Christophe Malaterre

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'.

The concept of “life” certainly is of some use to distinguish birds and beavers from water and stones. This pragmatic usefulness has led to its construal as a categorical predicate that can sift out living entities from non-living ones depending on their possessing specific properties—reproduction, metabolism, evolvability etc. In this paper, we argue against this binary construal of life. Using text-mining methods across over 30,000 scientific articles, we defend instead a degrees-of-life view and show how these methods can contribute to experimental philosophy of science and concept explication. We apply topic-modeling algorithms to identify which specific properties are attributed to a target set of entities (bacteria, archaea, viruses, prions, plasmids, phages and the molecule of adenine). Eight major clusters of properties were identified together with their relative relevance for each target entity (two that relate to metabolism and catalysis, one to genetics, one to evolvability, one to structure, and—rather unexpectedly—three that concern interactions with the environment broadly construed). While aligning with intuitions—for instance about viruses being less alive than bacteria—these quantitative results also reveal differential degrees of performance that have so far remained elusive or overlooked. Taken together, these analyses provide a conceptual “lifeness space” that makes it possible to move away from a categorical construal of life by empirically assessing the relative lifeness of more-or-less alive entities.

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’.

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.

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

Explanation in biology has long been characterized as being very different from explanation in other scientific disciplines, very much so from explanation in physics. One of the reasons was the existence in biology of explanation types that were unheard of in the physical sciences: teleological explanations (e.g. Hull 1974), evolutionary explanations (e.g. Mayr 1988), or even functional explanations (e.g. Neander 1991). More recently, and owing much to the rise of molecular biology, biological explanations have been depicted as mechanisms (e.g; Machamer, Darden and Craver 2000). The aim of this volume is to shed some new light on the diversity of explanation types in biology. What are the different types of explanation that occur in biology? Are these types of explanation specific to particular sub-disciplines of biology, or to particular types of problems across biology? How do they relate to each another? Do they compete with one another for answering the same questions? Or do they complement each other, providing insights to different questions? What are the reasons for such diversity? Can this diversity be overcome by a broader unifying model of explanation or is it more profound and irreducible? Why? This volume aims at making sense of this diversity of types of explanations that are found in biology, of their relationship with one another. After all, explanation in biology may prove not only different from explanation in the physical sciences, but also much more diverse than originally anticipated.

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.

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.

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