This chapter introduces the main research schools and paradigms along which the field of evolutionary biology has been developing. Evolutionary thinking was originally founded upon the Neo-Darwinian paradigm that combines the teachings of traditional Darwinism with those of the Modern Synthesis. The Neo-Darwinian paradigm has since further diversified into the Micro-, Meso-, and Macroevolutionary schools, and it has also started to integrate the school of Ecology. Together, these schools establish the paradigm called Ecological Evolutionary Developmental Biology (Eco-Evo-Devo). A (...) final school studies Reticulate Evolution as it occurs by means of symbiosis, symbiogenesis, lateral gene transfer, infective heredity, and hybridization. This chapter reviews the major tenets and points of differentiation that exist between these distinct evolution schools. The chapter ends by looking into how evolution can be defined and how distinct units, levels, and mechanisms underlie theorizing on evolutionary hierarchies and evolutionary causation. The following chapter examines how the different evolution schools are implemented into the symbolic sciences. (shrink)

1900 was a remarkable year for science. Several ground-breaking events took place, in physics, biology and psychology. Planck introduced the quantum concept, the work of Mendel was rediscovered, and Sigmund Freud published The Interpretation of Dreams . These events heralded the emergence of completely new areas of inquiry, all of which greatly affected the intellectual landscape of the 20 th century, namely quantum physics, genetics and psychoanalysis. What do these developments have in common? Can we discern a family likeness, (...) a basic affinity between them, so that we can use the one to deepen our understanding of the other? One common denominator is that they open up realms of inquiry that are significantly different from the world of everyday experience, namely the realm of elementary particles, of genes and genomes, and of the unconscious. But to what extent can we meaningfully argue, for instance, that the genome is the biological unconscious, and the unconscious the psychic genome? To address these questions, I will build on the work of two key intellectual figures who have explored the affinities of these developments in depth, namely Erwin Schrödinger (a quantum physicist and avid reader of Schopenhauer who initiated molecular biology) and Jacques Lacan (who reframed the specificity of psychoanalysis with the help of 20 th century science: the era of structural linguistics, but also of quantum physics, molecular biology, bioinformatics and DNA). (shrink)

The paper examines the relationship between the biological and the social in morals. Its conclusion is that the biological is one among other sources of moarls. The social developed as another, much more dynamic source. An important role is played by free will or the moral freedom, especially on the individual morals level. It is the consequences, and especially social consequences, that in the author's viewpoint to the actual state of social and individual morals.

I develop a distinction between two types of psychological hedonism. Inferential hedonism (or “I-hedonism”) holds that each person only has ultimate desires regarding his or her own hedonic states (pleasure and pain). Reinforcement hedonism (or “R–hedonism”) holds that each person's ultimate desires, whatever their contents are, are differentially reinforced in that person’s cognitive system only by virtue of their association with hedonic states. I’ll argue that accepting R-hedonism and rejecting I-hedonism provides a conciliatory position on the traditional altruism debate, and (...) that it coheres well with the neuroscientist Anthony Dickinson’s theory about the evolutionary function of hedonic states, the “hedonic interface theory.” Finally, I’ll defend R-hedonism from potential objections. (shrink)

We defend a realistic attitude towards biological species. We argue that two species are not different species because they differ in intrinsic features, be they phenotypic or genomic, but because they are separated with regard to gene flow. There are no intrinsic species essences. However, there are relational ones. We argue that bearing a gene flow relation to conspecifics may serve as the essence of a species. Our view of the species as a Gene-Flow Community differs from Mayr’s definition of (...) the species as a reproductive community. In a reproductive community, each organism is able to successfully reproduce with each other. However, there are species in which geographically distant organisms lost their ability to successfully reproduce, due to strong genetic adaptations to the respective local environmental conditions. Despite this loss of the ability to mutually reproduce, they are still bound by gene flow via continuous intermediate populations. This replacement of Mayr’s notion of an interbreeding potential as a criterion for species membership has important implications for the treatment of populations in allopatry and sympatry. (shrink)

The mathematical universe hypothesis is a theory that the physical universe is not merely described by mathematics, but is mathematics, specifically a mathematical structure. Our research provides evidence that the mathematical structure of the universe is biological in nature and all systems, processes, and objects within the universe function in harmony with biological patterns. Living organisms are the result of the universe’s biological pattern and are embedded within their physiology the patterns of this biological universe. Therefore physiological patterns in living (...) organisms can be used as models to structurally map analogies from the biological domain to any target domain to reveal and understand the biological nature of the target domain. Our paper explores various analogies, structurally mapping a red blood cell to a cup; proteins produced from ribosomes to music produced from instruments; a beating heart to the melting and freezing of Antartica; cells, tissue, organs and blood, to people, organizations, industries, and money, and; bio-economic concepts in cellular society to socioeconomic concepts in human society. It also discusses how phenomena in cellular mitosis can help explain phenomena in the universe, such as black holes, dark matter, dark energy, and the structure of the universe. Building upon the concept of perennial wisdom, our research has provided evidence that the ideas of a biological universe were expressed across many past cultures and historical periods. The implications of this theory are vast, encompassing fields such as physics, science, philosophy, religion, law, economics, politics, and engineering, thus serving as a unifying theory for all knowledge. Our theory is supported by meta-analysis of scientific, historic, and religious literature, observations and first principles logic. (shrink)

This essay explains Donald Hoffman's Interface Theory of Perception using The Biological Framework for a Mathematical Universe proposed by Ronald Williams. According to Hoffman, what we perceive is more like a “desktop interface with icons representing complex underlying processes, rather than a direct window into the true nature of the world." The theory of a biological framework for a mathematical universes suggests that these complex underlying processes of “the desktop interface with icons” contain correspondences to biological systems. For example, “the (...) desktop icons” of the ocean’s arctic currents and the melting and freezing of Antartica contain “complex underlying processes” which mirror the processes of a circulatory system and beating heart. While indeed we do interpret reality from a superficial perspective as Hoffman suggests, our cognitive abilities are enhanced enough to recognize correspondences to these patterns pertaining to these biological systems which reveal the true nature of the world/universe/reality and thus highlight our evolved perceptual systems which can enable us how to recognize these patterns and organize ourselves to them in order to best survive it. Another example of a “desktop icon” is human society—the order and properties of human society contain “complex underlying processes” that are analogous to the order and properties of cellular society—thus “socioeconomic problems” can be understood through cellular economic problems. Moreover, the solution to the cellular economic problem is the solution to the socioeconomic problem. (shrink)

Acknowledging that Nature is one unified whole, we expect that physics and biology are intimately related. Keeping in mind that physics became an exact science with which we are already familiar with, while, apparently, we do not have at present a similar knowledge about biology, we consider how can we make useful the clarity of physics to shed light to biology. The next question will be what are the most basic categories of physics and biology. If (...) we do not want to cut laws of Nature into different parts, we obtain a constraint, and the remaining part of physics will be the input data to the equations of physics. In these terms, our question will be: if we keep biological laws intact, as indivisible units, what remains in case of biology? This approach, just because it is more fundamental, has significant consequences for philosophy, and obviously offers a new conceptual framework considering the relation between the ontopoietic principle of Anna-Teresa Tymieniecka and the biological principle. The quintessence of science, namely, the first essentially complete scientific world picture is presented in a detailed form. (shrink)

How the visual systems of different species enable them to detect and discriminate colour patterns and how such visual abilities contribute to their survival is discussed. The influence of evolutionary and environmental pressures on both perceptual capacity and colour trait production is to be considered. Visual systems with different functional anatomy have evolved in response to such pressures.

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)

Searle offers an account of seeing as a conscious state not constituted by the object(s) seen. I focus in this article on his biological case for this thesis, and argue that the biological considerations he adduces neither establish his own position nor defeat a rival object-inclusive view. I show (among other things) that taking seeing to be a biological state is compatible with its being (partially) constituted by the object(s) seen.

The traditional emphasis on the physics of the very small is questioned, and the suggestion made that a crucial test of contributions to the philosophy of science ought to be their applicability to areas which are more representative of the scientific enterprise. Life science is cited as just such an area. It is quantum physics, rather than biology, which nurtures anti-realism. The most respected anti-realism today is that provided by Bas C van Fraassen; and the persuasiveness of his "Constructive (...) Empiricism" is attested to by the failure of avowed realists, such as Ian Hacking, to distance themselves very far from van Fraassen's ideas. A detailed critique of van Fraassen is presented with particular attention paid to his ideas on scientific explanation - the question of whether good explanations are true explanations being one which tends to divide realist and anti-realist. The conclusion is reached that, while realism raises - and fails to answer - a number of philosophical questions, the anti-realism provided by Bas van Fraassen is no better at answering those questions. Moreover, it is argued, van Fraassen's ideas lack plausibility as a description of science and the attitudes of scientists - particularly when attention is shifted from physics to biology. Finally, a number of suggestions are made as to how the philosophical questions posed by realism might be answered in the future. (shrink)

We introduce here evoText, a new tool for automated analysis of the literature in the biological sciences. evoText contains a database of hundreds of thousands of journal articles and an array of analysis tools for generating quantitative data on the nature and history of life science, especially ecology and evolutionary biology. This article describes the features of evoText, presents a variety of examples of the kinds of analyses that evoText can run, and offers a brief tutorial describing how to (...) use it. (shrink)

The aim of this paper is to show that for Kant, a combination of epigenesis and monogenesis is the condition of possibility of anthropology as he conceives of it and that moreover, this has crucial implications for the biological dimension of his account of human nature. More precisely, I begin by arguing that Kant’s conception of mankind as a natural species is based on two premises: firstly the biological unity of the human species (monogenesis of the human races); and secondly (...) the existence of ‘seeds’ which may or may not develop depending on the environment (epigenesis of human natural predispositions). I then turn to Kant’s account of man’s natural predispositions and show that far from being limited to the issue of races, it encompasses unexpected human features such as gender, temperaments and nations. These predispositions, I argue, are means to the realisation of Nature’s overall purpose for the human species. This allows me to conclude that man’s biological determinism leads to the species’ preservation, cultivation and civilisation. (shrink)

Robert Henman’s article, Can brain scanning and imaging techniques contribute to a theory of thinking? came to my attention recently. My own work over the years has included applications of mathematics in the biological sciences, collaboration in experimental work in biochemistry, as well as work in the philosophy of the biological sciences. Henman suggests something that, at present, would be out of the ordinary.

What are the conditions under which one biological object is a part of another biological object? This paper answers this question by developing a general, systematic account of biological parthood. I specify two criteria for biological parthood. Substantial Spatial Inclusionrequires biological parts to be spatially located inside or in the region that the natural boundary of t he biological whole occupies. Compositional Relevance captures the fact that a biological part engages in a biological process that must make a necessary contribution (...) to a condition that is minimally sufficient to one or more of the characteristic behaviors of the biological whole. Instead of emphasizing the diversity of part-whole relations in the biological world, this paper asks what biological part-whole relations have in common and what constrains their existence, in general. After presenting the two criteria for biological parthood I discuss in how far my account can cope with hard cases (e.g., redundant parts) and I reveal the merits and limits of monism. (shrink)

In contrast to the previously widespread view that Kant's work was largely in dialogue with the physical sciences, recent scholarship has highlighted Kant's interest in and contributions to the life sciences. Scholars are now investigating the extent to which Kant appealed to and incorporated insights from the life sciences and considering the ways he may have contributed to a new conception of living beings. The scholarship remains, however, divided in its interest: historians of science are concerned with the content of (...) Kant's claims, and the ways in which they may or may not have contributed to the emerging science of life, while historians of philosophy focus on the systematic justifications for Kant's claims, e.g., the methodological and theoretical underpinnings of Kant's statement that living beings are mechanically inexplicable. My aim in this paper is to bring together these two strands of scholarship into dialogue by showing how Kant's methodological concerns (specifically, his notion of reflective judgment) contributed to the ontological concern with life as a distinctive object of study. I argue that although Kant's explicit statement was that biology could not be a science, his implicit and more fundamental claim was that the study of living beings necessitates a distinctive mode of thought, a mode that is essentially analogical. I consider the implications of this view, and argue that it is by developing a new methodology for grasping organized beings that Kant makes his most important contribution to the new science of life. (shrink)

It is widely assumed that there is value in the biological tie between parent and child. An implication of this is that adoption is often considered a less desirable alternative to procreation. This paper offers a philosophical defence of adoptive parenthood as a valuable and authentic form of parenthood. While previous defences have suggested that society’s valorisation of the biological tie is unjustified, I argue herein that the conception of the biological tie that features in the normative discourse on parenthood (...) is too narrowly genocentric. Against this genocentric conception, recent work in the philosophy of biology has emphasised the roles of joint determination, dynamic construction, and extended inheritance in development, which I suggest can substantiate a more inclusive conception of the biological tie. Accordingly, I propose that adoptive parents form a rich variety of biological ties with their children, some of which are as heritable and formative as genetic relatedness. (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)

The aim of this paper is to show that for Kant, a combination of epigenesis and monogenesis is the condition of possibility of anthropology as he conceives of it and that moreover, this has crucial implications for the biological dimension of his account of human nature. More precisely, I begin by arguing that Kant’s conception of mankind as a natural species is based on two premises: firstly the biological unity of the human species (monogenesis of the human races); and secondly (...) the existence of ‘seeds’ which may or may not develop depending on the environment (epigenesis of human natural predispositions). I then turn to Kant’s account of man’s natural predispositions and show that far from being limited to the issue of races, it encompasses unexpected human features such as gender, temperaments and nations. These predispositions, I argue, are means to the realisation of Nature’s overall purpose for the human species. This allows me to conclude that man’s biological determinism leads to the species’ preservation, cultivation and civilisation. (shrink)

Following Hume’s lead, Paul Draper argues that, given the biological role played by both pain and pleasure in goal-directed organic systems, the observed facts about pain and pleasure in the world are antecedently much more likely on the Hypothesis of Indifference than on theism. I examine one by one Draper’s arguments for this claim and show how they miss the mark.

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)

Should we think of our universe as law-governed and “clockwork”-like or as disorderly and “soup”-like? Alternatively, should we consciously and intentionally synthesize these two extreme pictures? More concretely, how deterministic are the postulated causes and how rigid are the modeled properties of the best statistical methodologies used in the biological and behavioral sciences? The charge of this entry is to explore thinking about causation in the temporal evolution of biological and behavioral systems. Regression analysis and path analysis are simply explicated (...) with reference to a thought experiment of painting three universes (clockwork, soup, and conscious) useful for imagining our actual universe. Attention to historical, structural, and mechanistic explanatory perspectives broadens the palette of methodologies available for analyzing determinism in, and explanation of, biological and behavioral systems. Each justified methodology provides a partial perspective on complex reality. Is a total explanation of any system ever possible, and what would it require? (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)

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.] 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 and there are many new abstractions from advances in mathematics. 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 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 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 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)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

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

In my view all behavior is an expression of our evolved psychology and so intimately connected to religion, morals and ethics, if one knows how to look at them. -/- Many will find it strange that I spend little time discussing the topics common to most discussions of religion, but in my view it is essential to first understand the generalities of behavior and this necessitates a good understanding of biology and psychology which are mostly noticeable by their absence (...) in works on religion, politics, history, morals and ethics, etc. In my view most such efforts have no grasp at all of the operation of System 2, the slow cortical functions of the brain which can be equated to linguistic behavior or the mind, and which I call the Descriptive Psychology of Higher Order Thought and which I regard as the province of philosophy in the narrow sense. -/- It is my contention that the table of intentionality (rationality, mind, thought, language, personality etc.) that features prominently here describes more or less accurately, or at least serves as an heuristic for, how we think and behave, and so it encompasses not merely philosophy and psychology, but everything else (religion, history, literature, mathematics, politics etc.). Note especially that intentionality and rationality as I (along with Searle, Wittgenstein and others) view it, includes both conscious deliberative System 2 and unconscious automated System 1 actions or reflexes. -/- This collection of articles was written over the last 10 years and revised to bring them up to date (2019). All the articles are about human behavior (as are all articles by anyone about anything), and so about the limitations of having a recent monkey ancestry (8 million years or much less depending on viewpoint) and manifest words and deeds within the framework of our innate psychology as presented in the table of intentionality. As famous evolutionist Richard Leakey says, it is critical to keep in mind not that we evolved from apes, but that in every important way, we are apes. If everyone was given a real understanding of this (i.e., of human ecology and psychology to actually give them some control over themselves), maybe civilization would have a chance. As things are however the leaders of society have no more grasp of things than their constituents and so collapse into anarchy is inevitable is spite of the near universal views that religion, politics or technology can save us. See my Suicidal Utopian Delusions in the 21st Century 5th ed (2019), for a detailed exposition of this view. -/- It is critical to understand why we behave as we do and so I start with a brief review of the logical structure of rationality, which provides some heuristics for the description of language (mind, rationality, personality) and gives some suggestions as to how this relates to the evolution of social behavior. This centers around the two writers I have found the most important in this regard, Ludwig Wittgenstein and John Searle, whose ideas I combine and extend within the dual system (two systems of thought) framework that has proven so useful in recent thinking and reasoning research. As I note, there is in my view essentially complete overlap between philosophy, in the strict sense of the enduring questions that concern the academic discipline, and the descriptive psychology of higher order thought (behavior). Once one has grasped Wittgenstein’s insight that there is only the issue of how the language game is to be played, one determines the Conditions of Satisfaction (what makes a statement true or satisfied etc.) and that is the end of the discussion. No neurophysiology, no metaphysics, no postmodernism, no theology. -/- Along with many, I see it as the basic religious or moral issue of our times that America and the world are in the process of collapse from excessive population growth, most of it for the last century, and now all of it, due to 3rd world people. Consumption of resources and the addition of 3 billion more ca. 2100 will collapse industrial civilization and bring about starvation, disease, violence and war on a staggering scale. The earth loses at least 1% of its topsoil every year, so as it nears 2100, most of its food growing capacity will be gone. Billions will die and nuclear war is all but certain. In America, this is being hugely accelerated by massive immigration and immigrant reproduction, combined with abuses made possible by democracy. Depraved human nature inexorably turns the dream of democracy and diversity into a nightmare of crime and poverty. China will continue to overwhelm America and the world, as long as it maintains the dictatorship which limits selfishness and permits long term planning. The root cause of collapse is the inability of our innate psychology to adapt to the modern world, which leads people to treat unrelated persons as though they had common interests (which I suggest may be regarded as an unrecognized -- but the commonest and most serious-- psychological problem -- Inclusive Fitness Disorder). This, plus ignorance of basic biology and psychology, leads to the social engineering delusions of the partially educated who control democratic societies. Few understand that if you help one person you harm someone else—there is no free lunch and every single item anyone consumes destroys the earth beyond repair. Consequently, social policies everywhere are unsustainable and one by one all societies without stringent controls on selfishness will collapse into anarchy or dictatorship. Without dramatic and immediate changes, there is no hope for preventing the collapse of America, or any country that follows a democratic system, especially now that the Neomarxist Third World Supremacists are taking control of the USA and other Western Democracies, and helping the Seven Sociopaths who run China to succeed in their plan to eliminate peace and freedom and religion worldwide. Hence my concluding essays. Of course, it is an easily defensible point of view that Artificial Intelligence (aka Artificial Stupidity or Artificial Sociopathy) researchers are even more evil than the Democrats and the CCP, and I make brief comments on this as well. -/- Several articles touch on The One Big Happy Family Delusion, i.e., that we are genetically selected for cooperation with everyone, and that the euphonious ideals of Democracy, Diversity, Equality and Religion will lead us into utopia, if we just manage things correctly (the possibility of politics). Again, the No Free Lunch Principle ought to warn us it cannot be true, and we see throughout history and all over the contemporary world, that without strict controls, selfishness and stupidity gain the upper hand and soon destroy any nation that embraces these delusions. In addition, the monkey mind steeply discounts the future, and so we cooperate in selling our descendant’s heritage for temporary comforts, greatly exacerbating the problems. -/- I describe versions of this delusion (i.e., that we are basically ‘friendly’ if just given a chance) as it appears in some recent books on sociology/biology/economics. Even Sapolsky’s otherwise excellent “Behave” (2017) embraces leftist politics and group selection and gives space to a discussion of whether humans are innately violent. I end with two essays on the great tragedy playing out in America and the world, which can be seen as a direct result of our evolved psychology manifested as the inexorable machinations of System 1. Our psychology, eminently adaptive and eugenic on the plains of Africa from ca. 6 million years ago, when we split from chimpanzees, to ca. 50,000 years ago, when many of our ancestors left Africa (i.e., in the EEA or Environment of Evolutionary Adaptation), is now maladaptive and dysgenic and the source of our Suicidal Utopian Delusions. So, like all discussions of behavior (theology, philosophy, psychology, sociology, biology, anthropology, politics, law, literature, history, economics, soccer strategies, business meetings, etc.), this book is about evolutionary strategies, selfish genes and inclusive fitness (kin selection, natural selection), though of course few grasp this, regardless of whether they are academics or peasants, atheists or fundamentalists. (shrink)

In this article, two different claims about nature are discussed. On the one hand, environmental philosophy has forced us to reflect on our position within nature. We are not the masters of nature as was claimed before. On the other hand there are the recent developments within synthetic biology. It claims that, now at last, we can be the masters of nature we have never been before. The question is then raised how these two claims must be related to (...) one another. Rather than stating that they are completely irreconcilable, I will argue for a dialogue aimed to discuss the differences and similarities. The claim is that we should not see it as two successive temporal phases of our relation to nature, but two tendencies that can coexist. (shrink)

Feminist and trans theory challenges "the" binary sex/gender system, but can create a new binary opposition of subversive transgender versus conservative transsexual. This paper aims to shift debate concerning bodies as authentic/real versus constructed/mutable, arguing that such debate establishes a false dichotomy that may be overcome by reappraising scientific understandings of sex/gender. Much recent biology and neurology stresses nonlinearity, contingency, self-organization, and open-endedness. Engaging with this research offers ways around apparently interminable theoretical impasses.

One of the most influential arguments against the claim that computers can think is that while our intentionality is intrinsic, that of computers is derived: it is parasitic on the intentionality of the programmer who designed the computer-program. Daniel Dennett chose a surprising strategy for arguing against this asymmetry: instead of denying that the intentionality of computers is derived, he endeavours to argue that human intentionality is derived too. I intend to examine that biological plausibility of Dennett’s suggestion and show (...) that Dennett’s argument for the claim that human intentionality is derived because it was designed by natural selection is based on the misunderstanding of how natural selection works. (shrink)

Chapter 1st of the book. This chapter explores the fundamental ambiguity of the concept of plasticity – between openness and determination, change and stabilization of forms. This pluralism of meanings is used to unpack different instantiations of corporeal plasticity across various epochs, starting from ancient and early modern medicine, particularly humouralism. A genealogical approach displaces the notion that plasticity is a unitary phenomenon, coming in the abstract, and illuminates the unequal distribution of different forms of plasticities across social, gender, and (...) ethnic groups. Taking a longer view of the plastic body as a ubiquitous belief in traditions predating and coexisting with modern medicine will help contextualize the seeming radicalism of today’s turn to permeability and the exceptionalism of Western findings. By highlighting the complex biopolitical usages of plasticity in the past, the chapter warns against simplistic appropriations of the term in contemporary body/world configurations driven by findings in neuroscience, epigenetics and microbiomics. (shrink)

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

Racial constructionists, anti-naturalists, and anti-realists have challenged users of the biological race concept to provide and defend, from the perspective of biology, biological philosophy, and ethics, a biologically informed concept of race. In this paper, an ontoepistemology of biology is developed. What it is, by this, to be "biological real" and "biologically meaningful" and to represent a "biological natural division" is explained. Early 18th century race concepts are discussed in detail and are shown to be both sensible and (...) not greatly dissimilar to modern concepts. A general biological race concept (GBRC) is developed. It is explained what the GBRC does and does not entail and how this concept unifies the plethora of specific ones, past and present. Other race concepts as developed in the philosophical literature are discussed in relation to the GBRC. The sense in which races are both real and natural is explained. Racial essentialism of the relational sort is shown to be coherent. Next, the GBRC is discussed in relation to anthropological discourse. Traditional human racial classifications are defended from common criticisms: historical incoherence, arbitrariness, cluster discordance, etc. Whether or not these traditional human races could qualify as taxa subspecies – or even species – is considered. It is argued that they could qualify as taxa subspecies by liberal readings of conventional standards. Further, it is pointed out that some species concepts potentially allow certain human populations to be designated as species. It is explained why, by conventional population genetic and statistical standards, genetic differences between major human racial groups are at least moderate. Behavioral genetic differences associated with human races are discussed in general and in specific. The matter of race differences in cognitive ability is briefly considered. Finally, the race concept is defended from various criticisms. First, logical and empirical critiques are dissected. These include: biological scientific, sociological, ontological, onto-epistemological, semantic, and teleological arguments. None are found to have any merit. Second, moral-based arguments are investigated in context to a general ethical frame and are counter-critiqued. Racial inequality, racial nepotism, and the “Racial Worldview" are discussed. What is dubbed the Anti-Racial Worldview is rejected on both empirical and moral grounds. Finally, an area of future investigation – the politics of the destruction of the race concept – is pointed to. (shrink)

This paper discuss the phenomenon of empathy in social robotics and is divided into three main parts. Initially, I analyse whether it is correct to use this concept to study and describe people’s reactions to robots. I present arguments in favour of the position that people actually do empathise with robots. I also consider what circumstances shape human empathy with these entities. I propose that two basic classes of such factors be distinguished: biological and socio-cognitive. In my opinion, one of (...) the most important among them is a sense of group membership with robots, as it modulates the empathic responses to representatives of our- and other- groups. The sense of group membership with robots may be co-shaped by socio-cognitive factors such as one’s experience, familiarity with the robot and its history, motivation, accepted ontology, stereotypes or language. Finally, I argue in favour of the formulation of a pragmatic and normative framework for manipulations in the level of empathy in human–robot interactions. (shrink)

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their func- tionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adapta- tions, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In (...) particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an oppor- tunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would sug- gest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to imple- ment novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engi- neering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engi- neering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms. (shrink)

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

The nature and role of the patient in biomedicine comprise issues central to bioethical inquiry. Given its developmental history grounded firmly in a backlash against 20th-century cases of egregious human subjects abuse, contemporary medical bioethics has come to rely on a fundamental assumption: the unit of care is the autonomous self-directing patient. In this article we examine first the structure of the feminist social critique of autonomy. Then we show that a parallel argument can be made against relational autonomy as (...) well, demonstrating how this second concept of autonomy fails to take sufficiently into account an array of biological determinants, particularly those from microbial biology. Finally, in light of this biological critique, we question whether or to what extent any relevant and meaningful view of autonomy can be recovered in the contemporary landscape of bioethics. (shrink)

Philosophical inquiries into morality are as old as philosophy, but it may turn out that morality itself is much, much older than that. At least, that is the main thesis of prima- tologist Frans De Waal, who in this short book based on his Tanner Lectures at Princeton, elaborates on what biologists have been hinting at since Darwin’s (1871) book The Descent of Man and Hamilton’s (1963) studies on the evolution of altruism: morality is yet another allegedly human characteristic that (...) turns out to be built over evolutionary time by natural. (shrink)

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their functionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adaptations, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In particular, the (...) analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an opportunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would suggest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to implement novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engineering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engineering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms. (shrink)

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

Ita La recensione presenta la prospettiva enattivista difesa da Alva Noë, e ne discute alcuni aspetti specifici. Il pensiero, la coscienza e la cognizione non sono pienamente comprensibili, secondo l’enattivismo di Noë, senza un’adeguata considerazione del ruolo ricoperto dal corpo e dall’ambiente. Sarebbe quindi sbagliato continuare a pensare che il cervello da solo sia responsabile dei processi cognitivi umani: il programma che ricerca i correlati neurali della coscienza sarebbe quindi destinato al fallimento dal principio, perché tralascia in partenza corpo e (...) ambiente; i programmi di ricerca nel campo dell’intelligenza artificiale sarebbero ugualmente compromessi, non solo con una concezione computazionalista della cognizione, ma anche con la vecchia idea che un cervello artificiale sia sufficiente alla cognizione quanto un cervello naturale. Di seguito si prendono in esame due prospettive sperimentali su cui Noë fa grande affidamento: gli studi sulla plasticità neurale dei furetti svolti da Mriganka Sur e altri, e la realizzazione di un sistema di sostituzione visuo-tattile da parte di Paul Bach-Y-Rita. Per Noë si tratta di elementi cruciali in supporto alla propria prospettiva: in realtà, come emerge dalla breve analisi, l’attribuire loro un significato così chiaro e univoco pro-enattivismo è qualcosa di molto meno scontato. Infine, segue un breve bilancio del libro di Noë, dove gli elementi d’interesse del volume sono presentati insieme all’individuazione di alcuni punti deboli, che il testo condivide con la gran parte degli studi che in vario modo fanno leva sull’intuizione legata all’embodiement: da un lato una difficoltà strutturale riguarda la possibilità di identificare con chiarezza gli elementi costitutivi del mentale; dall’altro lato, il riferimento a forme di esternalismo radicale sembra ugualmente comportare diversi problemi. -/- Abstract Eng The review presents Alva Noë’s enactivist view, and aims at discussing some of its ideas. Thought, consciousness, and cognition are not understandable, Noë claims, without taking into proper consideration the role played by the body and the environment. It would be wrong indeed to go on thinking that our brain alone is responsible for human cognitive processes: the program searching for the neural correlates of consciousness is hopeless in principle, because it neglects from the beginning the body and the environment; research programs in artificial intelligence are as well compromised, not only with a computationalist view of cognition, but also with the old idea that an artificial brain will suffice for cognition just like a natural one. Thereafter, two experimental perspectives, that Noë uses to support his view, are examined: Mriganka Sur’s studies on neural plasticity of ferrets, and Paul Bach-Y-Rita’s tactile-visual substitution system. Noë argues that these results are crucial in supporting his view, but, as the discussion highlights, their pro-enactivism meaning is not so clear and unambiguous. Finally, a balance of the book follows, where the many elements of interest are presented together with the acknowledgment of some weak points, that the book shares with the majority of the proposals that deal with the embodiment’s insight: on the one hand, a structural difficulty concerns the possibility to identify clearly the constitutive elements of the mental; on the other hand, the reference to radical versions of externalism seems to entail many difficulties as well. (shrink)

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

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

Biosemiotics is a growing fi eld that investigates semiotic processes in the living realm in an attempt to combine the fi ndings of the biological sciences and semiotics. Semiotic processes are more or less what biologists have typically referred to as “ signals, ” “ codes, ”and “ information processing ”in biosystems, but these processes are here understood under the more general notion of semiosis, that is, the production, action, and interpretation of signs. Thus, biosemiotics can be seen as (...) class='Hi'>biology interpreted as a study of living sign systems — which also means that semiosis or sign process can be seen as the very nature of life itself. In other words, biosemiotics is a field of research investigating semiotic processes (meaning, signification, communication, and habit formation in living systems) and the physicochemical preconditions for sign action and interpretation. -/- (...). (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)

The hologenome concept of evolution is a hypothesis about the evolution of animals and plants. It asserts that the evolution of animals and plants was partially triggered by their interactions with their symbiotic microbiomes. In that vein, the hologenome concept posits that the holobiont (animal host + symbionts of the microbiome) is a unit of selection. -/- The hologenome concept has been severely criticized on the basis that selection on holobionts would only be possible if there were a tight transgenerational (...) host-genotype-to-symbiont-genotype connection. As our current evidence suggests that this is not the case for most of the symbiont species that compose the microbiome of animals and plants, the opportunity for holobiont selection is very low in relation to the opportunity for selection on each of the species that compose the host microbiome. Therefore, holobiont selection will always be disrupted ‘from below’, by selection on each of the species that compose the microbiome. -/- This thesis constitutes a conceptual effort to defend philosophically the hologenome concept. I argue that the criticism according to which holobiont selection requires tight transgenerational host-genotype-to-symbiont-genotype connection is grounded on a metaphysical view of the world according to which the biological hierarchy needs to be nested, such that each new level of selection includes every entity from below. Applied to hologenomes, it entails that the hologenome is a collection of genomes, and selection of hologenomes is assumed to entail cospeciation of the host with the species that constitute its microbiome. -/- Against that interpretation, I propose the ‘stability of traits’ account, according to which hologenome evolution is the result of the action of natural selection in a non-nested hierarchical world. In that vein, hologenome evolution does not entail cospeciation, and thus it does not require tight transgenerational host-genotype-to-symbiont-genotype connection. By embracing a multilevel selection perspective, I argue that hologenome evolution results from the simultaneous action of natural selection on each of the lineages that compose the microbiome, and on the assemblage composed by the host genome plus the functional traits of its microbiome. Hologenome selection occurs when the evolution of the traits of the microbiome result from their effects on the fitness of the host, and it can take the form of multilevel selection 1, or multilevel selection 2. In both cases, hologenome selection entails the evolution of microbiome traits, as well as evolution of the host genome, rather than cospeciation of lineages. (shrink)

The concept of mechanism in biology has three distinct meanings. It may refer to a philosophical thesis about the nature of life and biology (‘mechanicism’), to the internal workings of a machine-like structure (‘machine mechanism’), or to the causal explanation of a particular phenomenon (‘causal mechanism’). In this paper I trace the conceptual evolution of ‘mechanism’ in the history of biology, and I examine how the three meanings of this term have come to be featured in the (...) philosophy of biology, situating the new ‘mechanismic program’ in this context. I argue that the leading advocates of the mechanismic program (i.e., Craver, Darden, Bechtel, etc.) inadvertently conflate the different senses of ‘mechanism’. Specifically, they all inappropriately endow causal mechanisms with the ontic status of machine mechanisms, and this invariably results in problematic accounts of the role played by mechanism-talk in scientific practice. I suggest that for effective analyses of the concept of mechanism, causal mechanisms need to be distinguished from machine mechanisms, and the new mechanismic program in the philosophy of biology needs to be demarcated from the traditional concerns of mechanistic biology. (shrink)

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