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)

Many researchers consider cancer to have molecular causes, namely mutated genes that result in abnormal cell proliferation (e.g. Weinberg 1998). For others, the causes of cancer are to be found not at the molecular level but at the tissue level where carcinogenesis consists of disrupted tissue organization with downward causation effects on cells and cellular components (e.g. Sonnenschein and Soto 2008). In this contribution, I ponder how to make sense of such downward causation claims. Adopting a manipulationist account of causation (...) (Woodward 2003), I propose a formal definition of downward causation and discuss further requirements (in light of Baumgartner 2009). I then show that such an account cannot be mobilized in support of non-reductive physicalism (contrary to Raatikainen 2010). However, I also argue that such downward causation claims might point at particularly interesting dynamic properties of causal relationships that might prove salient in characterizing causal relationships (following Woodward 2010). (shrink)

Science is now studying biodiversity on a massive scale. These studies are occurring not just at the scale of larger plants and animals, but also at the scale of minute entities such as bacteria and viruses. This expansion has led to the development of a specific sub-field of “microbial diversity”. In this paper, I investigate how microbial diversity faces two of the classical issues encountered by the concept of “ biodiversity ”: the issues of defining the units of biodiversity and (...) of choosing a mathematical measure of diversity. I also show that the extension of the scope of biodiversity to microbial entities such as viruses and many other not-clearly-alive entities raises yet another foundational issue: that of defining a “lower-limit” of biodiversity. (shrink)

Do trees of life have roots? What do these roots look like? In this contribution, I argue that research on the origins of life might offer glimpses on the topology of these very roots. More specifically, I argue (1) that the roots of the tree of life go well below the level of the commonly mentioned ‘ancestral organisms’ down into the level of much simpler, minimally living entities that might be referred to as ‘protoliving systems’, and (2) that further below, (...) a system of roots gradually dissolves into non-living matter along several functional dimensions. In between non-living and living matter, one finds physico-chemical systems that I propose to characterize by a ‘lifeness signature’. In turn, this ‘lifeness signature’ might also account for a diverse range of biochemical entities that are found to be ‘less-than-living’ yet ‘more-than-non-living’. (shrink)

The plurality of definitions of life is often perceived as an unsatisfying situation stemming from still incomplete knowledge about ‘what it is to live’ as well as from the existence of a variety of methods for reaching a definition. For many, such plurality is to be remedied and the search for a unique and fully satisfactory definition of life pursued. In this contribution on the contrary, it is argued that the existence of such a variety of definitions of life undermines (...) the very feasibility of ever reaching a unique unambiguous definition. It is argued that focusing on the definitions of specific types of ‘living systems’ – somehow in the same way that one can define specific types of ‘flying systems’ – could be more fruitful from a heuristic point of view than looking for ‘the’ right definition of life, and probably more accurate in terms of carving Nature at its joints. (shrink)

In recent cancer research, strong and apparently conflicting epistemological stances have been advocated by different research teams in a mist of an ever-growing body of knowledge ignited by ever-more perplexing and non-conclusive experimental facts: in the past few years, an 'organicist' approach investigating cancer development at the tissue level has challenged the established and so-called 'reductionist' approach focusing on disentangling the genetic and molecular circuitry of carcinogenesis. This article reviews the ways in which 'organicism' and 'reductionism' are used and opposed (...) in this context, with an aim at clarifying the debate. Methodological, epistemological and ontological implications of both approaches are discussed. We argue that the 'organicist/reductionist' opposition in the present case of carcinogenesis is more a matter of diverging heuristics than a claim about theoretical or ontological (ir)reducibility. As a matter of fact, except for the downward causation claim, which we question, we argue that the organicist arguments are compatible with the reductionist approach. Moreover, we speculate that both approaches, which currently focus on specific entities i.e., genes versus tissues, will need to shift their conceptual frameworks to studying complex arrays of relationships potentially ranging over several levels of entities, as is the case with 'systems biology'. (shrink)

It is a most commonly accepted hypothesis that life originated from inanimate matter, somehow being a synthetic product of organic aggregates, and as such, a result of some sort of prebiotic synthetic biology. In the past decades, the newly formed scientific discipline of synthetic biology has set ambitious goals by pursuing the complete design and production of genetic circuits, entire genomes or even whole organisms. In this paper, I argue that synthetic biology might also shed some novel and interesting perspectives (...) on the question of the origin of life, and that, in addition, it might challenge our most commonly accepted definitions of life, thereby changing the ways we might think about life and its origin. (shrink)

Biochemical networks are often called upon to illustrate emergent properties of living systems. In this contribution, I question such emergentist claims by means of theoretical work on genetic regulatory models and random Boolean networks. If the existence of a critical connectivity Kc of such networks has often been coined “emergent” or “irreducible”, I propose on the contrary that the existence of a critical connectivity Kc is indeed mathematically explainable in network theory. This conclusion also applies to many other types of (...) formal networks and weakens the emergentist claim attached to bio-molecular networks, and by extension to living systems. (shrink)

This Special Issue of Origins of Life and Evolution of Biospheres contains papers based on the contributions presented at the Conference "Defining Life" held in Paris (France) on 4-5 February, 2008. The main objective of this Conference was to confront speakers from several disciplines--chemists, biochemists, biologists, exo/astrobiologists, computer scientists, philosophers and historians of science--on the topic of the definition of life. Different viewpoints of the problem approached from different perspectives have been expounded and, as a result, common grounds as well (...) as remaining diverging arguments have been identified. In addition to individual talks, two large roundtables gave ample room for speakers to discuss their diverging viewpoints. This volume collects almost all the contributions presented during the Conference and provides a rich spectrum of renewed answers to the ever-standing question "What is Life?". Besides the arguments directly regarding this question, more philosophical or historical reflections are also proposed in this issue that were not presented during the Conference. This volume also offers a synthesis written by J. Gayon taking each contribution into account. To conclude this foreword, we would like to thank all the participants and speakers who made this Conference a most stimulating event. Each provided novel ideas to "Defining Life" while highlighting the extreme difficulty to reach a consensus on this topic. We are also very grateful to the French CNRS Interdisciplinary Program Origines des Planètes et de la Vie (Origins of Planets and Life) for its generous support, as well as to the National Museum of Natural History in Paris for hosting the Conference. We also thank Alan W. Schwartz for generously offering this space for publishing the Proceedings of the Conference. (shrink)

Physicalism is the metaphysical thesis that everything is physical. According to this thesis, everything in the world, including chemical, biological, mental, and social entities and processes, is constituted by or results from physical entities and processes. In analytic philosophy, one might say that physicalism is the claim that everything supervenes on, or is necessitated by, the physical.

It is a most commonly accepted hypothesis that life originated from inanimate matter, somehow being a synthetic product of organic aggregates, and as such a result of some sort of prebiotic synthetic biology. In the past decades, the newly formed scientific discipline of synthetic biology has set ambitious goals by pursuing the complete design and production of genetic circuits, entire genomes, or even whole organisms. I argue that synthetic biology might also shed some novel and interesting perspectives on the question (...) of the origins of life, and that, in addition, it might challenge our most commonly accepted definitions of life, thereby changing the ways we might think about life and its origins. (shrink)

The notion of chemical evolution is controversially defined in reference to Darwinian evolution: for some, it is nothing but natural selection applied to chemical systems; yet, for others, it is precisely what happened before natural selection, the latter being the birthmark of life. Taking into account a plurality of evolutionary processes, I propose to construe chemical evolution as a composite theory within which natural selection might only be one of several evolutionary processes.

La vie est-elle un phénomène émergent ? Traduit-elle l'apparition de propriétés nouvelles au niveau d'un tout, qui seraient irréductibles aux propriétés et à l'organisation des composants de ce tout, ou encore imprédictibles à partir de ces mêmes éléments ? Développées à la charnière des XIXe et XXe siècles comme alternative aux deux approches antinomiques du vivant que sont le vitalisme et le mécanisme, la notion philosophique d'émergence connait aujourd'hui de nouveaux développements : avec la prise de conscience de la complexité (...) du vivant, un nouveau discours émergentiste refait surface en biologie et dans le champ scientifique des origines de la vie. Que signifie la notion d'émergence lorsqu'elle s'applique à l'apparition de la vie sur Terre ? Quelles sont sa pertinence et sa portée ? Dans ce livre, Christophe Malaterre propose une clarification conceptuelle de la notion philosophique d'émergence ; il en défend une conception epistémique et contextuelle, adossée à la notion d'explication. En s'inspirant des travaux les plus contemporains sur les origines de la vie, il montre que, selon le contexte epistémique dans lequel le phénomène est évalué, la qualification de l'apparition de la vie comme émergente est, ou non, justifié. Il défend alors la thèse selon laquelle la caractérisation émergentiste de l'apparition de la vie n'est qu'une conséquence temporaire des limites de nos connaissances scientifiques. (shrink)