Carol Cleland

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin.We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question.

In earlier work ( Cleland [2001], [2002]), I sketched an account of the structure and justification of ‘prototypical’ historical natural science that distinguishes it from ‘classical’ experimental science. This article expands upon this work, focusing upon the close connection between explanation and justification in the historical natural sciences. I argue that confirmation and disconfirmation in these fields depends primarily upon the explanatory (versus predictive or retrodictive) success or failure of hypotheses vis-à-vis empirical evidence. The account of historical explanation that I develop is a version of common cause explanation. Common cause explanation has long been vindicated by appealing to the principle of the common cause. Many philosophers of science (e.g., Sober and Tucker) find this principle problematic, however, because they believe that it is either purely methodological or strictly metaphysical. I defend a third possibility: the principle of the common cause derives its justification from a physically pervasive time asymmetry of causation (a.k.a. the asymmetry of overdetermination). I argue that explicating the principle of the common cause in terms of the asymmetry of overdetermination illuminates some otherwise puzzling features of the practices of historical natural scientists.

This chapter argues that doubts about the scientific status of the field sciences often rest on mistaken preconceptions about the nature of the evaluative relation between empirical evidence and hypothesis or theory, namely, that it is some sort of formal logical relation. It argues that there is a potentially more fruitful approach to understanding the nature of the support offered by empirical evidence to scientific hypotheses. The first part of the chapter briefly reviews the traditional philosophical take on the scientific method in order to clarify its most serious problems. It shows that these problems are greatly exacerbated when science moves from the artificially controlled environment of the laboratory to the messy uncontrollable world of nature. The second part ferrets out some highly general, causal components in the methodological reasoning of nonhistorical field scientists. It argues that differences in patterns of evidential reasoning in the experimental sciences versus the field sciences, and in the historical versus nonhistorical field sciences, seem tailored to pervasive causal differences in their epistemic situations.

The question ‘what is life?’ has long been a source of philosophical debate and in recent years has taken on increasing scientific importance. The most popular approach among both philosophers and scientists for answering this question is to provide a “definition” of life. In this article I explore a variety of different definitional approaches, both traditional and non-traditional, that have been used to “define” life. I argue that all of them are deeply flawed. It is my contention that a scientifically compelling understanding of the nature of life presupposes an empirically adequate scientific theory (vs. definition) of life; as I argue, scientific theories are not the sort of thing that can be encapsulated in definitions. Unfortunately, as I also discuss, scientists are currently in no position to formulate even a tentative version of such a theory. Recent discoveries in biology and biochemistry have revealed that familiar Earth life represents a single example that may not be representative of life. If this is the case, life on Earth today provides an empirically inadequate foundation for theorizing about life considered generally. I sketch a strategy for procuring the needed additional examples of life without the guidance of a definition or theory of life, and close with an application to NASA’s fledgling search for extraterrestrial life.

Bringing together the latest scientific advances and some of the most enduring subtle philosophical puzzles and problems, this book collects original historical and contemporary sources to explore the wide range of issues surrounding the nature of life. Selections ranging from Aristotle and Descartes to Sagan and Dawkins are organised around four broad themes covering classical discussions of life, the origins and extent of natural life, contemporary artificial life creations and the definition and meaning of 'life' in its most general form. Each section is preceded by an extensive introduction connecting the various ideas discussed in individual chapters and providing helpful background material for understanding them. With its interdisciplinary perspective, this fascinating collection is essential reading for scientists and philosophers interested in astrobiology, synthetic biology and the philosophy of life.

: Despite its amazing morphological diversity, life as we know it on Earth today is remarkably similar in its basic molecular architecture and biochemistry. The assumption that all life on Earth today shares these molecular and biochemical features is part of the paradigm of modern biology. This paper examines the possibility that this assumption is false, more specifically, that the contemporary Earth contains as yet unrecognized alternative forms of microbial life. The possibility that more than one form of life arose on Earth is consistent with our current understanding of conditions on the early Earth and the biochemical and molecular possibilities for life. Arguments that microbial descendents of an alternative origin of life could not co-exist with familiar life are belied by what we know of the complexity and diversity of microbial communities. Furthermore, the tools that are currently used to explore the microbial world – microscopy (with the aid of techniques such as DAPI staining and fluorescence in situ hybridization), cultivation and PCR amplification of rRNA genes – could not detect such organisms if they existed. Thus, the fact that we have not discovered any alternative life forms cannot be taken as evidence that they do not exist.

Pluralism is popular among philosophers of biology. This essay argues that negative judgments about universal biology, while understandable, are very premature. Familiar life on Earth represents a single example of life and, most importantly, there are empirical as well as theoretical reasons for suspecting that it may be unrepresentative. Scientifically compelling generalizations about the unity of life must await the discovery of forms of life descended from an alternative origin, the most promising candidate being the discovery of extraterrestrial life. Nonetheless, in the absence of additional examples of life, we are best off exploring the microbial world for promising explanatory concepts, principles, and mechanisms rather than prematurely giving up on universal biology. Unicellular microbes are by far the oldest, metabolically most diverse, and environmentally tolerant form of life on our planet. Yet somewhat ironically, much of our theorizing about life still implicitly privileges complex multicellular eukaryotes, which are now understood to be highly specialized, fragile latecomers to Earth. The problem with pursuing a pluralist approach to understanding life is that it is likely to blind us to the significance of just those entities and causal processes most likely to shed light on the underlying nature of life.

The Church-Turing thesis makes a bold claim about the theoretical limits to computation. It is based upon independent analyses of the general notion of an effective procedure proposed by Alan Turing and Alonzo Church in the 1930''s. As originally construed, the thesis applied only to the number theoretic functions; it amounted to the claim that there were no number theoretic functions which couldn''t be computed by a Turing machine but could be computed by means of some other kind of effective procedure. Since that time, however, other interpretations of the thesis have appeared in the literature. In this paper I identify three domains of application which have been claimed for the thesis: (1) the number theoretic functions; (2) all functions; (3) mental and/or physical phenomena. Subsequently, I provide an analysis of our intuitive concept of a procedure which, unlike Turing''s, is based upon ordinary, everyday procedures such as recipes, directions and methods; I call them mundane procedures. I argue that mundane procedures can be said to be effective in the same sense in which Turing machine procedures can be said to be effective. I also argue that mundane procedures differ from Turing machine procedures in a fundamental way, viz., the former, but not the latter, generate causal processes. I apply my analysis to all three of the above mentioned interpretations of the Church-Turing thesis, arguing that the thesis is (i) clearly false under interpretation (3), (ii) false in at least some possible worlds (perhaps even in the actual world) under interpretation (2), and (iii) very much open to question under interpretation (1)

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

Experimental research is commonly held up as the paradigm of "good" science. Although experiment plays many roles in science, its classical role is testing hypotheses in controlled laboratory settings. Historical science is sometimes held to be inferior on the grounds that its hypothesis cannot be tested by controlled laboratory experiments. Using contemporary examples from diverse scientific disciplines, this paper explores differences in practice between historical and experimental research vis-à-vis the testing of hypotheses. It rejects the claim that historical research is epistemically inferior. For as I argue, scientists engage in two very different patterns of evidential reasoning and, although there is overlap, one pattern predominates in historical research and the other pattern predominates in classical experimental research. I show that these different patterns of reasoning are grounded in an objective and remarkably pervasive time asymmetry of nature.

Many scientists believe that there is a uniform, interdisciplinary method for the prac- tice of good science. The paradigmatic examples, however, are drawn from classical ex- perimental science. Insofar as historical hypotheses cannot be tested in controlled labo- ratory settings, historical research is sometimes said to be inferior to experimental research. Using examples from diverse historical disciplines, this paper demonstrates that such claims are misguided. First, the reputed superiority of experimental research is based upon accounts of scientific methodology (Baconian inductivism or falsificationism) that are deeply flawed, both logically and as accounts of the actual practices of scientists. Second, although there are fundamental differences in methodology between experimental scien- tists and historical scientists, they are keyed to a pervasive feature of nature, a time asymmetry of causation. As a consequence, the claim that historical science is methodo- logically inferior to experimental science cannot be sustained.

Astrobiologists are aware that extraterrestrial life might differ from known life, and considerable thought has been given to possible signatures associated with weird forms of life on other planets. So far, however, very little attention has been paid to the possibility that our own planet might also host communities of weird life. If life arises readily in Earth-like conditions, as many astrobiologists contend, then it may well have formed many times on Earth itself, which raises the question whether one or more shadow biospheres have existed in the past or still exist today. In this paper, we discuss possible signatures of weird life and outline some simple strategies for seeking evidence of a shadow biosphere. Key Words: Weird life—Multiple origins of life—Biogenesis—Biomarkers—Extremophiles—Alternative biochemistry. Astrobiology 9, 241–249.

In the technical literature of computer science, the concept of an effective procedure is closely associated with the notion of an instruction that precisely specifies an action. Turing machine instructions are held up as providing paragons of instructions that "precisely describe" or "well define" the actions they prescribe. Numerical algorithms and computer programs are judged effective just insofar as they are thought to be translatable into Turing machine programs. Nontechnical procedures (e.g., recipes, methods) are summarily dismissed as ineffective on the grounds that their instructions lack the requisite precision. But despite the pivotal role played by the notion of a precisely specified instruction in classifying procedures as effective and ineffective, little attention has been paid to the manner in which instructions "precisely specify" the actions they prescribe. It is the purpose of this paper to remedy this defect. The results are startling. The reputed exemplary precision of Turing machine instructions turns out to be a myth. Indeed, the most precise specifications of action are provided not by the procedures of theoretical computer science and mathematics (algorithms) but rather by the nontechnical procedures of everyday life. I close with a discussion of some of the rumifications of these conclusions for understanding and designing concrete computers and their programming languages.

This book consists of notes of lectures given by G. E. Moore at Cambridge during the three terms of 1934-35. They were compiled by the editor, Alice Ambrose, who was then Student of Newnham College, and the late Margaret Macdonald, who was then Fellow of Girton College. The lectures contain discussions of some material on which Moore published little or nothing, for example, types and tokens, propositional functions and their relation to common properties and relations, and the objects of false judgements. They also include detailed examinations of the views of a number of Moore's contemporaries, including C. D. Broad, Bertrand Russell, F. P. Ramsey, W. E. Johnson, and John Wisdom. Moreover, the lectures do a nice job of illustrating Moore's general approach to the philosophical enterprise, highlighting his emphasis upon ordinary language and revealing the high standards of clarity and precision that he demanded of himself and others. It is clear, however, that Moore is not so much concerned with formulating philosophical positions as with exploring philosophical problems. This lends a certain lack of focus to the lectures and makes them a bit confusing at times. Nevertheless, the lectures provide valuable insight into the evolution of Moore's later thought about a number of important philosophical problems.

The assumption that all life on Earth today shares the same basic molecular architecture and biochemistry is part of the paradigm of modern biology. This paper argues that there is little theoretical or empirical support for this widely held assumption. Scientists know that life could have been at least modestly different at the molecular level and it is clear that alternative molecular building blocks for life were available on the early Earth. If the emergence of life is, like other natural phenomena, highly probable given the right chemical and physical conditions then it seems likely that the early Earth hosted multiple origins of life, some of which produced chemical variations on life as we know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer (LGT) or alternatively out-competed by our putatively more evolutionarily robust form of life. Besides, the argument continues, if such life forms still existed, we surely would have encountered telling signs of them by now. These arguments do not hold up well under close scrutiny. They reflect a host of assumptions that are grounded in our experience with large multicellular organisms and, most importantly, do not apply to microbial forms of life, which cannot be easily studied without the aid of sophisticated technologies. Significantly, the most powerful molecular biology techniques available—polymerase chain reaction (PCR) amplification of rRNA genes augmented by metagenomic analysis—could not detect such microbes if they existed. Given the profound philosophical and scientific importance that such a discovery would represent, a dedicated search for ‘shadow microbes’ (heretofore unrecognized ‘alien’ forms of terran microbial life) seems in order. The best place to start such a search is with puzzling (anomalous) phenomena, such as desert varnish, that resist classification as ‘biological’ or ‘nonbiological’.

Since the mid-twentieth century, the concept of the Turing machine has dominated thought about effective procedures. This paper presents an alternative to Turing's analysis; it unifies, refines, and extends my earlier work on this topic. I show that Turing machines cannot live up to their billing as paragons of effective procedure; at best, they may be said to provide us with mere procedure schemas. I argue that the concept of an effective procedure crucially depends upon distinguishing procedures as definite courses of action(- types) from the particular courses of action(-tokens) that actually instantiate them and the causal processes and/or interpretations that ultimately make them effective. On my analysis, effectiveness is not just a matter of logical form; `content' matters. The analysis I provide has the advantage of applying to ordinary, everyday procedures such as recipes and methods, as well as the more refined procedures of mathematics and computer science. It also has the virtue of making better sense of the physical possibilities for hypercomputation than the received view and its extensions, e.g. Turing's o-machines, accelerating machines.

Is one of the roles of theory in biology answering the question “What is life?” This is true of theory in many other fields of science. So why should not it be the case for biology? Yet efforts to identify unifying concepts and principles of life have been disappointing, leading some (pluralists) to conclude that life is not a natural kind. In this essay I argue that such judgments are premature. Life as we know it on Earth today represents a single example and moreover there is positive evidence that it may be unrepresentative of life considered generally. Furthermore, as I discuss, the prototype for theorizing about life has traditionally been based on multicellular plants and animals. Yet biologists have discovered that the latter represent a rare, exotic, and fairly recent form of Earth life. By far the oldest, toughest, most extensive, and diverse form of life on our planet is unicellular, prokaryotic microbes, and there are reasons to suppose that this is almost certainly true elsewhere in the universe as well. If there are explanatorily and predictively powerful, biologically distinctive principles for life that can be gleaned from our insular example of life it is more likely that they will be found among the microbes. I discuss some provocative ways in which unicellular microbes differ from multicellular eukaryotes and argue that some of them just might provide us with key insights into the nature of life.

The assumption that all life on Earth today shares the same basic molecular architecture and biochemistry is part of the paradigm of modern biology. This paper argues that there is little theoretical or empirical support for this widely held assumption. Scientists know that life could have been at least modestly different at the molecular level and it is clear that alternative molecular building blocks for life were available on the early Earth. If the emergence of life is, like other natural phenomena, highly probable given the right chemical and physical conditions then it seems likely that the early Earth hosted multiple origins of life, some of which produced chemical variations on life as we know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer (LGT) or alternatively out-competed by our putatively more evolutionarily robust form of life. Besides, the argument continues, if such life forms still existed, we surely would have encountered telling signs of them by now. These arguments do not hold up well under close scrutiny. They reflect a host of assumptions that are grounded in our experience with large multicellular organisms and, most importantly, do not apply to microbial forms of life, which cannot be easily studied without the aid of sophisticated technologies. Significantly, the most powerful molecular biology techniques available—polymerase chain reaction (PCR) amplification of rRNA genes augmented by metagenomic analysis—could not detect such microbes if they existed. Given the profound philosophical and scientific importance that such a discovery would represent, a dedicated search for ‘shadow microbes’ (heretofore unrecognized ‘alien’ forms of terran microbial life) seems in order. The best place to start such a search is with puzzling (anomalous) phenomena, such as desert varnish, that resist classification as ‘biological’ or ‘nonbiological’. Ó 2007 Elsevier Ltd..

In recent years, an increasing number of philosophers have come to doubt the viability of the empiricist program of analyzing the concepts of lawhood and causation in terms of nonnomic or noncausal concepts. The central thesis of Carroll's book is that these concepts cannot be so analyzed. Carroll is quite liberal about what he is willing to count as a reductive analysis. He does not identify an analysis with a definition, as traditional empiricists have insisted upon. He is willing to go along with contemporary empiricists who are satisfied that they have an analysis if they can identify necessary conditions or even just a supervenience base. Moreover, he is willing to include concepts with nomic and causal commitments in the supervenience base. Thus Carroll intends his conclusions to encompass all empiricist attempts, no matter how weak, to analyze the concepts of lawhood and causation.

Horsten and Roelants have raised a number of important questions about my analysis of effective procedures and my evaluation of the Church-Turing thesis. They suggest that, on my account, effective procedures cannot enter the mathematical world because they have a built-in component of causality, and, hence, that my arguments against the Church-Turing thesis miss the mark. Unfortunately, however, their reasoning is based upon a number of misunderstandings. Effective mundane procedures do not, on my view, provide an analysis of ourgeneral concept of an effective procedure; mundane procedures and Turing machine procedures are different kinds of procedure. Moreover, the same sequence ofparticular physical action can realize both a mundane procedure and a Turing machine procedure; it is sequences of particular physical actions, not mundane procedures, which enter the world of mathematics. I conclude by discussing whether genuinely continuous physical processes can enter the world of real numbers and compute real-valued functions. I argue that the same kind of correspondence assumptions that are made between non-numerical structures and the natural numbers, in the case of Turing machines and personal computers, can be made in the case of genuinely continuous, physical processes and the real numbers.