Philosophy of Biology, Miscellaneous

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

The notion of habit used in neuroscience is an inheritance from a particular theoretical origin, whose main source is William James. Thus, habits have been characterized as rigid, automatic, unconscious, and opposed to goal-directed actions. This analysis leaves unexplained several aspects of human behavior and cognition where habits are of great importance. We intend to demonstrate the utility that another philosophical conception of habit, the Aristotelian, may have for neuroscientific research. We first summarize the current notion of habit in neuroscience, (...) its philosophical inspiration and the problems that arise from it, mostly centered on the sharp distinction between goal-directed actions and habitual behavior. We then introduce the Aristotelian view and we compare it with that of William James. For Aristotle, a habit is an acquired disposition to perform certain types of action. If this disposition involves an enhanced cognitive control of actions, it can be considered a “habit-as-learning”. The current view of habit in neuroscience, which lacks cognitive control and we term “habit-as-routine”, is also covered by the Aristotelian conception. He classifies habits into three categories: (1) theoretical, or the retention of learning understood as “knowing that x is so”; (2) behavioral, through which the agent achieves a rational control of emotion-permeated behavior (“knowing how to behave”); and (3) technical or learned skills (“knowing how to make or to do”). Finally, we propose new areas of research where this “novel” conception of habit could serve as a framework concept, from the cognitive enrichment of actions to the role of habits in pathological conditions. In all, this contribution may shed light on the understanding of habits as an important feature of human action. Habits, viewed as a cognitive enrichment of behavior, are a crucial resource for understanding human learning and behavioral plasticity. (shrink)

Margulis’ evolutionary theory entails a revision of certain core concepts of traditional biology. One of these changes is related to the hot debate about units of selection. This paper considers Margulis’ proposal as a new research tradition (RT) and evaluates its consequences to the mentioned issue. Three ideas are suggested here: firstly, that her theory represents the revision of many classical biological concepts; secondly, that her position implies a reappraisal of many traditional issues in philosophy of biology; and thirdly, that (...) studying it from Lakatos and Laudan’s ideas about RT allows us to enlighten the richness of her theory. (shrink)

Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, holobiont detractors argue that they are just mere chimeras or ecological communities, but not individuals. Both parties in the dispute develop their arguments from the framework of the philosophy of biology, in terms (...) of what it takes for a “conglomerate” to be considered an interesting individual from a biological point of view. However, the debates about holobiont individuality have important ontological implications that have remained vaguely explored from a metaphysical framework. The purpose of this paper is to cover that gap by presenting a metaphysical approach to holobionts individuality. Drawing upon a conception of natural selection that puts the focus on the transgenerational recurrence of the traits and that supports the thesis that holobionts are units of selection, we argue that holobionts bear emergent traits and exert downward powers over the entities that compose them. In this vein, we argue, a reasonable argument can be made for conceiving holobionts as emergent biological individuals. (shrink)

In questo lavoro si dimostra che l'opinione comune, secondo cui è Heidegger a introdurre Jacob von Uexküll nel dibattito filosofico è scorretta, in quanto è Scheler, due decenni prima, a scoprire e valorizzare la portata filosofica di Uexküll. -/- Pure la distinzione fra mondo (Welt) e ambiente (Umwelt), come quella fra apertura al mondo e chiusura ambientale, non è introdotta da Heidegger nel 1929 (cfr. l'Introduzione di Marco Mazzeo al testo di Uexküll, Ambienti animali e ambienti umani, p.18 e seg.) (...) ma è già presente in Scheler negli scritti del periodo 1909-1913. (shrink)

How comes that two organisms can interact with each other or that we can comprehend what the other experiences? The theories of embodiment, intersubjectivity or empathy have repeatedly taken as their starting point an individualistic assumption (the comprehension of the other comes after the self-comprehension) or a cognitivist one (the affective dimension follows the cognitive process). The thesis of this book is that there are no two isolated entities at the origin which successively interact with each other. There is, rather, (...) an impersonal stratum – the original affectivity (Gefühlsdrang) – which lets the living organisms be constitutively attuned with the expressive dimension of the life from the very beginning. The book aims to rethink the issue of corporality on the basis of a biosemiotics of the interaction between lived body (Leib) and environment (Umwelt). The human emotions reveals themselves as devices that experiment further attunement levels and expose the human being – because of her ex-centricity – to the alienation in various forms of the psychopathological existence. This is an unprecedented perspective that turns to psychopathology to reread against the light the watermark weaving the structure of personal singularity. What emerges is an intermediate territory confining both with philosophy and psychiatry: the psychopathology of ordo amoris. The author advances the project of a new psychopathology of ordo amoris, not only tackling with the 19th-century tradition of psychiatry and phenomenological psychopathology, but also with the contemporary disputes on intersubjectivity in phenomenology and with those on schizophrenia as disruption of aida or as disembodiment process in psychiatry. What results from his project is the first systematic study on the international level showing the relevance of Schelerian concepts of body schema (Leibschema) and order of feeling (ordo amoris) to understand the disruptions of emotional regulation on the psychopathological dimension as well as on the formation process of the singularity. (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)

Through an empirical account of Knowledge Management-enabled research in systems biology, we argue that computational KM helps produce new first-order biological knowledge, in new ways. KM is enabled by conceiving of ‘knowledge’ as an object for computational science: explicated in the text of biological articles and computable via appropriate data and metadata. These founded concepts risk underestimating practice-based knowing in ensuring the validity of ‘manageable’ knowledge as knowledge.

Robert Wilson’s The Eugenic Mind Project is a major achievement of engaged scholarship and socially relevant philosophy and history of science. It exemplifies the virtues of interdisciplinarity. As principal investigator of the Living Archives on Eugenics in Western Canada project, while employed in the Department of Philosophy at the University of Alberta, Wilson encountered a proverbial big ball of mud with questions and issues that involved local individuals living through a painful set of memories and implicated his institutional home in (...) outstanding moral obligations. It is engaged scholarship because it required building relationships with affected persons and taking responsibility for his institution’s legacy, as well as transforming Wilson’s own outlook along the way. It is socially relevant philosophy and history of science because it brings to light issues that remain salient today, especially how eugenic themes are ubiquitous in societal discourse and evinced in everyday decisions. It is interdisciplinary because to accomplish this type of analysis requires intellectual gymnastics that range over diverse domains of research: from standpoint theory and disability studies to oral history and governmental policy; from the evolutionary biology of prosociality and variation to conceptual questions about the categorization of human traits and types. (shrink)

[A slightly revised version of this paper has been accepted by the BJPS] More attention has been devoted to providing evolutionary scenarios accounting for the development of beliefs, or belief-like states, than for desires or preferences. Here I articulate and defend an evolutionary rationale for the development of psychologically real preference states. Preferences token or represent the expected values of discriminated states, available actions, or action-state pairings. The argument is an application the ‘environmental complexity thesis’ found in Godfrey-Smith and Sterelny, (...) although my conclusions differ from Sterelny’s. I argue that tokening expected utilities can, under specified general conditions, be a powerful design solution to the problem of allocating the capacities of an agent in an efficient way. Preferences are for efficient action selection, and are a ‘fuel for success’ in the sense urged by Godfrey-Smith for true beliefs. They will tend to be favoured by selection when environments are complex in ways that matter to an organism, and when organisms have rich behavioural repertoires with heterogenous returns and costs. The rationale suggested here is conditional, especially on contingencies in what design options are available to selection and on trade-offs associated with the costs of generating and processing representations of value. The unqualified efficiency rationale for preferences suggests that organisms should represent expected utilities in a comprehensive and consistent way, but none of them do. In the final stages of the paper I consider some of the ways in which design trade-offs compromise the implementation of preferences in organisms that have them. (shrink)

The aim of this article is to identify the strongest evolutionary debunking argument against moral realism and to assess on which empirical assumptions it relies. In the recent metaethical literature, several authors have de-emphasized the evolutionary component of EDAs against moral realism: presumably, the success or failure of these arguments is largely orthogonal to empirical issues. I argue that this claim is mistaken. First, I point out that Sharon Street’s and Michael Ruse’s EDAs both involve substantive claims about the evolution (...) of our moral judgments. Next, I argue that combining their respective evolutionary claims can help debunkers to make the best empirical case against moral realism. Some realists have argued that the very attempt to explain the contents of our endorsed moral judgments in evolutionary terms is misguided, and have sought to escape EDAs by denying their evolutionary premise. But realists who pursue this reply can still be challenged on empirical grounds: debunkers may argue that the best, scientifically informed historical explanations of our moral endorsements do not involve an appeal to mind-independent truths. I conclude, therefore, that the empirical considerations relevant for the strongest empirically driven argument against moral realism go beyond the strictly evolutionary realm; debunkers are best advised to draw upon other sources of genealogical knowledge as well. (shrink)

We review some of the main implications of the free-energy principle (FEP) for the study of the self-organization of living systems – and how the FEP can help us to understand (and model) biotic self-organization across the many temporal and spatial scales over which life exists. In order to maintain its integrity as a bounded system, any biological system - from single cells to complex organisms and societies - has to limit the disorder or dispersion (i.e., the long-run entropy) of (...) its constituent states. We review how this can be achieved by living systems that minimize their variational free energy. Variational free energy is an information theoretic construct, originally introduced into theoretical neuroscience and biology to explain perception, action, and learning. It has since been extended to explain the evolution, development, form, and function of entire organisms, providing a principled model of biotic self-organization and autopoiesis. It has provided insights into biological systems across spatiotemporal scales, ranging from microscales (e.g., sub- and multicellular dynamics), to intermediate scales (e.g., groups of interacting animals and culture), through to macroscale phenomena (the evolution of entire species). A crucial corollary of the FEP is that an organism just is (i.e., embodies or entails) an implicit model of its environment. As such, organisms come to embody causal relationships of their ecological niche, which, in turn, is influenced by their resulting behaviors. Crucially, free-energy minimization can be shown to be equivalent to the maximization of Bayesian model evidence. This allows us to cast natural selection in terms of Bayesian model selection, providing a robust theoretical account of how organisms come to match or accommodate the spatiotemporal complexity of their surrounding niche. In line with the theme of this volume; namely, biological complexity and self-organization, this chapter will examine a variational approach to self-organization across multiple dynamical scales. (shrink)

How do we know what we know? • How do we perceive ourselves and the world around? • Is what we perceive the only reality that exists? (or) • Is there a different reality other than what we perceive? (Not referring to the source of C, but to the CoC, in the very limit of our physical structure).

Peña-Guzmán (2017) argues that empirical evidence and evolutionary theory compel us to treat the phenomenon of suicide as continuous in the animal kingdom. He defends a “continuist” account in which suicide is a multiply-realizable phenomenon characterized by self-injurious and self-annihilative behaviors. This view is problematic for several reasons. First, it appears to mischaracterize the Darwinian view that mind is continuous in nature. Second, by focusing only on surface-level features of behavior, it groups causally and etiologically disparate phenomena under a single (...) conceptual umbrella, thereby reducing the account’s explanatory power. Third, it obscures existing analyses of suicide in biomedical ethics and animal welfare literatures. A more promising naturalistic approach might seek a theoretical understanding of the social/ecological circumstances that drive humans and perhaps other animals to self-destruction. (shrink)

In the late 19th century Husserl studied our internal sense of time passing, maintaining that its deep connections into experience represent prima facie evidence for it as the basis for all investigations in the sciences: Phenomenology was born. Merleau-Ponty focused on perception pointing out that any theory of experience must in accord with established aspects of biology i.e. embodied. Recent analyses suggest that theories of experience require non-reductive, integrative information, together with a specific property connecting them to experience. Here we (...) elucidate a new class of information states with just such properties found at the loci of control of complex biological systems, including nervous systems. Complexity biology concerns states satisfying self-organized criticality. Such states are located at critical instabilities, commonly observed in biological systems, and thought to maximize information diversity and processing, and hence to optimize regulation. Major results for biology follow: why organisms have unusually low entropies; and why they are not merely mechanical. Criticality states form singular self-observing systems, which reduce wave packets by processes of perfect self-observation associated with feedback gain g=1. Analysis of their information properties leads to identification of a new kind of information state with high levels of internal coherence, and feedback loops integrated into their structure. The major idea presented here is that the integrated feedback loops are responsible for our ‘sense of self’, and also the feeling of continuity in our sense of time passing. Long-range internal correlations guarantee a unique kind of non-reductive, integrative information structure enabling such states to naturally support phenomenal experience. Being founded in complexity biology, they are ‘embodied’; they also fulfill the statement that ‘The self is a process’, a singular process. High internal correlations and RenéThom-style catastrophes support non-digital forms of information, gestalt cognition, and information transfer via quantum teleportation. Criticality in complexity biology can ‘embody’ cognitive states supporting gestalts, and phenomenology’s senses of ‘self,’ time passing, existence and being. (shrink)

In this paper we challenge the notion of ‘normativity’ used by some enactive approaches to cognition. We define some varieties of enactivism and their assumptions and make explicit the reasoning behind the co-emergence of individuality and normativity. Then we argue that appealing to dispositions for explaining some living processes can be more illuminating than claiming that all such processes are normative. For this purpose, we will present some considerations, inspired by Wittgenstein, regarding norm-establishing and norm-following and show that attributions of (...) normativity to non-social agents are deeply paradoxical. The main conclusions of our discussion are: (1) circular and internal explanations centred on the stability of living systems are insufficient to account for processes where the environment plays an important role, such as adaptation. Enactivism is not an explanatory alternative to evolutionary biology but needs it as a complement to accounts focused on the internal self-assembly of organisms; (2) though we share enactivism’s anti-representational spirit, we argue that ecological psychology can offer a better account of perception. (shrink)

This article develops an account of local epistemic practices on the basis of case studies from ethnobiology. I argue that current debates about objectivity often stand in the way of a more adequate understanding of local knowledge and ethnobiological practices in general. While local knowledge about the biological world often meets criteria for objectivity in philosophy of science, general debates about the objectivity of local knowledge can also obscure their unique epistemic features. In modification of Ian Hacking’s suggestion to discuss (...) “ground level questions” instead of objectivity, I propose an account that focuses on both epistemic virtues and vices of local epistemic practices. (shrink)

Definition The authors’ definition of the autopoietic system has evolved through the years. One of them states that an autopoietic system is organized (defined as a unity) as a network of processes of production (transformation and destruction) of components that produces the components which: (1) through their interactions and transformations regenerate and realize the network of processes (relations) that produced them; and (2) constitute it (the machine) as a concrete unity in the space in which they exist by specifying the (...) topological domain of its realization as such a network (Varela 1979, p. 13). Nearly the same formula was earlier used to define an autopoietic machine (Maturana and Varela 1973/1980, 1984/1987, p. 135). (shrink)

Although they are continually compositionally reconstituted and reconfigured, organisms nonetheless persist as ontologically unified beings over time – but in virtue of what? A common answer is: in virtue of their continued possession of the capacity for morphological invariance which persists through, and in spite of, their mereological alteration. While we acknowledge that organisms‟ capacity for the “stability of form” – homeostasis - is an important aspect of their diachronic unity, we argue that this capacity is derived from, and grounded (...) in a more primitive one – namely, the homeodynamic capacity for the “specified variation of form”. In introducing a novel type of causal power – a „structural power‟ – we claim that it is the persistence of their dynamic potential to produce a specified series of structurally adaptive morphologies which grounds organisms‟ privileged status as metaphysically “one over many” over time. (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)

Part of a special issue, Ontologies of Living Beings, guest-edited by A. M. Ferner and Thomas Pradeu.

Since the fundamental challenge that I laid at the doorstep of the pluralists was to defend, with nonderivative models, a strong notion of genic cause, it is fatal that Waters has failed to meet that challenge. Waters agrees with me that there is only a single cause operating in these models, but he argues for a notion of causal ‘parsing’ to sustain the viability of some form of pluralism. Waters and his colleagues have some very interesting and important ideas about (...) the sciences, involving pluralism and parsing or partitioning causes, but they are ideas in search of an example. He thinks he has found an example in the case of hierarchical and genic selection. I think he has not. (shrink)

With neurons emergence, life alters itself in a remarkable way. This embodied neurons become carriers of signals, and processing devices: it begins an inexorable progression of functional complexity, from increasingly drawn behaviors to the mind and eventually to consciousness [Damasio, 2010]. In which moment has awareness arisen in the history of life? The emergence of human consciousness is associated with evolutionary developments in brain, behavior and mind, which ultimately lead to the creation of culture, a radical novelty in natural history. (...) It is in this context of biological evolution of conscious brains that we raise the question: how conscious brains connect with each other? In order to answer it, I will explore how brain states and conscious states each participate in dynamic interactive processes involving the whole organism. I will argue that a possible way to overcome the hard problem of consciousness might be based on the notion of embodiment as a process of embedding the mental in the living organism relating dynamically with the environment through the sensorymotor experience. In order to do so, I will provide an assembly between an anthropologic perspective of consciousness with contemporary Philosophy of Mind, Interaction Theory [Gallagher 2001, 2008; Zahavi 2001, 2008; Fuchs and De Jaegher 2009]. (shrink)

Judgments of plausibility involve appearance of the truth or reasonableness, which is always a function of background knowledge. What anyone will countenance is conditioned by what they already know (or think they know). Marc Kirschner (professor of systems biology at Harvard) and John Gerhart (professor of molecular and cell biology at the University of California—Berkeley) aim to show that molecular, cellular, and developmental processes relevant to the generation of phenotypic variation in anatomy, physiology, and behavior demonstrate how evolutionary processes, especially (...) the origins of novelty, are plausible. The outstanding question for Kirschner and Gerhart concerns not the modification of structures but their origination—a question unanswered by the theoretical framework of the modern synthesis. (shrink)

Sterelny (2003) develops an idealised natural history of folk-psychological kinds. He argues that belief-like states are natural elaborations of simpler control systems, called detection systems, which map directly from environmental cue to response. Belief-like states exhibit robust tracking (sensitivity to multiple environmental states), and response breadth (occasioning a wider range of behaviours). The development of robust tracking and response-breadth depend partly on properties of the informational environment. In a transparent environment the functional relevance of states of the world is directly (...) detectable. Outside transparent environments, selection can favour decoupled representations. Sterelny maintains that these arguments do not generalise to desire. Unlike the external environment, the internal processes of an organism, he argues, are selected for transparency. Parts of a single organism gain nothing from deceiving one another, but gain significantly from accurate signalling of their states and needs. Key conditions favouring the development of belief-like states are therefore absent in the case of desires. Here I argue that Sterelny’s reasons for saying that his treatment of belief does not generalise to motivation (desires, or preferences) are insufficient. There are limits to the transparency that internal environments can achieve. Even if there were not, tracking the motivational salience of external states suggests possible gains for systematic tracking of outcome values in any system in which selection has driven the production of belief-like states. (shrink)

The is the Editorial of the 2015 JPBMB Special Issue on Integral Biomathics: Life Sciences, Mathematics and Phenomenological Philosophy.

Background— Although one of the main characteristics of psychopaths is a deficit in emotion, it is unknown whether they show a fundamental impairment in appropriately recognizing their own body sensations during an emotion-inducing task. Method— Skin conductance and heart rate were recorded in 138 males during a social stressor together with subjective reports of body sensations. Psychopathic traits were assessed using the Psychopathy Checklist – Revised (PCL-R) 2nd edition (Hare, 2003). Results— Nonpsychopathic controls who reported higher body sensations showed higher (...) heart rate reactivity, but this verbal-autonomic consistency was not found in psychopathic individuals. This mind-body disconnection is particularly associated with the interpersonal-affective factor of psychopathy. Conclusions— Findings are the first to document this body sensations– autonomic mismatch in psychopaths, and suggest that somatic aphasia the inaccurate identification and recognition of one‘s own somatic states may partly underlie the interpersonal-affective features of psychopaths. (shrink)

When a group of processes achieves such closure that a set of states of affairs recurs continually, then the effect of that coherence on the world differs from what would occur in the absence of that closure. Such altered effectiveness is an attribute of the system as a whole, and would have consequences. This indicates that the network of processes, as a unit, has ontological significance. Whenever a network of processes generates continual return to a limited set of states of (...) affairs, the system may function as a “whole”— with respect to appropriate interaction partners. The balance achieved by the processes provides the form of definiteness of a unified agent. The causal powers of such coherent aggregates are indeed just the powers of the “constituents acting in concert”. However, the components act in concert in the specific way they do only because of their inclusion in the closed set of interactions that defines the coherence. This renders the causal powers of the coherence defined by that closure non-redundant, and hence the coherence, as a unit, is ontologically significant. The form of definiteness that provides internal coherence also grounds external efficacy of the societal aggregation. The closure is a structural feature of the coherence — possibly, but not necessarily, apparent in spatial structuring. This approach can provide a unified account that includes quantum microphysics, systems biology, and the philosophy of organism ─ without reducing any of these to another. (shrink)

In this paper I provide a frequentist philosophical-methodological solution for the stopping rule problem presented by Lindley & Phillips in 1976, which is settled in the ecological realm of testing koalas’ sex ratio. I deliver criteria for discerning a stopping rule, an evidence and a model that are epistemically more appropriate for testing the hypothesis of the case studied, by appealing to physical notion of probability and by analyzing the content of possible formulations of evidence, assumptions of models and meaning (...) of the ecological hypothesis. First, I show the difference in the evidence taken into account in different frequentist sampling procedures presented in the problem. Next, I discuss the inapplicability of the Carnapian principle of total evidence in deciding which formulation of evidence associated with a given sampling procedure and statistical model is epistemically more appropriate for testing the hypothesis in question. Then I propose a double-perspective (evidence and model) frequentist solution based on the choice of evidence which better corresponds to the investigated ecological hypothesis, as well as on the choice of a model that embraces less unrealistic ontological assumptions. Finally, I discuss two perspectives of the stopping rule dependence. (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)

This paper shows that the identity of living things is a composite reality. It also suggests that the immune system constitutes a unifying process for the organism.

The articles in this issue represent the pursuit of a new understanding of the human past, one that can replace the neo-saltationist view of a human revolution with models that can account for the complexities of the archaeological record and of human social lives. The articulation of archaeological, philosophical, and biological perspectives seems to offer a strong foundation for exploring available evidence, and this was the rationale for collecting these particular articles. Even at this preliminary stage there is a coherence (...) emerging in proposals: the origin and operation of symbolically rich, complexly signaling human social systems was the consequence of the long-term evolution of multiple components of perceiving and negotiating social interactions, a contingent outcome of myriad adaptive shifts rather than a single event. (shrink)

In the past five years, there have been a series of papers in the journal Evolution debating the relative significance of two theories of evolution, a neo-Fisherian and a neo-Wrightian theory, where the neo-Fisherians make explicit appeal to parsimony. My aim in this paper is to determine how we can make sense of such an appeal. One interpretation of parsimony takes it that a theory that contains fewer entities or processes, (however we demarcate these) is more parsimonious. On the account (...) that I defend here, parsimony is a ‘local’ virtue. Scientists’ appeals to parsimony are not necessarily an appeal to a theory’s simplicity in the sense of it’s positing fewer mechanisms. Rather, parsimony may be proxy for greater probability or likelihood. I argue that the neo-Fisherians appeal is best understood on this interpretation. And indeed, if we interpret parsimony as either prior probability or likelihood, then we can make better sense of Coyne et al. argument that Wright’s three phase process operates relatively infrequently. (shrink)

The articles in this issue reflect the results of the 25th Altenberg Workshop in Theoretical Biology on ‘‘The Meaning of ‘Theory’ in Biology’’ held at the Konrad Lorenz Institute for Evolution and Cognition Research, Altenberg, Austria, 30 June–3 July, 2011.

Issues of nature conservation, and socio-cultural movement called ecologism, are vivid becouse of it’s many controvertions and actual validity in terms of sustainable development. This paper presents contemporary motives of preserving the nature, scientific ways of it’s realization, and chosen issues of so called „ecological spirituality”. Reflection on the abilities and perils of science and spirituality, with reference to philosophy and practical conservation activity, will be led. Finally, there will be an attemption to answer the question about relation between nature (...) preservation, science and ecological spirituality, and to define the spiritual condition and trends in contemporary ecologism. (shrink)

Medical science conceives the human body as a system comprised of many subsystems at a variety of levels. At the highest level are bodily systems proper, such as the endocrine system, which are central to our understanding of human anatomy, and play a key role in diagnosis and in dynamic modeling as well as in medical pedagogy and computer visualization. But there is no explicit definition of what a bodily system is; such informality is acceptable in documentation created for human (...) beings, but falls short of what is needed for computer representations. Our analysis is intended as a first step towards filling this gap. (shrink)

Povinelli and colleagues ask whether chimpanzees can understand the concept of weight, answering with a resounding ‘‘no’’. They justify their answer by appeal to over thirty previously unpublished experiments. I here evaluate in detail Povinelli’s arguments against his targets, questioning the assumption that such comparative questions will be resolved with an unequivocal ‘‘yes’’ or ‘‘no’’.

A descriptive role is suggested for uracil as a temporal divide in the immediate aspects of metabolism verses long term maintained genetic transmission. In particular, details of the mechanism of excision repair of uracil from DNA based on differential parameters of spatial distortion of the planar uracil molecule within the DNA helix verses RNA, when viewed in analogy to a proposed model for space involving the substitution of the act of mirroring for the element of time in processes and a (...) descending complexity of structure with time of evolution, suggest the possibility that negative selection against decreased lifetime is the singular motive force of natural selection. The geometry of the Mobius strip, as it has a plane of mirroring symmetry, a twist able to account for torque in nature, an inversion of inside and out seen in biological structures, and an endless surface that can be accommodated to an atemporal account of physical processes is employed in a holistic model to elaborate a negative selection opposing death as zero volume or the logical existence of physical constraint to volumes that is represented as the ubiquitous inability of witnessing objects of any type to witness simultaneously both a self reflection and the reflection of self reflection. A role for uracil and its’ physical structure, in a model in which both are evolved from the mirroring of events of the witnessing of energies, is elaborated in which temporal aspects such as those entailed in existing models of natural evolution are considered inappropriate in perspectives that are oriented positively towards a successful comprehension of processes; focus is placed instead upon the geometry and arrangement of physical spaces. (shrink)

Are living organisms--as Descartes argued--just machines? Or is the nature of life such that it can never be fully explained by mechanistic models? In this thought-provoking and controversial book, eminent geophysicist Walter M. Elsasser argues that the behavior of living organisms cannot be reduced to physico-chemical causality. Suggesting that molecular biology today is at the same point as Newtonian physics on the eve of the quantum revolution, Elsasser lays the foundation for a theoretical biology that points the way toward a (...) natural philosophy of organic life. Explicitly repudiating "vitalism" (the notion that the laws of nature need to be modified when applied to living organisms), Elsasser argues instead that the structural complexity of even a single living cell is "transcomputational"--that is, beyond the power of any imaginable system to compute. Beginning from this insight, Elsasser leads the reader through a step-by-step process that ultimately arrives at the conclusion that living and non-living matter are separated by "a no-man's land of irrationality." Trained in Germany as a physicist, Elsasser first pondered the implications of quantum mechanics for biology as early as 1951. The more closely he studied the inherent complexity of life, the more skeptical he became of the reductionist view of organisms as tiny machines. "An organism," he concluded, "is a source of causal chains which cannot be traced beyond a terminal point because they are lost in the unfathomable complexity of the organism." Like the physicist who works within the bounds of an unfathomable universe, Elsasser argues, the biologist must seek answers within a system that is no less unfathomable. (shrink)

The so-called “Baldwin Effect” has been studied for years in the fields of Artificial Life, Cognitive Science, and Evolutionary Theory across disciplines. This idea is often conflated with genetic assimilation, and has raised controversy in trans-disciplinary scientific discourse due to the many interpretations it has. This paper revisits the “Baldwin Effect” in Baldwin’s original spirit from a joint historical, theoretical and experimental approach. Social Heredity – the inheritance of cultural knowledge via non-genetic means in Baldwin’s term – is also taken (...) into consideration. I shall argue that the Baldwin Effect can occur via social heredity without necessity for genetic assimilation. Computational experiments are carried out to show that when social heredity is permitted with high fidelity, there is no need for the assimilation of acquired characteristics; instead the Baldwin Effect occurs as promoting more plasticity to facilitate future intelligence. The role of mind and intelligence in evolution and its implications in an extended synthesis of evolution are briefly discussed. (shrink)

Synthetic biology is described as a new field of biotechnology that models itself on engineering sciences. However, this view of synthetic biology as an engineering field has received criticism, and both biologists and philosophers have argued for a more nuanced and heterogeneous understanding of the field. This paper elaborates the heterogeneity of synthetic biology by clarifying the role of design and the variability of design methodologies in synthetic biology. I focus on two prominent design methodologies: rational design and directed evolution. (...) Rational design resembles the design methodology of traditional engineering sciences. However, it is often replaced and complemented by the more biologically-inspired method of directed evolution, which models itself on natural evolution. These two approaches take philosophically different stances to the design of biological systems. Rational design aims to make biological systems more machine-like, whereas directed evolution utilizes variation and emergent features of living systems. I provide an analysis of the methodological basis of these design approaches, and highlight important methodological differences between them. By analyzing the respective benefits and limitations of these approaches, I argue against the engineering-dominated conception of synthetic biology and its “methodological monism”, where the rational design approach is taken as the default design methodology. Alternative design methodologies, like directed evolution, should be considered as complementary, not competitive, to rational design. (shrink)

Review of: Sophia Roosth, Synthetic: How Life Got Made (University of Chicago Press, 2017); and Andrew S. Balmer, Katie Bulpin, and Susan Molyneux-Hodgson, Synthetic Biology: A Sociology of Changing Practices (Palgrave Macmillan, 2016).

Much of the basic non-technical vocabulary of artificial intelligence is surprisingly ambiguous. Some key terms with unclear meanings include intelligence, embodiment, simulation, mind, consciousness, perception, value, goal, agent, knowledge, belief, optimality, friendliness, containment, machine and thinking. Much of this vocabulary is naively borrowed from the realm of conscious human experience to apply to a theoretical notion of “mind-in-general” based on computation. However, if there is indeed a threshold between mechanical tool and autonomous agent (and a tipping point for singularity), projecting (...) human conscious-level notions into the operations of computers creates confusion and makes it harder to identify the nature and location of that threshold. There is confusion, in particular, about how—and even whether—various capabilities deemed intelligent relate to human consciousness. This suggests that insufficient thought has been given to very fundamental concepts—a dangerous state of affairs, given the intrinsic power of the technology. It also suggests that research in the area of artificial general intelligence may unwittingly be (mis)guided by unconscious motivations and assumptions. While it might be inconsequential if philosophers get it wrong (or fail to agree on what is right), it could be devastating if AI developers, corporations, and governments follow suit. It therefore seems worthwhile to try to clarify some fundamental notions. (shrink)

La educación en el periodo digital en el que vivimos está alcanzando retos nunca antes vistos, precedidos por fenómenos que involucran no solamente a unidades sociales tradicionales, sino también a las nuevas comunidades virtuales; innovar es difícil, es un reto, no obstante, hay que pensar en nuevos métodos de enseñanza que impacten a la actual generación de estudiantes, los mismos que llegan con nuevas necesidades y expectativas. La construcción del conocimiento desde el sujeto y el mundo virtual que lo rodea, (...) establece la base para el desarrollo de un nuevo modelo de enseñanza, donde el salón de clase es la representación particular de un nuevo ecosistema físico-cibernético compuesto por las tres grandes dimensiones que forman parte de esta nueva convergencia tecno-social (humano – información – maquina); permitiendo una interrelación entre el estudiante, la información, la máquina y el profesor; usando métodos Biocibernéticos de influencia, control y replica, mediante el vector masivo de impacto (i); además, el desarrollo de nuevas estrategias asistidas por la cibernética y la actualización del contenido académico acorde al nuevo ambiente de enseñanza. De ahí la importancia de este estudio, el cual nos lleva a la necesidad de un nuevo modelo transformador de instrucción académica, el cual no se base en un conglomerado de herramientas tecnológicas, más establezca un nuevo modelo educativo y transformador, basado en el “pensamiento colaborativo” y la ubicuidad de la información, estableciendo así la relación entre el sujeto y objeto de estudio, permitiéndonos de esta manera establecer el nuevo paradigma educativo Biocibernético en el periodo digital. (shrink)

El humanismo tradicional del siglo XX, inspirado por la cultura del libro, se distanció sistemáticamente de la nueva sociedad de la información digital; el Internet y las herramientas de procesamiento de información revolucionaron el mundo, la sociedad en el transcurso de este periodo desarrolló ciertas características adaptativas, basadas en la convivencia (Humano – Maquina), esta transformación establece su base en el impacto de tres segmentos tecnológicos: Los dispositivos, las aplicaciones y la infraestructura de comunicación social, las cuales están envueltas en (...) diversos cambios físicos, conductuales y cognitivos del ser humano; así como el surgimiento de nuevos modelos de influencia y control social, mediante la nueva comunicación ubicua; no obstante en este nuevo proceso de convivencia se desarrollan nuevos modelos como el “pensamiento colaborativo” y el “InfoSharing”; que gestionan la información social bajo tres dimensiones ontológicas Humano (h) – Información (i) – Maquina (m), el cual es la base de un nuevo ecosistema físico-cibernético, donde coexisten y se desarrollan nuevas unidades sociales llamadas “Comunidades virtuales”. Esta nueva infraestructura de comunicación y gestión social de información a dado descubierto áreas de vulnerabilidad denominada “Perspectiva social del riesgo”, impactando a todas las unidades sociales por medio del vector masivo de impacto (i); El entorno virtual “H + i + M”; y sus componentes, así como el ciclo de vida de la gestión de información social nos permite entender la trayectoria de la integración “Tecno – Social”, y estableciendo de la nueva cibernética, dentro de la convergencia de la tecnología con la sociedad y su nuevos retos de convivencia, encaminados en una nueva visión holística y no pragmática, ya que el componente humano (h) en este entorno virtual es el precursor del futuro y necesita ser estudiado no como una aplicación, sino como el eje de una nueva sociedad. (shrink)