The interests of synthetic biologists may appear to differ greatly from those of evolutionary biologists. The engineering of organisms must be distinguished from the tinkering action of evolution; the ambition of synthetic biologists is to overcome the limits of natural evolution. But the relations between synthetic biology and evolutionary biology are more complex than this abrupt opposition: Synthetic biology may play an important role in the increasing interactions between functional and evolutionary biology. In practice, (...) synthetic biologists have learnt to submit the proteins and modules they construct to a Darwinian process of selection that optimizes their functioning. More importantly, synthetic biology can provide evolutionary biologists with decisive tools to test the scenarios they have elaborated by resurrecting some of the postulated intermediates in the evolutionary process, characterizing their properties, and experimentally testing the genetic changes supposed to be the source of new morphologies and functions. This synthetic, experimental evolution will renew and clarify many debates in evolutionary biology: It will lead to the explosion of some vague concepts as constraints, parallel evolution, and convergence, and replace them with precise mechanistic descriptions. In this way, synthetic biology resurrects the old philosophical debate about the relations between the real and the possible. (shrink)

RésuméIl n'y a pas de sujet plus idoine à justifier la philosophie ouverte qui est celle de Dialectica que l'étude de l'évolution du concept de raison dans la pensée occidentale.C'est avec la création de la géométrie déductive que le mot raison prit un sens chez les Grecs du ***Ve siècle av. J.‐C. A l'évidence sensible qui résulte du témoignage de nos sens et ne constate que le comment d'un fait observé, les géomètres grecs substituent l'évidence intelligible qui en explique le (...) pourquoi, en montrant qu'il est la conséquence nécessaire d'un petit nombre de propositions admises comme évidentes. S'élevant du concret à l'abstrait, ils dégagent l'essence intelligible de l'accident sensible et substituent au réel le possible. Les disciplines empiriques des Orientaux font place aux sciences théoriques et explicatives: l'astronomie, la mécanique, l'optique, la théorie musicale. Toutefois, au lieu de voir dans les concepts mathématiques une création de l'esprit, les penseurs‐géomètres de la Grèce les assimilent à une découverte par les yeux de l'ǎme d'essences préexistantes. Ils méprisèrent, en outre, les applications pratiques qui seules peuvent stimuler les sciences expérimentales. De là procèdent les limites, puis l'arrět de la science hellénique.Les conquětes d'Alexandre déversèrent sur l'Occident méditerranéen les religions de salut de l'Orient. A la recherche désintéressée du vrai se substitue la gnose, la révélation de mystères transcendants à la raison. Lorsque le message chrétien devint une philosophie puis une théologie, on en vint à distinguer » la démonstration hellénique « par le raisonnement et la dialectique, et » la démonstration hébraique « par les prophéties et les miracles des articles de la foi. La Scolastique rechercha l'accord de la raison et de la foi, en entendant par raison l'apport de la science et de la philosophie helléniques, assimilées, à partir du XIIIe siècle dans la Latinité, à l'encyclopédie aristotélicienne. La Scolastique échoua dans cette tentative. La doctrine de » la double vérité « fut l'aveu de cette impuissance.Pour se libérer de la mentalité scolastique, il fallut s'affranchir dans l'étude des phénomènes naturels de l'autorité d'Aristote, du joug de la théologie et parvenir à une théorie correcte de la connaissance, en particulier de la valeur des idées abstraites et de la distinction des vérités formelles et des vérités empiriques. Il fallut interpréter comme une création de l'esprit ce que les Grecs assimilaient à une découverte de vérités préexistantes. La désagrégation de l'a priori synthétique, conçu à la façon des Cartésiens et des Kantiens, conduit à se demander ce qui subsiste des exigences a priori de la raison. C'est à quoi s'évertue de répondre la dernière partie de l'article.ZusammenfassungEs gibt keinen geeigneteren Gegenstand zur Rechtfertigung der offenen Philosophie, die von der Dialectica vertreten wird, als das Studium der Entwicklung des Vernunftsbegriffes im abendländischen Denken.Mit der Entstehung der deduktiven Geometrie erhält das Wort Vernunft bei den Griechen des 5. Jahrhunderts vor Christo einen Sinn. An Stelle der gefühlsmässigen Evidenz, die auf der Gewissheit unserer Sinne beruht und lediglich das Wieeiner beobachteten Tatsache feststellt, setzen die griechischen Geometer die logische Evidenz, die das Warum erklärt, indem sie zeigt, dass es eine Folge einer kleinen Zahl von Voraussetzungen ist, die als evident angesehen werden können. Sich vom Konkreten zum Abstrakten erhebend, befreien sie das intelligible Wesen von der Zufälligkeit des Sinnlichen und ersetzen das Reelle durch das Mögliche. Die empirischen Disziplinen der Morgenländer schaffen Platz für die theoretischen und erklärenden Wissenschaften wie Astronomie, Mechanik, Optik, Musiktheorie. Immerhin, anstatt in den mathematischen Konzepten eine Schöpfung des Geistes zu sehen, setzen die geometrischen Denker Griechenlands diese der Entdeckung präexistenter Essenzen durch die Augen der Seele gleich. Sie verachten im übrigen die praktischen Anwendungen, die nur die Experimentalwissen‐schaften anregen können. Daher kommt es, dass die griechische Wissenschaft bei einer gewissen Grenze Halt machen musste.Die Schlachten Alexanders verschlangen im Abendland des Mittelmeeres die Heilsreligionen des Orients. An Stelle des uneigennützigen Suchens nach der Wahrheit tritt die Gnosis, das Erheben des mysteriös‐Transzendenten in den Bereich der Vernunft. Als die christliche Botschaft eine Philosophie, darauf eine Theologie wurde, begann man zu unterscheiden zwischen der » griechischen Beweisführung « mittels Vernunft und Dialektik und der » hebräischen Beweisführung « mittels Prophezeiungen und Wundern des zu Glaubenden. Die Scholastik forschte nach dem Zusammenhang zwischen Vernunft und Glaube, indem sie unter Vernunft den Beitrag der griechischen Wissenschaft und Philosophie verstand, der Aristotelischen Enzyklopädie angeglichen in der Folgezeit des 13. Jahrhunderts im Römischen Reich. Die Scholastik scheiterte in diesem Versuch. Die Lehre der » doppelten Wahrheit « war das Geständnis dieses Unvermögens.Um sich von der scholastischen Mentalität zu befreien, hiess es sich im Studium der Naturereignisse von der Autorität des Aristoteles befreien, vom Joch der Theologie und zu einer korrekten Theorie der Erkenntnis zu gelangen, speziell des Wertes der abstrakten Ideen und der Unterscheidung zwischen formellen und empirischen Wahrheiten. Was die Griechen einer Entdeckung von präexistenten Wahrheiten gleichsetzten, musste als Schöpfung des Geistes interpretiert werden. Die Desagregation des synthetischen Apriori, aufgefasst im Sinne von Descartes und Kant, führte zur Frage, was vorhanden sei von den apriori‐Erfordernissen der Vernunft.Dies zu beantworten, bemüht sich der letzte Teil des Artikels.There is no subject more suitable to the open philosophy of Dialectica than the study of the development of the concept of reason in Western thought.The word » reason « acquired a meaning with the creation of deductive geometry by the Greeks of the Vth cent. B. C. These geometers substituted for the sensible evidence, which only establishes the » what « of an observed fact, the intelligible evidence which explains the » why « of such an observed fact, by showing that it is the necessary result of a small number of statements, accepted as self‐evident. Rising from the concrete to the abstract, the geometers isolated the intelligible essence from the sensible accident, and substituted for the real the possible. The empirical technics of the Orientals made place for the theoretical sciences of the Greeks: astronomy, mechanics, optics and musical theory. Instead, however, of seeing mathematical concepts as creations of the mind, the Greek geometers considered them as preexisting entities, discovered by the eyes of the soul. They furthermore disregarded the practical applications which alone can stimulate experimental sciences. These were the limitations and the causes of the eventual end of hellenic science.The conquests of Alexander brought to the Western Mediterranean the religions of salvation of the East. The gnose, revelation of mysteries transcending reason, took the place of the disinterested search for truth. As the Christian message became a philosophy and then a theology, the distinction came to be made between the » hellenic demonstration of the faith « by logic and dialectics, and the » hebrew demonstration « by the prophecies and the miracles. The scholastics sought to reconcile reason with faith, by defining reason as the legacy of Greek science and philosophy, identified, after the XIIIth century, with the Aristotelian Encyclopedia. They failed in this endeavour. The doctrine of the » double truth « was the admission of this failure.In order to progress beyond the scholastic outlook, it was necessary to reject the precepts of Aristotle in the study of natural phenomena, to become free of the tyranny of theology, to develop a correct theory of knowledge, especially as regards the role of abstract ideas and the distinction between formal and empirical truths. It was necessary to interpret as a creation of the mind what the Greeks considered the discovery of preexisting truths. The breakdown of the synthetic apriori of the Cartesians and the Kantians leads one to wonder what remains of the a priori requisites of reason. The last part of the article suggests an answer to this question. (shrink)

Social robotics entertains a particular relationship with anthropomorphism, which it neither sees as a cognitive error, nor as a sign of immaturity. Rather it considers that this common human tendency, which is hypothesized to have evolved because it favored cooperation among early humans, can be used today to facilitate social interactions between humans and a new type of cooperative and interactive agents - social robots. This approach leads social robotics to focus research on the engineering of robots that activate anthropomorphic (...) projections in users. The objective is to give robots "social presence" and "social behaviors" that are sufficiently credible for human users to engage in comfortable and potentially long-lasting relations with these machines. This choice of ’applied anthropomorphism’ as a research methodology exposes the artifacts produced by social robotics to ethical condemnation: social robots are judged to be a "cheating" technology, as they generate in users the illusion of reciprocal social and affective relations. This article takes position in this debate, not only developing a series of arguments relevant to philosophy of mind, cognitive sciences, and robotic AI, but also asking what social robotics can teach us about anthropomorphism. On this basis, we propose a theoretical perspective that characterizes anthropomorphism as a basic mechanism of interaction, and rebuts the ethical reflections that a priori condemns "anthropomorphism-based" social robots. To address the relevant ethical issues, we promote a critical experimentally based ethical approach to social robotics, "synthetic ethics," which aims at allowing humans to use social robots for two main goals: self-knowledge and moral growth. (shrink)

Biologists in the last 50 years have increasingly emphasized the role of historical contingency in explaining the distribution and dynamics of biological systems. However, recent work in philosophy of biology has shown that historical contingency carries various interpretations and that we are still lacking a general understanding of historicity, i.e., a framework from which to interpret why and to what extent history matters in biological processes. Building from examples and analyses of the long-term experimental evolution (LTEE) project, this (...) paper argues that historicity possess three essential conditions: (1) multiple possible pasts, (2) multiple possible outcomes at a given instant, and (3) a relationship of causal dependence between these two sets. These criteria can be further specified in two general forms of historicity: dependence on initial conditions and path dependence. More attention is devoted to developing a rigorous account of the latter, which captures the type of historicity displayed by stochastic processes. This paper also highlights that it is often more productive to adopt an instant-relative approach and think in terms of degree of historicity instead of trying to maintain a rigid and absolute dichotomy between historical and ahistorical (completely convergent) processes. (shrink)

The premise of biological modularity is an ontological claim that appears to come out of practice. We understand that the biological world is modular because we can manipulate different parts of organisms in ways that would only work if there were discrete parts that were interchangeable. This is the foundation of the BioBrick assembly method widely used in synthetic biology. It is one of a number of methods that allows practitioners to construct and reconstruct biological pathways and devices using (...) DNA libraries of standardized parts with known functions. In this paper, we investigate how the practice of synthetic biology reconfigures biological understanding of the key concepts of modularity and evolvability. We illustrate how this practice approach takes engineering knowledge and uses it to try to understand biological organization by showing how the construction of functional parts and processes can be used in synthetic experimental evolution. We introduce a new approach within synthetic biology that uses the premise of a parts-based ontology together with that of organismal self-organization to optimize orthogonal metabolic pathways in E. coli. We then use this and other examples to help characterize semisynthetic categories of modularity, parthood, and evolvability within the discipline. (shrink)

The increasing place of evolutionary scenarios in functional biology is one of the major indicators of the present encounter between evolutionary biology and functional biology (such as physiology, biochemistry and molecular biology), the two branches of biology which remained separated throughout the twentieth century. Evolutionary scenarios were not absent from functional biology, but their places were limited, and they did not generate research programs. I compare two examples of these past scenarios with two present-day ones. At least three characteristics distinguish (...) present and past efforts: An excellent description of the systems under study, a rigorous use of the evolutionary models, and the possibility to experimentally test the evolutionary scenarios. These three criteria allow us to distinguish the domains in which the encounter is likely to be fruitful, and those where the obstacles to be overcome are high and in which the proposed scenarios have to be considered with considerable circumspection. (shrink)

Discussions of reproducibility are casting doubts on the credibility of experimental outcomes in the life sciences. Although experimental evolution is not typically included in these discussions, this field is also subject to low reproducibility, partly because of the inherent contingencies affecting the evolutionary process. A received view in experimental studies more generally is that standardization (i.e., rigorous homogenization of experimental conditions) is a solution to some issues of significance and internal validity. However, this solution hides (...) several difficulties, including a reduction of external validity and reproducibility. After explaining the meaning of these two notions in the context of experimental evolution, we import from the fields of animal research and ecology and suggests that systematic heterogenization of experimental factors could prove a promising alternative. We also incorporate into our analysis some philosophical reflections on the nature and diversity of research objectives in experimental evolution. (shrink)

In this paper the relationship between phenomenology of perception and synthetic phenomenology is discussed. Synthetic phenomenology is presented on the basis of the issues in A.I. and Robotics that required to address the question of what enables artificial agents to have phenomenal access to the environment. Phenomenology of perception is construed as a theory with autonomous structure and domain, which can be embedded in a philosophical as well as a scientific theory. Two attempts at specifying the phenomenal content (...) of artificial agents are discussed. Concepts and experimental evidence on the independence of perception and the coordination of motion and appearances are set out to submit that phenomenology of perception makes a contribution to synthetic phenomenology. (shrink)

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio‐engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to (...) synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine‐tuning through evolution is suggested. (shrink)

Since the 1940s, microbiologists, biochemists and population geneticists have experimented with the genetic mechanisms of microorganisms in order to investigate evolutionary processes. These evolutionary studies of bacteria and other microorganisms gained some recognition from the standard-bearers of the modern synthesis of evolutionary biology, especially Theodosius Dobzhansky and Ledyard Stebbins. A further period of post-synthesis bacterial evolutionary research occurred between the 1950s and 1980s. These experimental analyses focused on the evolution of population and genetic structure, the adaptive gain of (...) new functions, and the evolutionary consequences of competition dynamics. This large body of research aimed to make evolutionary theory testable and predictive, by giving it mechanistic underpinnings. Although evolutionary microbiologists promoted bacterial experiments as methodologically advantageous and a source of general insight into evolution, they also acknowledged the biological differences of bacteria. My historical overview concludes with reflections on what bacterial evolutionary research achieved in this period, and its implications for the still-developing modern synthesis. (shrink)

Few topics have intrigued biologists as much as the evolution of sex. Understanding why sex persists despite its costs requires not just rigorous theoretical study, but also empirical data on related fundamental issues, including the nature of genetic variance for fitness, patterns of genetic interactions, and the dynamics of adaptation. The increasing feasibility of examining genomes in an experimental context is now shedding new light on these problems. Using this approach, McDonald et al. recently demonstrated that sex uncouples (...) beneficial and deleterious mutations, allowing selection to proceed more effectively with sex than without. Here we discuss the insights provided by this study, along with other recent empirical work, in the context of the major theoretical models for the evolution of sex. (shrink)

Several paleontologists have recently challenged the explanatory adequacy of the modern synthetic theory of evolution. Their position is that, contrary to the prevailing view that evolutionary change is gradual, the fossil record manifests long periods of species stasis (equilibrium) punctuated by periods of rapid species formation. And, they argue, this punctuated equilibria pattern challenges the gradualist, adaptationist and extrapolationist assumptions of the modern synthetic theory of evolution and supports a hierarchical, non-extrapolationist (non-reductionist) view of evolution. (...) In this paper I argue that the challenge rests on an inadequate characterization of the modern synthetic theory and that, even accepting punctuated equilibria and an irreducible evolutionary hierarchy, the modern synthetic theory is adequate to explain evolutionary change at all levels of the hierarchy. (shrink)

Several paleontologists have recently challenged the explanatory adequacy of the modern synthetic theory of evolution. Their position is that, contrary to the prevailing view that evolutionary change is gradual, the fossil record manifests long periods of species stasis punctuated by periods of rapid species formation. And, they argue, this punctuated equilibria pattern challenges the gradualist, adaptationist and extrapolationist assumptions of the modern synthetic theory of evolution and supports a hierarchical, non-extrapolationist view of evolution. In this (...) paper I argue that the challenge rests on an inadequate characterization of the modern synthetic theory and that, even accepting punctuated equilibria and an irreducible evolutionary hierarchy, the modern synthetic theory is adequate to explain evolutionary change at all levels of the hierarchy. (shrink)

The theory of evolution has beenused in arguments regarding animalexperimentation. Two such arguments areanalyzed, one against and one in favor. Eachargument stresses the relevance of the theoryof evolution to normative ethics but attemptsexplicitly to avoid the so-called naturalisticfallacy.According to the argument against animalexperimentation, the theory of evolution`undermines' the idea of a special humandignity and supports `moral individualism'. Thelatter view implies that if it is wrong to usehumans in experiments, then it is also wrong touse animals, unless there (...) are relevantdifferences between them that justify adifference in treatment. No such differencescan be found with regard to animals which lead`biographical lives'.The argument in favor of animal experimentationis based on evolutionary psychology. It statesthat humans, as all social animals, arespeciesist by nature and stresses that thisshould be taken seriously in normative ethics.This does not mean that animal interests shouldnot be considered, only that vital humaninterests may outweigh them.In order to assess the arguments, one has totake a stand on certain more basic issues: `is'versus `ought', impartiality versus specialobligations, and feelings/intuitions versusreason. Given the author's own position withregard to these more basic considerations, theevolutionary argument in favor of animalexperimentation is judged to be more convincingthan the one against but not decisive. It isalso maintained that not all animal experimentsare acceptable. Which animal experiments areacceptable and which are not has to be decidedon a case-by-case basis. (shrink)

This study explores the history of nanotechnology from the perspective of protein engineering, which differs from the history of nanotechnology that has arisen from mechanical and materials engineering; it also demonstrates points of convergence between the two. Focusing on directed evolution—an experimental system of molecular biomimetics that mimics nature as an inspiration for material design—this study follows the emergence of an evolutionary experimental system from the 1960s to the present, by detailing the material culture, practices, and techniques (...) involved. Directed evolution, as an aspect of nanobiotechnology, is also distinct from the dominant biotechnologies of the 20th century. The experimental systems of directed evolution produce new ways of thinking about molecular diversity that could affect concepts concerning both biology and life. (shrink)

Synthetic biology is a dynamic, young, ambitious, attractive, and heterogeneous scientific discipline. It is constantly developing and changing, which makes societal evaluation of this emerging new science a challenging task, prone to misunderstandings. Synthetic biology is difficult to capture, and confusion arises not only regarding which part of synthetic biology the discussion is about, but also with respect to the underlying concepts in use. This book offers a useful toolbox to approach this complex and fragmented field. It (...) provides a biological access to the discussion using a 'layer' model that describes the connectivity of synthetic or semisynthetic organisms and cells to the realm of natural organisms derived by evolution. Instead of directly reviewing the field as a whole, firstly our book addresses the characteristic features of synthetic biology that are relevant to the societal discussion. Some of these features apply only to parts of synthetic biology, whereas others are relevant to synthetic biology as a whole. In the next step, these new features are evaluated with respect to the different areas of synthetic biology. Do we have the right words and categories to talk about these new features? In the third step, traditional concepts like "life" and "artificiality" are scrutinized with regard to their discriminatory power. This approach may help to differentiate the discussion on synthetic biology. Lastly our refined view is utilized for societal evaluation. We have investigated the public views and attitudes to synthetic biology. It also includes the analysis of ethical, risk and legal questions, posed by present and future practices of synthetic biology. This book contains the results of an interdisciplinary research project and presents the authors' main findings and recommendations. They are addressed to science, industry, politics and the general public interested in this upcoming field of biotechnology. (shrink)

The comparison between natural evolution and the action of a tinkerer has become highly popular since its reintroduction by François Jacob at the end of the 1970s. It has been used as a weapon against the existence of an “intelligent design” as well as a way for synthetic biologists to promote their ambitious projects. I will describe the complex history of this metaphor, and examine its pertinence. Whereas Darwin considered it as a way to describe how evolution (...) proceeded, Jacob linked it with a description of the imperfections of organisms, while Stephen Jay Gould and Richard Lewontin criticized what they called the “Panglossian” vision of most evolutionary biologists. The distinction between the work of engineers and that of tinkerers is not obvious. There are limits to the process of evolution, but their alleged description so far reflects the limits of knowledge on the part of evolutionary biologists more than the existence of true barriers to the evolutionary process. And, in their work, synthetic biologists crucially need the optimizing action of natural selection. To give a definition of synthetic biology is no easy task; the false distinction drawn between the work of synthetic biologists and the action of evolution is of no help. (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)

Experimental modeling in biology involves the use of living organisms (not necessarily so-called "model organisms") in order to model or simulate biological processes. I argue here that experimental modeling is a bona fide form of scientific modeling that plays an epistemic role that is distinct from that of ordinary biological experiments. What distinguishes them from ordinary experiments is that they use what I call "in vivo representations" where one kind of causal process is used to stand in for (...) a physically different kind of process. I discuss the advantages of this approach in the context of evolutionary biology. (shrink)

Maintaining the coherence of the distinction between nature and artefact has long been central to environmental thinking. By building genomes from scratch out of 'bio-bricks', synthetic biology promises to create biotic artefacts markedly different from anything created thus far in biotechnology. These new biotic artefacts depart from a core principle of Darwinian natural selection – descent through modification – leaving them with no causal connection to historical evolutionary processes. This departure from the core principle of Darwinism presents a challenge (...) to the normative foundation of a number of leading positions in environmental ethics. As a result, environmental ethicists with a commitment to the normative significance of the historical evolutionary process may see synthetic biology as a moral 'line in the sand'. (shrink)

No single theory so far proposed gives a wholly satisfactory account of the origin and maintenance of bird-song dialects. This failure is the consequence of a weak comparative literature that precludes careful comparisons among species or studies, and of the complexity of the issues involved. Complexity arises because dialects seem to bear upon a wide range of features in the life history of bird species. We give an account of the principal issues in bird-song dialects: evolution of vocal learning, (...) experimental findings on song ontogeny, dialect descriptions, female and male reactions to differences in dialect, and population genetics and dispersal.We present a synthetic theory of the origin and maintenance of song dialects, one that accommodates most of the different systems reported in the literature. The few data available suggest that large, regional dialect populations are genetically differentiated; this pattern is correlated with reduced dispersal between dialects, assortative mating by females, and male-male exclusion. At the same time, “subdialects” may be formed within regional dialects. Subdialect clusters are usually small and may represent vocal mimicry among a few adjacent territorial males. The relative importance of genetic and social adaptation may contribute to the emergence of subdialects; their distinctiveness may be correlated with the degree of polygyny, for example. Thus, subdialect formation is linked to one theory of the evolution of repertoire size, but data are too fragmentary to examine this idea critically. (shrink)

In this short contribution we explore the historical roots of recent synthetic approaches in biology and try to assess their real potential, as well as identify future hurdles or the reasons behind some of the main difficulties they currently face. We suggest that part of these difficulties might not be just the result of our present lack of adequate technical skills or understanding, but could spring directly from the nature of the biological phenomenon itself. In particular, if life is (...) conceived as autonomy in open-ended evolution, which would help to explain the highly complex and dynamic organization of the simplest known organisms (i.e., genetically-instructed cellular metabolisms), external synthetic implementations of such systems, or interventions on them, are bound to interfere with some of their characteristic transformation processes, both at the ontogenetic and phylogenetic scales. In any case, this will prove very revealing and productive, technologically and scientifically speaking, since the knowledge gathered from those implementations/interventions will be extremely valuable in establishing our capacities and limitations to fully comprehend, utilize, and expand the living domain as we know it today. (shrink)

Probably the most distinctive feature of synthetic biology is its being “synthetic” in some sense or another. For some, synthesis plays a unique role in the production of knowledge that is most distinct from that played by analysis: it is claimed to deliver knowledge that would otherwise not be attained. In this contribution, my aim is to explore how synthetic biology delivers knowledge via synthesis, and to assess the extent to which this knowledge is distinctly synthetic. (...) On the basis of distinctions between knowledge-how and knowledge-why, and between syntheses that succeed and syntheses that fail, I argue that the contribution of synthesis to knowledge is best understood when syntheses are construed as experimental interventions that aim at probing causal relationships between properties of the entities that are combined through these syntheses and properties of their target products. The distinctiveness of synthetic biology in its quest for knowledge through synthesis stems from its ability to sample at will a space of empirical possibilities that is not only huge but also that has been so scarcely sampled by nature. (shrink)

The recent discussion of fictional models has focused on imagination, implicitly considering fictions as something nonconcrete. We present two cases from synthetic biology that can be viewed as concrete fictions. Both minimal cells and alternative genetic systems are modal in nature: they, as well as their abstract cousins, can be used to study unactualized possibilia. We approach these synthetic constructs through Vaihinger’s notion of a semi-fiction and Goodman’s notion of semifactuality. Our study highlights the relative existence of such (...) concrete fictions. Before their realizations neither minimal cells nor alternative genetic systems were any well-defined objects, and the subsequent experimental work has given more content to these originally schematic imaginings. But it is as yet unclear whether individual members of these heterogeneous groups of somewhat functional synthetic constructs will eventually turn out to be fully realizable, remain only partially realizable, or prove outright impossible. (shrink)

In this essay, I discuss Dennett’s From Bacteria to Bach and Back: The Evolution of Minds and Godfrey Smith’s Other Minds: The Octopus and The Evolution of Intelligent Life from a methodological perspective. I show that these both instantiate what I call ‘synthetic philosophy.’ They are both Darwinian philosophers of science who draw on each other’s work. In what follows I first elaborate on synthetic philosophy in light of From Bacteria and Other Minds; I also explain (...) my reasons for introducing the term; and I close by looking at the function of Darwinism in contemporary synthetic philosophy. (shrink)

The paper tries to show that an evolutionary perspective helps us to address what is called the adaptation problem, that is, the remarkable coherence, and seemingly successful design, existing between our cognitive tools and the phenomena of the material world. It argues that a fine-grained description of the structure and function of experimental techniques—as a special type amongst evolving scientific practices—is a condition for a better understanding and, ultimately, an explanation of how adaptation among the heterogeneous elements of (...) class='Hi'>experimental knowledge is attained. Some apparently contradictory features of techniques, such as their high context-dependency and their capabilities to reproduce and diversify outside their original contexts, are addressed with the help of the concepts of technical variation and the historical entrenchment of phenomena in techniques. In order to do so, a case-study on the construction of satellite-DNA and the evolution of nucleic acid hybridization, a research project carried out by Roy J. Britten and his colleagues in the 1960s, is presented in detail. This case illustrates the close relationship existing between the evolution of techniques and the stabilization of phenomena in experimental biology. (shrink)

This text answers the question, posed by the editor, on the philosophical and social issues resulting from the synthetic assembly of a modified bacterial genome that was introduced in an existing bacterial species (M.mycoides)and so it was claimed to represent the first ever kind of synthetic life produced by human manipulation.

Computation and philosophy intersect three times in this essay. Computation is considered as an object, as a method, and as a model used in a certain line of philosophical inquiry concerning the relation of mind to matter. As object, the question considered is whether computation and related notions of mental representation constitute the best ways to conceive of how physical systems give rise to mental properties. As method and model, the computational techniques of artificial life and embodied evolutionary connectionism are (...) used to conduct prosthetically enhanced thought experiments concerning the evolvability of mental representations. Central to this essay is a discussion of the computer simulation and evolution of three‐dimensional synthetic animals with neural network controllers. The minimally cognitive behavior of finding food by exhibiting positive chemotaxis is simulated with swimming and walking creatures. These simulations form the basis of a discussion of the evolutionary and neurocomputational bases of the incremental emergence of more complex forms of cognition. Other related work has been used to attack computational and representational theories of cognition. In contrast, I argue that the proper understanding of the evolutionary emergence of minimally cognitive behaviors is computational and representational through and through. (shrink)

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their func- tionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adapta- tions, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In (...) particular, the analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an oppor- tunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would sug- gest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to imple- ment novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engi- neering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engi- neering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms. (shrink)

Computation and philosophy intersect three times in this essay. Computation is considered as an object, as a method, and as a model used in a certain line of philosophical inquiry concerning the relation of mind to matter. As object, the question considered is whether computation and related notions of mental representation constitute the best ways to conceive of how physical systems give rise to mental properties. As method and model, the computational techniques of artificial life and embodied evolutionary connectionism are (...) used to conduct prosthetically enhanced thought experiments concerning the evolvability of mental representations. Central to this essay is a discussion of the computer simulation and evolution of three-dimensional synthetic animals with neural network controllers. The minimally cognitive behavior of finding food by exhibit- ing positive chemotaxis is simulated with swimming and walking creatures. These simulations form the basis of a discussion of the evolutionary and neurocomputa- tional bases of the incremental emergence of more complex forms of cognition. Other related work has been used to attack computational and representational theories of cognition. In contrast, I argue that the proper understanding of the evolutionary emergence of minimally cognitive behaviors is computational and representational through and through. (shrink)

Jürgen Renn examines the role of knowledge in global transformations going back to the dawn of civilization while providing vital perspectives on the complex challenges confronting us today in the Anthropocene--this new geological epoch shaped by humankind. Renn reframes the history of science and technology within a much broader history of knowledge, analyzing key episodes such as the evolution of writing, the emergence of science in the ancient world, the Scientific Revolution of early modernity, the globalization of knowledge, industrialization, (...) and the profound transformations wrought by modern science. He investigates the evolution of knowledge using an array of disciplines and methods, from cognitive science and experimental psychology to earth science and evolutionary biology. The result is an entirely new framework for understanding structural changes in systems of knowledge--and a bold new approach to the history and philosophy of science. (shrink)

This paper analyses conceptual and experimental work in synthetic biology on different types of interactions considered as minimal examples or models of communication. It discusses their pertinence and relevance for the wider understanding of this biological and cognitive phenomenon. It critically analyses their limits and it argues that a conceptual framework is needed. As a possible solution, it provides a theoretical account of communication based on the notion of organisation, and characterised in terms of the functional influence exerted (...) by the sender upon the receiver. It shows that this account can be operationalised in synthetic biology, and that it can supply criteria and guidelines for the design and evaluation of synthetic models. (shrink)

The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their functionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adaptations, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In particular, the (...) analogy with human-made machines falters when we move down to the level of molecular biology and genetics. Living organisms are far more messy and less transparent than human-made machines. Notoriously, evolution is an opportunistic tinkerer, blindly stumbling on ‘‘designs’’ that no sensible engineer would come up with. Despite impressive technological innovation, the prospect of artificially designing new life forms from scratch has proven more difficult than the superficial analogy with ‘‘programming’’ the right ‘‘software’’ would suggest. The idea of applying straightforward engineering approaches to living systems and their genomes— isolating functional components, designing new parts from scratch, recombining and assembling them into novel life forms—pushes the analogy with human artifacts beyond its limits. In the absence of a one-to-one correspondence between genotype and phenotype, there is no straightforward way to implement novel biological functions and design new life forms. Both the developmental complexity of gene expression and the multifarious interactions of genes and environments are serious obstacles for ‘‘engineering’’ a particular phenotype. The problem of reverse-engineering a desired phenotype to its genetic ‘‘instructions’’ is probably intractable for any but the most simple phenotypes. Recent developments in the field of bio-engineering and synthetic biology reflect these limitations. Instead of genetically engineering a desired trait from scratch, as the machine/engineering metaphor promises, researchers are making greater strides by co-opting natural selection to ‘‘search’’ for a suitable genotype, or by borrowing and recombining genetic material from extant life forms. (shrink)

The theory of punctuated equilibrium has been proposed as a challenge to the modern synthesis of evolutionary theory. Two important issues are raised. The first is scientific: whether morphological change as observed in the paleontological record is essentially always associated with speciation events. This paper argues that there is at present no empirical support for this claim: the alleged evidence is based on a definitional fallacy. The second issue is epistemological: whether macroevolution is an autonomous field of study, independent from (...) microevolutionary knowledge. It is herein argued that macroevolution and microevolution are not decoupled in two senses: identity at the level of events and compatibility of theories. But macroevolution is autonomous in the epistemologically important sense: macroevolutionary theories are not reducible to microevolutionary principles. It is finally pointed out that the discipline of macroevolution is notoriously lacking in theoretical constructs of great import and generality. (shrink)

This book reconceptualizes the ancient philosophy of "dualism" and a "trinity" applied to classical and quantum nonequilibrium phenomena. In addition to classical mechanics and electrodynamics, a remarkable connection of this philosophy with quantum mechanics is established which can be useful for quantum computing and the development of quantum artificial intelligence. Packed with the recent theoretical models, quantum simulations of black holes, and experimental observations of quantum phase transitions, this book brings a holistic approach that can be useful to refine (...) the concept of the 'Creation', evolution of the Universe from the condensed state of matter, and explain the artificial vision. (shrink)

This interdisciplinary volume brings together expert researchers coming from primatology, anthropology, ethology, philosophy of cognitive sciences, neurophysiology, mathematics and psychology to discuss both the foundations of non-human primate and human social cognition as well as the means there currently exist to study the various facets of social cognition. The first part focusses on various aspects of social cognition across primates, from the relationship between food and social behaviour to the connection with empathy and communication, offering a multitude of innovative approaches (...) that range from field-studies to philosophy. The second part details the various epistemic and methodological means there exist to study social cognition, in particular how to ascertain the proximal and ultimate mechanisms of social cognition through experimental, modelling and field studies. In the final part, the mechanisms of cultural transmission in primate and human societies are investigated, and special attention is given to how the evolution of cognitive capacities underlie primates’ abilities to use and manufacture tools, and how this in turn influences their social ecology. A must-read for both, young scholars as well as established researchers! (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)

Synthetic biology is an umbrella term that covers a range of aims, approaches, and techniques. They are all brought together by common practices of analogizing, synthesizing, mechanicizing, and kludging. With a focus on kludging as the connection point between biology, engineering, and evolution, I show how synthetic biology’s successes depend on custom-built kludges and a creative, “make-it-work” attitude to the construction of biological systems. Such practices do not fit neatly, however, into synthetic biology’s celebration of rational (...) design. Nor do they straightforwardly embody Richard Feynman’s “last blackboard” statement that without creating something it cannot be understood. Reflecting further on the relationship between synthetic construction and knowledge making gives philosophy of science new avenues of insight into scientific practice. (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)

To some, a misguided Lamarckian and a fraud, to others a martyr in the fight against Darwinism, the Viennese zoologist Paul Kammerer (1880-1926) remains one of the most controversial scientists of the early 20th century. Here his work is reconsidered in light of turn-of-the-century problems in evolutionary theory and experimental methodology, as seen from Kammerer's perspective in Vienna. Kammerer emerges not as an opponent of Darwinism, but as one would-be modernizer of the 19th-century theory, which had included a role (...) for the inheritance of acquired characteristics. Kammerer attempted a synthesis of Darwinism with genetics and the chromosome theory, while retaining the modifying effects of the environment as the main source of favorable variation, and he developed his program of experimentation to support it. Kammerer never had a regular university position, but worked at a private experimental laboratory, with sidelines as a teacher and a popular writer and lecturer. On the lecture circuit he held forth on the significance of his science for understanding and furthering cultural evolution and he satisfied his passion for the arts and performance. In his dual career as researcher and popularizer, he did not always follow academic convention. In the contentious and rapidly changing fields of heredity and evolution, some of his stances and practices, as well as his outsider status and part-Jewish background, aroused suspicion and set the stage for the scandal that ended his career and prompted his suicide. (shrink)