In this book the editors invited prominent researchers with different perspectives and deep insights into the various facets of the relationship between reality and representation in the following three classes of agent: in humans, in other living beings, and in machines. -/- The book enriches our views on representation and deepens our understanding of its different aspects, a question that connects philosophy, computer science, logic, anthropology, psychology, sociology, neuroscience, linguistics, information and communication science, systems theory and engineering, computability, cybernetics, (...) synthetic biology, and bioinformatics biosemiotics. This book will be relevant to researchers in these fields. (shrink)

The integration of computer science, biology, and engineering has resulted in the emergence of rapidly growing interdisciplinary fields such as bioinformatics, bioengineering, DNA computing, and systems and synthetic biology. Ideas derived from computer science and engineering can provide innovative solutions to biological problems and advance research in new directions. Although interdisciplinary research has become increasingly prevalent in recent years, the scientists contributing to these efforts largely remain specialists in their original disciplines and are not fully capable of (...) covering the many facets of multidisciplinary problems, which impedes the development of truly integrated solutions. It would be .. (shrink)

Synthetic biology emerged around 2000 as a new biological discipline. It shares with systems biology the same modular vision of organisms, but is more concerned with applications than with a better understanding of the functioning of organisms. A herald of this new discipline is Craig Venter who aims to create an artificial microorganism with the minimal genome compatible with life and to implement into it different 'functional modules' to generate new micro-organisms adapted to specific tasks. Synthetic (...) biology is based on the possibilities raised by genetic engineering, but it aims to engineer organisms, and not simply to modify them, mimicking the practice of computer engineers. Three points will be discussed: In what regard does synthetic biology represent a new epistemology of the life sciences? What are the relations between synthetic biology and evolutionary biology? What is the raison d'être of synthetic biology as a discipline independent of nanotechnologies? (shrink)

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)

Synthetic biology is designing and creating biological tools and systems for useful purposes. It uses knowledge from biology, such as biotechnology, molecular biology, biophysics, biochemistry, bioinformatics, and other disciplines, such as engineering, mathematics, computer science, and electrical engineering. It is recognized as both a branch of science and technology. The scope of synthetic biology ranges from modifying existing organisms to gain new properties to creating a living organism from non-living components. Synthetic biology (...) has many applications in important fields such as energy, chemistry, medicine, environment, agriculture, national security, and nanotechnology. The development of synthetic biology also raises ethical and social debates. This article aims to identify the place of ethics in synthetic biology. In this context, the theoretical ethical debates on synthetic biology from the 2000s to 2020, when the development of synthetic biology was relatively faster, were analyzed using the systematic review method. Based on the results of the analysis, the main ethical problems related to the field, problems that are likely to arise, and suggestions for solutions to these problems are included. The data collection phase of the study included a literature review conducted according to protocols, including planning, screening, selection and evaluation. The analysis and synthesis process was carried out in the next stage, and the main themes related to synthetic biology and ethics were identified. Searches were conducted in Web of Science, Scopus, PhilPapers and MEDLINE databases. Theoretical research articles and reviews published in peer-reviewed journals until the end of 2020 were included in the study. The language of publications was English. According to preliminary data, 1,453 publications were retrieved from the four databases. Considering the inclusion and exclusion criteria, 58 publications were analyzed in the study. Ethical debates on synthetic biology have been conducted on various issues. In this context, the ethical debates in this article were examined under five themes: the moral status of synthetic biology products, synthetic biology and the meaning of life, synthetic biology and metaphors, synthetic biology and knowledge, and expectations, concerns, and problem solving: risk versus caution. (shrink)

Synthetic biology, as an engineering approach to biological systems, has the potential to disruptively innovate the development of vaccines, therapeutics, and diagnostics. Data accessibility and differences in data-usage capabilities are important factors in shaping this innovation landscape. In this paper, the data that underpin synthetic biology responses to the COVID-19 pandemic are analyzed as positional information goods—goods whose value depends on exclusivity. The positionality of biological data impacts the ability to guide innovations toward societally preferred goals. (...) From both an ethical and economic point of view, positionality can lead to suboptimal as well as beneficial situations. When aiming for responsible innovation (i.e. embedding societal deliberation in the innovation process), it is important to consider hurdles and facilitators in data access and use. Central governance and knowledge commons provide routes to mitigate the negative effects of data positionality. (shrink)

This paper uses the theory of technoscience to shed light on the current criticisms against the emerging science of Artificial Life. We see that the science of Artificial Life is criticized for the synthetic nature of its research and its over reliance on computer simulations which is seen to be contrary to the traditional goals and methods of science. However, if we break down the traditional distinctions between science and technology using the theory of technoscience, then we can begin (...) to see that all science has a synthetic nature and reliance on technology. Artificial Life researchers are not heretical practitioners of some pseudoscience; they are just more open about their reliance on technology to help realize their theories and modeling. Understanding that science and technology are not as disparate as was once thought is an essential step in helping us create a more humane technoscience in the future. (shrink)

The field of synthetic biology is looking forward engineering framework for safely designing reliable de-novo biological functions. In this undertaking, Computer-Aided-Design environments should play a central role for facilitating the design. Although, CAD environment is widely used to engineer artificial systems the application in synthetic biology is still in its infancy. In this article we address the problem of the design of a high level language which at the core of CAD environment. More specifically the Gubs (...) language is a specification language used to describe the observations of the expected behaviour. The compiler appropriately selects components such that the observation of the synthetic biological function resulting to their assembly complies to the programmed behaviour. (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)

The field of synthetic biology is looking forward engineering framework for safely designing reliable de-novo biological functions. In this undertaking, Computer-Aided-Design environments should play a central role for facilitating the design. Although, CAD environment is widely used to engineer artificial systems the application in synthetic biology is still in its infancy. In this article we address the problem of the design of a high level language which at the core of CAD environment. More specifically the Gubs (...) language is a specification language used to describe the observations of the expected behaviour. The compiler appropriately selects components such that the observation of the synthetic biological function resulting to their assembly complies to the programmed behaviour. (shrink)

In synthetic biology the use of engineering metaphors to describe biological organisms and their behavior has become a common practice. The concept of noise provides one of the most compelling examples of such transfer. But this notion is also confusing: While in engineering noise is a destructive force perturbing artificial systems, in synthetic biology it has acquired an additional functional meaning. It has been found out that noise is an important factor in driving biological processes such (...) as gene regulation, development, and evolution. How did noise acquire this dual meaning in the field of synthetic biology? In this paper we study the emergence of the functional meaning of noise in relation to synthetic modeling. We will pay particular attention to the interdisciplinary aspects of this process highlighting the way borrowed concepts, analogical reasoning and the use of cross-disciplinary computational templates were entwined in it. (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)

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)

Neosentience, a potentially new branch of scientific inquiry related to artificial intelligence, was first suggested in a paper by Bill Seaman as part of a new embodied robotic paradigm, arising out of ongoing theoretical research with Otto E. Rossler. Seaman, artist-researcher, and Rossler, theoretical biologist and physicist, have been examining the potential of generating an intelligent, embodied, multimodal sensing and computational robotic system. Although related to artificial intelligence the goal of this system is the creation of an entity exhibiting (...) a new form of sentience. Its unique qualities will be discussed. Sentience is not yet used in the formal languages of either cognitive science or artificial intelligence. Two related approaches are (1) the generation of artificial minds via parallel processing, in a robotic system; (2) an alternative approach is the generation of an electrochemical computer as a robotic system. Biomimetics, along with state-of-the-art computer visualization is employed. The electrochemical paradigm has a complexity that exceeds standard computational means. The scientific and the poetic elements of the project are motivated by human sentience. The sentient entity is initially modelled on our functional definition of human sentience. The system involves synthetic drives as a new element. We seek to articulate the differences to living brains. This transdisciplinary approach necessitates different forms of inquiry to inform this project such as cognitive science including psychology, education/learning, neuroscience, linguistics, philosophy, anthropology, biology and the arts. We believe that this area of research to be of importance. (shrink)

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)

Based on a conference on the nature and origin of biological information held at Cornell University in 2011, this edited volume presents new research by experts in information theory, computer science, numerical simulation, thermodynamics, evolutionary theory, whole organism biology, developmental biology, molecular biology, genetics, physics, biophysics, mathematics, and linguistics.

Synthetic biology aims at reconstructing life to put to the test the limits of our understanding. It is based on premises similar to those which permitted invention of computers, where a machine, which reproduces over time, runs a program, which replicates. The underlying heuristics explored here is that an authentic category of reality, information, must be coupled with the standard categories, matter, energy, space and time to account for what life is. The use of this still elusive category (...) permits us to interact with reality via construction of self-consistent models producing predictions which can be instantiated into experiments. While the present theory of information has much to say about the program, with the creative properties of recursivity at its heart, we almost entirely lack a theory of the information supporting the machine. We suggest that the program of life codes for processes meant to trap information which comes from the context provided by the environment of the machine. (shrink)

Big data biology—bioinformatics, computational biology, systems biology (including ‘omics’), and synthetic biology—raises a number of issues for the philosophy of science. This article deals with several such: Is data-intensive biology a new kind of science, presumably post-reductionistic? To what extent is big data biology data-driven? Can data ‘speak for themselves?’ I discuss these issues by way of a reflection on Carl Woese’s worry that “a society that permits biology to become an (...) engineering discipline, that allows that science to slip into the role of changing the living world without trying to understand it, is a danger to itself.” And I argue that scientific perspectivism, a philosophical stance represented prominently by Giere, Van Fraassen, and Wimsatt, according to which science cannot as a matter of principle transcend our human perspective, provides the best resources currently at our disposal to tackle many of the philosophical issues implied in the modeling of complex, multilevel/multiscale phenomena. (shrink)

This paper links two domains of recent interest in science and technology studies, complexity and ignorance, in the context of knowledge practices observed among synthetic biologists. Synthetic biologists are recruiting concepts and methods from computer science and electrical engineering in order to design and construct novel organisms in the lab. Their field has taken shape amidst revised assessments of life’s complexity in the aftermath of the Human Genome Project. While this complexity is commonly taken to be an immanent (...) property of biological systems, this article presents an epistemological view of complexity according to which complexity relates to a specific scientific theory or model and refers to that which exceeds the theory or model’s explanatory power. This epistemological view allows us to narrate a particular story about the changing relationship between biology and synthetic biology in the last decade and accounts for early knowledge practices in synthetic biology that “ignored” biology. This article further argues that while the failure of ignorance to produce clear-cut results for synthetic biologists has led practitioners back to biology, the entanglements between different pragmatic orientations and ways of knowing trouble the implications of this return for assessments of the complexity of biological systems. (shrink)

Within French epistemology the question is central whether the present can be a reference point for the history of science or whether scientific practices should be understood within their own historical context. Both positions are linked with problems: either it results in a ‘whig history’ written from the perspective of the victors or it leads to the accusation of relativism and to resistance from the scientists themselves. Isabelle Stengers claims that this resistance by scientists must be considered as an essential (...) element in the historiography of the sciences. She is part of a more recent generation of French philosophers of science, who build on the work of the earlier generation but with significant differences. Stengers interprets the scientist’s work as ‘in the service of history’: everyone must be forced to recognize their work not as the product of personal construction but as a necessary discovery in the history of science. The work of the historian of science is in conflict with the aims of the scientists themselves, who want to be seen as the norm of the present by which one should read the history of science. This service of history is not some external ideological factor, but an internal part of the scientific practice itself. The construction of the difference between the discovery of a pre-given fact and the construction of a fiction is for Stengers the core of the scientific practices. This use of history will be illustrated by the case of synthetic biology, as described by Bernadette Bensaude-Vincent. Synthetic biologists are invoking specific past or future scenario’s, such as that of synthetic chemistry or computer engineering, to legitimatize their current research projects and ambitions. From this perspective, the problematic tension between the past and the present is so hard to cope with because it is not merely a struggle among historians and philosophers of science, but also among the scientists themselves. (shrink)

Wie unterscheidet sich ein Betriebssystem wie bspw. Linux von einer Mikrobe? Der Beitrag untersucht, wie technische Objekte im »Jahrhundert der Biologie« aufgefasst werden. Anhand des Werks von Gilbert Simondon wird gefragt, welche Existenzweisen biotechnische Objekte aufweisen. Die Prozesse von Abstraktion und Konkretisierung, die auf dem Feld der Synthetischen Biologie stattfinden, können einen Weg aufweisen, diese Fragen zu beantworten. How does a computer operating system such as Linux differ from a microbe? This paper explores how technical objects are envisaged in the (...) »century of biology«. Via the work of Gilbert Simondon, it asks what modes of existence biotechnical objects will display. The processes of abstraction and concretisation taking place in the field of synthetic biology offer one way to address these questions. (shrink)

What is a language? What do scientific grammars tell us about the structure of individual languages and human language in general? What kind of science is linguistics? These and other questions are the subject of Ryan M. Nefdt's Language, Science, and Structure. -/- Linguistics presents a unique and challenging subject matter for the philosophy of science. As a special science, its formalisation and naturalisation inspired what many consider to be a scientific revolution in the study of mind and (...) language. Yet radical internal theory change, multiple competing frameworks, and issues of modelling and realism have largely gone unaddressed in the field. Nefdt develops a structural realist perspective on the philosophy of linguistics which aims to confront the aforementioned topics in new ways while expanding the outlook toward new scientific connections and novel philosophical insights. On this view, languages are real patterns which emerge from complex biological systems. Nefdt's exploration of this novel view will be especially valuable to those working in formal and computational linguistics, cognitive science, and the philosophies of science, mathematics, and language. (shrink)

Computing as a science is the study of computers, both the hardware and their programs, and all that goes with them (Newell and Simon 1976). The philosophy of computer science is concerned with problems of a philosophical kind raised by the discipline's goals, fundamental ideas, techniques or methods, and findings. It parallels other parts of philosophy ‐ for example, the philosophy of economics or linguistics or biology ‐ in primarily considering problems raised by one discipline, rather than issues (...) raised by a group of disciplines, as does the philosophy of science in general. (shrink)

If complexity is a necessary but not sufficient premise for the existence and expression of the living, anticipation is the distinguishing characteristic of what is alive. Anticipation is at work even at levels of existence where we cannot refer to intelligence. The prospect of artificially generating aesthetic artifacts and ethical constructs of relevance to a world in which the natural and the artificial are coexistent cannot be subsumed as yet another product of scientific and technological advancement. Beyond the artificial, the (...) synthetic conjures the understanding of aesthetics and ethics no longer from the perspective of the How? type of question, but rather the Why? Given the current infatuation with synthetic biology (i.e., making life from non-life), there is a practical consequence to such considerations. Synthetic life, as any other form of life, implies the possibility of evolution. Anticipation, which is the underlying factor of evolution, is thus expected. At the level of human existence, anticipation is expressed, for instance (but not exclusively), in aesthetic forms and ethical values. This translates, in turn, into an argument for the role aesthetics and ethics play in the process. Consequently, to qualify as life, the synthesis of the physical and the living will have to efficiently handle ambiguity. Current computational facilities, regardless of their nature or performance, operate exclusively in the semiotic domain of the well defined non-ambiguous. (shrink)

The metaphorical nature of biological language is examined and the use of metaphors for providing the linguistic context in which similarities and differences are made is described. Certain pervasive metaphors which are characterised by systemic properties are noted, and in order to provide some focus to the study, systemic metaphors associated with machine, text and organism are discussed. Other systemic metaphors such as society and circuit are also reported. Some details concerning interrelations between automaton and organism are presented in the (...) light of the previous discussion.An approach towards the analysis of biosystem metaphors is outlined which relates part-whole, organisational level and systemic metaphors in a single model. Examples are provided throughout the discussion and mainly come from computing. The potential for metaphorical transfers between these domains is considered. (shrink)

The computational program for theoretical neuroscience initiated by Marr and Poggio (1977) calls for a study of biological information processing on several distinct levels of abstraction. At each of these levels — computational (defining the problems and considering possible solutions), algorithmic (specifying the sequence of operations leading to a solution) and implementational — significant progress has been made in the understanding of cognition. In the past three decades, computational principles have been discovered that are common to a (...) wide range of functions in perception (vision, hearing, olfaction) and action (motor control). More recently, these principles have been applied to the analysis of cognitive tasks that require dealing with structured information, such as visual scene understanding and analogical reasoning. Insofar as language relies on cognition-general principles and mechanisms, it should be possible to capitalize on the recent advances in the computational study of cognition by extending its methods to linguistics. (shrink)

Synthetic biology, as a research field, brings together molecular life scientists, computational biologists, and social scientists to engineer biological systems toward societally desired goals. Given the field’s broad multidisciplinarity and relatively young age, innovative educational methods are required to provide students with the needed background knowledge to push the field forward in the future. The international Genetically Engineered Machine competition is such an example where education and high-level research merge, providing the synthetic biology field with (...) trained students, new ideas, and novel results. In the 2021 edition alone, 343 teams from across the world completed the competition to tackle societal problems with synthetic biology. As Wageningen University & Research celebrates 10 years of participation in iGEM, we share our thoughts and experiences on supervising iGEM teams, which is especially relevant to organizers of current and new teams, and also others interested in the iGEM competition. (shrink)

A new theoretical model of oncogenesis that incorporates a systemic view of biodynamics was developed and analyzed. According to our model, the emergent behavior at the cell population level is the result of nonlinear interactions between the neoplastic and immune subsystems. Our approach allows subsequent extensions of the model to span multiple levels of biological organization. The model opens the possibility of a flexible connection between the molecular and tissue level descriptions of oncogenesis.

This article considers naturalistic analyses of the concepts of health and disease in light of the possibility of constructing novel living systems. The article begins by introducing the vision of synthetic biology as the application of engineering principles to the construction of biological systems, the main analyses of the concepts of health and disease, and the standard theories of function in artefacts and organisms. The article then suggests that reflection on the possibility of artefactual organisms amounts to a (...) challenge to the functional theories of health and disease proposed by Wakefield and Boorse. More specifically, Wakefield and Boorse's theories are reconstructed as responses to a dilemma concerning how to allow for the ascription of health and disease to artefactual organisms without at the same time opening up the possibility of diseased nonliving artefacts such as cars and computers. It is argued that neither response will enable us to ascribe health and disease to artefactual organisms, because both theories, in order to rule out the possibility of ascribing health and disease to nonliving artefacts, make such ascriptions conditional on having a natural-selection history or being part of a species which has been designed by evolution. (shrink)

This volume comprises a selection of papers that were contributed to the 7th International Congress of Logic, Methodology and Philosophy of Science, which was held in Salzburg from the 11th - 16th July, 1983. There were 14 sections in this congress: 1. proof theory and foundations of mathematics 2. model theory and its applica ti on 3. recursion theory and theory of computation 4. axiomatic set theory 5. philosophical logic 6. general methodology of science 7. foundations of probability and induction (...) 8. foundations and philosophy of the physical sciences 9. foundati ons and phi 1 osophy of biology 10. foundations and philosophy of psychology foundations and philosophy 11. of the social sciences 12. foundati ons and philosophy of linguistics 13. history of logic, methodology and philosophy of science 14. fundamental principles of the ethics of science In each section, three or four invited addresses were given, which will be published in the Congress Proceedings (Ruth Barcan Marcus, Georg J. W. Dorn and Paul Weingartner, eds. : Logic, Metho dology and Philosophy of Science VII. Proceedings of the Seventh International Congress of Logic, Methodology and Philosophy of v PREFACE Science, Salzburg, 1983. - Amsterdam, New York, Oxford: North-Holland Publishing 'Company, 1985. ) Every section with the exception of section 14 also contained contributed papers. (shrink)

Language, according to Jackendoff, is more than just an instrument of communication and cultural transmission. It is also a tool which helps us to think. It does so, he suggests, by expanding the range of our conscious contents and hence allowing processes of attention and reflection to focus on items which would not otherwise be available for scrutiny. I applaud Jackendoff s basic vision, but raise some doubts concerning the argument. In particular, I wonder what it is about public language (...) that uniquely fits it to play the functional role which Jackendoff isolates — why couldn't expression in a private inner code induce the same computational benefits? I suggest a weaker position in which the communicative role of public language moulds it into a suitably expressive resource, such that natural language emerges as the logically and technologically contingent filler of a functional role which could, in principle, be filled by other means. I also compare and contrast Jackendoff's position with some related ideas due to Daniel Dennett and others, concluding with a sketch of my own view of language as an external artifact whose computational properties complement those of the basic biological brain. (shrink)

Language, according to Jackendoff, is more than just an instrument of communication and cultural transmission. It is also a tool which helps us to think. It does so, he suggests, by expanding the range of our conscious contents and hence allowing processes of attention and reflection to focus on items which would not otherwise be available for scrutiny. I applaud Jackendoff s basic vision, but raise some doubts concerning the argument. In particular, I wonder what it is about public language (...) that uniquely fits it to play the functional role which Jackendoff isolates — why couldn't expression in a private inner code induce the same computational benefits? I suggest a weaker position in which the communicative role of public language moulds it into a suitably expressive resource, such that natural language emerges as the logically and technologically contingent filler of a functional role which could, in principle, be filled by other means. I also compare and contrast Jackendoff's position with some related ideas due to Daniel Dennett and others, concluding with a sketch of my own view of language as an external artifact whose computational properties complement those of the basic biological brain. (shrink)

This paper offers a contribution to debates around integrative aspects of systems biology and engages with issues related to the circumstances under which physicists look at biological problems. We use oral history as one of the methodological tools to gather the empirical material, conducting interviews with physicists working in systems biology. The interviews were conducted at several institutions in Brazil, Germany, Israel and the U.S. Biological research has been increasingly dependent on computational methods, high-throughput technologies, and multidisciplinary (...) skills. Quantitative scientists are joining biological departments and collaborations between physicists and biologists are particularly vigorous. This state of affairs raises a number of questions, such as: What are the circumstances under which physicists approach biological problems in systems biology? What kind of interdisciplinary challenges must be tackled? The paper suggests that, concerning physicists’ move to work on biological systems, there are common reasons to move, the transition must be understood in terms of degrees, physicists have a rationale for simplifying systems, and distinct conceptions of model and modeling strategies are recurrent. We identified problems regarding linguistic clarity and integration of epistemological aims. We conclude that cultural unconformities within the systems biology community have important consequences to the flow of scientific knowledge. (shrink)

Descartes argued that productivity, namely our ability to generate an unlimited number of new thoughts or ideas from previous ones, derives from a single undividable source in the human soul. Cognitive scientists, in contrast, have viewed productivity as a modular phenomenon. According to this latter view, syntactic, semantic, musical or visual productivity emerges each from their own generative engines in the human brain. Recent evidence has, however, led some authors to revitalize the Cartesian theory. According to this view, a single (...) source or a single mechanism in the human brain produces productivity in every cognitive domain, whether in the domain of music, semantics or syntax. In this article, we will address recent evidence concerning the single source hypothesis from brain-imaging studies, linguistics, cognitive theories of music perception, biology of cognition and cognitive development, along with several objections that have been presented against this hypothesis. We formulate two versions of the Cartesian theory which combine the more recent computational theory of cognition with Descartes' view on productivity. (shrink)

Evolution exploits the physics of non‐neural bioelectricity to implement anatomical homeostasis: a process in which embryonic patterning, remodeling, and regeneration achieve invariant anatomical outcomes despite external interventions. Linear “developmental pathways” are often inadequate explanations for dynamic large‐scale pattern regulation, even when they accurately capture relationships between molecular components. Biophysical and computational aspects of collective cell activity toward a target morphology reveal interesting aspects of causation in biology. This is critical not only for unraveling evolutionary and developmental events, but (...) also for the design of effective strategies for biomedical intervention. Bioelectrical controls of growth and form, including stochastic behavior in such circuits, highlight the need for the formulation of nuanced views of pathways, drivers of system‐level outcomes, and modularity, borrowing from concepts in related disciplines such as cybernetics, control theory, computational neuroscience, and information theory. This approach has numerous practical implications for basic research and for applications in regenerative medicine and synthetic bioengineering. (shrink)

According to the so-called Quantum Darwinist approach, the emergence of “classical islands” from a quantum background is assumed to obey a principle of maximal information. We illustrate this idea by considering the coupling of two oscillators. As our approach suggests that the classical limit could have emerged throughout a long and progressive Evolution mechanism, it is likely that primitive living organisms behave in a “more quantum”, “less classical” way than more evolved ones. This brings us to seriously consider the possibility (...) to measure departures from classicality exhibited by biological systems. We describe an experimental proposal the aimed at revealing the presence of entanglement in the biophotonic radiation emitted by biological sources. (shrink)

The goal of synthetic biology is to create artificial organisms. To achieve this it is essential to understand what life is. Metabolism-replacement systems, or (M, R)-systems, constitute a theory of life developed by Robert Rosen, characterized in the statement that organisms are closed to efficient causation, which means that they must themselves produce all the catalysts they need. This theory overlaps in part with other current theories, including autopoiesis, the chemoton, and autocatalytic sets, all of them invoking some (...) idea of closure. A simple model of an (M, R)-system has been implemented in the computer, and behaves in ways that may shed light on the requirements for a prebiotic self-organizing system. In addition to a trivial steady state in which nothing happens, it can establish a non-trivial steady state in which all intermediates have finite concentrations, with their rates of degradation balanced by their rates of synthesis. The system can be regenerated from the set of food components plus a single intermediate, and maintain itself in that state indefinitely, despite continuous degradation. At the very low compartment volumes that may have existed in prebiotic conditions, for example in cavities in minerals, or in micelles formed by simple amphiphiles, statistical fluctuations in the numbers of molecules need to be taken into account. With the stochastic approach there is no non-trivial steady state in strict mathematical terms, because the system will always collapse to the trivial state after sufficient time. However, the average time before collapse is so long for volumes greater than $10^{-19}\;{\textsc{l}}$ (much smaller than the volume of the order of $10^{-15}\;{\textsc{l}}$ for a typical bacterial cell) that for practical purposes the self-maintaining state of non-null concentrations becomes significant, recalling the situation of bistability that is observed in deterministic analysis. In turn, there exists a minimum size below which the self-organizing system cannot maintain itself on chemically relevant time scales. The value of the critical volume depends on the particular concentrations and rate constants assumed, but the principle could apply generally. (shrink)

In this paper I aim to defend a twofold thesis. On one hand, I will sup-port, against Perini [7], the indispensability of diagrams when structurally complex biomolecules are concerned, since it is not possible to satisfactorily use linguistic-sentential representations at that domain. On the other hand, even when diagrams are dispensable I will defend than they will generally be more effective than other representations in encoding biomolecular knowledge, relying on Kulvicki-Shimojima’s diagrammatic effectiveness thesis. Finally, I will ground many epistemic virtues (...) of biomolecular diagrams (understandability, explanatory power, prediction and hypothesis evaluation) on their cognitive-computational indispensability and their semantic-epistemic effectiveness. (shrink)

The papers in this series of five volumes provide a snapshot of current trends in European Cognitive Science. Each of the volumes deals with problems in cognitive science from a different perspective, covering the interacting disciplines of cognitive psychology, logic and linguistics, human-computer interaction, neuroscience and artificial intelligence respectively. Linguistics is concerned with the structure and use of languages, and logic with the form and correctness of argumentation in ordinary and scientific language. The two fields are presented with (...) respect to their role in cognitive science and artificial intelligence: How are they realised by psychological mechanisms or biological processes on the one hand or programmed or wired in machines on the other. The contributions in this volume give introductions to the state-of-the-art, emphasizing the analysis of complexity and flexibility in logic and language in the framework of classical approaches (Chapters 3, 4, 5, 7). At the same time some contributions present a broader perspective in which an integration of the formal structure with the structure of the processing systems might be possible (Chapters 2 & 6). In this context, the differences and the perspectives of the classical approaches on the one hand and of connectionist approaches on the other are compared. (Chapters 1 & 6).contributions present a broader perspective in which an integration of the formal structure with the structure of the processing systems might be possible (Chapters 2 & 6). In this context, the differences and the perspectives of the classical approaches on the one hand and of connectionist approaches on the other are compared. (Chapters 1 & 6). (shrink)

The ArgumentThis paper focuses on the opening of a discursive space: the emergence of informational and scriptural representations of life and their self-negating consequences for the construction of biological meaning. It probes the notion of writing and the book of life and shows how molecular biology's claims to a status of language and texuality undermines its own objective of control. These textual significations were historically contingent. The informational representations of heredity and life were not an outcome of the internal (...) cognitive momentum of molecular biology; they were not a logical necessity of the unravelling of the base-pairing of the DNA double-helix. They were transported into molecular biology still within the protein paradigm of the gene in the 1940s and permeated nearly every discipline in the life and social sciences. These information-based models, metaphors, linguistic, and semiotic tools which were central to the formulation of the genetic code were transported into molecular biology from cybernetics, information theory, electronic computing, and control and communication systems — technosciences that were deeply embedded with the military experiences of world war II and the Cold War. The information discourse thus became fixed in molecular biology not because it worked in the narrow epistemic sense (it did not), but because it positioned molecular biology within postwar discourse and culture, perhaps within the transition to a post-modern information-based society. (shrink)

The first promising results from “streamlined,” minimal genomes tend to support the notion that these are a useful tool in biological systems engineering. However, compared with the speed with which genomic microbial sequencing has provided us with a wealth of data to study biological functions, it is a slow process. So far only a few projects have emerged whose synthetic ambition even remotely matches our analytic capabilities. Here, we survey current technologies converging into a future ability to engineer large‐scale (...) biological systems. We argue that the underlying synthetic technology, de novo DNA synthesis, is already rather mature – in particular relative to the scope of our current synthetic ambitions. Furthermore, technologies towards rationalizing the design of the newly synthesized DNA fragment are emerging. These include techniques to implement complex regulatory circuits, suites of parts on a DNA and RNA level to fine tune gene expression, and supporting computational tools. As such DNA fragments will, in most cases, be destined for operating in a cellular context, attention has to be paid to the potential interactions of the host with the functions encoded on the engineered DNA fragment. Here, the need of biological systems engineering to deal with a robust and predictable bacterial host coincides with current scientific efforts to theoretically and experimentally explore minimal bacterial genomes. (shrink)

A range of views on the morality of synthetic biology and its place in public policy and political discourse.

The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including (...) transporters and the ribosome construction machinery, behave as would behave a material implementation of the informationmanaging agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell’s demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy-efficient way that is vastly better than our contemporary computers. (shrink)

The present study explores the idea that human linguistic communication co-opted a pre-existing population-wide behavioural system that was shared among social group members and whose structure reflected the structure of the environment. This system is hypothesized to have emerged from interactions among individuals who had evolved the capacity to imitate arbitrary, functionless behaviour. A series of agent-based computer simulations test the separate and joint effects of imitation, pattern completion behaviour, environment structure and level of social interaction on such a population-wide (...) behavioural system. The results support the view that a system that could be co-opted for linguistic communication might arise in a population of agents equipped with arbitrary imitation for the purposes of pattern completion interacting in certain kinds of structured environments. Such pre-linguistic behavioural system could have bootstrapped communication and paved the way for biological capacities widely believed to be necessary for communication, such as shared intentionality and symbolicity, to evolve. (shrink)

The development of form in living organisms continues to challenge biological research. The concept of biological information encoded in the genetic program that controls development forms a major part of the semiotic metaphor in biology. Development is here seen in analogy to an execution of a program, written in a formal language in the computer. Other versions of the semiotic or "nature-as-language" metaphor use other formal or informal aspects of language to comprehend the specific structural relations in nature as (...) explored by molecular and evolutionary biology. This intuitively appealing complex of related ideas, which has a long history in the philosophy of nature and biology, is critically reviewed. The general nature of metaphor in science is considered, and different levels of metaphorical transfer of signification is distinguished. It is argued, that the metaphors may be of considerable value, not only heuristically, but in order to comprehend the irreducible nature of living organisms. In arguing for a semiotic perspective on living nature, it makes a marked difference whether the departure is made from the tradition of F. de Saussure´s structural linguistics or from the tradition of general semiotics of C. S. Peirce. An agenda is made for a Peircean perspective on the semiotics of nature. (shrink)

Synthetic biology presents a challenge to traditional accounts of biology: Whereas traditional biology emphasizes the evolvability, variability, and heterogeneity of living organisms, synthetic biology envisions a future of homogeneous, humanly engineered biological systems that may be combined in modular fashion. The present paper approaches this challenge from the perspective of the epistemology of technoscience. In particular, it is argued that synthetic-biological artifacts lend themselves to an analysis in terms of what has been called (...) ‘thing knowledge’. As such, they should neither be regarded as the simple outcome of applying theoretical knowledge and engineering principles to specific technological problems, nor should they be treated as mere sources of new evidence in the general pursuit of scientific understanding. Instead, synthetic-biological artifacts should be viewed as partly autonomous research objects which, qua their material-biological constitution, embody knowledge about the natural world—knowledge that, in turn, can be accessed via continuous experimental interrogation. (shrink)

Synthetic biology is an increasingly high-profile area of research that can be understood as encompassing three broad approaches towards the synthesis of living systems: DNA-based device construction, genome-driven cell engineering and protocell creation. Each approach is characterized by different aims, methods and constructs, in addition to a range of positions on intellectual property and regulatory regimes. We identify subtle but important differences between the schools in relation to their treatments of genetic determinism, cellular context and complexity. These distinctions (...) tie into two broader issues that define synthetic biology: the relationships between biology and engineering, and between synthesis and analysis. These themes also illuminate synthetic biology's connections to genetic and other forms of biological engineering, as well as to systems biology. We suggest that all these knowledge-making distinctions in synthetic biology raise fundamental questions about the nature of biological investigation and its relationship to the construction of biological components and systems. (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)

Synthetic biology aims at making life easier to an engineer by applying biotechnology engineering principles such as standardization and modularity. I argue that living organisms are inherently non-machine, non-standardized entities and that the current state-of-the-art in SynBio combines pre- and post-standardization efforts, in a scenario without evidence that full standardization in biology is even possible. I finally propose a new view on SynBio based on purpose rather than on technicalities.

It has become commonplace to say that with the advent of technologies like synthetic biology the line between artifacts and living organisms, policed by metaphysicians since antiquity, is beginning to blur. But that line began to blur 10,000 years ago when plants and animals were first domesticated; and has been thoroughly blurred at least since agriculture became the dominant human subsistence pattern many millennia ago. Synthetic biology is ultimately only a late and unexceptional offshoot of this (...) prehistoric development. From this perspective, then, synthetic biology is a red herring, distracting us from more thorough philosophical consideration of the most truly revolutionary human practice—agriculture. In the first section of this paper I will make this case with regard to ontology, arguing that synthetic biology crosses no ontological lines that were not crossed already in the Neolithic. In the second section I will construct a parallel case with regard to cognition, arguing that synthetic biology as biological engineering represents no cognitive advance over what was required for domestication and the new agricultural subsistence pattern it grounds. In the final section I will make the case with regard to human existence, arguing that synthetic biology, even if wildly successful, is not in a position to cause significant existential change in what it is to be human over and above the massive existential change caused by the transition to agriculture. I conclude that a longer historical perspective casts new light on some important issues in philosophy of technology and environmental philosophy. (shrink)