Funding organizations around the world are adopting open science policies, resulting in a pressing need for open science programs. In response to the 2011 decadal survey, NASA sought to expand and accelerate omics research, releasing its GeneLab Strategic Plan in 2014. GeneLab is an open science data repository and analysis portal for spaceflight and space-relevant omics data. GeneLab’s output has been outstanding, but its full potential as a way to transform space biology has not yet been achieved. (...) NASA should pursue the development of GeneLab as an open science platorm in earnest. (shrink)

We provide a new perspective on the relation between the space of description of an object and the appearance of novelties. One of the aims of this perspective is to facilitate the interaction between mathematics and historical sciences. The definition of novelties is paradoxical: if one can define in advance the possibles, then they are not genuinely new. By analyzing the situation in set theory, we show that defining generic (i.e., shared) and specific (i.e., individual) properties of elements of (...) a set are radically different notions. As a result, generic and specific definitions of possibilities cannot be conflated. We argue that genuinely stating possibilities requires that their meaning has to be made explicit. For example, in physics, properties playing theoretical roles are generic; then, generic reasoning is sufficient to define possibilities. By contrast, in music, we argue that specific properties matter, and generic definitions become insufficient. Then, the notion of new possibilities becomes relevant and irreducible. In biology, among other examples, the generic definition of the space of DNA sequences is insufficient to state phenotypic possibilities even if we assume complete genetic determinism. The generic properties of this space are relevant for sequencing or DNA duplication, but they are inadequate to understand phenotypes. We develop a strong concept of biological novelties which justifies the notion of new possibilities and is more robust than the notion of changing description spaces. These biological novelties are not generic outcomes from an initial situation. They are specific and this specificity is associated with biological functions, that is to say, with a specific causal structure. Thus, we think that in contrast with physics, the concept of new possibilities is necessary for biology. (shrink)

Reductionism--understanding complex processes by breaking them into simpler elements--dominates scientific thinking around the world and has certainly proved a powerful tool, leading to major discoveries in every field of science. But reductionism can be taken too far, especially in the life sciences, where sociobiological thinking has bordered on biological determinism. Thus popular science writers such as Richard Dawkins, author of the highly influential The Selfish Gene, can write that human beings are just "robot vehicles blindly programmed to preserve the selfish (...) molecules known as genes." Indeed, for many in science, genes have become the fundamental unit for understanding human existence: genes determine every aspect of our lives, from personal success to existential despair: genes for health and illness, genes for criminality, violence, and sexual orientation. Others would say that this is reductionism with a vengeance. In Lifelines, biologist Steven Rose offers a powerful alternative to the ultradarwinist claims of Dawkins, E.O. Wilson, Daniel Dennett and others. Rose argues against an extreme reductionist approach that would make the gene the key to understanding human nature, in favor of a more complex and richer vision of life. He urges instead that we focus on the organism and in particular on the organism's lifeline: the trajectory it takes through time and space. Our personal lifeline, Rose points out, is unique--even identical twins, with identical genes at birth, will differ over time. These differences are obviously not embedded in our genes, but come about through our developmental trajectory in which genes, as part of the biochemical orchestra of trillions of cells in each human body, have an important part--but only a part--to play. To illustrate this idea, Rose examines recent research in modern biology, and especially two disciplines--genetics (which looks at the impact of genes on form) and developmental biology (which examines the interaction between the organism and the environment)--and he explores new ideas on biological complexity proposed by scientists such as Stuart Kauffman. He shows how our lifelines are constructed through the interplay of physical forces--such as the intrinsic chemistry of lipids and proteins, and the self-organizing and stabilizing properties of complex metabolic webs--and he reaches a startling conclusion: that organisms are active players in their own fate, not simply the playthings of the gods, nature, or the inevitable workings out of gene-driven natural selection. The organism is both the weaver and the pattern it weaves. Lifelines will be a rallying point for all who seek an alternative to the currently fashionable, deeply determinist accounts which dominate popular science writing and, in fact, crowd the pages of some of the major scientific journals. Based on solid, state-of-the-art research, it not only makes important contributions to our understanding of Darwin and natural selection, but will swing the pendulum back to a richer, more complex view of human nature and of life. (shrink)

A classic analytic approach to biological phenomena seeks to refine definitions until classes are sufficiently homogenous to support prediction and explanation, but this approach founders on cases where a single process produces objects with similar forms but heterogeneous behaviors. I introduce object spaces as a tool to tackle this challenging diversity of biological objects in terms of causal processes with well-defined formal properties. Object spaces have three primary components: (1) a combinatorial biological process such as protein synthesis that generates objects (...) with parts that are modular, independent, and organized according to an invariant syntax; (2) a notion of “distance” that relates the objects according to rules of change over time as found in nature or useful for algorithms; (3) mapping functions defined on the space that map its objects to other spaces or apply an evaluative criterion to measure an important quality, such as parsimony or biochemical function. Once defined, an object space can be used to represent and simulate the dynamics of phenomena on multiple scales; it can also be used as a tool for predicting higher-order properties of the objects, including stitching together series of causal processes. Object spaces are the basis for a strategy of theorizing, discovery, and analysis in biology: as heuristic idealizations of biology, they help us transform inchoate, intractable problems into articulated, well-structured ones. Developing an object space is a research strategy with a long, successful history under many other names, and it offers a unifying but not overreaching approach to biological theory. (shrink)

The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, such as life, reproduction, and agency. There (...) has been a focus in some recent discussions by both philosophers and biologists on how evolutionary individuals are created and regulated, as well as continuing work on the evolution of individuality. (shrink)

I consider recent uses of the notion of neutrality in evolutionary biology and ecology, questioning their relevance to the kind of explanation recently labeled ‘topological explanation’. Focusing on fitness landscapes and genotype-phenotype maps, I explore the explanatory uses of neutral subspaces, as modeled in two perspectives: hyperdimensional fitness landscapes and RNA sequence-structure maps. I argue that topological properties of such spaces account for features of evolutionary systems: respectively, capacity for adaptive evolution toward global optima and mutational robustness of genotypes. (...) Thus many models appealing to “neutral” manifolds provide topological alternatives to hypothetical mechanisms. (shrink)

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

Purpose: To consider the implications of the operation of the nervous system -- and of the constitution of cultures as closed networks of languaging and emotioning -- for how we understand and generate so-called "virtual realities." Findings: The nervous system is a detector of configurations within itself and thus cannot represent reality. The distinction between virtual and non-virtual realities does not apply to the operation of the nervous system; rather it pertains to the operation of the observer as a languaging (...) being. Our human existence has changed as virtual realities have become non-virtual through their systemic cultural inclusion in the realization of our biological human manner of living. Implications: Virtual realities are never trivial, because we always become transformed as we live them according to the emotioning of the psychic space that they bring about in our living, and this is so regardless of whether we like it or not. (shrink)

Biological modalities, i.e., biologically possible, impossible, or necessary states of affairs have not received much attention from philosophers. Yet, it is widely agreed that there are biological constraints on physically possible states of affairs, such that not everything that is physically possible is also biologically possible, even if everything that is biologically possible is also physically possible. Furthermore, biologists use concepts that appear to be modal in nature, such as the concept of evolvability in evolutionary developmental biology, or “evo-devo.” (...) The present chapter investigates what kind of modality underlies the concept of evolvability. This concept tries to capture the capacity of an organism or a lineage to sustain genetic changes that enable it to evolve or to evolve adaptively. The basic idea of the proposed approach is to construe evolvability as a kind of accessibility in a modal space. The difficult part is to specify this modal space and the relevant accessibility relation. While there may not be a general way of defining such a relation, there exist model systems for which it is possible, e.g., evolving small RNAs. The modal space in such cases turns out to be quite distinct from those constructed by philosophers, e.g., David Lewis’s similarity metric for possible worlds. Even though the biological case examined here is quite special, attending to the way in which biological possibilities are modeled in this case harbors some general lessons about biological modalities, in particular their dependence on the explanatory goals of the models modeling modality. (shrink)

Space and time, which should properly be taken conjointly, are both communicatively produced and created with certain contextual perspectives—they are not independent physical entities. The standpoint of production makes the relationship between space and time comprehensible. They can either be mental-subjective, physical-objective, or social-intersubjective. Social and intersubjective (or E-series) spacetime might shed new light on biological thinking. For general readers, this paper provides a clue regarding an alternative conceptualization of spacetime based on biology.

It’s recently been argued that biological fitness can’t change over the course of an organism’s life as a result of organisms’ behaviors. However, some characterizations of biological function and biological altruism tacitly or explicitly assume that an effect of a trait can change an organism’s fitness. In the first part of the paper, I explain that the core idea of changing fitness can be understood in terms of conditional probabilities defined over sequences of events in an organism’s life. The result (...) is a notion of “conditional fitness” which is static but which captures intuitions about apparent behavioral effects on fitness. The second part of the paper investigates the possibility of providing a systematic foundation for conditional fitness in terms of spaces of sequences of states of an organism and its environment. I argue that the resulting “organism–environment history conception” helps unify diverse biological perspectives, and may provide part of a metaphysics of natural selection. (shrink)

Biological sexes (male, female, hermaphrodite) are defined by different gametic strategies for reproduction. Sexes are regions of phenotypic space which implement those gametic reproductive strategies. Individual organisms pass in and out of these regions – sexes - one or more times during their lives. Importantly, sexes are life-history stages rather than applying to organisms over their entire lifespan. This fact has been obscured by concentrating on humans, and ignoring species which regularly change sex, as well as those with non-genetic (...) or facultatively genetic sex determination systems. But the general point applies equally to humans. Assigning sexes to pre-reproductive life history stages involves ‘prospective narration’ – classifying the present in terms of its anticipated future. Assigning sexes to adult stages of non-reproductive castes or non-reproductive individuals is a complex matter whose biological meaning differs from case to case. The chromosomal and phenotypic ‘definitions’ of biological sex that are contested in philosophical discussions of sex are actually operational definitions which track gametic sex more or less effectively in some species or group of species. Neither ‘definition’ can be stated for species in general except by defining them in terms of gametic sex. The gametic definition of sex also features in widely accepted models which explain why two biological sexes – either in separate individuals or combined in hermaphroditic individuals - are almost universal in multicellular species. Finally, the fact that a species has only two biological sexes does not imply that every member of the species is either male, female or hermaphroditic, or that the sex of every individual organism is clear and determinate. The idea of biological sex is critical for understanding the diversity of life, but ill-suited to the job of determining the social or legal status of human beings as men or women. (shrink)

Contemporary psychiatry faces serious challenges because it has failed to incorporate accumulated knowledge from basic neuroscience, neurophilosophy, and brain–mind relation studies. As a consequence, it has limited explanatory power, and effective treatment options are hard to come by. A new conceptual framework for understanding mental health based on underlying neurobiological spatial-temporal mechanisms of mental disorders (already gained by the experimental studies) is beginning to emerge.

Deweyan pedagogy seeks to promotes growth, characterized as an increased sensitivity, responsiveness, and ability to participate in an environment. Growth, Dewey says, is fostered by the development of habits that enable further habit formation. Unfortunately, humans have their own habitual ways of encountering other species, which often do not support growth. In this article, I briefly review some common conceptions of learning and the process of habit-formation to scope out the landscape of a more responsible and responsive approach to taking (...) growth seriously. What emerges is a reflexive biosemiotics that has humans explicitly concerned with the in situ emergence of new signification in themselves and in other organisms. This requires we take a pedagogical stance in our attitudes and practices towards other species, which we can enrich with insights derived from re-interpreting traditional empirical studies. By freeing the habit-forming process from confining stereotype, a biological pedagogy can enable a more fluid and creative biosphere, unencumbered to explore unfolding possibilities in semiotic space. (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)

This book proposes the foundation of the relational approach to biology, rejecting the deterministic and reductionist approach of molecular biology. Although biology has made enormous progress in the last seventy years, onto genesis is still conceived as a “revelation” of information (DNA). Recovering the geometric tradition, relational biology conceives scientific and epistemological tools (cause, probability, space etc.) of science in a new way. If probabilistic biology and organicism still proposes a biology based on (...) physics, with a fundamental invariant, relational biology is based on variation: its fundamental invariant is variation, one of the most important elements of life. This is an indispensable book for academics who consider biology from a new theoretical approach, in particular for those working in the domains of cancer, ontogenesis and evolution. (shrink)

Many scientific models in biology are how-possibly models. These models depict things as they could be, but do not necessarily capture actual states of affairs in the biological world. In contemporary philosophy of science, it is customary to treat how-possibly models as second-rate theoretical tools. Although possibly important in the early stages of theorizing, they do not constitute the main aim of modelling, namely, to discover the actual mechanism responsible for the phenomenon under study. In the paper it is (...) argued that this prevailing picture does not do justice to the synthetic strategy that is commonly used in biological engineering. In synthetic biology, how-possibly models are not simply speculations or eliminable scaffolds towards a single how-actually model, but indispensable design hypotheses for a field whose ultimate goal is to build novel biological systems. The paper explicates this by providing an example from the study of alternative genetic systems by synthetic biologist Steven Benner and his group. The case will also highlight how the method of synthesis, even when it fails, provides an effective way to limit the space of possible models for biological systems. (shrink)

This article proposes a new bi-directional way of understanding the convergence of biology and computing. It argues for a reciprocal interaction in which biology and computing have shaped and are currently reshaping each other. In so doing, we qualify both the view of a natural marriage and of a digital shaping of biology, which are common in the literature written by scientists, STS, and communication scholars. The DNA database is at the center of this interaction. We argue (...) that DNA databases are spaces of convergence for computing and biology that change in form, meaning, and function from the 1960s to the 2000s. The first part of the article shows how, in the 1980s, DNA sequencing shifted from passively incorporating computers to be increasingly modeled in digital coding and decoding. Information retrieval algorithms, reciprocally, were altered according to the peculiarities of DNA in the first sequence-storage databases. The second part of the article investigates the impact of these reciprocal interactions and globalization on the organization of research centers, ways of conducting big science, and scientific values. Through convergence and new technologies such as data mining, biology and computing were transformed technologically, institutionally, and culturally into a new bio-data enterprise called genomics. (shrink)

Space and time have been explained not in terms of physical entities but in terms of practice, that is, based on communication, which includes spacetime code in the _A-series_, _B-series_, and _E-series_. Each code has a unique grammar, and it progresses through _boundary operation_, i.e., setting the limit and transgressing it, but in each distinct way. The purpose of this paper is to introduce the notion of _event matching_ to elucidate the mechanism of meaning-making through _boundary operations_. Biological spacetime (...) production is an incessant _effort after meaning_ in the adaptive process, where the _dia-metric_ scale in the _E-series_ necessitates anticipatory (retrocausal) actions in the steps of interaction. This paper suggests that the three terms — _event matching_, meaning making, and spacetime production — are synonymous with each other in biological worlds. Evidence-based examples are provided to support the arguments. (shrink)

This paper reviews the location of Responsible Research and Innovation approaches within the access and benefit sharing policy spaces of the Convention on Biological Diversity and Nagoya Protocol. We describe how a range of dialogues on ethical research practices found a home, almost inadvertently, within the ABS policy process. However, more recent RRI dialogues around emerging technologies have not been similarly absorbed into ABS policy, due in part to the original framing of ABS and associated definitional and scope issues. Consideration (...) is given to the challenges posed to these policy processes by the transformative and rapid nature of scientific and technological change today, including the emerging field of synthetic biology. Drawing on experiences from regulating ABS, we emphasize that the integration of RRI into policies for new, emerging, or poorly understood activities such as synthetic biology faces deficiencies such as limits to government capacity, jurisdictional confusion, shortages in funds, and an absence of strategic approaches. We conclude that a coordinated combination of diverse policy processes within the CBD might provide an invaluable space for RRI dialogues on social justice, sustainability, biosafety, and other issues raised by emerging technologies. (shrink)

The question What is an individual? goes back beyond Aristotle’s discussion of substance to the Ionians’ preoccupation with the paradox of change -- the fact that if anything changes it must stay the same. Mere reflection on this fact and the common-sense notion of a countable thing yields a concept of a “minimal individual”, which is particular (a logical matter) specific (a taxonomic matter), and unique (an evaluative empirical matter). Individuals occupy space, and therefore might be dislodged. Even minimal (...) individuals, therefore (Strawsonian individual or Aristotelian substance) already contain the potential for competition or conflict. What is added by biology to this basic notion? It emerges from some recent work on the evolution of metazoan animals that individuals as we know them are minimal individuals towhich four features have been added, and which appear to be inseparable: differentiated multicellularity; sexual reproduction; segregation of germ from somatic cells; and obligatory death. Whether or not individuals are to be counted as units of selection, they are not the beneficiaries of natural selection. (shrink)

Due to the variation, contingency and complexity of living systems, biology is often taken to be a science without fundamental theories, laws or general principles. I revisit this question in light of the quest for design principles in systems biology and show that different views can be reconciled if we distinguish between different types of generality. The philosophical literature has primarily focused on generality of specific models or explanations, or on the heuristic role of abstraction. This paper takes (...) a different approach in emphasizing a theory-constituting role of general principles. Design principles signify general dependency-relations between structures and functions, given a set of formally defined constraints. I contend that design principles increase our understanding of living systems by relating specific models to general types. The categorization of types is based on a delineation of the scope of biological possibilities, which serves to identify and define the generic features of classes of systems. To characterize the basis for general principles through generic abstraction and reasoning about possibility spaces, I coin the term constraint-based generality. I show that constraint-based generality is distinct from other types of generality in biology, and argue that general principles play a unifying role that does not entail theory reduction. (shrink)

Abstract.At the heart of the most radical proposals in Stuart Kauffman's Investigations is his attempt to show that we find in evolutionary biology some configuration spaces—the sets of possible developments for any given system—that (unlike those in traditional physics of Newtonian, relativistic, and quantum stripes) cannot be completely described in advance. We bring Charles Peirce's work on the philosophy of continuity to bear on the problem and discover, first, that Kauffman's arguments do not succeed; second, that Peirce's metaphysics provide (...) new and sounder arguments for the same propositions; third, that Peirce's rigorous but nonstandard treatment of mathematical continuity shows great promise for modeling the unpredictability and growth we find in evolutionary biology; fourth, that it also strengthens a development only hinted at by biologists thus far—the inevitable involvement of the observer's mind in constituting the objects of science. We close with a logical argument for the surprising relevance of metaphysical hypotheses in the natural sciences and with suggestions for future work that will connect these questions to what Kauffman terms the “narrative stance” in biology. (shrink)

Altruism may be learned (behavioral evolution) in a way similar to that proposed in the target article for its biological evolution. Altruism (over social space) corresponds to self-control (over time). In both cases, one must learn to ignore the rewards to a particular (person or moment) and behave to maximize the rewards to a group (of people or moments).

This paper describes a pattern of explanation prevalent in the biological sciences that I call a ‘lineage explanation’. The aim of these explanations is to make plausible certain trajectories of change through phenotypic space. They do this by laying out a series of stages, where each stage shows how some mechanism worked, and the differences between each adjacent stage demonstrates how one mechanism, through minor modifications, could be changed into another. These explanations are important, for though it is widely (...) accepted that there is an ‘incremental constraint’ on evolutionary change, in an important class of cases it is difficult to see how to satisfy this constraint. I show that lineage explanations answer important questions about evolutionary change, but do so by demonstrating differences between individuals rather than invoking population processes, such as natural selection.1. Introduction2. Turning a ‘Scale’ into a ‘Plume’3. Lineage Explanations in Biology3.1. The evolution of eyes3.2. The evolution of feathers4. The Two Dimensions of a Lineage Explanation4.1. The production dimension4.2. The continuity dimension4.3. The dual role of the parts5. Constraining the Explanations6. Operational and Generative Lineages7. Explaining Change Without Populations8. Conclusion. (shrink)

By focusing on biorobotics, this article explores the epistemological foundations necessary to support the transition from biological models to technological artifacts. To address this transition, I analyze the position of the German philosopher Thomas Fuchs, who represents one possible approach to the problem of the relationship between bio-inspired technology and biology. While Fuchs defends the idea of a unique ontological space for humans, this article contends that his categorical distinctions face challenges in establishing a robust epistemic foundation necessary (...) to ground the transition from biology to technology. After identifying at least three interwoven reasons for rejecting Fuchs’ epistemic foundation, I ask how, through what methods, and by means of which practices the newly bio-inspired object is accessed and shaped. Expanding on philosophy of science and technology in practice, I argue that the plurality of answers to this question provides a possible epistemological foundation _within_ the different frameworks of practices that produce the bio-inspired object. In addressing the potential epistemological foundation for pluralistically grounding the transition from biological models to technological ones, my approach helps us: (i) concretize and examine the relationship between biological and technological models, and (ii) investigate the features and validity of bio-inspired objects, effectively offering a more concrete and pluralistic picture of what bio-inspired sciences and technologies are and what they can (or cannot) do. (shrink)

Lake Tanganiyka has lefty and righty cichlid fish that show there can be natural selection for a trait over its mirror image counterpart.This raises the question Can there be biological selection of a whole organism over its mirror image counterpart? That is, could the fitness of a fish be altered by simply changing it into its own enantaniomorph? My answer is no. I present Flatlander thought experiment to demonstrate that mirror imagecounterparts are duplicates because they only differ in how they (...) happen to be oriented in space. The counterparts have the same intrinsic properties and are in the same environment,so there can be no difference in fitness. (shrink)

Evolutionary systems biology (ESB) aims to integrate methods from systems biology and evolutionary biology to go beyond the current limitations in both fields. This article clarifies some conceptual difficulties of this integration project, and shows how they can be overcome. The main challenge we consider involves the integration of evolutionary biology with developmental dynamics, illustrated with two examples. First, we examine historical tensions between efforts to define general evolutionary principles and articulation of detailed mechanistic explanations of (...) specific traits. Next, these tensions are further clarified by considering a recent case from another field focused on developmental dynamics: stem cell biology. In the stem cell case, incompatible explanatory aims block integration. Experimental approaches aim at mechanistic explanation while dynamical system models offer explanation in terms of general principles. We then discuss an ESB case in which integration succeeds: search for general attractors using a dynamical systems framework synergizes with the experimental search for detailed mechanisms. Contrasts between the positive and negative cases suggest general lessons for achieving an integrated understanding of developmental and evolutionary dynamics. The key integrative move is to acknowledge two complementary aims, both relevant to explanation: identifying the space of possible dynamic states and trajectories, and mechanistic understanding of causal interactions underlying a specific phenomenon of interest. These two aims can support one another in a joint project characterizing dynamic aspects of evolving lineages. This more inclusive project can lead to insights that cannot be reached by either approach in isolation. (shrink)

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

Several disciplines share an interest in the evolutionary selection pressures that shaped human physical functioning and appearance, psyche, and behavior. The methodologies invoked from the disciplines studying these domains are often based on different rhetorics, and hence may conflict. Progress in one field is thereby hampered from effective transfer to others. Topics at the intersection of anthropometry and psychometry, such as the impact of sexual selection on the hominin face, are a typical example. Since the underlying theory explicitly places facial (...) form in the middle of a causal chain as the mediating variable between biological causes and psychological effects, a particularly convenient conceptual and analytic scenario arises as follows. Modern morphometrics allows analysis of shape both “backwards” and “forwards” . The two computations are commensurate, hence the two kinds of effects can be compared and evaluated as directions in the same morphospace. We suggest translating the morphometric methodology of “Darwinian aesthetics” into this space, where psychological and other processes of interest can be coded commensurately. Such a translation permits researchers to relate the effects of biological processes on form to the perceptions of the same processes in one unified “psychomorphospace.”. (shrink)

Formal spaces have become commonplace conceptual and computational tools in a large array of scientific disciplines, including both the natural and the social sciences. Morphological spaces are spaces describing and relating organismal phenotypes. They play a central role in morphometrics, the statistical description of biological forms, but also underlie the notion of adaptive landscapes that drives many theoretical considerations in evolutionary biology. We briefly review the topological and geometrical properties of the most common morphospaces in the biological literature. In (...) contemporary geometric morphometrics, the notion of a morphospace is based on the Euclidean tangent space to Kendall’s shape space, which is a Riemannian manifold. Many more classical morphospaces, such as Raup’s space of coiled shells, lack these metric properties, e.g., due to incommensurably scaled variables, so that these morphospaces typically are affine vector spaces. Other notions of a morphospace, like Thomas and Reif’s skeleton space, may not give rise to a quantitative measure of similarity at all. Such spaces can often be characterized in terms of topological or pretopological spaces. (shrink)

The human attempts to access, measure and organize physical phenomena have led to a manifold construction of mathematical and physical spaces. We will survey the evolution of geometries from Euclid to the Algebraic Geometry of the 20th century. The role of Persian/Arabic Algebra in this transition and its Western symbolic development is emphasized. In this relation, we will also discuss changes in the ontological attitudes toward mathematics and its applications. Historically, the encounter of geometric and algebraic perspectives enriched the mathematical (...) practices and their foundations. Yet, the collapse of Euclidean certitudes, of over 2300 years, and the crisis in the mathematical analysis of the 19th century, led to the exclusion of “geometric judgments” from the foundations of Mathematics. After the success and the limits of the logico-formal analysis, it is necessary to broaden our foundational tools and re-examine the interactions with natural sciences. In particular, the way the geometric and algebraic approaches organize knowledge is analyzed as a cross-disciplinary and cross-cultural issue and will be examined in Mathematical Physics and Biology. We finally discuss how the current notions of mathematical (phase) “space” should be revisited for the purposes of life sciences. (shrink)

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

Critics of multiple realizability have recently argued that we should concentrate solely on actual here-and-now realizations that are found in nature. The possibility of alternative, but unactualized, realizations is regarded as uninteresting because it is taken to be a question of pure logic or an unverifiable scenario of science fiction. However, in the biological context only a contingent set of realizations is actualized. Drawing on recent work on the theory of neutral biological spaces, the paper shows that we can have (...) ways of assessing the modal dimension of multiple realizability that do not have to rely on mere conceivability. (shrink)

Different cell lineages growing in microgravity undergo a spontaneous transition leading to the emergence of two distinct phenotypes. By returning these populations in a normal gravitational field, the two phenotypes collapse, recovering their original configuration. In this review, we hypothesize that, once the gravitational constraint is removed, the system freely explores its phenotypic space, while, when in a gravitational field, cells are “constrained” to adopt only one favored configuration. We suggest that the genome allows for a wide range of (...) “possibilities” but it is unable per se to choose among them: the emergence of a specific phenotype is enabled by physical constraints that drive the system toward a preferred solution. These findings may help in understanding how cells and tissues behave in both development and cancer. In microgravity, cells undergo spontaneous and reversible transitions between different phenotypes. In the absence of physical constraints, living systems could yield bi-stable decisions. On the contrary, physical ‘boundaries’ constrain cells to acquire only a specific configuration by selecting and shaping different gene expression patterns provided by the intrinsic genetic stochasticity. (shrink)

Reasoning from a naturalistic perspective, viewing the mind as an evolved biological organ with a particular structure and function, a number of influential philosophers and cognitive scientists claim that science is constrained by human nature. How exactly our genetic constitution constrains scientific representations of the world remains unclear. This is problematic for two reasons. Firstly, it often leads to the unwarranted conclusion that we are cognitively closed to certain aspects or properties of the world. Secondly, it stands in the way (...) of a nuanced account of the relationship between our cognitive and perceptual wiring and scientific theory. In response, I propose a typology or classification of the different kinds of biological constraints and their sources on science. Using Boden’s notion of a conceptual space, I distinguish between constraints relating to the ease with which we can reach representations within our conceptual space and constraints causing possible representations to fall outside of our conceptual space. This last kind of constraints does not entail that some aspects or properties of the world cannot be represented by us – as argued by advocates of ‘cognitive closure’ – merely that some ways of representing the world are inaccessible to us. It relates to what Clark and Rescher have framed as ‘the alien scientist hypothesis’. The purpose of this typology is to provide some much needed clarity and structure to the debate about biological constraints on science. (shrink)

On October 11, 2003, the Talk Reason website posted an article by Nicholas Matzke titled "Evolution in (Brownian) Space: A Model for the Origin of the Bacterial Flagellum" (http://www.talkreason.org/articles/flagellum.cfm). Talk Reason advertises itself as a website that presents a collection of articles which aim to defend genuine science from numerous attempts by the new crop of creationists to replace it with theistic pseudo-science under various disguises and names." The most obvious target here is intelligent design. Indeed, Matzke's article attempts (...) to rebut one of the main challenges that intelligent design has raised against Darwinian evolution, namely, how to explain the emergence of irreducibly complex biochemical machines like the bacterial flagellum. (shrink)

Boltzmann's gas model representing the second law of thermodynamics is based on the improbability of certain molecular distributions in space. Maxwell argued that a hypothetical ‘being’ with the faculty of seeing individual molecules could bring about such improbable distributions, thus violating the law of entropy. However, it appears that to render the molecules visible for any observer would increase the entropy more than the demon could decrease it, hence ‘Maxwell's Demon cannot operate’ . In the study presented here Maxwell's (...) Demon is interpreted in a general way as a biological observer system within systems which can upset thermodynamic probabilities provided that the relative magnitudes between observer system and observed system are appropriate.Maxwell's Demon within Boltzmann's Gas Model thus appears only as a special case of inappropriate, relative magnitude between the two systems. (shrink)

Model organisms are at the centre of progress in biology but attributing them an excessive representational power and concentrating on a limited group of them, although efficient for research, can have negative consequences, mainly of epistemic nature. Here, I argue that model organisms are exploratory models with a perspectival modelling function, and that a deflated representational power is needed for their proper use. In support of this argument, I will analyse developmental biology as a case study. Firstly, I (...) show that model organisms in developmental biology are not selected because of their representational capabilities, but mainly based on practical criteria. Secondly, I defend that the epistemic organization of developmental biology around questions fosters exploration and perspectival modelling and I propose that developmental biology is a ‘model organism situated knowledge’. Lastly, I use the study of the mechanisms of cell fate acquisition during early embryonic development in _C. elegans_ and mice as a case study to illustrate how a plurality of model organisms allows exploration and perspectival modelling. The use of model organisms for exploration and perspectival modelling, with a limited representational power, should allow more adequate inferences about human embryonic development and encourage the introduction of more model organisms for a comprehensive navigation of the space of possibilities. (shrink)

The current debate over extending inheritance and its evolutionary impact has focused on adding new categories of non-genetic factors to the classical transmission of DNA, and on trying to redefine inheritance. Transmitted factors have been mainly characterized by their directions of transmission and the way they store variations. In this paper, we leave aside the issue of defining inheritance. We rather try to build an evolutionary conceptual framework that allows for tracing most, if not all forms of transmission and makes (...) sense of their different tempos and modes. We discuss three key distinctions that should in particular be the targets of theoretical and empirical investigation, and try to assess the interplay among them and evolutionary dynamics. We distinguish two channels of transmission, two measurements of the temporal dynamics of transmission, respectively across and within generations, and two types of transmitted factors according to their evolutionary relevance. By implementing these three distinctions we can then map different forms of transmission over a continuous space describing the combination of their varying dynamical features. While our aim is not to provide yet another model of inheritance, putting together these distinctions and crossing them, we manage to offer an inclusive conceptual framework of transmission, grounded in empirical observation, and coherent with evolutionary theory. This interestingly opens possibilities for qualitative and quantitative analyses, and is a necessary step, we argue, in order to question the interplay between the dynamics of evolution and the dynamics of multiple forms of transmission. (shrink)

We used agent-based modelling to highlight the advantages and disadvantages of several management styles in biology, ranging from centralized to egalitarian ones. In egalitarian groups, all team members are connected with each other, while in centralized ones, they are only connected with the principal investigator. Our model incorporated time constraints, which negatively influenced weakly connected groups such as centralized ones. Moreover, our results show that egalitarian groups outperform others if the questions addressed are relatively simple or when the communication (...) among agents is limited. Complex epistemic spaces are explored best by centralized groups. They outperform other team structures because the individual members can develop their own ideas with less interference of the opinions of others. The optimal ratio between time spent on experimentation and dissemination varies between different organizational structures. Furthermore, if the evidence is shared only after a relevant degree of certainty is reached, all investigated groups epistemically profit. We discovered that the introduction of seminars to the model changes the epistemic performance in favour of weakly connected teams. Finally, the abilities of the principal investigator do not seem to outperform cognitive diversity, as group performances were not strongly influenced by the increase of her abilities. (shrink)

Biologists increasingly report anthropogenic disruptions of both organisms and ecosystems, suggesting that these processes are a fundamental, qualitative component of the Anthropocene. Nonetheless, the notion of disruption has not yet been theorized in biology. To progress in that regard, we work on a special case. Relatively minor temperature changes impact plant-pollinator synchrony, disrupting mutualistic interaction networks. Understanding this phenomenon requires a specific rationale since models describing them use both historical and systemic reasoning. Specifically, history justifies that the system is (...) initially in a very narrow part of the possibility space where it is viable, and the disruption randomizes this configuration. Building on this rationale, we develop a formal framework inspired by Boltzmann's entropy. With empirical networks, we show historical trends depending on latitude. Then we propose an initial definition of disruption in ecology. When a specific historical outcome contributes to a system's viability, disruption randomizes this outcome, decreasing viability. (shrink)

As urbanization accelerates, diminishing green spaces pose growing public health challenges, exacerbating pollution exposure, stress, and chronic illnesses. This narrative review synthesizes research on the biological and psychological pathways through which urban plants promote human health. Biologically, urban greenery enhances air quality by filtering pollutants, strengthens immune function by increasing microbial diversity, and regulates stress physiology via endocrine mechanisms. Psychologically, nature exposure restores cognitive function, reduces stress, and fosters emotional resilience, as evidenced by neuroimaging and epidemiological studies. The findings suggest (...) that integrating green infrastructure into urban environments yields measurable public health benefits, including lower mortality rates, reduced cardiovascular and respiratory disease prevalence, and improved mental well-being. However, critical research gaps remain regarding the optimal “doses” of nature for health, cultural differences in nature perception, and the potential role of incorporating insights from quantum and informational theories to study cognitive-environment interactions (e.g., Granular Interaction Thinking Theory). Addressing these gaps through interdisciplinary collaboration, artificial intelligence integration, and data-driven urban planning can help cities evolve into healthier, more sustainable ecosystems. (shrink)

Several authors have used the notion of causal specificity in order to defend non-parity about genetic causes (Waters 2007, Woodward 2010, Weber 2017, forthcoming). Non-parity in this context is the idea that DNA and some other biomolecules that are often described as information-bearers by biologists play a unique role in life processes, an idea that has been challenged by Developmental Systems Theory (e.g., Oyama 2000). Indeed, it has proven to be quite difficult to state clearly what the alleged special role (...) of genetic causes consists in. In this paper, I show that the set of biomolecules that are normally considered to be information-bearers (DNA, mRNA) can be shown to be the most specific causes of protein primary structure, provided that causal specificity is measured over a relevant space of biological possibilities, disregarding physical as well as logically possible states of the causal variables. (shrink)

German Idealism still dominates most approaches in theoretical biology. This has led to a conception of organisms as tightly regulated self-forming systems where the demands of the whole organism dominate how the parts are coordinated. This article troubles this approach by presenting aspects of biology that refuse to be synthesized into a specific whole. I call this approach “goth biology” as it recognizes the murkiness of systems of knowledge, the loosely composite nature of most living things, and (...) the continual haunting of life by death. Methodologically, I use insights gleaned from the history of post-punk goth music to explore the role of aesthetics, timbres, and forms as elements of lives that bound disparate times and spaces without providing a unified synthesis. A form of biological experience, and a theory of how the body works, goth biology demands that one lose a conception of “self” in order to embrace the complexity of biological interactions. As the goth performance artist Anna-Varney Cantodea recently confessed in an interview: “I have long given up on any goals I might have had,” but this doesn’t keep me from being inspired by everything around me. (shrink)