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)

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)

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)

The social, behavioral, and a good chunk of the biological sciences concern the nature of individual agency, where our paradigm for an individual is a human being. Theories of economic behavior, of mental function and dysfunction, and of ontogenetic development, for example, are theories of how such individuals act, and of what internal and external factors are determinative of that action. Such theories construe individuals in distinctive ways.

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.

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 received several critical comments regarding the "The Science of Spiritual Biology." We reply to those criticisms in order to further clarify some of the important points that were made. It is only to be expected that a strong emotional response may be evoked by the revolution in scientific thinking that the modern paradigm of cognitive biology presents. We have to be prepared to accept that, and maintain the integrity of the scientific approach.

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

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

This is an English translation of my essay: Alfred Gierer Wissenschaft, Religion und die deutungsoffenen Grundfragen der Biologie. Mpi for the History of Science, preprint 388, 1-21, also in philpapers. Range and limits of science are given by the universal validity of physical laws, and by intrinsic limitations, especially in self-referential contexts. In particular, neurobiology should not be expected to provide a full understanding of consciousness and the mind. Science cannot provide, by itself, an unambiguous interpretation of the natural order (...) at the philosophical, cultural and religious level. The diversity of interpretations, however appears as a positive factor of cultural dynamics. Historically, the revival of the philosophy of nature in the middle ages included remarkable biological thoughts such as those of Eriugena and Thierry of Chartres. In this essay, emphasis is placed on basic issues of modern biology – the distinction of man and animal, the evolution of human mental capabilities, the physics of the universe as precondition for biological evolution, and the intricasies of the brain-mind-relation. They are open to agnostic as well as religious interpretations, the individual choice being mainly a matter of wisdom and not just of knowledge. -/-. (shrink)

Research in ecology and evolutionary biology (evo-eco) often tries to emulate the “hard” sciences such as physics and chemistry, but to many of its practitioners feels more like the “soft” sciences of psychology and sociology. I argue that this schizophrenic attitude is the result of lack of appreciation of the full consequences of the peculiarity of the evo-eco sciences as lying in between a-historical disciplines such as physics and completely historical ones as like paleontology. Furthermore, evo-eco researchers (...) have gotten stuck on mathematically appealing but philosophi- cally simplistic concepts such as null hypotheses and p-values defined according to the frequentist approach in statistics, with the consequence of having been unable to fully embrace the complexity and subtlety of the problems with which ecologists and evolutionary biologists deal with. I review and discuss some literature in ecology, philosophy of science and psychology to show that a more critical methodological attitude can be liberating for the evo-eco scientist and can lead to a more fecund and enjoyable practice of ecology and evolutionary biology. With this aim, I briefly cover concepts such as the method of multiple hypotheses, Bayesian analysis, and strong inference. (shrink)

"Living systems are cognitive systems, and living as a process is a process of cognition." -H.R. Maturana, The Biology of Cognition (1970/1980) Just as the cell has gradually come to be understood as a highly regulated and unctionally integrated whole, so too is the biosphere now recognized as a finely balanced ecological whole in which local disturbances can create world-wide climatic catastrophe. The oversimplified ideas of biology that characterized the field in its immature beginning led to the theories of a (...) progressive cumulative development or evolution to explain the present state of Nature. However, today, a more mature understanding of biology has brought with it the realization that Nature can not be the product of a gradual development, based only on the reductionist principles of chemistry and physics. In an ideal situation, where there are no strong interactions with the environment, isolated and purified chemicals may react in a mechanically simple manner, but in a living organism there are no isolated molecules. Everything within the cell interacts with everything else. The constituents of a cell are produced by the cell as much as they produce the cell itself. As the German philosopher Immanuel Kant understood, the unique judgment that allows us to identify a living organism as distinct from non-living matter, is that a living organism is both the cause and effect of itself. Thus, the life of a cell, as much as the life of the biosphere, can only be properly understood as an integrated organic whole. (shrink)

Genes and the Agents of Life undertakes to rethink the place of the individual in the biological sciences, drawing parallels with the cognitive and social sciences. Genes, organisms, and species are all agents of life but how are each of these conceptualized within genetics, developmental biology, evolutionary biology, and systematics? The 2005 book includes highly accessible discussions of genetic encoding, species and natural kinds, and pluralism above the levels of selection, drawing on work from across the (...) class='Hi'>biological sciences. The book is a companion to the author's Boundaries of the Mind (2004), also available from Cambridge, where the focus is the cognitive sciences. The book will appeal to a broad range of professionals and students in philosophy, biology, and the history of science. You can download the table of contents and the first chapter here. (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)

The scientific status of evolutionary theory seems to be more or less perennially under question. I am not referring here (just) to the silliness of young Earth creation- ism (Pigliucci 2002; Boudry and Braeckman 2010), or even of the barely more intel- lectually sophisticated so-called Intelligent Design theory (Recker 2010; Brigandt this volume), but rather to discussions among scientists and philosophers of science concerning the epistemic status of evolutionary theory (Sober 2010). As we shall see in what follows, this debate (...) has a long history, dating all the way back to Darwin, and it is in great part rooted in the fundamental dichotomy between what French biologist and Nobel laureate Jacques Monod (1971) called chance and necessity—i.e., the inevitable and inextricable interplay of deterministic and stochastic mechanisms operating during the course of evolution. (shrink)

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

Review of: "Biology as a postmodern science: Universals, historicity, and context".

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)

Aristotle is a political scientist and a student of biology. Political science, in his view, is concerned with the human good and thus it includes the study of ethics. He approaches many subjects from the perspective of both political science and biology: the virtues, the function of humans, and the political nature of humans. In light of the overlap between the two disciplines, I look at whether or not Aristotle’s views in biology influence or explain some of his theses in (...) political science. I show that we should not seek a unified answer to this question, for the relationship between the two disciplines varies depending on the topic. In some cases, e.g. the nature of the human function, the biological background is likely to be endorsed as one of the presuppositions of the ethical enquiry. In other cases, e.g. the study of social hierarchies, even though the ethical works and the biological works come to similar conclusions, it is hard to establish that the biological approach is intended to provide support to the ethico-political approach. In conclusion, I show that Aristotle’s political science and his biology are in conflict at least in two important cases: his account of justice towards non-human animals and his exhortation to contemplate. (shrink)

For some the gene-centered reductionism that permeates contemporary neo-Darwinism is an obstacle for finding a common explanatory framework for both biological and cultural evolution. Thus social scientists are tempted to find new concepts that might bridge the divide between biology and sociology. Yet since Aristotle we know that the level of explanation must be commensurate with the particular question to be answered. In modern natural science there are many instances where a reductionist approach has failed to provide the right (...) answer to the corresponding question. Thus social scientists risk becoming non-relevant when mimicking some features of the natural sciences (such as hard or soft reductionism) just for the sake of it, instead of finding autonomous explanations commensurate with the level of phenomena studied by social science. (shrink)

Investigations into inter-level relations in computer science, biology and psychology call for an *empirical* turn in the philosophy of mind. Rather than concentrate on *a priori* discussions of inter-level relations between 'completed' sciences, a case is made for the actual study of the way inter-level relations grow out of the developing sciences. Thus, philosophical inquiries will be made more relevant to the sciences, and, more importantly, philosophical accounts of inter-level relations will be testable by confronting them with (...) what really happens in science. Hence, close observation of the ever-changing reduction relations in the developing sciences, and revision of philosophical positions based on these empirical observations, may, in the long run, be more conducive to an adequate understanding of inter-level relations than a traditional *a priori* approach. (shrink)

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

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)

This paper discusses the epistemic status of biology from the standpoint of the systemic approach to living systems based on the notion of biological autonomy. This approach aims to provide an understanding of the distinctive character of biological systems and this paper analyses its theoretical and epistemological dimensions. The paper argues that, considered from this perspective, biological systems are examples of emergent phenomena, that the biological domain exhibits special features with respect to other domains, and that (...) biology as a discipline employs some core concepts, such as teleology, function, regulation among others, that are irreducible to those employed in physics and chemistry. It addresses the claim made by Jacques Monod that biology as a science is marginal. It argues that biology is general insofar as it constitutes a paradigmatic example of complexity science, both in terms of how it defines the theoretical object of study and of the epistemology and heuristics employed. As such, biology may provide lessons that can be applied more widely to develop an epistemology of complex systems. (shrink)

This paper is an attempt to provide an adequate theoretical framework to understand the biological basis of human rights. We argue that the skepticism about human rights is increasing especially among the most rational, innovative and productive community of intellectuals belonging to the applied sciences. By using examples of embryonic stem cell research, a clash between applied scientists and legal scientists cum human rights activists has been highlighted. After an extensive literature review, this paper concludes that the advances (...) in applied sciences proven by empirical evidence should not be restricted by normative theories and philosophies of the social sciences. If we agree on these premises that Human Rights are biological, then biology can provide a framework of cooperation for social and applied scientists. (shrink)

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

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)

For two reasons, physics occupies a preeminent position among the sciences. On the one hand, due to its recognized position as a fundamental science, and on the other hand, due to the characteristic of its obvious certainty of knowledge. For both reasons it is regarded as the paradigm of scientificity par excellence. With its focus on the issue of epistemic certainty, philosophy of science follows in the footsteps of classical epistemology, and this is also the basis of its 'judicial' (...) pretension vis-à-vis physics. Whereas physics is in a strong competitive relationship to philosophy and epistemology with respect to its position as a fundamental science - even on the subject of cognition, as the pretension of 'reductionism' shows. It is the thematic focus on epistemic certainty itself, however, that becomes the root of a profound epistemological misunderstanding of physics. The reason for this is twofold: first, the idea of epistemic certainty as a criterion of 'demarcation' between physics and metaphysics obscures the view of the much deeper heuristic differences between the two kinds of knowledge. The second, related, reason is that epistemology does not ask the question of the reason for the epistemic certainty of physics; instead, it sets itself the task of 'legitimating' physical knowledge, and this, crucially, with reference to the interpretation of the process of cognition. Thus, as a matter of course, all epistemological assumptions about this process – including the common descriptive understanding of knowledge and its ontological premises – flow into the interpretation of physics as a science. Consequently, this undertaking is not only doubtful from the ground up, because it presupposes for its meaningfulness nothing less than certainty of knowledge concerning (the interpretation of) the process of knowledge, thereby relying on mere convictions; moreover, by projecting the descriptive, 'metaphysical' concept of knowledge onto physics, it leads to unsolvable epistemological problems and corresponding resignative conclusions concerning the claim of knowledge of physics. In other words, epistemology itself builds, due to its basic assumptions, a major obstacle for an adequate understanding of physics. Physics' cross-object, deconstructive approach to knowledge implies a completely different, non-descriptive understanding of its concepts, with consequences that extend far beyond itself due to its status as a basic science. (shrink)

Andrea Wiggins and John Wilbanks’ article (2019) presents us with a welcome overview of the neglected, novel ethical issues raised by the advent of citizen science in health and biomedical contexts. This contribution takes a rather different approach, focusing on a very specific (yet also overlooked) problem in this context - the ethical implications of self-administered genetic testing. This problem, however, is particularly illustrative of the “ethics gap” between traditional medical settings and new public-driven scientific practices, emphasized by Wiggins and (...) Wilbanks in their more wide-ranging treatment. (shrink)

Hans Jonas’ “philosophical biology,” although developed several decades ago, is still fundamental to the contemporary reflection upon the meaning of life in a systems thinking perspective. Jonas, in fact, closely examines the reasons of modern science, and especially of Wiener’s Cybernetics and Bertalanffy’s General System Theory, and at the same time points out their basic limits, such as their having a reductionistic attitude to knowledge and ontology. In particular, the philosopher highlights the problematic consequences of scientific reductionism for human nature. (...) As the final result of an overall process of naturalization, the essence of the human being is reduced to its quantitative features only, while the “meaning” of life as such becomes no different from the “fact” of its material consistency. However, the problem is that by such a process, the human being is deprived of his specificity. (shrink)

I motivate the concept of styles of scientific investigation, and differentiate two styles, formal and compositional. Styles are ways of doing scientific research. Radically different styles exist. I explore the possibility of the unification of biology and social science, as well as the possibility of unifying the two styles I identify. Recent attempts at unifying biology and social science have been premised almost exclusively on the formal style. Through the use of a historical example of defenders of compositional biological (...) social science, the Ecology Group at the University of Chicago from, roughly, the 1930s to the 1950s, I attempt to show the coherence and possibility, if not utility, of employing the compositional style to effect the synthesis of biology and social science. I also relate the efforts of the Ecology Group to those of investigators in the Sociology Department of the University of Chicago. In my conclusion, I discuss the usefulness both of employing the category of styles of scientific investigation in historical and philosophical studies of science, as well as the concept of compositionality in scientific studies. I end the paper with some tentative suggestions regarding the importance of compositionality for an analysis of human society. (shrink)

A minimal essentialism (‘intrinsic biological essentialism’) about natural kinds is required to explain the projectability of human science terms. Human classifications that yield robust and ampliative projectable inferences refer to biological kinds. I articulate this argument with reference to an intrinsic essentialist account of HPC kinds. This account implies that human sciences (e.g., medicine, psychiatry) that aim to formulate predictive kind categories should classify biological kinds. Issues concerning psychiatric classification and pluralism are examined.

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

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

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)

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 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)

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

This third paper locates the synthetic neurorobotics research reviewed in the second paper in terms of themes introduced in the first paper. It begins with biological non-reductionism as understood by Searle. It emphasizes the role of synthetic neurorobotics studies in accessing the dynamic structure essential to consciousness with a focus on system criticality and self, develops a distinction between simulated and formal consciousness based on this emphasis, reviews Tani and colleagues' work in light of this distinction, and ends by (...) forecasting the increasing importance of synthetic neurorobotics studies for cognitive science and philosophy of mind going forward, finally in regards to most- and myth-consciousness. (shrink)

The biological sciences have always proven a fertile ground for philosophical analysis, one from which has grown a rich tradition stemming from Aristotle and flowering with Darwin. And although contemporary philosophy is increasingly becoming conceptually entwined with the study of the empirical sciences with the data of the latter now being regularly utilised in the establishment and defence of the frameworks of the former, a practice especially prominent in the philosophy of physics, the development of that tradition (...) hasn’t received the wider attention it so thoroughly deserves. This review will briefly introduce some recent significant topics of debate within the philosophy of biology, focusing on those whose metaphysical themes (in everything from composition to causation) are likely to be of wide-reaching, cross-disciplinary interest. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises (...) ENVO’s motivation, content, structure, adoption, and governance approach. (shrink)

In recent years, a proliferation of books about empathy, cooperation and pro-social behaviours (Brooks, 2011a) has significantly influenced the discourse of the life-sciences and reversed consolidated views of nature as a place only for competition and aggression. In this article I describe the recent contribution of three disciplines – moral psychology (Jonathan Haidt), primatology (Frans de Waal) and the neuroscience of morality – to the present transformation of biology and evolution into direct sources of moral phenomena, a process here (...) named the ‘moralization of biology’. I conclude by addressing the ambivalent status of this constellation of authors, for whom today ‘morality comes naturally’: I explore both the attractiveness of their message, and the problematic epistemological assumptions of their research programmes in the light of new discoveries in developmental and molecular biology. (shrink)

Although biological autonomy is widely discussed, its description in scientific terms remains elusive. I present here a series of recent evidences on the existence of genuine biological autonomy. Nevertheless, nowadays it seems that the only acceptable ground to account for any natural phenomena, including biological autonomy, is physics. But if this were the case, then arguably there would be no way to account for genuine biological autonomy. The way out of such a situation is to build (...) up an exact theoretical biology, and one of the first steps is to clarify the basic concepts of biology, among them biological aim, function and autonomy. We found a physical mechanism to realize biological autonomy, namely, biologically initiated vacuum processes. In the newly emerging picture, biological autonomy shows up as a new, fundamental and inevitable element in our scientific world picture. It offers new perspectives for solving problems regarding the origin and nature of life, connecting ancient Greek philosophy with modern science. Namely, our proposal sheds light in what sense can the God as conceived by Xenophanes can move the material objects of the Universe by its thoughts without toil. (shrink)

We take the potentialities that are studied in the biological sciences (e.g., totipotency) to be an important subtype of biological dispositions. The goal of this paper is twofold: first, we want to provide a detailed understanding of what biological dispositions are. We claim that two features are essential for dispositions in biology: the importance of the manifestation process and the diversity of conditions that need to be satisfied for the disposition to be manifest. Second, we demonstrate (...) that the concept of a disposition (or potentiality) is a very useful tool for the analysis of the explanatory practice in the biological sciences. On the one hand it allows an in-depth analysis of the nature and diversity of the conditions under which biological systems display specific behaviors. On the other hand the concept of a disposition may serve a unificatory role in the philosophy of the natural sciences since it captures not only the explanatory practice of biology, but of all natural sciences. Towards the end we will briefly come back to the notion of a potentiality in biology. (shrink)

How does evolutionary biology fit with Thomas Kuhn's famous distinction between puzzle solving and paradigm shifts in science?

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

The vision of natural kinds that is most common in the modern philosophy of biology, particularly with respect to the question whether species and other taxa are natural kinds, is based on a revision of the notion by Mill in A System of Logic. However, there was another conception that Whewell had previously captured well, which taxonomists have always employed, of kinds as being types that need not have necessary and sufficient characters and properties, or essences. These competing views employ (...) different approaches to scientific methodologies: Mill’s class-kinds are not formed by induction but by deduction, while Whewell’s type-kinds are inductive. More recently, phylogenetic kinds (clades, or monophyletic-kinds) are inductively projectible, and escape Mill’s strictures. Mill’s version represents a shift in the notions of kinds from the biological to the physical sciences. (shrink)

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