This paper proposes an abstract mathematical frame for describing some features of biological time. The key point is that usual physical (linear) representation of time is insufficient, in our view, for the understanding key phenomena of life, such as rhythms, both physical (circadian, seasonal …) and properly biological (heart beating, respiration, metabolic …). In particular, the role of biological rhythms do not seem to have any counterpart in mathematical formalization of physical clocks, which are based (...) on frequencies along the usual (possibly thermodynamical, thus oriented) time. We then suggest a functional representation of biological time by a 2-dimensional manifold as a mathematical frame for accommodating autonomous biological rhythms. The “visual” representation of rhythms so obtained, in particular heart beatings, will provide, by a few examples, hints towards possible applications of our approach to the understanding of interspecific differences or intraspecific pathologies. The 3- dimensional embedding space, needed for purely mathematical reasons, allows to introduce a suitable extra-dimension for “representation time”, with a cognitive significance. (shrink)

I propose that, in addition to the commonly recognized increase of entropy, two more time arrows influence living beings. The increase of damage reactions, which produce aging and genetic variation, and the decrease of the rate of entropy production involved in natural selection are neglected arrows of time. Although based on the statistical theory of the arrow of time, they are distinguishable from the general arrow of the increase of entropy. Physiology under healthy conditions only obeys the (...) increase of entropy arrow. But aging, death, and evolution are determined by the other time arrows as well. Paradoxes emerge from conflicts among the specific determinisms associated with each arrow. These conflicts, along with uncertainties intrinsic to the low-number statistics of the arrows of damage reactions and decrease of the rate of production of entropy, highlight the limits of determinism at different levels of biology and its dependence on time span and number of organisms. The recognition of the three time arrows opens new perspectives for the problem of compatibility of the flow of time in physics and psychology. (shrink)

While many aspects of cognition have been shown to be shared between humans and non-human animals, there remains controversy regarding whether the capacity to mentally time travel is a uniquely human one. In this paper, we argue that there are four ways of representing when some event happened: four kinds of temporal representation. Distinguishing these four kinds of temporal representation has five benefits. First, it puts us in a position to determine the particular benefits these distinct temporal representations afford (...) an organism. Second, it provides the conceptual resources to foster a discussion about which of these representations is necessary for an organism to count as having the capacity to mentally time travel. Third, it enables us to distinguish stricter from more liberal views of mental time travel that differ regarding which kind(s) of temporal representation is taken to be necessary for mental time travel. Fourth, it allows us to determine the benefits of taking a stricter or more liberal view of mental time travel. Finally, it ensures that disagreement about whether some species can mentally time travel is not merely the product of unrecognised disagreement about which temporal representation is necessary for mental time travel. We argue for a more liberal view, on the grounds that it allows us to view mental time travel as an evolutionarily continuous phenomenon, and to recognise that differences in the ways that organisms mentally time travel might reflect different temporal representations, or combinations thereof, that they employ. Our ultimate aim, however, is to create the conceptual framework for further discussion regarding what sorts of temporal representations are required for mental time travel. (shrink)

This article proposes an abstract mathematical frame for describing some features of cognitive and biological time. We focus here on the so called “extended present” as a result of protentional and retentional activities (memory and anticipation). Memory, as retention, is treated in some physical theories (relaxation phenomena, which will inspire our approach), while protention (or anticipation) seems outside the scope of physics. We then suggest a simple functional representation of biological protention. This allows us to introduce the (...) abstract notion of “biological inertia”. (shrink)

This paper presents and defends an account of the coincidence of biological organisms with mereological sums of their material components. That is, an organism and the sum of its material components are distinct material objects existing in the same place at the same time. Instead of relying on historical or modal differences to show how such coincident entities are distinct, this paper argues that there is a class of physiological properties of biological organisms that their coincident mereological (...) sums do not have. The account answers some of the most pressing objections to coincidence, for example the so-called grounding problem , that material coincidence seems to require that coinciding objects have modal differences that do not supervene on any other properties. (shrink)

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

Much has been made of how Darwinian thinking destroyed proofs for the existence of God from ‘design’ in the universe. I challenge that prevailing view by looking closely at classical ‘teleological’ arguments for the existence of God. One version championed by Aristotle and Thomas Aquinas stems from how chance is not a sufficient kind of ultimate explanation of the universe. In the course of constructing this argument, I argue that the classical understanding of teleology is no less necessary in modern (...) Darwinian biology than it was in Aristotle's time. In fact, modern biology strengthens the claims that teleological arguments make by vindicating many of their key features. As a consequence, I show how Aristotle and Aquinas' teleological argument for an intelligent First Cause remains valid. (shrink)

This paper examines two parallel discussions of scientific modeling which have invoked experimentation in addressing the role of models in scientific inquiry. One side discusses the experimental character of models, whereas the other focuses on their exploratory uses. Although both relate modeling to experimentation, they do so differently. The former has considered the similarities and differences between models and experiments, addressing, in particular, the epistemic value of materiality. By contrast, the focus on exploratory modeling has highlighted the various kinds of (...) exploratory functions of models in the early stages of inquiry. These two perspectives on modeling are discussed through a case study in the field of synthetic biology. The research practice in question explores biological control by making use of an ensemble of different epistemic means: mathematical models and simulations, synthetic genetic circuits and intracellular measuring devices, and finally electronic circuits. We argue that the study of exploratory modeling should trace the ways different epistemic means, in different materialities, are being combined over time. Finally, the epistemic status of such novel investigative objects as synthetic genetic circuits is evaluated, with the conclusion that they can function as both experiments and models. (shrink)

Background: how mind functions is subject to continuing scientific discussion. A simplistic approach says that, since no convincing way has been found to model subjective experience, mind cannot exist. A second holds that, since mind cannot be described by classical physics, it must be described by quantum physics. Another perspective concerns mind's hypothesized ability to interact with the world of quanta: it should be responsible for reduction of quantum wave packets; physics producing 'Objective Reduction' is postulated to form the basis (...) for mind-matter interactions. This presentation describes results derived from a new approach to these problems. It is based on well-established biology involving physics not previously applied to the fields of mind, or consciousness studies, that of critical feedback instability. -/- Methods: 'self-organized criticality' in complexity biology places system loci of control at critical instabilities, physical properties of which, including information properties, are presented. Their elucidation shows that they can model hitherto unexplained properties of experience. -/- Results: All results depend on physical properties of critical instabilities. First, at least one feed-back or feed-forward loop must have feedback gain, g = 1: information flows round the loop impress perfect images of system states back on themselves: they represent processes of perfect self-observation. This annihilates system quanta: system excitations are instability fluctuations, which cannot be quantized. Major results follow: -/- 1. Information vectors representing criticality states must include at least one attached information loop denoting self-observation. -/- 2. Such loop structures are attributed a function, 'registering the state's own existence', explaining -/- a. Subjective 'awareness of one's own presence' -/- b. How content-free states of awareness can be remembered (Jon Shear) -/- c. Subjective experience of time duration (Immanuel Kant) -/- d. The 'witness' property of experience – often mentioned by athletes 'in the zone' -/- e. The natural association between consciousness and intelligence -/- This novel, physically and biologically sound approach seems to satisfactorily model subjectivity. -/- Further significant results follow: -/- 1. Registration of external information in excited states of systems at criticality reduces external wave-packets: the new model exhibits 'Objective Reduction' of wave packets. -/- 2. High internal coherence (postulated by Domash & Penrose) leading to a. Non-separable information vector bundles. b. Non-reductive states (Chalmers's criterion for experience). -/- 3. Information that is: a. encoded in coherence negentropy; b. non-digitizable, and therefore c. computationally without digital equivalent (posited by Penrose). -/- Discussion and Conclusions: instability physics implies anharmonic motion, preventing excitation quantization, and totally different from the quantum physics of simple harmonic motion at stability. Instability excitations are different from anything hitherto conceived in information science. They can model aspects of mind never previously treated, including genuine subjectivity, objective reduction of wave-packets, and inter alia all properties given above. (shrink)

There are two fundamentally distinct kinds of biological theorizing. "Formal biology" focuses on the relations, captured in formal laws, among mathematically abstracted properties of abstract objects. Population genetics and theoretical mathematical ecology, which are cases of formal biology, thus share methods and goals with theoretical physics. "Compositional biology," on the other hand, is concerned with articulating the concrete structure, mechanisms, and function, through developmental and evolutionary time, of material parts and wholes. Molecular genetics, biochemistry, developmental biology, and physiology, (...) which are examples of compositional biology, are in serious need of philosophical attention. For example, the very concept of a "part" is understudied in both philosophy of biology and philosophy of science. ;My dissertation is an attempt to clarify the distinction between formal biology and compositional biology and, in so doing, provide a clear philosophical analysis, with case studies, of compositional biology. Given the social, economic, and medical importance of compositional biology, understanding it is urgent. For my investigation, I draw on the philosophical fields of metaphysics and epistemology, as well as philosophy of biology and philosophy of science. I suggest new ways of thinking about some classic philosophy of science issues, such as modeling, laws of nature, abstraction, explanation, and confirmation. I hint at the relevance of my study of two kinds of biological theorizing to debates concerning the disunity of science. (shrink)

As a sort of intellectual provocation and as a lateral thinking strategy for creativity, this chapter seeks to determine what the study of the dynamics of biodiversity can offer linguists. In recent years, the analogical equation "language = biological species" has become more widespread as a metaphorical source for conceptual renovation, and, at the same time, as a justification for the defense of language diversity. Language diversity would be protected in a way similar to the mobilization that has (...) taken place to protect endangered species. Nevertheless, one must be careful when uncritically transferring conceptualizations and theoretical frameworks from one field to another, since obviously, these two phenomena are quite different in the real world. The dialogue with bioecologists starts by asking about the formation of diversity, i.e., about specialization. Here, one can observe the similarity between the processes of linguistic and genetic fragmentation, in the sense that both phenomena have a (socio)geographical basis for dispersion and consequently, for the loss of their original compact nature and their intercommunication. The self-organizing and creative properties of human beings favor the development of specific varieties for each subset, varieties that continue to evolve constantly, through the unceasing "languaging" of humanity. Regarding the continuity of species or languages, one can also observe the decisive role of intragroup relations. The staying power of linguistic varieties will increase in direct proportion to the intensity of the relationship among the components of the subset. On the other hand, if exotic elements are introduced, especially if these elements are aggressive in nature, the alteration of the ecological niche may turn out to be fatal for the continuity of the previously existing forms. This suggests to us the need to make an in-depth study of what the minimal contextual conditions would be so that a set linguistic group could be assured a sustainable continuity within a framework of linguistic contact. What type of minimum (socio-)ecological niche would a language have to have if we wished to ensure its habitual reproduction? A proposal is made here to explore the ideas of "exclusive functions" and "non-hierarchical functional distribution" for codes in situations where there is high contact and a danger of disuse. As regards change, this phenomenon is seen as an inherent element in the tendency of life to create new developments, which may or not be accompanied by an adaptation to changing environmental conditions. It is pointed out that, similar to what happens in biology, much of linguistic innovation stems from a systemically reorganized mixture of solutions from different codes. An important research question would be, however, to determine why some of these innovations disappear and others survive and extend throughout the community. The big question mark, as Mufwene points out, is, then how to manage to understand how "the evolution of language proceeds by naturally selecting from among the competing alternatives available through the idiolects of individual speakers". Extinction, whether it be of languages or of species, is caused in most cases "by a combination of demographic processes and environmental changes", as Brown points out. Thus, the environment plays a fundamental role in the direction of evolution, since the "the survival of the fittest is, in actuality, the survival of those who fit into the context (Allen and Hoekstra)". This allows us to see the great degree of importance of political-economic contexts in the case of languages. In the same way, migratory movements are also one of the major variables determining the extinction of biodiversity and language diversity. Species and habitat form the basic unit of existence, and this is the major point of departure for understanding the problem of the preservation and recovery of species or languages. Given the increase in the degree of linguistic contact, the continuity of language diversity depends on determining, as exactly as possible, as Prigogine, the physicist, would say, what precise conditions of imbalance may prove to be stable. The great challenge is not so much avoiding contact but managing it. And "restorative ecology" can also be of help to us here. Being able to reach sustainable solutions for language diversity implies a profound knowledge of the dynamics for determining the ways in which language is used in contact situations. The general conclusion is that linguistics is still terminologically and conceptually ill prepared to deal with the dynamic character of human languages. The world and our objects must be conceived of as elements in a state of flux, as changing systems in an unstable equilibrium. With respect to language policy, it would be necessary to make an effort to manage to establish some general principles regarding the linguistic organization of the human species that would make it possible for local linguistic diversity and communication on a planetary scale, which must necessarily take place, to be compatible with each other. To succeed, it will be necessary to continue promoting an autonomous socio-ecological perspective devoted to the comprehension of language phenomena. Such a perspective would be based on a paradigm of complexity, and would, at the same time, place human beings at the center of its theoretical underpinnings. (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)

Essentialism in philosophy is the position that things, especially kinds of things, have essences, or sets of properties, that all members of the kind must have, and the combination of which only members of the kind do, in fact, have. It is usually thought to derive from classical Greek philosophy and in particular from Aristotle’s notion of “what it is to be” something. In biology, it has been claimed that pre-evolutionary views of living kinds, or as they are sometimes called, (...) “natu-ral kinds”, are essentialist. This static view of living things presumes that no tran-sition is possible in time or form between kinds, and that variation is regarded as accidental or inessential noise rather than important information about taxa. In contrast it is held that Darwinian, and post-Darwinian, biology relies upon varia-tion as important and inevitable properties of taxa, and that taxa are not, therefore, kinds but historical individuals. Recent attempts have been made to undercut this account, and to reinstitute essentialism in biological kind terms. Others argue that essentialism has not ever been a historical reality in biology and its predecessors. In this chapter, I shall outline the many meanings of the notion of essentialism in psychology and social science as well as science, and discuss pro- and anti-essentialist views, and some recent historical revisionism. It turns out that nobody was essentialist to speak of in the sense that is antievolutionary in biology, and that much confusion rests on treating the one word, “essence” as meaning a single notion when in fact there are many. I shall also discuss the philosophical implica-tions of essentialism, and what that means one way or the other for evolutionary biology. Teaching about evolution relies upon narratives of change in the ways the living world is conceived by biologists. This is a core narrative issue. (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 mathematical constructions, physical structure and manifestations of physical time are reviewed. The nature of insight and mathematics used to understand and deal with physical time associated with classical, quantum and cosmic processes is contemplated together with a comprehensive understanding of classical time. Scalar time (explicit time or quantitative time), vector time (implicit time or qualitative time), biological time, time of and in conscious awareness are discussed. The mathematical (...) understanding of time in special and general theories of relativity is critically analyzed. The independent nature of classical, quantum and cosmic physical times from one another, and the manifestations of respective physical happenings, distinct from universal time, are highlighted. The role of a universal time related or unrelated to origin, being etc., of universe or cosmos as common thread in all happenings is reviewed. The missing of time is identified and concept of absence of time is put forward. The complex nature of time and the real and imaginary dimensions of physical time are also elaborately discussed together with human time- consciousness as past, present and future. (shrink)

Psychopaths appear to be ‘creatures apart’ – grandiose, shameless, callous and versatile in their violence. I discuss biological underpinnings to their pale affect, their selective inability to discern fear and sadness in others and a predatory orienting towards images that make most startle and look away. However, just because something is biologically underpinned does not mean that it is innate. I show that while there may be some genetic determination of fearlessness and callous-unemotionality, these and other features of the (...) personality may arise from developmental failures in the interpersonal reception of their emotions, needs and their sense of self. One is unlikely to be able to own inner experiences if shamed for having them, or if, having them, one does not know how to regulate and soothe. So psychopaths may learn to attend away and suppress them. Rather than a fully inherited difficulty, they may have become unable to reflect on inner states, so meta-emotions and self-reflective emotions like guilt and shame do not fully arise. They retain enough sensitivity to know their difference, and hide. I suggest that psychopaths are characterised by a nested sense of self, arising from the surprising effect of shame on these seemingly shameless characters. They do not have an integrated sense of self across context or across time or in relation to a generalised social other. With a nested sense of self, diminished intensity and scope of affective experience (in both directly experienced and vicarious forms) they lack textured access to a personal, owned and integrated past. Thus they lack the kind of access to the past required for a motivationally compelling planning of the future. They lack the emotional investment in the future that enables us to overcome the motivation to act opportunistically and myopically. These individuals live strangely in time. They have a fugitive sense of self and live nimbly among many pasts. They present an elegant and coherent mask to the person they are addressing in the moment and generate possible futures without conviction. (shrink)

The mathematical constructions, physical structure and manifestations of physical time are reviewed. The nature of insight and mathematics used to understand and deal with physical time associated with classical, quantum and cosmic processes is contemplated together with a comprehensive understanding of classical time. Scalar time (explicit time or quantitative time), vector time (implicit time or qualitative time), biological time, time of and in conscious awareness are discussed. The mathematical (...) understanding of time in special and general theories of relativity is critically analyzed. The independent nature of classical, quantum and cosmic physical times from one another, and the manifestations of respective physical happenings, distinct from universal time, are highlighted. The role of a universal time related or unrelated to origin, being etc., of universe or cosmos as common thread in all happenings is reviewed. The missing of time is identified and concept of absence of time is put forward. The complex nature of time and the real and imaginary dimensions of physical time are also elaborately discussed together with human time- consciousness as past, present and future. (shrink)

The nature and structure of time and time-intervals in physical, chemical and biological systems will be elucidated. The relation and dependence among time, energy and taking place of natural processes will be critically analyzed. The bio-processes taking place in nano-time intervals will be identified. Their relevance to nano-bio-science and nano-bio-technology will be developed and nano-time interval-aspect of nano-sciences and nano-technology will be advanced. -/- .

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

It is argued that at a sufficiently deep level the conventional quantitative approach to the study of nature faces difficult problems, and that biological processes should be seen as more fundamental, in a way that can be elaborated on the basis of Peircean semiotics and Yardley's Circular Theory. In such a world-view, Wheeler's observer-participation and emergent law arise naturally, rather than having to be imposed artificially. This points the way to a deeper understanding of nature, where meaning has a (...) fundamental role to play that is invisible to quantitative science. (shrink)

We argue that C. Darwin and more recently W. Hennig worked at times under the simplifying assumption of an eternal biosphere. So motivated, we explicitly consider the consequences which follow mathematically from this assumption, and the infinite graphs it leads to. This assumption admits certain clusters of organisms which have some ideal theoretical properties of species, shining some light onto the species problem. We prove a dualization of a law of T.A. Knight and C. Darwin, and sketch a decomposition result (...) involving the internodons of D. Kornet, J. Metz and H. Schellinx. A further goal of this paper is to respond to B. Sturmfels’ question, “Can biology lead to new theorems?”. (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. (shrink)

Some investigators of the rubber hand illusion (RHI) have suggested that when standard RHI induction procedures are employed, if the rubber hand is experienced by participants as owned, their corresponding biological hands are experienced as disowned. Others have demurred: drawing upon a variety of experimental data and conceptual considerations, they infer that experience of the RHI might include the experience of a supernumerary limb, but that experienced disownership of biological hands does not occur. Indeed, some investigators even categorically (...) deny that any experimental paradigm has been employed or any evidence can be adduced to support the claim that disownership experiences occur during the RHI. It goes without saying that RHI experiences can be elusive, and that there is some evidence to support claims that supernumerary limb experiences can sometimes occur. Here, however, we test the claim that the conscious experience of disownership can occur during the RHI. In order to test this claim, we developed two new online proxies—onset time for the illusion and illusion duration—and combined these with established questionnaires that concern the conscious contents of the RHI, in particular ownership/disownership experiences. Both online proxy data and post hoc questionnaire data converge in supporting the claim that disownership experiences do occur, at least when the left hand is the object of investigation. Our findings that onset time and illusion duration are reliable measures suggest that investigations of the RHI stand to benefit by devoting more attention to data collected while the RHI is being experienced, in particular data concerning temporal dynamics. (shrink)

Advances in biology, at least over the past two centuries, have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. The field of theoretical biology used to primarily provide a basis, similar to theoretical physics in the physical sciences, to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical (...) biology. This could in part be explained by a relatively recent tendency in which a "data first", rather than a "theory first", approach is preferred. Moreover, generating hypotheses has at times become procedural rather than theoretical, therefore perhaps inadvertently leading some hypotheses to become perfunctory in nature. This situation leaves our understanding enmeshed in data, which should be disentangled from much noise. Given the many unresolved questions in biology and medicine, big and small, ranging from the problem of protein folding to unifying causative frameworks of complex non-Mendelian human diseases, it seems apt to revive the role of pure theory in the biological sciences. This paper, using the current biomedical literature and historical precedents, makes the case for a "philosophical biology" (philbiology), distinct from but quite complementary to philosophy of biology (philobiology), which would entail biological investigation through philosophical approaches. Philbiology would thus be a reincarnation of theoretical biology, adopting the true sense of the word "theory" and making use of a rich tradition of serious philosophical approaches in the natural sciences. A philbiological investigation, after clearly defining a given biological problem, would aim to propose a set of empirical questions, along with a class of possible solutions, about that problem. Importantly, whether or not the questions can be tested using current experimental paradigms would be secondary to whether the questions are inherently empirical or not. These issues will be illustrated using a range of specific examples. The final goal of a philbiological investigation would be to develop a theoretical framework that can lead observational and/or interventional experimental studies of the defined problem, a framework that is structured, generative and expandable, and, crucially, one that simplifies some aspect(s) of the said problem. (shrink)

Throughout the ages, people of all creeds, backgrounds, and cultures have dedicated their lives to search for a higher reality where the visionary experience of Cosmic Consciousness brought about through mystical union, is part of an inner process which may lead to enlightenment. Traditions in India hold that this urge to find the truth involves awakening kundalini energy. In its dormant state, this serpent energy is said to lie coiled up at the base of the spine. In search of a (...) biological basis of the religious impulse, we look at early embryonic human development, which is seen as being guided by higher cosmic forces. On approximately day 30-33, the human embryo begins to grow a tail, which then disappears. The corresponding development of the heart during this phase resembles that of reptiles. Linking the time lapse between the formation and absorption of the tail with an increase in voltage between the tail and the head suggests that on intake, the increase in charge could result in the potential at the base of the spine where it lies dormant until used either for procreation or reverse itself up to join the cosmic source from which it originated. To further our understanding of kundalini energy and its connection to light, we also consider these terms from various perspectives, including quantum physics. (shrink)

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

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

Walter M. Miller, Jr.’s 1959 novel A Canticle for Leibowitz is on one level a theological reflection on the human propensity to sin. Not coincidentally, the story is located in an Albertinian abbey in the former American southwest six hundred years after a nuclear holocaust, recounting three separate historical periods over the following twelve hundred years: a dark age, a scientific renaissance, and finally a time of technological achievement where a second nuclear holocaust is imminent. Miller asks the question (...) of whether humans as a species cannot avoid committing acts of sin that cumulatively and continually lead to acts of societal and technological self-destruction; his response oscillates between a fatalistic pessimism (the final extinction of the human species) and a vague optimism (the “new creature,” the mutant Rachel, or perhaps a last group of humans leaving the Earth as the curtain falls). It is my thesis in this article that theological questions about sin (as explored by Augustine and later scholars) can be fruitfully approached by analogous genetic processes; more precisely by reference to the rising science of Epigenetics, which explores how genes can express themselves differently without mutating in response to life stressors. In light of the idea of a genetic and epigenetic expression of moral rules of existence, Augustine’s thesis of original sin as something that is inherited makes new sense. In this light, it may also be possible to approach the question that the Canticle proposes: are we destined to self-destruction, or is there a way out of this destructive cycle? (shrink)

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

Ernst Mayr argued that the emergence of biology as a special science in the early nineteenth century was possible due to the demise of the mathematical model of science and its insistence on demonstrative knowledge. More recently, John Zammito has claimed that the rise of biology as a special science was due to a distinctive experimental, anti-metaphysical, anti-mathematical, and anti-rationalist strand of thought coming from outside of Germany. In this paper we argue that this narrative neglects the important role played (...) by the mathematical and axiomatic model of science in the emergence of biology as a special science. We show that several major actors involved in the emergence of biology as a science in Germany were working with an axiomatic conception of science that goes back at least to Aristotle and was popular in mid-eighteenth-century German academic circles due to its endorsement by Christian Wolff. More specifically, we show that at least two major contributors to the emergence of biology in Germany—Caspar Friedrich Wolff and Gottfried Reinhold Treviranus—sought to provide a conception of the new science of life that satisfies the criteria of a traditional axiomatic ideal of science. Both C.F. Wolff and Treviranus took over strong commitments to the axiomatic model of science from major philosophers of their time, Christian Wolff and Friedrich Wilhelm Joseph Schelling, respectively. The ideal of biology as an axiomatic science with specific biological fundamental concepts and principles thus played a role in the emergence of biology as a special science. (shrink)

The study of organisms within the range of their existence from fertilization to birth is referred to as embryology. The process of progressive change during that period is called development. That development does not stop at birth but continues on throughout the entire life-span of the organism as the process of growth and decay — catabolism, anabolism, and metabolism. The study of this entire range of life has recently become known as developmental biology. The belief that the development from an (...) initial stage of a fertilized egg or zygote to a fully formed adult represents, in compressed time, the whole process of evolution that occurred over millions of years, has recently been named evo-devo, or evolutionary development. The more science advances, the more it studies Nature in its intimate details, the more it comes to realize the existence of a pervasive reason, an inherent natural intelligence that is working in even the most insignificant portions of the universe. Francis Bacon (1561–1626) said, “A little philosophy (science) inclineth man's mind to atheism, but depth in philosophy (science) bringeth men's minds about to religion.” This point is especially true today. It is not from ignorance that men come to have faith in God, but from a maturity of reason and experience. Vedanta philosophy teaches that there is a conscious intelligence that underlies all experienced existence. Being self-evident, this should hardly have to be argued. Yet modern science has failed to integrate this truth into its materialist/naturalistic paradigm. Correcting this deficiency will be the challenge of 21st century science, and the highest reward for humanity. (shrink)

In this paper I argue that it is finally time to move beyond the Nagelian framework and to break new ground in thinking about epistemic reduction in biology. I will do so, not by simply repeating all the old objections that have been raised against Ernest Nagel’s classical model of theory reduction. Rather, I grant that a proponent of Nagel’s approach can handle several of these problems but that, nevertheless, Nagel’s general way of thinking about epistemic reduction in terms (...) of theories and their logical relations is entirely inadequate with respect to what is going on in actual biological research practice. (shrink)

The term “Complex Systems Biology” was introduced a few years ago [Kaneko, 2006] and, although not yet of widespread use, it seems particularly well suited to indicate an approach to biology which is well rooted in complex systems science. Although broad generalizations are always dangerous, it is safe to state that mainstream biology has been largely dominated by a gene-centric view in the last decades, due to the success of molecular biology. So the one gene - one trait approch, which (...) has often proved to be effective, has been extended to cover even complex traits. This simplifying view has been appropriately criticized, and the movement called systems biology has taken off. Systems biology [Noble, 2006] emphasizes the presence of several feedback loops in biological systems, which severely limit the range of validity of explanations based upon linear causal chains (e.g. gene → behaviour). Mathematical modelling is one the favourite tools of systems biologists to analyze the possible effects of competing negative and positive feedback loops which can be observed at several levels (from molecules to organelles, cells, tissues, organs, organisms, ecosystems). Systems biology is by now a well-established field, as it can be inferred by the rapid growth in number of conferences and journals devoted to it, as well as by the existence of several grants and funded projects.Systems biology is mainly focused upon the description of specific biological items, like for example specific organisms, or specific organs in a class of animals, or specific genetic-metabolic circuits. It therefore leaves open the issue of the search for general principles of biological organization, which apply to all living beings or to at least to broad classes. We know indeed that there are some principles of this kind, biological evolution being the most famous one. The theory of cellular organization also qualifies as a general principle. But the main focus of biological research has been that of studying specific cases, with some reluctance to accept (and perhaps a limited interest for) broad generalizations. This may however change, and this is indeed the challenge of complex systems biology: looking for general principles in biological systems, in the spirit of complex systems science which searches for similar features and behaviours in various kinds of systems. The hope to find such general principles appears well founded, and I will show in Section 2 that there are indeed data which provide support to this claim. Besides data, there are also general ideas and models concerning the way in which biological systems work. The strategy, in this case, is that of introducing simplified models of biological organisms or processes, and to look for their generic properties: this term, borrowed from statistical physics, is used for those properties which are shared by a wide class of systems. In order to model these properties, the most effective approach has been so far that of using ensembles of systems, where each member can be different from another one, and to look for those properties which are widespread. This approach was introduced many years ago [Kauffman, 1971] in modelling gene regulatory networks. At that time one had very few information about the way in which the expression of a given gene affects that of other genes, apart from the fact that this influence is real and can be studied in few selected cases (like e.g. the lactose metabolism in E. coli). Today, after many years of triumphs of molecular biology, much more has been discovered, however the possibility of describing a complete map of gene-gene interactions in a moderately complex organism is still out of reach. Therefore the goal of fully describing a network of interacting genes in a real organism could not be (and still cannot be) achieved. But a different approach has proven very fruitful, that of asking what are the typical properties of such a set of interacting genes. Making some plausible hypotheses and introducing some simplifying assumptions, Kauffman was able to address some important problems. In particular, he drew attention to the fact that a dynamical system of interacting genes displays selforganizing properties which explain some key aspects of life, most notably the existence of a limited number of cellular types in every multicellular organism (these numbers are of the order of a few hundreds, while the number of theoretically possible types, absent interactions, would be much much larger than the number of protons in the universe). In section 3 I will describe the ensemble based approach in the context of gene regulatory networks, and I will show that it can describe some important experimental data. Finally, in section 4 I will discuss some methodological aspects. (shrink)

Biological individuality is without a doubt a key concept in philosophy of biology. Questions around the individuality of organisms, species, and biological systems can be traced throughout the philosophy of biology since the discipline’s inception, not to mention the sustained attention they have received in biology and philosophy more broadly. It’s high time the topic got its own Cambridge Element. McConwell’s Biological Individuality falls short of an authoritative overview of the debate on biological individuality. However, (...) it sends a welcome message to new and seasoned scholars to reorient the debate towards practically and politically relevant themes. (shrink)

Pierre-Henri Castel provides a short but richly argued precis of his recently published two-volume 1,000-page masterwork on the history of obsessive-compulsive disorder. Having not read the as-yet-untranslated books, I write this commentary from Plato’s cave, trying to infer the reality of Castel’s analysis from expository shadows. I am unlikely to be more successful than Plato’s poor troglodytes, so I apologize ahead of time for any misunderstandings. Moreover, I cannot assess Castel’s detailed evidential case for his substantive theses.1 I thus (...) focus on some key philosophical issues that impinge on an area of my concern, the concept of mental disorder. Castel is a rare breed of French.. (shrink)

Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed studies (...) of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. (shrink)

Neurological syndromes in which consciousness seems to malfunction, such as temporal lobe epilepsy, visual scotomas, Charles Bonnet syndrome, and synesthesia offer valuable clues about the normal functions of consciousness and ‘qualia’. An investigation into these syndromes reveals, we argue, that qualia are different from other brain states in that they possess three functional characteristics, which we state in the form of ‘three laws of qualia’. First, they are irrevocable: I cannot simply decide to start seeing the sunset as green, or (...) feel pain as if it were an itch; second, qualia do not always produce the same behaviour: given a set of qualia, we can choose from a potentially infinite set of possible behaviours to execute; and third, qualia endure in short-term memory, as opposed to non-conscious brain states involved in the on-line guidance of behaviour in real time. We suggest that qualia have evolved these and other attributes because of their role in facilitating non-automatic, decision-based action. We also suggest that the apparent epistemic barrier to knowing what qualia another person is experiencing can be overcome by using a ‘bridge’ of neurons; and we offer a hypothesis about the relation between qualia and one's sense of self. (shrink)

In 2012, the Geological Time Scale, which sets the temporal framework for studying the timing and tempo of all major geological, biological, and climatic events in Earth’s history, had one-quarter of its boundaries moved in a widespread revision of radiometric dates. The philosophy of metrology helps us understand this episode, and it, in turn, elucidates the notions of calibration, coherence, and consilience. I argue that coherence testing is a distinct activity preceding calibration and consilience, and I highlight the (...) value of discordant evidence and trade-offs scientists face in calibration. The iterative nature of calibration, moreover, raises the problem of legacy data. (shrink)

Norbert Wiener’s idea of “cybernetics” is linked to temporality as in a physical as in a philosophical sense. “Time orders” can be the slogan of that natural cybernetics of time: time orders by itself in its “screen” in virtue of being a well-ordering valid until the present moment and dividing any totality into two parts: the well-ordered of the past and the yet unordered of the future therefore sharing the common boundary of the present between them when (...) the ordering is taking place by choices. Thus, the quantity of information defined by units of choices, whether bits or qubits, describes that process of ordering happening in the present moment. The totality (which can be considered also as a particular or “regional” totality) turns out to be divided into two parts: the internality of the past and the externality of the future by the course of time, but identifiable to each other in virtue of scientific transcendentalism (e.g. mathematical, physical, and historical transcendentalism). A properly mathematical approach to the “totality and time” is introduced by the abstract concept of “evolutionary tree” (i.e. regardless of the specific nature of that to which refers: such as biological evolution, Feynman trajectories, social and historical development, etc.), Then, the other half of the future can be represented as a deformed mirror image of the evolutionary tree taken place already in the past: therefore the past and future part are seen to be unifiable as a mirrorly doubled evolutionary tree and thus representable as generalized Feynman trajectories. The formalism of the separable complex Hilbert space (respectively, the qubit Hilbert space) applied and further elaborated in quantum mechanics in order to uniform temporal and reversible, discrete and continuous processes is relevant. Then, the past and future parts of evolutionary tree would constitute a wave function (or even only a single qubit once the concept of actual infinity be involved to real processes). Each of both parts of it, i.e. either the future evolutionary tree or its deformed mirror image, would represented a “half of the whole”. The two halves can be considered as the two disjunctive states of any bit as two fundamentally inseparable (in virtue of quantum correlation) “halves” of any qubit. A few important corollaries exemplify that natural cybernetics of time. (shrink)

The physical singularity of life phenomena is analyzed by means of comparison with the driving concepts of theories of the inert. We outline conceptual analogies, transferals of methodologies and theoretical instruments between physics and biology, in addition to indicating significant differences and sometimes logical dualities. In order to make biological phenomenalities intelligible, we introduce theoretical extensions to certain physical theories. In this synthetic paper, we summarize and propose a unified conceptual framework for the main conclusions drawn from work spanning (...) a book and several articles, quoted throughout. (shrink)

This paper provides an answer to the question why birth parents have a moral right to keep and raise their biological babies. I start with a critical discussion of the parent-centred model of justifying parents’ rights, recently proposed by Harry Brighouse and Adam Swift. Their account successfully defends a fundamental moral right to parent in general but, because it does not provide an account of how individuals acquire the right to parent a particular baby, it is insufficient for addressing (...) the question whether and why there is a right to parent one’s biological child. Such a right is important because, in its absence, fairness towards adequate prospective parents who are involuntarily childless would demand a ‘babies redistribution’; moreover, in societies with entrenched histories of injustice there may be reasons of fairness for shuffling babies amongst all recent parents. I supplement the Brighouse-Swift account of fundamental parental rights by an account of how adequate parents acquire the right to parent their biological babies. I advance two arguments to this conclusion: by the time of birth, the birth parents will have already shouldered various burdens in order to bring children into existence, and are likely to have formed an intimate relationship with the future baby. Denying birth parents who would make at least adequate parents the right to keep their baby would be unfair to them and would destroy already formed parent-baby relationships which, I assume, are intrinsically valuable. (shrink)

Historical explanations in evolutionary biology are commonly characterized as narrative explanations. Examples include explanations of the evolution of particular traits and explanations of macroevolutionary transitions. In this paper I present two case studies of explanations in accounts of pathogen evolution and host-pathogen coevolution, respectively, and argue that one of them is captured well by established accounts of time-sequenced narrative explanation. The other one differs from narrative explanations in important respects, even though it shares some characteristics with them as it (...) is also a population-level historical explanation. I thus argue that the second case represents a different kind of explanation that I call historical explanation of type phenomena. The main difference between the two kinds of explanation is the conceptualization of the explanandum phenomena as particulars or type phenomena, respectively. Narrative explanations explain particulars but also deal with generalization, regularities and type phenomena. Historical explanations of type phenomena, on the other hand, explain multiply realizable phenomena but also deal with particulars. The two kinds of explanation complement each other because they explain different aspects of evolution. (shrink)

Multicellular organisms contain numerous symbiotic microorganisms, collectively called microbiomes. Recently, microbiomic research has shown that these microorganisms are responsible for the proper functioning of many of the systems of multicellular organisms. This has inclined some scholars to argue that it is about time to reconceptualise the organism and to develop a concept that would place the greatest emphasis on the vital role of microorganisms in the life of plants and animals. We believe that, unfortunately, there is a problem with (...) this suggestion, since there is no such thing as a universal concept of the organism which could constitute a basis for all biological sciences. Rather, the opposite is true: numerous alternative definitions exist. Therefore, comprehending how microbiomics is changing our understanding of organisms may be a very complex matter. In this paper we will demonstrate that this pluralism proves that claims about a change in our understanding of organisms can be treated as both true and untrue. Mainly, we assert that the existing concepts differ substantially, and that only some of them have to be reconsidered in order to incorporate the discoveries of microbiomics, while others are already flexible enough to do so. Taking into account the plurality of conceptualisations within different branches of modern biology, we will conduct our discussion using the developmental and the cooperation–conflict concepts of the organism. Then we will explain our results by referring to the recent philosophical debate on the nature of the concept of the organism within biology. (shrink)

The idea behind this special theme journal issue was to continue the work we have started with the INBIOSA initiative (www.inbiosa.eu) and our small inter-disciplinary scientific community. The result of this EU funded project was a white paper (Simeonov et al., 2012a) defining a new direction for future research in theoretical biology we called Integral Biomathics and a volume (Simeonov et al., 2012b) with contributions from two workshops and our first international conference in this field in 2011. The initial impulse (...) for this effort was given a year earlier by a publication of one of the guest editors of this issue (Simeonov, 2010) in this journal. This time we wish to provide a broader forum and more space to elaborate in detail some of the most interesting concepts we have encountered in our discussions, as well as to invite some new contributions of particular interest in the field. Another goal we had in mind was to collect and review as many provocative perspectives as possible on the same key topic we are interested before making a decision to follow a more focused notion that would lead to a funded research program. Therefore we welcomed the generous suggestion of Professor Denis Noble, FRS, who is also editor of this journal to prepare a special theme issue entitled: “Can biology create a profoundly new mathematics and computation?” It has taken a while to invite and collect the contributions. Most of them had a couple of revision cycles and adjustments after having been thoroughly discussed with colleagues, incl. the editors of this issue. We think that the result we have obtained at the end is a satisfactory one, since we succeeded to integrate a diversity of original, but sometimes controversial and mutually excluding concepts organized within chapters of a self-contained volume. The task of compiling all this was not easy at all. Despite our efforts to position the articles of different authors and themes in a way allowing their easy comprehension and relation to each other within the individual chapters, some of them still require a sort of introduction to dissolve possible ambiguities. This is what we are going to do in the following few paragraphs with the hope that the reader (and some of the authors) would excuse our failures. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented (...) and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

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

Modes of teaching and learning have had to rapidly shift amid the COVID-19 pandemic. As an emergency response, students from Philippine public schools were provided learning modules based on a minimized list of essential learning competencies in Biology. Using a cross-sectional survey method, we investigated students’ perceptions of the Biology self-learning modules (BSLM) that were designed in print and digitized formats according to a constructivist learning approach. Senior high school STEM students from grades 11 (n = 117) and 12 (n (...) = 104) participated in a survey using a 3-point Likert-scale questionnaire uploaded online through Google Forms. The survey results indicate that majority of the students perceived the modules positively, suggesting that aspects of the modules that were salient to students corresponded to essential elements of constructivist pedagogies. However, during interviews, students reported several difficulties in learning with BSLM as it was constrained by, to name a few, the use of unfamiliar words, lack of access to supporting resources, slow internet connection, and time constraints. To address these problems, teachers reported that they gave deadline extensions, complemented modules with other channels of support, and used online and offline platforms for reaching out to students to answer their queries and plan out their schedule for the week. The findings across the data sources point to the complex demands of emergency distance education that teachers, as curriculum designers and enactors, need to bear in mind in order to craft productive pedagogies, constructivist or otherwise, during this unprecedented time. (shrink)

Among the many causes of an event, how do we distinguish the important ones? Are there ways to distinguish among causes on principled grounds that integrate both practical aims and objective knowledge? Psychologist Tania Lombrozo has suggested that causal explanations “identify factors that are ‘exportable’ in the sense that they are likely to subserve future prediction and intervention” (Lombrozo 2010, 327). Hence portable causes are more important precisely because they provide objective information to prediction and intervention as practical aims. However, (...) I argue that this is only part of the epistemology of causal selection. Recent work on portable causes has implicitly assumed them to be portable within the same causal system at a later time. As a result, it has appeared that the objective content of causal selection includes only facts about the causal structure of that single system. In contrast, I present a case study from systems biology in which scientists are searching for causal factors that are portable across rather than within causal systems. By paying careful attention to how these biologists find portable causes, I show that the objective content of causal selection can extend beyond the immediate systems of interest. In particular, knowledge of the evolutionary history of gene networks is necessary for correctly identifying causal patterns in these networks that explain cellular behavior in a portable way. (shrink)

This paper does two things. First, it interprets the work of W. E. B. Du Bois to reveal that the meanings of race terms are grounded by both a historical and an aspirational component. Race terms refer to a backward-looking component that traces the history of the group to its present time, as well as a forward-looking component that sets out values and goals for the group. Race terms thus refer to a complex cluster of concepts that involve (...) class='Hi'>biological, sociological, historical, moral, and political properties. Second, the paper defends W. E. B. Du Bois’s conservationist thesis about races, which holds that we should maintain race talk and racial distinctions. But instead of offering philosophical evidence, this paper defends the plausibility of the conservationist thesis with evidence from contemporary biology and psychology. It argues that, instead of eliminating race terms or concepts, we should conserve and revise them. (shrink)