Three puzzles about self-deception make this mental phenomenon an intriguing explanatory target. The first relates to how to define it without paradox; the second is about how to make sense of self-deception in light of the interpretive view of the mental that has become widespread in philosophy; and the third concerns why it exists at all. In this paper I address the first and third puzzles. First, I define self-deception. Second, I criticize Robert Trivers' attempt to use adaptionist evolutionary psychology (...) to solve the third puzzle (existence). Third, I sketch a theory to replace that of Trivers. Self-deception is not an adaptation, but a spandrel in the sense that Gould and Lewontin give the term: a byproduct of other features of human (cognitive) architecture. Self-deception is so undeniable a fact of human life that if anyone tried to deny its existence, the proper response would be to accuse this person of it. (Allen Wood, 1988). (shrink)

In this paper we present a new framework of idealization in biology. We characterize idealizations as a network of counterfactual and hypothetical conditionals that can exhibit different “degrees of contingency”. We use this idea to say that, in departing more or less from the actual world, idealizations can serve numerous epistemic, methodological or heuristic purposes within scientific research. We defend that, in part, this structure explains why idealizations, despite being deformations of reality, are so successful in scientific practice. For illustrative (...) purposes, we provide an example from population genetics, the Wright-Fisher Model. (shrink)

Biological atomism postulates that all life is composed of elementary and indivisible vital units. The activity of a living organism is thus conceived as the result of the activities and interactions of its elementary constituents, each of which individually already exhibits all the attributes proper to life. This paper surveys some of the key episodes in the history of biological atomism, and situates cell theory within this tradition. The atomistic foundations of cell theory are subsequently dissected (...) and discussed, together with the theory’s conceptual development and eventual consolidation. This paper then examines the major criticisms that have been waged against cell theory, and argues that these too can be interpreted through the prism of biological atomism as attempts to relocate the true biological atom away from the cell to a level of organization above or below it. Overall, biological atomism provides a useful perspective through which to examine the history and philosophy of cell theory, and it also opens up a new way of thinking about the epistemic decomposition of living organisms that significantly departs from the physicochemical reductionism of mechanistic biology. (shrink)

Are living organisms--as Descartes argued--just machines? Or is the nature of life such that it can never be fully explained by mechanistic models? In this thought-provoking and controversial book, eminent geophysicist Walter M. Elsasser argues that the behavior of living organisms cannot be reduced to physico-chemical causality. Suggesting that molecular biology today is at the same point as Newtonian physics on the eve of the quantum revolution, Elsasser lays the foundation for a theoretical biology that points the way toward a (...) natural philosophy of organic life. Explicitly repudiating "vitalism" (the notion that the laws of nature need to be modified when applied to living organisms), Elsasser argues instead that the structural complexity of even a single living cell is "transcomputational"--that is, beyond the power of any imaginable system to compute. Beginning from this insight, Elsasser leads the reader through a step-by-step process that ultimately arrives at the conclusion that living and non-living matter are separated by "a no-man's land of irrationality." Trained in Germany as a physicist, Elsasser first pondered the implications of quantum mechanics for biology as early as 1951. The more closely he studied the inherent complexity of life, the more skeptical he became of the reductionist view of organisms as tiny machines. "An organism," he concluded, "is a source of causal chains which cannot be traced beyond a terminal point because they are lost in the unfathomable complexity of the organism." Like the physicist who works within the bounds of an unfathomable universe, Elsasser argues, the biologist must seek answers within a system that is no less unfathomable. (shrink)

In this paper I first offer a systematic outline of a series of conceptual novelties in the life-sciences that have favoured, over the last three decades, the emergence of a more social view of biology. I focus in particular on three areas of investigation: (1) technical changes in evolutionary literature that have provoked a rethinking of the possibility of altruism, morality and prosocial behaviours in evolution; (2) changes in neuroscience, from an understanding of the brain as an isolated data processor (...) to the ultrasocial and multiply connected social brain of contemporary neuroscience; and (3) changes in molecular biology, from the view of the gene as an autonomous master of development to the ‘reactive genome’ of the new emerging field of molecular epigenetics. In the second section I reflect on the possible implications for the social sciences of this novel biosocial terrain and argue that the postgenomic language of extended epigenetic inheritance and blurring of the nature/nurture boundaries will be as provocative for neo-Darwinism as it is for the social sciences as we have known them. Signs of a new biosocial language are emerging in several social-science disciplines and this may represent an exciting theoretical novelty for twenty-first social theory. (shrink)

This paper has two parts: In the first part, I give a general survey of the various reasons 17th and 18th century life scientists and metaphysicians endorsed the theory of pre-existence according to which God created all living beings at the creation of the universe, and no living beings are ever naturally generated anew. These reasons generally fall into three categories. The first category is theological. For example, many had the desire to account for how all humans are stained (...) by original sin (we were all there). As another example of a theological motivation, some take the organism as an obvious starting point for a teleological argument for God’s existence, and this staring point is sometimes developed into a full-blown theory of pre-existence. The second category could be thought of as non-theological metaphysical, and paramount here is the desire to deal with the metaphysical problem of individuation. So, for example, Leibniz embraces a version of hylomorphism in order to overcome difficulties with Descartes’ theory of material substance, including the difficulty of how to account for enduring material individuals, and Leibniz’s hylomorphism is closely linked with his embrace of pre-existence. The third category might be termed “biological”, and one example of such a concern is how to explain the organic unity of living beings where the whole seems to ontologically precede the parts. This is frequently translated into a temporal priority of whole to parts, and thus pre-existence is posited. Of course, many natural philosophers of the early modern period embrace pre-existence for more than one reason, but in general, these are the three classes of motivations one might have for embracing the theory. In the second part of the paper I examine in detail one argument that appears in the work of Malebranche. On the face of it, this argument seems to be a biological one, specifically the biological or organic holism argument mentioned above. But upon closer examination, I shall argue, Malebranche’s reasons for endorsing pre-existence bring together several of the arguments discussed in the first part of the paper. I conclude with some considerations about what we can learn about Malebranche as a natural philosopher from his motivations for holding the pre-existence doctrine of generation. (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)

Three metascientific concepts that have been object of philosophical analysis are the concepts oflaw, model and theory. The aim ofthis article is to present the explication of these concepts, and of their relationships, made within the framework of Sneedean or Metatheoretical Structuralism (Balzer et al. 1987), and of their application to a case from the realm of biology: Population Dynamics. The analysis carried out will make it possible to support, contrary to what some philosophers of science in general and (...) of biology in particular hold, the following claims: a) there are "laws" in biological sciences, b) many of the heterogeneous and different "models" of biology can be accommodated under some "theory", and c) this is exactly what confers great unifying power to biological theories. (shrink)

We characterize access to empirical objects in biology from a theoretical perspective. Unlike objects in current physical theories, biological objects are the result of a history and their variations continue to generate a history. This property is the starting point of our concept of measurement. We argue that biological measurement is relative to a natural history which is shared by the different objects subjected to the measurement and is more or less constrained by biologists. We call symmetrization the (...) theoretical and often concrete operation which leads to considering biological objects as equivalent in a measurement. Last, we use our notion of measurement to analyze research strategies. Some strategies aim to bring biology closer to the epistemology of physical theories, by studying objects as similar as possible, while others build on biological diversity. (shrink)

I analyze the importance of parts in the style of biological theorizing that I call compositional biology. I do this by investigating various aspects, including partitioning frames and explanatory accounts, of the theoretical perspectives that fall under and are guided by compositional biology. I ground this general examination in a comparative analysis of three different disciplines with their associated compositional theoretical perspectives: comparative morphology, functional morphology, and developmental biology. I glean data for this analysis from canonical textbooks and defend (...) the use of such texts for the philosophy of science. I end with a discussion of the importance of recognizing formal and compositional biology as two genuinely different ways of doing biology – the differences arising more from their distinct methodologies than from scientific discipline included or natural domain studied. Ultimately, developing a translation manual between the two styles would be desirable as they currently are, at times, in conflict. (shrink)

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

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)

Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...) form and matter has yet to similarly earn its keep. In this chapter, I offer a first step toward showing that the hylomorphic framework is up to that task. To do so, I return to the birthplace of that doctrine - the biological realm. Utilising recent advances in developmental biology, I argue that the hylomorphic framework is an empirically adequate and conceptually rich explanatory schema with which to model the nature of organisms. (shrink)

Stapp and others have proposed that reality involves a fundamental life process, or creative process. It is shown how this process description may be unified with the description that derives from quantum physics. The methods of the quantum physicist and of the biological sciences are seen to be two alternative approaches to the understanding of nature, involving two distinct modes of description which can usefully supplement each other, and neither on its own contains the full story. The unified view (...) explains the major features of quantum mechanics and suggests that biological systems may function more effectively than would be expected on the basis of quantum mechanics alone. (shrink)

The aim of this paper is to describe and analyze the epistemological justification of a proposal initially made by the biomathematician Robert Rosen in 1958. In this theoretical proposal, Rosen suggests using the mathematical concept of “category” and the correlative concept of “natural equivalence” in mathematical modeling applied to living beings. Our questions are the following: According to Rosen, to what extent does the mathematical notion of category give access to more “natural” formalisms in the modeling of living beings? Is (...) the so -called “naturalness” of some kinds of equivalences (which the mathematical notion of category makes it possible to generalize and to put at the forefront) analogous to the naturalness of living systems? Rosen appears to answer “yes” and to ground this transfer of the concept of “natural equivalence” in biology on such an analogy. But this hypothesis, although fertile, remains debatable. Finally, this paper makes a brief account of the later evolution of Rosen’s arguments about this topic. In particular, it sheds light on the new role played by the notion of “category” in his more recent objections to the computational models that have pervaded almost every domain of biology since the 1990s. (shrink)

The articles in this issue reflect the results of the 25th Altenberg Workshop in Theoretical Biology on ‘‘The Meaning of ‘Theory’ in Biology’’ held at the Konrad Lorenz Institute for Evolution and Cognition Research, Altenberg, Austria, 30 June–3 July, 2011.

Reichenbach’s early solution to the scientific problem of how abstract mathematical representations can successfully express real phenomena is rooted in his view of coordination. In this paper, I claim that a Reichenbach-inspired, ‘layered’ view of coordination provides us with an effective tool to systematically analyse some epistemic and conceptual intricacies resulting from a widespread theorising strategy in evolutionary biology, recently discussed by Okasha (2018) as ‘endogenization’. First, I argue that endogenization is a form of extension of natural selection theory (...) that comprises three stages: quasi-axiomatisation, functional extension, and semantic extension. Then, I argue that the functional extension of one core principle of natural selection theory, namely, the principle of heritability, requires the semantic extension of the concept of inheritance. This is because the semantic extension of ‘inheritance’ is necessary to establish a novel form of coordination between the principle of heritability and the extended domain of phenomena that it is supposed to represent. Finally, I suggest that – despite the current lack of consensus on the right semantic extension of ‘inheritance’ – we can fruitfully understand the reconceptualization of ‘inheritance’ provided by niche construction theorists as the result of a novel form of coordination. (shrink)

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)

The selected effects or ‘etiological’ theory of Proper function is a naturalistic and realist account of biological teleology. It is used to analyse normativity in philosophy of language, philosophy of mind, philosophy of medicine and elsewhere. The theory has been developed with a simple and intuitive view of natural selection. Traits are selected because of their positive effects on the fitness of the organisms that have them. These ‘selected effects’ are the Proper functions of the traits. Proponents (...) argue that this analysis of biological teleology has the unique advantage that the selected effect function of a trait is also a causal explanation of the trait: the trait exists because it performs this function. We show, however, that selected effect functions as currently defined explain the existence of traits only under highly restrictive assumptions about evolutionary dynamics. In many common scenarios in which traits evolve by natural selection, selected effect functions do not explain those traits. This is because definitions of selected effect function extract from any evolutionary scenario only the information that would be explanatorily relevant in the simple evolutionary scenario implicit in those definitions. When applied to more complex scenarios selected effect functions omit the key information that is explanatorily relevant in those scenarios. The assumptions required for selected effect functions to be explanatory are particularly unlikely to hold in the domain that its proponents care most about - the evolution of representation. A more adequate selected effects theory of Proper functions may be possible, but will require much greater attention to the structure of actual evolutionary explanations. (shrink)

Since Boorse [Philos Sci 44(4):542–573, 1977] published his paper “Health as a theoretical concept” one of the most lively debates within philosophy of medicine has been on the question of whether health and disease are in some sense ‘objective’ and ‘value-free’ or ‘subjective’ and ‘value-laden’. Due to the apparent ‘failure’ of pure naturalist, constructivist, or normativist accounts, much in the recent literature has appealed to more conciliatory approaches or so-called ‘hybrid accounts’ of health and disease. A recent paper by Matthewson (...) and Griffiths [J Med Philos 42(4):447–466, 2017], however, may bear the seeds for the revival of purely naturalist approach to health and disease. In this paper, I defend their idea of Biological Normativity against recent criticism by Schwartz [J Med Philos Forum Bioethics Philos Med 42(4):485–502, 2017] and hope to help it flower into a revival of naturalist approaches in the philosophy of medicine. (shrink)

Serial Endosymbiosis Theory, or SET, was conceived and developed by Lynn Margulis, to explain the greatest discontinuity in the history of life, the origin of eukaryotic cells. Some predictions of SET, namely the origin of mitochondria and chloroplasts, withstood the test of the most recent evidence from a variety of disciplines including phylogenetics, biochemistry, and cell biology. Even though some other predictions fared less well, SET remains a seminal theory in biology. In this paper, I focus on two (...) aspects of SET. First, using the concept of "universal symbiogenesis”, developed by Freeman Dyson to search for commonalities in astronomy and biology, I propose that SET can be extended beyond eukaryogenesis. The extension refers to the possibility that even prokaryotic organisms, themselves subject to the process of symbiogenesis in SET, could have emerged symbiotically. Second, I contrast a recent “viral eukaryogenesis” hypothesis, according to which the nucleus evolved from a complex DNA virus, with a view closer to SET, according to which the nucleus evolved through the interplay of the archaeal host, the eubacterial symbiont, and a non-LTR transposon, or telomerase. Viruses joined in later, through the process of viral endogenization, to shape eukaryotic chromosomes in the process of karyotype evolution. These two proposals based on SET are a testament to its longevity as a scientific theory. (shrink)

The fracture in the emerging discipline of biosemiotics when the code biologist Marcello Barbieri claimed that Peircian biosemiotics is not genuine science raises anew the question: What is science? When it comes to radically new approaches in science, there is no simple answer to this question, because if successful, these new approaches change what is understood to be science. This is what Galileo, Darwin and Einstein did to science, and with quantum theory, opposing interpretations are not merely about what (...) theory is right, but what is real science. Peirce's work, as he acknowledged, is really a continuation of efforts of Schelling to challenge the heritage of Newtonian science for the very good reason that the deep assumptions of Newtonian science had made sentient life, human consciousness and free will unintelligible, the condition for there being science. Pointing out the need for such a revolution in science has not succeeded as a defence of Peircian biosemiotics, however. In this paper, I will defend the scientific credentials of Peircian biosemiotics by relating it to the theoretical biology of the bio-mathematician, Robert Rosen. Rosen's relational biology, focusing on anticipatory systems and giving a place to final causes, should also be seen as a rigorous development of the Schellingian project to conceive nature in such a way that the emergence of sentient life, mind and science are intelligible. Rosen has made a very strong case for the characterization of his ideas as a real advance not only in science, but in how science should be understood, and I will argue that it is possible to provide a strong defence of Peircian biosemiotics as science through Rosen's defence of relational biology. In the process, I will show how biosemiotics can and should become a crucial component of anticipatory systems theory. (shrink)

In her landmark book, Language, Thought, and Other Biological Categories (Millikan1984),1 Ruth Garrett Millikan utilizes the idea of a biological function to solve philosophical problems associated with the phenomena of language, thought, and meaning. Language and thought are activities of biological organisms, according to Millikan, and we should treat them as such when trying to answer related philosophical questions. Of special interest is Millikan’s treatment of intentionality. Here Millikan employs the notion of a biological function to (...) explain what it is for one thing in nature, a bee dance (43), for example, to be about another, in this case, the location of a nectar source. My concern in this paper is to understand whether Millikan’s account of intentionality adequately explains how humans achieve reference, in language or thought, to individuals and groups in their environment. In bringing her theory of intentional content to bear on human activities, Millikan focuses largely on natural language. Thus, in what follows, I begin by laying out the biology-based principles that underlie Millikan’s theory of content, then proceed with an explanation of how the theory is to apply to natural language. As it appears, Millikan’s account of how content is determined for natural language terms and sentences rests on the determinacy of intentional content at the psychological level. This leads me to take a careful look at what Millikan says about the content of mental representations, in hopes of finding a sufficient basis there for the application of Millikan’s theory of content to natural language. Ultimately, I conclude that Millikan’s theory faces a problem of vacuity. If we approach the theory as a theory of intentional content, intended to explain the nature of reference, the theory is lacking in an extremely important respect: Millikan explains how it could be one of the biological functions of a mental or natural language term to refer, without telling us precisely what in the natural order constitutes the reference relation.. (shrink)

Open peer commentary on the article “Circularity and the Micro-Macro-Difference” by Manfred Füllsack. Upshot: The target article defends the fundamental role of circularity for systems sciences and the necessity to develop a conceptual and methodological approach to it. The concept of circularity, however, is multifarious, and two of the main challenges in this respect are to provide distinctions between different forms of circularities and explore in detail the roles they play in organizations. This commentary provides some suggestions in this direction (...) with the aim to supplement the perspective presented in the target article with some insights from theoretical biology. (shrink)

Waters’s (2007) actual difference making and Weber’s (2013, 2017) biological normality approaches to causal selection have received many criticisms, some of which miss their target. Disagreement about whether Waters’s and Weber’s views succeed in providing criteria that uniquely singles out the gene as explanatorily significant in biology has led philosophers to overlook a prior problem. Before one can address whether Waters’s and Weber’s views successfully account for the explanatory significance of genes, one must ask whether either view satisfactorily meets (...) the necessary conditions for causal selection in the first place. An adequate defense of causal selection must meet two desiderata. First, there must be an explanatory property that sets some causes apart from others. Second, the property identified must be one that is recognized by biologists as relevant to their domain(s) of inquiry. I argue that both fall short of meeting the second condition. I demonstrate this by showing how many of the biological technologies crucial to experimentation do not fit either view very well. I offer a more adequate proposal that accommodates non-actual and artificial causal variables. A consequence of my view is the following: When analyzing the causal selection practices of biologists, philosophers should consider the explanatory targets relevant to a research program – including ones whose explanans must appeal to biological technologies. I then explain how this proposal can inform the existing debate between Weber (2017) and Griffiths et al. (2015). (shrink)

The theory of evolution, which provides the conceptual framework for all modern research in organismal biology and informs research in molecular bi- ology, has gone through several stages of expansion and refinement. Darwin and Wallace (1858) of course proposed the original idea, centering on the twin concepts of natural selection and common descent. Shortly thereafter, Wallace and August Weismann worked toward the complete elimination of any Lamarckian vestiges from the theory, leaning in particular on Weismann’s (1893) concept of (...) the separation of soma and germ, resulting in what is some- times referred to as “neo-Darwinism”. (shrink)

In his famous article “The Unreasonable Effectiveness of Mathematics in the Natural Sciences” Eugen Wigner argues for a unique tie between mathematics and physics, invoking even religious language: “The miracle of the appropriateness of the language of mathematics for the formulation of the laws of physics is a wonderful gift which we neither understand nor deserve”. The possible existence of such a unique match between mathematics and physics has been extensively discussed by philosophers and historians of mathematics. Whatever the merits (...) of this claim are, a further question can be posed with regard to mathematization in science more generally: What happens when we leave the area of theories and laws of physics and move over to the realm of mathematical modeling in interdisciplinary contexts? Namely, in modeling the phenomena specific to biology or economics, for instance, scientists often use methods that have their origin in physics. How is this kind of mathematical modeling justified? (shrink)

Biology seems to present local and transitory regularities rather than immutable laws. To account for these historically constituted regularities and to distinguish them from mathematical invariants, Montévil and Mossio (Journal of Theoretical Biology 372:179–191, 2015) have proposed to speak of constraints. In this article we analyse the causal power of these constraints in the evolution of biodiversity, i.e., their positivity, but also the modality of their action on the directions taken by evolution. We argue that to fully account for the (...) causal power of these constraints on evolution, they must be thought of in terms of normativity. In this way, we want to highlight two characteristics of the evolutionary constraints. The first, already emphasised as reported by Gould (The structure of evolutionary theory, Harvard University Press, 2002), is that these constraints are both produced by and producing biological evolution and that this circular causation creates true novelties. The second is that this specific causality, which generates unpredictability in evolution, stems not only from the historicity of biological constraints, but also from their internalisation through the practices of living beings. (shrink)

In the framework of materialism, the major attention is to find general organizational laws stimulated by physical sciences, ignoring the uniqueness of Life. The main goal of materialism is to reduce consciousness to natural processes, which in turn can be translated into the language of math, physics and chemistry. Following this approach, scientists have made several attempts to deny the living organism of its veracity as an immortal soul, in favor of genes, molecules, atoms and so on. However, advancement in (...) various fields of biology has repeatedly given rise to questions against such a denial and has supplied more and more evidence against the completely misleading ideological imposition that living entities are particular states of matter. In the recent past, however, the realization has arisen that cognitive nature of life at all levels has begun presenting significant challenges to the views of materialism in biology and has created a more receptive environment for the soul hypothesis. Therefore, instead of adjudicating different aprioristic claims, the development of an authentic theory of biology needs both proper scientific knowledge and the appropriate tools of philosophical analysis of life. In a recently published paper the first author of present essay made an attempt to highlight a few relevant developments supporting a sentient view of life in scientific research, which has caused a paradigm shift in our understanding of life and its origin [1]. The present essay highlights the uniqueness of biological systems that offers a considerable challenge to the mainstream materialism in biology and proposes the Vedāntic philosophical view as a viable alternative for development of a biological theory worthy of life. (shrink)

Probably the most distinctive feature of synthetic biology is its being “synthetic” in some sense or another. For some, synthesis plays a unique role in the production of knowledge that is most distinct from that played by analysis: it is claimed to deliver knowledge that would otherwise not be attained. In this contribution, my aim is to explore how synthetic biology delivers knowledge via synthesis, and to assess the extent to which this knowledge is distinctly synthetic. On the basis of (...) distinctions between knowledge-how and knowledge-why, and between syntheses that succeed and syntheses that fail, I argue that the contribution of synthesis to knowledge is best understood when syntheses are construed as experimental interventions that aim at probing causal relationships between properties of the entities that are combined through these syntheses and properties of their target products. The distinctiveness of synthetic biology in its quest for knowledge through synthesis stems from its ability to sample at will a space of empirical possibilities that is not only huge but also that has been so scarcely sampled by nature. (shrink)

Eric Olson argues in The Human Animal that thought-experiments involving body-swapping do not in the end offer any support to psychological continuity theories, nor do they pose any threat to his Biological View. I argue that he is mistaken in at least the second claim.

Cancer biology features the ascription of normal functions to parts of cancers. At least some ascriptions of function in cancer biology track local normality of parts within the global abnormality of the aberration to which those parts belong. That is, cancer biologists identify as functions activities that, in some sense, parts of cancers are supposed to perform, despite cancers themselves having no purpose. The present paper provides a theory to accommodate these normal function ascriptions—I call it the Modeling Account (...) of Normal Function (MA). MA comprises two claims. First, normal functions are activities whose performance by the function-bearing part contributes to the self-maintenance of the whole system and, thereby, results in the continued presence of that part. Second, MA holds that models of system-level activities that are (partly) constitutive of self-maintenance are improved by including a representation of the relevant function-bearing part and by making reference to the activity/activities that part performs which contribute(s) to those system-level activities. I contrast MA with two other accounts that seek to explicate the ascription of normal functions in biology, namely, the organizational account and the selected effects account. Both struggle to extend to cancer biology. However, I offer ecumenical readings which allow them to recover some ascriptions of normal function to parts of cancers. So, though I contend that MA excels in this respect, the purpose of this paper is served if it provides materials for bridging the gap between cancer biology, philosophy of cancer, and the literature on function. (shrink)

Standpoint theory is based on the insight that those who are marginalized or oppressed have distinctive epistemic resources with which to understand social structures. Inasmuch as these structures shape our understanding of the natural and lifeworlds, standpoint theorists extend this principle to a range of biological and physical as well as social sciences. Standpoint theory has been articulated as a social epistemology and as an aligned methodological stance. It provides the rationale for ‘starting research from the margins’ (...) and for expanding the diversity of backgrounds and experience represented in scientific communities. (shrink)

We argue that genuine biological autonomy, or described at human level as free will, requires taking into account quantum vacuum processes in the context of biological teleology. One faces at least three basic problems of genuine biological autonomy: (1) if biological autonomy is not physical, where does it come from? (2) Is there a room for biological causes? And (3) how to obtain a workable model of biological teleology? It is shown here that the (...) solution of all these three problems is related to the quantum vacuum. We present a short review of how this basic aspect of the fundamentals of quantum theory, although it had not been addressed for nearly 100 years, actually it was suggested by Bohr, Heisenberg, and others. Realizing that the quantum mechanical measurement problem associated with the “collapse” of the wave function is related, in the Copenhagen Interpretation of quantum mechanics, to a process between self-consciousness and the external physical environment, we are extending the issue for an explanation of the different processes occurring between living organisms and their internal environment. Definitions of genuine biological autonomy, biological aim, and biological spontaneity are presented. We propose to improve the popular two-stage model of decisions with a biological model suitable to obtain a deeper look at the nature of the mind-body problem. In the newly emerging picture biological autonomy emerges as a new, fundamental and inevitable element of the scientific worldview. (shrink)

Modern life sciences research is increasingly relying on artificial intelligence (AI) approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, (...) yet it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research – protein structure prediction and single cell RNA-sequencing – we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems. (shrink)

One of the central aims of science is explanation: scientists seek to uncover why things happen the way they do. This chapter addresses what kinds of explanations are formulated in biology, how explanatory aims influence other features of the field of biology, and the implications of all of this for biology education. Philosophical treatments of scientific explanation have been both complicated and enriched by attention to explanatory strategies in biology. Most basically, whereas traditional philosophy of science based explanation on derivation (...) from scientific laws, there are many biological explanations in which laws play little or no role. Instead, the field of biology is a natural place to turn for support for the idea that causal information is explanatory. Biology has also been used to motivate mechanistic accounts of explanation, as well as criticisms of that approach. Ultimately, the most pressing issue about explanation in biology may be how to account for the wide range of explanatory styles encountered in the field. This issue is crucial, for the aims of biological explanation influence a variety of other features of the field of biology. Explanatory aims account for the continued neglect of some central causal factors, a neglect that would otherwise be mysterious. This is linked to the persistent use of models like evolutionary game theory and population genetic models, models that are simplified to the point of unreality. These explanatory aims also offer a way to interpret many biologists’ total commitment to one or another methodological approach, and the intense disagreements that result. In my view, such debates are better understood as arising not from different theoretical commitments, but commitments to different explanatory projects. Biology education would thus be enriched by attending to approaches to biological explanation, as well as the unexpected ways that these explanatory aims influence other features of biology. I suggest five lessons for teaching about explanation in biology that follow from the considerations of this chapter. (shrink)

Biology and theology are interdependent theoretical sciences for Aristotle. In prominent discussions of the divine things (the stars and their unmoved movers) Aristotle appeals to the science of living things, and in prominent discussions of the nature of plants and animals Aristotle appeals to the nature of the divine. There is in fact a single continuous series of living things that includes gods, humans, animals, and plants, all of them in a way divine. Aristotle has this continuum of divine beings, (...) and a theory of value that corresponds to it, in mind not only in key parts of his theology and biology, but also in his practical philosophy. Here I call attention to some important texts and attempt to offer a coherent account of them, without being able to enter into the usual interpretive disputes. I begin by clarifying the terms “theology” and “biology” and their place in Aristotle's division of philosophy. Next, I discuss how Aristotle’s theology is informed by his biology, and then how his biology is informed by his theology. I end by discussing some implications of the interdependence of biology and theology for Aristotle’s ethics and exhortation to philosophy. (shrink)

A strong motivation for the human genome project was to relate biological features to the structure and function of small sets of genes, and ideally to individual genes. However, it is now increasingly realized that many problems require a "systems" approach emphasizing the interplay of large numbers of genes, and the involvement of complex networks of gene regulation. This implies a new emphasis on integrative, systems theoretical approaches. It may be called 'holistic' if the term is used without irrational (...) overtones, in the general sense of directing attention to integrated features of organs and organisms. In the history of biology, seemingly conflicting reductionist and holistic notions have alternated, with bottom-up as well as top-down approaches eventually contributing to the solutions of basic problems. By now, there is no doubt that biological features and phenomena are rooted in physico-chemical processes of the molecules involved; and yet, integrated systems aspects are becoming more and more relevant in developmental biology, brain and behavioural science, and socio-biology. -/- . (shrink)

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

Some moral realists claim that moral facts are a species of natural fact, amenable to scientific investigation. They argue that these moral facts are needed in the best explanations of certain phenomena and that this is evidence that they are real. In this paper I present part of a biological account of the function of morality. The account allows the identification of a plausible natural kind that could play the explanatory role that a moral kind would play in naturalist (...) realist theories. It is therefore a candidate for being the moral kind. I argue, however, that it will underdetermine the morally good, that is, identifying the kind is not sufficient to identify what is good. Hence this is not a natural moral kind. Its explanatory usefulness, however, means that we do not have to postulate any further (moral) facts to provide moral explanations. Hence there is no reason to believe that there are any natural moral kinds. (shrink)

It should now be recognized that codes are central to life and to understanding its more complex forms, including human culture. Recognizing the ‘conventional’ nature of codes provides solid grounds for rejecting efforts to reduce life to biochemistry and justifies according a place to semantics in life. The question I want to consider is whether this is enough. Focussing on Eigen’s paradox of how a complex code could originate, I will argue that along with Barbieri’s efforts to account for the (...) origins of life based on the ribosome and then to account for the refined codes through a process of ambiguity reduction, something more is required. Barbieri has not provided an adequate account of emergence, or the basis for providing such an account. I will argue that Stanley Salthe has clarified to some extent the nature of emergence by conceptualizing it as the interpolation of new enabling constraints. Clearly, codes can be seen as enabling constraints. How this actually happens, though, is still not explained. Stuart Kauffman has grappled with this issue and shown that it radically challenges the assumptions of mainstream science going back to Newton. He has attempted to reintroduce real possibilities or potentialities into his ontology, and argued that radically new developments in nature are associated with realizing adjacent possibles. This is still not adequate. What is also involved, I will suggest, utilizing concepts developed by the French natural philosopher Gilbert Simondon, is ‘transduction’ as part of ‘ontogenesis’ of individuals in a process of ‘individuation’, that is, the emergence of ‘individuals’ from preindividual fields or milieux. (shrink)

In this enquiry I attempt to establish Universal Desire Theory as the nominal designation of my active ethical framework, a system heavily influenced by the natural essentialists Philippa Foot and Jenny Teichman, wherein the comparative amalgamation of all subjectively experienced biological harm and benefit is the foundation of objective normativity. Highlights of this paper include the sections where I discuss the moral life of the cell, as well as the moral fallibility of hallucinating persons under this system which (...) combines biological observation with conscious awareness of action. I hope you enjoy. (shrink)

Clark and Chalmers claim that an external resource satisfying the following criteria counts as a memory: the agent has constant access to the resource; the information in the resource is directly available; retrieved information is automatically endorsed; information is stored as a consequence of past endorsement. Research on forgetting and metamemory shows that most of these criteria are not satisfied by biological memory, so they are inadequate. More psychologically realistic criteria generate a similar classification of standard putative external memories, (...) but the criteria still do not capture the function of memory. An adequate account of memory function, compatible with its evolution and its roles in prospection and imagination, suggests that external memory performs a function not performed by biological memory systems. External memory is thus not memory. This has implications for: extended mind theorizing, ecological validity of memory research, the causal theory of memory. (shrink)

Synthetic biology has a strong modal dimension that is part and parcel of its engineering agenda. In turning hypothetical biological designs into actual synthetic constructs, synthetic biologists reach towards potential biology instead of concentrating on naturally evolved organisms. We analyze synthetic biology’s goal of making biology easier to engineer through the combinatorial theory of possibility, which reduces possibility to combinations of individuals and their attributes in the actual world. While the last decades of synthetic biology explorations have shown (...) biology to be much more difficult to engineer than originally conceived, synthetic biology has not given up its combinatorial approach. (shrink)

Although it may seem like a truism to assert that biology is the science that studies organisms, during the second half of the twentieth century the organism category disappeared from biological theory. Over the past decade, however, biology has begun to witness the return of the organism as a fundamental explanatory concept. There are three major causes: (a) the realization that the Modern Synthesis does not provide a fully satisfactory understanding of evolution; (b) the growing awareness of the (...) limits of reductionism in molecular biology; and (c) the renewed interest in the nature of life as a genuine scientific problem. This essay examines these recent developments and considers the new epistemological roles being played by the organism in each of them. It also reflects on what the present resurgence of the organism means for the philosophy of biology. (shrink)

Modeling mechanisms is central to the biological sciences – for purposes of explanation, prediction, extrapolation, and manipulation. A closer look at the philosophical literature reveals that mechanisms are predominantly modeled in a purely qualitative way. That is, mechanistic models are conceived of as representing how certain entities and activities are spatially and temporally organized so that they bring about the behavior of the mechanism in question. Although this adequately characterizes how mechanisms are represented in biology textbooks, contemporary biological (...) research practice shows the need for quantitative, probabilistic models of mechanisms, too. In this paper we argue that the formal framework of causal graph theory is well-suited to provide us with models of biological mechanisms that incorporate quantitative and probabilistic information. On the ba-sis of an example from contemporary biological practice, namely feedback regulation of fatty acid biosynthesis in Brassica napus, we show that causal graph theoretical models can account for feedback as well as for the multi-level character of mechanisms. However, we do not claim that causal graph theoretical representations of mechanisms are advantageous in all respects and should replace common qualitative models. Rather, we endorse the more balanced view that causal graph theoretical models of mechanisms are useful for some purposes, while being insufficient for others. (shrink)

Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress that (...) symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not just processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), variability is at the core of these transitions. (shrink)

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)

It is illegitimate to read any ontology about "race" off of biological theory or data. Indeed, the technical meaning of "genetic variation" is fluid, and there is no single theoretical agreed-upon criterion for defining and distinguishing populations (or groups or clusters) given a particular set of genetic variation data. Thus, by analyzing three formal senses of "genetic variation"—diversity, differentiation, and heterozygosity—we argue that the use of biological theory for making epistemic claims about "race" can only seem (...) plausible when it relies on the user’s own assumptions about race; the move from biological measures to claims about “race” inevitably amounts to a pernicious reification. We also excavate assumptions in the history of the technical discourse over the concept of "race" (e.g., Livingstone's and Dobzhansky's 1962 exchange, Edwards' 2003 response to Lewontin 1972, as well as contemporary discussions of cladistic "race", and "races" as clusters). We show that claims about the existence (or non-existence) of "race" are underdetermined by biological facts, methods, and theories. Biological theory does not force the concept of "race" upon us; our social discourse, social ontology, and social expectations do. We become prisoners of our abstractions at our own hands, and at our own expense. (shrink)