Can there be higher level laws of nature even though everything is reducible to the fundamental laws of physics? The computer science notion of level of abstraction explains how there can be.

Radboud Universiteit Nijmegen, 06 september 2010.

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)

The term “biology” was introduced in 1802 by a German, Treviranus, and by a Frenchman whose name would remain well known to posterity, Jean-Baptiste Lamarck.

Abstract In this paper, I argue that the traditional philosophical approach of taking cognitively and emotionally competent adult people to be the prototypical instances of agency should be revised in light of current work in the behavioral sciences. Logical consistency in application is better served by taking simple goal-directed and feedback-governed systems such as insects as the prototypes of the concept of agency, with people being agents ?by extension? in the same sense as countries or corporations.

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)

Many believe that a suitably programmed computer could act for its own goals and experience feelings. I challenge this view and argue that agency, mental causation and qualia are all founded in the unique, homeostatic nature of living matter. The theory was formulated for coherence with the concept of an agent, neuroscientific data and laws of physics. By this method, I infer that a successful action is homeostatic for its agent and can be caused by a feeling - which does (...) not motivate as a force, but as a control signal. From brain research and the locality principle of physics, I surmise that qualia are a fundamental, biological form of energy generated in specialized neurons. Subjectivity is explained as thermodynamically necessary on the supposition that, by converting action potentials to feelings, the neural cells avert damage from the electrochemical pulses. In exchange for this entropic benefit, phenomenal energy is spent as and where it is produced - which precludes the objective observation of qualia. (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)

In this paper, I will reread the history of molecular genetics from a psychoanalytical angle, analysing it as a case history. Building on the developmental theories of Freud and his followers, I will distinguish four stages, namely: (1) oedipal childhood, notably the epoch of model building (1943–1953); (2) the latency period, with a focus on the development of basic skills (1953–1989); (3) adolescence, exemplified by the Human Genome Project, with its fierce conflicts, great expectations and grandiose claims (1989–2003) and (4) (...) adulthood (2003–present) during which revolutionary research areas such as molecular biology and genomics have achieved a certain level of normalcy—have evolved into a normal science. I will indicate how a psychoanalytical assessment conducted in this manner may help us to interpret and address some of the key normative issues that have been raised with regard to molecular genetics over the years, such as ‘relevance’, ‘responsible innovation’ and ‘promise management’. (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 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.

Recent years have witnessed rapidly increasing interests in developing quantum theoretical models of human cognition. Quantum mechanisms have been taken seriously to describe how the mind reasons and decides. Papers in this special issue report the newest results in the field. Here we discuss why the two levels of commitment, treating the human brain as a quantum computer and merely adopting abstract quantum probability principles to model human cognition, should be integrated. We speculate that quantum cognition models gain greater modeling (...) power due to a richer representation scheme. (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)

Crane envisions the speculative conjecture that intelligent civilizations might want and be able to produce black holes in the very far future. He implicitly suggests two main purposes of this enterprise: (i) energy production and (ii) universe production. We discuss those two options. The commentary is obviously highly speculative and should be read accordingly.

Presented is a discourse on the contextual nature of physical qualities. The realistic and observational contexts in which a system exists are demonstrated as equally involved in defining its qualities. Each quality could be consequently considered as natural and experiential at the same time. The subsequently proposed thesis of the contextual co-definition of natural/experiential qualities in the relationship between the human mind and Nature is shown to possess numerous favorable ethical and aesthetical implications. The contextual nature of experiential qualities is (...) further correlated with the holistic character of natural systems and events, which is illustrated by several real-life examples. A systemic approach to knowledge is shown to naturally emanate from the acceptance of the contextual definition of physical qualities and the holistic nature of experiences. Methodological problems of the standard, reductionist explanatory frameworks are additionally discussed with an emphasis on the major descriptive flaws of quantificational approaches and in respect to cybernetic and autopoietic organization of physical and biological systems. (shrink)

Behaviour is central to many fields, but metatheoretical definitions specifying the most basic assumptions about what is considered behaviour and what is not are largely lacking. This transdisciplinary research explores the challenges in defining behaviour, highlighting anthropocentric biases and a frequent lack of differentiation from physiological and psychical phenomena. To meet these challenges, the article elaborates a metatheoretical definition of behaviour that is applicable across disciplines and that allows behaviours to be differentiated from other kinds of phenomena. This definition is (...) used to explore the phenomena of language and to scrutinise whether and under what conditions language can be considered behaviour and why. The metatheoretical concept of two different levels of meaning conveyed in human language is introduced, highlighting that language inherently relies on behaviours and that the content of what-is-being-said, in and of itself, can constitute behaviour under particular conditions. The analyses reveal the ways in which language meaningfully extends human's behavioural possibilities, pushing them far beyond anything enabled by non-language behaviours. These novel metatheoretical concepts can complement and expand on existing theories about behaviour and language and contribute a novel piece of theoretical explanation regarding the crucial role that language has played in human evolution. (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)

The study of information based on the approach of Shannon was detached from problems of meaning. Also, it did not allow analysis of the structural characteristics of information, nor describe the way structures carry information. An outline of a different theory of information, including its semantics, was earlier proposed by the author. This theory was using closure spaces to model information. In the present paper, structures (called syllogistics) underlying syllogistic reasoning as well as ethnoscientific classifications are identified together with the (...) conditions for the lattice of closed subsets describing information to allow its existence. The structures can be used for logical analysis outside of language at the more general level of information, which in turn can be applied to the description of semantic relations in the context of information. (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)

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)

Niche construction theory concerns how organisms can change selection pressures by altering the feature–factor relationship between themselves and their environment. These alterations are standardly understood to be brought about through two kinds of organism–environment interaction: perturbative and relocational niche construction. We argue that a reconceptualization is needed on the grounds that if a niche is understood as the feature–factor relationship, then there are three fundamental ways in which organisms can engage in niche construction: constitutive, relational, and external niche construction. We (...) further motivate our reconceptualization by showing some examples of organismic activities that fall outside of the current categorization of niche construction, but nonetheless should be included. We end by discussing two objections to niche construction and show how our reconceptualization helps to undercut these objections. 1Introduction2Niche Construction Theory 2.1The standard account of niche construction2.2Two problems with the standard account of niche construction3Three Kinds of Niche Construction 3.1Constitutive niche construction3.2Relational niche construction3.3External niche construction4Conceptual Improvement on Niche Construction Theory 4.1Constitutive niche construction4.2Relational niche construction4.3External niche construction5The Status of Niche Construction Theory within Evolutionary Theory 5.1Is niche construction a helpful addition to evolutionary theory?5.2Is niche construction an evolutionary process?6Conclusion. (shrink)

Summary Franz Brentano, 1838–1917, introduced the intriguing concept of “plerosis” in order to account for aspects of the continuum that were “explained” by formal mathematics in ways that he considered absurd from the perspective of intuition, especially visual awareness and imagery. In doing this, he pointed in directions later developed by the Dutch mathematician Luitzen Brouwer. Brentano’s notion of plerosis involves distinct though coincident points, which one might call “atomic entities with parts”. This notion fits the modern concepts of “receptive (...) field” in neurophysiology, “perceptive field” in psychology and “differential operator” in the formal theory of scale space. We identify Brentano’s boundary points as the primordial atomic Gestalts of visual imagery. The concept deserves to play a key role in Gestalt theory. (shrink)

Genes are often described by biologists using metaphors derived from computa- tional science: they are thought of as carriers of information, as being the equivalent of ‘‘blueprints’’ for the construction of organisms. Likewise, cells are often characterized as ‘‘factories’’ and organisms themselves become analogous to machines. Accordingly, when the human genome project was initially announced, the promise was that we would soon know how a human being is made, just as we know how to make airplanes and buildings. Impor- tantly, (...) modern proponents of Intelligent Design, the latest version of creationism, have exploited biologists’ use of the language of information and blueprints to make their spurious case, based on pseudoscientific concepts such as ‘‘irreducible complexity’’ and on flawed analogies between living cells and mechanical factories. However, the living organ- ism = machine analogy was criticized already by David Hume in his Dialogues Concerning Natural Religion. In line with Hume’s criticism, over the past several years a more nuanced and accurate understanding of what genes are and how they operate has emerged, ironically in part from the work of computational scientists who take biology, and in particular developmental biology, more seriously than some biologists seem to do. In this article we connect Hume’s original criticism of the living organism = machine analogy with the modern ID movement, and illustrate how the use of misleading and outdated metaphors in science can play into the hands of pseudoscientists. Thus, we argue that dropping the blueprint and similar metaphors will improve both the science of biology and its understanding by the general public. (shrink)

To explain consciousness as a physical process we must acknowledge the role energy plays in the brain. Energetic activity is fundamental to all physical processes and causally drives biological behaviour. Recent neuroscientific evidence can be interpreted in a way that suggests consciousness is a product of the organization of energetic activity in the brain. The nature of energy itself, though, remains largely mysterious, and we do not fully understand how it contributes to brain function or consciousness. According to the prin-ciple (...) outlined here, energy, along with forces and work, can be described in terms of actu-alized differences of motion and tension. By observing physical systems, we can infer there is something it is like to undergo states of actualized difference from the intrinsic perspective of the system. Consciousness occurs because there is something it is like, in-trinsically, to undergo a certain organization of actualized differences in the brain. (shrink)

La biología sintética mantiene una relación muy singular con la teoría evolutiva: por un lado, parte de una interpretación ingenieril de la evolución para fundar su aproximación al diseño de bioartefactos; por otro, la biología sintética aspira, en última instancia, a deshacerse de la evolución creando organismos de novo que se comporten de un modo predecible. Tras examinar las tres grandes propiedades que aparecen recurrentemente en la descripción sintética de los nuevos artefactos orgánicos, argumentaré que la biología sintética se erige (...) sobre una concepción de los organismos y en particular de la relación de estos con su legado histórico que ha sido profundamente cuestionada por la biología evolucionista contemporánea. (shrink)

The multi-millennial philosophical discussion about life after death has received a recent boost in the prospect of immortality attained via technologies. In this newer version, humans generally are considered mortal but may develop means of making themselves immortal. If “immortal” means not mortal, thus existing for infinity, and if the proposed infinite-existing entity is material, it must inhabit an infinite material universe. If the proposed entity is not material, there must be means by which it can shed its material substance (...) and exist nonmaterially. The article examines arguments for how an infinite life would be possible given current physical understanding. The paper considers a Pascalian-style wager weighing the likelihood of adjusting to existence wholly within a finite universe versus betting on there being some way to construe the universe(s) as a viable medium for infinite beings. Conclusion: The case for a finite being to exist infinitely has little viable support. (shrink)

It is a most commonly accepted hypothesis that life originated from inanimate matter, somehow being a synthetic product of organic aggregates, and as such, a result of some sort of prebiotic synthetic biology. In the past decades, the newly formed scientific discipline of synthetic biology has set ambitious goals by pursuing the complete design and production of genetic circuits, entire genomes or even whole organisms. In this paper, I argue that synthetic biology might also shed some novel and interesting perspectives (...) on the question of the origin of life, and that, in addition, it might challenge our most commonly accepted definitions of life, thereby changing the ways we might think about life and its origin. (shrink)

This essay argues that nano-images would be best understood with an aesthetical approach rather than with an epistemological critique. For this aim, I propose a ‘techno-aesthetical’ approach: an enquiry into the way instruments and machines transform the logic of the sensible itself and not just the way by which it represents something else. Unlike critical epistemology, which remains self-evidently grounded on a representationalist philosophy, the approach developed here presents the advantage of providing a clear-cut distinction between image-as-representation and other modes (...) of existence of images, such as the one of ‘ imaginaction ’ that I draw from a comparison between far-field and near-field microscopies. Once this regime of imaginaction is distinguished from representation, I focus on nanotechnological percepts and argue that they follow a transmodal logic. I then draw the implications of this enquiry in terms of a new sensible condition that changes the way we think of non-living objects. Finally, I conclude that if techno-aesthetics dares to posit and articulate sensibility beyond the privileged sphere of subject/object relationships, it simultaneously engages us to consider the political character of our responsibilities towards the design of nano-engineered sensorial spaces. (shrink)

Atoms theory and symmetry theory dominated physics. Symmetry propagation and interactions verify the Curie principle. But its violation by symmetry breaking is spontaneous.Fragility is creative. An information breaks a generalized symmetry. Results on symmetry breakings are not valid for fuzzy symmetries. The breaking of a fuzzy symmetry leads only to a pour symmetry. Homogeneity breaking, and atom of time are not usual concepts. We examine in this work symmetry breakings which generate the living time.

The common opinion has been that evolution results in the continuing development of more complex forms of life, generally understood as more complex organisms. The arguments supporting that opinion have recently come under scrutiny and been found wanting. Nevertheless, the appearance of increasing complexity remains. So, is there some sense in which evolution does grow complexity? Artificial life simulations have consistently failed to reproduce even the appearance of increasing complexity, which poses a challenge. Simulations, as much as scientific theories, are (...) obligated at least to save the appearances! We suggest a relation between these two problems, understanding biological complexity growth and the failure to model even its appearances. We present a different understanding of that complexity which evolution grows, one that genuinely runs counter to entropy and has thus far eluded proper analysis in information-theoretic terms. This complexity is reflected best in the increase in niches within the biosystem as a whole. Past and current artificial life simulations lack the resources with which to grow niches and so to reproduce evolution’s complexity. We propose a more suitable simulation design integrating environments and organisms, allowing old niches to change and new ones to emerge. (shrink)

The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists by (...) drawing analogies between the different fields of inquiry. We will study analogical reasoning in synthetic biology through the emergence of the functional meaning of noise, which marks an important shift in how engineering concepts are employed in this field. The notion of noise serves also to highlight the differences between the two branches of synthetic biology: the basic science-oriented branch and the engineering-oriented branch, which differ from each other in the way they draw analogies to various other fields of study. Moreover, we show that fixing the mapping between a source domain and the target domain seems not to be the goal of analogical reasoning in actual scientific practice. (shrink)