Philosophy of Biology, Misc

The biochemistry of geotropism in plants and gravisensing in e.g. cyanobacteria or paramacia is still not well understood today [1]. Perhaps there are more ways than one for organisms to sense gravity. The two best known relatively old explanations for gravity sensing are sensing through the redistribution of cellular starch statoliths and sensing through redistribution of auxin. The starch containing statoliths in a gravity field produce pressure on the endoplasmic reticulum of the cell. This enables the cell to sense direction. (...) Alternatively, there is the redistribution of auxin under the action of gravity. This is known as the Cholodny-Went hypothesis [2], [3]. The latter redistribution coincides with a redistribution of electrical charge in the cell. With the present study the aim is to add a mathematical unified field explanation to gravisensing. (shrink)

(This version was submitted to Behavioral and Brain Science. A revised version was published by Biological Theory) Estimates of autism’s incidence increased 5-10 fold in ten years, an increase which cannot be genetic. Though many mutations are associated with autism, no mutation seems directly to cause autism. We need to find the direct cause. Complexity science provides a new paradigm - confirmed in biology by extensive hard data. Both the body and the personality are complex dynamic systems which spontaneously self-organize (...) from simple dynamic systems. Autism may therefore be caused by the failure of a simple dynamic system. We know that infants who cannot track their mother’s face often become autistic, that eye-contact initiates intersubjectivity which is blocked in autism, and that the infant-mother pair seems designed to promote eye-contact, as does the eye’s appearance. This author earlier proposed that failure of eye-contact might directly cause autism and that early non-maternal childcare, including television/video, would therefore be statistically linked to autism. Waldman et al. (2008; 2006) recently proved that autism is strongly linked to precipitation (indoor activity) and to the introduction of cable. The most plausible explanation? Early exposure to television/video is linked to autism. Furthermore a normal developmental cascade (blocked in autism) has been deciphered: (a) Infant-mother eye-contact triggers increased maternal attention. (b) Early maternal attention permanently increases not only baseline vasopressin but also that oxytocin release which is triggered by subsequent maternal attention. (c) Vasopressin and oxytocin promote face recognition, gazing-at-the-eyes, emotion recognition, and social bonding. The eye-contact hypothesis suggests a clinical study addressing prevention: recruit prospective parents who agree to curtail television/video/computer/wi-fi in their families; measure autism’s incidence in their children. (shrink)

Abstract: Without directly taking sides in the design/anti-design debate, this paper defends the following position: the assertion that biological evolution “is” design-free presupposes the possibility to model biological evolution in a design-free way. Certainly, there are design-free models of evolution based on cumulative selection. But “to model” is a verb denoting “modeling” as the process leading to a model. So any modeling – trivially – needs “previous human design.” Nevertheless, contrary to other scientific activities which legitimately consider models while ignoring (...) the process leading to them, evolution theory must take into account the human activity of modeling required by its corresponding models. (shrink)

The foundations of biology have been disputed since the last decades. The inherited view of Modern Synthesis, where organisms are passive objects and explanatory inert in evolutionary theory, is being replaced by one where organisms are active agents and responsible for adaptively constructing their own phenotypic traits. Given this picture, in this article, we wonder if the current biological theory is transiting a Cognitive Revolution. This question may have two interpretations. On the one hand, a theoretical interpretation: is the explanatory (...) apparatus of the cognitive sciences central to current theoretical biology? On the other hand, there is a historical interpretation: could the current picture in theoretical biology be described by its resemblance to the Cognitive Revolution in the mid-20th century? Both answers will be affirmative, even though important remarks will be highlighted: the explanatory framework of the cognitive sciences is used to account for the agentive properties of organisms, and there is a clear parallelism between the Cognitive Revolution and the current situation in theoretical biology. (shrink)

Various understandings and definitions of time will be reviewed. The nature and structure of time will be reviewed and the concepts of time and passage of time will be refreshed. The fundamental role played by energy and four natural forces in the actions, reactions and interactions concerning matter, anti-matter, energy in space and time will be critically analyzed. The reality how time is constructed during the construction of materials will be presented and discussed. The classical and quantum ideas in this (...) regard will be comprehensively studied. How these ideas will give us a fresh insight about the nature, structure and role of time in the construction of materials through natural scientific and manmade processes will be highlighted. The relations among matter, anti-matter, energy and time will be freshly stated. The milli-, micro-, nano, pico-, femto-, atto-times will be qualitatively analyzed considering physical, inorganic, organic and bio-materials and their construction and structure. The physics of timelessness also will be put forward. -/- . (shrink)

I respond to Karola Stotz's criticisms of my previously published challenges to the inference from developmental systems theory to an extended view of cognition.

While the homology concept has taken on importance in thinking about the nature of psychological kinds, no one has shown how comparative psychological and behavioral evidence can distinguish between competing homology claims. I adapt the operational criteria of homology to accomplish this. I consider two competing homology claims that compare human anger with putative aggression systems of nonhuman animals, and demonstrate the effectiveness of these criteria in adjudicating between these claims.

Shadmehr and Ahmed’s book is a welcome extension of optimal foraging theory and neuroeconomics, achieved by integrating both with parameters relating to effort and rate of movement. Their most persuasive and prolific data comes from saccades, where times before and after decision are reasonably determinate. Skeletal movements are less likely to exhibit such tidy temporal organisation.

Millikan’s (1984. Language, Thought, and Other Biological Categories: New Foundations for Realism. MIT Press) selected effects theory of functions states that functions are effects for which the ancestors of a trait were selected for. As the function is an effect a thing’s ancestors produced, only things that are reproductions in some sense can have functions. Against this reproduction requirement, Garson (2019. What Biological Functions Are and Why They Matter. Cambridge University Press) argues that not only processes of differential reproduction but (...) also processes of differential persistence can lead to new functions. Since such “persistence functions” have the same explanatory power as traditional selected effects functions, selected effects theorists should include them in their theory. In this paper, I will defend Millikan’s theory against this argument. I will show that the proponents of the generalized theory have yet to provide a working notion of populations that avoids a liberality problem. Further, I will argue that persistence functions are at best a marginal case of functions due to their restricted explanatory power. (shrink)

Originating in the work of Ernst Haeckel and Wilhelm Preyer, and advanced by a Prussian embryologist, Wilhelm Roux, the idea of struggle for existence between body parts helped to establish a framework, in which population cell dynamics rather than a predefined harmony guides adaptive changes in an organism. Intended to provide a causal-mechanical view of functional adjustments in body parts, this framework was also embraced later by early pioneers of immunology to address the question of vaccine effectiveness and pathogen resistance. (...) As an extension of these early efforts, Elie Metchnikoff established an evolutionary vision of immunity, development, pathology, and senescence, in which phagocyte-driven selection and struggle promote adaptive changes in an organism. Despite its promising start, the idea of somatic evolution lost its appeal at the turn of the twentieth century giving way to a vision, in which an organism operates as a genetically uniform, harmonious entity. (shrink)

I argue that an explicit distinction between cognitive characters and cognitive phenotypes is needed for empirical progress in the cognitive sciences and their integration with evolution-guided sciences. I elaborate what ontological commitment to characters involves and how such a commitment would clarify ongoing debates about the relations between human and nonhuman cognition and the extent of cognitive abilities across biological species. I use theoretical proposals in episodic memory, language, and sociocultural bases of cognition to illustrate how cognitive characters are being (...) introduced in scientific practice. (shrink)

According to the current scientific paradigm, what we call ‘life’, ‘mind’, and ‘consciousness’ are considered epiphenomenal occurrences, or emergent properties or functions of matter and energy. Science does not associate these with an inherent and distinct existence beyond a materialistic/energetic conception. ‘Life’ is a word pointing at cellular and multicellular processes forming organisms capable of specific functions and skills. ‘Mind’ is a cognitive ability emerging from a matrix of complex interactions of neuronal processes, while ‘consciousness’ is an even more elusive (...) concept, deemed a subjective epiphenomenon of brain activity. Historically, however, this has not always been the case, even in the scientific and academic context. Several prominent figures took vitalism seriously, while some schools of Western philosophical idealism and Eastern traditions promoted conceptions in which reality is reducible to mind or consciousness rather than matter. We will argue that current biological sciences did not falsify these alternative paradigms and that some forms of vitalism could be linked to some forms of idealism if we posit life and cognition as two distinct aspects of consciousness preeminent over matter. However, we will not argue in favor of vitalistic and idealistic conceptions. Rather, contrary to a physicalist doctrine, these were and remain coherent worldviews and cannot be ruled out by modern science. (shrink)

"The author tells a history of the study of cancer-causing viruses from the early twentieth century to the development of an HPV vaccine for cervical cancer in 2006. He profiles the "cancer virus hunters" who made breakthroughs in tumor virology"--.

This paper develops the conceptual framework of ’sex contextualism’ for the study of sex-related variables in biomedical research. Sex contextualism offers an alternative to binary sex essentialist approaches to the study of sex as a biological variable. Specifically, sex contextualism recognizes the pluralism and context-specificity of operationalizations of ’sex’ across experimental laboratory research. In light of recent policy mandates to consider sex as a biological variable, sex contextualism offers constructive guidance to biomedical researchers for attending to sex-related biological variation. As (...) an alternative to and critique of biological binary sex essentialism, sex contextualism contributes to current debates in philosophy of biology, feminist science studies, and social ontology on the construction of categories of gender/sex differences in scientific research. (shrink)

The free-energy principle states that all systems that minimize their free energy resist a tendency to physical disintegration. Originally proposed to account for perception, learning, and action, the free-energy principle has been applied to the evolution, development, morphology, anatomy and function of the brain, and has been called a postulate, an unfalsifiable principle, a natural law, and an imperative. While it might afford a theoretical foundation for understanding the relationship between environment, life, and mind, its epistemic status is unclear. Also (...) unclear is how the free-energy principle relates to prominent theoretical approaches to life science phenomena, such as organicism and mechanism. This paper clarifies both issues, and identifies limits and prospects for the free-energy principle as a first principle in the life sciences. (shrink)

L’article poursuit un double objectif. D’une part, il propose une revue de l’articulation des concepts de genre et de sexe au prisme de la biologie de l’évolution dans le champ des études féministes francophones (cette délimitation tenant à la fois à des raisons de place, de pertinence scientifique et d’accessibilité au public non spécialiste). A cette fin, il propose également une définition du concept de constructivisme qui soit compatible avec le naturalisme, s’inscrivant en cela dans l’état contemporain de la philosophie (...) générale des sciences. Une fois mis en place ces éléments de cartographie du débat, le second objectif de l’article consiste à prendre au sérieux la diversité actuelle des concepts de sexe en biologie. Il insiste sur la nécessité d’une clarification conceptuelle des différents niveaux impliqués, et propose pour cela d’en finir avec la terminologie unique du sexe : celle-ci, en favorisant des confusions entre différents concepts, constitue un coût cognitif qu’il faut dépasser. Ce coût cognitif s’articule à un coût social. En effet, un tel flou conceptuel favorise en même temps dans la sphère publique une naturalisation abusive – puisque scientifiquement douteuse – de comportements sociaux inégalitaires. L’approche constructiviste ne consiste donc pas à nier la contrainte empirique de la nature. Il s’agit plutôt, à partir de la mise en évidence de la circulation des représentations entre la société en général et la science en particulier, de se doter d’outils d’analyse réflexifs et scientifiquement maîtrisés pour aborder les problématiques éthiques, politiques et épistémiques impliquées par cette circulation. (shrink)

Dieser Aufsatz behandelt moderne "Naturphilosophie" am Beispiel von Rupert Riedls evolutionärer Erkenntnistheorie und Carl Friedrich von Weizsäckers Philosophie der Physik. Es wird darin im Anschluss das menschliche Erkennen im Hinblick auf die Ordnung der Natur reflektiert. Schließlich wird das Phänomen der Erkenntnis sowohl im von Weizsäcker und Riedl erschlossenen Zugang zur Realität als auch in wissenschaftsphilosophischer Hinsicht erfasst.

The article Thinking embodiment with genetics: epigenetics and postgenomic biology in embodied cognition and enactivism, written by Maurizio Meloni and Jack Reynolds, was originally published electronically on the publisher’s internet portal on 18 June 2020 without open access. With the author’ decision to opt for Open Choice the copyright of the article changed on 6 November 2020 to ©The Author 2020 and the article is forthwith distributed under a Creative Commons Attribution.

In 1976, the Genetics Society of America published a document entitled “Resolution of Genetics, Race, and Intelligence.” This document laid out the Society’s position in the IQ controversy, particularly that on scientific and ethical questions involving the genetics of intellectual differences between human populations. Since the GSA was the largest scientific society of geneticists in the world, many expected the document to be of central importance in settling the controversy. Unfortunately, the Resolution had surprisingly little influence on the discussion. In (...) 1979, William Provine analyzed the possible factors that decreased the impact of the Resolution, among them scientists’ limited understanding of the relationship between science and ethics. Through the analysis of unpublished versions of the Resolution and exchanges between GSA members, I will suggest that the limited impact of the statement likely depended on a shift in the aims of the GSA due to the controversies that surrounded the preparation of the document. Indeed, the demands of the membership made it progressively more impartial in both scientific and political terms, decreasing its potential significance for a wider audience. Notably, the troubled history of the Resolution raises the question of what can make effective or ineffective the communication between scientists and the public—a question with resonance in past and present discussions on topics of social importance. (shrink)

We look to mitonuclear ecology and the phenomenon of Mother’s Curse to argue that the sex of parents and offspring among populations of eukaryotic organisms, as well as the mitochondrial genome, ought to be taken into account in the conceptualization of evolutionary fitness. Subsequently, we show how characterizations of fitness considered by philosophers that do not take sex and the mitochondrial genome into account may suffer. Last, we reflect on the debate regarding the fundamentality of trait versus organism fitness and (...) gesture at the idea that the former lies at the conceptual basis of evolutionary theory. (shrink)

This paper poses a problem for traditional phylogenetics: The identity of organisms that reproduce through fission can be understood in several different ways. This prompts questions about how to differentiate parent organisms from their offspring, making vertical gene transfer unclear. Differentiating between parents and offspring stems from what I call the identity problem. How the problem is resolved has implications for phylogenetic groupings. If the identity of a particular asexual organism persists through fission, the vertical lineage on a phylogenetic tree (...) will split differently than if the identity of an organism does not survive the fission process. (shrink)

The aim of this article is to investigate the relevance and implications of synthetic models for the study of the interactive dimension of minimal life and cognition, by taking into consideration how the use of artificial systems may contribute to an understanding of the way in which interactions may affect or even contribute to shape biological identities. To do so, this article analyzes experimental work in synthetic biology on different types of interactions between artificial and natural systems, more specifically: between (...) protocells and between biological living cells and protocells. It discusses how concepts such as control, cognition, communication can be used to characterize these interactions from a theoretical point of view, which criteria of relevance and evaluation of synthetic models can be applied to these cases, and what are their limits. (shrink)

At the intersection of taxonomy and nomenclature lies the scientific practice of typification. This practice occurs in biology with the use of holotypes (type specimens), in geology with the use of stratotypes, and in metrology with the use of measurement prototypes. In this paper I develop the first general definition of a scientific type and outline a new philosophical theory of types inspired by Pierre Duhem. I use this general framework to resolve the necessity-contingency debate about type specimens in philosophy (...) of biology, to advance the debate over the myth of the absolute accuracy of standards in metrology, and to address the definition-correlation debate in geology. I conclude that just as there has been a productive synergy between philosophical accounts of natural kinds and scientific taxonomic practices, so too there is much to be gained from developing a deeper understanding of the practices and philosophy of scientific types. (shrink)

The thesis of this paper is that our understanding of life, as reflected in the biological and medical sciences but also in our everyday transactions, has been hampered by an inappropriate metaphysics. The metaphysics that has dominated Western philosophy, and that currently shapes most understanding of life and the life sciences, sees the world as composed of things and their properties. While these things appear to undergo all kinds of changes, it has often been supposed that this amounts to no (...) more than a change in the spatial relations of their unchanging parts. From antiquity, however, there has been a rival to this view, the process ontology, associated in antiquity with the fragmentary surviving writings of Heraclitus. In the last century it has been especially associated with the work of the British metaphysician and logician, Alfred North Whitehead. For process ontology, what most fundamentally exists is change, or process. What we are tempted to think of as constant things are in reality merely temporary stabilities in this constant flux of change, eddies in the flux of process. My main claim in this paper will be that a metaphysics of this latter kind is the only kind adequate to making sense of the living world. After explaining in more detail, the differences between these ontological views, I shall illustrate the advantages of a process ontology with reference to the category of organism. Finally I shall explore some further implications of a process ontology for biology and for philosophy. (shrink)

The concept of information and its relation to biosemiotics is a major area of contention among biosemioticians. Biosemioticians influenced by von Uexküll, Sebeok, Bateson and Peirce are critical of the way the concept as developed in information science has been applied to biology, while others believe that for biosemiotics to gain acceptance it will have to embrace information science and distance biosemiotics from Peirce’s philosophical work. Here I will defend the influence of Peirce on biosemiotics, arguing that information science and (...) biosemiotics as these were originally formulated are radically opposed research traditions. Failure to appreciate this will undermine the challenge of biosemiotics and other anti-reductionist traditions to mainstream science with its reductionist ambition to explain everything through physics. However, for this challenge to be successful, it will be necessary to respond to criticisms of Peircian ideas, jettisoning ideas that are no longer defensible and integrating ideas allied to his anti-reductionist agenda. Here I will argue that the natural philosophy of Gilbert Simondon, offering a searching critique of the application of the new concept of information and cybernetics to the life and human sciences, provides the means to defend and advance Peirce’s core ideas and thereby defend post-reductionist biosemiotics. (shrink)

Biological order provided by α-helical secondary protein structures is an important resource exploitable by living organisms for increasing the efficiency of energy transport. In particular, self-trapping of amide I energy quanta by the induced phonon deformation of the hydrogen-bonded lattice of peptide groups is capable of generating either pinned or moving solitary waves following the Davydov quasiparticle/soliton model. The effect of applied in-phase Gaussian pulses of amide I energy, however, was found to be strongly dependent on the site of application. (...) Moving solitons were only launched when the amide I energy was applied at one of the α-helix ends, whereas pinned solitons were produced in the α-helix interior. In this paper, we describe a general mechanism that launches moving solitons in the interior of the α-helix through phase-modulated Gaussian pulses of amide I energy. We also compare the predicted soliton velocity based on effective soliton mass and the observed soliton velocity in computer simulations for different parameter values of the isotropy of the exciton-phonon interaction. The presented results demonstrate the capacity for explicit control of soliton velocity in protein α-helices, and further support the plausibility of gradual optimization of quantum dynamics for achieving specialized protein functions through natural selection. (shrink)

The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of generalized Davydov equations that govern the quantum dynamics of multiple amide I exciton quanta propagating along the hydrogen-bonded peptide groups in α-helices. Computational simulations have confirmed the generation of moving Davydov solitons by applied pulses of amide I energy for protein α-helices of varying length. The stability and mobility (...) of these solitons depended on the uniformity of dipole-dipole coupling between amide I oscillators, and the isotropy of the exciton-phonon interaction. Davydov solitons were also able to quantum tunnel through massive barriers, or to quantum interfere at collision sites. The results presented here support a nontrivial role of quantum effects in biological systems that lies beyond the mechanistic support of covalent bonds as binding agents of macromolecular structures. Quantum tunneling and interference of Davydov solitons provide catalytically active macromolecular protein complexes with a physical mechanism allowing highly efficient transport, delivery, and utilization of free energy, besides the evolutionary mandate of biological order that supports the existence of such genuine quantum phenomena, and may indeed demarcate the quantum boundaries of life. (shrink)

In this review of Milan Ćirković’s The Great Silence: Science and Philosophy of Fermi’s Paradox, we attempt to reconstruct the logic of Fermi’s paradox as understood by the author, and we critically examine the reasoning that leads to the paradox. We show that there is no plausible solution to Fermi’s paradox that can satisfy all of Ćirković’s proposed desiderata, which in turn suggests that the author’s standards for hypothesis adjudication need to be revised.

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)

The task of this essay is to put biological individuals in formal terms. This approach is not directly interested in matters of time (for example, in evolution), but rather in the formal shape of biological objects. So it is different from, but not opposed to, natural science. In his later years, Wittgenstein made similar investigations in psychology and mathematics. Unfortunately, he found no time to make extensive remarks on philosophy of biology. This is what we are going to advance here.

Review of William B Irvine's "You: A Natural History".

This paper adds to the philosophical literature on mechanistic explanation by elaborating two related explanatory functions of idealisation in mechanistic models. The first function involves explaining the presence of structural/organizational features of mechanisms by reference to their role as difference-makers for performance requirements. The second involves tracking counterfactual dependency relations between features of mechanisms and features of mechanistic explanandum phenomena. To make these functions salient, we relate our discussion to an exemplar from systems biological research on the mechanism for countering (...) heat shock—the heat shock response system—in Escherichia coli bacteria. This research also reinforces a more general lesson: ontic constraint accounts in the literature on mechanistic explanation provide insufficiently informative normative appraisals of mechanistic models. We close by outlining an alternative view on the explanatory norms governing mechanistic representation. (shrink)

The volume Philosophy and Life Sciences in Dialogue is a result of the IV. International Summer School Bioethics in Context, organized by Sofia University “St. Kliment Ohridski” and FernUniversität in Hagen. The book is exemplary in many ways. It contains 11 high-quality articles on fundamental themes and concepts with real philosophical depth – nature, autonomy, the future of trans- and post-humanism, the meta-topic of bioethics and its relations with life sciences. The authors present illuminating historical backgrounds as a context to (...) these theoretical discussions and a source of interesting or forgotten arguments. Most of the articles analyze recent and avantgarde scientific research with its social implications: CRISPR-Cas9 technology, digitalization of health care, justification of animal experiments, questions of human cloning, moral enhancement and the artificial synthesis of life. The main idea of the book is that bioethics is necessarily connected to human practice: it is not just knowledge but a living culture. (shrink)

This note discusses the importance of Natural History (biology) in the development of Aristotle philosophy and scientific outlook, and so the importance of considering Aristotle's philosophy as a necessary and useful background for contemporary biology.

Pluralisms of various sorts are popular in philosophy of science, including those that imply some scientific concept x should be eliminated from science in favour of a plurality of concepts x1, x2, … xn. This article focuses on influential and representative arguments for such eliminative pluralism about the concept species. The main conclusions are that these arguments fail, that all other extant arguments also fail, and that this reveals a quite general dilemma, one that poses a defeasible presumption against many (...) eliminative pluralisms about various scientific concepts. The article ends by outlining a novel integrative alternative in defence of species. 1) Introduction 2) The species Concept, the Category ‘Species’, and the ‘Species’ Category Problem 3) What Are Eliminative Pluralism about species, and the Arguments for It? 4) Evaluation of Arguments 4.1 Splitting? 4.2 Lumping? 4.3 The eliminative pluralist’s dilemma 5) More General Lessons6Species Cohesion: An Integrative Alternative7Conclusion. (shrink)

This paper proposes a new and testable view about the nature of species and other evolving lineages, according to which they are feedback systems. On this view, it is a mistake to think gene flow, niche sharing, and trait frequency similarities between populations are among variables that interact to cause some further downstream variable that distinguishes evolving lineages from each other, some sort of “species cohesion” for example. Instead, gene flow, niche sharing, similarities between populations, and other causal variables feed (...) into each other—instances of these at earlier times help cause instances of these same variables at later times. And any lineage-identifying cohesion just is the recurrence or cycling of these feedback relations within metapopulations over generations. Such cohesion can then be represented as variable M within multi-dimensional variable spaces, where values of M vary dynamically with the frequency and magnitude of feedback relations. Related conditions for being a species or other evolving lineage are then clarified. To argue for the development and testing of this view, the paper shows how it improves upon others. (shrink)

The aim of this paper is to provide a theoretical framework to understand how multicellular systems realize functionally integrated physiological entities by organizing their intercellular space. From a perspective centered on physiology and integration, biological systems are often characterized as organized in such a way that they realize metabolic self-production and self-maintenance. The existence and activity of their components rely on the network they realize and on the continuous management of the exchange of matter and energy with their environment. One (...) of the virtues of the organismic approach focused on organization is that it can provide an understanding of how biological systems are functionally integrated into coherent wholes. Organismic frameworks have been primarily developed by focusing on unicellular life. Multicellularity, however, presents additional challenges to our understanding of biological systems, related to how cells are capable to live together in higher-order entities, in such a way that some of their features and behaviors are constrained and controlled by the system they realize. Whereas most accounts of multicellularity focus on cell differentiation and increase in size as the main elements to understand biological systems at this level of organization, we argue that these factors are insufficient to provide an understanding of how cells are physically and functionally integrated in a coherent system. In this paper, we provide a new theoretical framework to understand multicellularity, capable to overcome these issues. Our thesis is that one of the fundamental theoretical principles to understand multicellularity, which is missing or underdeveloped in current accounts, is the functional organization of the intercellular space. In our view, the capability to be organized in space plays a central role in this context, as it enables (and allows to exploit all the implications of) cell differentiation and increase in size, and even specialized functions such as immunity. We argue that the extracellular matrix plays a crucial active role in this respect, as an evolutionary ancient and specific (non-cellular) control subsystem that contributes as a key actor to the functional specification of the multicellular space and to modulate cell fate and behavior. We also analyze how multicellular systems exert control upon internal movement and communication. Finally, we show how the organization of space is involved in some of the failures of multicellular organization, such as aging and cancer. (shrink)

Philosophy of biology before biology -/- Edited by Cécilia Bognon-Küss & Charles T. Wolfe -/- Table of contents -/- Cécilia Bognon-Küss & Charles T. Wolfe. Introduction -/- 1. Cécilia Bognon-Küss & Charles T. Wolfe. The idea of “philosophy of biology before biology”: a methodological provocation -/- Part I. FORM AND DEVELOPMENT -/- 2. Stéphane Schmitt. Buffon’s theories of generation and the changing dialectics of molds and molecules 3. Phillip Sloan. Metaphysics and “Vital” Materialism: The Gabrielle Du Châtelet Circle and French (...) Vitalism 4. John Zammito. The Philosophical Reception of C. F. Wolff’s Epigenesis in Germany, 1770-1790: Herder, Tetens and Kant -/- Part II. ORGANISM & ORGANIZATION 5. François Duchesneau. Senebier and the Advent of General Physiology 6. Tobias Cheung. Organization and Process. Living Systems Between Inner and Outer Worlds: Cuvier, Hufeland, Cabanis. -/- Part III. SYSTEMS 7. Georg Toepfer. Philosophy of Ecology Long Before Ecology: Kant’s Idea of an Organized System of Organized Beings 8. Ina Goy. "All is leaf". Goethe's plant philosophy and poetry 9. Snait Gissis. ‘Biology’, Lamarck, Lamarckisms -/- POSTSCRIPTS 1. Lynn Nyhart. A Historical Proposal Around Prepositions -/- 2. Philippe Huneman. Philosophy after Philosophy of Biology before Biology -/- Cécilia Bognon-Küss and Charles T. Wolfe. Conclusion . (shrink)

According to the Academy of Nutrition and Dietetics’ influential position statement on vegetarianism, meat and seafood can be replaced with milk, soy/legumes, and eggs without any negative effects in children. The United States Department of Agriculture endorses a similar view. The present paper argues that the Academy of Nutrition and Dietetics ignores or gives short shrift to direct and indirect evidence that vegetarianism may be associated with serious risks for brain and body development in fetuses and children. Regular supplementation with (...) iron, zinc, and B12 will not mitigate all of these risks. Consequently, we cannot say decisively that vegetarianism or veganism is safe for children. (shrink)

Lynch, Parke, and O’Malley highlight the need for better evaluative criteria for causal explanations in microbiome research. They propose new interventionist criteria, show that paradigmatic examples of microbiome explanations are flawed using those criteria, and suggest numerous ways microbiome explanations can be improved. While we endorse their primary criticisms and suggestions for improvements in microbiome research, we make several observations regarding the use of mooted causal models in microbiome research that have significant implications for their overall argument. In sum, we (...) contend that their critique is too modest and that even flawed causal inferences like those they criticize can be valuable for generating better causal models and evaluating explanatory outcomes in individual cases. (shrink)

Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...) are framed by an interventionist causal framework, it is clearer what the H. pylori explanation achieves and where its explanatory strengths lie. After assessing this ‘simple’, single-microbe case, we apply the interventionist framework to two key areas of microbiome research, in which obesity and mental health states are purportedly explained by microbiomes. Despite the experimental data available, interventionist criteria for explanation show that many of the causal claims generated by microbiome research are weak or misleading. We focus on the stability, specificity and proportionality of proposed microbiome causal explanations, and evaluate how effectively these dimensions of causal explanation are achieved in some promising avenues of research. We suggest some conceptual and explanatory strategies to improve how causal claims about microbiomes are made. (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 2016, a multidisciplinary body of scholars within the International Commission on Stratigraphy—the Anthropocene Working Group—recommended that the world officially recognize the Anthropocene as a new geological epoch. The most contested claim about the Anthropocene, that humans are a major geological and environmental force on par with natural forces, has proven to be a hotbed for discussion well beyond the science of geology. One reason for this is that it compels many natural and social scientists to confront problems and systems (...) that transgress traditional disciplinary boundaries, and as a result, calls for interdisciplinary research are now gaining traction. Proponents of such transgressions have dubbed the new scientific order that will result “Anthropocene Science”, and rhetoric notwithstanding, such discussions exemplify how recent changes within science justify rethinking a prevailing image of how science is done, and with it, the working relationship between scholars in the humanities, natural scientists, and social scientists. (shrink)