of Biomedical Investigations (OBI), an OBO Foundry ontology supported by some 20 communities. Currently, OBCS contains 686 terms, including 381 classes imported from OBI and 147 classes specific to OBCS. The goal of this paper is to present OBCS for community critique and to describe a (...) number of use cases designed to illustrate its potential applications. The OBCS project and source code are available at http://obcs.googlecode.com. (shrink)

A consensus exists among contemporary philosophers of biology about the history of their field. According to the received view, mainstream philosophy of science in the 1930s, 40s, and 50s focused on physics and general epistemology, neglecting analyses of the 'special sciences', including biology. The subdiscipline of philosophy of biology emerged (and could only have emerged) after the decline of logical positivism in the 1960s and 70s. In this article, I present bibliometric data from four major philosophy of (...) science journals (Erkenntnis, Philosophy of Science, Synthese, and the British Journal for the Philosophy of Science), covering 1930-59, which challenge this view. (shrink)

Philosophy of biology is often said to have emerged in the last third of the twentieth century. Prior to this time, it has been alleged that the only authors who engaged philosophically with the life sciences were either logical empiricists who sought to impose the explanatory ideals of the physical sciences onto biology, or vitalists who invoked mystical agencies in an attempt to ward off the threat of physicochemical reduction. These schools paid little attention to actual biological science, (...) and as a result philosophy of biology languished in a state of futility for much of the twentieth century. The situation, we are told, only began to change in the late 1960s and early 1970s, when a new generation of researchers began to focus on problems internal to biology, leading to the consolidation of the discipline. In this paper we challenge this widely accepted narrative of the history of philosophy of biology. We do so by arguing that the most important tradition within early twentieth-century philosophy of biology was neither logical empiricism nor vitalism, but the organicist movement that flourished between the First and Second World Wars. We show that the organicist corpus is thematically and methodologically continuous with the contemporary literature in order to discredit the view that early work in the philosophy of biology was unproductive, and we emphasize the desirability of integrating the historical and contemporary conversations into a single, unified discourse. (shrink)

The publication in 2015 (ed. Li) of Chap. 6 of the rediscovered Sanskrit text of Candrakīrti’s Madhyamakāvatāra (MA) allows us to witness more directly Candrakīrti’s careful and deliberate critique of the ‘chariot argument’ for the merely conventional existence of the self in Indian Abhidharmic thought. I argue that in MA 6.140–141, Candrakīrti alludes to the use of the chariot argument in the Milindapañha as negating only the view of a permanent self (compared to an elephant), rather than negating ego-identification (compared (...) to a snake in its hole). In contrast to this misuse of the chariot argument, in MA 6.150–165 Candrakīrti uses the chariot argument as an allegory to enable the meditator to refute the basis of ego-identification in seven ways. Candrakīrti’s use of the chariot argument does not establish any theory about the self or not-self, but acts as a guide to meditation as part of philosophy as a spiritual practice with the goal of liberation. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Biological conservation practices and approaches take many forms. Conservation projects do not only differ in their aims and methods, but also concerning their conceptual and normative background assumptions and their underlying motivations and objectives. We draw on philosophical distinctions from the ethics of conservation to explain variances of different positions on conservation projects along six dimensions: (1) conservation ideals, (2) intervention intuitions, (3) the moral considerability of nonhuman beings, (4) environmental values, (5) views on nature and (6) human roles in (...) nature. The result is a map of the moral landscape of biological conservation, on which these six dimensions are layered. This map functions as a heuristic tool to understand conceptual and normative foundations of specific conservation projects, which we will illustrate with four paradigmatic examples: the Pisavaara Strict Nature Reserve, Predator Free New Zealand, the Oostvaardersplassen Nature Reserve and the Great Green Wall Project. With this map as a heuristic tool, we aim to conceptually illuminate disagreement and clarify misunderstandings between representatives of different environmental protection strategies and to show that the same project can be supported (or criticised) on different grounds. (shrink)

The complexity that we observe in nature can often be explained in terms of cooperative behavior. For example, the major transitions of evolution required the emergence of cooperation among the lower-level units of selection, which led to specialization through division-of-labor ultimately resulting in spontaneous order. There are two aspects to address explaining how such cooperation is sustained: how free-riders are prevented from free-riding on the benefits of cooperative tasks, and just as importantly, how those social benefits arise. We review these (...) problems from an economic perspective, and highlight how ideas from economics can help us to better understand how the benefits of social interactions arise, how they are sustained, and how they affect the underlying social dilemmas. (shrink)

Philosophy of biology, perhaps more than any other philosophy of science, is a discipline in flux. What counts as consensus and key arguments in certain areas changes rapidly.The publication of Contemporary Debates in Philosophy of Biology (2010 Wiley-Blackwell) is reviewed and is used as a catalyst to a discussion of the recent expansion of subjects and perspectives in the philosophy of biology as well as their diverse epistemological and methodological commitments.

We introduce the virtual special issue on content in signalling systems. The issue explores the uses and limits of ideas from evolutionary game theory and information theory for explaining the content of biological signals. We explain the basic idea of the Lewis-Skyrms sender-receiver framework, and we highlight three key themes of the issue: (i) the challenge of accounting for deception, misinformation and false content, (ii) the relevance of partial or total common interest to the evolution of meaningful signals, and (iii) (...) how the sender-receiver framework relates to teleosemantics. (shrink)

The paper addresses the formation of striking patterns within originally near-homogenous tissue, the process prototypical for embryology, and represented in particularly purist form by cut sections of hydra regenerating, by internal reorganisation of the pre-existing tissue, a complete animal with head and foot. The essential requirements are autocatalytic, self-enhancing activation, combined with inhibitory or depletion effects of wider range – “lateral inhibition”. Not only de-novo-pattern formation, but also well known, striking features of developmental regulation such as induction, inhibition, and proportion (...) regulation can be explained on this basis. The theory provides a mathematical recipe for the construction of molecular models with criteria for the necessary non-linear interactions. It has since been widely applied to different developmental processes. (shrink)

The aim of this paper is to call the attention, especially that of feminists, to the current progress in biology. It appears gender studies still confine themselves to outdated ideas of sex chromosomes like XX, XY (§10). However, science has been making progress. It no longer sticks to such matters as XX, XY. Its interest is now in Sry, a kind of gene (§11), and MIS, a kind of sex hormone (§14). Abnormalities of sex chromosomes are no longer evidence (...) to deny the biological approaches, for example. We shed light on this fact, putting gender studies in the context of chronologies of science as well (§§2-9). (shrink)

The aim of this article is to discuss the conditions under which functional neuroimaging can contribute to the study of higher cognition. We begin by presenting two case studies—on moral and economic decision making—which will help us identify and examine one of the main ways in which neuroimaging can help advance the study of higher cognition. We agree with critics that functional magnetic resonance imaging (fMRI) studies seldom “refine” or “confirm” particular psychological hypotheses, or even provide details of the neural (...) implementation of cognitive functions. However, we suggest that neuroimaging can support psychology in a different way—namely, by selecting among competing hypotheses of the cognitive mechanisms underlying some mental function. One of the main ways in which neuroimaging can be used for hypothesis selection is via reverse inferences, which we here examine in detail. Despite frequent claims to the contrary, we argue that successful reverse inferences do not assume any strong or objectionable form of reductionism or functional locationism. Moreover, our discussion illustrates that reverse inferences can be successful at early stages of psychological theorizing, when models of the cognitive mechanisms are only partially developed. (shrink)

I show how archaeologists have two problems. The construction of scenarios accounting for the raw data of Archaeology, the material remains of the past, and the explanation of pre-history. Within Archaeology, there has been an ongoing debate about how to constrain speculation within both of these archaeological projects, and archaeologists have consistently looked to biological mechanisms for constraints. I demonstrate the problems of using biology, either as an analogy for cultural processes or through direct application of biological principles to (...) material remains. This is done through setting out the requirements of a Darwinian Archaeology, and then measuring various approaches against these requirements. This approach leads to the conclusion that archaeologist's explanations of the past must include within their formulations an account of human cognitive capacities within their explanatory framework. The limits of our understanding of the human past will be the limits of our understanding of Homo sapiens. (shrink)

Much disease and disability is the result of lifestyle behaviours. For example, the contribution of imprudence in the form of smoking, poor diet, sedentary lifestyle, and drug and alcohol abuse to ill-health is now well established. More importantly, some of the greatest challenges facing humanity as a whole – climate change, terrorism, global poverty, depletion of resources, abuse of children, overpopulation – are the result of human behaviour. In this chapter, we will explore the possibility of using advances in the (...) cognitive sciences to develop strategies to intentionally manipulate human motivation and behaviour. While our arguments apply also to improving prudential motivation and behaviour in relation to health, we will focus on the more controversial instance: the deliberate targeted use of biomedicine to improve moral motivation and behaviour. We do this because the challenge of improving human morality is arguably the most important issue facing humankind (Persson and Savulescu, forthcoming). We will ask whether using the knowledge from the biological and cognitive sciences to influence motivation and behaviour erodes autonomy and, if so, whether this makes it wrong. (shrink)

The article presents a perspective on the scientific explanation of the subjectivity of conscious experience. It proposes plausible answers for two empirically valid questions: the ‘how’ question concerning the developmental mechanisms of subjectivity, and the ‘why’ question concerning its function. Biological individuation, which is acquired in several different stages, serves as a provisional description of how subjective perspectives may have evolved. To the extent that an individuated informational space seems the most efficient way for a given organism to select biologically (...) valuable information, subjectivity is deemed to constitute an adaptive response to informational overflow. One of the possible consequences of this view is that subjectivity might be (at least functionally) dissociated from consciousness, insofar as the former primarily facilitates selection, the latter action. (shrink)

A new theory that naturalizes biological function is explained and compared with earlier etiological and causal role theories. Etiological theories explain functions from how they are caused over their evolutionary history. Causal role theories analyze how functional mechanisms serve the current capacities of their containing system. The new proposal unifies the key notions of both kinds of theories, but goes beyond them by explaining how functions in an organism can exist as factors with autonomous causal efficacy. The goal-directedness and normativity (...) of functions exist in this strict sense as well. The theory depends on an internal physiological or neural process that mimics an organism’s fitness, and modulates the organism’s variability accordingly. The structure of the internal process can be subdivided into subprocesses that monitor specific functions in an organism. The theory matches well with each intuition on a previously published list of intuited ideas about biological functions, including intuitions that have posed difficulties for other theories. (shrink)

Many philosophers are skeptical about the scientific value of the concept of biological information. However, several have recently proposed a more positive view of ascribing information as an exercise in scientific modeling. I argue for an alternative role: guiding empirical data collection for the sake of theorizing about the evolution of semantics. I clarify and expand on Bergstrom and Rosvall’s suggestion of taking a “diagnostic” approach that defines biological information operationally as a procedure for collecting empirical cases. The more recent (...) modeling-based accounts still perpetuate a theory-centric view of scientific concepts, which motivated philosophers’ misplaced skepticism in the first place. (shrink)

Symbiosis plays a fundamental role in contemporary biology, as well as in recent thinking in philosophy of biology. The discovery of the importance and universality of symbiotic associations has brought new light to old debates in the field, including issues about the concept of biological individuality. An important aspect of these debates has been the formulation of the hologenome concept of evolution, the notion that holobionts are units of natural selection in evolution. This review examines the philosophical assumptions (...) that underlie recent proposal of the hologenome concept of evolution, and traces those debates back in time to their historical origins, to the moment when the connection between the topics of symbiosis and biological individuality first caught the attention of biologists. The review is divided in two parts. The first part explores the historical origins of the connection between the notion of symbiosis and the concept of biological individuality, and emphasizes the role of A. de Bary, R. Pound, A. Schneider and C. Merezhkowsky in framing the debate. The second part examines the hologenome concept of evolution and explores four parallelisms between contemporary debates and the debates presented in the first part of the essay, arguing that the different debates raised by the hologenome concept were already present in the literature. I suggest that the novelty of the hologenome concept of evolution lies in the wider appreciation of the importance of symbiosis for maintaining life on Earth as we know it. Finally, I conclude by suggesting the importance of exploring the connections among contemporary biology, philosophy of biology and history of biology in order to gain a better understanding of contemporary biology. (shrink)

Life as self-organization is philosophically understood by L. Polo in terms of co-causality between matter, formal configuration and intrinsic efficiency. This characterization provides a dynamic account of life and soul, capable to explain both its identity and its continuous renovation. In this article I especially highlight in this author the metaphysical notions of finality, unity and cosmos, which may be helpful to understand the sense of biological systems in the universe.

An influential position in the philosophy of biology claims that there are no biological laws, since any apparently biological generalization is either too accidental, fact-like or contingent to be named a law, or is simply reducible to physical laws that regulate electrical and chemical interactions taking place between merely physical systems. In the following I will stress a neglected aspect of the debate that emerges directly from the growing importance of mathematical models of biological phenomena. My main aim is (...) to defend, as well as reinforce, the view that there are indeed laws also in biology, and that their difference in stability, contingency or resilience with respect to physical laws is one of degrees, and not of kind . (shrink)

Bence Nanay has argued that we must abandon the etiological theory of teleological function because this theory explains functions and functional categories in a circular manner. Paul Griffiths argued earlier that we should retain the etiological theory and instead prevent the circularity by making etiologies independent of functional categories. Karen Neander and Alex Rosenberg reply to Nanay similarly, and argue that we should analyze functions in terms of natural selection acting not on functional categories, but merely on lineages. Nanay replies (...) that these lineages cannot be individuated except by reference to functional categories. Worryingly, Neander and Rosenberg themselves have previously argued persuasively that homology often depends on function. This article addresses their arguments and shows how to escape them: Regardless whether the arguments are right about long-term homological categories, they do not apply to generation-to-generation homology. The latter, moreover, is sufficient for individuating the lineages needed to explain teleological functions. (shrink)

In this paper I attempt to open a new horizon in the field of civilization studies by examining the concept of painless civilization from the perspective of the philosophy of biological evolution. Since the space is limited, the priority will be given to the clarification of an overall structure. Modern civilization has created systems that seek “comfort and pleasure” and eliminate “pain and suffering” and has spread them to every corner of our society. It is progressing like a great wave (...) in many developed countries. I have called a civilization advancing in this direction a “painless civilization.” At first glance, the elimination of pain and suffering seems like a good thing. Of course, it is considered good if unbearable suffering (such as the pain of terminal cancer) that we encounter in our lives can be avoided through technology. This is not the problem. The problem is that modern civilization is moving in a direction where various forms of suffering that we might experience in the future are going to be erased from our lives, one after another, through preventive technologies (preventive elimination of pain). ... (shrink)

The problem with reductionism in biology is not the reduction, but the implicit attitude of determinism that usually accompanies it. Methodological reductionism is supported by deterministic beliefs, but making such a connection is problematic when it is based on an idea of determinism as fixed predictability. Conflating determinism with predictability gives rise to inaccurate models that overlook the dynamic complexity of our world, as well as ignore our epistemic limitations when we try to model it. Furthermore, the assumption of (...) a strictly deterministic framework is unnecessarily hindering to biology. By removing the dogma of determinism, biological methods, including reductive methods, can be expanded to include stochastic models and probabilistic interpretations. Thus, the dogma of reductionism can be saved once its ties with determinism are severed. In this paper, I analyze two problems that have faced molecular biology for the last 50 years—protein folding and cancer. Both cases demonstrate the long influence of reductionism and determinism on molecular biology, as well as how abandoning determinism has opened the door to more probabilistic and unconstrained reductive methods in biology. (shrink)

The writings of Joseph Henry Woodger (1894–1981) are often taken to exemplify everything that was wrongheaded, misguided, and just plain wrong with early twentieth-century philosophy of biology. Over the years, commentators have said of Woodger: (a) that he was a fervent logical empiricist who tried to impose the explanatory gold standards of physics onto biology, (b) that his philosophical work was completely disconnected from biological science, (c) that he possessed no scientific or philosophical credentials, and (d) that his (...) work was disparaged – if not altogether ignored – by the biologists and philosophers of his era. In this paper, we provide the first systematic examination of Woodger’s oeuvre, and use it to demonstrate that the four preceding claims are false. We argue that Woodger’s ideas have exerted an important influence on biology and philosophy, and submit that the current consensus on his legacy stems from a highly selective reading of his works. By rehabilitating Woodger, we hope to show that there is no good reason to continue to disregard the numerous contributions to the philosophy of biology produced in the decades prior to the professionalization of the discipline. (shrink)

I was asked to argue a polarizing stance on the issue of Large Language Models and the future of adaptive education. The following paper is what resulted, and may not represent my actual stance on the most valuable step forward.