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P1: KAF/KAA P2: KaF 0521829496c09.xml CY335B/Dembski 0 521 82949 6 March 10, 2004 1:5 9 Darwinism,Design,andComplexSystemsDynamics Bruce H. Weber and David J. Depew 1. the argument from incredulity When Saint Augustine was a young man he could not imagine how evil could possibly have come into the world. Later, he came to realize that this line of questioning was dangerous and could bring religion into disrepute (Confessions VI, Chapter 5; VII, Chapters 3–5). His was a wise realization. ‘How possibly’ types of questions may do effective rhetorical work in the early stages of a line of inquiry or argumentation, but the types of answers they en- gender are open to refutation by the answers to other types of questions, such as ‘why actually’ or ‘why necessarily’ questions. ‘Why actually’ questions – or at least an important class of them that are asked by scientists – have a remarkable way of shutting down ‘how possibly’ questions. When looking at the functional complexity of the living world, ‘how pos- sibly’ questions emerge rather intuitively. As Michael Ruse has pointed out, the traditional argument from design actually has two steps (Ruse 2002). The first move is from observed functional complexity to the notion that such phenomena appear to have been designed, the argument to design. During this process, alternative, natural explanations are rejected using the criterion of incredulity: how possibly could the vertebrate eye appear as a result of random events, even under natural processes and laws? This was the line of argument taken by William Paley some two centuries ago (Paley 1802). In effect, he dared anyone to come up with a fully natural explana- tion of biological functional complexity. The remainder of the project of natural theology is to argue from design to the existence of a designer, and even to deduce attributes of the designer God from the properties of His designed Creation. Darwin, who as an undergraduate had read and admired Paley, took Paley’s dare and made his research program that of finding a natural ex- planation of apparent design by way of biological adaptation. Darwin’s ex- planatory mechanism was natural selection acting upon the random but 173 P1: KAF/KAA P2: KaF 0521829496c09.xml CY335B/Dembski 0 521 82949 6 March 10, 2004 1:5 174 Bruce H. Weber and David J. Depew heritable variations of reproducing organisms in particular environments. This selective process produced, over generational time, adaptive traits in lineages, as well as diversification – descent with modification. Much of Darwin’s “long argument” was to show that natural selection could account for the empirical claim of a common descent for all living beings. 1 Many of Darwin’s sympathizers, John Stuart Mill among them, thought the ar- gument no stronger than that (Mill 1874, 328). But Darwin was not just responding to the ‘how possibly’ question posed by Paley; he was also pro- viding a conceptual framework within which ‘why actually’ questions could be coherently formulated and answered. The Darwinian research tradition developed through a succession of research programs over the course of the twentieth century. Under the aegis of rubrics such as genetical Darwinism or the Modern Evolutionary Synthesis, questions about adaptation, geograph- ical distribution, speciation, and related matters were asked and answered with ever greater empirical and theoretical richness. The Synthesis may not have been a complete theory of evolution, but it has resolved enough ques- tions to create a presumption in its favor. Thus, even though contention over the very idea of evolution remained in the general culture, the project of natural theology receded from view. In recent times, however, there have been attempts to revive natural the- ology based on new notions derived from physics (the anthropic principle) and from biochemistry (irreducible complexity). It is the latter approach, advanced by Michael Behe and a number of other “intelligent design the- orists,” that most directly attempts to recover Paley’s argument and that in consequence will concern us (Behe 1996, 2001). 2 Behe summarizes the functional complexity at the molecular level of a variety of biological phe- nomena, such as the clotting of blood, the locomotion of bacteria, the im- mune system, the biochemistry that underlies vision, and even the origin of life. He concedes early on that he accepts natural selection and com- mon descent; he even concedes that there are plausible accounts of how the vertebrate eye could have evolved (see, for example, Futuyma 1998; Gilbert 2000). He thus bears witness to the changed presumptions in favor of selectionist explanations. Having done so, however, Behe shifts the ar- gument to the greater complexity and functional intricacy of the molecules that underwrite macroscopic biological adaptations. How possibly, he asks, could this particular biochemical feature or trait, which requires X num- ber of components, each with a precise structure and function, have arisen by natural selection, when a loss or defect in any one of the components must cause a loss of the function of the trait? Any system, that is, with X−1 components will have no function, no fitness – nothing upon which nat- ural selection can act. Indeed, Behe claims that “many biochemical sys- tems cannot be built up by natural selection working on mutation; no di- rect, gradual route exists to these irreducibly complex systems” (Behe 1996, p. 202). P1: KAF/KAA P2: KaF 0521829496c09.xml CY335B/Dembski 0 521 82949 6 March 10, 2004 1:5 Darwinism,Design,andComplexSystemsDynamics 175 Behe’s argument from incredulity takes the following schematic form: (1) Natural selection has to be gradual, linear, and sequential if it is to result in adapted traits. (2) Observed molecular functional complexity of Y is inconsistent with (1). (3) Natural selection cannot possibly account for Y. Behe tacitly assumes that the molecular components of cells, if not cells themselves, are little machines, artifacts with moving parts. Since the an- swer to the question of whether natural selection could possibly have been the causal explanation of the appearance of a particular adaptive trait is negative, and since Behe denies that there is any other possible natural ex- planation, he reasons by disjunctive syllogism that the only other possible explanation is intelligent design. We can call this “the argument to the only alternative.” The rhetorical advantage of this strategy is that, having elimi- nated the only other possibility, it is not necessary to provide any positive argument for design. But the strategy will persuade only if three conditions are fulfilled: (1) there are no empirically adequate answers to the ‘how pos- sibly’ questions Behe poses; (2) cells and their molecular components are no more than machines; and (3) there is a simple dichotomy at the level of possible explanations. We will consider Behe’s argument in the light of these three conditions. We will find reason to doubt whether any of them is strong enough to sustain Behe’s argument. 2. the argument against incredulity When considering ‘how possibly’ questions, one needs to think about the kinds of systems in which changes occur over time (i.e., the nature and dy- namics of these systems). Intelligent Design (ID) theorists, such as Behe, presuppose that the only possible systems are ones that are highly decompos- able. This is implicit in the strong analogy they draw between biological or biochemical systemsand man-made machines; the latter presume a linear as- sembly model of systems. Unfortunately, contemporary hyper-adaptationist versions of Darwinism – arguments that look for an adaptationist explana- tion for virtually every trait or evolutionary phenomenon – meet ID on the same ground by employing similar classes of models (Dawkins 1986; Dennett 1995). 3 In effect, the ID theorists and the hyper-adaptationists are taking in each other’s laundry when they both use the terminology of design, even as they differ in the source of the design. This way of framing the debate between evolutionists and creationists foreshortens the space of what will count as possible explanations. Unfortunately, too, this is something both camps seem to prefer. Both assume that there are only two alternatives and P1: KAF/KAA P2: KaF 0521829496c09.xml CY335B/Dembski 0 521 82949 6 March 10, 2004 1:5 176 Bruce H. Weber and David J. Depew argue that the other alternative is impossible. A knockout blow is the aim of both a Dennett and a Behe, a Dawkins and a Dembski. But deploying ‘how possibly’ questions in order to foreclose any but one answer to ‘why actually’ questions is a very risky business. Because ‘how pos- sibly’ claims seldom, if ever, reach the status of ‘why necessarily’ answers in favor of the disjunct they prefer, they can be upended by plausible ‘why actually’ hypotheses that put the burden of proof back onto the questioner. Suppose for a moment that ‘why actually’ scenarios or hypotheses are given as plausible answers to questions posed by an ID theorist about the origin of a particular biological mechanism. Then either (1) a retreat from the claim of the ‘irreducible complexity’ of that trait must be made, or (2) it must be acknowledged – especially if the number of such retreats accumulates – that the assumption of decomposable systems acted upon by gradual, linear, sequential selection is not valid. Both eventualities weaken the ID case. If evolutionary theory is merely a stalking horse for materialism, then ID argu- ments do have a certain rhetorical point. However, the problem is that ID theorists foreclose the ‘how possibly’ question too quickly, slyly converting the ‘why actually’ question into a dichotomy of either external design or selection. What if natural systems are not strongly decomposable but in fact are gen- erated by and composed of parallel processes? What if such natural systems can “limp along” when they open new survival space with the beginning of the emergence of novel properties, and what if these properties can be polished by selection to a shine of apparent design? Such scenarios, if bio- chemically plausible, could take the force out of the appeal to irreducible complexity and the argument from incredulity. That is why well-documented processes, such as gene duplication, are relevant. They allow for parallel and divergent evolution of enzyme functions that can open new energy sources, produce new metabolic pathways andcomplex functions, and cope with potentially lethal mutations (Shanks and Joplin 1999; Thornhill and Ussery 2000; Deacon 2003). Behe argues that “the impotence of Darwinian theory in accounting for the molecular basis of life is evident .from the complete absence in the professional scientific literature of any detailed models by which complex biochemical system could have been produced” (Behe 1996, 187). Yet liter- ature published before Behe wrote, and subsequent papers in the profes- sional scientific literature, have provided just such ‘how possibly’ scenarios; and further research in some cases is shifting to the ‘why actually’ issues. For example, a chemically plausible route for the evolutionary origin of the Krebs citric acid cycle has been proposed. It might serve as a more gen- eral model for the emergence of complex metabolic pathways (Melendex- Hevia, Waddell, and Cascante 1996). Behe could respond to such arguments with the admission that this particular system, the Krebs cycle, has turned out not to be irreducibly complex, since an explanation of its emergence can be P1: KAF/KAA P2: KaF 0521829496c09.xml CY335B/Dembski 0 521 82949 6 March 10, 2004 1:5 Darwinism,Design,andComplexSystemsDynamics 177 plausibly advanced. Behe has taken just such a position about the emergent phenomena of patterns of chemical reactions in the Belousov-Zhabotinsky (BZ) reaction, which was originally developed to model the functional com- plexity of the Krebs cycle (Belousov 1958; Behe 2000; Shanks 2001). It turns out that the BZ reaction can be understood in terms of theories of nonlin- ear chemical kinetics and nonequilibrium thermodynamics, even though the emergent phenomena were not anticipated by the decomposability as- sumption of conventional chemical descriptions (Tyson 1976, 1994). The BZ reaction can be used as a model to explore the dynamics of other com- plex systems, including biological ones (Shanks and Joplin 1999; Shanks 2001). Behe does concede that the origin of some biochemical systems may also be explainable by natural processes, and hence by processes not fitting his definition of irreducible complexity (Behe 2000). But wait a minute. We were assured by Behe that no complex biochemical system, including metabolic pathways such as the Krebs cycle, had been given a Darwinian explanation in response to his ‘how possibly’ questions (Behe 1996). There are many classes of Darwinian explanations, and Darwinian explanations are only a subclass of naturalistic explanations. All we need at present is a plausible naturalistic explanation, whether Darwinian or not. As similar ar- guments are extended to other metabolic pathways, however, the scope of the phenomena that Behe claims to explain by ID shrinks. Well, Behe will say, even if metabolism is capable of naturalistic explanation, still there are other very complex phenomena that surely resist explanation. But at a cer- tain point, it is this very assertion that is in dispute. Consider the following case, in which explicitly Darwinian naturalism figures. Behe has claimed that “no one on earth has the vaguest idea how the co- agulation cascade came to be” (Behe 1996, 97, emphasis in original). But there are, it turns out, plausible scenarios by which crude, primitive blood clotting could have occurred in organisms that employed proteins from other func- tions to achieve a marginal stoppage of bleeding (Doolittle and Feng 1987; Xu and Doolittle 1990; Doolittle 1993; Miller 1999). Through gene dupli- cation and shuffling of the subregions of genes coding for domains within the proteins produced, such protein functions could expand, diverge, and become targets of selection that could lead to improved clotting. Proposals such as this can be tested by making predictions about both the specific relationships of sequences of the various genes within the pathway and to sequences of genes for proteins in more primitive organisms that might have been the origin of the original genetic information. This kind of work is proceeding and is beginning to provide the basis for shifting to the ques- tion of ‘why actually’ such a complex cascade has actually arisen in evolution by natural selection. Again, Behe asserts that “the only way a cell could make a flagellum is if the structure were already coded for in its DNA” (Behe 1996, 192, em- phasis added). The bacterial flagella that Behe considers have over forty P1: KAF/KAA P2: KaF 0521829496c09.xml CY335B/Dembski 0 521 82949 6 March 10, 2004 1:5 178 Bruce H. Weber and David J. Depew protein components, and it would seem that he has a strong case here. Yet only thirty-three proteins are needed for fully functional flagella in some bacteria not considered by Behe. Even so, such a number constitutes an explanatory challenge. Clues to how such a system might have evolved, em- ploying processes of protein “recruitment” and gene duplication followed by divergence, are provided by the roles of ion gradients in the organiza- tion of bacterial metabolism and their possible role in self-organizational and emergent phenomena, a subject to which we will return (Harold 1991; Harold 2001). Another example Behe uses is the truly complex vertebrate immune sys- tem of over ten thousand genes. He claims that “the scientific literature has no answers to the origin of the immune system” (Behe 1996, 138). But shortly after Behe published his book, the discovery of the RAG transposases and transposons in contemporary vertebrate immune systems suggested possi- ble routes by which “reverse transcription” (similar to the way in which the HIV virus converts its RNA message into DNA and incorporates it into T-cells) could have worked, in addition to gene duplication and domain shuffling through RNA splicing mechanisms, to generate the immune sys- tem (Agrawal, Eastman, and Schatz 1998; Agrawal 2000; Kazazian 2000). There is, to be sure, a long way to go in developing our understanding of how immunity came into existence. But it should be clear that the reason- able way to proceed is through pursuing the combined research programs of molecular genetics, genomics, proteomics, and informatics rather than simply by declaring the immune system to be too complex for any other than ID explanations (if indeed they can be called explanations). In time, Behe may be forced to concede that the immune system, as well as blood clotting and metabolic pathways, are subject to naturalistic explanations and, although complex, are not in the end irreducibly complex. We are just now entering a new age in understanding the relationship between genes and biochemical pathways and systems. Why does Behe think that, just as this new cascade of research gets under way, he can put a stop to the whole business? Finally, let us return to Paley’s example of the eye. Behe concedes, as men- tioned earlier, that the eye as an organ might have a Darwinian explanation. But he argues that the biochemistry of vision is too complex to have any other than a design explanation. What can be said about this? Photosensi- tive enzyme systems exist in bacteria, functioning in energy metabolism, and indeed may be quite ancient (Harold 1986; Nicholls and Ferguson 1992). Proteins that function in the lens turn out to be similar to the sequences of amino acids in heat shock proteins, and to various metabolic enzymes that function in the liver (Wistow 1993), suggesting once again a process of parallel processing via gene duplication and divergence as a new function becomes selectively advantageous. More dramatically, recent developments in our understanding of the molecular basis of biological developmental P1: KAF/KAA P2: KaF 0521829496c09.xml CY335B/Dembski 0 521 82949 6 March 10, 2004 1:5 Darwinism,Design,andComplexSystemsDynamics 179 processes reveals that certain genes responsible for the development of eyes, such as the pax 6 gene, arose only once in the history of life and, although not coding for eyes per se, code for the processes that lead to the construc- tion of eyes in various lineages (Gehring 1998; Gilbert 2000, 705; Carroll, Grenier, and Weatherbee 2001). Comparisons of the genes regulating de- velopment in different species hold the promise of giving us clues to the origin and evolution of complex, multicellular organisms and their organs (Carroll, Grenier, and Weatherbee 2001). A recurring theme in the specific research areas just mentioned is that evolutionary processes occur through parallel processing rather than by se- quentially adding one perfected component to another. Thus evolutionary biologists, other than those committed to an extreme form of adaptationism, have explanatory resources that ID theorists deny (see, for example, Thornhill and Ussery 2000). (That is why ID creationists and hyper-adaptationists have a common interest in narrowing what counts as evolutionary theory and as Darwinism.) Even if organisms are conceived as decomposable artifacts – a position against which we will argue later – they are not analogous to the assembly protocols for watches, in which the components are specifically designed and perfected for unique functions and then put together in a specified sequence. Interestingly, engineers now find that in designing complex machines (such as a processor composed of over forty million transistors), it is more efficacious to have the components combined in a functional pattern than to assemble them from perfect components. Indeed, the best strategy is to get as quickly as possible to a crudely functional whole and then to remove and replace less reliable subsystems. Challet and Johnson estimate that one-half of the components could be significantly imperfect and yet the system as a whole would function reliably (Challet and Johnson 2002). With complexity comes redundancy and parallelism that can give functionality; and with functionality comes pressure for improved components over time. Thus, even allowing ID theory its artifact metaphor, it poses its ‘how possibly’ arguments the wrong way around. The function of the whole system does not depend upon perfectly designed and articulated components. 4 The questions that need to be addressed, then, are what types of systems are living organisms – and ecosystems as well? What are the dynamical prin- ciples of such systems? Do design and selection exhaust the possibilities of explanatory space in such systems, or are there other relevant natural pro- cesses, such as self-organization? To these issues we now turn our attention. 3. self-organization and emergence in complex natural systems Both ID and hyper-adaptationist Darwinian (HD) theorists share assump- tions about the nature of organisms and systems. These shared assumptions imply that self-organization is not a serious contending explanatory resource P1: KAF/KAA P2: KaF 0521829496c09.xml CY335B/Dembski 0 521 82949 6 March 10, 2004 1:5 180 Bruce H. Weber and David J. Depew for apparent design in natural systems. ID and HD theorists both view cells and organisms as machines with independent components that can be ei- ther designed separately or selected for their contribution to optimal fitness. By contrast, the sort of complex system dynamical perspective for which we have argued views cells and organisms as lineages of developing entities in which everything changes at the same time, in parallel fashion, during life cycles and over generational time. In this view, organisms are open thermo- dynamic systems with gradients stabilized by the actions of macromolecules that have a degree of autopoeisis; their parts do not aggregate but rather de- velop by differentiation (Depew and Weber 1995; Weber and Depew 1996, 2001). They do not passively, and only incidentally, conform to the require- ments of the Second Law of Thermodynamics. They exploit that law in becoming the kinds of systems they are. Behe’s key claim is that there is no way that natural explanations can possibly account for the origin of life. Hence, for Behe, life itself must be irreducibly complex, and so the product of intelligent design. We agree with him about the complexity. But we would prefer to frame the question as one about the emergence of life through a complex process rather than as the product of a specific event, or series of events, as Behe (and his hyper- adaptationist counterparts) assume. Our own guiding ideas about the origin of life are integral to our ap- proach to how complexsystemsdynamics might enrich Darwinian theory. Darwin himself famously sought to sidestep the issue of the origin of life by placing it outside of his explanatory framework. But in the late twentieth century, biologists have increasingly sought to articulate proposals describ- ing how living things came to be within a broader Darwinian framework. Some of them, placing emphasis on replication and the role of genes in directing all other biological processes, have put the focus on naked, repli- cating RNA as the starting point of life, with the rest of cellular structures and processes viewed as “survival machines” for the genes (Dawkins 1976; Dawkins 1989). A quite different view arises, however, when the problem of the emergence of life is addressed in the context of complexity theory (for recent, reader-friendly introductions to complexity theory, see Casti 1994; Taylor 2001). The complexsystemsdynamics to which we have drawn attention in- cludes the energetic driving force of far-from-equilibrium thermodynamics (that is, far from the equilibrium state in which there is no change in the energy of the system as a whole). This gives rise to matter-energy gradi- ents and to internal structures, breaking symmetries and producing inter- nal order and organization at the expense of increases in entropy (disorder and/or degraded energy) in the environment (Schr¨odinger 1944; Nicolis and Prigogine 1977; Prigogine 1980; Wicken 1987; Prigogine 1997). A conse- quence of such a state of affairs is the appearance of nonlinear (nonadditive, potentially amplifying) interactions between components and processes in P1: KAF/KAA P2: KaF 0521829496c09.xml CY335B/Dembski 0 521 82949 6 March 10, 2004 1:5 Darwinism,Design,andComplexSystemsDynamics 181 such systems through which organized structures emerge. The appearance of higher-order, macroscopic (whole, global, or collective) properties and structures from lower-order microscopic (part or individual) components is called “self-organization” though perhaps “system organization” would be a more apt phrase. Stuart Kauffman is one of the theorists who have modeled the dynamics of such systems by exploring, through computer simulations, the dynam- ics of systems in which nonlinearity obtains and self-organization can occur (Kauffman 1993, 1995, 2000). ID theorists, including Behe, have attacked Kauffman as if he were the only advocate of self-organizing complexity, and as if his simulations were cut off from any physical or biological reality (Behe 1996, 156, 189–92). (Similar objections have been raised against the mag- num opus of Stephen Wolfram [Wolfram 2002]). Kauffman’s approach is dismissed by Behe as irrelevant, since, according to Behe, self-organization is only a mathematical phenomenon that occurs in computer simulations un- der specific initial and boundary conditions – as well as rules of component interaction – that are set by the programmer. To this criticism there are two responses. First, any computer simulation requires constraints that are introduced by the programmer; the question is whether the constraints are realistic. Kauffman does argue that the con- straints that he introduces in various modeling applications are plausible and reflect the essence, if not the minute detail, of energetic and molecular properties and propensities of the natural system – or at least that they reflect the consequences of such systems being far from equilibrium and having nonlinearity (Kauffman 1993, 1995, 2000). It is unreasonable to argue that Kauffman has to avoid any constraints to totally random interactions in his models, since analogous constraints do exist in nature. Second, there is the response that self-organization is not just a mathe- matical, theoretical concept, but rather is a real phenomenon. In summa- rizing a series of recent studies in cell biology, Tom Misteli recently argued that “[t]hese studies have permitted the direct and quantitative testing of the role of self-organization in the formation of cytoskeletal networks, thus elevating the concept of self-organization from a largely theoretical con- sideration to a cell biological reality” (Misteli 2001, 182, emphasis added). Self-organizing metabolic and signaling networks that display systemwide dy- namics are viewed by Richard Strohman as playing a coequal role with genes in controlling human disease phenotypes (Strohman 2002). An even more wide-ranging review of the phenomena of self-organization and its appropri- ate simulations has recently appeared, according to which self-organization, rather than limiting the action of natural selection, enhances its efficacy through economical use of information and by providing the formation of whole patterns upon which selection can act (Camazine et al. 2001). We have argued in a similar vein that, although selection and self-organization can be conceptualized as interacting in a variety of logically possible ways, P1: KAF/KAA P2: KaF 0521829496c09.xml CY335B/Dembski 0 521 82949 6 March 10, 2004 1:5 182 Bruce H. Weber and David J. Depew these two principles can and should be viewed as complementary phenomena (Weber and Depew 1996). Energy, primarily from the sun, would be expected to drive the chem- istry of the primitive Earth to greater molecular complexity under the con- straints of atomic and molecular properties and propensities under far-from- equilibrium conditions (Wicken 1987; Williams and Frausto da Silva 1996, 1999). At some point, there would have arisen sufficient chemical complex- ity and catalysis of reactions that regions on the abiotic Earth would have produced chemical self-organization, in which some chemical components would have acted as catalysts for reaction sequences that produced more of themselves – the phenomenon of autocatalysis. Under such conditions, at least some amino acids, which are the building blocks of proteins, as well as the purine and pyrimidine bases, which are components of nucleic acids, would have been produced. Even polymers of these can be stabilized by var- ious mechanisms. Even though such polymers would not contain “specified information,” they could be weakly catalytic and would contribute to the overall autocatalytic system (Kauffman 1993; Weber 1998). Kauffman has applied his flexible NK model (where N = the num- ber of components and K = the number of interactions between com- ponents) to model both the range of possible sequences of proteins and their autocatalytic interactions. Kauffman modeled a “catalytic task space” that represents all the conceivable chemical reactions (on the order of a few million) and mapped that onto the protein sequence space. In an array or ensemble of random sequences of amino acids in proteins, a large number of chemical reactions would appear that would be weakly catalyzed by subpopulations of protein sequences. Then a chemical-type selection (favoring enhanced catalytic activity) would act on protein se- quences in such a way that it would enhance the catalytic efficiency of the catalysts and contribute to the overall thermodynamic efficiency of the system. Even if there were no physical or chemical boundary for such autocatalytic systems – but very much more likely, if there were clo- sure bounded by a chemical barrier from the rest of the chemical envi- ronment – such systems could become sufficiently interactive to achieve “catalytic closure.” They would generate, that is to say, a system of auto- catalytic chemical transformations that would become self-contained – able to generate all its constituents by pulling in available chemical sub- strates and to exhibit weakly heritable information, even in the absence of macromolecular memory molecules such as RNA. It is likely that such catalytic closure did not occur in dilute sea water (contra the naked RNA approach), but instead within a barrier composed of molecules with water-avoiding and water-seeking ends (amphiphiles). These would have served the same function as that provided by modern cellular membranes (Morowitz, Deamer, and Smith 1991; Morowitz 1992). Plausible [...]... 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