Conventional methods of genetic engineering and more recent genome editing techniques focus on identifying genetic target sequences for manipulation. This is a result of historical concept of the gene which was also the main assumption of the ENCODE project designed to identify all functional elements in the human genome sequence. However, the theoretical core concept changed dramatically. The old concept of genetic sequences which can be assembled and manipulated like molecular bricks has problems in explaining the natural genome-editing competences of (...) viruses and RNA consortia that are able to insert or delete, combine and recombine genetic sequences more precisely than random-like into cellular host organisms according to adaptational needs or even generate sequences de novo. Increasing knowledge about natural genome editing questions the traditional narrative of mutations (error replications) as essential for generating genetic diversity and genetic content arrangements in biological systems. This may have far-reaching consequences for our understanding of artificial genome editing. (shrink)

This paper explores some of the factors that make complex systems complex. We first examine the history of complex systems. It was Aristotle’s insight that how elements are joined together helps determine the properties of the resulting whole. We find (a) that scientific reductionism does not provide a sufficient explanation; (b) that to understand complex systems, one must identify and trace energy flows; and (c) that disproportionate causality, including global tipping points, are all around us. Disproportionate causality results from the (...) wide availability of energy stores. We discuss three categories of emergent phenomena—static, dynamic, and adaptive—and recommend retiring the term emergent, except perhaps as a synonym for creative. Finally, we find that virtually all communication is stigmergic. (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)

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)

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)

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)

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)

Perhaps there has been no greater opportunity than in this “VOLUME FIFTEEN of our Death And Anti-Death set of anthologies” to write about how might think about life and how to avoid death. There are two reasons to discuss “life”, the first being enhancing our understanding of who we are and why we may be here in the Universe. The second is more practical: how humans meet the physical challenges brought about by the way they have interacted with their environment. (...) Many persons discussing “life” beg the question about what “life” is. Surely, when one discusses how to overcome its opposite, death, they are not referring to another “living” thing such as a plant. There seems to be a commonality, though, and it is this commonality is one needing elaboration. It ostensibly seems to be the boundary condition separating what is completely passive (inert) from what attempts to maintain its integrity, as well as fulfilling other conditions we think “life” has. In our present discussion, there will be a reminder that it by no means has been unequivocally established what life really is by placing quotes around the word, namely, “life”. Consider it a tag representing a bundle of philosophical ideas that will be unpacked in this paper. (shrink)

This paper deals with the question of agency and intentionality in the context of the free-energy principle. The free-energy principle is a system-theoretic framework for understanding living self-organizing systems and how they relate to their environments. I will first sketch the main philosophical positions in the literature: a rationalist Helmholtzian interpretation (Hohwy 2013; Clark 2013), a cybernetic interpretation (Seth 2015b) and the enactive affordance-based interpretation (Bruineberg and Rietveld 2014; Bruineberg et al. 2016) and will then show how agency and intentionality (...) are construed differently on these different philosophical interpretations. I will then argue that a purely Helmholtzian is limited, in that it can account only account for agency in the context of perceptual inference. The cybernetic account cannot give a full account of action, since purposiveness is accounted for only to the extent that it pertains to the control of homeostatic essential variables. I will then argue that the enactive affordance-based account attempts to provide broader account of purposive action without presupposing goals and intentions coming from outside of the theory. In the second part of the paper, I will discuss how each of these three interpretations conceives of the sense agency and intentionality in different ways. (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 general sketch on how the problem of space dimensionality depends on anthropic arguments is presented. Several examples of how life has been used to constraint space dimensionality (and vice-versa) are reviewed. In particular, the influences of three-dimensionality in the solar system stability and the origin of life on Earth are discussed. New constraints on space dimensionality and on its invariance in very large spatial and temporal scales are also stressed.

The connection between brain and mind is an important scientific and philosophical question that we are still far from completely understanding. A crucial point to our work is noticing that thermodynamics provides a convenient framework to model brain activity, whereas cognition can be modeled in information-theoretical terms. In fact, several models have been proposed so far from both approaches. A second critical remark is the existence of deep theoretical connections between thermodynamics and information theory. In fact, some well-known authors claim (...) that the laws of thermodynamics are nothing but principles in information theory. Unlike in physics or chemistry, a formalization of the relationship between information and energy is currently lacking in neuroscience. In this paper we propose a framework to connect physical brain and cognitive models by means of the theoretical connections between information theory and thermodynamics. Ultimately, this article aims at providing further insight on the formal relationship between cognition and neural activity. (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)

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

Biosemiotics is the synthesis of biology and semiotics, and its main purpose is to show that semiosis is a fundamental component of life, i.e., that signs and meaning exist in all living systems. This idea started circulating in the 1960s and was proposed independently from enquires taking place at both ends of the Scala Naturae. At the molecular end it was expressed by Howard Pattee’s analysis of the genetic code, whereas at the human end it took the form of Thomas (...) Sebeok’s investigation into the biological roots of culture. Other proposals appeared in the years that followed and gave origin to different theoretical frameworks, or different schools, of biosemiotics. They are: (1) the physical biosemiotics of Howard Pattee and its extension in Darwinian biosemiotics by Howard Pattee and by Terrence Deacon, (2) the zoosemiotics proposed by Thomas Sebeok and its extension in sign biosemiotics developed by Thomas Sebeok and by Jesper Hoffmeyer, (3) the code biosemiotics of Marcello Barbieri and (4) the hermeneutic biosemiotics of Anton Markoš. The differences that exist between the schools are a consequence of their different models of semiosis, but that is only the tip of the iceberg. In reality they go much deeper and concern the very nature of the new discipline. Is biosemiotics only a new way of looking at the known facts of biology or does it predict new facts? Does biosemiotics consist of testable hypotheses? Does it add anything to the history of life and to our understanding of evolution? These are the major issues of the young discipline, and the purpose of the present paper is to illustrate them by describing the origin and the historical development of its main schools. (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)

Fundamental to Computer Science is the distinction between abstractions and implementations. When that distinction is applied to various philosophical questions it yields the following conclusions. -/- • EMERGENCE. It isn’t as mysterious as it’s made out to be; the possibility of strong emergence is not a threat to science. -/- • INTERACTIONS BETWEEN HIGHER-LEVEL ENTITIES. Physical interaction among higher-level entities is illusory. Abstract interactions are the source of emergence, new domains of knowledge, and complex systems. -/- • PHYSICS and the (...) SPECIAL SCIENCES. The new domains of knowledge derived from abstract interactions are the basis of the autonomy of the special sciences. -/- • DOWNWARD CAUSATION. It’s a zombie idea that should have a stake put through its heart and be replaced by downward entailment. (shrink)

The Snooks/Panov curve is discussed, concerning the economic history of human societies as energy transduction systems; a first formulization is proposed. World system energetics falls into the scientific context of the mathematics of planet earth & sustainability, futurizing the energy wave patterns of the global village.

This brief systems back-casting of statistical post portems on the US economy documents the quantitative heuristic errors of financial decision-making; the need for sound monetary reform is explained.

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)

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)

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)

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.

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)

A general definition of consciousness is: ‘consciousness is a mental aspect of a system or a process, which is a conscious experience, a conscious function, or both depending on the context’, where the term context refers to metaphysical views, constraints, specific aims, and so on. One of the aspects of visual consciousness is the visual subjective experience (SE) or the first person experience that occurs/emerges in the visual neural-network of thalamocortical system (which includes dorsal and ventral visual pathways and frontal (...) cortex) during dynamic interactions among widely distributed neuronal groups. In this article, however, consciousness and SE are interchangeably used unless noted. Consciousness can be either access (reportable) or phenomenal consciousness. For access consciousness, the interactions are between feed forward stimulus dependent signals and fronto-parietal feedback attentional signals. The necessary ingredients for access (reportable) consciousness are (i) wakefulness, (ii) reentrant interactions among neural populations, (iii) fronto-parietal and thalamic-reticular-nucleus attentional signals that modulate consciousness, (iv) working memory that retains information for consciousness, (v) stimulus at or above threshold level, and (vi) neural-network proto-experiences (PEs) that are superposed SEs embedded in a neural-network. Attention and the ability to report are not necessary for phenomenal consciousness. The neural source for the arousal system is the ascending reticular activating system in the brain stem, which brings the thalamocortical neural networks to wakeful state as a baseline for consciousness to occur. Reentrant interactions among neural populations bind stimulus attributes (such as location and features) and entail consciousness. Attention could be the results of reentry and competitive interactions, and modulates the stimulus related feed forward signal and consciousness. The ‘sources’ of attention may be thalamic reticular nucleus for bottom-up or frontal cortex for top-down direction. The ‘target’ of visual attention is ‘V4/V8/VO’ for Red-Green (R-G) channel. The neural correlates of the psychophysical entity R-G channel appear to be ‘V4/V8/VO’-neural-network (retina → LGN ↔ V1 ↔ V2 ↔ ‘V4/V8/VO’, and areas for attention, memory, and wakefulness). The psychophysical Red-Green Channel, its neurophysiological correlates V4/V8/VO-neural-network, and related experience (such as redness) are integrated. The dual-aspect-dual-mode PE-SE framework (Vimal, J Integr Neurosci 7:49–73, 2008) was used to address the explanatory gap problem of materialism. Neural-network and related SEs are the results of the co-evolution and co-development of the material aspect (mass, charge, spin, force, quanta, and space-time) and the mental aspect of fundamental particles (strings or elementary particles (fermions and bosons)). Their mental aspects are considered as the carriers of superposed multiple possible experiences (SEs/PEs) in unexpressed form. These possibilities are actualized when neural-networks are formed via neural Darwinism, and a specific SE is selected by a matching process when the necessary ingredients of consciousness/SE are satisfied. A simple experimental design is suggested to address the necessary and sufficient attributes of consciousness. (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 biological sciences study (bio)complex living systems. Research directed at the mechanistic explanation of the "live" state truly requires a pluralist research program, i.e. BioComplexity research. The program should apply multiple intra-level and inter-level theories and methodologies. We substantiate this thesis with analysis of BioComplexity: metabolic and modular control analysis of metabolic pathways, emergence of oscillations, and the analysis of the functioning of glycolysis.

Extract from Hofstadter's revew in Bulletin of American Mathematical Society : http://www.ams.org/journals/bull/1980-02-02/S0273-0979-1980-14752-7/S0273-0979-1980-14752-7.pdf -/- "Aaron Sloman is a man who is convinced that most philosophers and many other students of mind are in dire need of being convinced that there has been a revolution in that field happening right under their noses, and that they had better quickly inform themselves. The revolution is called "Artificial Intelligence" (Al)-and Sloman attempts to impart to others the "enlighten- ment" which he clearly regrets not having (...) experienced earlier himself. Being somewhat of a convert, Sloman is a zealous campaigner for his point of view. Now a Reader in Cognitive Science at Sussex, he began his academic career in more orthodox philosophy and, by exposure to linguistics and AI, came to feel that all approaches to mind which ignore AI are missing the boat. I agree with him, and I am glad that he has written this provocative book. The tone of Sloman's book can be gotten across by this quotation (p. 5): "I am prepared to go so far as to say that within a few years, if there remain any philosophers who are not familiar with some of the main developments in artificial intelligence, it will be fair to accuse them of professional incom- petence, and that to teach courses in philosophy of mind, epistemology, aesthetics, philosophy of science, philosophy of language, ethics, metaphysics, and other main areas of philosophy, without discussing the relevant aspects of artificial intelligence will be as irresponsible as giving a degree course in physics which includes no quantum theory." -/- (The author now regrets the extreme polemical tone of the book.). (shrink)

In this paper, we examine the use of the term ‘life’ in the debates within and about synthetic biology. We review different positions within these debates, focusing on the historical background, the constructive epistemology of laboratory research and the pros and cons of metaphorical speech. We argue that ‘life’ is used as buzzword, as folk concept, and as theoretical concept in inhomogeneous ways. Extending beyond the review of the significant literature, we also argue that ‘life’ can be understood as aBurstwordin (...) two concrete senses. Firstly, terms such as life easily turn into fuzzy, foggy and buzzy clouds of nonsense, if their use is not appropriately reflected. In these cases, the semantic orientation is detonated. This is theBurstword Icharacteristic of the concept of ‘life’ that we reveal for its unclear terminological use. Secondly, and in contrast toBurstword I, we show that the concept of ‘life’ can be used in a methodologically controlled way. We call this kind of useBurstword II. Here the concept of ‘life’ fulfils the function of expanding an inadequately narrow disciplinary or conceptual focus in different discursive contexts. In this second sense, ‘life’ receives an important operational function, for instance as a transdisciplinary research principle. It turns out that the innovative function and paradigm-changing power of metaphorical speech belong here as well. Finally, we illustrate three ethically relevant examples that show how ‘life’ can be applied asBurstword IIin the context of synthetic biology. (shrink)

Radboud Universiteit Nijmegen, 06 september 2010.

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.

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)

Morphological Computation is based on the observation that biological systems seem to carry out relevant computations with their morphology (physical body) in order to successfully interact with their environments. This can be observed in a whole range of systems and at many different scales. It has been studied in animals – e.g., while running, the functionality of coping with impact and slight unevenness in the ground is "delivered" by the shape of the legs and the damped elasticity of the muscle-tendon (...) system – and plants, but it has also been observed at the cellular and even at the molecular level – as seen, for example, in spontaneous self-assembly. The concept of morphological computation has served as an inspirational resource to build bio-inspired robots, design novel approaches for support systems in health care, implement computation with natural systems, but also in art and architecture. As a consequence, the field is highly interdisciplinary, which is also nicely reflected in the wide range of authors that are featured in this e-book. We have contributions from robotics, mechanical engineering, health, architecture, biology, philosophy, and others. (shrink)

Language, through the discrete nature of linguistic names and strictly determined grammatical rules, creates absolute, “quantized”, sharply separated “facts” within the external world that is continuous, “fuzzy” and relational in its essence. Therefore, it is similar, in some important sense, to magic, which attributes causal and creative power to magical words and formulas. On the one hand, language increases greatly the effectiveness of the processes of thinking and interpersonal communication, yet, on the other hand, it determines and distorts to a (...) large extent the picture of the world created within the mind. The relatively smallest (but still significant) magical admixture is present in science, because of its relatively reliable methodology, while the largest is found in religion and a large part of philosophy. The magical nature of language also manifests itself in logic and mathematics that refer to ill determined, fuzzy objects, sets and relations in the real world. The meaning of linguistic names is based on the conceptual network—an epiphenomenon (continuous in its essence) of the neural network—where interactions between particular concepts are based on the relation of connotation. The names and formulas of language correspond to these concepts which are best separated and determined. A direct relation of denotation between the elements of language and “facts” of the world is an illusion. While we cannot dispense with language because of its immense usefulness, we must remember about its “fact-creating” nature and influence on our thought and cognitive processes. The picture of the reality created as the result of them is to a large extent formed and deformed by the nature of language, and not by the “immanent” properties of the world in itself. (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)

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)

We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: living is information processing, in which memory is maintained by both molecular states and ecological states as well as the more obvious nucleic acid coding; this information processing has one overall function—to perpetuate itself; and the processing method is filtration of, and synthesis of, information at lower levels to appear at higher levels in complex (...) systems . We show how information patterns, are united by the creation of mutual context, generating persistent consequences, to result in ‘functional information’. This constructive process forms arbitrarily large complexes of information, the combined effects of which include the functions of life. Molecules and simple organisms have already been measured in terms of functional information content; we show how quantification may be extended to each level of organisation up to the ecological. In terms of a computer analogy, life is both the data and the program and its biochemical structure is the way the information is embodied. This idea supports the seamless integration of life at all scales with the physical universe. The innovation reported here is essentially to integrate these ideas, basing information on the ‘general definition’ of information, rather than simply the statistics of information, thereby explaining how functional information operates throughout life. (shrink)

Philosophy may relate to interdisciplinarity in two distinct ways On the one hand, philosophy may play an auxiliary role in the process of interdisciplinarity, typically through conceptual analysis, in the understanding that the disciplines themselves are the main epistemic players. This version of the relationship I characterise as ‘normal’ because it captures the more common pattern of the relationship, which in turn reflects an acceptance of the division of organized inquiry into disciplines. On the other hand, philosophy may be itself (...) the site for the production of interdisciplinary knowledge, understood as a kind of second-order understanding of reality that transcends the sort of knowledge that the disciplines provide, left to their own devices. This is my own position, which I dub ‘deviant’ and to which most of this article is devoted. I begin by relating the two types of interdisciplinarity to the organization of inquiry, especially their respective attitudes to the history of science. Underlying the two types are contrasting notions of what constitutes the ‘efficient’ pursuit of knowledge. This difference is further explored in terms of the organization of the university. The normal/deviant distinction was already marked in the institution’s medieval origins in terms of the difference between Doctors and Masters, respectively, an artefact of which remains in the postgraduate/undergraduate degree distinction. In the context of the history of the university, the prospects for deviant interdisciplinarity were greatest from the early sixteenth to the early nineteenth century—the period called ‘early modern’ in the philosophy curriculum. Towards the end of that period, due to Kant and the generation of idealists who followed him, philosophy was briefly the privileged site for deviant interdisciplinarity. After Hegel’s death, the mantle of deviant interdisciplinarity increasingly passed to some version of ‘biology’. I explore the ‘Natur-’ and ‘Geisteswissenschaft’ versions of that post-philosophical vision, which continue to co-exist within today’s biological science. I then briefly examine the chequered reputation of Jean-Baptiste Lamarck, someone who exemplified the promise and perils of deviant interdisciplinarity over the past 200 years. I conclude with an Epilogue that considers contemporary efforts to engage philosophy in interdisciplinary work, invoking William James as an exemplar. (shrink)

Famously, James Watson credited the discovery of the double-helical structure of DNA in 1953 to an X-ray diffraction photograph taken by Rosalind Franklin. Historians of molecular biology have long puzzled over a remarkably similar photograph taken two years earlier by the physicist and pioneer of protein structure William T. Astbury. They have suggested that Astbury’s failure to capitalize on the photograph to solve DNA’s structure was due either to his being too much of a physicist, with too little interest in (...) or knowledge of biology, or to his being misled by an erroneous theoretical model of the gene. Drawing on previously unpublished archival sources, this paper offers a new analysis of Astbury’s relationship to the problem of DNA’s structure, emphasizing a previously overlooked element in Astbury’s thinking: his concept of biological specificity. (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.

We discuss the meaning of “being alive” and “being dead.” Our primary aim is to pave the way for a sound and accurate ethical debate concerning these two concepts. In particular, we analyze a metabolic approach and a genetic one and discuss the reasons for their failure to constitute a good starting point for successive debates. We argue that any ethical or social discussion of topics involving life and death must introduce cultural constructs such as, on the one hand, the (...) concept of clinical death and, on the other hand, the concept of existence. We argue that these two cultural constructs, although consistent with biomedical knowledge, cannot be ontologically grounded in it. To conclude, we apply our findings to the case of human embryos. (shrink)