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Abstract and Keywords

This article provides insights on emerging discipline of origins of life studies. It answers various questions such as the logics behind scientific concepts and the scope and limit of biological science. It is now generally accepted that life existed around 3.5 billion years ago on earth. If life began elsewhere, then the time window for life's origin might be wide open. Narrowing the gap puts the idea that there is room for God to explain the gaps in nature left by scientific uncertainty. Some fundamental heuristic principles are discussed based on continuity, microreversibility, actualism. The origin of life appeared to be a problem, when it was realized how complex the interrelations between DNA as the carrier of genetic information and protein were. Origins of life researchers use biological, chemical, and physical laboratories to challenge how life might have emerged in the harsh conditions of early Earth.

Keywords: life, origins, earth, DNA, genetics

Big Questions, Big Problems

Origins of life studies attempt to answer questions about when, where, why, and how life originated on Earth. The big questions include (1) did life begin with metabolism, a bounding membrane, a “naked” replicator, or some combination of these? (2) was first life autotrophic (making all of its necessary components itself from simple, small molecules and a source of energy) or heterotrophic (taking in key nutrients from the environment)? (3) did life begin in a soup or at a solid surface; with a hot or cold start; in a strongly, weakly, or nonreducing atmosphere; with photons, hydrogen, heat, or something else as energy source? (4) did first life evolve over a long period of time or arise in an improbable flash of chemical emergence? (5) did first life resemble modern life “in outline” or was it fundamentally different and “taken over” by modern forms that evolved from it? (6) did life on Earth begin on Earth or in outer space? (6) was life an unlikely, wildly improbable, lucky accident or (nearly) inevitable, once the starting materials and conditions were present? Extending Gould's question (1989), would life exist at all if Earth's tape were rewound and replayed? Because answers to the big questions are not settled, the field has changed names, from origin of life to origins of life, reflecting uncertainty about whether life even had a single origin (and one evolutionary path to the last common ancestor of modern life) or many.1

Scientists involved in origins of life studies are quite specialized, and the field often has the feel of the proverbial blind men studying different parts of an (p. 264) elephant. They generally take a naturalistic stance toward the big questions, considering evolutionary‐biological and physical‐chemical processes (including stochastic ones) as possible explanations while rejecting supernatural design as out of court. There is little debate with antinaturalists of the sort still evident in discussions about evolution versus creation, perhaps because discussion of the origins of life, unlike the origin of humans, has been so lopsided: Creationists have often assumed science cannot answer the question of life's origin scientifically, and many scientists have been inclined to agree. Evolutionary theory is a pretty good theory of transformations, but not such a good theory of origins. Mayr famously noted that Darwin's book, despite its title, failed to give a satisfying account of the origin of species (Mayr 1964). Indeed, scientific theories generally don't handle questions of origins, generation, innovation, or emergence very well. When Darwin adopted the strategy of ignoring the question in On the Origin of Species, he let scientists off the hook, as Harriet Martineau and others noted at the time, ceding origins to creationists with his famous poetic cop‐out: “There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one” (1859, 484). Evolutionary biologists ever since have tended to follow suit, ignoring the question of life's origins as out of scientific bounds.

The science of origins has meanwhile grown up, moved on, gotten technical, and now has its own problems of internal consistency, empirical adequacy, and theoretical power to worry about. Perhaps the biggest theoretical challenge to the field is to settle into a set of theoretical principles and strategies of heuristic reasoning that are robust in regard to the daily empirical discoveries announced in the news, new extremophiles pushing the limits of what life can be (and what it can withstand), evidence of liquid water on Mars, new advances in synthetic chemistry. The field will remain somewhat unstable, subject to major conceptual swings, “pre‐paradigmatic” (Kuhn 1970) until it no longer experiences radical shifts of theory and approach with each new discovery—life based on sulfur metabolism, “bio”chemicals in comets, surface catalysis by pyrite, catalytic RNA.

It is high time that philosophers of biology looked in on the field, since there are many conceptual challenges to be met. The conceptual instability makes it exciting and a good place to study disciplines and interdisciplines in formation (and decline). A fundamental challenge for philosophers of biology weaned on evolutionary theory, Mendelian genetics, and units of selection questions is how the origins of units of life are related to the evolutionary process: If life evolved from nonlife, then the units of evolution need not have properties of familiar contemporary units of life, else life must not have originated by evolution. Either way, a philosophical world view built on evolutionary theory and units of contemporary selection must be incomplete. One of the most interesting social‐epistemological aspects of origins of life research as it is now practiced is just how many sciences must be brought together to make any single, apparently simple point. At every turn, the physics matters, the chemistry matters, the geology matters, and the biology—including the biggest problem of all: What is life?—matters. Even the astronomy matters. Just when the bombardment of the Earth‐in‐formation by (p. 265) comets and planetesimals ceased is a hot topic in origins of life work, for example, because that sets the lower bound on when life could have emerged and persisted. Current practices of origins of life research should be of interest to philosophers concerned with the social organization of research, questions of disciplines and interdisciplines, collaboration and integration, unity and disunity. Hazen (2005) gives a nice, personal, narrative introduction to these sorts of questions and some of the major players.

As with other disciplines organized around “big questions,” approaches and methods are eclectic, theories and principles are diverse. Research methods range from database analyses of millions of organic molecular species (e.g., Morowitz et al. 2000), to inferences from geophysical and fossil data (e.g., Schopf 1983, 2002), chemical synthesis of cell‐like components (e.g., replicators: Rebek 1994; von Kiedrowski 1986; coacervates and membranes: Oparin 1924; Fox and Harada 1958; Hargreaves et al. 1977; Hanczyc et al. 2003), to experiments on hypothesized early Earth conditions (e.g., Miller 1953; Orgel 1994), historical reconstructions of the last universal common ancestor of modern life (LUCA, see Woese 1998; Delaye et al. 2005; Doolittle 1999a), abstract models of cells and theoretical deductions from core functions of extant life (e.g., Gánti 1971; Morowitz et al. 1988; Morowitz 1992; Gánti 2003a, 2003b; Smith and Morowitz 2004), to geochemical and biological observations of deep‐sea hydrothermal vents (e.g., Schwartz and Chang 2002; Miller and Lazcano 2002) and other planets (e.g., Bibring et al. 2004).

Theories and principles are equally diverse, from replicator‐first theories (e.g., Eigen 1971, 1992; Pross 2004), to protein‐first theories (e.g., Fox and Harada 1958; Kauffman 1986, 1993), metabolism‐first theories (e.g., Wächtershäuser 1988, 1990; Morowitz 1992), dual‐origin theories (e.g., Dyson 1985), ribosome‐first theories (e.g., Poole et al. 1998, 1999; Penny 2005), to thioester and iron‐sulphur worlds, surface metabolism, and “takeover” theories (De Duve 1991; Wächtershäuser 1988, 1990; Cairns‐Smith 1985), exobiology (Sagan 1961), and (neo)panspermia (Crick 1981).

It is perhaps misleading to pigeonhole researchers on the big questions, since theoretical views are usually more complex than the simple contrasts and dichotomies around a single question can convey. For example, Morowitz is concerned that energy flow in far‐from‐equilibrium conditions, where persistence requires dissipative flows of matter and energy, generally requires some kind of phase separation, so probably membranes of some kind arose along with metabolism. For him, the important theoretical contrast is with genes‐first views that neglect energetic considerations and with otherwise friendly views like Wächtershäuser's and Cairns‐Smith's, which suggest that primordial phase separation was due to surface catalysis rather than reactions in membrane‐enclosed solutions, and with De Duve's, which suggests that the first metabolism‐driving energy system was probably sulfur‐based rather than phosphorus‐based (as in modern metabolism with its central role for ATP). Other theories are equally nuanced, but simple contrasts can be instructive, and the concern to answer the question “with whom” did life begin?—which are the significant molecular actors to first put chemical systems on the road to life?—is shared by all.

(p. 266)

There is ample scope for philosophical work on origins of life studies to explore broad questions such as (1) whether and to what extent the many and diverse scientific concepts, hypotheses, and principles fit together logically, metaphysically, methodologically, theoretically, and empirically; (2) how and to what extent diverse empirical methods can provide good evidence to support claims about origins, including traditional questions of explanation and confirmation; and (3) what are the scope and limits of biological science in relation to other sciences, including traditional questions about reduction and emergence. More than a century after Darwin, many philosophers of biology have, in my humble opinion, become somewhat complacent about the general problem structure of biological theory, concepts, modes of reasoning, and indeed the basic accepted facts of life—as comfortable with broadly Darwinian explanations of adaptation and evolutionary diversification, for example, as Darwin was with his old stuffed chair and writing desk. His vision no longer seems grand enough, however, in the face of our vastly greater knowledge of chemistry, biochemistry, molecular developmental biology, phylogenetic systematics, evo‐devo, epigenetics, genomics, proteomics, and metabolomics, in addition to paleobiology, geophysics, geochemistry, mineralogy, climatology, and astrobiology. We want to know not only how adaptation and divergence among organisms and molecules in populations are driven by variation, competition among fitness variants, inheritance, and stochastic processes, but also how the levels of life originated in the first place—including not just the familiar level of animals and plants, but cells with genomes organized into chromatin packaged in nuclei, multicellular organization in several kingdoms of life and colony‐grade organization in others, species organized into sexually reproducing family units, species with eusocial division of reproduction labor, species with epigenetic, behavioral, neural, and symbolic communication systems, and possibly ecological organizations with evolutionary potential above the population or species level (Margulis 1981; Buss 1987; Maynard Smith and Szathmáry 1995; Griesemer 2000a, 2000b, 2000c; Jablonka and Lamb 2005).

Origins of life studies have advanced significantly since Darwin (1859) took what was then a prudent course, limiting his remarks in On the Origin of Species to the speculation that life was “first breathed” into one or a few forms. Today, origins of life studies present such a number of challenging puzzles and foundational problems that philosophers of biology will miss important opportunities to test their ideas and arguments if they neglect the topic of origins. Origins of life studies are “extreme biology,” which may need to be matched by equally extreme philosophy. New philosophical as well as biological ideas may be needed to answer the big questions and address the big problems, since many biological assumptions, upon which contemporary philosophical notions were built, must be reexamined in the light of origins research. It is good engineering practice (Wimsatt 2007) to take engineered concepts to extremes to find out how they break down and to learn how to fix them from studying the breakage patterns. Origins of life research is a good test bed for philosophical ideas about biology, as has been philosophical work (p. 267) pushing ideas about organisms and units of selection to extremes in the contexts of group, species, and genic selection.

One of the most exciting contributions that origins of life studies can make to philosophy stems from the challenges they present to philosophical concepts developed for the biology of modern living things. Can replicator theories of the units of selection explain the evolutionary origin of replicators? Not if our concept of evolution entails the existence of replicators as a precondition of the operation of Darwinian selection. Can theories of the gene work to explain the origin of genotype‐phenotype maps? Not if gene concepts entail the existence of transcription and translation processes with nucleic acid polymers long enough to code for protein enzymes. Can theories of phylogenetic inference describe the deepest ancestors of modern life? Not if monophyly is required for such inference, since primordial life may not even be “lineage‐like,” let alone monophyletic (see Woese 1998; Doolittle 1999a). Indeed, can evolution explain the origin of life if life is defined as that which is capable of evolving (e.g., Maynard Smith 1986)?

Some fruitful entry points for philosophers of biology into the scientific and philosophical literature include Penny's (2005) excellent interpretive review, Fry's (2000) and Strick's (2000) insightful historical books, Deamer and Fleischaker's (1994) superb anthology of key papers from 1908 to 1992 (including excellent introductions to themes and concepts plus an additional bibliography), and books by Dyson (1985), De Duve (1991), Eigen (1992), Maynard Smith and Szathmáry (1999), Schopf (2002), Gánti (2003a), Knoll (2003), Hazen (2005), and Gesteland et al. (2006). Ruse's (1998) anthology has pertinent essays on the concept of life, including a 1985 essay by Mayr on the improbability of life.

Boundary problems, such as the nature of units of life and evolution in the extreme context of the physical‐chemical origin of units, raises conceptual challenges for the philosophy of biology as does no other topic: All of our biological assumptions must be reassessed or risk begging questions, e.g., that genes are made of nucleic acids, that life must be cellular, and even that evolution is the driving process. In origins of life studies, one learns to honor the converse of Dobzhansky's dictum. True, nothing in biology makes sense except in the light of evolution (Dobzhansky 1973), but by the same token, at the origins of life, evolution doesn't make sense except in light of the rest of biology. The problem is to understand what it is to be distinctively biological without begging questions.

The temporal remoteness of the originating events and conditions and the obscurity of the necessary fundamental principles leave many people supposing that origins of life studies are doomed to idle speculation, unfit for serious scientific investigation, or worse: fit only for an unresolvable confrontation of science with religious beliefs. Ethical questions about producing synthetic life forms which are not genealogically related to life on Earth are only beginning to be addressed (on synthetic life, see Bartel and Unrau 1999; Szostak et al. 2001; on the ethics of synthetic biology, see Economist 2006).

The history of the (Western) scientific study of life's origins is as challenging as the philosophical puzzles: It might be traced to Aristotle's work on the nature of (p. 268) generation, to sixteenth‐, seventeenth‐, or eighteenth‐century views on spontaneous generation, to nineteenth‐century panspermia theories—that life is as old as the universe itself—to Darwinian evolutionary ideas about the monophyletic ancestry of all life, to Chamberlin and Chamberlin's, Troland's, Oparin's, or Haldane's early twentieth‐century speculations about primitive Earth conditions and their consequences for geophysicochemical theories of origins, or finally to mid‐twentieth‐century experimental chemical syntheses of biochemicals beginning with Miller's famous experiment in 1953 (recounted by Orgel 1994; see also the introductions and essays reprinted in Deamer and Fleischaker 1994; Fry 2000; Strick 2000). An interesting early theme in the emergence of the origin of life question in the nineteenth century is that the question arose as a consequence of the final demise of spontaneous generation in the mid‐nineteenth century with Pasteur's work, together with the apparent inability of Darwin's contemporary evolutionary theory (or Darwin's unwillingness) to explain the origin of first life (Farley 1977; Fry 2000; Strick 2000; see also Orgel 1994; Penny 2005). How did/could it arise? Can an evolutionary theory explain the evolution of life from nonlife?

How one thinks about the history of the field has everything to do with one's conception of what the field is. The historiography of this field and its heroic myths are a bit fresher than those for genetics, evolution, and ecology, which are well known to the philosophy of biology community. There are opportunities here for comparative studies of discipline formation. Fry's historiographic hypothesis is intriguing and worth coordinating with historical work on molecular biology more broadly. She proposes that the early blossoming of origins of life studies in the 1920s and 1930s, centering on Oparin's coacervate droplet theory (1924) and Haldane's (1929) warm dilute soup, built on the key idea that early Earth presented a strongly reducing environment (no oxygen). The program they started stalled midcentury with the DNA revolution (Fry 2000, 86). After Watson‐Crick (and the Miller experiment) in 1953, attention shifted to gene‐centric theories of origins, fueled by the RNA world hypothesis building from the work of Woese and Orgel, and boosted by key discoveries about the catalytic properties of RNA by Cech and Altman (see Fry 2000; Deamer and Fleischaker 1994 for historical review). The questions Oparin and Haldane asked, however, were pushed aside rather than answered, despite the theoretical promise of their starting points.

Despite significant disagreement on many fronts in origins of life studies, there is emerging scientific consensus that life is indeed a natural property of certain types of organized matter (Morowitz 1992; Gánti 2003a; Penny 2005). A fairly rapid, naturalistic origin of life is deemed much more plausible than was supposed even in the 1960s. Some even suggest that the major problems will be solved through a combination of theoretical and empirical work in the next ten to twenty years (Penny 2005, 667).

Solving problems, however, does not mean that a coherent and satisfying theory of origins will be achieved. The integration of empirical and theoretical results from a variety of specialties will be required, and that presents additional opportunities for philosophers interested in problems of theory integration. Nor (p. 269) does solving big problems mean that controversy about fundamentals will abate, since the conceptual basis for problem solutions seems to be undermined periodically by new empirical discoveries (e.g., hydrothermal vents and associated organisms with unusual metabolisms, water on Mars, catalytic RNA, massive lateral gene transfer among archaea, bacteria, and eucaryota, and so on). One might be tempted to call origins research perpetual “pre‐paradigm” science (Kuhn 1970), were it not for the fact that debate within and across the specialties involved is so highly articulated and so supremely commensurable. Although nearly every proposal is hotly contested and it is hard to keep score, with distinguished scientists drawing on a wealth of data from many different fields and perspectives to promote very distinct views, it is clear to all when new empirical discoveries threaten favored assumptions and why. Yes, catalytic and self‐catalytic RNA is a big discovery, but how did these “naked replicators” get the energy to carry out catalysis? If it's from high‐energy phosphate bonds in ATP or GTP, which intriguingly are involved both in energy metabolism and nucleic acid synthesis and as coenzymes in proto‐translation (Poole et al. 1998), then where did the high‐energy phosphate bonds come from? No incommensurability here—everyone can see where the problem lies. Perhaps the pre‐paradigmatic nature of origins research has less to do with the lack of a consensus paradigm and incommensurable concepts than with the challenge of attending to, and integrating, diverse discoveries and proposals.

The diverse nature of the subject matter—involving astronomy, thermodynamics, geology, paleontology, many branches of organic and inorganic chemistry, molecular biology, systematics, evolutionary biology, ecology, and much more—precludes a comprehensive survey of origins of life research and may compromise the consistency and coherence of even a partial perspective. The field is a giant jigsaw puzzle that tempts, but resists, simple historical narrative and clean conceptual reconstruction. It is, in short, a philosophical challenge. As William Wimsatt might say, origins of life studies will appeal to philosophers interested in dense rainforest ontology rather than spare desert landscapes, webs of heuristic inferences rather than straightforward tales of reduction (or supervenience), and of course, diverse modeling, experimental, and observational practices in which to muck about. The field should especially appeal to those who feel that philosophical controversies (e.g., units of selection; phylogenetic inference; concepts of gene, organism, species, function) are increasingly being settled by shifts of interest and attention rather than by good philosophical arguments, since it seems that everybody's arguments break down when applied to problems of origins. This is not an accident: Our philosophical theories about biology were framed in the twentieth century by Darwin's nineteenth century theory of evolutionary transformations. We need a fresh start to deal with problems of biological origins.

In the remainder of this chapter, I sketch (of necessity, idiosyncratically) some ways in which origins of life studies have been invigorated in the last half‐century by advances that combine theoretical, empirical, and conceptual insights. This thematic focus on confluences of the theoretical, empirical, and conceptual helps to cut a path (p. 270) through terrain so dense that it is hard to know even the scale of the problem. I focus on five topics: (1) the time window in which life arose or appeared on Earth, which has been narrowed significantly by empirical discoveries about the early Earth, leading to a substantially changed outlook on the broadest “why” question: Did life on Earth arise due to a statistically improbable, all‐at‐once chance event or to some step‐by‐step mechanistic pathway making the appearance of life not only explicable, but likely? (2) the development of heuristic principles that serve to guide reasoning about laboratory experiments, field observations, and theoretical inferences about historical processes and patterns; (3) the pursuit, in many distinct specialties, of a conceptual strategy of “narrowing the gaps,” through which incremental progress in specialized research produces continual theoretical revolution by radically altering the plausibility of origins scenarios that must draw on work across many specialties; (4) the RNA world hypothesis, which promises to resolve some chicken‐and‐egg paradoxes of origins, e.g., the origin of differentiated functions of proteins and DNA in all life traceable to the last universal common ancestor, but which threatens to create new ones, such as which came first, the autocatalytic or heterocatalytic function? and (5) the structure and pattern of material overlap and lineage‐like relations between the chemical and biological worlds (see Griesemer 2000a, 2000b, 2000c, 2003) in light of the apparently nonmonophyletic (several times over) relations linking the pre‐RNA chemical world (Woese 1998; Doolittle 1999a) to the pre‐organism RNP world (ribonucleoprotein; see Poole at al. 1999; Penny 2005) to the “progenote” world (pretranslation, high lateral gene transfer; see Woese 1998) prior to the LUCA, which in turn may not be “an organism” with genealogical, lineage‐like relations to modern life at all but a complex community without a phylogenetically resolvable clade (Woese 1998, 6856).

Closing the Time Window on Life's Origins

Prior to the 1960s, the antiquity of life on Earth was traced to the origin of multicellular animals with hard parts at the beginning of the Phanerozoic, 540–550 million years ago (Schopf 2002, ch. 6). The Earth is about 4.5 billion years old, so life as it was then known spanned only about one‐ninth of Earth's history, perhaps one‐eighth after the planet cooled sufficiently that life could persist. Thus, it seemed that it took in the neighborhood of 3.5 billion years for life to emerge—a very long time, consistent with the view that life is highly improbable (Monod 1971; Mayr 1985, reprinted in Ruse 1998). Since then, more ancient soft‐bodied faunae have been discovered, and the date of the earliest fossils has moved steadily backward (Knoll 2003). It is now generally accepted that life existed around 3.5 billion years ago, near the beginning of the Archean era, in chert formations around the world (e.g., the (p. 271) Warrawoona group in Australia) in which can be found stromatolites thought to be the fossilized remains of microbial mats (Morowitz 1992, 34; Schopf 2002, ch. 6). Isotope evidence from the Isua supercrustal group in Greenland may extend the record back to as early as 3.8 or 3.9 billion years ago, at most a few hundred million years after the planet became suitable for habitation, roughly around 4.0 to 4.2 billion years ago (Morowitz 1992, 36; Fry 2000, 123–26; Schopf 2002, ch. 6). It is widely believed that Earth was too hot and too violent for anything remotely like life to have arisen earlier than 4.1 to 4.2 billion years ago (Joyce 1991; Morowitz 1992); the oldest evidence of crustal rocks dates from 4 billion years ago (Knoll 2003). High temperatures would have denatured fragile biochemical polymers and driven chemical reactions in unsuitable directions. Frequent bombardment by large meteorites would have boiled away whatever water was present at the surface, sending proto‐life back to the drawing board. This narrows the time window for life's origin on Earth to a span of 0.2 to 0.4 billion years. Some close the window even more, to a mere 100 million years (Penny 2005, 660). A few close the window to a mere crack: 10 or even 5 million years, based on arguments from impact data, the universality of metabolic reactions using a small set of small molecules as building blocks, and the plausibility of rapid genome evolution by gene duplication (Lazcano and Miller 1994, cited in Fry 2000, 126).

Of course, this reasoning presumes that life on Earth began on Earth. If life (or its significant biochemical constituents) began elsewhere, e.g., Mars, comets, or interstellar space (Crick 1981; Chyba and Sagan 1992), then the time window for life's origin might be wide open, with only the last steps or finishing touches passing through Earth's narrow window. Evidence and theory both suggest that extraterrestrial processes contributed substantially to the origins of life on Earth, in the form of a huge input of carbohydrates, amino acids, nucleic acids, metals with catalytic significance, and water from comets and meteorites (as much as 50,000 tons of organic material per year by one estimate; see Fry 2000, 115). All of the water on Earth could have been carried in approximately 1,000 comets that fell to Earth during the bombardment period (Fry 2000, 115). On the other hand, it is not known whether Earth's water is in fact derived from comets or mainly from the condensation of outgassing volcanoes. New evidence of (recently) liquid water on Mars raises the possibility of a Mars origin of life (Bibring et al. 2004), since it is known that material from Mars can be ejected by impacts on that planet to rain down on Earth.

Whether one takes the best estimate to be 0.01, 0.1, or 0.4 billion years, the window is dramatically narrower than it was once thought to be. Even at 0.4 billion years, the window is narrower than the whole Phanerozoic and roughly half the span since the Ediacaran fauna.

The significance of this narrowing is not only that the geological context in which life first appeared on Earth is better resolved, circumscribing the search for the chemical, lithospheric, geospheric, and atmospheric conditions. It also provides increased reason to think that life, per se, is probable. The concept that life took a long time to appear helped to fuel the notion that it arose stochastically, all at once (see Fry 2000; Penny 2005). Ironically, a long time frame seems to support a (p. 272) chance origin while a short time frame seems to support a “deterministic” (causal‐mechanistic) origin. The long time frame could be interpreted as the waiting time necessary for a highly improbable chance event to occur “all at once.”

The spontaneous, chance emergence of life, in turn, explained away (for some) the air of paradox in the origins problem as well—that all of the parts of living systems are functionally interlocking and mutually dependent, so there could not be a drawn‐out process and pathway to the origin of functioning living systems, fulfilling a wealth of life criteria from self‐maintenance and growth, to movement and sensation, to reproduction, inheritance, and evolvability (see Gánti 2003a on life criteria). That point raises still other problems, but however the magic was worked to fit together a metabolism, a membrane, and a genetic system capable of replication, transcription, and translation, it reinforced the idea that life would take a long time to emerge. How strange that adaptationist evolutionary biologists like Mayr (1985[1998]), following in Darwin's gradualist footsteps, should resist the idea that complex systems would arise in a sequence of incremental steps and instead endorse sudden emergence in a very improbable chance event because they think that life must have taken a long time to arise.

The origin of life problem may be the last scientific refuge for doubts about the explanatory power of Darwinian argument. Darwin was wise to avoid it, choosing to defer to the conventional wisdom that life was “breathed” into existence (1859, 484). Just as Darwin's nineteenth‐century critics doubted that a simple mechanism like natural selection together with his theory of descent with modification could explain the origin of complex adaptations or new species, doubts about the nature of the steps toward life are swept aside if life originated in a grand, stochastic, accidental flash of chemical emergence. This style of explanation provided an opening to twentieth‐century religious doubters, who exploited the chance view of life's origins to push doubts about probabilities to extremes as a way of endorsing the alternative view that life is simply too complex to arise all at once by any naturalistic means and therefore must have been designed (see discussion of the views of Hoyle and Wickramasinghe and intelligent designers in Fry 2000, ch. 13). It would be amusing indeed if it took an initial push from creationists for evolutionists to realize that defending a long time window for the origins of life actually seems to run contrary to the expectation that life evolved from nonlife.

If the time window is narrowed to as little as 100 or 10 million years, life begins to look like the product of natural forces operating continuously on (admittedly, poorly known or unknown) natural mechanisms rather than on improbable chance events that take a really long time to occur. If 100 million years could do it under early Earth conditions, then why not on other planets, in a similar phase of a planetary and solar system life cycle? Why not, indeed, wherever and whenever the chemical starting kit is to be found? The narrowed window doesn't close the gap sufficiently to distinguish plausible from implausible chemical pathways to life from the chemical realm, but it does close it sufficiently to shift the weight of attention toward chemical mechanisms and the structuring of a mechanistic path and away from “mere” chance (Penny 2005). Narrowing the gap reduces the plausibility of (p. 273) chance explanations of life's origin at the same time that it puts the squeeze on the idea that there is room for God to explain the gaps in nature left by scientific uncertainty.

Heuristic Principles for a Science of Viva Incognita

Definitions and heuristic criteria

Many contributors to origins of life studies offer definitions or criteria for life, living things, the living state, or the living world (e.g., Maynard Smith 1986; Fleischaker 1994; Gánti 2003a; Deamer and Fleischaker 1994; Luisi 1998; Cleland and Chyba 2002; Ruiz‐Mirazo et al. 2004). In the definitional approach to heuristic research strategies, the idea is to define life and then use the definition to probe for satisfaction of the definition among real or hypothetical chemical systems. If one of these definitions could gain wide acceptance or at least serve to reduce controversy about the nature of life, it might serve as a general heuristic to guide research into the unknown terrain of what life was like before the last universal common ancestor, which was clearly a unit of selection in the accepted sense of something that could exhibit heritable variation in fitness, lived in populations of such entities, and was cellular in organization, having all of the major constituent subsystems of modern cells: a lipid bilayer membrane; a DNA polymer genetic subsystem engaged in replication, transcription, and translation; and a robust metabolism with phosphate‐based energy transduction, photosynthesis, and biosynthetic pathways. In short, the LUCA was too similar to modern life to be much of a guide to how life of that sort could have originated from mere chemicals.

Because there is a constant risk of embedding biological assumptions about the nature of life in the theories, models, principles, hypotheses, and heuristics used to explore and explain origins, there is a continual risk of begging the question in the definitional strategy for producing reasoning heuristics for a field like this. Origins of life researchers may be more explicit than most in their attempt to define and delimit the entities they talk about and concepts they use, but the risks of circularity and question begging are greater as well. The goal of this section is not to canvass all definitions and life criteria, but rather to indicate the role that conceptual work to articulate heuristics plays in relation to empirical studies. As I have argued elsewhere (Griesemer 2003), the heuristic benefit of “definitions,” or rather, criteria, depends on conjunction with a model of a minimal living system. The benefit of teaming criteria with a model is that the two together facilitate an iterative process of interrogation and improvement of criteria and model through application to real‐world phenomena.

(p. 274) Heuristic principles

An alternative to the definitional approach is to develop metaheuristics that delimit the evaluation of criteria, models, and evidence rather than attempting to delimit what constitutes life. Several fundamental heuristics principles are used by a wide variety of origins of life researchers. This section considers some of the central ones that raise philosophical questions. Penny (2005) lists a dozen or so such principles, which cannot all be considered here.

Continuity, microreversibility, actualism

Morowitz (1992) and Penny (2005), among others, endorse a principle of “continuity” in reasoning about origins of life. Penny (2005, 637) likens the principle to Lyell's principle of actualism in geology: “Basically, we aim to explain the past by, in Lyell's phrase, ‘causes now in operation.’ ” (See Ruse 1999 for an introduction to Lyell's and Herschel's actualism.) Morowitz (1992, 14) uses the principle as a means to limit investigation “to those hypotheses that are subject to analysis using the experimental, theoretical, and epistemological tools of normative science.” This means, roughly, that those speculative hypotheses which propose stages in the history of life that would entail radical “takeovers” by modern forms replacing very different ancient ones are ruled out of consideration, not because they are impossible, but because they are much less open to investigation. Morowitz (1992, 90) rejects Cairns‐Smith's (1985) “genetic take‐over” of a clay‐mineral world of surface catalysis by the nucleic acid world on grounds of discontinuity (among other reasons). He also rejects Wächtershäuser's (1988) iron‐sulphur world of pyrite surface catalysis (that life began on rock surfaces with pyrite as the catalyst, without benefit of membranes to hold in reactants and products, with energy coming from energetic sulfur at hydrothermal vents) and panspermic theories (that life originated in space, cold and slow rather than hot and fast) for similar reasons.

Penny (2005, 640) elaborates on the continuity principle, arguing that it is equivalent to a principle of microreversibility: In the many intermediate, mechanistic small steps toward life, each is to be assumed reversible, so there is no “miracle” in a succession of them. It is open to question whether this principle is equivalent to continuity as stated or that its use is equivalent in practice. Maynard Smith and Szathmáry (1995) make much of a principle of “contingent irreversibility,” in which a sequence of presumably reversible steps add up to a contingently irreversible result, such as the sequential loss of genes of endosymbiotic bacteria to the host, leading to the evolution of organelles. If Penny's principle is “micro,” in the sense that it operates in the chemical or quantum domain, it should be fully consistent with Maynard Smith and Szathmáry's contingent irreversibility in the “macro” domain of cells and organisms. But it is not entirely clear what should count as micro in this context. How many chemical steps can be microreversible, (p. 275) yet add up to biologically contingent irreversibility? The slippery slope here should hold some interest for philosophers.

Pushing beyond the current literature somewhat, consider the following sort of microreversible, multistep process: the eventual emergence of genetic coding, and whether its origin is consistent with the spirit of the continuity principle. There are many scenarios for this process. Here I consider only two in order to formulate the question.

On Penny's hypothesis about the origin of the code, the proto‐ribosome was a complex of RNA molecules involved in RNA replication rather than translation, binding single‐stranded RNA (the precursor of mRNA) in order to replicate it (Jeffares et al. 1998; Poole at al. 1998, 1999; Penny 2005). The precursors to tRNA were nucleotide triplet donors. That is, in the pretranslation world, proto‐tRNAs were nucleotide triplets donating packets to replicating RNA molecules, rather than the triplet serving as “anti‐codon” in a larger tRNA molecule (of about seventy nucleotides) to pair with mRNA in translation of mRNA sequence into amino acid sequence (protein). In the model, the precursor to the anti‐codon triplet in the precursor to tRNA exchanges functions with an amino acid coenzyme “handle” attached to the other end of the “tRNA.” A modern tRNA is a complex, folded RNA molecule with the triplet anti‐codon at one end and an amino acid attached at the other end (by the operation of a protein enzyme, the aminoacyl tRNA synthetase). In the model, the amino acid is attached as a coenzyme to help catalyze the addition of the nucleotide triplet in RNA replication. Instead of the amino acid remaining on the proto‐tRNA as coenzyme and the nucleotide triplet being donated to the replicating single‐stranded RNA as in the hypothesized ancient RNA replication mechanism, after the exchange of functions in the evolutionary pathway to modern translation (of RNA to protein), the anti‐codon triplet becomes the catalyst, retained in the tRNA, and the amino acid is donated to a growing polypeptide (Penny 2005, 650).

In Szathmáry's (1993) coenzyme handle hypothesis, coding arose before translation. The amino acid attached to a nucleotide triplet, the primordial tRNA anti‐codon, was supposed to improve the efficiency of a larger RNA ribozyme that functioned as a synthetase enzyme. The ribozyme would “grab” the amino acid coenzyme by its RNA triplet handle via base‐pair hydrogen bonding. In other words, the anti‐codon triplet filled the role of a handle for the amino acid as coenzyme to the ribozyme. In this model, the proto‐tRNA and coenzyme handle amino acid serve in the catalytic enzyme function of ancient RNA rather than serving RNA replication, as in Penny's model. In Szathmáry's model, coding originated as a means of improving the catalytic efficiency of RNA enzymes (“ribozymes”). Eventually, the amino acid coenzyme evolved into the protein synthetase enzyme, by addition of amino acids to the original one to improve the catalytic efficiency of the ribozyme still further, and the triplet handle evolved into the tRNA of modern translation, so the RNA ribozyme and amino acid coenzyme exchanged functions.

Penny's ribosomal RNA replication hypothesis and Szathmáry's coenzyme handle hypothesis both involve the exchange or transfer of function, as opposed to mere “change” of function, as is common in Darwinian explanations of the (p. 276) evolution of complex adaptations. After an exchange of function in which A formerly did F and B formerly did G, A does G and B does F. In a transfer of function in which A formerly did F to B, B does F, either to A or to some C. These sorts of cases involve interactions among entities that carry out distinct functions, but also provide “scaffolding” services to the other entity with which they interact (see Fry 2000, 185–90). For example, when a clay or mineral surface provides catalytic opportunities to molecules interacting at the surface, as in Cairns‐Smith's clay surfaces or Wächtershäuser's iron‐pyrite surfaces, the surface catalyzes the reaction so that the reactants don't have to, lowering the “fitness cost” of proceeding at a slower rate than they otherwise would. Scaffolding provides a fitness benefit to what it scaffolds (Bickhard 1992; see Wimsatt and Griesemer 2007). When a scaffold A (that also happens to do F) plays a role in the realization of function G in entity B, there is an opportunity for the function F to be transferred to entity B and, conversely, for function G to be transferred to A (if B scaffolds A as well). (Wimsatt and Griesemer, 2007, discuss the central role of scaffolding in biological and cultural evolution.) The important question in the present context is whether exchanges and transfers of function of the sort described above in the evolution of translation and coding are consistent with the kind of heuristic continuity principle endorsed by Morowitz and Penny. Exchanges and transfers involving scaffolding seem to implicate the sort of takeover (of function) arguments that Morowitz rejects, yet they seem entirely in the spirit of Penny's microreversibility principle, since each of the scaffolding steps in the models are chemically reversible processes in the relevant sense.

Multiplicity of approaches

This heuristic principle is not stated as such, but the bottom‐up and top‐down approaches are generally endorsed as complementary and both necessary, and the combination favored over either one alone (Morowitz 1992; Penny 2005). Bottom‐up, or “forward,” reasoning runs from the physical‐chemical realm and early Earth conditions to the biological realm. Top‐down, or “backward,” reasoning runs from modern life to the chemical realm and the deep past. Of particular interest is that pursuing the dual approach generally requires ranging outside one's specialty and often seems to generate “gaps,” whose closing constitutes a major research activity.

The closing of the time window discussed above is a good example of the multiple‐approaches heuristic strategy: Physics, chemistry, and geology are used in bottom‐up reasoning to describe the conditions prior to and preparatory for life. Paleontology, comparative biochemistry, and phylogenetic inference (drawing heavily on molecular studies of, e.g., universally distributed molecules like rRNA) form the core of the top‐down approach, reasoning backward from contemporary life and fossils to the last universal common ancestor. The gap that arises between precellular systems and “ur‐cells,” on the one hand, and the LUCA, on the other, is considerable, but serves to delimit problems and to focus research.

(p. 277)

For example, Morowitz (1992, 88) urges that the first living cells arose by physical‐chemical principles, but the last universal common ancestor of modern life is far too complex to be the result of continuing operations and that the two must be bridged by an evolutionary account. So, the applicability of evolutionary explanations becomes a new kind of project to narrow that gap (see below). Arguments about phylogenetic inference based on monophyly criteria break down at the time of the LUCA because of massive lateral gene transfer, among other reasons, creating a deep theoretical problem to apply evolutionary reasoning in the gap (Woese 1983, 1998; Doolittle 1999a, 1999b). New theoretical tools will probably be needed (Woese 1998; see below).

Current utility

Penny (2005, 650) argues against teleological principles, suggesting that the origin of the ribosome and triplet coding cannot be explained as arising for the sake of protein synthesis (a teleological explanation). He points out that ribosomes are so complex that they must have evolved for a different function and then changed functions. As discussed above, he proposes that ribosomes were originally involved in RNA replication and were later recruited for protein synthesis (see Poole et al. 1998, 1999). This is standard evolutionary reasoning about a change of function. It supposes that the pretranslation world was one with units of evolution capable of undergoing this kind of Darwinian process. It would be interesting to apply contemporary conceptual tools to evaluate how the science fares in cases like this, given that many models and proposed mechanisms are not variation and selection models, but rely on appeals to chemical interactions leading to novel functions, with little attention to the competitive processes that would make such cases evolutionary. Put differently, if evolutionary arguments don't apply anyway, what's the argument for the current utility heuristic? Presumably, no one is tempted to offer them in chemical explanations, and it would seem important to establish that evolutionary explanation is relevant before enforcing a current utility principle.

Penny (2005) lists many more principles, including (1) respecting the “Eigen limit” (on the sequence length that can be maintained for a given mutational error rate of replication and strength of selection), (2) the prohibition on reversals from more‐efficient to less‐efficient mechanisms (such as the takeover of a catalytic function of a more‐efficient protein by a less‐efficient RNA), and (3) the commitment to rest arguments on universally distributed, common materials rather than rare ones. Morowitz, for example, argues for the origin of life from a metabolism‐first point of view, rather than involving proteins or nucleic acids, in part because the former involves only the most common atomic elements, C, H, O, and P (lipids also require S), while the latter require N as well. Morowitz concludes from this that life may have started in a “pre‐nitrogen” world lacking amino acids and nucleotides (1992, 134). That is a parsimony principle of sorts, but it is not at all (p. 278) clear whether it squares with the kinds of defenses or attacks philosophers have mounted on parsimony in other realms of biology.

My purpose in this section has been to indicate the richness and philosophical interest in the kinds of principles at work in origins of life studies and their heuristic role in guiding reasoning about experimental results and theory alike. There is much more to do than this preliminary report can convey.

Mind the Gaps

As described above, the combination of bottom‐up and top‐down approaches can leave gaps that provide a focus for further research. Bringing together concepts and results from the two approaches often generates gaps as well because the methods and theories brought to bear often differ substantially. In this section, I consider several contrasting views about the conditions, contexts, and properties considered to apply at life's origins, which illustrate both the gaps and some of the fruitful research problems they generate.

A key issue in contemporary discussion is whether life had a “hot start” or a “cold start” (Penny 2005, 658). Haldane (1929, reprinted in Deamer and Fleischaker 1994) imagined that life began in a “hot dilute soup” (Haldane [1929]1994, 78), supposing that life began more or less as soon as the Earth had cooled enough to form a crust and organic constituents had built up in the oxygen‐free, nitrogen‐rich oceans. (The richness of the soup also suggested to Haldane that the first living systems were heterotrophic, relying on the rich broth to supply new components to keep a reproductive process going.) More recently, the theory that life first started around sulfur‐rich, deep hydrothermal ocean vents created by undersea volcanoes emitting superheated water suggested another reason to support a hot start. Moreover, phylogenetic reconstructions place the LUCA among thermophiles, organisms that live in the hottest environments known on Earth today, upward of 113° C.

Penny (2005, 658) is not so sure (see also Trinks et al. 2005). He points out that the phylogeny is flawed, that ribonucleotides and RNA are unstable and fail to fold correctly at high temperatures. He cites Bada and Lazcano (2002), who endorse a cold start. Moreover, ordered structures form more readily in the cold, freezing concentrates chemicals, rates of reaction may not be limiting if large amounts of time are available, and temperature falls off with distance at hot vents, so it isn't clear whether vent life was all that hot (Penny 2005, 659).

My purpose isn't to evaluate the two contrasting hypotheses, but to point to the productive nature of the gap separating them. Those who endorse a hot, deep‐sea start also must consider whether the correlative high pressure makes for a plausible start. Those who endorse a cold start, e.g., inside comets, must establish that suitable reactions will actually occur. The pair of alternatives arises from trying (p. 279) to bring different bottom‐up and top‐down data together, and in the process spawns new questions, as Penny points out, such as whether nucleotides are stable at high pressure and whether pressure promotes or inhibits polymerization (2005, 660). Alternatively, cold‐start scenarios more easily take advantage of evidence of the delivery of organic materials developed in comets and meteorites, or that the materials are synthesized in the shock impact (Chyba and Sagan 1992). Closing the gap requires of each set of proponents that they reconcile not only the two hypotheses, but make sure that all the data are consistent with the assumptions of their starting points from above (in biology) and below (in physics and chemistry).

Another, similar contrast is whether life started in the wet or the dry and, if wet, whether shallow or deep. Shallow water (i.e., in intertidal zones) is subject to cycles of wetting and drying, which can serve to concentrate chemicals, but on the other hand, the chemistry may not be very “aqueous” during the drying phases, so theories that are based on aqueous‐phase chemistry may be inadequate even if the hypothesis includes a water phase. Deep water, such as around hydrothermal vents, raises other chemical puzzles, as mentioned above. The point here is that each empirical or theoretical development on either side of the gap has ramifications for the other, and the subject advances by point and counterpoint: “No, it's absurd to think life could exist on Mars; there's no water.” “Ah, but there is water, just beneath the surface, and possibly liquid until recently.” Each of these debating positions entails diverse and ramifying consequences, each potentially relevant, as if each step in the argument shifts the magnitude of a fundamental constant such that the whole character of the universe has to be rethought at each step. Narrowing the gaps thus breeds new problems as pressure is put on other dimensions of every scenario consistent with that one dimension: hot or cold, wet or dry, autotrophic or heterotrophic, reducing or neutral atmosphere, includes or excludes nitrogen, soup or surface.

Which Came Second, DNA or Protein?

The RNA world hypothesis made the (modern) world safe for DNA and protein. The origin of life appeared to be an intractable problem, even a paradox, when it was realized how intricate were the interrelations between DNA as the carrier of genetic information and protein as the coded catalytic agent of the cell. The central dogma (“once genetic information gets into protein, it cannot get out again”; Crick 1958, 1970) and a division of molecular labor between DNA and protein were worked out after Watson and Crick's model of the structure of DNA was presented in 1953. The genetic code and basic outlines of the processes of replication, transcription, and translation were established in the 1960s (described in Kay 2000). It seemed hopelessly unlikely that there could be a long series of intermediate steps to (p. 280) produce the DNA‐protein system de novo since DNA only “acts” in replication and transcription as a function of protein enzymes while protein enzymes only function in accordance with the specification of their structure by DNA genes. The pedigree of this chicken‐and‐egg problem of structure, function, and process (Eigen 1971; Cech 1986) can be traced back, through distinctions between gene structure and gene activity, genotype and phenotype, and gene and character, to the interlocking problem of germ and soma in the nineteenth century (Maynard Smith 1975; Griesemer and Wimsatt 1989; Yamashita 2006).

The RNA world hypothesis neatly undoes the paradox that DNA and proteins can only exist together but cannot arise together by suggesting that RNA once served both the replicative information‐carrying function of DNA and the catalytic metabolic function of protein. Or, as Penny (2005, 644) pithily put it: “The RNA‐world: no protein, no DNA—no chicken, no egg.” The realization that RNA must have played a central role in both primordial autocatalysis and heterocatalysis goes back much further, to work in the 1960s by Woese, Crick, Orgel, and others (discussed in Cech 1986; see also Gánti 1971, 2003a; Eigen 1971). The hypothesis, named by Gilbert (1986), has become highly articulated in the wake of studies of RNA self‐splicing introns, the discovery that RNA has catalytic activity (Cech 1983; Guerrier‐Takada et al. 1983), and the subsequent demonstration of an increasing (and astonishing) variety of RNA abilities (reviewed in Doudna and Cech 2002; Penny 2005, 645–46).

The basic story is one of evolutionary advantage created by division of labor. RNA is an inefficient catalyst, and there would be an evolutionary benefit to better ones made of protein. Similarly, DNA is more stable than RNA, due to both the dehydroxylation of ribose and the methylation of uridine (U) to thymidine (T), which would be a benefit to genetic information storage and retrieval. Orgel (1994) recounts that it seemed plausible to evolve DNA from RNA (ribonucleotides are easier to synthesize than deoxyribonucleotides), securing a specialized function of storing genetic information in the former, but not to evolve RNA and DNA from autocatalytic, uncoded sets of proteins (but see Kauffman 1986; Mossel and Steel 2005; Goldstein 2006 on autocatalytic protein or metabolic sets). Orgel's arguments depend on the notion that what is easy or hard for a chemist to synthesize reflects the ease or difficulty of synthesis in nature, under early Earth conditions.

The evidence in support of the RNA world hypothesis following the discovery of catalytic RNA is strong: Szostak has shown in artificial selection experiments that RNA molecules can be selected for a wide variety of catalytic activities (Wilson and Szostak 1995), Joyce has shown that RNA can cleave peptide bonds (see Joyce 1989), and Noller has shown that the RNA rather than the protein in modern ribosomes performs the catalytic activity in protein synthesis, e.g., the translocation step moving tRNA within the ribosome (Fredrick and Noller 2003).

Familiar challenges of adaptive evolution apply to these early stages in the evolution of the LUCA. How did life get to the world of polyfunctional RNA in the first place, and how did life get from the RNA world to the division of labor present (p. 281) in the LUCA? Was it a classic story of duplication and divergence: duplication of RNA molecules, release of the extra copies from selective constraint, and divergence to more‐efficient DNA and protein specialists? But what exactly would it mean to say that a duplicated RNA molecule could “specialize” if the function had to be transferred (see above) to DNA or to protein? A lot of biochemical evolution has to be worked out to make this scenario plausible.

And if the model is duplication and divergence, at what level: duplication of RNA molecules in some local “hypercycle” system (Eigen 1971, 1992), or duplication of proto‐cells in something like Szathmáry's “stochastic corrector” model (Szathmáry 1986; Grey, Hutson, and Szathmáry 1995; Maynard Smith and Szathmáry 1995; Zintzaras, Mauro, and Szathmáry 2002)? Because RNA is not a very accurate catalyst, Eigen argued that the size of a replicating catalytic polymer would be limited by the replication error rate, which restricts the evolution of RNA catalysts to a maximum of around 100 nucleotides in length, which is too small to code for modern proteins (Eigen 1992). This problem could be overcome, in theory, if genetic information were distributed in a set of such catalysts which served to catalyze one another's replication, forming a hypercycle. Szathmáry's stochastic corrector model was introduced to solve problems with the hypercycle model (products would diffuse away if not enclosed in a membrane, but if enclosed, the hypercyclic organization appears unnecessary to overcome the Eigen limit, given other plausible assumptions). Szathmáry's model is a group selection model while Eigen's looks like a “genic” selection model—shades of the units of selection debate of the 1970s and 1980s, recast in chemical and molecular terms.

On the former problem of the origin of the RNA world in the first place, how did RNA gain the energy and component nucleotides to function as naked ribozymic replicator organisms? Nucleotides are not easy to produce in abiotic synthesis (Orgel 2000). And what about energy metabolism in the RNA world? For Szostak's discovery to support the RNA world hypothesis, we must still presume that phosphate energy was available in the RNA world and was what drove proto‐life as well as the LUCA.

On the latter problem, getting from the RNA world to the LUCA involves solving the problem of the origin of the genetic code, changeover (if necessary) from a primordial energy and nutrient metabolism to the contemporary one, and a host of related chemical problems. How did replication work in a mixed world of RNA and DNA before the advent of protein enzymes, or did protein enzymes come before DNA? Could a proto‐ribosome of the sort envisioned by Penny and collaborators (see above) handle DNA as well as RNA? It seems that the question “which came second, DNA or protein?” must be answered in order to build plausible scenarios from the RNA world to the LUCA (Poole et al. 1998).

More fundamentally, the RNA world hypothesis represents the extension of a genetic view of life to its ultimate conclusion in the sort of popular, yet theoretically inspired vision of Dawkins (1976). In order for there to be a world of evolvable living entities, they must have some means of preserving and transmitting those traits that survive selection's gauntlet. That is, the units of life are units of inheritance (p. 282) , carriers of heritability, as well as units of selection, carriers of variations correlated with fitness. It is beyond the scope of this chapter to reprise the units and levels of selection controversies that still continue, other than to point out that they are reinvigorated by the field of evolutionary transition studies, which attempts to explain the origins of levels of biological organization and not only adaptation and natural selection at those levels (Buss 1987; Maynard Smith and Szathmáry 1995; Griesemer 2000c). Because the origin of life represents the first possible evolutionary transition, in which there first arose units of inheritance capable of evolution, the question of which function (inheritance or selection) was logically first in the origin of life is an important issue, philosophically, theoretically, and empirically.

Phylogenetic Inference and the Origins of Life

The problem of phylogenetic relationships at the origins of life is central to many inferences made from the top‐down or backward strategy—reasoning back from contemporary organisms and taxa to what the last universal common ancestor must have been like. For example, Orgel (1994, 77) states:

One can safely infer that intricate features present in all modern varieties of life also appeared in that common ancestor. After all, it is next to impossible for such universal traits to have evolved separately. The rationale is the same as would apply to discovery of two virtually identical screenplays, differing only in a few words. It would be unreasonable to think that the scripts were created independently by two separate authors.

This safe inference depends on two assumptions: the heuristic assumption of continuity (discussed above) and the standard assumption of monophyly in phylogenetic methodology, i.e., that all members of a clade (group of related taxa) are related in hierarchical, genealogical relations of parent and offspring groups, which share a more‐recent common ancestor than any of the members of the clade do with any other taxon or clade. Monophyletic clades contain all and only the descendants of a given ancestor. Monophyletic clades have a branching tree structure such that the clade can be picked out of the overall “tree of life” by the ancestral node. The assumptions of continuity and monophyly together support inferences about patterns of character evolution and reconstructions of ancestry relations based on those patterns.

If these assumptions are violated, then cladistic inference cannot follow the usual methods (see Felsenstein 2004 for a review). Historically, there have been major debates in systematics about whether classifications should be purely and (p. 283) strictly monophyletic—e.g., Mayr defended so‐called evolutionary taxonomy against cladistics to allow for paraphyletic groups like birds in order to emphasize, in classifications, the important adaptation of flight in this group, even though elevating Aves to the same rank as “reptiles” implies that “reptiles” is not a monophyletic group because it does not include all and only the descendants of the common ancestor that birds share with lizards, snakes, turtles, and dinosaurs. Today, this debate has largely been won by phylogeneticists in favor of the view that, in order to properly analyze adaptation, ancestry must first be established (see Haber 2005 on phylogenetic thinking).

It appears that at least one stage in the early history of life violates these general assumptions of modern phylogenetic inference. Life overall is not monophyletic and, according to Woese (1998), not even “genealogical.” The modern living world is still basically a world at the bacterial “grade” of organization, and only human prejudice leads us not to notice. Just as David Hull once complained of “vertebrate bias” in philosophical thinking about the nature of organisms and units of selection (Hull 1988), there is “eukarya bias” in thinking about the vertical, lineage‐like structure of phylogeny. Two of the three domains (“superkingdoms”) of life are at this grade: the bacteria (true bacteria, mitochondria, chloroplasts) and the archaea (methanogens, halophiles, sulfolobus), while only one, the eukarya (protists, plants, fungi, animals), contains what most people, most of the time, think of as “life” (see Tree of Life Web Project 1997). Alternatively, Forterre and Philippe (1999) argue that the tree of life should be rooted in the eukarya, that confidence in molecular phylogenies is often misplaced, and that the fundamental fact challenging contemporary approaches to phylogenetics is that each of the three domains of life is a mosaic of the other two.

Because the earliest history of life back to the LUCA is about the bacterial grade of organization, the phylogenetic patterns created by its activities and mechanisms dominate the tree of life overall. A hallmark of this period of life's history and this grade of organization is lateral gene transfer, the transfer of genes (and other components) “horizontally,” rather than “vertically” within organism lineages. When genes are transferred laterally, it no longer follows that genes (and therefore the traits determined by genes) need be universally distributed due to common ancestry down vertical, monophyly‐producing organism lineages. A genetic mechanism, e.g., for disease resistance, can evolve in one lineage or clade and spread to many others. As Woese (1998) and Doolittle (1999b) observe, the phylogenetic patterns in this early phase of life's history are more web‐ or net‐like than tree‐like, as Darwin supposed and as modern phylogenetic methods assume.

This problem for phylogenetic inference is compounded at the origins of life if Woese's theory of universal ancestry in a progenote is correct (Woese 1983, 1998). Woese thinks that the most primitive forms of cellular life were so different from modern cells that he refrains from calling them organisms, introducing the neologism “progenote” (see Woese 1998, 6855). The hallmark of a progenote is that its translation mechanism is so primitive that modern (i.e., large) proteins could not be produced. Lack of modern proteins would mean that only small genomes could (p. 284) be maintained due to high error rates of replication (up to the Eigen limit). Hence, progenotes were “more or less bags of semi‐autonomous genetic elements … that would come and go, especially on an evolutionary time scale” (1998, 6856). Woese concludes:

Progenotes were very unlike modern cells. Their component parts had different ancestries, and the complexion of their componentry changed drastically over time. All possessed the machinery for gene expression and genome replication and at least some rudimentary capacity for cell division. But even these common functions had no genealogical continuity, for they too were subject to the confusion of lateral gene transfer. Progenotes are cell lines without pedigrees, without long‐term genetic histories. With no organismal history, no individuality or “self‐recognition,” progenotes are not “organisms in any conventional sense.” (Woese 1998, 6856)

Deep‐seated taxonomic beliefs, e.g., that the cellular world is divided into prokaryotes and eukaryotes, are likely false. That dichotomy apparently has to go, just as the notion that reptiles are a monophyletic clade had to go when it became clear that birds are dinosaurs. If Woese is right, then diagrams like Morowitz's (1992, 89, fig. 4), which show two radiations—one from the first proto‐cell to the time of the universal ancestor and one from the universal ancestor to modern microbes—are misleading. They show branching “cones of diversity” (Gould 1989), trees rooted in unique ancestors. Woese's view is that there was no such “ancestor,” but rather a community of entities engaged in so much lateral gene transfer that there are not well‐defined lineage‐like relations among the entities bearing the genes. Differently put, there may be gene trees back to the origin of genes, but nothing like organism trees back to the origin of cellular life.

One explanation for the gap between the last universal common ancestor and first life is, therefore, that the LUCA is the earliest point at which organisms with resolvable vertical organism lineages emerged. But what is the nature of that process of emergence? It does not coincide, apparently, with the origin of life, so we have a new problem of emergence, which is biological, but not yet familiar from the top‐down approaches involving phylogenetic inference based on assumptions violated at the time of emergence. Woese (1998) invokes an analogy with physics to introduce an alternative phylogenetic model of “genetic annealing” (see also Felsenstein 2004). At the very least, the problem of how phylogenetic structure itself emerges should be of interest to philosophers of systematics.


This review has only scratched the surface of a vast, emerging discipline of origins of life studies. The primary literature is rich with deep insights and provocative philosophical positions expressed by some of the best scientists of our time, including (p. 285) quite a few Nobel laureates (and quite a few others who deserve such prizes). There are problems of philosophical interest at all levels of detail, from metaphysical questions and heuristic metaprinciples, to epistemological questions raised by the complex disciplinary and interdisciplinary histories of the many interacting sciences involved, to questions of reduction and emergence relating biology and chemistry, to particular processes, mechanisms, functions, and structures of a more or less biological or chemical nature (including many important ones not discussed here at all, e.g., how the chirality of nucleic acids and sugars could emerge from chemical processes tending to produce mixtures, or how the side reactions that tend to poison biosynthetic pathways were controlled).

Versions of many traditional problems in the philosophy of biology arise in origins of life studies, e.g., units and levels of selection, group versus genic selection, the nature of replicators, genotype‐phenotype relations, function, and concepts of the gene, organism, species, and clade, as well as problems not touched on here, such as how developmental systems and niche construction theories might apply to the chemical systems of proto‐biology, and whether problems of modularity, quasi‐independence, near‐decomposability, and integration might work similarly or differently in this realm than elsewhere in biology. Many of the basic attitudes and assumptions that philosophers of biology bring to their considerations of modern biology are of dubious value in a world without genes, a world without organisms, and a world without genealogy as commonly understood. Origins of life studies offer to philosophers of biology a “laboratory” in which to test concepts and arguments designed for contemporary life and biology, by taking ideas to extremes and testing them under harsh conditions, just as origins of life researchers use biological, chemical, and physical laboratories to challenge and test their speculative scenarios about how life might have emerged in the harsh conditions of early Earth.


I wish to thank Michael Ruse and all of the authors in this volume for their forbearance and continued friendship. This chapter was a long time coming, and I appreciate the opportunity to add my voice to theirs.


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                                                                                                                                                                                                                            (1.) The premier journal in the field is Origins of Life and Evolution of Biospheres. It pluralized “Biosphere” in 2005. Other prominent journals in which origins research is published, besides the general ones like Science and Nature, include Journal of Molecular Evolution and Journal of Theoretical Biology.