Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971, and further developed in several recent articles.The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well (...) as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an internal re-structuring of major submodules of the genome and Interactome networks related to cell cycling and cell growth. Contrary to the commonly held view of `standard’ Darwinist models of evolution, the evolution of organisms and species occurs through coupled multi-molecular transformations induced not only by the environment but actually realized through internal re-organizations of genome and interactome networks. The biological, evolutionary processes involve certain epigenetic transformations that are responsible for phenotypic expression of the genome and Interactome transformations initiated at the quantum-molecular level. It can thus be said that only quantum genetics can provide correct explanations of evolutionary processes that are initiated at the quantum—multi-molecular levels and propagate to the higher levels of organismal and species evolution. Biological evolution should be therefore regarded as a multi-scale process which is initiated by underlying quantum multi-molecular transformations of the genomic and interactomic networks, followed by specific phenotypic transformations at the level of organism and the variable biogroupoids associated with the evolution of species which are essential to the survival of the species. The theoretical framework introduced in this article also paves the way to a Quantitative Biology approach to biological evolution at the quantum-molecular, as well as at the organismal and species levels. This is quite a substantial modification of the `established’ modern Darwinist, and also of several so-called `molecular evolution’ theories. (shrink)

A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...) extension of Hull’s view to the ubiquitous phenomenon of symbiosis. Finally, using immunology as a key example, it shows that the genidentity view suggests that the main interest of a process approach is epistemological rather than ontological and that its principal claim is one of priority, namely that processes precede and define things, and not vice versa. (shrink)

This chapter draws on insights from non-equilibrium thermodynamics to demonstrate the ontological inadequacy of the machine conception of the organism. The thermodynamic character of living systems underlies the importance of metabolism and calls for the adoption of a processual view, exemplified by the Heraclitean metaphor of the stream of life. This alternative conception is explored in its various historical formulations and the extent to which it captures the nature of living systems is examined. Following this, the chapter considers the metaphysical (...) implications of reconceptualizing the organism from complex machine to flowing stream. What do we learn when we reject the mechanical and embrace the processual? Three key lessons for biological ontology are identified. The first is that activity is a necessary condition for existence. The second is that persistence is grounded in the continuous self-maintenance of form. And the third is that order does not entail design. (shrink)

Abstracts of each chapter may be found by typing in your browser search bar, "Jeremy Horne, Managing Complexity Through Social Intelligence: Foundations of the Modern Organic Corporatist State", going to the Springer Publishing website and reading the abstracts for each chapter.

Big History has been developing very fast indeed. We are currently observing a ‘Cambrian explosion’ in terms of its popularity and diffusion. Big History courses are taught in the schools and universities of several dozen countries, including China, Korea, the Netherlands, the USA, India, Russia, Japan, Australia, Great Britain, Germany, and many more. The International Big History Association (IBHA) is gaining momentum in its projects and membership. Conferences are beginning to be held regularly (this edited volume has been prepared on (...) the basis of the proceedings of the International Big History Association Inaugural Conference [see below for details]). Hundreds of researchers are involved in studying and teaching Big History. (shrink)

If complexity is a necessary but not sufficient premise for the existence and expression of the living, anticipation is the distinguishing characteristic of what is alive. Anticipation is at work even at levels of existence where we cannot refer to intelligence. The prospect of artificially generating aesthetic artifacts and ethical constructs of relevance to a world in which the natural and the artificial are coexistent cannot be subsumed as yet another product of scientific and technological advancement. Beyond the artificial, the (...) synthetic conjures the understanding of aesthetics and ethics no longer from the perspective of the How? type of question, but rather the Why? Given the current infatuation with synthetic biology (i.e., making life from non-life), there is a practical consequence to such considerations. Synthetic life, as any other form of life, implies the possibility of evolution. Anticipation, which is the underlying factor of evolution, is thus expected. At the level of human existence, anticipation is expressed, for instance (but not exclusively), in aesthetic forms and ethical values. This translates, in turn, into an argument for the role aesthetics and ethics play in the process. Consequently, to qualify as life, the synthesis of the physical and the living will have to efficiently handle ambiguity. Current computational facilities, regardless of their nature or performance, operate exclusively in the semiotic domain of the well defined non-ambiguous. (shrink)

This book argues that a plausible account of emergence requires replacing the traditional assumption that what primarily exists are particular entities with generic processes. Traversing contemporary physics and issues of identity over time, it then proceeds to develop a metaphysical taxonomy of emergent entities and of the character of human life.

Quantum–mechanical systems may be understood in terms of information. When they interact, they modify the information they carry or represent in two, and only two, ways: by selecting a part of the initial amount of (potential) information and by sharing information with other systems. As a consequence, quantum systems are informationally shielded. These features are shown to be general features of nature. In particular, it is shown that matter arises from quantum–mechanical processes through the constitution of larger ensembles that share (...) some information while living organisms make use of a special form of information selection. (shrink)

According to the working definition of the International Big History Association, ‘Big History seeks to understand the integrated history of the Cosmos, Earth, Life and Humanity, using the best available empirical evidence and scholarly methods’. In recent years Big History has been developing very fast indeed. Big History courses are taught in the schools and universities of several dozen countries. Hundreds of researchers are involved in studying and teaching Big History. The unique approach of Big History, the interdisciplinary genre of (...) history that deals with the grand narrative of 13.8 billion years, has opened up a vast amount of research agendas. Big History brings together constantly updated information from the scientific disciplines and merges it with the contemplative realms of philosophy and the humanities. It also provides a connection between the past, present, and future. Big History is a colossal and extremely heterogeneous field of research encompassing all the forms of existence and all timescales. Unsurprisingly, Big History may be presented in very different aspects and facets. In this volume the Big History is presented and discussed in three different ways. In its first part, Big History is explored in terms of methodology, theories of knowledge, as well as showcasing the personal approach of scholars to Big History. The second section comprises such articles that could clarify Big History's main trends and laws. The third part of this book explores the nature of teaching Big History as well as profiling a number of educational methods. This volume will be useful both for those who study interdisciplinary macroproblems and for specialists working in focused directions, as well as for those who are interested in evolutionary issues of Astrophysics, Geology, Biology, History, Anthropology, Linguistics and other areas of study. (shrink)

This paper develops a dialectical methodology for assessing technoscience during the Anthropocene. How to practice Hegelian dialectics of technoscience today? First of all, dialectics is developed here in close interaction with contemporary technoscientific research endeavours, which are addressed from a position of proximity and from an ‘oblique’ perspective. Contrary to empirical research, the focus is on how basic concepts of life, nature and technology are acted out in practice. Notably, this paper zooms in on a synthetic cell project called BaSyC (...) as a concrete instantiation of converging views of life, nature and technology currently at work in technoscience. While dialectics is used to explore the significance of this project, the synthetic cell as a case study also allows us to demonstrate the remarkable relevance of dialectics for understanding contemporary research, notably because it incites us to see the synthetic cell project as a concrete exemplification of life under Anthropocenic conditions. Should we assess the synthetic cell as the ultimate realisation of the technoscientific will to control and optimise life, or rather as an effort to bridge the disruptive collision between technoscience and nature, or both? (shrink)

This paper develops a dialectical methodology for assessing technoscience during the Anthropocene. How to practice Hegelian dialectics of technoscience today? First of all, dialectics is developed here in close interaction with contemporary technoscientific research endeavours, which are addressed from a position of proximity and from an ‘oblique’ perspective. Contrary to empirical research, the focus is on how basic concepts of life, nature and technology are acted out in practice. Notably, this paper zooms in on a synthetic cell project called BaSyC (...) as a concrete instantiation of converging views of life, nature and technology currently at work in technoscience. While dialectics is used to explore the significance of this project, the synthetic cell as a case study also allows us to demonstrate the remarkable relevance of dialectics for understanding contemporary research, notably because it incites us to see the synthetic cell project as a concrete exemplification of life under Anthropocenic conditions. Should we assess the synthetic cell as the ultimate realisation of the technoscientific will to control and optimise life, or rather as an effort to bridge the disruptive collision between technoscience and nature, or both? (shrink)

Debates on the role of biotechnology in food production are beset with notorious ambiguities. This already applies to the term “biotechnology” itself. Does it refer to the use and modification of living organisms in general, or rather to a specific set of technologies developed quite recently in the form of bioengineering and genetic modification? No less ambiguous are discussions concerning the question to what extent biotechnology must be regarded as “unnatural.” In this article it will be argued that, in order (...) to disentangle some of the ambiguities involved, we have to broaden the temporal horizon of the debate. Ideas about biotechniques and naturalness have evolved in various socio-historical contexts and their historical origins will determine to a considerable extent their actual meaning and use in contemporary deliberations. For this purpose, a comprehensive timetable is developed, beginning with the Neolithic revolution ~10,000 years ago (resulting in the emergence of agriculture and the Common Human Pattern) up to the biotech revolution as it has evolved from the 1970s onwards—sometimes referred to as a second “Genesis.” The concept of nature that emerged in the context of the “Common Human Pattern” differs considerably from traditional philosophical concepts of nature (such as coined by Aristotle), as well as from the scientific view of nature conveyed by the contemporary life sciences. A clarification of these different historical backdrops will allow us to understand and elucidate the conceptual ambiguities that are at work in contemporary debates on biotechnology and the place of human beings in nature. (shrink)

The position and role of humanity in the world of life is examined in the light of the ontological structure of life itself. This problem is approached by considering the possible units of life representing various modes of life phenomena. I argue that the only meaningful unit of life without interposing some special external conditions is “global life” framed in a star‐planet system. Any other possible unit of life exhibited by various kinds of individuals is conditional in the sense that (...) it would leave out an essential part as “co‐life.” The relationship between human being and the global life should be understood in this general scheme of individual and global life. It is emphasized, however, that human being occupies a unique position in global life in the sense that humanity can promote either a cancerous situation or a healthy higher‐order enhancement of the global life. (shrink)

The ‘French reading’ of Nietzsche crystallized almost 50 years ago at the 1972 conference at Cerisy-la-Salle, Nietzsche aujourd’hui. An earlier version of this paper was presented at the annual conference of the Friedrich Nietzsche Society, with the theme of ‘The Politics of Difference’, Newcastle University, 20–21 September 2018. Nietzsche’s fortunes have since undergone some dramatic shifts in France, but there are signs that he is once again on the ascendency, in particular the 2016 edited collection Pourquoi nous sommes Nietzschéens (a (...) direct riposte to the 1991 Pourquoi nous ne sommes pas Nietzschéens). Taking a bearing from the French readings, I want to explore the question of what ‘Nietzsche today’ might mean for us today. At Cerisy in 1972, the meaning of Nietzsche was centred on the twin critiques of humanism and capitalism. While these issues persist, several articles in the 2016 collection indicate that they are now inflected through the vast contemporary significance of technology. One of the key debates here is Nietzsche’s significance for transhumanism. For Bernard Stiegler, transhumanism is the culmination of nihilism, understood as the reign of big data and the total quantification of the self. In this regard, he alludes to a ‘hypernihilism’ of the contemporary era, characterised by the quantifying effects of information technologies, which work in conjunction with capitalism to produce an ultimate ‘averaging’ force. I will argue that Stiegler gives an essential corrective to the largely critical engagements with neonihilism of the Nietzscheans of the previous generation, but that his emphasis on the value of negentropy risks reaffirming the logic of the transhumanism he critiques. Nietzscheanism today, I will argue, requires an appreciation of the dual tendencies of nihilism – identified here as neonihilism and hypernihilism – such that we must draw on contributions from both generations of French Nietzscheans in order to think and respond to the problems of our contemporary era. (shrink)

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

Erwin Schrödinger’s 1944 publication What is Life? is a classic of twentieth century science writing. In his book, Schrödinger discussed the chromosome fibre as the seat of heredity and variation thanks to a hypothetical aperiodic structure – a suggestion that famously spurred on a generation of scientists in their pursuit of the gene as a physico-chemical entity. While historical attention has been given to physicists who were inspired by the book, little has been written about its biologist readers. This paper (...) examines the case of the English evolutionary botanist and cytologist Irène Manton, who took an interest in What is Life? for its relevance to her own research in chromosome structure as a clue to plant phylogeny. Drawing on recently discovered correspondence between Manton and Schrödinger, the paper reconstructs Manton ‘s path to the book and her response to it by way of throwing new light on a pivotal moment in the history of the debate on chromosome structure. (shrink)

The sequence of nucleotide bases occurring in an organism’s DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical machine, which the information constrains in such a way as to direct the process of construction. In reality, any biochemical machine for which a DNA codescript is efficacious is itself produced through the mechanical interpretation of an identical or very similar codescript. In these (...) terms the origin of life can be described as a bootstrap process involving the simultaneous accumulation of genetic information and the generation of a machine that interprets it as instructions for its own construction. This problem is discussed within the theoretical frameworks of thermodynamics, informatics and self-reproducing automata, paying special attention to the physico-chemical origin of genetic coding and the conditions, both thermodynamic and informatic, that a system must fulfil in order for it to sustain semiosis. The origin of life is equated with biosemiosis. (shrink)

The Darwinian concept of natural selection was conceived within a set of Newtonian background assumptions about systems dynamics. Mendelian genetics at first did not sit well with the gradualist assumptions of the Darwinian theory. Eventually, however, Mendelism and Darwinism were fused by reformulating natural selection in statistical terms. This reflected a shift to a more probabilistic set of background assumptions based upon Boltzmannian systems dynamics. Recent developments in molecular genetics and paleontology have put pressure on Darwinism once again. Current work (...) on self-organizing systems may provide a stimulus not only for increased problem solving within the Darwinian tradition, especially with respect to origins of life, developmental genetics, phylogenetic pattern, and energy-flow ecology, but for deeper understanding of the very phenomenon of natural selection itself. Since self-organizational phenomena depend deeply on stochastic processes, self-organizational systems dynamics advance the probability revolution. In our view, natural selection is an emergent phenomenon of physical and chemical selection. These developments suggest that natural selection may be grounded in physical law more deeply than is allowed by advocates of the autonomy of biology, while still making it possible to deny, with autonomists, that evolutionary explanations can be modeled in terms of a deductive relationship between laws and cases. We explore the relationship between, chance, self-organization, and selection as sources of order in biological systems in order to make these points. (shrink)

Over the past fifteen years there has been a considerable amount of debate concerning what theoretical population dynamic models tell us about the nature of natural selection and drift. On the causal interpretation, these models describe the causes of population change. On the statistical interpretation, the models of population dynamics models specify statistical parameters that explain, predict, and quantify changes in population structure, without identifying the causes of those changes. Selection and drift are part of a statistical description of population (...) change; they are not discrete, apportionable causes. Our objective here is to provide a definitive statement of the statistical position, so as to allay some confusions in the current literature. We outline four commitments that are central to statisticalism. They are: 1. Natural Selection is a higher order effect; 2. Trait fitness is primitive; 3. Modern Synthesis (MS)-models are substrate neutral; 4. MS-selection and drift are model-relative. (shrink)

A notion of delegated causality is introduced here. This subtle kind of causality is dual to interventional causality. Delegated causality elucidates the causal role of dynamical systems at the “edge of chaos”, explicates evident cases of downward causation, and relates emergent phenomena to Gödel’s incompleteness theorem. Apparently rich implications are noticed in biology and Chinese philosophy. The perspective of delegated causality supports cognitive interpretations of self-organization and evolution.

This article searches for a way of theorizing the interconnectedness of processes of individuation, relationality and affect, with the aim of clearing the ground for an approach that establishes the basis of this interconnectedness by reference to mechanisms common to all living things. It establishes a number of shifts that enable us to think the categories and concepts like the individual, the subject, the group, the threshold, relationality, co-implication and so on according to a fundamental decentring, finally breaking with both (...) subject-centredness and its privilege of the individual as model or starting point; the same epistemological shift implies the rejection of the anthropocentric divide between humans and animals, while avoiding species of sociobiologism, pre-formationism, geneticism and other monocausal paradigms. What the new problematic of life enjoins us to rethink are the standpoint of singularity rather than that of the individual, coupled to the standpoint of relationality as a principle enabling us to think the self—other, human—animal, nature—culture and human—world in terms of compossibility and complex becoming. This view about the co-constitution of all life has major implications regarding responsibility for the other and responsibility for the world, grounded in the standpoint of the temporality and historicity of being as existential condition circumscribing the relation to the other. This shift at the level of ontology is explored via an engagement with the work of Simondon and his conceptual apparatus, particularly ideas of psychic and collective individuation, the pre-and transindividual, the associated milieu; this perspective is re-articulated by way of the work of Merleau-Ponty, Haraway’s notion of ‘companion species’, Ettinger’s concept of the ‘I—other plurality’, and cognate concepts that point to a new terrain for theorizing affect. (shrink)

In 1869, Johann Friedrich Miescher discovered a new substance in the nucleus of living cells. The substance, which he called nuclein, is now known as DNA, yet both Miescher’s name and his theoretical ideas about nuclein are all but forgotten. This paper traces the trajectory of Miescher’s reception in the historiography of genetics. To his critics, Miescher was a “contaminator,” whose preparations were impure. Modern historians portrayed him as a “confuser,” whose misunderstandings delayed the development of molecular biology. Each of (...) these portrayals reflects the disciplinary context in which Miescher’s work was evaluated. Using archival sources to unearth Miescher’s unpublished speculations—including an analogy between the hereditary material and language, and a speculation that a series of asymmetric carbon atoms could account for hereditary variation—this paper clarifies the ways in which the past was judged through the lens of contemporary concerns. It also shows how organization, structure, function, and information were already being considered when nuclein was first discovered nearly 150 years ago. (shrink)

Attempts to define life should focus on the transition from molecules to cells and the “closure” aspects of this event. Rather than classifying existing objects into living and non-living entities I believe the challenge is to understand how the transition from non-life to life can take place, that is, the how the closure in Jagers op Akkerhuis’s hierarchical classification of operators, comes about.

The free energy principle is sometimes put forward as accounting for biological self-organization and cognition. It states that for a system to maintain non-equilibrium steady-state with its environment it can be described as minimising its free energy. It is said to be entirely scale-free, applying to anything from particles to organisms, and interactive machines, spanning from the abiotic to the biotic. Because the FEP is so general in its application, one might wonder whether this framework can capture anything specific to (...) biology. We take steps to correct for this here. We first explicate the worry, taking pebbles as examples of an abiotic system, and then discuss to what extent the FEP can distinguish its dynamics from an organism’s. We articulate the notion of ‘autonomy as precarious operational closure’ from the enactive literature, and investigate how it can be unpacked within the FEP. This enables the FEP to delineate between the abiotic and the biotic; avoiding the pebble worry that keeps it out of touch with the living systems we encounter in the world. (shrink)

The free energy principle (FEP) portends to provide a unifying principle for the biological and cognitive sciences. It states that for a system to maintain non-equilibrium steady-state with its environment it must minimise its (information-theoretic) free energy. Under the FEP, to minimise free energy is equivalent to engaging in approximate Bayesian inference. According to the FEP, therefore, inference is at the explanatory base of biology and cognition. In this paper, we discuss a specific challenge to this inferential formulation of adaptive (...) self-organisation. We call it the universal ethology challenge: it states that the FEP cannot unify biology and cognition, for life itself (or adaptive self-organisation) does not require inferential routines to select adaptive solutions to environmental pressures (as mandated by the FEP). We show that it is possible to overcome the universal ethology challenge by providing a cautious and exploratory treatment of inference under the FEP. We conclude that there are good reasons for thinking that the FEP can unify biology and cognition under the notion of approximate Bayesian inference, even if further challenges must be addressed to properly draw such a conclusion. (shrink)

Psychological empirical research has shown that human choice behavior often violates the assumptions of classical rational choice models. In the last few decades a new research field has emerged which aims to account for the observed choice behavior by resorting to the concepts and mathematical techniques developed in the realm of quantum physics, such as the “mental state vector” defined in a Hilbert space and the interference of quantum probability. This article is a short introduction to the quantum-like approach to (...) the description of cognitive processes. I argue that the mathematical apparatus of quantum physics can account for the observed violations of classical logic and can help develop effective models of psychological and cognitive phenomena. This is illustrated through the so-called conjunction and disjunction fallacies by providing an alternative interpretation of the results of Linda test and Hawaii test. No-fallacy configurations are made possible in the quantum-like approach by sequential modeling of mental states transitions. (shrink)

Recalling the title of Yoxen’s classical paper on the influence of Schrödinger’s book, I analyze the role that the work of H. Pattee might have played, if any, in the development of Biosemiotics. I take his 1969 paper “How does a molecule become a message?” (Developmental Biology Supplement) as a first target due to several circumstances that make it especially salient. On the one hand, even if Pattee has obviously developed further his ideas on later papers, the significance of this (...) one springs out right from the title, the journal and date of publication and, of course, its content. On the other, this paper in particular has been somehow rediscovered recently and not only within the frame of biosemiotics (eg, in history and philosophy of biology by E.F. Keller). Following the parallelism with Yoxen’s perspective, I contend that Pattee’s work was relatively influential with respect to a good amount of attempts to rethink living systems within theoretical biology around the 70s. This influence diminished together with the decay or even collapse of those attempts under the impact of molecular biology as it was being developed those years. Eventually, Pattee’s work has been taken up again. Notwithstanding, it is quite clear that Pattee himself was not intending to contribute specifically to Biosemiotics and that he was probably unaware of any such discipline, at least until recently. Then, we should as well ask (as Yoxen wonders with respect to Schrödinger) to which extent Pattee’s influence has been a direct one or rather an indication of the relevance of his ideas and the resonance of his hypotheses with those of biosemiotics. For this task I will sketch a few points of convergence and divergence and examine the work of some authors who either address directly this issue or have contributed significantly to build up the history of Biosemiotics. (shrink)

A simple molecular system is described consisting of the reciprocal linkage between an autocatalytic cycle and a self-assembling encapsulation process where the molecular constituents for the capsule are products of the autocatalysis. In a molecular environment sufficiently rich in the substrates, capsule growth will also occur with high predictability. Growth to closure will be most probable in the vicinity of the most prolific autocatalysis and will thus tend to spontaneously enclose supportive catalysts within the capsule interior. If subsequently disrupted in (...) the presence of new substrates, the released components will initiate production of additional catalytic and capsule components that will spontaneously re-assemble into one or more autocell replicas, thereby reconstituting and sometimes reproducing the original. In a diverse molecular environment, cycles of disruption and enclosure will cause auto-cells to incidentally encapsulate other molecules as well as reactive substrates. To the extent that any captured molecule can be incorporated into the autocatalytic process by virtue of structural degeneracy of the catalytic binding sites, the altered autocell will incorporate the new type of component into subsequent replications. Such altered autocells will be progenitors of “lineages” with variant characteristics that will differentially propagate with respect to the availability of commonly required substrates. Autocells are susceptible to a limited form of evolution, capable of leading to more efficient, more environmentally fitted, and more complex forms. This provides a simple demonstration of the plausibility of open-ended reproduction and evolvability without self-replicating template molecules or maintenance of persistent nonequilibrium chemistry. This model identifies an intermediate domain between prebiotic and biotic systems and bridges the gap from nonequilibrium thermodynamics to life. (shrink)

A key challenge in conceptualizing ecological complexity is to allow simultaneously for particularity, contingency, and structure, and for such structure to be internally differentiated,dynamically tied to its context, and subject torestructuring. Because all organisms live insuch dynamic ecological circumstances, philosophy of ecology could become the leading site for addressing difficult conceptual questions concerning the situatedness or positionality of organisms –humans included – in their changing and intersecting worlds.

There has been a long-standing opposition to genetically modified organisms worldwide. Some studies have tried to identify the deep-lying philosophical, conceptual as well as psychological motivations for this opposition. Philosophical essentialism, psychological essentialism, and vitalism have been proposed as possible candidates. I approach the plausibility of the claim that these notions are related to GMO opposition from a historical perspective. Vitalism and philosophical essentialism have been associated with anti-GMO stance on account of their purported hostility to species and organismic mutability. (...) I show that vitalism has often been associated to various mutabilist theories, whereas the case for philosophical essentialism as motivating GMO opposition depends on the now discredited Essentialism Story that had constructed essentialism as a predominant view in pre-Darwinian science. Further, as philosophical essentialism taken seriously is incompatible with the reality of genetic engineering, it is unlikely to be a reason for opposition. Psychological essentialism, involving an instinctive repulsion from the practice of manipulating what is thought to be the essence of living beings, is a more likely reason for resistance to transgenesis. Yet even here, historical considerations are crucial. Not only lay people tend to essentialize genes, but scientists themselves can be shown to have been complicit in essentialist tendencies. From the advent of modern genetics, the imagery of the all-powerful genes, often depicted by scientists themselves metaphorically as material counterparts of the now obsolete vitalistic agent, has permeated the language of leading scientific figures, whose influence in shaping public opinion should not be downplayed. Enthusiasm for genetic engineering and the abhorrence from it might both derive from the same unrealistic image of the essential gene, the revision of which thus holding out the hope for transcending the present impasse of the GMO controversy. (shrink)

In present cultural debate, the theme of biodiversity is considered one of the most important topic because it does not treat only the variety of living forms but it includes also the value of itself and its preservation. Analysing a lot of its peculiar aspects we take conscious about uniqueness of life and relationship with other fields of knowledge: science, epistemology, aesthetics, ethics, politics. This essay focus especially on the origin of life, the processes of morphogenesis in living forms and (...) appearing of “aesthetics” qualities in biological world. The relation between biodiversity and aesthetic can help to understand the origin of human aesthetic sense. (shrink)

The paper introduces mathematical encoding for subjective experience and meaning in natural cognition. The code is based on a quantum-theoretic qubit structure supplementing classical bit with circular dimension, functioning as a process-causal template for representation of contexts relative to the basis decision. The qubit state space is demarcated in categories of emotional experience of animals and humans. Features of the resulting spherical map align with major theoreties in cognitive and emotion science, modeling of natural language, and semiotics, suggesting several generalizations (...) and improvements. The developed model bridges psychological, quantum-theoretic, and semiotic perspectives, allowing for an integrative account of subjectivity, agency, and meaning in living Nature.Graphical abstract. (shrink)

In "The Indeterministic Character of Evolutionary Theory: No 'Hidden Variables Proof' But No Room for Determinism Either," Brandon and Carson (1996) argue that evolutionary theory is statistical because the processes it describes are fundamentally statistical. In "Is Indeterminism the Source of the Statistical Character of Evolutionary Theory?" Graves, Horan, and Rosenberg (1999) argue in reply that the processes of evolutionary biology are fundamentally deterministic and that the statistical character of evolutionary theory is explained by epistemological rather than ontological considerations. In (...) this paper I focus on the topic of mutation. By focusing on some of the theory and research on this topic from early to late, I show how quantum indeterminism hooks up to point mutations (via tautomeric shifts, proton tunneling, and aqueous thermal motion). I conclude with a few thoughts on some of the wider implications of this topic. (shrink)

Whatever we take “life” to mean, it must involve an attempt to describe the objective reality beyond scientists’ biases. Traditionally, this is thought to involve comparing our scientific categories to “natural kinds.” But this approach has been tainted with an implicit metaphysics, inherited from Aristotle, that does not fit biological reality. In particular, we must accept that biological categories will never be specifiable in terms of necessary and sufficient conditions or shared underlying physical structures that produce clean boundaries. Biology blurs (...) all lines and failure to embrace this unique feature has blocked attempts to reach consensus on the meaning of “life.” Thus, while the three classical accounts all fall short of offering a complete definition, their advocates fail to realize that they share the same view of life’s ultimate, functional hallmark: its uniquely rich adaptive capacity. I develop an account of life as adaptive capacity that sidesteps debates about the relative importance of specific mechanisms and the precise location of boundaries to bring the three classical accounts together under a shared conceptual framework. (shrink)

Well-being depends not only on what happens but also on when it happens. There are temporal aspects of well-being, and to a large extent those aspects are about relative timing—about being “in-tact.” On the one hand, there is a perspectival aspect about being in-tact with one’s past, present, and future or, in a less involved sense, with one’s life as a whole. On the other hand, there is a synchronization aspect of being in-tact; and this aspect occurs on different levels: (...) It might be about the alignment between different temporal domains—such as time as individually perceived and physical or intersubjective time. Or it might be about a single domain, especially the inner dynamics of individual time. The danger of not experiencing and acknowledging the relational character of these different timings likely leads to a substantial loss in the variety of human experience. Important aspects of subjective and intersubjective experience might fade away. The present paper discusses these aspects of well-being along the lines of distinctions and concepts prominently used in the metaphysics and the phenomenology of time. Thus, the paper also aims to complement the existing literature by bringing together important strands of current philosophical research. (shrink)

In contrast to the traditional relational semiotics, biosemiotics decisively deviates towards dynamical aspects of signs at the evolutionary and developmental time scales. The analysis of sign dynamics requires constructivism to explain how new components such as subagents, sensors, effectors, and interpretation networks are produced by developing and evolving organisms. Semiotic networks that include signs, tools, and subagents are multilevel, and this feature supports the plasticity, robustness, and evolvability of organisms. The origin of life is described here as the emergence of (...) simple self-constructing semiotic networks that progressively increased the diversity of their components and relations. Primitive organisms have no capacity to classify and track objects; thus, we need to admit the existence of proto-signs that directly regulate activities of agents without being associated with objects. However, object recognition and handling became possible in eukaryotic species with the development of extensive rewritable epigenetic memory as well as sensorial and effector capacities. Semiotic networks are based on sequential and recursive construction, where each step produces components that are needed for the following steps of construction. Construction is not limited to repair and reproduction of what already exists or is unambiguously encoded, it also includes production of new components and behaviors via learning and evolution. A special case is the emergence of new levels of organization known as metasystem transition. Multilevel semiotic networks reshape the phenotype of organisms by combining a mosaic of features developed via learning and evolution of cooperating and/or conflicting subagents. (shrink)

This essay provides an introduction to the terminology, concepts, methods, and challenges of image‐based modeling in biology. Image‐based modeling and simulation aims at using systematic, quantitative image data to build predictive models of biological systems that can be simulated with a computer. This allows one to disentangle molecular mechanisms from effects of shape and geometry. Questions like “what is the functional role of shape” or “how are biological shapes generated and regulated” can be addressed in the framework of image‐based systems (...) biology. The combination of image quantification, model building, and computer simulation is illustrated here using the example of diffusion in the endoplasmic reticulum. (shrink)

Drawing from field theory, Gestalt therapy conceives psychological suffering and psychotherapy as two intentional field phenomena, where unprocessed and chaotic experiences seek the opportunity to emerge and be assimilated through the contact between the patient and the therapist (i.e., the intentionality of contacting). This therapeutic approach is based on the therapist’s aesthetic experience of his/her embodied presence in the flow of the healing process because (1) the perception of beauty can provide the therapist with feedback on the assimilation of unprocessed (...) experiences; (2) the therapist’s attentional focus on intrinsic aesthetic diagnostic criteria can facilitate the modification of rigid psychopathological fields by supporting the openness to novel experiences. The aim of the present manuscript is to review recent evidence from psychophysiology, neuroaesthetic research, and neurocomputational models of cognition, such as the free energy principle (FEP), which support the notion of the therapeutic potential of aesthetic sensibility in Gestalt psychotherapy. Drawing from neuroimaging data, psychophysiology and recent neurocognitive accounts of aesthetic perception, we propose a novel interpretation of the sense of beauty as a self-generated reward motivating us to assimilate an ever-greater spectrum of sensory and affective states in our predictive representation of ourselves and the world and supporting the intentionality of contact. Expecting beauty, in the psychotherapeutic encounter, can help therapists tolerate uncertainty avoiding impulsive behaviours and to stay tuned to the process of change. (shrink)

?Emergence? can be analyzed into evolutionary and developmental kinds. The latter can be further analyzed into intensional and extensional kinds of emergence. Evolutionary emergence occurs each time a uniqueness enters the world. Intensional emergence (supervenience) explicitly involves the categories of an observer. Extensional emergence (cohesion) is constructed as an attempt to see developmental emergence as a result of the imposition of larger scale constraints on a system. In all cases there is a sudden jump from pre?emergent to post?emergent stages so (...) that the transformation may be said to defy continuous description, which is also hampered by the fact that knowledge of properties of the pre?emergent condition alone does not allow us to predict post?emergent properties. (shrink)

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

The Earth agglomerates and heats. Convection cells within the planetary interior expedite the cooling process. Volcanoes evolve steam, carbon dioxide, sulfur dioxide and pyrophosphate. An acidulous Hadean ocean condenses from the carbon dioxide atmosphere. Dusts and stratospheric sulfurous smogs absorb a proportion of the Sun’s rays. The cooled ocean leaks into the stressed crust and also convects. High temperature acid springs, coupled to magmatic plumes and spreading centers, emit iron, manganese, zinc, cobalt and nickel ions to the ocean. Away from (...) the spreading centers cooler alkaline spring waters emanate from the ocean floor. These bear hydrogen, formate, ammonia, hydrosulfide and minor methane thiol. The thermal potential begins to be dissipated but the chemical potential is dammed. The exhaling alkaline solutions are frustrated in their further attempt to mix thoroughly with their oceanic source by the spontaneous precipitation of biomorphic barriers of colloidal iron compounds and other minerals. It is here we surmise that organic molecules are synthesized, filtered, concentrated and adsorbed, while acetate and methane—separate products of the precursor to the reductive acetyl-coenzyme-A pathway—are exhaled as waste. Reactions in mineral compartments produce acetate, amino acids, and the components of nucleosides. Short peptides, condensed from the simple amino acids, sequester ‘ready-made’ iron sulfide clusters to form protoferredoxins, and also bind phosphates. Nucleotides are assembled from amino acids, simple phosphates carbon dioxide and ribose phosphate upon nanocrystalline mineral surfaces. The side chains of particular amino acids register to fitting nucleotide triplet clefts. Keyed in, the amino acids are polymerized, through acid–base catalysis, to alpha chains. Peptides, the tenuous outer-most filaments of the nanocrysts, continually peel away from bound RNA. The polymers are concentrated at cooler regions of the mineral compartments through thermophoresis. RNA is reproduced through a convective polymerase chain reaction operating between 40 and 100°C. The coded peptides produce true ferredoxins, the ubiquitous proteins with the longest evolutionary pedigree. They take over the role of catalyst and electron transfer agent from the iron sulfides. Other iron–nickel sulfide clusters, sequestered now by cysteine residues as CO-dehydrogenase and acetyl-coenzyme-A synthase, promote further chemosynthesis and support the hatchery—the electrochemical reactor—from which they sprang. Reactions and interactions fall into step as further pathways are negotiated. This hydrothermal circuitry offers a continuous supply of material and chemical energy, as well as electricity and proticity at a potential appropriate for the onset of life in the dark, a rapidly emerging kinetic structure born to persist, evolve and generate entropy while the sun shines. (shrink)

Despite many attempts to achieve an adequate definition of living systems by means of a set of necessary and sufficient conditions, the opinion that such an enterprise is inexorably destined to fail is increasingly gaining support. However, we believe options do not just come down to either having faith in a future success or endorsing skepticism. In this paper, we aim to redirect the discussion of the problem by shifting the focus of attention from strict definitions towards a philosophical framework (...) that allows conceiving of living systems as a natural kind, but whereby natural kinds are not to be defined by fixed necessary and sufficient conditions. We argue for a property-cluster kind approach according to which living systems constitute a natural kind with vague boundaries, capable of changing, and whose members do not need to instantiate every property. We draw from Boyd’s homeostatic property-cluster theory and introduce two modifications, one regarding homeostatic mechanisms and another related to the scientific role of kinds. Thus, our view overcomes some difficulties of Boyd’s theory and we are able to account for the natural kindhood of living things. We also emphasize the most appealing features of our approach for specific research fields and address three objections to this sort of approach. (shrink)

The consolidation of the informational paradigm in molecular biology research concluded on a system to convert the epistemic object into an operational technological object and a stable epistemic product. However, the acceptance of the informational properties of genetic acids failed to clarify the meaning of the concept of information. The “information”’ as a property of the genetic molecules remained as an informal notion that allows the description of the mechanism of inheritance, but it was not specified in a logic–semantic structure. (...) The metaphorical implications associated with the idea of genes as molecules with meaning, questioned the linguistics that seemed too foreign to molecular biology. A reformulation of the concept of information in molecular biology was developed upon the theory of Claude Shannon. The node for the structural coupling between biology, physics and information theory was the identification of an analog structure between the coded messages of Shannon’s theory. (shrink)

On the occasion of the centennial of his birth, Schrödinger's life and views are sketched and his critique of the interpretation of quantum mechanics accepted at his time is examined. His own interpretation, which he had to abandon after a short time, provides a prime example of the way in which the tentative meaning of central theoretical terms in a new and revolutionary theory often fails. Schrödinger's strong philosophical convictions have played a key role in his refusal to break with (...) many of the notions of classical physics. At the same time, they made him into a keen and incisive critic of the Copenhagen interpretation. His criticism is compared with present views on quantum mechanics. (shrink)

It has long been thought that gene expression is tightly regulated in multicellular eukaryotes, so that expression profiles match functional profiles. This conception emerged from the assumption that gene activity is synonymous with gene function. This paradigm was first challenged by comparative protein electrophoresis studies showing extensive differences in expression patterns among related species. The paradigm is now being challenged by evolutionary transcriptomics using microarray technologies. Most gene expression profiles display features that lack any obvious functional significance. The so‐called “ectopic” (...) expression refers to the expression of genes at times and locations where the target gene is not known to have a function. However, ectopic expression might be associated with genuine function even if this function is not essential or has yet to be ascertained. Alternatively, ectopic expression might come about as a superfluous by‐product of regulatory systems, which would call for a revision of prevailing ideas about the specificity of gene regulation. We herein review available evidence for ectopic expression and the hypotheses proposed for its origin and evolution. We propose that ectopic expression must be regarded as part of an integrated phenotypic whole. It seems likely that ectopic expression represents a leak in the evolution of regulatory systems, but one that is endowed with considerable evolutionary possibilities. BioEssays 27:592–601, 2005. © 2005 Wiley Periodicals, Inc. (shrink)