The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

Over the course of the last three decades, computer simulations have become a major tool of doing science and engaging with the world, not least in an effort to predict and intervene in a future to come. Born in the context of the Second World War and the discipline of physics, simulations have long spread into most diverse fields of enquiry and technological application. This paper introduces a topical collection focussing on simulations in the life sciences. Echoing (...) the current state of tinkering, fast developments, segmentation of knowledge and interdisciplinary collaboration, and in an effort to bridge the science-humanities divide, the contributors to this collection come from multiple disciplinary backgrounds, including information studies, cognitive sciences, philosophy and biology. The ambiguous character of simulations, their cutting across scientific disciplines, analysis and prediction, understanding and doing, gave rise to their success in contemporary life sciences and has been the object of much scientific debate. One of the main aims of this topical collection, by contrast, is to call into question the assumption of an obvious use and easy transfer of methods between fields of knowledge as diverse as, e.g. physics and biology. The collection presents historical case studies from various biological sub-fields. The articles study how simulations are used and the ways they contribute specifically to our understanding of life. Taking up Sergio Sismondo’s description of simulations as “compromises” and “glue”, they also critically engage with the question of what exactly the life sciences have been gluing together over the last two decades. (shrink)

Since the outbreak of COVID-19, governments have turned their attention to digital contact tracing. In many countries, public debate has focused on the risks this technology poses to privacy, with advocates and experts sounding alarm bells about surveillance and mission creep reminiscent of the post 9/11 era. Yet, when Apple and Google launched their contact tracing API in April 2020, some of the world’s leading privacy experts applauded this initiative for its privacy-preserving technical specifications. In an interesting twist, the tech (...) giants came to be portrayed as greater champions of privacy than some democratic governments. This article proposes to view the Apple/Google API in terms of a broader phenomenon whereby tech corporations are encroaching into ever new spheres of social life. From this perspective, the advantage these actors have accrued in the sphere of the production of digital goods provides them with access to the spheres of health and medicine, and more worrisome, to the sphere of politics. These sphere transgressions raise numerous risks that are not captured by the focus on privacy harms. Namely, a crowding out of essential spherical expertise, new dependencies on corporate actors for the delivery of essential, public goods, the shaping of public policy by non-representative, private actors and ultimately, the accumulation of decision-making power across multiple spheres. While privacy is certainly an important value, its centrality in the debate on digital contact tracing may blind us to these broader societal harms and unwittingly pave the way for ever more sphere transgressions. (shrink)

The purpose of this study is to examine how trends in the use of images in modern life science journals have changed since the spread of computer-based visual and imaging technology. To this end, a new classification system was constructed to analyze how the graphics of a scientific journal have changed over the years. The focus was on one international peer-reviewed journal in life sciences, Cell, which was founded in 1974, whereby 1725 figures and 160 tables (...) from the research articles in Cell were sampled. The unit of classification was defined as a graphic and the figures and tables were divided into 5952 graphics. These graphics were further classified into hierarchical categories, and the data in each category were aggregated every five years. The following categories were observed: data graphics, explanation graphics, and hybrid graphics. Data graphics increased by more than sixfold between 1974 and 2014, and some types of data graphics including mechanical reproduction images and bar charts displayed notable changes. The representation of explanatory graphics changed from hand-painted illustrations to diagrams of Bezier-curves. It is suggested that in addition to the development of experimental technologies such as fluorescent microscopy and big data analysis, continuously evolving application software for image creation and researchers’ motivation to convince reviewers and editors have influenced these changes. (shrink)

Digital computers play a special role in cognitive science—they may actually be instances of the phenomenon they are being used to model. This paper surveys some of the main issues involved in understanding the relationship between digital computers and cognition. It sketches the role of digital computers within orthodox computational cognitive science, in the light of a recently emerging alternative approach based around dynamical systems.

The present paper discusses a topic often neglected by contemporary philosophy of biology: The relation between metaphorical notions of living organisms as information processing systems, the attempts to model such systems by computational means (e.g., Artificial Life research), and the idea that life itself is a computational phenomenon. This question has ramifications in theoretical biology and thedefinition of Iife, in theoretical computer science and the concept of computation, and in semiotics (the study of signs in the most (...) general sense, including information, signification, and meaning), and the concept of the interpreter. It is argued, that the theory of autopoietic systems known from theoretical biology should be integrated with a biosemiotic reflection on the natural history of signs. (shrink)

Here moral problems created by the use of constructive imaging technologies within the life sciences are discussed. It specifically deals with the creation of dichotomies, such as gender, race and other differences, created and manifested through the contingent use of scientific and computational models and methods, channelling the production process of scientific results and images. Gender in technology studies has been concerned with destabilizing essentialist and dichotomous co-constructions of gender and technology. In the technological construction process gendered social (...) constructions of stereotypes and inequalities both of the technological models and of the presumptions in life sciences become structural properties of the artefacts, again flowing back into the seemingly objective results and knowledge of the life sciences. Here we will deal with the construction of gender differences via biomedical imaging and the creation of norms in atlases. Additionally, the de-contextualized images, showing idiosyncratic selections and reducing complexity are used to popularize gendered assumptions about biological facts. (shrink)

To study the interaction of forces that produce chest wall motion, we propose a model based on the lever system of Hillman and Finucane (J Appl Physiol 63(3):951–961, 1987 ) and introduce some dynamic properties of the respiratory system. The passive elements (rib cage and abdomen) are considered as elastic compartments linked to the open air via a resistive tube, an image of airways. The respiratory muscles (active) force is applied to both compartments. Parameters of the model are identified in (...) using experimental data of airflow signal measured by pneumotachography and rib cage and abdomen signals measured by respiratory inductive plethysmography on eleven healthy volunteers in five conditions: at rest and with four level of added loads. A breath by breath analysis showed, whatever the individual and the condition are, that there are several breaths on which the airflow simulated by our model is well fitted to the airflow measured by pneumotachography as estimated by a determination coefficient R 2 ≥ 0.70. This very simple model may well represent the behaviour of the chest wall and thus may be useful to interpret the relative motion of rib cage and abdomen during quiet breathing. (shrink)

��This article reviews a theory of explanatory coherence that provides a psychologically plausible account of how people evaluate competing explanations. The theory is implemented in a computational model that uses simple artificial neural networks to simulate many important cases of scientific and legal reasoning. Current research directions include extensions to emotional thinking and implementation in more biologically realistic neural networks.

Because evolution in natural systems happens so slowly, it is dif- ficult to design inquiry-based labs where students can experiment and observe evolution in the way they can when studying other phenomena. New research in evolutionary computation and artificial life provides a solution to this problem. This paper describes a new A-Life software environment – Avida-ED – in which undergraduate students can test evolutionary hypotheses directly using digital organisms that evolve on their own through the very mechanisms that (...) Darwin discovered. (shrink)

A short review of complexity research from the perspective of history and philosophy of biology is presented. Complexity and its emergence has scientific and metaphysical meanings. From its beginning, biology was a science of complex systems, but with the advent of electronic computing and the possibility of simulating mathematical models of complicated systems, new intuitions of complexity emerged, together with attempts to devise quantitative measures of complexity. But can we quantify the complex?

Where humans can manipulate and integrate the information they receive in subtle and ever-changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, (...) chemistry, mathematics, medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

What is life? Is it just the biologically familiar--birds, trees, snails, people--or is it an infinitely complex set of patterns that a computer could simulate? What role does intelligence play in separating the organic from the inorganic, the living from the inert? Does life evolve along a predestined path, or does it suddenly emerge from what appeared lifeless and programmatic? In this easily accessible and wide-ranging survey, Claus Emmeche outlines many of the challenges and controversies involved in (...) the dynamic and curious science of artificial life. Emmeche describes the work being done by an international network of biologists, computer scientists, and physicists who are using computers to study life as it could be, or as it might evolve under conditions different from those on earth. Many artificial-life researchers believe that they can create new life in the computer by simulating the processes observed in traditional, biological life-forms. The flight of a flock of birds, for example, can be reproduced faithfully and in all its complexity by a relatively simple computer program that is designed to generate electronic "boids." Are these "boids" then alive? The central problem, Emmeche notes, lies in defining the salient differences between biological life and computer simulations of its processes. And yet, if we can breathe life into a computer, what might this mean for our other assumptions about what it means to be alive? The Garden in the Machine touches on every aspect of this complex and rapidly developing discipline, including its connections to artificial intelligence, chaos theory, computational theory, and studies of emergence. Drawing on the most current work in the field, this book is a major overview of artificial life. Professionals and nonscientists alike will find it an invaluable guide to concepts and technologies that may forever change our definition of life. (shrink)

The pervasive use of computer simulations in the sciences brings novel epistemological issues discussed in the philosophy of science literature since about a decade. Evolutionary biology strongly relies on such simulations, and in relation to it there exists a research program (Artificial Life) that mainly studies simulations themselves. This paper addresses the specificity of computer simulations in evolutionary biology, in the context (described in Sect. 1) of a set of questions about their scope as explanations, the (...) nature of validation processes and the relation between simulations and true experiments or mathematical models. After making distinctions, especially between a weak use where simulations test hypotheses about the world, and a strong use where they allow one to explore sets of evolutionary dynamics not necessarily extant in our world, I argue in Sect. 2 that (weak) simulations are likely to represent in virtue of the fact that they instantiate specific features of causal processes that may be isomorphic to features of some causal processes in the world, though the latter are always intertwined with a myriad of different processes and hence unlikely to be directly manipulated and studied. I therefore argue that these simulations are merely able to provide candidate explanations for real patterns. Section 3 ends up by placing strong and weak simulations in Levins’ triangle, that conceives of simulations as devices trying to fulfil one or two among three incompatible epistemic values (precision, realism, genericity). (shrink)

The experimental practice in contemporary molecular biology oscillates between the creativity of the researcher in tinkering with the experimental system, and the necessity of standardization of methods of inquiry. Experimental procedures, when standardized in lab protocols, might definitely be seen as actual recipes. Considering these protocols as recipes can help us understand some epistemological characteristics of current practice in molecular biology. On the one hand, protocols represent a common ground, i.e. the possibility of reproducibility, which constitutes one of the essential (...) properties for contemporary science to define an actual discovery. At the same time, however, protocols are flexible enough to be adapted by the individual researcher (within a space of maneuver given by the experimental system and by the practices that each individual discipline gives to itself) to his/her specific needs. These variations, just like the recipes, remind us that the legitimacy of an experimental practice, involves both objective and subjective constraints and it is articulated on a fuzzy background rather than a rigid and clear context. Moreover, looking at experiments according to this perspective can provide a key to understanding how different forms of science (which adopt different methodologies but which investigate the same phenomena), such as computational biology, are precisely different in the use of a different “cookbook”.Indeed, given the procedural/operational realism of biologists towards phenomena, the clash of different procedures has opened a discussion also about the nature and the meaning of the obtained results. Thus, according to the recipe-perspective that, the methodological struggle over the nature of biological phenomena (and their ways of discovery) among scientists, might be seen as a not always explicit, epistemological debate, however coming from the practice of science itself. (shrink)

This book examines the interface between mathematics and applied sciences. The editor examines the present and future needs for the interaction between various science and engineering areas. This edited book brings together the cutting-edge research on mathematics, combining various fields of science and engineering. The book begins with an introduction to computing and modeling. Next, computation and modeling trends are covered, along with chapters on structural static and vibration problems, heat conduction and diffusion problems, and fluid dynamics problems. Soft (...) computing and machine intelligence based modeling are also discussed, along with bio medical problems. The book concludes with a chapter on modeling in mining, electrical, electronics, and chemical problems. This book is a reference for students and researchers in various fields of engineering such as computer, mechanical, civil, aerospace, electrical, and chemical, as well as and other sciences such as applied mathematics, physics, chemistry, and life sciences. (shrink)

Brain-Computer interfacing is a highly promising and fast developing field of modern life sciences. Recent advances in neuroscience together with progressing miniaturization in micro systems provide insights in structure and functioning of the human brain and enable connections of technical components to neuronal structures as well. This possibly offers a future therapy for paralysed patients through neuronal motor pros-theses. This paper identifies central ethical aspects which have to be considered in further progressing research in this scientific field (...) and the development of neuronal motor prostheses. (shrink)

Images of Middle Eastern women in the Western media tend toward the exotic, erotic, or abject. The women are often styled as the victims of patriarchal institutions and depicted as in need of being saved by their supposedly more enlightened Western sisters. These stereotypes carry over into Western media assumptions about the participation of Arab women in science and technology as well; few people are aware of the existence of professional women in STEM (science, technology, engineering, and mathematics) fields in (...) the Middle East. This article discusses the experiences of expatriate Arab women in high-tech start-ups and other scientific enterprises in the United Arab Emirates and other countries of the Middle East. Among the issues addressed are experiences in the field and on temporary job locations, citizenship quandaries, family and community responsibilities, private versus governmental and semigovernmental employers, apparel/veiling considerations, and gender and racial prejudice. The essay is based on conversations with young women from Belorussia, Egypt, Jordan, Kuwait, Lebanon, and Palestine who work primarily as engineers and computer scientists. (shrink)

Summarizes and illuminates two decades of research Gathering important papers by both philosophers and scientists, this collection illuminates the central themes that have arisen during the last two decades of work on the conceptual foundations of artificial intelligence and cognitive science. Each volume begins with a comprehensive introduction that places the coverage in a broader perspective and links it with material in the companion volumes. The collection is of interest in many disciplines including computer science, linguistics, biology, information science, (...) psychology, neuroscience, iconography, and philosophy. Examines initial efforts and the latest controversies The topics covered range from the bedrock assumptions of the computational approach to understanding the mind, to the more recent debates concerning cognitive architectures, all the way to the latest developments in robotics, artificial life, and dynamical systems theory. The collection first examines the lineageof major research programs, beginning with the basic idea of machine intelligence itself, then focuses on specific aspects of thought and intelligence, highlighting the much-discussed issue of consciousness, the equally important, but less densely researched issue of emotional response, and the more traditionally philosophical topic of language and meaning. Provides a gamut of perspectives The editors have included several articles that challenge crucial elements of the familiar research program of cognitive science, as well as important writings whose previous circulation has been limited. Within each volume the papers are organized to reflect a variety of research programs and issues. The substantive introductions that accompany each volume further organize the material and provide readers with a working sense of the issues and the connection between articles. (shrink)

This volume is a collection of selected papers presented at the Second Asia-Pacific Computing and Philsosophy Conference, which was held in Bangkok, Thailand in January 2005. The conference was organized by the Center for Ethics of Science and Technology, Chulalongkorn University on behalf of the International Association of Computing and Philosophy (www.ia-cap.org). Computing have had a long relationship with philosophy, starting from the problem of how symbols being manipulated in computing bear a relation to the outside world, to those of (...) artificial intelligence, robotics, computer simulation, and so on. Moreover, as computer technologies have become thoroughly pervasive in today's environment, there are also issues concerning social and ethical impacts brought about by them. The papers in the volume represent a wide variety of concerns and various dimensions within which computing and philosophy are related. Furthermore, it also represents some of the first attempts to highlight cultural dimensions of computing and philosophy, which became prominent when the conference was held for the first time within the milieu of an Asian culture. (The First Asia-Pacific Computing and Philosophy was held in Canberra, Australia.) Hence, many of the papers in the volume address this added dimension. Apart form the usual problems of how computers and human lives are interconnected, the papers here also discuss how computers are related to human lives as lived in a specific culture. Thus the book breaks a new ground and should be of interest to a wide range of scholars and students who are interested, not only on computing and philosophy generally construed, but also on this exciting new dimension of how the cultures of Asia, the West, and others bear upon the traditional issues in computing and philosophy, and on how this dimension raises some new concerns and agenda. Among the topics discussed in this volume are: political online forums in Saudi Arabia, e-democracy and structural transformation of public sphere, the Buddhist informational person, a glance into the lives of computerized generation in Thailand, technology and journalism in the market, local approaches and global potential (?) of information ethics, computer-enhanced good life, computer teaching ethics, and many others. (shrink)

Embodied approach to cognition has taken roots in cognitive studies with developments in diverse fields such as robotics, artificial life and cognitive linguistics. Taking cue from the metaphor of a Watt governor, this approach stresses on the coupling between the organism and the environment and the continuous nature of the cognitive processes. This results in questioning the viability of computational–representational understanding of mind as a comprehensive theory of cognition. The paper, after giving an overview of embodied approach based on (...) some examples from conceptual metaphor theory, looks into a special case of Orwell’s problem in cognitive science. The problem is that there is so much evidence for embodiment to be true, yet there is little understanding of the same. I shall try to solve this problem by pointing out that it is our inveterate habits of perceiving ourselves that makes the embodied approach appear implausible. Studies on free will as well as the importance of the unconscious in overall cognitive processing raise challenging questions on our self-conception. A revision in the self-conception in the light of these findings will pave the way for a better appreciation of the embodied approach to cognition. (shrink)

Computer models and simulations have become, since the 1960s, an essential instrument for scientific inquiry and political decision making in several fields, from climate to life and social sciences. Philosophical reflection has mainly focused on the ontological status of the computational modeling, on its epistemological validity and on the research practices it entails. But in computational sciences, the work on models and simulations are only two steps of a longer and richer process where operations on data (...) are as important as, and even more time and energy-consuming than modeling itself. Drawing on two study cases—computational embryology and computational epidemiology—this article contributes to filling the gap by focusing on the operations of producing and re-using data in computational sciences. The different phases of the scientific and artisanal work of modelers include data collection, aggregation, homogenization, assemblage, analysis and visualization. The article deconstructs the ideas that data are self-evident informational aggregates and that data-driven approaches are exempted from theoretical work. More importantly, the paper stresses the fact that data are constructed and theory laden not only in their fabrication, but also in their reusing. (shrink)

Farming computer games enable the ‘desk chair countryside’—millions of people actively engaged in performing farming and rural activities on-line—to co-produce their desired representations of rural life, in line with the parameters set by game creators. In this paper, I critique the narratives and images of farming life expressed in the popular computer game ‘Stardew Valley’. Stardew is based on a scenario whereby players leave a [meaningless] urban desk job to revitalize the family farm. Player are given (...) a choice to invest in the Community Center or to support ‘JojaMart’, a ‘big-box’ development. The farming narrative demonstrates the hallmarks of classical American agrarianism: farming as the basic profession on which other occupations depend, the virtue of hard work, the ‘natural’ and moral nature of agricultural life, and the economic independence of the farmer. More recent discourses of critical agrarianism are noticeably absent, particularly in relation to environmental protection. Conflict is centred on urban-based big business, whereas the farm is represented as a ‘bolt-hole’ or sanctuary from urban life. I argue that embedding issues of big-box development in gameplay enrols players in active reflection and debate on desirable responses, whereas the emphasis on reproducing classical agrarian tropes risks desensitizing game players to contemporary agrarian social and environmental justice issues. However, Stardew Valley gameplay implicitly reinforces the ideal that low input farming is the way that agriculture should be practiced. The success of the game in eliciting on-line debates, and the requirement for active performance and decision-making, demonstrates the specific potential of computer games as mediums for influencing and intervening in ongoing reworking of farming imaginaries, and enabling more critically engagement of the ‘desk chair countryside’ in important global debates. (shrink)

Nowadays, it has become almost a matter of course to say that the human mind is like a computer. Folks in all walks of life talk of ‘programming’ themselves, ‘multitasking’, running different ‘operating systems’, and sometimes of ‘crashing’ and being ‘rebooted’. Few who have used computers have not been touched by the appeal of the..

Alan M. Turing, pioneer of computing and WWII codebreaker, is one of the most important and influential thinkers of the twentieth century. In this volume for the first time his key writings are made available to a broad, non-specialist readership. They make fascinating reading both in their own right and for their historic significance: contemporary computational theory, cognitive science, artificial intelligence, and artificial life all spring from this ground-breaking work, which is also rich in philosophical and logical insight. An (...) introduction by leading Turing expert Jack Copeland provides the background and guides the reader through the selection. About Alan Turing Alan Turing FRS OBE, (1912-1954) studied mathematics at King's College, Cambridge. He was elected a Fellow of King's in March 1935, at the age of only 22. In the same year he invented the abstract computing machines - now known simply as Turing machines - on which all subsequent stored-program digital computers are modelled. During 1936-1938 Turing continued his studies, now at Princeton University. He completed a PhD in mathematical logic, analysing the notion of 'intuition' in mathematics and introducing the idea of oracular computation, now fundamental in mathematical recursion theory. An 'oracle' is an abstract device able to solve mathematical problems too difficult for the universal Turing machine. In the summer of 1938 Turing returned to his Fellowship at King's. When WWII started in 1939 he joined the wartime headquarters of the Government Code and Cypher School (GC&CS) at Bletchley Park, Buckinghamshire. Building on earlier work by Polish cryptanalysts, Turing contributed crucially to the design of electro-mechanical machines ('bombes') used to decipher Enigma, the code by means of which the German armed forces sought to protect their radio communications. Turing's work on the version of Enigma used by the German navy was vital to the battle for supremacy in the North Atlantic. He also contributed to the attack on the cyphers known as 'Fish'. Based on binary teleprinter code, Fish was used during the latter part of the war in preference to morse-based Enigma for the encryption of high-level signals, for example messages from Hitler and other members of the German High Command. It is estimated that the work of GC&CS shortened the war in Europe by at least two years. Turing received the Order of the British Empire for the part he played. In 1945, the war over, Turing was recruited to the National Physical Laboratory (NPL) in London, his brief to design and develop an electronic computer - a concrete form of the universal Turing machine. Turing's report setting out his design for the Automatic Computing Engine (ACE) was the first relatively complete specification of an electronic stored-program general-purpose digital computer. Delays beyond Turing's control resulted in NPL's losing the race to build the world's first working electronic stored-program digital computer - an honour that went to the Royal Society Computing Machine Laboratory at Manchester University, in June 1948. Discouraged by the delays at NPL, Turing took up the Deputy Directorship of the Royal Society Computing Machine Laboratory in that year. Turing was a founding father of modern cognitive science and a leading early exponent of the hypothesis that the human brain is in large part a digital computing machine, theorising that the cortex at birth is an 'unorganised machine' which through 'training' becomes organised 'into a universal machine or something like it'. He also pioneered Artificial Intelligence. Turing spent the rest of his short career at Manchester University, being appointed to a specially created Readership in the Theory of Computing in May 1953. He was elected a Fellow of the Royal Society of London in March 1951 (a high honour). (shrink)

This rare publication continues an exploratory journey in relational biology, a study of biology in terms of the organization of networked connections in living systems. It builds on the author's two earlier monographs which looked at the epistemology of life and the ontogeny of life. Here the emphasis is on the intangibility of life, that the real nature of living systems is conveyed not by their tangible material basis but by their intangible inherent processes. Relational biology is (...) the approach that hails 'function dictates structure'; it is mathematics decoded into biological realizations. Therefore, the work begins with a concise introduction to category theory, equiping the reader with the mathematical metalanguage of relation biology. The book is organized around three parts: Part I is a comprehensive study of the most important functor in relational biology, the power set functor. The author lays the set-theoretic foundations of the functorial connections in relational biology, exploring relations, mappings, and set-valued mappings. In Part II, Natural Law receives a new mathematical formulation founded on two axioms: 'Everything is a set.' and 'Every process is a set-valued mapping.' The reader sees how Metabolism-Repair networks, equipped with set-valued processors, expand their role from models of biological entities to generic models of all natural systems. Part III expounds the various shades of invertibility in general, and the inversion of encoding to decoding in particular. A plethora of mathematical and biological examples illustrate the category-theoretic concepts of equivalence and adjunction. This book's algebraic approach to biological models will appeal to researchers and graduate students in mathematics, biology, and the philosophy of science. (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)

This volume brings together contributions from leading researchers in the field of agent-based modelling and simulation. This approach has grown out of some recent and innovative ideas in the social sciences, computer sciences, life sciences, physics and game theory. It is proving helpful in understanding complexity in many domains. The opportunities it offers to explore the experimental approach to social and human behaviour is proving of theoretical and empirical value across a wide range of fields. (...) With contributions from researchers whose work has served to define this new field such as Nigel Gilbert, Robert Axtell (in economics and social science) and Jacques Ferber (in multi-agent systems), as well as practitioners who are working at the cutting edge of the new domain, this collection of essays has been assembled by two of its leading exponents: Frédéric Amblard and Denis Phan. The research, case studies and theoretical approaches discussed in this book are designed to introduce beginners and experts alike to the current state of play in this new and exciting field of social science. (shrink)

Alan Turing, pioneer of computing and WWII codebreaker, is one of the most important and influential thinkers of the twentieth century. In this volume for the first time his key writings are made available to a broad, non-specialist readership. They make fascinating reading both in their own right and for their historic significance: contemporary computational theory, cognitive science, artificial intelligence, and artificial life all spring from this ground-breaking work, which is also rich in philosophical and logical insight.

Biodiversity scientists often describe their field as aiming to save life and humanity, but the field has yet to reckon with the history and contemporary practices of colonialism and systematic racism inherited from natural history. The online data portals scientists use to store and share biodiversity data are a growing class of organizations whose governance can address or perpetuate and further institutionalize the implicit assumptions and inequitable social impacts from this extensive history. In this context, researchers and Indigenous Peoples (...) are developing and implementing new strategies to examine and change assumptions about which agents should count as salient participants to scientific projects, especially projects that build and manage large digital data portals. Two notable efforts are the FAIR and CARE Principles for scientific data management and governance. To characterize how these influence the governance of biodiversity data portals, we develop an account of fitness-for-use that makes explicit its social as well as technical conditions in relation to agents and purposes. The FAIR Principles, already widely adopted by biodiversity data projects, prioritize machine agents and efficient computation, while the CARE Principles prioritize Indigenous Peoples and their data sovereignty. Both illustrate the potency of an emerging general strategy by which groups of actors craft and implement governance principles for data fitness-of-use to change assumptions about salient participants to data science. (shrink)

The bookModeling Reality covers a wide range of fascinating subjects, accessible to anyone who wants to learn about the use of computer modeling to solve a diverse range of problems, but who does not possess a specialized training in mathematics or computer science. The material presented is pitched at the level of high-school graduates, even though it covers some advanced topics (cellular automata, Shannon's measure of information, deterministic chaos, fractals, game theory, neural networks, genetic algorithms, and Turing machines). (...) These advanced topics are explained in terms of well known simple concepts: Cellular automata - Game of Life, Shannon's formula - Game of twenty questions, Game theory - Television quiz, etc. The book is unique in explaining in a straightforward, yet complete, fashion many important ideas, related to various models of reality and their applications. Twenty-five programs, written especially for this book, are provided on an accompanying CD. They greatly enhance its pedagogical value and make learning of even the more complex topics an enjoyable pleasure. (shrink)

Computational modeling has long been one of the traditional pillars of cognitive science. Unfortunately, the computer models of cognition being developed today have not kept up with the enormous changes that have taken place in computer technology and, especially, in human-computer interfaces. For all intents and purposes, modeling is still done today as it was 25, or even 35, years ago. Everyone still programs in his or her own favorite programming language, source code is rarely made available, (...) accessibility of models to non-programming researchers is essentially non-existent, and even for other modelers, the profusion of source code in a multitude of programming languages, written without programming guidelines, makes it almost impossible to access, check, explore, re-use, or continue to develop. It is high time to change this situation, especially since the tools are now readily available to do so. We propose that the modeling community adopt three simple guidelines that would ensure that computational models would be accessible to the broad range of researchers in cognitive science. We further emphasize the pivotal role that journal editors must play in making computational models accessible to readers of their journals. (shrink)

In this philosophical paper, we explore computational and biological analogies to address the fine-tuning problem in cosmology. We first clarify what it means for physical constants or initial conditions to be fine-tuned. We review important distinctions such as the dimensionless and dimensional physical constants, and the classification of constants proposed by Lévy-Leblond. Then we explore how two great analogies, computational and biological, can give new insights into our problem. This paper includes a preliminary study to examine the two analogies. Importantly, (...) analogies are both useful and fundamental cognitive tools, but can also be misused or misinterpreted. The idea that our universe might be modelled as a computational entity is analysed, and we discuss the distinction between physical laws and initial conditions using algorithmic information theory. Smolin introduced the theory of "cosmological natural selection" with a biological analogy in mind. We examine an extension of. (shrink)

All epistemic agents physically consist of parts that must somehow comprise an integrated cognitive self. Biological individuals consist of subunits (organs, cells, molecular networks) that are themselves complex and competent in their own context. How do coherent biological Individuals result from the activity of smaller sub-agents? To understand the evolution and function of metazoan bodies and minds, it is essential to conceptually explore the origin of multicellularity and the scaling of the basal cognition of individual cells into a coherent larger (...) organism. In this paper I synthesize ideas in cognitive science, evolutionary biology, and developmental physiology toward a hypothesis about the origin of Individuality: “Scale-Free Cognition”. I propose a fundamental definition of an Individual based on the ability to pursue goals at an appropriate level of scale and organization, and suggest a formalism for defining and comparing the cognitive capacities of highly diverse types of agents. Any Self is demarcated by a computational surface – the spatio-temporal boundary of events that it can measure, model, and try to affect. This surface sets a functional boundary - a cognitive “light cone” which defines the scale and limits of its cognition. I hypothesize that higher-level goal-directed activity and agency, resulting in larger cognitive boundaries, evolve from the primal homeostatic drive of living things to reduce stress – the difference between current conditions and life-optimal conditions. The mechanisms of developmental bioelectricity - the ability of all cells to form electrical networks that process information - suggests a plausible set of gradual evolutionary steps that naturally lead from physiological homeostasis in single cells to memory, prediction, and ultimately complex cognitive agents, via scale-up of the drive of infotaxis. Recent data on the molecular mechanisms of pre-neural bioelectricity suggest a model of how increasingly sophisticated cognitive functions emerge smoothly from cell-cell communication used to guide embryogenesis and regeneration. This set of hypotheses provides a novel perspective on numerous phenomena, such as cancer, and makes several unique, testable predictions for interdisciplinary research that have implications not only for evolutionary developmental biology but also for biomedicine and perhaps artificial intelligence and exobiology. (shrink)

To what extent should humans transfer, or abdicate, responsibility to computers? In this paper, I distinguish six different senses of responsible and then consider in which of these senses computers can, and in which they cannot, be said to be responsible for deciding various outcomes. I sort out and explore two different kinds of complaint against putting computers in greater control of our lives: (i) as finite and fallible human beings, there is a limit to how far we can acheive (...) increased reliability through complex devices of our own design; (ii) even when computers are more reliable than humans, certain tasks (e.g., selecting an appropriate gift for a friend, solving the daily crossword puzzle) are inappropriately performed by anyone (or anything) other than oneself. In critically evaluating these claims, I arrive at three main conclusions: (1) While we ought to correct for many of our shortcomings by availing ourselves of the computer''s larger memory, faster processing speed and greater stamina, we are limited by our own finiteness and fallibility (rather than by whatever limitations may be inherent in silicon and metal) in the ability to transcend our own unreliability. Moreover, if we rely on programmed computers to such an extent that we lose touch with the human experience and insight that formed the basis for their programming design, our fallibility is magnified rather than mitigated. (2) Autonomous moral agents can reasonably defer to greater expertise, whether human or cybernetic. But they cannot reasonably relinquish background-oversight responsibility. They must be prepared, at least periodically, to review whether the expertise to which they defer is indeed functioning as he/she/it was authorized to do, and to take steps to revoke that authority, if necessary. (3) Though outcomes matter, it can also matter how they are brought about, and by whom. Thus, reflecting on how much of our lives should be directed and implemented by computer may be another way of testing any thoroughly end-state or consequentialist conception of the good and decent life. To live with meaning and purpose, we need to actively engage our own faculties and empathetically connect up with, and resonate to, others. Thus there is some limit to how much of life can be appropriately lived by anyone (or anything) other than ourselves. (shrink)

The papers collected in this volume are based on the best contributions to the conference of the Italian Society for Logic and Philosophy of Science (SILFS) that took place in Milan on 8-10 October 2007. The aim of the Society, since its foundation in 1952, has always been that of bringing together scholars - working in the broad areas of Logic, Philosophy of Science and History of Science - who share an open-minded approach to their disciplines and regard them as (...) essentially requiring continuous confrontation and bridge-building to avoid the danger of over-specialism. In this perspective, logicians and philosophers of science should not indulge in inventing and cherishing their own "internal problems" - although these may occasionally be an opportunity for conceptual clarification - but should primarily look at the challenging conceptual and methodological questions that arise in any genuine attempt to extend our objective knowledge. As Ludovico Geymonat used to put it: " good] philosophy should be sought in the folds of science itself." Contributions are distributed into six sections, five of which - "Logic and Computing," "Physics and Mathematics," "Life Sciences," "Economics and Social Sciences," "Neuroscience and Philosophy of Mind" - are devoted to the discussion of cutting-edge problems that arise from current-day scientific research, while the remaining section on "General Philosophy of Science" is focused on foundational and methodological questions that are common to all areas. (shrink)

In considering how to best deploy robotic systems in public and private sectors, we must consider what individuals will expect from the robots with which they interact. Public awareness of robotics—as both military machines and domestic helpers—emerges out of a braided stream composed of science fiction and popular science. These two genres influence news media, government and corporate spending, and public expectations. In the Euro-American West, both science fiction and popular science are ambivalent about the military applications for robotics, and (...) thus we can expect their readers to fear the dangers posed by advanced robotics while still eagerly anticipating the benefits to be accrued through them. The chief pop science authors in robotics and artificial intelligence have a decidedly apocalyptic bent and have thus been described as leaders in a social movement called "Apocalyptic AI." In one form or another, such authors look forward to a transcendent future in which machine life succeeds human life, thanks to the march of evolutionary progress. The apocalyptic promises of popular robotics presume that presently exponential growth in computing will continue indefinitely, producing a "Singularity." During the Singularity, technological progress will be so rapid that undreamt of changes will take place on earth, the most important of which will be the evolutionary succession of human beings by massively intelligent robots and the "uploading" of human consciousness into computer bodies. This supposedly inevitable transition into post-biological life looms across the entire scope of pop robotics and artificial intelligence, and it is from beneath that shadow that all popular books engage the military and the ethics of warfare. Creating a just future will require that we transcend the apocalyptic discourse of pop science and establish an ethical approach to researching and deploying robots, one that emphasizes human rather than robot welfare; doing so will require the collaboration of social scientists, humanists, and scientists. (shrink)

Cognitive science is considered to be the study of mind (consciousness and thought) and intelligence in humans. Under such definition variety of unsolved/unsolvable problems appear. This article argues for a broad understanding of cognition based on empirical results from i.a. natural sciences, self-organization, artificial intelligence and artificial life, network science and neuroscience, that apart from the high level mental activities in humans, includes sub-symbolic and sub-conscious processes, such as emotions, recognizes cognition in other living beings as well as (...) extended and distributed/social cognition. The new idea of cognition as complex multiscale phenomenon evolved in living organisms based on bodily structures that process information, linking cognitivists and EEEE (embodied, embedded, enactive, extended) cognition approaches with the idea of morphological computation (info-computational self-organisation) in cognizing agents, emerging in evolution through interactions of a (living/cognizing) agent with the environment. (shrink)

As a result of the developments in science and technology, humanity began to experience a digital transformation after the 19th century. With this digital transformation, it is seen that a serious change has occurred in human beings biologically, socially, and, more specifically, religiously. One could say that different trends have emerged at many points where human relations, the relationship of the human with the environment and with God are also affected. Among the most comprehensive and prominent of these trends is (...) transhumanism because of its aims for humanity and the world. Transhumanism, which views technology as the main point of reference for the future of humanity, is also considered a cultural, social, and ideological human movement with its statements intended for society. It considers immortality as a goal, along with such claims as improving welfare, extending human life, and wiping out diseases by using technology in every aspect of human life. Transhumanists, who claim that they can achieve immortality thanks to technology, argue that this will happen in two ways. The first is biological immortality. It will be achieved by eliminating all kinds of biological factors that lead to humans aging and death. The second is digital or virtual immortality, which is achieved by transferring human consciousness from the biological body to computer interfaces and installing it in any desired entity. This perspective must be critically examined as it can be considered an attempt to challenge death, which is the basic doctrine of classical religions. In the present study, human immortality, considered the most important claim made by transhumanists, is criticized within kalām, Islamic theology. Of course, transhumanists’ account of human immortality is impossible, according to kalām. It can be said that transhumanists view of immortal human can be considered in the category of created beings, which is defined in kalām as "the being created later and needs another being in order to exist and to continue its existence". Given that transhumanists base the idea of the immortal being upon biological healing or digital transmission, it is clear that both types of beings need someone else. Therefore, one could say that it would be more reasonable to define transhumanists’ notion of immortality as the act of prolonging human life. It is because the life of immortal beings, accepted as biological or digital entities, is shaped by many factors. If these factors disappear, so does the being. On the other hand, the attribute of immortality, which belongs to the eternal being only, according to kalām, must come from itself without needing any other being. Therefore, the notion of immortal being suggested by the transhumanists must be reexamined within kalām and be redefined as the extension of life. The redefined immortality as the extension of life hardly poses kalāmī (or theological) problems. In fact, Islam encourages using all types of tools and equipment to enable humans to have a healthy and blissful life. (shrink)

This ground-breaking and timely book explores how big data, artificial intelligence and algorithms are creating new types of agency, and the impact that this is having on our lives and the rule of law. Addressing the issues in a thoughtful, cross-disciplinary manner, the authors examine the ways in which data-driven agency is transforming democratic practices and the meaning of individual choice. Leading scholars in law, philosophy, computer science and politics analyse the latest innovations in data science and machine learning, (...) assessing the actual and potential implications of these technologies. They investigate how this affects our understanding of such concepts as agency, epistemology, justice, transparency and democracy, and advocate a precautionary approach that takes the effects of data-driven agency seriously without taking it for granted. Scholars and students of law, ethics and philosophy, in particular legal, political and democratic theory, will find this book a compelling and invaluable read, as will computer scientists interested in the implications of their own work. It will also prove insightful for academics and activists working on privacy, fairness and anti-discrimination. Contributors include: J.E. Cohen, G. de Vries, S. Delacroix, P. Dumouchel, C. Ess, M. Garnett, E.H. Gerding, R. Gomer, C. Graber, M. Hildebrandt, C. Maple, K. O'Hara, P. Ohm, m.c. schraefel, D. Stevens, N. van Dijk, M. Veale. (shrink)

An exploration of the moral and ethical implications of new biotechnologies Many of the ethical issues raised by new technologies have not been widely examined, discussed, or indeed settled. For example, robotics technology challenges the notion of personhood. Should a robot, capable of making what humans would call ethical decisions, be held responsible for those decisions and the resultant actions? Should society reward and punish robots in the same way that it does humans? Likewise, issues of safety, environmental concerns, and (...) distributive justice arise with the increasing acceptance of genetically modified organisms in food production nanotechnology in engineering and medicine, and human gene therapy and enhancement. The problem of dual-use—when a technology can be used both to benefit and to harm—exists with virtually all new technologies but is central in the context of emerging 21st century technologies ranging from artificial intelligence and robotics to human gene-editing and brain-computer interfacing. In Re-Creating Nature: Science, Technology, and Human Values in the Twenty-First Century, James T. Bradley addresses emerging biotechnologies with prodigious potential to benefit humankind but that are also fraught with ethical consequences. Some actually possess the power to directly alter the evolution of life on earth including human. Specifically, these topics include stem cells, synthetic biology, GMOs in agriculture, nanotechnology, bioterrorism, CRISPR gene-editing technology, three-parent babies, robotics and roboethics, artificial intelligence, and human brain research and neurotechnologies. Offering clear explanations of these various technologies, a pragmatic presentation of the conundrums involved, and questions that illuminate hypothetical situations, Bradley guides discussions of these and other thorny issues resulting from the development of new biotechnologies. He also highlights the responsibilities of scientists to conduct research in an ethical manner and the responsibilities of nonscientists to become “science literate” in the twenty-first century. (shrink)

The proliferation of digital data has been the impetus for the emergence of a new discipline for the study of social life: ‘computational social science’. Much research in this field is founded on the premise that society is a complex system with emergent structures that can be modeled or reconstructed through digital data. This paper suggests that computational social science serves practical and legitimizing functions for digital capitalism in much the same way that neoclassical economics does for neoliberalism. In (...) recognition of this homology, this paper develops a critique of the complexity perspective of computational social science and argues for a heterodox computational social science founded on the meta-theory of critical realism that is critical, methodological pluralist, interpretative and explanative. This implies diverting computational social science’ computational methods and digital data so as to not be aimed at identifying invariant laws of social life, or optimizing state and corporate practices, but to instead be used as part of broader research strategies to identify contingent patterns, develop conjunctural explanations, and propose qualitatively different ways of organizing social life. (shrink)

Global development initiatives frequently promote agricultural commodity chain projects to improve livelihoods. In Morocco, development projects, including the Plan Maroc Vert, have promoted apple production in rural regions of the country. In order to access domestic markets, these new apple producers often use pesticides to meet market standards. Through situated ethnographic inquiry and commodity chain analysis, using a combination of surveys and interviews with apple wholesalers, government officials, along with farmers, this paper works to critique the PMV’s development approach that (...) implicitly values commodification. By exploring interconnected processes of commodification, I link subsidized apple saplings and cold storage infrastructure to the dependence on pesticide usage, which has become a part of daily village life. This has important implications for community health and riparian ecosystems. Alternatively, I propose how we can imagine different development trajectories that decommodify livelihoods by focusing on local knowledge creation and diversification strategies. (shrink)

Games are more varied and occupy more of daily life than ever before. At the same time, the tools available to study game play and players are more powerful than ever, especially massive data sets from online platforms and computational engines that can accurately evaluate human decisions. This essay offers six suggestions for future cognitive science research on games: Don't forget about chess, Look beyond action games and chess, Use -optimal play to understand human play and players, Investigate social (...) phenomena, Raise the standards for studies of games as treatments, Talk to real experts. (shrink)

The autobiography of one of the most versatile of American scientists of his generation, the first to be trained largely in his own country. A scientific generalist, Morse has made significant contributions to atomic physics, quantum mechanics, plasma physics, astrophysics, acoustics, machine computation, and operations research. Philip Morse has surely been one of the most versatile of American scientists of his generation, the first to be trained largely in his own country. A scientific generalist, he has made significant contributions to (...) atomic physics, quantum mechanics, plasma physics, astrophysics, acoustics, machine computation, and operations research. His life-long commitment to teaching, through his authorship of a series if standard-setting textbooks and through his personal guidance of unnumbered individual students, has extended this scope to include thermodynamics, statistical mechanics, and the methods of theoretical physics as well. Moreover, as this autobiography relates at a fast-moving pace, Morse has also been involved in the high-pressure concerns of war research, scientific administration and consultation, policy formation, the education of key groups and wider publics beyond the classroom, and the real-world utilization of scientific techniques and discoveries. For all these accomplishments, Morse writes that his experience as a scientist and as a participant in the affairs of his time "has been at the second, rather than at the top, level." It may be that this circumstance of being neat, rather than at, the top makes this autobiography more, rather than less, relevant to other and younger scientists, to those considering a life in science, and to general readers curious as to what such a life is really like. Only a miniscule few reach, say. Einsteinian levels, and their lives and work tend to be unique unto themselves; what Morse reports is truer to the experience of the great majority of the members of the scientific community. While his actual accomplishments, his range, and his eminence certainly far exceed those of a "typical" scientist, they do so more in degree than in kind. Morse's style is straightforward and nontechnical, direct, and personal. Some of the lighter moments and revealingly human incidents of his experience are recorded along with the problems and breakthroughs in the near-private world of pure science and the public worlds of policy, high-level consultation, and practical applications. (shrink)