Computer simulations constitute a significant scientific tool for promoting scientific understanding of natural phenomena and dynamic processes. Substantial leaps in computational force and software engineering methodologies now allow the design and development of large-scale biological models, which – when combined with advanced graphics tools – may produce realistic biological scenarios, that reveal new scientific explanations and knowledge about real life phenomena. A state-of-the-art simulation system termed Reactive Animation (RA) will serve as a study case to examine the contemporary philosophical (...) debate on the scientific value of simulations, as we demonstrate its ability to form a scientific explanation of natural phenomena and to generate new emergent behaviors, making possible a prediction or hypothesis about the equivalent real-life phenomena. (shrink)

Background: how mind functions is subject to continuing scientific discussion. A simplistic approach says that, since no convincing way has been found to model subjective experience, mind cannot exist. A second holds that, since mind cannot be described by classical physics, it must be described by quantum physics. Another perspective concerns mind's hypothesized ability to interact with the world of quanta: it should be responsible for reduction of quantum wave packets; physics producing 'Objective Reduction' is postulated to form the basis (...) for mind-matter interactions. This presentation describes results derived from a new approach to these problems. It is based on well-established biology involving physics not previously applied to the fields of mind, or consciousness studies, that of critical feedback instability. -/- Methods: 'self-organized criticality' in complexity biology places system loci of control at critical instabilities, physical properties of which, including information properties, are presented. Their elucidation shows that they can model hitherto unexplained properties of experience. -/- Results: All results depend on physical properties of critical instabilities. First, at least one feed-back or feed-forward loop must have feedback gain, g = 1: information flows round the loop impress perfect images of system states back on themselves: they represent processes of perfect self-observation. This annihilates system quanta: system excitations are instability fluctuations, which cannot be quantized. Major results follow: -/- 1. Information vectors representing criticality states must include at least one attached information loop denoting self-observation. -/- 2. Such loop structures are attributed a function, 'registering the state's own existence', explaining -/- a. Subjective 'awareness of one's own presence' -/- b. How content-free states of awareness can be remembered (Jon Shear) -/- c. Subjective experience of time duration (Immanuel Kant) -/- d. The 'witness' property of experience – often mentioned by athletes 'in the zone' -/- e. The natural association between consciousness and intelligence -/- This novel, physically and biologically sound approach seems to satisfactorily model subjectivity. -/- Further significant results follow: -/- 1. Registration of external information in excited states of systems at criticality reduces external wave-packets: the new model exhibits 'Objective Reduction' of wave packets. -/- 2. High internal coherence (postulated by Domash & Penrose) leading to a. Non-separable information vector bundles. b. Non-reductive states (Chalmers's criterion for experience). -/- 3. Information that is: a. encoded in coherence negentropy; b. non-digitizable, and therefore c. computationally without digital equivalent (posited by Penrose). -/- Discussion and Conclusions: instability physics implies anharmonic motion, preventing excitation quantization, and totally different from the quantum physics of simple harmonic motion at stability. Instability excitations are different from anything hitherto conceived in information science. They can model aspects of mind never previously treated, including genuine subjectivity, objective reduction of wave-packets, and inter alia all properties given above. (shrink)

Natural Computing is a field of research in Computer Science aimed at reinterpreting biological phenomena as computing mechanisms. This allows unconventional computing architectures to be proposed in which computations are performed by atoms, DNA strands, cells, insects or other biological elements. Membrane Computing is a branch of Natural Computing in which biological phenomena of interest are related with interactions between molecules inside cells. The research in Membrane Computing has lead to very important theoretical results that show how, in principle, cells (...) could be used to solve any (computable) computational problem with performances that cannot be obtained by conventional computers. However, the implementation of a cell-based computational architecture seems not easily achievable. On the other hand, models of Membrane Computing have found an alternative application to the description of biological systems, with the aim of developing simulators and other analysis tools for the study of biological problems. (shrink)

Investigations into inter-level relations in computer science, biology and psychology call for an *empirical* turn in the philosophy of mind. Rather than concentrate on *a priori* discussions of inter-level relations between 'completed' sciences, a case is made for the actual study of the way inter-level relations grow out of the developing sciences. Thus, philosophical inquiries will be made more relevant to the sciences, and, more importantly, philosophical accounts of inter-level relations will be testable by confronting them with what really (...) happens in science. Hence, close observation of the ever-changing reduction relations in the developing sciences, and revision of philosophical positions based on these empirical observations, may, in the long run, be more conducive to an adequate understanding of inter-level relations than a traditional *a priori* approach. (shrink)

This paper connects information with computation and cognition via concept of agents that appear at variety of levels of organization of physical/chemical/cognitive systems – from elementary particles to atoms, molecules, life-like chemical systems, to cognitive systems starting with living cells, up to organisms and ecologies. In order to obtain this generalized framework, concepts of information, computation and cognition are generalized. In this framework, nature can be seen as informational structure with computational dynamics, where an (info-computational) agent is needed (...) for the potential information of the world to actualize. Starting from the definition of information as the difference in one physical system that makes a difference in another physical system – which combines Bateson and Hewitt’s definitions, the argument is advanced for natural computation as a computational model of the dynamics of the physical world, where information processing is constantly going on, on a variety of levels of organization. This setting helps us to elucidate the relationships between computation, information, agency and cognition, within the common conceptual framework, with special relevance for biology and robotics. (shrink)

The idea behind this special theme journal issue was to continue the work we have started with the INBIOSA initiative (www.inbiosa.eu) and our small inter-disciplinary scientific community. The result of this EU funded project was a white paper (Simeonov et al., 2012a) defining a new direction for future research in theoretical biology we called Integral Biomathics and a volume (Simeonov et al., 2012b) with contributions from two workshops and our first international conference in this field in 2011. The initial (...) impulse for this effort was given a year earlier by a publication of one of the guest editors of this issue (Simeonov, 2010) in this journal. This time we wish to provide a broader forum and more space to elaborate in detail some of the most interesting concepts we have encountered in our discussions, as well as to invite some new contributions of particular interest in the field. Another goal we had in mind was to collect and review as many provocative perspectives as possible on the same key topic we are interested before making a decision to follow a more focused notion that would lead to a funded research program. Therefore we welcomed the generous suggestion of Professor Denis Noble, FRS, who is also editor of this journal to prepare a special theme issue entitled: “Can biology create a profoundly new mathematics and computation?” It has taken a while to invite and collect the contributions. Most of them had a couple of revision cycles and adjustments after having been thoroughly discussed with colleagues, incl. the editors of this issue. We think that the result we have obtained at the end is a satisfactory one, since we succeeded to integrate a diversity of original, but sometimes controversial and mutually excluding concepts organized within chapters of a self-contained volume. The task of compiling all this was not easy at all. Despite our efforts to position the articles of different authors and themes in a way allowing their easy comprehension and relation to each other within the individual chapters, some of them still require a sort of introduction to dissolve possible ambiguities. This is what we are going to do in the following few paragraphs with the hope that the reader (and some of the authors) would excuse our failures. (shrink)

This volume offers very selected papers from the 2014 conference of the “International Association for Computing and Philosophy” (IACAP) - a conference tradition of 28 years. - - - Table of Contents - 0 Vincent C. Müller: - Editorial - 1) Philosophy of computing - 1 Çem Bozsahin: - What is a computational constraint? - 2 Joe Dewhurst: - Computing Mechanisms and Autopoietic Systems - 3 Vincenzo Fano, Pierluigi Graziani, Roberto Macrelli and Gino Tarozzi: - Are Gandy Machines really (...) local? - 4 Doukas Kapantais: - A refutation of the Church-Turing thesis according to some interpretation of what the thesis says - 5 Paul Schweizer: - In What Sense Does the Brain Compute? - 2) Philosophy of computer science & discovery - 6 Mark Addis, Peter Sozou, Peter C R Lane and Fernand Gobet: - Computational Scientific Discovery and Cognitive Science Theories - 7 Nicola Angius and Petros Stefaneas: - Discovering Empirical Theories of Modular Software Systems. An Algebraic Approach. - 8 Selmer Bringsjord, John Licato, Daniel Arista, Naveen Sundar Govindarajulu and Paul Bello: - Introducing the Doxastically Centered Approach to Formalizing Relevance Bonds in Conditionals - 9 Orly Stettiner: - From Silico to Vitro: - Computational Models of Complex Biological Systems Reveal Real-world Emergent Phenomena - 3) Philosophy of cognition & intelligence - 10 Douglas Campbell: - Why We Shouldn’t Reason Classically, and the Implications for Artificial Intelligence - 11 Stefano Franchi: - Cognition as Higher Order Regulation - 12 Marcello Guarini: - Eliminativisms, Languages of Thought, & the Philosophy of Computational Cognitive Modeling - 13 Marcin Miłkowski: - A Mechanistic Account of Computational Explanation in Cognitive Science and Computational Neuroscience - 14 Alex Tillas: - Internal supervision & clustering: - A new lesson from ‘old’ findings? - 4) Computing & society - 15 Vasileios Galanos: - Floridi/Flusser: - Parallel Lives in Hyper/Posthistory - 16 Paul Bello: - Machine Ethics and Modal Psychology - 17 Marty J. Wolf and Nir Fresco: - My Liver Is Broken, Can You Print Me a New One? - 18 Marty J. Wolf, Frances Grodzinsky and Keith W. Miller: - Robots, Ethics and Software – FOSS vs. Proprietary Licenses. (shrink)

Since the sixties, computational modeling has become increasingly important in both the physical and the social sciences, particularly in physics, theoretical biology, sociology, and economics. Sine the eighties, philosophers too have begun to apply computational modeling to questions in logic, epistemology, philosophy of science, philosophy of mind, philosophy of language, philosophy of biology, ethics, and social and political philosophy. This chapter analyzes a selection of interesting examples in some of those areas.

Synthetic biology is a field of research that concentrates on the design, construction, and modification of new biomolecular parts and metabolic pathways using engineering techniques and computational models. By employing knowledge of operational pathways from engineering and mathematics such as circuits, oscillators, and digital logic gates, it uses these to understand, model, rewire, and reprogram biological networks and modules. Standard biological parts with known functions are catalogued in a number of registries (e.g. Massachusetts Institute of Technology Registry of (...) Standard Biological Parts). Biological parts can then be selected from the catalogue and assembled in a variety of combinations to construct a system or pathway in a microbe. Through the innovative re-engineering of biological circuits and the optimization of certain metabolic pathways, biological modules can be designed to reprogram organisms to produce products or behaviors. Synthetic biology is what is known as a “platform technology”. That is, it generates highly transferrable theoretical models, engineering principles, and know-how that can be applied to create potential products in a wide variety of industries. Proponents suggest that applications of synthetic biology may be able to provide scientific and engineered solutions to a multitude of worldwide problems from health to energy. Synthetic biology research has already been successful in constructing microbial products which promise to offer cheaper pharmaceuticals such as the antimalarial synthetic drug artemisinin, engineered microbes capable of cleaning up oil spills, and the engineering of biosensors that can detect the presence of high concentrations of arsenic in drinking water. One of the potential benefits of synthetic biology research is in its application to biofuel production. It is this application which is the focus of this entry. The term “biofuel” has referred generally to all liquid fuels that are sourced from plant or plant byproducts and are used for energy necessary for transportation vehicles (Thompson 2012). Biofuels that are produced using synthetic biological techniques re-engineer microbes into biofuel factories are a subset of these. (shrink)

A classic analytic approach to biological phenomena seeks to refine definitions until classes are sufficiently homogenous to support prediction and explanation, but this approach founders on cases where a single process produces objects with similar forms but heterogeneous behaviors. I introduce object spaces as a tool to tackle this challenging diversity of biological objects in terms of causal processes with well-defined formal properties. Object spaces have three primary components: (1) a combinatorial biological process such as protein synthesis that generates objects (...) with parts that are modular, independent, and organized according to an invariant syntax; (2) a notion of “distance” that relates the objects according to rules of change over time as found in nature or useful for algorithms; (3) mapping functions defined on the space that map its objects to other spaces or apply an evaluative criterion to measure an important quality, such as parsimony or biochemical function. Once defined, an object space can be used to represent and simulate the dynamics of phenomena on multiple scales; it can also be used as a tool for predicting higher-order properties of the objects, including stitching together series of causal processes. Object spaces are the basis for a strategy of theorizing, discovery, and analysis in biology: as heuristic idealizations of biology, they help us transform inchoate, intractable problems into articulated, well-structured ones. Developing an object space is a research strategy with a long, successful history under many other names, and it offers a unifying but not overreaching approach to biological theory. (shrink)

To study climate change, scientists employ computer models, which approximate target systems with various levels of skill. Given the imperfection of climate models, how do scientists use simulations to generate knowledge about the causes of observed climate change? Addressing a similar question in the context of biological modelling, Levins (1966) proposed an account grounded in robustness analysis. Recent philosophical discussions dispute the confirmatory power of robustness, raising the question of how the results of computer modelling studies contribute to the body (...) of evidence supporting hypotheses about climate change. Expanding on Staley’s (2004) distinction between evidential strength and security, and Lloyd’s (2015) argument connecting variety-of-evidence inferences and robustness analysis, I address this question with respect to recent challenges to the epistemology robustness analysis. Applying this epistemology to case studies of climate change, I argue that, despite imperfections in climate models, and epistemic constraints on variety-of-evidence reasoning and robustness analysis, this framework accounts for the strength and security of evidence supporting climatological inferences, including the finding that global warming is occurring and its primary causes are anthropogenic. (shrink)

Although Paul Churchland and Jerry Fodor both subscribe to the so-called theory-theory– the theory that folk psychology (FP) is an empirical theory of behavior – they disagree strongly about FP’s fate. Churchland contends that FP is a fundamentally flawed view analogous to folk biology, and he argues that recent advances in computational neuroscience and connectionist AI point toward development of a scientifically respectable replacement theory that will give rise to a new common-sense psychology. Fodor, however, wagers that FP (...) will be largely preserved and vindicated by scientific investigations of behavior. Recent findings by developmental psychologists, I argue, will push both Churchlandians and Fodorians toward the pessimistic view that FP is a misguided theory that will never be displaced, because it is, so to speak, built into our cognitive systems. I explore the possibility of preserving optimism by rejecting the theory-theory and adopting the simulation theory, a competing view developed by Robert Gordon, Alvin Goldman, and Jane Heal. According to simulationists, common-sense interpretation of behavior is accomplished by means of pretense-like operations that deploy the cognitive system’s own reasoning capabilities in a disengaged manner. Since on this view no theory-like set of principles would be needed, the simulation theory seems to enjoy a simplicity advantage over the theory-theory. Steven Stich and Shawn Nichols, however, contend that as the cognitive system would require special mechanisms for disengaged operation, the simplicity question cannot be resolved until suitable computational models are developed. I describe a set of models I have constructed to meet this need, and I discuss the contribution such models can make to determining FP’s fate. (shrink)

In this paper a possible general framework for the representation of concepts in cognitive artificial systems and cognitive architectures is proposed. The framework is inspired by the so called proxytype theory of concepts and combines it with the heterogeneity approach to concept representations, according to which concepts do not constitute a unitary phenomenon. The contribution of the paper is twofold: on one hand, it aims at providing a novel theoretical hypothesis for the debate about concepts in cognitive sciences by providing (...) unexplored connections between different theories; on the other hand it is aimed at sketching a computational characterization of the problem of concept representation in cognitively inspired artificial systems and in cognitive architectures. (shrink)

The journal of Cognitive Computation is defined in part by the notion that biologically inspired computational accounts are at the heart of cognitive processes in both natural and artificial systems. Many studies of various important aspects of cognition (memory, observational learning, decision making, reward prediction learning, attention control, etc.) have been made by modelling the various experimental results using ever-more sophisticated computer programs. In this manner progressive inroads have been made into gaining a better understanding of the many components (...) of cognition. Concomitantly in both science and science fiction the hope is periodically re-ignited that a manmade system can be engineered to be fully cognitive and conscious purely in virtue of its execution of an appropriate computer program. However, whilst the usefulness of the computational metaphor in many areas of psychology and neuroscience is clear, it has not gone unchallenged and in this article I will review a group of philosophical arguments that suggest either such unequivocal optimism in computationalism is misplaced—computation is neither necessary nor sufficient for cognition—or panpsychism (the belief that the physical universe is fundamentally composed of elements each of which is conscious) is true. I conclude by highlighting an alternative metaphor for cognitive processes based on communication and interaction. (shrink)

Direct neurological and especially imaging-driven investigations into the structures essential to naturally occurring cognitive systems in their development and operation have motivated broadening interest in the potential for artificial consciousness modeled on these systems. This first paper in a series of three begins with a brief review of Boltuc’s (2009) “brain-based” thesis on the prospect of artificial consciousness, focusing on his formulation of h-consciousness. We then explore some of the implications of brain research on the structure of consciousness, finding limitations (...) in biological approaches to the study of consciousness. Looking past these limitations, we introduce research in artificial consciousness designed to test for the emergence of consciousness, a phenomenon beyond the purview of the study of existing biological systems. (shrink)

The emerging contemporary natural philosophy provides a common ground for the integrative view of the natural, the artificial, and the human-social knowledge and practices. Learning process is central for acquiring, maintaining, and managing knowledge, both theoretical and practical. This paper explores the relationships between the present advances in understanding of learning in the sciences of the artificial (deep learning, robotics), natural sciences (neuroscience, cognitive science, biology), and philosophy (philosophy of computing, philosophy of mind, natural philosophy). The question is, what (...) at this stage of the development the inspiration from nature, specifically its computational models such as info-computation through morphological computing, can contribute to machine learning and artificial intelligence, and how much on the other hand models and experiments in machine learning and robotics can motivate, justify, and inform research in computational cognitive science, neurosciences, and computing nature. We propose that one contribution can be understanding of the mechanisms of ‘learning to learn’, as a step towards deep learning with symbolic layer of computation/information processing in a framework linking connectionism with symbolism. As all natural systems possessing intelligence are cognitive systems, we describe the evolutionary arguments for the necessity of learning to learn for a system to reach human-level intelligence through evolution and development. The paper thus presents a contribution to the epistemology of the contemporary philosophy of nature. (shrink)

I go deep into the biology of the human organism to argue that the psychological features and functions of persons are realized by cellular and molecular parallel distributed processing networks dispersed throughout the whole body. Persons supervene on the computational processes of nervous, endocrine, immune, and genetic networks. Persons do not go with brains.

We have been left with a big challenge, to articulate consciousness and also to prove it in an artificial agent against a biological standard. After introducing Boltuc’s h-consciousness in the last paper, we briefly reviewed some salient neurology in order to sketch less of a standard than a series of targets for artificial consciousness, “most-consciousness” and “myth-consciousness.” With these targets on the horizon, we began reviewing the research program pursued by Jun Tani and colleagues in the isolation of the formal (...) dynamics essential to either. In this paper, we describe in detail Tani’s research program, in order to make the clearest case for artificial consciousness in these systems. In the next paper, the third in the series, we will return to Boltuc’s naturalistic non-reductionism in light of the neurorobotics models introduced (alongside some others), and evaluate them more completely. (shrink)

According to some critics, if biology is a kind of reverse engineering for the nature, it is quite poorly prepared for the task. Thus, the issue is more likely with its ontology. Multiple hypotheses and conjectures found in papers on methodological issues claim that living systems should be viewed as complex networks of signal-transmitting paths, both neural and non-neural, that feature modularity and feedback circuits and are prone to emergent properties and increasing complexity. If so, we are on the (...) eve of a new stage in computer models development where not only computers are used to emulate life, but life itself is construed as a complex network of interacting natural computers. (shrink)

This third paper locates the synthetic neurorobotics research reviewed in the second paper in terms of themes introduced in the first paper. It begins with biological non-reductionism as understood by Searle. It emphasizes the role of synthetic neurorobotics studies in accessing the dynamic structure essential to consciousness with a focus on system criticality and self, develops a distinction between simulated and formal consciousness based on this emphasis, reviews Tani and colleagues' work in light of this distinction, and ends by forecasting (...) the increasing importance of synthetic neurorobotics studies for cognitive science and philosophy of mind going forward, finally in regards to most- and myth-consciousness. (shrink)

‘‘Theoretical biology’’ is a surprisingly heter- ogeneous field, partly because it encompasses ‘‘doing the- ory’’ across disciplines as diverse as molecular biology, systematics, ecology, and evolutionary biology. Moreover, it is done in a stunning variety of different ways, using anything from formal analytical models to computer sim- ulations, from graphic representations to verbal arguments. In this essay I survey a number of aspects of what it means to do theoretical biology, and how they compare with the (...) allegedly much more restricted sense of theory in the physical sciences. I also tackle a recent trend toward the presentation of all-encompassing theories in the biological sciences, from general theories of ecology to a recent attempt to provide a conceptual framework for the entire set of biological disciplines. Finally, I discuss the roles played by philosophers of science in criticizing and shap- ing biological theorizing. (shrink)

Molecular biology is a relatively new and very successful branch of science but currently it faces challenges posed by very complex issues that cannot be addressed by a traditional reductionist approach. However, despite its origins in the providential shift of some theoretical physicists to biology, currently molecular biology is immersed in a blind trend in which high-throughput technology, able to generate trillions of data, is becoming the leading edge of a discipline that has traded rational and critical (...) thinking for computer power, data crunching and statistics in hope of finding, once more, its way. However, the complex questions facing MB may only be solved by a paradigm shift in the causal way of thinking, so that complex, emergent, non-linear phenomena may be effectively understood in top-down and not in bottom-up terms. (shrink)

“Morphological computation” is an increasingly important concept in robotics, artificial intelligence, and philosophy of the mind. It is used to understand how the body contributes to cognition and control of behavior. Its understanding in terms of "offloading" computation from the brain to the body has been criticized as misleading, and it has been suggested that the use of the concept conflates three classes of distinct processes. In fact, these criticisms implicitly hang on accepting a semantic definition of what constitutes computation. (...) Here, I argue that an alternative, mechanistic view on computation offers a significantly different understanding of what morphological computation is. These theoretical considerations are then used to analyze the existing research program in developmental biology, which understands morphogenesis, the process of development of shape in biological systems, as a computational process. This important line of research shows that cognition and intelligence can be found across all scales of life, as the proponents of the basal cognition research program propose. Hence, clarifying the connection between morphological computation and morphogenesis allows for strengthening the role of the former concept in this emerging research field. (shrink)

Criticism of big data has focused on showing that more is not necessarily better, in the sense that data may lose their value when taken out of context and aggregated together. The next step is to incorporate an awareness of pitfalls for aggregation into the design of data infrastructure and institutions. A common strategy minimizes aggregation errors by increasing the precision of our conventions for identifying and classifying data. As a counterpoint, we argue that there are pragmatic trade-offs between precision (...) and ambiguity that are key to designing effective solutions for generating big data about biodiversity. We focus on the importance of theory-dependence as a source of ambiguity in taxonomic nomenclature and hence a persistent challenge for implementing a single, long-term solution to storing and accessing meaningful sets of biological specimens. We argue that ambiguity does have a positive role to play in scientific progress as a tool for efficiently symbolizing multiple aspects of taxa and mediating between conflicting hypotheses about their nature. Pursuing a deeper understanding of the trade-offs and synthesis of precision and ambiguity as virtues of scientific language and communication systems then offers a productive next step for realizing sound, big biodiversity data services. (shrink)

The paper provides a critical review of the debate on the foundations of Computer Ethics (CE). Starting from a discussion of Moor’s classic interpretation of the need for CE caused by a policy and conceptual vacuum, five positions in the literature are identified and discussed: the “no resolution approach”, according to which CE can have no foundation; the professional approach, according to which CE is solely a professional ethics; the radical approach, according to which CE deals with absolutely unique issues, (...) in need of a unique approach; the conservative approach, according to which CE is only a particular applied ethics, discussing new species of traditional moral issues; and the innovative approach, according to which theoretical CE can expand the metaethical discourse with a substantially new perspective. In the course of the analysis, it is argued that, although CE issues are not uncontroversially unique, they are sufficiently novel to render inadequate the adoption of standard macroethics, such as Utilitarianism and Deontologism, as the foundation of CE and hence to prompt the search for a robust ethical theory. Information Ethics (IE) is proposed for that theory, as the satisfactory foundation for CE. IE is characterised as a biologically unbiased extension of environmental ethics, based on the concepts of information object/infosphere/entropy rather than life/ecosystem/pain. In light of the discussion provided in this paper, it is suggested that CE is worthy of independent study because it requires its own application-specific knowledge and is capable of supporting a methodological foundation, IE. (shrink)

Advances in biology, at least over the past two centuries, have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. The field of theoretical biology used to primarily provide a basis, similar to theoretical physics in the physical sciences, to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with (...) class='Hi'>computational and mathematical biology. This could in part be explained by a relatively recent tendency in which a "data first", rather than a "theory first", approach is preferred. Moreover, generating hypotheses has at times become procedural rather than theoretical, therefore perhaps inadvertently leading some hypotheses to become perfunctory in nature. This situation leaves our understanding enmeshed in data, which should be disentangled from much noise. Given the many unresolved questions in biology and medicine, big and small, ranging from the problem of protein folding to unifying causative frameworks of complex non-Mendelian human diseases, it seems apt to revive the role of pure theory in the biological sciences. This paper, using the current biomedical literature and historical precedents, makes the case for a "philosophical biology" (philbiology), distinct from but quite complementary to philosophy of biology (philobiology), which would entail biological investigation through philosophical approaches. Philbiology would thus be a reincarnation of theoretical biology, adopting the true sense of the word "theory" and making use of a rich tradition of serious philosophical approaches in the natural sciences. A philbiological investigation, after clearly defining a given biological problem, would aim to propose a set of empirical questions, along with a class of possible solutions, about that problem. Importantly, whether or not the questions can be tested using current experimental paradigms would be secondary to whether the questions are inherently empirical or not. These issues will be illustrated using a range of specific examples. The final goal of a philbiological investigation would be to develop a theoretical framework that can lead observational and/or interventional experimental studies of the defined problem, a framework that is structured, generative and expandable, and, crucially, one that simplifies some aspect(s) of the said problem. (shrink)

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

What is philosophy of science? Numerous manuals, anthologies or essays provide carefully reconstructed vantage points on the discipline that have been gained through expert and piecemeal historical analyses. In this paper, we address the question from a complementary perspective: we target the content of one major journal of the field—Philosophy of Science—and apply unsupervised text-mining methods to its complete corpus, from its start in 1934 until 2015. By running topic-modeling algorithms over the full-text corpus, we identified 126 key research topics (...) that span across 82 years. We also tracked their evolution and fluctuating significance over time in the journal articles. Our results concur with and document known and lesser-known episodes of the philosophy of science, including the rise and fall of logic and language-related topics, the relative stability of a metaphysical and ontological questioning (space and time, causation, natural kinds, realism), the significance of epistemological issues about the nature of scientific knowledge as well as the rise of a recent philosophy of biology and other trends. These analyses exemplify how computational text-mining methods can be used to provide an empirical large-scale and data-driven perspective on the history of philosophy of science that is complementary to other current historical approaches. (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)

Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed (...) studies of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. (shrink)

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been (...) more fact-oriented and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. -/- This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. -/- Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. -/- The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses. (shrink)

One of the most influential arguments against the claim that computers can think is that while our intentionality is intrinsic, that of computers is derived: it is parasitic on the intentionality of the programmer who designed the computer-program. Daniel Dennett chose a surprising strategy for arguing against this asymmetry: instead of denying that the intentionality of computers is derived, he endeavours to argue that human intentionality is derived too. I intend to examine that biological plausibility of Dennett’s suggestion and show (...) that Dennett’s argument for the claim that human intentionality is derived because it was designed by natural selection is based on the misunderstanding of how natural selection works. (shrink)

Despite the impressive amount of financial resources recently invested in carrying out large-scale brain simulations, it is controversial what the pay-offs are of pursuing this project. One idea is that from designing, building, and running a large-scale neural simulation, scientists acquire knowledge about the computational performance of the simulating system, rather than about the neurobiological system represented in the simulation. It has been claimed that this knowledge may usher in a new era of neuromorphic, cognitive computing systems. This study (...) elucidates this claim and argues that the main challenge this era is facing is not the lack of biological realism. The challenge lies in identifying general neurocomputational principles for the design of artificial systems, which could display the robust flexibility characteristic of biological intelligence. (shrink)

Moral reasoning traditionally distinguishes two types of evil:moral (ME) and natural (NE). The standard view is that ME is the product of human agency and so includes phenomena such as war,torture and psychological cruelty; that NE is the product of nonhuman agency, and so includes natural disasters such as earthquakes, floods, disease and famine; and finally, that more complex cases are appropriately analysed as a combination of ME and NE. Recently, as a result of developments in autonomous agents in cyberspace, (...) a new class of interesting and important examples of hybrid evil has come to light. In this paper, it is called artificial evil (AE) and a case is made for considering it to complement ME and NE to produce a more adequate taxonomy. By isolating the features that have led to the appearance of AE, cyberspace is characterised as a self-contained environment that forms the essential component in any foundation of the emerging field of Computer Ethics (CE). It is argued that this goes someway towards providing a methodological explanation of why cyberspace is central to so many of CE's concerns; and it is shown how notions of good and evil can be formulated in cyberspace. Of considerable interest is how the propensity for an agent's action to be morally good or evil can be determined even in the absence of biologically sentient participants and thus allows artificial agents not only to perpetrate evil (and fort that matter good) but conversely to `receive' or `suffer from' it. The thesis defended is that the notion of entropy structure, which encapsulates human value judgement concerning cyberspace in a formal mathematical definition, is sufficient to achieve this purpose and, moreover, that the concept of AE can be determined formally, by mathematical methods. A consequence of this approach is that the debate on whether CE should be considered unique, and hence developed as a Macroethics, may be viewed, constructively,in an alternative manner. The case is made that whilst CE issues are not uncontroversially unique, they are sufficiently novel to render inadequate the approach of standard Macroethics such as Utilitarianism and Deontologism and hence to prompt the search for a robust ethical theory that can deal with them successfully. The name Information Ethics (IE) is proposed for that theory. Itis argued that the uniqueness of IE is justified by its being non-biologically biased and patient-oriented: IE is an Environmental Macroethics based on the concept of data entity rather than life. It follows that the novelty of CE issues such as AE can be appreciated properly because IE provides a new perspective (though not vice versa). In light of the discussion provided in this paper, it is concluded that Computer Ethics is worthy of independent study because it requires its own application-specific knowledge and is capable of supporting a methodological foundation, Information Ethics. (shrink)

The aim of this paper is to describe and analyze the epistemological justification of a proposal initially made by the biomathematician Robert Rosen in 1958. In this theoretical proposal, Rosen suggests using the mathematical concept of “category” and the correlative concept of “natural equivalence” in mathematical modeling applied to living beings. Our questions are the following: According to Rosen, to what extent does the mathematical notion of category give access to more “natural” formalisms in the modeling of living beings? Is (...) the so -called “naturalness” of some kinds of equivalences (which the mathematical notion of category makes it possible to generalize and to put at the forefront) analogous to the naturalness of living systems? Rosen appears to answer “yes” and to ground this transfer of the concept of “natural equivalence” in biology on such an analogy. But this hypothesis, although fertile, remains debatable. Finally, this paper makes a brief account of the later evolution of Rosen’s arguments about this topic. In particular, it sheds light on the new role played by the notion of “category” in his more recent objections to the computational models that have pervaded almost every domain of biology since the 1990s. (shrink)

Moral reasoning traditionally distinguishes two types of evil: moral and natural. The standard view is that ME is the product of human agency and so includes phenomena such as war, torture and psychological cruelty; that NE is the product of nonhuman agency, and so includes natural disasters such as earthquakes, floods, disease and famine; and finally, that more complex cases are appropriately analysed as a combination of ME and NE. Recently, as a result of developments in autonomous agents in cyberspace, (...) a new class of interesting and important examples of hybrid evil has come to light. In this paper, it is called artificial evil and a case is made for considering it to complement ME and NE to produce a more adequate taxonomy. By isolating the features that have led to the appearance of AE, cyberspace is characterised as a self-contained environment that forms the essential component in any foundation of the emerging field of Computer Ethics. It is argued that this goes some way towards providing a methodological explanation of why cyberspace is central to so many of CE’s concerns; and it is shown how notions of good and evil can be formulated in cyberspace. Of considerable interest is how the propensity for an agent’s action to be morally good or evil can be determined even in the absence of biologically sentient participants and thus allows artificial agents not only to perpetrate evil but conversely to ‘receive’ or ‘suffer from’ it. The thesis defended is that the notion of entropy structure, which encapsulates human value judgement concerning cyberspace in a formal mathematical definition, is sufficient to achieve this purpose and, moreover, that the concept of AE can be determined formally, by mathematical methods. A consequence of this approach is that the debate on whether CE should be considered unique, and hence developed as a Macroethics, may be viewed, constructively, in an alternative manner. The case is made that whilst CE issues are not uncontroversially unique, they are sufficiently novel to render inadequate the approach of standard Macroethics such as Utilitarianism and Deontologism and hence to prompt the search for a robust ethical theory that can deal with them successfully. The name Information Ethics is proposed for that theory. It is argued that the uniqueness of IE is justified by its being non-biologically biased and patient-oriented: IE is an Environmental Macroethics based on the concept of data entity rather than life. It follows that the novelty of CE issues such as AE can be appreciated properly because IE provides a new perspective. In light of the discussion provided in this paper, it is concluded that Computer Ethics is worthy of independent study because it requires its own application-specific knowledge and is capable of supporting a methodological foundation, Information Ethics. (shrink)

In spite of being ubiquitous in life sciences, the concept of information is harshly criticized. Uses of the concept other than those derived from Shannon's theory are denounced as pernicious metaphors. We perform a computational experiment to explore whether Shannon's information is adequate to describe the uses of said concept in commonplace scientific practice. Our results show that semantic sequences do not have unique complexity values different from the value of meaningless sequences. This result suggests that quantitative theoretical frameworks (...) do not account fully for the complex phenomenon that the term “information” refers to. We propose a restructuring of the concept into two related, but independent notions, and conclude that a complete theory of biological information must account completely not only for both notions, but also for the relationship between them. (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)

This essay presents arguments for the claim that in the best of all possible worlds (Leibniz) there are sources of unpredictability and creativity for us humans, even given a pancomputational stance. A suggested answer to Chaitin’s questions: “Where do new mathematical and biological ideas come from? How do they emerge?” is that they come from the world and emerge from basic physical (computational) laws. For humans as a tiny subset of the universe, a part of the new ideas comes (...) as the result of the re-configuration and reshaping of already existing elements and another part comes from the outside as a consequence of openness and interactivity of the system. For the universe at large it is randomness that is the source of unpredictability on the fundamental level. In order to be able to completely predict the Universe-computer we would need the Universe-computer itself to compute its next state; as Chaitin already demonstrated there are incompressible truths which means truths that cannot be computed by any other computer but the universe itself. (shrink)

n this text, we revisit part of the analysis of anti-entropy in Bailly and Longo (2009} and develop further theoretical reflections. In particular, we analyze how randomness, an essential component of biological variability, is associated to the growth of biological organization, both in ontogenesis and in evolution. This approach, in particular, focuses on the role of global entropy production and provides a tool for a mathematical understanding of some fundamental observations by Gould on the increasing phenotypic complexity along evolution. Lastly, (...) we analyze the situation in terms of theoretical symmetries, in order to further specify the biological meaning of anti-entropy as well as its strong link with randomness. (shrink)

Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein (...) complexes, epigenetic modifications, and natural genetic engineering activities, the genome can serve as a read-write storage system. An interactive informatic conceptualization of the genome allows us to understand the functional importance of DNA that does not code for protein or RNA structure, clarifies the essential multidirectional and systemic nature of genomic information transfer, and emphasizes the need to investigate how cellular computation operates in reproduction and evolution. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

We argue that the mathematization of science should be understood as a normative activity of advocating for a particular methodology with its own criteria for evaluating good research. As a case study, we examine the mathematization of taxonomic classification in systematic biology. We show how mathematization is a normative activity by contrasting its distinctive features in numerical taxonomy in the 1960s with an earlier reform advocated by Ernst Mayr starting in the 1940s. Both Mayr and the numerical taxonomists sought (...) to formalize the work of classification, but Mayr introduced a qualitative formalism based on human judgment for determining the taxonomic rank of populations, while the numerical taxonomists introduced a quantitative formalism based on automated procedures for computing classifications. The key contrast between Mayr and the numerical taxonomists is how they conceptualized the temporal structure of the workflow of classification, specifically where they allowed meta-level discourse about difficulties in producing the classification. (shrink)

With increasing publication and data production, scientific knowledge presents not simply an achievement but also a challenge. Scientific publications and data are increasingly treated as resources that need to be digitally ‘managed.’ This gives rise to scientific Knowledge Management : second-order scientific work aiming to systematically collect, take care of and mobilise first-hand disciplinary knowledge and data in order to provide new first-order scientific knowledge. We follow the work of Leonelli, Efstathiou and Hislop in our analysis of the use of (...) KM in semantic systems biology. Through an empirical philosophical account of KM-enabled biological research, we argue that KM helps produce new first-order biological knowledge that did not exist before, and which could not have been produced by traditional means. KM work is enabled by conceiving of ‘knowledge’ as an object for computational science: as explicated in the text of biological articles and computable via appropriate data and metadata. However, these founded knowledge concepts enabling computational KM risk focusing on only computationally tractable data as knowledge, underestimating practice-based knowing and its significance in ensuring the validity of ‘manageable’ knowledge as knowledge. (shrink)

Review of: "Computation, Information, Cognition: The Nexus and the Liminal", Ed. Susan Stuart & Gordana Dodig Crnkovic, Newcastle: Cambridge Scholars Publishing, September 2007, xxiv+340pp, ISBN: 9781847180902, Hardback: £39.99, $79.99 ---- Are you a computer? Is your cat a computer? A single biological cell in your stomach, perhaps? And your desk? You do not think so? Well, the authors of this book suggest that you think again. They propose a computational turn, a turn towards computational explanation and towards the (...) explanation of computation itself. The explanation of computation is the core of the present volume, but the computational turn to regard a wide variety of systems as computational is a potentially very wide-ranging project. (shrink)

Endowing artificial systems with explanatory capacities about the reasons guiding their decisions, represents a crucial challenge and research objective in the current fields of Artificial Intelligence (AI) and Computational Cognitive Science [Langley et al., 2017]. Current mainstream AI systems, in fact, despite the enormous progresses reached in specific tasks, mostly fail to provide a transparent account of the reasons determining their behavior (both in cases of a successful or unsuccessful output). This is due to the fact that the classical (...) problem of opacity in artificial neural networks (ANNs) explodes with the adoption of current Deep Learning techniques [LeCun, Bengio, Hinton, 2015]. In this paper we argue that the explanatory deficit of such techniques represents an important problem, that limits their adoption in the cognitive modelling and computational cognitive science arena. In particular we will show how the current attempts of providing explanations of the deep nets behaviour (see e.g. [Ritter et al. 2017] are not satisfactory. As a possibile way out to this problem, we present two different research strategies. The first strategy aims at dealing with the opacity problem by providing a more abstract interpretation of neural mechanisms and representations. This approach is adopted, for example, by the biologically inspired SPAUN architecture [Eliasmith et al., 2012] and by other proposals suggesting, for example, the interpretation of neural networks in terms of the Conceptual Spaces framework [Gärdenfors 2000, Lieto, Chella and Frixione, 2017]. All such proposals presuppose that the neural level of representation can be considered somehow irrelevant for attacking the problem of explanation [Lieto, Lebiere and Oltramari, 2017]. In our opinion, pursuing this research direction can still preserve the use of deep learning techniques in artificial cognitive models provided that novel and additional results in terms of “transparency” are obtained. The second strategy is somehow at odds with respect to the previous one and tries to address the explanatory issue by avoiding to directly solve the “opacity” problem. In this case, the idea is that one of resorting to pre-compiled plausible explanatory models of the word used in combination with deep-nets (see e.g. [Augello et al. 2017]). We argue that this research agenda, even if does not directly fits the explanatory needs of Computational Cognitive Science, can still be useful to provide results in the area of applied AI aiming at shedding light on the models of interaction between low level and high level tasks (e.g. between perceptual categorization and explanantion) in artificial systems. (shrink)

In his book "The Structure of Behavior", the philosopher Maurice Merleau-Ponty proposes a solution to the mind-body problem. Merleau-Ponty argues that there is a nested hierarchy of three orders—the physical order, the biological order, and the mental order—in which each lower order composes each higher order. Through the structuration or organization of a lower order, a higher order is created. Merleau-Ponty’s solution is promising, but it leaves an explanatory chasm between the biological order and the mental order that cannot be (...) crossed without introducing an intermediary order. I propose just that: the addition of a fourth order—the computational order—to bridge the chasm. (shrink)

Upshot: The variety of commentaries has shown that IC impacts on many disciplines, from physics to biology, to cognitive science, to ethics. Given its young age, IC still needs to fill in many gaps, some of which were pointed out by the commentators. My goal is both to illuminate some general topics of info-computationalism, and to answer specific questions in that context.

The students’ academic performance is the key element for both learners and teachers in examining the educational objectives for all subjects. This work is entitled “Factors contributing to Students' Academic Performance in Biology State Examination at Upper Secondary Schools in Gitega commune, Burundi” explores the factors that influence the students’ academic performance in biology national examination, particularly in Gitega commune. All school directors, laboratory, and library staff, and six senior students who did biology national examination over five (...) school years from 2016 to 2020 in all upper secondary schools with Biology-Chemistry and Earth sciences combination formed a study population. The stratified sampling technique to carry out this correlational study for choosing the upper secondary schools from urban and rural school areas. This study covered 12 upper secondary schools, 12 library staff and 3 laboratory staff, and 1961 senior six students who were selected purposively according to the above learning combination six in 1961 senior students over five consecutive school years (2016 to 2020) as a sample. The instruments used for collecting data were questionnaires and the document review checklist. Descriptive statistics, Analysis of variance (ANOVA) and multiple linear Regression test were used to analyze the collected data and the interpretation was guided by a literature review. The findings of this study indicated that teachers’ academic qualifications were inversely associated with the students’ academic performance whereas the teachers’ professional qualifications and students’ academic performance were also negatively linked. Also, there was statistically a significant association between teaching experience and students’ academic performance while professional training of biology Teachers are significantly associated with students’ academic performance. Other contributing factors to students’ academic achievement such as physical facilities (laboratory, library, staff room, computer lab and biology textbooks were significantly and positively linked with students' academic performance. Based on these findings, recommendations were made. (shrink)

We present a technique for the analysis of pattern formation by a class of models for the formation of ocular dominance stripes in the striate cortex of some mammals. The method, which employs the adiabatic approximation to derive a set of ordinary differential equations for patterning modes, has been successfully applied to reaction-diffusion models for striped patterns [1]. Models of ocular dominance stripes have been studied [2,3] by computation, or by linearization of the model equations. These techniques do not provide (...) a rationale for the origin of the stripes. We show here that stripe formation is a non-linear property of the models. Our analysis indicates that stripe selection is closely linked to a property in the dynamics of the models which arises from a symmetry between ipsilateral and contralateral synapses to the visual cortex of a given hemisphere. (shrink)