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 key assumption behind evolutionary epistemology is that animals are active learners or ‘knowers’. In the present study, I updated the concept of natural learning, developed by Henry Plotkin and John Odling-Smee, by expanding it from the animal-only territory to the biosphere-as-a-whole territory. In the new interpretation of natural learning the concept of biological information, guided by Peter Corning’s concept of “control information”, becomes the ‘glue’ holding the organism–environment interactions together. The control information guides biological systems, from bacteria (...) to ecosystems, in the process of natural learning executed by the universal algorithm. This algorithm, summarized by the acronym IGPT (information-gain-process-translate) incorporates natural cognitive methods including sensing/perception, memory, communication, and decision-making. Finally, the biosphere becomes the distributed network of communicative interactions between biological systems termed the interactome. The concept of interactome is based on Gregory Bateson’s natural epistemology known as the “ecology of mind”. Mimicking Bateson’s approach, the interactome may also be designated “physiology of mind”—the principle behind regulating the biosphere homeostasis. (shrink)

Following an analysis of the state of investigations and clinical outcomes in the Alzheimer's research field, I argue that the widely-accepted 'amyloid cascade' mechanistic explanation of Alzheimer's disease appears to be fundamentally incomplete. In this context, I propose that a framework termed 'principled mechanism' (PM) can help with remedying this problem. First, using a series of five 'tests', PM systematically compares different components of a given mechanistic explanation against a paradigmatic set of criteria, and hints at various ways of making (...) the mechanistic explanation more 'complete'. These steps will be demonstrated using the amyloid explanation, and its missing or problematic mechanistic elements will be highlighted. Second, PM makes an appeal for the discovery and application of 'biological principles' (BPs), which approximate ceteris paribus laws and are operative at the level of a biological cell. As such, although thermodynamic, evolutionary, ecological and other laws or principles from chemistry and the broader life sciences could inform them, BPs should be considered ontologically unique. BPs could augment different facets of the mechanistic explanation but also allow further independent nomological explanation of the phenomenon. Whilst this overall strategy can be complementary to certain 'New Mechanist' approaches, an important distinction of the PM framework is its equal attention to the explanatory utility of biological principles. Lastly, I detail two hypothetical BPs, and show how they could each inform and improve the potentially incomplete mechanistic aspects of the amyloid explanation and also how they could provide independent explanations of the cellular features associated with Alzheimer's disease. (shrink)

The notion of a physiological individuals has been developed and applied in the philosophy of biology to understand symbiosis, an understanding of which is key to theorising about the major transition in evolution from multi-organismality to multi-cellularity. The paper begins by asking what such symbiotic individuals can help to reveal about a possible transition in the evolution of cognition. Such a transition marks the movement from cooperating individual biological cognizers to a functionally integrated cognizing unit. Somewhere along the way, (...) did such cognizing units simultaneously have cognizers as parts? Expanding upon the multiscale integration view of the Free Energy Principle, this paper develops an account of reciprocal integration, demonstrating how some coupled biological cognizing systems, when certain constraints are met, can result in a cognizing unit that is in ways greater than the sum of its cognizing parts. Symbiosis between V. Fischeri bacteria and the bobtail squid is used to provide an illustration this account. A novel manner of conceptualizing biological cognizers as gradient is then suggested. Lastly it is argued that the reason why the notion of ontologically nested cognizers may be unintuitive stems from the fact that our folk-psychology notion of what a cognizer is has been deeply influenced by our folk-biological manner of understanding biological individuals as units of reproduction. (shrink)

Autoinhibition is a design principle realized in many molecular mechanisms in biology. After explicating the notion of a design principle and showing that autoinhibition is such a principle, we focus on how researchers discovered instances of autoinhibition, using research establishing the autoinhibition of the molecular motors kinesin and dynein as our case study. Research on kinesin and dynein began in the fashion described in accounts of mechanistic explanation but, once the mechanisms had been discovered, researchers discovered that they exhibited a (...) second phenomenon, autoinhibition. The discovery of autoinhibition not only reverses the pattern in terms of which philosophers have understood mechanism discovery but runs counter to the one phenomenon-one mechanism principle assumed to relate mechanisms and the phenomena they explain. The ubiquity of autoinhibition as a design principle, therefore, necessitates a philosophical understanding of mechanisms that recognizes how they can participate in more than one phenomenon. Since mechanisms with this design are released from autoinhibition only when they are acted on by control mechanisms, we advance a revised account of mechanisms that accommodates attribution of multiple phenomena to the same mechanism and distinguishes them from other processes that control them. (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)

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

Synthetic biology is a field of research that concentrates on the design, construction, and modification of new biomolecular parts and metabolic pathways using engineering techniques and computational models. By employing knowledge of operational pathways from engineering and mathematics such as circuits, oscillators, and digital logic gates, it uses these to understand, model, rewire, and reprogram biological networks and modules. Standard biological parts with known functions are catalogued in a number of registries (e.g. Massachusetts Institute of Technology Registry of (...) Standard Biological Parts). Biological parts can then be selected from the catalogue and assembled in a variety of combinations to construct a system or pathway in a microbe. Through the innovative re-engineering of biological circuits and the optimization of certain metabolic pathways, biological modules can be designed to reprogram organisms to produce products or behaviors. Synthetic biology is what is known as a “platform technology”. That is, it generates highly transferrable theoretical models, engineering principles, and know-how that can be applied to create potential products in a wide variety of industries. Proponents suggest that applications of synthetic biology may be able to provide scientific and engineered solutions to a multitude of worldwide problems from health to energy. Synthetic biology research has already been successful in constructing microbial products which promise to offer cheaper pharmaceuticals such as the antimalarial synthetic drug artemisinin, engineered microbes capable of cleaning up oil spills, and the engineering of biosensors that can detect the presence of high concentrations of arsenic in drinking water. One of the potential benefits of synthetic biology research is in its application to biofuel production. It is this application which is the focus of this entry. The term “biofuel” has referred generally to all liquid fuels that are sourced from plant or plant byproducts and are used for energy necessary for transportation vehicles (Thompson 2012). Biofuels that are produced using synthetic biological techniques re-engineer microbes into biofuel factories are a subset of these. (shrink)

Is it possible to know anything about life we have not yet encountered? We know of only one example of life: our own. Given this, many scientists are inclined to doubt that any principles of Earth’s biology will generalize to other worlds in which life might exist. Let’s call this the “N = 1 problem.” By comparison, we expect the principles of geometry, mechanics, and chemistry would generalize. Interestingly, each of these has predictable consequences when applied to biology. (...) The surface-to-volume property of geometry, for example, limits the size of unassisted cells in a given medium. This effect is real, precise, universal, and predictive. Furthermore, there are basic problems all life must solve if it is to persist, such as resistance to radiation, faithful inheritance, and energy regulation. If these universal problems have a limited set of possible solutions, some common outcomes must consistently emerge. In this chapter, I discuss the N = 1 problem, its implications, and my response (Mariscal 2014). I hold that our current knowledge of biology can justify believing certain generalizations as holding for life anywhere. Life on Earth may be our only example of life, but this is only a reason to be cautious in our approach to life in the universe, not a reason to give up altogether. In my account, a candidate biological generalization is assessed by the assumptions it makes. A claim is accepted only if its justification includes principles of evolution, but no contingent facts of life on Earth. (shrink)

Synthetic biologists aim to generate biological organisms according to rational design principles. Their work may have many beneficial applications, but it also raises potentially serious ethical concerns. In this article, we consider what attention the discipline demands from bioethicists. We argue that the most important issue for ethicists to examine is the risk that knowledge from synthetic biology will be misused, for example, in biological terrorism or warfare. To adequately address this concern, bioethics will need to broaden (...) its scope, contemplating not just the means by which scientific knowledge is produced, but also what kinds of knowledge should be sought and disseminated. (shrink)

In this paper, I defend the agent/patient distinction against critics who argue that causal interactions are symmetrical. Specifically, I argue that there is a widespread type of causal interaction between distinct entities, resulting in a type of ontological asymmetry that provides principled grounds for distinguishing agents from patients. The type of interaction where the asymmetry is found is when one of the entities undergoes a change in kind, structure, powers, or intrinsic properties as a result of the interaction while the (...) other does not. Interactions of this type are widespread in molecular biology and chemistry. I focus specifically on (i) the actions of enzymes on substrates and (ii) water molecules breaking the bonds of polarized molecules. Finally, I respond to objections by laying out and to a limited extent defending three commitments of my account: emergent entities and powers, realism about chemical kinds or structures, and the assumption of the agent/patient distinction in functional attributions in biology. (shrink)

Basal cognition investigates cognition working upward from nonneuronal organisms. Because basal cognition is committed to empirically testable hypotheses, a methodological challenge arises: how can experiments avoid using zoocentric assumptions that ignore the ecological contexts that might elicit cognitively driven behavior in nonneuronal organisms? To meet this challenge, I articulate the principle of dynamic holism (PDH), a methodological principle for guiding research on nonneuronal cognition. I describe PDH’s relation to holistic research programs in human-focused cognitive science and psychology then present an (...) argument from analogy based on holistic developmental biology. Last, I examine two experiments exemplifying the need for PDH. (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)

The perception of reality by biosystems is based on different, and in certain respects more effective, principles than those utilized by the more formal procedures of science. As a result, what appears as random pattern to the scientific method can be meaningful pattern to a living organism. The existence of this complementary perception of reality makes possible in principle effective use by organisms of the direct interconnections between spatially separated objects shown to exist in the work of J. S. (...) Bell. (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)

Is life a simple result of a conjunction of physico-chemical processes? Can be reduced to a mere juxtaposition of spatially determined events? What epistemology or world-view allows us to comprehend it? Aristotle built a novel philosophical system in which nature is a dynamical totality which is in constant movement. Life is a manifestation of it, and is formed and governed by the psyche. Psyche is the organizational principle of the different biological levels: nutritive, perceptive and intelective. Driesch's crucial experiment (...) provided empirical proof of the principle of life, which he called entelechy. Entelechy is an intensive manifoldness and cannot be comprehended by the usual extensive parameters. The entelechian's own ambiance is duration. This allows the reintroduction of the concept of teleology in the sphere of the living, understood not as a final cause, but as an order born from desire and leading to action. (shrink)

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

A formal model of the processes of digestion in a hypothetical cell is developed and discussed as a case study of how the threefold logic of Peircean semiotics works within Rosen’s paradigm of relational ontology. The formal model is used to demonstrate several fundamental differences between a relational description of biological processes and a mechanistic description. The formal model produces a logic of embodied generalization that is mediated and determined by the cell through its interactions with the environment. Specifically, (...) the synchronization of the functions of pattern recognition and semantic attribution results in an open and adaptive learning system that is stabilized by a hermeneutical circle. The relational principles of biosemiotics demonstrated through this case study are applicable to other biological systems, as well as to the relational ontology of systems theory, artificial intelligence systems, and relativistic quantum theory. (shrink)

According to the Thomistic tradition, the Principle of Totality (TPoT) articulates a secondary principle of natural law which guides the exercise of human ownership or dominium over creation. In its general signification, TPoT is a principle of distributive justice determining the right ordering of wholes to their parts. In the medical field it is traditionally understood as entailing an absolute prohibition of bodily mutilation as irrational and immoral, and an imperfect obligation to use the parts of one’s body for the (...) perfection of the bodily whole. TPoT is thus a key element of the system of principles within which an individual exercises her right to life: it helps specify the nature, scope and limits of those actions by which an agent permissibly acts in order to preserve her life. While the Thomistic tradition and the Catholic Church have drawn clear conclusions from the principle regarding, e.g., direct sterilization and non-therapeutic experimentation on human subjects, less attention has been given to the implications of TPoT for non-therapeutic procedures that may positively impact biological functioning or supra-biological goals–that is, for human “enhancement.” We will explore the degree to which TPoT non-univocally guides our use of both artifacts and bodies. We will argue that a careful analysis of these distinct kinds of totalities suggests that the application of TPoT to artifacts and bodies is strongly isomorphic, which is what tempts advocates of the Principle of Autonomy to invalidly infer the absolute dominium of the individual over her body. The inference is invalid because this isomorphism also includes a principle of intrinsic value whose function is to resist the instrumentalization of both artifacts and bodies in some contexts; we are not even related to artifacts as advocates of absolute autonomy believe we are, let alone to our bodies. Rather, the limits of human dominium are determined by the nature and finalities, inherent or acquired, of the objects in question, and it will be argued that articulating these limits raises important, understudied, and fascinating questions about the permissibility of various kinds of human enhancement. (shrink)

Our concept of the universe and the material world is foundational for our thinking and our moral lives. In an earlier contribution to the URAM project I presented what I called 'the ultimate organizational principle' of the universe. In that article (Grandpierre 2000, pp. 12-35) I took as an adversary the wide-spread system of thinking which I called 'materialism'. According to those who espouse this way of thinking, the universe consists of inanimate units or sets of material such as atoms (...) or elementary particles. Against this point of view on reality, I argued that it is 'logic', which exists in our inner world as a function of our mind, that is the universal organizing power of the universe. The present contribution builds upon this insight. Then I focussed on rationality; now I am interested in the responsibility that is the driving force behind our effort to find coherence and ultimate perspectives in our cosmos. It is shown that biology fundamentally differs from physics. Biology has its own fundamental principle, which is formulated for the first time in history in a scientific manner by Ervin Bauer. This fundamental principle is the cosmic life principle. I show that if one considers the physical laws as corresponding to reality, as in scientific realism, than physicalism becomes fundamentally spiritual because the physical laws are not material. I point out that the physical laws originate from the fundamental principle of physics which is the least action principle. I show that the fundamental principle of physics can be considered as the "instinct of atoms". Our research has found deep and meaningful connections between the basic principle of physics and the ultimate principles of the universe: matter, life and reason. Therefore, the principle of least action is not necessarily an expression of sterile inanimateness. On the contrary, the principle of physics is related to the life principle of the universe, to the world of instincts behind the atomic world, in which the principles of physics, biology, and psychology arise from the same ultimate principle. Our research sheds new light to the sciences of physics, biology, and psychology in close relation to the basic principles. These ultimate principles have a primary importance in our understanding of the nature of Man and the Universe, together with the relations between Man and Nature, Man and the Universe. The results offer new foundations for our understanding our own role in the Earth, in the Nature and in the Universe. Even the apparently inanimate world of physics shows itself to be animate on long timescales and having a kind of pre- human consciousness in its basic organisation. This hypothesis offers a way to understand when and how the biological laws may direct physical laws, and, moreover, offers a new perspective to study and understand under which conditions can self-consciousness govern the laws of biology and physics. This point of view offers living beings and humans the possibility of strengthening our natural identity, and recognising the wide perspective arising from having access to the deepest ranges of our own human resources and realising the task for which human and individual life has been created. (shrink)

Since Aristotle the central question in biology was the origin of organic form; a question put in the backyard by neo-Darwinism that considers organic form as a side effect of the interactions between genes and their products. On the other hand, the fashionable notion of self-organization also fails to provide a true causal explanation for organic form. For Aristotle form is both a cause and the principle of intelligibility and this coupled to the classical concepts of potentiality and actuality provides (...) a rational framework,currently embodied in the contemporary concept of ‘attractor’, for understanding the origin of organic form. (shrink)

It is now increasingly accepted that many existing biological and medical ontologies can be improved by adopting tools and methods that bring a greater degree of logical and ontological rigor. In this chapter we will focus on the merits of a logically sound approach to ontologies from a methodological point of view. As we shall see, one crucial feature of a logically sound approach is that we have clear and functional definitions of the relational expressions such as ‘is a’ (...) and ‘part of ’. (shrink)

Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction form the building blocks of the (Neo-)Darwinian research program, and several of these have been called “Darwinian principles.” Here, we suggest that caution should be taken in calling these principles Darwinian because of the important role played by reticulate evolutionary mechanisms and processes in also bringing about these phenomena. Reticulate mechanisms and processes include symbiosis, symbiogenesis, lateral gene transfer, infective heredity mediated by genetic and organismal mobility, and (...) hybridization. Because the “Darwinian principles” are brought about by both vertical and reticulate evolutionary mechanisms and processes, they should be understood as foundational for a more pluralistic theory of evolution, one that surpasses the classic scope of the Modern and the Neo-Darwinian Synthesis. Reticulate evolution moreover demonstrates that what conventional (Neo-)Darwinian theories treat as intra-species features of evolution frequently involve reticulate interactions between organisms from very different taxonomic categories. Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction therefore cannot be understood as “traits” or “properties” of genes, organisms, species, or ecosystems because the phenomena are irreducible to specific units and levels of an evolutionary hierarchy. Instead, these general principles of evolution need to be understood as common goods that come about through interactions between different units and levels of evolutionary hierarchies, and they are exherent rather than inherent properties of individuals. (shrink)

I examine to what extent accounts of mechanisms based on formal interventionist theories of causality can adequately represent biological mechanisms with complex dynamics. Using a differential equation model for a circadian clock mechanism as an example, I first show that there exists an iterative solution that can be interpreted as a structural causal model. Thus, in principle, it is possible to integrate causal difference-making information with dynamical information. However, the differential equation model itself lacks the right modularity properties for (...) a full integration. A formal mechanistic model will therefore have to leave out either noncausal or causal explanatory relations. (shrink)

The free energy principle is notoriously difficult to understand. In this paper, we relate the principle to a framework that philosophers of biology are familiar with: Ruth Millikan’s teleosemantics. We argue that: systems that minimise free energy are systems with a proper function; and Karl Friston’s notion of implicit modelling can be understood in terms of Millikan’s notion of mapping relations. Our analysis reveals some surprising formal similarities between the two frameworks, and suggests interesting lines of future research. We hope (...) this will aid further philosophical evaluation of the free energy principle. (shrink)

Biological sex should be “acknowledged” and “accepted”—but which responses to gender dysphoria might this preclude? Trans-identified people may factually acknowledge their biological sex and regard transition as purely palliative. While generally some level of self-deception and even a high level of nonlying deception of others are sometimes justified, biological sex is important, and there is a nontrivial onus against even palliative, nonsexually motivated cross-dressing. The onus is higher against co-opting the body, even in a minor and/or reversible (...) way, to make a false communication concerning one’s sex. Hardest to defend is the destruction of sexual–reproductive functions and causally downstream functions such as lactation: due to the transcendent nature of sexual–reproductive functions, an appeal to the “principle of totality” here is misplaced. This is not to say that social, and milder medical, transition is absolutely excluded even for severe unmanageable dysphoria, nor that subsequent to any transition, detransition is necessarily required. (shrink)

Causal selection is the task of picking out, from a field of known causally relevant factors, some factors as elements of an explanation. The Causal Parity Thesis in the philosophy of biology challenges the usual ways of making such selections among different causes operating in a developing organism. The main target of this thesis is usually gene centrism, the doctrine that genes play some special role in ontogeny, which is often described in terms of information-bearing or programming. This paper is (...) concerned with the attempt of confronting the challenge coming from the Causal Parity Thesis by offering principles of causal selection that are spelled out in terms of an explicit philosophical account of causation, namely an interventionist account. I show that two such accounts that have been developed, although they contain important insights about causation in biology, nonetheless fail to provide an adequate reply to the Causal Parity challenge: Ken Waters's account of actual-difference making and Jim Woodward's account of causal specificity. A combination of the two also doesn't do the trick, nor does Laura Franklin-Hall's account of explanation (in this volume). We need additional conceptual resources. I argue that the resources we need consist in a special class of counterfactual conditionals, namely counterfactuals the antecedents of which describe biologically normal interventions. (shrink)

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

A model of brain function is presented that is consistently based on the biological principle of equilibrium. The neuronal modules of the cerebral cortex are proposed as units in which equilibrium between incoming signals and the synaptic structure is determined or established. Because of the electromagnetic activity of the brain, the electromagnetic properties of thecells are brought into focus. Due to the synaptic changes of the modules -essentially during sleep -an electromagnetic resting balance between the modules is established. Incoming (...) signals during the day, disturb the electromagnetic resting equilibrium and are detected and understood by this. The connecting nodes within the neuronal network are given by the equilibrium modules. Incoming information is represented in the form of the specific pathway of the network, while recognized information is represented by the equilibrium states within the modules. The paper leads to an understanding of information storage and processing in the brain. It even provides a hypothesis for understanding the emergence of the "self". Finally, the consideration of electromagnetic wave properties of neurons opens up a biophysical starting point to understanding conscious perceptions. In neuroscience, we lack a unifying theory of the brain. The reason for this may be an important detail –a missing link –that we do not yet see. Following the "track of biological equilibrium" in this paper leads to the hypothesis that the electromagnetic properties of the neurons are potential candidates to fill that gap. A hypothesis is developed describing their physiological significance in the processing of neurological information. (shrink)

This work addresses the autonomous organization of biological systems. It does so by considering the boundaries of biological systems, from individual cells to Home sapiens, in terms of the presence of Markov blankets under the active inference scheme—a corollary of the free energy principle. A Markov blanket defines the boundaries of a system in a statistical sense. Here we consider how a collective of Markov blankets can self-assemble into a global system that itself has a Markov blanket; thereby (...) providing an illustration of how autonomous systems can be understood as having layers of nested and self-sustaining boundaries. This allows us to show that: (i) any living system is a Markov blanketed system and (ii) the boundaries of such systems need not be co-extensive with the biophysical boundaries of a living organism. In other words, autonomous systems are hierarchically composed of Markov blankets of Markov blankets—all the way down to individual cells, all the way up to you and me, and all the way out to include elements of the local environment. (shrink)

I show how archaeologists have two problems. The construction of scenarios accounting for the raw data of Archaeology, the material remains of the past, and the explanation of pre-history. Within Archaeology, there has been an ongoing debate about how to constrain speculation within both of these archaeological projects, and archaeologists have consistently looked to biological mechanisms for constraints. I demonstrate the problems of using biology, either as an analogy for cultural processes or through direct application of biological (...) class='Hi'>principles to material remains. This is done through setting out the requirements of a Darwinian Archaeology, and then measuring various approaches against these requirements. This approach leads to the conclusion that archaeologist's explanations of the past must include within their formulations an account of human cognitive capacities within their explanatory framework. The limits of our understanding of the human past will be the limits of our understanding of Homo sapiens. (shrink)

Polger and Shapiro (2016) claim that unlike human-made artifacts cases of multiple realization in naturally occurring systems are uncommon. Drawing on cases from systems biology, I argue that multiple realization in naturally occurring systems is not as uncommon as Polger and Shapiro initially thought. The relevant cases, which I draw from systems biology, involve generalizable design principles called network motifs which recur in different organisms and species and perform specific functions. I show that network motifs with entirely different underlying (...) causal structures can perform the same function of interest. The article also considers the scope problem of multiple realization. (shrink)

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

Full applicability of physics to human biology does not necessarily imply that one can uncover a comprehensive, algorithmic correlation between physical brain states and corresponding mental states. The argument takes into account that information processing is finite in principle in a finite world. Presumbly the brain-mind-relation cannot be resolved in all essential aspects, particularly when high degrees of abstraction or self-analytical processes are involved. Our conjecture plausibly unifies the universal validity of physics and a logical limitation of human thought, and (...) it does not regard consciousness -the most basic human experience - as a marginal phenomenon. (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)

The notion of antifragility, an attribute of systems that makes them thrive under variable conditions, has recently been proposed by Nassim Taleb in a business context. This idea requires the ability of such systems to ‘tinker’, i.e., to creatively respond to changes in their environment. A fairly obvious example of this is natural selection-driven evolution. In this ubiquitous process, an original entity, challenged by an ever-changing environment, creates variants that evolve into novel entities. Analyzing functions that are essential during stationary-state (...) life yield examples of entities that may be antifragile. One such example is proteins with flexible regions that can undergo functional alteration of their side residues or backbone and thus implement the tinkering that leads to antifragility. This in-built property of the cell chassis must be taken into account when considering construction of cell factories driven by engineering principles. (shrink)

In her landmark book, Language, Thought, and Other Biological Categories (Millikan1984),1 Ruth Garrett Millikan utilizes the idea of a biological function to solve philosophical problems associated with the phenomena of language, thought, and meaning. Language and thought are activities of biological organisms, according to Millikan, and we should treat them as such when trying to answer related philosophical questions. Of special interest is Millikan’s treatment of intentionality. Here Millikan employs the notion of a biological function to (...) explain what it is for one thing in nature, a bee dance (43), for example, to be about another, in this case, the location of a nectar source. My concern in this paper is to understand whether Millikan’s account of intentionality adequately explains how humans achieve reference, in language or thought, to individuals and groups in their environment. In bringing her theory of intentional content to bear on human activities, Millikan focuses largely on natural language. Thus, in what follows, I begin by laying out the biology-based principles that underlie Millikan’s theory of content, then proceed with an explanation of how the theory is to apply to natural language. As it appears, Millikan’s account of how content is determined for natural language terms and sentences rests on the determinacy of intentional content at the psychological level. This leads me to take a careful look at what Millikan says about the content of mental representations, in hopes of finding a sufficient basis there for the application of Millikan’s theory of content to natural language. Ultimately, I conclude that Millikan’s theory faces a problem of vacuity. If we approach the theory as a theory of intentional content, intended to explain the nature of reference, the theory is lacking in an extremely important respect: Millikan explains how it could be one of the biological functions of a mental or natural language term to refer, without telling us precisely what in the natural order constitutes the reference relation.. (shrink)

A current advance within the agricultural industry is the use of genetic engineering to produce novel crops for food production. This technology raises questions about how societies should position themselves with respect to genetically modified (GM) crop development and implementation; namely, how should the potentials and risks of this technology be evaluated? We argue that current methods to evaluate the risks and benefits of GM crops are inadequate and not conducive to the strategic development of this technology, where a way (...) to ameliorate technology assessments for GM crops is to include farmers in the research process of evaluating these crops prior to their commercialization. However, particularities concerning the ethical status of such research require special consideration and vigilance. For example, in such technology assessment initiatives, farmers would occupy both the roles of research participant and research investigator. Other particularities surface due to factors related to the nature of GM crops. These particularities are examined with reference to concepts drawn from the field of research ethics, namely informed consent, compensatory decisions, and issues of participant inclusion/exclusion. (shrink)

The theory proposing a biological framework for a mathematical universe hypothesis posits that biological patterns define the fundamental nature of reality. These biological patterns are initially hidden from view, but can only be unveiled and understood through the knowledge of biology’s patterns and structurally mapping correspondences from the biological domain to a target domain. This perspective aligns with the ideas establishing perennial wisdom, a concept that encompasses universal and timeless spiritual truths found across various traditions. By (...) exploring the parallels between perennial wisdom's core ideas and the theory of a biological universe, we can assert that the mystical concepts of Pnimiyut and Chitzoniyut from Kabbalah may have been attempting to express the underlying principles surrounding a biological universe. In this essay, we will delve into the concepts of Pnimiyut and Chitzniyut and their potential connection to the biological nature of the universe. (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)

Disagreement about how best to think of the relation between theories and the realities they represent has a longstanding and venerable history. We take up this debate in relation to the free energy principle (FEP) - a contemporary framework in computational neuroscience, theoretical biology and the philosophy of cognitive science. The FEP is very ambitious, extending from the brain sciences to the biology of self-organisation. In this context, some find apparent discrepancies between the map (the FEP) and the territory (target (...) systems) a compelling reason to defend instrumentalism about the FEP. We take this to be misguided. We identify an important fallacy made by those defending instrumentalism about the FEP. We call it the literalist fallacy: this is the fallacy of inferring the truth of instrumentalism based on the claim that the properties of FEP models do not literally map onto real-world, target systems. We conclude that scientific realism about the FEP is a live and tenable option. (shrink)

Among the factors necessary for the occurrence of some event, which of these are selectively highlighted in its explanation and labeled as causes — and which are explanatorily omitted, or relegated to the status of background conditions? Following J. S. Mill, most have thought that only a pragmatic answer to this question was possible. In this paper I suggest we understand this ‘causal selection problem’ in causal-explanatory terms, and propose that explanatory trade-offs between abstraction and stability can provide a principled (...) solution to it. After sketching that solution, it is applied to a few biological examples, including to a debate concerning the ‘causal democracy’ of organismal development, with an anti-democratic (though not a gene-centric) moral. (shrink)

Ever since the advent of molecular biology in the 1970s, mechanical models have become the dogma in the field, where a "true" understanding of any subject is equated to a mechanistic description. This has been to the detriment of the biomedical sciences, where, barring some exceptions, notable new feats of understanding have arguably not been achieved in normal and disease biology, including neurodegenerative disease and cancer pathobiology. I argue for a "mechanism-plus-X" paradigm, where mainstay elements of mechanistic models such as (...) hierarchy and correlation are combined with nomological principles such as general operative rules and generative principles. Depending on the question at hand and the nature of the inquiry, X could range from proven physical laws to speculative biological generalizations, such as the notional principle of cellular synchrony. I argue that the "mechanism-plus-X" approach should ultimately aim to move biological inquiries out of the deadlock of oft-encountered mechanistic pitfalls and reposition biology to its former capacity of illuminating fundamental truths about the world. (shrink)

Much has been written about the free energy principle (FEP), and much misunderstood. The principle has traditionally been put forth as a theory of brain function or biological self-organisation. Critiques of the framework have focused on its lack of empirical support and a failure to generate concrete, falsifiable predictions. I take both positive and negative evaluations of the FEP thus far to have been largely in error, and appeal to a robust literature on scientific modelling to rectify the situation. (...) A prominent account of scientific modelling distinguishes between model structure and model construal. I propose that the FEP be reserved to designate a model structure, to which philosophers and scientists add various construals, leading to a plethora of models based on the formal structure of the FEP. An entailment of this position is that demands placed on the FEP that it be falsifiable or that it conform to some degree of biological realism rest on a category error. To this end, I deliver first an account of the phenomenon of model transfer and the breakdown between model structure and model construal. In the second section, I offer an overview of the formal elements of the framework, tracing their history of model transfer and illustrating how the formalism comes apart from any interpretation thereof. Next, I evaluate existing comprehensive critical assessments of the FEP, and hypothesise as to potential sources of existing confusions in the literature. In the final section, I distinguish between what I hold to be the FEP—taken to be a modelling language or modelling framework—and what I term “FEP models.”. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these (...) goals was that the OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Synthetic biology offers a powerful method to design and construct biological devices for human purposes. Two prominent design methodologies are currently used. Rational design adapts the design methodology of traditional engineering sciences, such as mechanical engineering. Directed evolution, in contrast, models its design principles after natural evolution, as it attempts to design and improve systems by guiding them to evolve in a certain direction. Previous work has argued that the primary difference between these two is the way they (...) treat variation: rational design attempts to suppress it, whilst direct evolution utilizes variation. I argue that this contrast is too simplistic, as it fails to distinguish different types of variation and different phases of design in synthetic biology. I outline three types of variation and show how they influence the construction of synthetic biological systems during the design process. Viewing the two design approaches with these more fine-grained distinctions provides a better understanding of the methodological differences and respective benefits of rational design and directed evolution, and clarifies the constraints and choices that the different design approaches must deal with. (shrink)

Kant’s theory of biology in the Critique of the Power of Judgment may be rejected as obsolete and attacked from two opposite perspectives. In light of recent advances in biology one can claim contra Kant, on the one hand, that biological phenomena, which Kant held could only be explicated with the help of teleological principles, can in fact be explained in an entirely mechanical manner, or on the other, that despite the irreducibility of biology to physico-mechanical explanations, it (...) is nonetheless proper science. I argue in response that Kant’s analysis of organisms is by no means obsolete. It reveals biology’s uniqueness in much the same way as several current theorists do. It brings to the fore the unique purposive characteristics of living phenomena, which are encapsulated in Kant’s concept of “natural end” and which must be explicated in natural terms in order for biology to become a science. I maintain that Kant’s reluctance to consider biology proper science is not a consequence of his critical philosophy but rather of his inability to complete this task. Kant lacked an appropriate theoretical framework, such as provided later by modern biology, which would enable the integration of the unique features of biology in an empirical system. Nevertheless, as I show in this paper, the conceptual problems with which Kant struggled attest more to the relevance and depth of his insights than to the shortcomings of his view. His contribution to the biological thought consists in insisting on an empirical approach to biology and in providing the essential philosophical underpinning of the autonomous status of biology. (shrink)

The anti-reductionist character of the recent philosophy of biology and the dynamic development of the science of emergent properties prove that the time is ripe to reintroduce the thought of Aristotle, the first advocate of a “top-down” approach in life-sciences, back into the science/philosophy debate. His philosophy of nature provides profound insights particularly in the context of the contemporary science of evolution, which is still struggling with the questions of form, teleology, and the role of chance in evolutionary processes. However, (...) although Aristotle is referenced in the evolutionary debate, a thorough analysis of his theory of hylomorphism and the classical principle of causality which he proposes is still needed in this exchange. Such is the main concern of the first part of the present article which shows Aristotle’s metaphysics of substance as an open system, ready to incorporate new hypothesis of modern and contemporary science. The second part begins with the historical exploration of the trajectory from Darwin to Darwinism regarded as a metaphysical position. This exploration leads to an inquiry into the central topics of the present debate in the philosophy of evolutionary biology. It shows that Aristotle’s understanding of species, teleology, and chance – in the context of his fourfold notion of causality – has a considerable explanatory power which may enhance our understanding of the nature of evolutionary processes. This fact may inspire, in turn, a retrieval of the classical theology of divine action, based on Aristotelian metaphysics, in the science/theology dialogue. The aim of the present article is to prepare a philosophical ground for such project. (shrink)

Chance and necessity are mainstays of explanation in current biology, dominated by the neo-Darwinian outlook, a blend of the theory of evolution by natural selection with the basic tenets of population genetics. In such a framework the form of living organisms is somehow a side effect of highly contingent, historical accidents. Thus, at a difference of other sciences, biology apparently lacks theoretical principles that in a law-like fashion may explain the emergence and persistence of the characteristic forms of living (...) organisms that paradoxically, given the current importance attributed to chance, can be grouped into organized structural typologies. Nevertheless, the present essay shows that since its origins in Aristotelian natural history, biology aimed at achieving rational, non-accidental, explanations for the wide variety of living forms endowed with characteristic behaviors that constitute the landscape of biological species. (shrink)