In this paper we give a new proof of Richardson's theorem [31]: a global function G[MATHEMATICAL DOUBLE-STRUCK CAPITAL A] of a cellular automaton [MATHEMATICAL DOUBLE-STRUCK CAPITAL A] is injective if and only if the inverse of G[MATHEMATICAL DOUBLE-STRUCK CAPITAL A] is a global function of a cellular automaton. Moreover, we show a way how to construct the inverse cellular automaton using the method of feasible interpolation from [20]. We also solve two problems regarding complexity of cellular (...) automata formulated by Durand [12]. (shrink)

Recall that for any Boolean algebra (BA) A, the cellularity of A is c(A) = sup{|X| : X is a pairwise-disjoint subset of A}. A pseudo-tree is a partially ordered set (T, ≤) such that for every t in T, the set {r ∊ T : r ≤ t} is a linear order. The pseudo-tree algebra on T, denoted Treealg(T), is the subalgebra of ℘(T) generated by the cones {r ∊ T : r ≥ t}, for t in T. We (...) characterize the cellularity of pseudo-tree algebras in terms of cardinal functions on the underlying pseudo-trees. For T a pseudo-tree, c(Treealg(T)) is the maximum of four cardinals c\sbT, ι\sbT, φ\sbT, and μ\sbT : roughly, c\sbT measures the "tallness" of the pseudo-tree T; ι\sbT the "breadth"; φ\sbT the number of "finite branchings"; and μ\sbT the number of places where T "does not branch." We give examples to demonstrate that all four of these cardinals are needed. (shrink)

We exhibit a bridge between the theory of cellular categories, used in algebraic topology and homological algebra, and the model-theoretic notion of stable independence. Roughly speaking, we show that the combinatorial cellular categories (those where, in a precise sense, the cellular morphisms are generated by a set) are exactly those that give rise to stable independence notions. We give two applications: on the one hand, we show that the abstract elementary classes of roots of Ext studied by (...) Baldwin–Eklof–Trlifaj are stable and tame. On the other hand, we give a simpler proof (in a special case) that combinatorial categories are closed under 2-limits, a theorem of Makkai and Rosický. (shrink)

Let T be an infinite pseudo-tree. In [2], we showed that the cellularity of the pseudo-tree algebra Treealg(T) was the maximum of four cardinals cT, lT, ϕT, and μT: roughly, cT is the "tallness" of T; lT is the "width" of T; ϕ is the number of "points of finite branching" in T; and μ is the number of "sections of no branching" in T. Here we ask: which inequalities among these four cardinals may be satisfied, in some sense, by (...) a pseudo-tree? We show that the possible inequalities among cT, lT, ϕT, and μT attained by pseudo-trees T are closely related to the existence of generalized Suslin trees. (shrink)

We prove two results intended to streamline proofs about cellularity that pass through mutual algebraicity. First, we show that a countable structure M is cellular if and only if M is \-categorical and mutually algebraic. Second, if a countable structure M in a finite relational language is mutually algebraic non-cellular, we show it admits an elementary extension adding infinitely many infinite MA-connected components. Towards these results, we introduce MA-presentations of a mutually algebraic structure, in which every atomic formula (...) is mutually algebraic. This allows for an improved quantifier elimination and a decomposition of the structure into independent pieces. We also show this decomposition is largely independent of the MA-presentation chosen. (shrink)

The paradox of biological diversity is the key problem of theoretical ecology. The paradox consists in the contradiction between the competitive exclusion principle and the observed biodiversity. The principle is important as the basis for ecological theory. On a relatively simple model we show a mechanism of indefinite coexistence of complete competitors which violates the known formulations of the competitive exclusion principle. This mechanism is based on timely recovery of limiting resources and their spatio-temporal allocation between competitors. Because of limitations (...) of the black-box modeling there was a problem to formulate the exclusion principle correctly. Our white-box multiscale model of two-species competition is based on logical deterministic individual-based cellular automata. This approach provides an automatic deductive inference on the basis of a system of axioms, and gives a direct insight into mechanisms of the studied system. It is one of the most promising methods of artificial intelligence. We reformulate and generalize the competitive exclusion principle and explain why this formulation provides a solution of the biodiversity paradox. In addition, we propose a principle of competitive coexistence. (shrink)

A complete Boolean algebra ${\mathbb{B}}$ satisfies property ${(\hbar)}$ iff each sequence x in ${\mathbb{B}}$ has a subsequence y such that the equality lim sup z n = lim sup y n holds for each subsequence z of y. This property, providing an explicit definition of the a posteriori convergence in complete Boolean algebras with the sequential topology and a characterization of sequential compactness of such spaces, is closely related to the cellularity of Boolean algebras. Here we determine the position of (...) property ${(\hbar)}$ with respect to the hierarchy of conditions of the form κ-cc. So, answering a question from Kurilić and Pavlović (Ann Pure Appl Logic 148(1–3):49–62, 2007), we show that ${``\mathfrak{h}{\rm -cc}\Rightarrow (\hbar)"}$ is not a theorem of ZFC and that there is no cardinal ${\mathfrak{k}}$ , definable in ZFC, such that ${``\mathfrak{k} {\rm -cc} \Leftrightarrow (\hbar)"}$ is a theorem of ZFC. Also, we show that the set ${\{ \kappa : {\rm each}\, \kappa{\rm -cc\, c.B.a.\, has}\, (\hbar ) \}}$ is equal to ${[0, \mathfrak{h})}$ or ${[0, {\mathfrak h}]}$ and that both values are consistent, which, with the known equality ${{\{\kappa : {\rm each\, c.B.a.\, having }\, (\hbar )\, {\rm has\, the}\, \kappa {\rm -cc } \} =[{\mathfrak s}, \infty )}}$ completes the picture. (shrink)

Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized into (...) hierarchies via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances. (shrink)

Protein post‐translational modifications (PTMs) play a crucial role in all cellular functions by regulating protein activity, interactions and half‐life. Despite the enormous diversity of modifications, various PTM systems show parallels in their chemical and catalytic underpinnings. Here, focussing on modifications that involve the addition of new elements to amino‐acid sidechains, I describe historical milestones and fundamental concepts that support the current understanding of PTMs. The historical survey covers selected key research programmes, including the study of protein phosphorylation as a (...) regulatory switch, protein ubiquitylation as a degradation signal and histone modifications as a functional code. The contribution of crucial techniques for studying PTMs is also discussed. The central part of the essay explores shared chemical principles and catalytic strategies observed across diverse PTM systems, together with mechanisms of substrate selection, the reversibility of PTMs by erasers and the recognition of PTMs by reader domains. Similarities in the basic chemical mechanism are highlighted and their implications are discussed. The final part is dedicated to the evolutionary trajectories of PTM systems, beginning with their possible emergence in the context of rivalry in the prokaryotic world. Together, the essay provides a unified perspective on the diverse world of major protein modifications. (shrink)

What sets someone on a life trajectory? This question is at the heart of studies of 21st-century neurosciences that build on scientific models developed over the last 150 years that attempt to link psychopathology risk and human development. Historically, this research has documented persistent effects of singular, negative life experiences on people’s subsequent development. More recently, studies have documented neuromolecular effects of early life adversity on life trajectories, resulting in models that frame lives as disproportionately affected by early negative experiences. (...) This view is dominant, despite little evidence of the stability of the presumably early-developed molecular traits and their potential effects on phenotypes. We argue that in the context of gaps in knowledge and the need for scientists to reason across molecular and phenotypic scales, as well as time spans that can extend beyond an individual’s life, specific interpretative frameworks shape the ways in which individual scientific findings are assessed. In the process, scientific reasoning oscillates between understandings of cellular homeostasis and organisms’ homeorhesis, or life trajectory. Biologist and historian François Jacob described this framework as the “attitude” that researchers bring to bear on their “objects” of study. Through an analysis of, first, historical and contemporary scientific literature and then ethnographic research with neuroscientists, we consider how early life trauma came to be associated with specific psychological and neurobiological effects grounded in understandings of life trajectories. We conclude with a consideration of the conceptual, ontological, and ethical implications of interpreting life trajectories as the result of the persistence of long-embodied biological traits, persistent life environments, or both. (shrink)

Although it has not been much noticed, reproduction is the central theme of François Jacob’s important history of biology, La logique du vivant (The Logic of Life). In a book ostensibly devoted to heredity, this molecular biologist had reproduction integrate levels of organization from organisms to molecules and play a major role in each historical transition between them, not just in the influential argument for a shift “from generation to reproduction.” Moreover, I claim, La logique was the first general (...) history of (research on) reproduction. Earlier histories had tackled only aspects of generation and reproduction; none historicized the latter. Jacob’s innovation came out of the rising prominence of reproduction in neo-Darwinist studies of populations and in his own field, the cellular genetics of bacteria and their viruses, and engagement with history and philosophy of science. The discovery of bacterial “sex” enabled microbial genetics but, ironically, led Jacob to a sexless concept of reproduction. This approach molded a history that reached across the living world but slighted sex and the complexities of reproduction in multicellular organisms. Readers can learn from its strength and limitations. (shrink)

We show that if a countable structure M in a finite relational language is not cellular, then there is an age-preserving $N \supseteq M$ such that $2^{\aleph _0}$ many structures are bi-embeddable with N. The proof proceeds by a case division based on mutual algebraicity.

This book is an introduction, entirely by example, to the possibilities of using computer models as tools in phosophical research in general and in philosophical logic in particular. Topics include chaos, fractals, and the semantics of paradox; epistemic dynamics; fractal images of formal systems; the evolution of generosity; real-valued game theory; and computation and undecidability in the spatialized Prisoner's Dilemma.

When a boat disappears over the horizon, does a distant observer detect the last moment in which the boat is visible, or the first moment in which the boat is not visible? This apparently ludicrous way of reasoning, heritage of long-lasting medieval debates on decision limit problems, paves the way to sophisticated contemporary debates concerning the methodological core of mathematics, physics and biology. These ancient, logically-framed conundrums throw us into the realm of bounded objects with fuzzy edges, where our mind (...) fails to provide responses to plain questions such as: given a closed curve with a boundary (say, a cellular membrane) how do you recognize what is internal and what is external? We show how the choice of an alternative instead of another is not arbitrary, rather points towards entirely different ontological, philosophical and physical commitments. This paves the way to novel interpretations and operational approaches to challenging issues such as black hole singularities, continuous time in quantum dynamics, chaotic nonlinear paths, logarithmic plots, demarcation of living beings. In the sceptical reign where judgements seem to be suspended forever, the contemporary scientist stands for a sort of God equipped with infinite power who is utterly free to dictate the rules of the experimental settings. (shrink)

Formal systems are standardly envisaged in terms of a grammar specifying well-formed formulae together with a set of axioms and rules. Derivations are ordered lists of formulae each of which is either an axiom or is generated from earlier items on the list by means of the rules of the system; the theorems of a formal system are simply those formulae for which there are derivations. Here we outline a set of alternative and explicitly visual ways of envisaging and analyzing (...) at least simple formal systems using fractal patterns of infinite depth. Progressively deeper dimensions of such a fractal can be used to map increasingly complex wffs or increasingly complex 'value spaces', with tautologies, contradictions, and various forms of contingency coded in terms of color. This and related approaches, it turns out, offer not only visually immediate and geometrically intriguing representations of formal systems as a whole but also promising formal links (1) between standard systems and classical patterns in fractal geometry, (2) between quite different kinds of value spaces in classical and infinite-valued logics, and (3) between cellular automata and logic. It is hoped that pattern analysis of this kind may open possibilities for a geometrical approach to further questions within logic and metalogic. (shrink)

This essay evaluates the moral logic of ‘liberal eugenics’: the ideal of genetic control which leaves decisions about what sort of people to produce in the hands of individual parents, absent government intervention. I argue that liberal eugenics cannot be justified on the basis of the underlying liberal theory which inspires it. I introduce an alternative to Rawls's social primary goods that might be called natural primary goods: hereditable mental and physical capacities and dispositions that are valued across a (...) range of projects and pursuits. I suggest that reproductive genetic biotechnologies like embryo selection, cellular surgery, and genetic engineering, which aim to enhance ‘general purpose’ traits in offspring are less like childrearing practices a liberal government leaves to the discretion of parents than like practices the state makes compulsory. I argue that if the liberal commitment to autonomy is important enough for the state to mandate childrearing practices such as health care and basic education, that very same interest is important enough for the state to mandate safe, effective, and functionally integrated genetic practices that act on analogous all‐purpose traits such as resistance to disease and general cognitive functioning. I conclude that the liberal case for compulsory eugenics is a reductio against liberal theory. (shrink)

We may now ask the question: In what historical perspective should we place the work of Richard Goldschmidt? There is no doubt that in the period 1910–1950 Goldschmidt was an important and prolific figure in the history of biology in general, and of genetics in particular. His textbook on physiological genetics, published in 1938, was an amazing compendium of ideas put forward in the previous half-century about how genes influence physiology and development. His earlier studies on the genetic and geographic (...) distribution of the various species and races of Lymantria contributed soundly to an understanding of the inheritance and development of sex, as well as the genetics of speciation. He was a curious mixture of the experimentalist, empiricist, and theorizer, who could grasp both the large and the small at once and wrap them into the same integrated and coherent package.In insisting on trying to relate genetics to development, Goldschmidt was continually forced to speculate and to forsake experimental fact for generalized theory. In refusing to reconcile a physiological and developmental conception with a corpuscular theory of the gene, he forced himself to substitute for a large body of experimentally verified evidence, vague and general speculations which did not lead in any precise direction. L. C. Dunn summarizes succinctly the effect of Goldschmidt's thinking on the development of genetic theory: Although Goldschmidt's ideas had a considerable influence in directing attention to the developmental processes intervening between genes and characters, they did not lead to the establishment of a general theory of development in genetical terms. In fact, at the end of the period, as signalized by Goldschmidt's book of 1938 [Physiological Gentics] doubt remained whether there was a field with a defined problem which could be identified as developmental genetics.Yet the frequency with which Goldschmidt is cited by later writers suggests that there is a more positive side to his contribution than this. The early Mendelians had recognized the genic constitution of organisms and the Drosophila workers had uncovered in detail the chromosomal mechanism of heredity. These great discoveries were of classical character, solidly based on a multitude of well established facts. By themselves, however, they would not have been sufficient to place genetics in the central position within biology which it was to assume. Beyond the “static” analysis of gene transmission an insight was needed into the dynamic role of genes in cellular physiology, biochemistry, and development. Goldschmidt recognized this aspect and outlined in brilliant generalizations a physiological theory of genetics. Necessarily the prophetic nature of this achievement — romantic in the sense of Ostwald's classification of great scientists and their discoveries — transcended its factual basis. It was the audacity of the theoretician unimpeded by the still scanty data which gave a new focus to biological thought.Some have called Goldschmidt an “obstructionist” in the history of genetics—one whose efforts were largely directed toward useless and continual criticism — challenge for the sake of challenge. As this line of argument goes, time wasted answering Goldschmidt's poorly conceived criticisms could have been better used to pursue new lines of thought within the classical gene theory. Sometimes historians are upbraided for studying the work of such “obstructionists,” or even the work of those whose ideas have later proved to be inadequate. This argument misses the point of history and the lessons which it can teach. Perhaps Goldschmidt did take the time of a number of the classical geneticists who tried to answer his objections to the gene theory; and perhaps many of his own ideas about genes were, by today's view, “wrong.” These are always easier judgments to make by hindsight than at the moment. But that is not the point. Goldschmidt had a considerable influence on his contemporaries, and to dismiss him as an obstructionist because his opponents later proved to be more nearly right, distorts history and obscures significant questions which we might well be asking. It might be valuable to know why Goldschmidt felt compelled to be an iconoclast —and how that impulse, psychological in orgin, led him to overlook critical items of evidence which his opponents considered more carefully. It might also be valuable to try and understand how a contemporary of Goldschmidt or. Morgan really viewed the gene theory — what were its strong and weak point? Such questions are not readily answered by studying the work of only those men who were correct by later standards.Answers to some of the above questions can be gleaned from this study of Goldschmidt — though the first, and most psychologically oriented, question is largely untouched here.On the one hand, Goldschmidt forced classical geneticists to reexamine the foundation of their ideas about the nature, inviolability, and even physical dimensions of genes. He also kept alive the very real problems of gene physiology and its relations to development — a relationship that was given less attention by the Drosophila school in their pursuit of the transmission process. On a broader level he emphasized to the biological community a principle that was in danger of being lost in the enthusiasm surrounding the expansion of the Mendelian-chromosome theory. The point was that all theories in science are transient, logical constructs which should not be held as sacred. Time and again, as the history of science has shown, theories become rigid structures which retard new modes of thought. From Goldschmidt's perspective, the gene theory was in danger of performing just that function, for it was preventing workers from viewing the gene in a functional as well as a structural light.On the other hand, examining the work of critics (or even of outright “obstructionists”) gives the historian an opportunity to observe how the more established community of scholars at some point in time reacts to challenges of its cherished ideas. The fact that many workers in his own day (such as Beadle, Luria, Delbruck, Sturtevant, Bridges, and others), as well as most geneticists today, saw Goldschmidt as having been largely “obstructionist” is useful historical (and/or sociological) data. Clearly, as this paper has tried to show, Goldschmidt's ideas were not all obstructionist, and his viewpoint that genes must be considered functionally was one which was clearly valid, premature as it may have been from an experimental and technique point of view. Perhaps Goldschmidt's major fault was that he developed alternative theories which were not easily testable. Nonetheless, his challenge to a fundamental and established idea brought forth a reaction from many members of the genetic community which indicates how unwilling they were to reconsider the formalized theory on which their work was based. While many of Goldschmidt's criticisms — and particularly his way of making them — arose out of his own idiosyncrasies, they were also a product of his times. His view of the nature of theory-construction, and his rejection of old-style reductionism and mechanism, were part of a growing awareness within the world scientific community that explanations based on reducing complex phenomena to ultimate particles or units were clearly inadequate. The success of the Mendelian-chromosome theory had obscured that fact for many geneticists, but to Goldschmidt it was a point that could not be allowed to pass unnoticed. (shrink)

In the target article “How molecules became signs” I offer a molecular “thought experiment” that provides a paradigm for resolving the major incompatibilities between biosemiotic and natural science accounts of living processes. To resolve these apparent incompatibilities I outline a plausible empirically testable model system that exemplifies the emergence of chemical processes exhibiting semiotic causal properties from basic nonliving chemical processes. This model system is described as an autogenic virus because of its virus-like form, but its nonparasitic self-repair and reproductive (...) dynamics. The 16 commentaries responding to this proposal recognize its material plausibility but are divided on its value in resolving this basic biosemiotic challenge. In response, I have addressed some of the most serious criticisms raised and have attempted to diagnose the major sources of incompatible assumptions that distinguish the autogenic paradigm from other major paradigms. In particular, I focus on four main issues: the significance of the shift from a cellular to a viral perspective, the relevance of intrinsic versus extrinsic initiation and channeling of interpretive work, the insufficiency of molecular replication as a basis for grounding biological semiosis, and a (universal?) three step scaffolding logic that enables referential displacement of sign vehicle properties without loss of referential continuity (as exemplified by DNA-protein relations). Although I can’t conclude that this is the only way that biosemiotic properties can emerge from physical-chemical relations that otherwise lack these properties, I contend that this approach offers a biologically plausible demonstration that it is possible. (shrink)

Digital physics claims that the entire universe is, at the very bottom, made out of bits; as a result, all physical processes are intrinsically computational. For that reason, many digital physicists go further and affirm that the universe is indeed a giant computer. The aim of this article is to make explicit the ontological assumptions underlying such a view. Our main concern is to clarify what kind of properties the universe must instantiate in order to perform computations. We analyse the (...) logical form of the two models of computation traditionally adopted in digital physics, namely, cellular automata and Turing machines. These models are computationally equivalent, but we show that they support different ontological commitments about the fundamental properties of the universe. In fact, cellular automata are compatible with a rather traditional form of physicalism, whereas Turing machines support a dualistic ontology, which could be understood as a realism about the laws of nature or, alternatively, as a kind of panpsychism. (shrink)

Explaining the nature and mechanisms of conscious experience in neurobiological terms seems to be an attainable, if yet unattained, goal. Research at many levels is important, including research at the cellular level that explores the role of recurrent pathways between thalamic nuclei and the cortex, and research that explores consciousness from the perspective of action. Conceptually, a clearer understanding of the logic of expressions such as ‘‘causes’’ and ‘‘correlates’’, and about what to expect from a theory of consciousness (...) are required. The logic of some terms, such as ‘‘qualia’’ and ‘‘reductionism’’, continues to generate misunderstandings about the scientific possibilities and limits. Experimentally, a deeper understanding of the role of the thalamus in coordinating activity across cortical levels, and a readiness to reconsider the orthodox approach to thalamocortical organization are also required. (shrink)

A recurrent theme in ethnomethodological research is that of instructed actions. Contrary to the classic traditions in the social and cognitive sciences, which attribute logical priority or causal primacy to instructions, rules, and structures of action, ethnomethodologists investigate the situated production of actions which enable such formulations to stand as adequate accounts. Consequently, a recitation of formal structures can not count as an adequate sociological description, when no account is given of the local production ofwhat those structures describe. The natural (...) sciences can be described as a domain of practical action in whichthe use of methods enables the intersubjective reproduction of naturalistic observations and experiments. As numerous sociological studies of laboratory practices have shown, the achievement of intersubjective order cannot be reduced to formal methods; instead, it arises from the work of custom-fitting relevant methods to the local circumstances of the research. In this paper we discuss a possible extension of this idea to cover two intertwined aspects of molecular biology: (1) the work of following instructions on how to perform routine laboratory procedures, and (2) the relationship between cellular orders and the encoded instructions contained in the DNA molecule. We suggest that a classic conception of scientific action is implied by the way formal instructions are treated as a primary basis, both for molecular biologists' actions and the cellular functions they study, and we envision an ethnomethodological alternative to those conceptions of social and biological order. (shrink)

The observed complexity of nature is often attributed to an intrinsic propensity of matter to self-organize under certain (e.g., dissipative) conditions. In order better to understand and test this vague thesis, we define complexity as “logical depth,” a notion based on algorithmic information and computational time complexity. Informally, logical depth is the number of steps in the deductive or causal path connecting a thing with its plausible origin. We then assess the effects of dissipation, noise, and spatial and other symmetries (...) of the initial conditions and equations of motion on the asymptotic complexity-generating abilities of statistical-mechanical model systems. We concentrate on discrete, spatially-homogeneous, locally-interacting systems such as kinetic Ising models and cellular automata. (shrink)

“There’s Plenty of Room at the Bottom”, said the title of Richard Feynman’s 1959 seminal conference at the California Institute of Technology. Fifty years on, nanotechnologies have led computer scientists to pay close attention to the links between physical reality and information processing. Not all the physical requirements of optimal computation are captured by traditional models—one still largely missing is reversibility. The dynamic laws of physics are reversible at microphysical level, distinct initial states of a system leading to distinct final (...) states. On the other hand, as von Neumann already conjectured, irreversible information processing is expensive: to erase a single bit of information costs ~3 × 10−21 joules at room temperature. Information entropy is a thermodynamic cost, to be paid in non-computational energy dissipation. This paper addresses the problem drawing on Edward Fredkin’s Finite Nature hypothesis: the ultimate nature of the universe is discrete and finite, satisfying the axioms of classical, atomistic mereology. The chosen model is a cellular automaton with reversible dynamics, capable of retaining memory of the information present at the beginning of the universe. Such a CA can implement the Boolean logical operations and the other building bricks of computation: it can develop and host all-purpose computers. The model is a candidate for the realization of computational systems, capable of exploiting the resources of the physical world in an efficient way, for they can host logical circuits with negligible internal energy dissipation. (shrink)

My research is centred upon how architecture is invigorated by cyberspace, the blurred boundary between the virtual and the actual, and how the different parameters of these spaces can be used to inform one another. My early experience in practice was that buildings are limited by the inert materials used to construct them and by the unimaginative ideas of what a building should look like and be. My research draws upon a variety of different disciplines to inform one architecture. The (...) areas of research are multidisciplinary and include the changing status of the architectural drawing, smart materials, computer-aided architectural drawing, computer-aided manufacture, emergent systems, responsive environments, the architectural design of cyberspace, interactivity, cybernetics and evolving systems and algorithmic design. To create responsive, non-prescriptive designs for architectural intervention was the starting point that led to an interest in the logic of algorithms and open-ended systems. These problem-solving diagrams used by computer programmers are very useful as a way of describing fluctuating conditions in responsive environments. This led to an interest in other computing paradigms such as cellular automata, complexity and emergence. These and other ideas I attempted to bring into the arena of architectural design to help architects cope with the rapid growth of computational technology, which is starting to revolutionize the way buildings are designed, drawn and built. We are at another of the important perturbations in technology and epistemology that seems to affect us so often these days. Cell biology is the new cyber-space and nanotechnology. Once we fully understand the exact nature of how our world makes us and, indeed how it sometimes kills us, we will be able to make true architectures of ecological connectability. This is our profession's future. Small steps have been made, but much more remains to be done. (shrink)

Transposable elements are no longer considered to be “junk” DNA. Here, we review how TEs can impact gene regulation systematically. TEs encode various regulatory elements that enables them to regulate gene expression. RJ Britten and EH Davidson hypothesized that TEs can integrate the function of various transcriptional regulators into gene regulatory networks. Uniquely TEs can deposit regulatory sites across the genome when they transpose, and thereby bring multiple genes under control of the same regulatory logic. Several studies together have (...) robustly established that TEs participate in embryonic development and oncogenesis. We discuss the regulatory characteristics of TEs in context of evolution to understand the extent of their impact on gene networks. Understanding these features of TEs is central to future investigations of TEs in cellular processes and phenotypic presentations, which are applicable to development and disease studies. We re-visit the Britten–Davidson “gene-battery” model and understand the genetic and transcriptional impact of TEs in innovating gene regulatory networks. Transposable elements are exogenous sequences that have either been co-opted or repurposed for host functions. The vast amounts of TE sequence in the genome provides raw material for gene expression regulation, and still remains to be fully understood; the “gene-battery” model provides the basis for understanding this. (shrink)

This paper examines the notion of the biopolitical body from the standpoint of Foucault’s logic of the security mechanism and the history he tells of vaccine technology. It then investigates how the increasing importance of the genetic code for determining the meaning and limits of the human in the field of 20th century cell biology has been a cause for ongoing transformation in the practices that currently extend vaccine research and development. I argue that these transformations mark the emergence (...) of a new kind of medical subject – the stabilized and infinitely reproducible human cell line – and that the practices and markets exploiting this new form of organism have had a destabilizing effect on the very biopolitical structures that engendered them and, in fact, mark a new way of conceiving the possibilities of cellular life. I call these new ways of organizing power that intervene in the logic of the security measure by mediating the relationship between populations and persons the microbiopolitical. (shrink)

This article explores the critical limitations of the now decades-long shift toward digital culture in the material and cultural constitution of biotechnology. It does this by telling the story of three contemporary efforts to reimagine the logic of life on the logic of the digital and the struggles attendant to building the infrastructures needed to actualize that re-imagination and make it profitable. In tracing these stories, it lifts out how biotechnologists, once caught in the spell of the digital (...) sublime, are having to confront the ways in which dreams of a data-driven and automated biology, far from eliciting an exalted future of health, wealth, and security, are simply reinforcing at the level of the organism a world already boxed in by algorithmic modes of reason and governed by imperatives of optimization. In the midst of these binds, this article points to a pathos which is beginning to stir at the bench as blue-collar technologists seek to activate an older feel for craftwork, and how this pathos signals a familiar but vital reciprocity between the maker and the made. It concludes that, in the end, breakdowns in the digital sublime make space for a more interesting biotechnical proposition, one in which the living thing being crafted has to be accommodated rather than rendered algorithmic: the cellular targets of biotechnical intervention must be coerced, cajoled, and enticed into playing along with our biotechnical imaginations. To act differently proves to be the real source of our trouble. The stories in this article draw on fieldwork conducted by the author through multiple experiments in collaborative anthropology. These experiments began in connection to a then-emerging brand of biotechnology called synthetic biology, were carried forward in view of a “post-engineering” approach to systems biology, and are currently (as of the writing of this essay) being conducted among biologists and technologists working to build “digital infrastructures” for the life sciences (i.e., digital tools for assembling, mediating, and synthesizing post-genomic biology). (shrink)

The interactions among the components of a biological system can be given a logical representation that is useful for reasoning about them. One of the relevant problems that may be raised in this context is finding what would explain a given behaviour of some component; in other terms, generating hypotheses that, when added to the logical theory modelling the system, imply that behaviour. Temporal aspects have to be taken into account, in order to model the causality relationship that may link (...) the behaviour of a given component to that of another one. This paper presents a hypothesis generation method for linear temporal logic theories whose formulae have a restricted syntactic form, which is however sufficient to model cellular and molecular interactions, as they are often represented by biologists. The method exploits the duality between hypothesis generation and consequence finding, and can therefore be also used to infer the consequences of a given fact. It is based on a resolution system proposed by Cavalli and Fariñas del Cerro in 1984. (shrink)

Microbes perfect social interactions with intuitive logics and goal-directed reciprocity. These multilevel, cognition-resembling adaptations in Dictyostelid cellular molds enable individual-to-group viability through public/private bacterial farming and dynamic marketspaces. Like humans and animals, Dictyostelid livestock-ownership depends on environmental sensing, cooperation, and competition. Moreover, social-norm policing of cosmopolitan colonies coordinates farmer decisions, phenotypes, and ownership identities with bacteria herding, privatization, and consumption.

With the advent of the cloud computing model allowing a shared access to massive computing facilities, a surging demand emerges for the protection of the intellectual property tied to the programs executed on these uncontrolled systems. If novel paradigm as confidential computing aims at protecting the data manipulated during the execution, obfuscating techniques (in particular at the source code level) remain a popular solution to conceal the purpose of a program or its logic without altering its functionality, thus preventing (...) reverse-engineering on the program even with the help of computing resources. The many advantages of code obfuscation, together with its low cost, makes it a popular technique. This paper proposes a novel methodology for source code obfuscation that can be used together with other traditional obfuscation techniques, making the code more robust against reverse engineering attacks. Three program complexity metrics are used to define three different single-objective combinatorial optimization versions of the problem, which are solved and analysed. Additionally, three multi-objective problems are defined, those considering each of the selected metrics together with the program execution time, in order to avoid strong obfuscations penalizing the performance. The goal of the defined problems is to find sequences of LLVM optimizations that lead to highly obfuscated versions of the original code. These transformations are applied to the back-end pseudo-assembly code (i.e., LLVM Intermediate Representation), thus avoiding any further optimizations by the compiler. Classical genetic algorithms (GAs) are used to solve the studied problems, namely a basic cellular GA for the single-objective problems and the popular NSGA-II for the multi-objective ones. The promising results show the potential of the proposed technique. (shrink)

Translation as philosophical program: An explorative reviewWhat does the concept of translation mean in the expression ‘translational neuroscience’? What are the different steps, or components, in the translation of neuroscientific findings to psychiatry? There are serious concerns about the validity and productivity of the traditional idea of a translational pipeline, starting in the fundamental sciences (chemistry, molecular and cellular biology) and ending in the practice of clinical medicine, including psychiatry. The article defends the thesis that the difficulties in the (...) traditional approach result, at least partially, from insufficient reflection on the philosophical premises upon which the concept of translation is based. The linear pipeline model is strongly determined by the traditional biomedical approach to disease. The translation crisis signifies some of the limitations of this approach, especially in the realm of clinical practice and patient experience. The biomedical model suggests that illness manifestations should be conceived as causally determined expressions of an underlying biological derailment or dysfunction. This model lacks the language and conceptual tools to address the role of contextual and person-bound factors in the manifestation of illness. It is only recently that personalized and context-sensitive approaches to psychopathology have gained scientific attention. In the wake of this conceptual and practical reform, network-like approaches to translation have emerged. These network approaches are based on a different conception of transdisciplinarity. They address all stakeholders, by asking them what kind of translation they need. Stakeholders are not only scientists and clinicians, but also patient- and family support groups; and parties that are responsible for the institutional embedding, the financial and logistic infrastructure, and the legal frameworks that support psychiatric care. It is the interaction between science (as producer of knowledge) and the contexts that are supposed to benefit from this knowledge, that should be put at the centre of conceptual reflection. The degree and fruitfulness of this interaction will be decisive for the future of both psychiatry and clinical neuroscience. Philosophy can play an important role in this interaction, by making explicit underlying logical and practical tensions and ambiguities in this interaction. (shrink)

While genomic and proteomic information describe the overall cellular machinery available to an organism, the metabolic profile of an individual at a given time provides a canvas as to the current physiological state. Concentration levels of relevant metabolites vary under different conditions, in particular, in the presence or absence of different disorders. Metabolite concentrations thus mediate an important link between chemistry and biology, contributing to a systems-wide understanding of biological processes and pathways. However, there are a number of challenges (...) in the ontological representation of such information. Firstly, concentration information is numeric and ranges over continuous values, while ontologies consist of discrete classes. Secondly, ontologies usually model only what is certain, and their logical formalisms are adapted to reasoning from certain axioms to logical deductions, however, the link between chemicals and diseases via concentration levels, like many threshold phenomena, is both uncertain and vague. In this paper we evaluate the representation of this knowledge using a combination of concrete domains and probabilistic reasoning. We parse concentration values from HMDB and create an ontology able to distinguish normal from abnormal concentrations and able to evaluate a probabilistic risk category for the presence of an associated disorder. (shrink)

Stuart Hameroff opens with an extended and updated exposition of the Penrose/Hameroff Orch-OR model, and subsequently addresses recent criticisms of quantum approaches to the brain. Evan Walker presents his view on consciousness from the perspective of a new approach to the integration of quantum theory and relativity. Friedrich Beck elaborates on the Beck/Eccles quantum approach to consciousness. Karl Pribram puts the holographic view on consciousness in perspective of his life long work. Peter Marcer and Edgar Mitchell explain the relevance of (...) quantum holography for consciousness. Gordon Globus discusses the relation between postmodern philosophical theories and quantum consciousness. Chris Clarke develops a theory in terms of a specific type of formal logic to reconcile the phenomenology of consciousness with the physical world. Ilya Prigogine summarizes his view on complexity, and on the future of quantum theory, which goes beyond the present formalism, and goes on to comment on the problem of consciousness. Matti Pitkanen identifies the place for consciousness in a unifying topological geometro-dynamics theory. Colin McGinn argues against classical materialism. Dick Bierman gives an overview of anomalous phenomena. He identifies a decline effect, and discusses different possible interpretations. Philip Van Loocke closes the volume with a discussion on how deep teleology in cellular systems may relate to consciousness. (shrink)

Of the many genes mutated on the road to tumor formation, few have received as much attention as p53. The gene has come to occupy center stage for the simple reason that it is more frequently altered in human tumors than any other known gene, undergoing mutation at a significant rate in almost every tumor type in which it has been studied. This association between p53 mutation and tumorigenesis has spurred a flurry of research attempting to delineate the normal function (...) of p53 and, by extension, the role of p53 mutation in tumor formation. At the cellular level, p53 has been shown to suppress growth. Recent efforts to further discern the function of p53 have centered on the underlying molecular basis for this growth suppression. In particular, research has focused on the identification of cellular molecules (specifically DNA and proteins) with which the p53 protein associates. p53 has now been shown to bind DNA in a sequence‐specific manner, and mounting evidence suggests that p53 acts as a transcription factor, perhaps regulating the expression levels of genes involved in the inhibition of cell growth. The logical next step in understanding p53 function involves the resolution of two questions: (1) what are the physiological transcriptional targets of p53, and (2) what cellular proteins regulate or mediate the ability of p53 to modulate transcription? Some initial clues to these puzzles are now emerging, and these form the subject of this review. (shrink)

Cascades of transcriptional regulation are the common source of the forward drive in all developmental systems. Increases in complexity and specificity of gene expression at successive stages are based on the collaboration of varied combinations of transcription factors already expressed in the cells to turn on new genes, and the logical relationships between the transcription factors acting and becoming newly expressed from stage to stage are best visualized as gene regulatory networks. However, gene regulatory networks used in different developmental contexts (...) underlie processes that actually operate through different sets of rules, which affect the kinetics, synchronicity, and logical properties of individual network nodes. Contrasting early embryonic development in flies and sea urchins with adult mammalian hematopoietic development from stem cells, major differences are seen in transcription factor dosage dependence, the silencing or damping impacts of repression, and the impact of cellular regulatory history on the parts of the genome that are accessible to transcription factor action in a given cell type. These different features not only affect the kinds of models that can illuminate developmental mechanisms in the respective biological systems, but also reflect the evolutionary needs of these biological systems to optimize different aspects of development. (shrink)

The qigong state of bigu is believed to be supported by the absorption of qi from the universe. Gamma radiation is ubiquitous in the cosmos and, according to some, may be a possible source of energy for cellular functioning. When the concept of energy is integrated with the concept of dynamical systems, the logic leads to the theory—termed systemic memory—that predicts all systems, from the micro to macro, store information and energy to various degrees. New research indicates that (...) the human body absorbs gamma radiation from the environment and emits high-frequency X rays. There are substantial individual differences in these effects that appear to be related, in part, to the psychological state of the person. Future research can determine if bigu is associated with increased absorption of gamma radiation and/or decreased emission of high frequency X rays. The hypothesis that qi can be viewed as quality information is proposed. (shrink)

The African-American philosopher William Fontaine (1909-1968) inaugurated a neo-Kantian philosophical analysis of the original biological theories of fellow African-American Ernest Everett Just (1883-1941), and his thesis regarding the “space-time” structure of biological systems deserves our renewed consideration today. First comparing Just’s methodology in his 1939 text Biology of the Cell Surface to Immanuel Kant’s Critique of Pure Reason (1781/1787), Fontaine then suggested a parallel reading of Just’s irreducible theory of cellular structure to Samuel Alexander’s (1859-1938) Gifford Lectures of 1920 (...) on the metaphysical possibility of non-Euclidean or multidimensional space-time — Along these lines, Just had written of life’s constituents, because “assembled both in space and time, its investigation is limited”. Since Kant was well-known and also later criticized for his logical commitments to three-dimensional Euclidean space-time, it is clear that Fontaine’s reading of Just’s statements departed from traditional Kantian philosophy. However, since Just’s Biology of the Cell Surface emphasized the whole-part relation of living organisms as well the distinction between reductionistic mechanism and emergent theories — metaphysical views that Kant also expounded — Fontaine’s analysis charted a new route for bringing Kantian philosophy into the context of contemporary theories of non-Euclidean and higher-dimensional space-time. This paper first reviews the original contributions of Ernest Everett Just to biology as well as William Fontaine’s philosophical commentary upon them, and then considers the current scientific basis for non-Euclidean and higher-dimensional geometries in the biological sciences. (shrink)

The structuralist program has developed a useful metascientific resource: ontological reductive links (ORLs) between the constituents of the potential models of reduced and reducing theories. This resource was developed initially to overcome an objection to structuralist ``global'' accounts of the intertheoretic reduction relation. But it also illuminates the way that concepts at a higher level of scientific investigation (e.g., cognitive psychology) become ``structured through reduction'' to lower-level investigations (e.g., cellular/molecular neuroscience). After (briefly) explaining this structuralist background, I demonstrate how (...) this resource illuminates an actual, emerging scientific example: the link between the psychological concept of a ``consolidation switch'' from short-term to long-term memory and the cellular/molecular mechanisms of the transition from early- to late-phases of long-term potentiation (LTP) (an important type of synaptic plasticity in mammalian hippocampus and cortex). (shrink)

Neurophysiological research suggests our mental life is related to the cellular processes of particular nerves. In the spirit of Occam’s razor, some authors take these connections as reductions of psychological terms and kinds to molecular- biological mechanisms and patterns. Bickle’s ‘intervene cellularly/molecularly and track behaviourally’ reduction is one example of this. Here the mental is being reduced to the physical in two steps. The first is, through genetically altered mammals, to causally alter activity of particular nerve cells, i.e. neurons, (...) at the molecular level and then, under controlled experimental conditions, to use generally-accepted rules of behaviour within psychology to monitor the results of these manipulations. In this article, we argue that Bickle’s case example for molecular reduction, i.e. the reduction of long-term memory to its cellular-molecular mechanisms, cannot support his claims, because it turns out that his chosen molecular pathway is neither a sufficient nor a necessary condition for the memory consolidation switch, and thus, instead of rejecting the multiple realization argument, Bickle’s argument actually speaks in favour of it. Therefore the idea of reductive connections between our mental life and the activity of particular nerves is, at present, still more fiction than reality. (shrink)

In this article, the author attempts to explicate the notion of the best known Talmudic inference rule called qal wa-omer. He claims that this rule assumes a massive-parallel deduction, and for formalizing it, he builds up a case of massive-parallel proof theory, the proof-theoretic cellular automata, where he draws conclusions without using axioms.

Hutto and Myin famously argue that basic minds are not contentful and content exists only as far as it is scaffolded with social and linguistic practices. This view, however, rests on a troublesome distinction between basic and scaffolded minds. Since Hutto and Myin have to account for language purely in terms of joint action guidance, there is no reason why simpler communication systems, such as cellular signaling pathways, should not give rise to scaffolded content as well. This conclusion remains (...) valid even if one rejects the view of language as mediated through public symbols and embraces global antirepresentationalism. Content evolves spontaneously in complex regulatory systems, such as human, animal, and cellular communication. (shrink)

We prove that colouring of pairs from 2 with strong properties exists. The easiest to state problem it solves is: there are two topological spaces with cellularity 1 whose product has cellularity 2; equivalently, we can speak of cellularity of Boolean algebras or of Boolean algebras satisfying the 2-c.c. whose product fails the 2-c.c. We also deal more with guessing of clubs.

The sequences produced by the cryptographic sequence generator known as the shrinking generator can be modelled as the output sequences of linear elementary cellular automata. These sequences are composed of interleaved m-sequences produced by linear structures based on feedback shifts. This profitable characteristic can be used in the cryptanalysis of this generator. In this work we propose an algorithm that takes advantage of the inherent linearity of these CA and the interleaved m-sequences. Although irregularly decimated generators have been conceived (...) and designed as non-linear ones, in practice they can be easily analysed in terms of simple linear structures. (shrink)