The ISSOL Trail Guide (DRAFT)
The NASA Astrobiology program has been very successful in bringing together a diverse group of investigators ranging from astronomers to ecologists. One of the four main goals of Astrobiology is to understand the origin of life, and this goal falls directly within the purview of ISSOL.
An important part of the Astrobiology program is that NASA activates a planning process every three years to establish research goals. This effort was led in 2002 by ISSOL member Dave Desmarais, and 20 scientists met weekly by teleconference over a six month period to develop the plan. The draft was then released for public comment. The final result, called the Astrobiology Road Map will be used both by scientists and administrators to guide future research.
ISSOL does not have the resources to undertake such an effort, nor is it required to do so as part of our charter. Our goal is to foster a community of scientists through this newsletter, our journal and our triennial meeting. A second goal is to introduce young investigators to the most significant problems in the field. To this end, it is useful to share ideas in a published forum, and we have invited members of the ISSOL Board and other prominent scientists to answer the following question: "In your judgment, what are some of the most interesting and significant new directions for research on the origin of life over the next five years?" Several initial responses are summarized here, not as a Road Map, but instead as a kind of "trail guide" in which experienced hikers share their knowledge with other workers who wish to explore the vast wilderness related to the origin of life. We will publish other comments as they are received, and invite members of ISSOL to share their ideas as well.
Prebiotic synthesis of adenosine
Alan Schwartz
While the RNA World scenario is generally accepted as providing a powerful insight as well as a productive starting point for thinking about many aspects of the origin of life, the realization of a convincing synthetic scheme for the synthesis of RNA has not been achieved. Because of the difficulties in achieving de novo synthesis of RNA and its components, many researches have concentrated instead on the possibility that some precursor of RNA, which may have been more easily synthesized on the primitive earth than RNA itself, may have first been formed and then evolved into RNA. However, at least one approach to the problem of nucleoside synthesis has possibly been somewhat neglected. It is conceivable that purine synthesis, which proceeds biochemically by the build-up of the purine ring on ribose, may have proceeded prebiotically in a similar fashion. One approach in this spirit, although related to the attempted synthesis of a pyrimidine nucleoside, was that of Sanchez and Orgel (1970), in which a mixture of nucleoside-like products were obtained by reactions of ribose and arabinose with cyanamide and cyanoacetylene. The synthesis of adenine by means of HCN oligomerization provides another model reaction system (Sanchez et al., 1967). What modifications of these reactions might be linked to a preexisting ribose scaffold, so that closure of the ring would produce adenosine?
Sanchez, R.A., Ferris, J.P., Orgel, L.E. (1967) J. Mol. Biol. 30, 223-253.
Sanchez, R.A. and Orgel, L.E. (1970) J. Mol. Biol. 47, 531-543.
Energy capture and life’s origins
Dave Deamer
A reasonable conjecture is that the origin of life occurred as the chance self-assembly of a system of molecules that did not remain at equilibrium, but instead could respond to a flow of energy so that smaller molecules could be used as nutrient monomers to construct larger molecules in the form of polymers. At some point in the process, one such structure happened to incorporate a set of molecules that could not only grow, but also catalyze the growth process and store information as sequences of monomers in polymers.
From this perspective, a fundamental question is how energy can be captured by self-assembled structures that might plausibly arise from organic compounds available on the prebiotic Earth. One such energy source is the chemical energy made available when electrons flow from a reduced molecule such as hydrogen to an oxidant such as iron or sulfur. A second potential energy source would have been light energy, in which a pigment molecule accepts photons and is elevated to a higher energy state that can release electrons to a second molecule, thereby capturing the light energy as chemical energy.
What are some plausible energy sources that might have been available on the early Earth? There are several possibilities, but none have been extensively studied. Three alternatives that immediately come to mind include chemical bond energy, such as the energy available in pyrophosphate bonds or aldehydes, the energy available in redox couples such as hydrogen gas and a mineral oxidant, and light energy. It seems to me that energy sources such as light or redox energy would have required a membrane-bounded compartment, just as cells do today. This should be a very fruitful area for future experimentation. We are likely to find that electrochemical gradients of protons or other ions are relatively easy to produce when light or redox energy is available, and that these gradients can be coupled to the activation of monomers, most likely by phosphorylation, in such a way that polymerization chemistry becomes possible.
Thoughts on future directions for origin of life research
Jack Szostak
At the level of prebiotic chemistry, the fundamental problem is to understand how genetic systems, which would seem to require a relatively homogeneous chemical makeup, could arise from very heterogeneous mixtures of small molecules such as are seen in interstellar molecular clouds, comets, meteorites, and earthbound prebiotic simulations. Many theories have been proposed - now is the time to go beyond speculation and do the experiments that will test these ideas.
At a higher level of organization, we still lack an experimental demonstration of a self-replicating genetic polymer. Despite major advances, achieving a true RNA replicase remains a major challenge. A very exciting possibility that I expect to open up in the coming decade is the ability to carry out directed evolution experiments with non-standard genetic polymers such as TNA, 2'-linked RNA and others. This could lead to the ability to assess the functional capacities of many new polymers. Ultimately, self-replication may be found to be possible in diverse genetic systems. A demonstration of self-replication in a genetic polymer that was chemically simpler than RNA could lead to a major simplification of the origin of life problem.
Finally, there are a host of fascinating issues related to compartmentalization and the origins of cellular evolution that should be explored in the coming decade. A variety of strategies for compartmentalization have been proposed, ranging from the localization of genetic materials to the surface of mineral particles or within aqueous droplets dispersed in an organic phase, or within the more biological membrane vesicles. With respect to vesicles, we need to know a lot more about prebiotic amphiphiles and the properties of membranes composed of such molecules. How could such vesicles grow and divide? How did genetic polymers and membrane vesicles first begin to interact? How did membranes begin to capture energy from the environment in such a way that it could be converted into useful chemical energy?
There are clearly many, many interesting and important questions outstanding in the origin of life field. Many of these are becoming experimentally tractable for the first time, so I expect the coming decade to be the most exciting since the field of prebiotic chemistry began with the Urey-Miller experiment.
Autocatalysis and a second genesis
André Brack
Life - defined as a chemical system capable of self-reproduction and of evolution - originated from the reaction of reduced carbon-based organic matter in liquid water. The organic molecules required for the appearance of terrestrial life might have been formed in Earth's atmosphere, in submarine hydrothermal systems or delivered to the Earth via interplanetary dust. Schematically, the prebiotic ressources needed for the emergence of life can be compared to parts of a chemical robot. By chance, some parts assembled to form a robot capable of assembling other parts to form a second identical robot. From time to time, a minor error in the assembly process generated more efficient robots. Since the oldest fossils of microorganisms discovered so far have been identified in geological horizons associated with hydrothermal systems, either subaerial or submarine, it is reasonable to consider that the robots were driven by thermal energy, around 85°C. The robots had therefore to protect themselves against hydrolysis that was also boosted by the high temperatures. They probably faced this difficulty by growing on, or within, mineral surfaces such as sulfides and/or clays.
The number of parts required for that first robot is still not known. The problem is that, on Earth, those earliest parts have been erased by geological processes such as plate tectonics. The chances of understanding the emergence of life on Earth by recreating a similar process in a test tube will obviously depend upon the simplicity of the chemical reactions leading to life. The discovery of a second genesis of life on another celestial body would strongly support the idea of a rather simple genesis of terrestrial life. The possibility that life may have evolved on Mars during an early period when water existed on the surface, and the possibility that life may still exist deep below the surface, marks it as a prime candidate in the search for life beyond the Earth. Cryovolcanic flows at the surface of Europa point to a possible subsurface ocean of water and of hydrothermal vents, which might harbour a basic life form. The discovery of the exoplanets opens the search for extraterrestrial life to the whole Universe.
To sum up, over the next 5 - 10 years we should search for:
- autocatalytic systems active on mineral surfaces in water at 85 °C.
- a second genesis of life on Mars, Europa, exoplanets with space missions and SETI
Synthetic biology may provide the "Aha!"
Steve Benner
A realistic look at the "origins" problem finds few hypotheses clearly worthy of experimental test. This is in marked contrast to the situation 50 years ago, when the experiments of Stanley Miller created the expectation that all biomolecules, including perhaps DNA and RNA, would be shown to self-assemble as the consequence of normal chemical reactivity in environments plausible for early Earth.
It is now clear that Miller-like experiments create too many biological molecules, in mixtures that are too complex to self-organize in a way rationally likely to lead to replication. The intrinsic reactivity of organic material under the inflluence of energy is to create tar, not life; the enviable ability of minerals to fractionate themselves into organized forms is not displayed by organic materials in standard solvents at surface temperatures and pressures on Earth. Every additional molecule can be as easily an inhibitor for the formation of life rather than a contributor.
This means, of course, nothing more than that we need some new insights, an "Aha!" experience that might create clarity from confusion. Today, fields surrounding the origins of life have themselves come of age. We know much, much more about the history of the solar system and the environments that it has offered than we did 50 years ago. Exploration of Titan, Mars, Venus, Europa, comets, meteorites and elsewhere cannot help but provide new insights, on organic chemistry in the cosmos, on the transformation of organic molecules on a planetary scale, and on the fractionation of these in planetary environments. The "Aha!" might lie within these observations.
Pushing backwards in time from the present day, exploration of the terrean planetary genome is proceeding. With post-genomic bioinformatic and interpretive proteomic techniques, both in silico and laboratory, we are well on our way to understanding the relation between the planet, the biosphere, and the genosphere for the Phanerozoic, the period of time when multicellular life has been prominent on the planet. Our understanding of very ancient microbial life has also advanced, certainly back 2 billion years, and possibly further. While we appear to be still not at the origin of life, and while the protogenome may be biochemically advanced relative to the first genome, the combined efforts of paleontology, microbiology, geology, and genomics have placed important constraints on the first form of life.
Last, the emerging field of synthetic biology may provide the "Aha!". Our understanding of organic chemistry has been driven for two centuries by the effort to create molecules that reproduce the behavior of living systems without reproducing their structures. Teams around the globe now are trying to do the same for the chemistry that we call "living". Obtaining in the laboratory self-replicating systems capable of Darwinian evolution will certainly provide insight into how chemical reactivity is intimately coupled with natural selection, even if it does not directly provide us with an answer to the historical question: How did terrean life, specifically, emerge?
Direct evidence of life's origin?
Bill Schopf
Three lines of evidence have traditionally been used to help decipher the what, when, and how of life's beginnings:
- inferences drawn from the biology (including the molecular biology and metabolism) of living microorganisms -- the reductionist strategy of using the traits of present-day microbes to infer the path of evolution, "top-down";
- inferences drawn from laboratory experiments designed to synthesize biologic-like organic compounds (monomers, polymers, vesicles, etc.) under conditions designed to simulate those of the pre-life Earth -- the constructionist strategy of using the products of prebiotic syntheses to infer the path of evolution, "bottom-up"; and
- inferences drawn from direct evidence (microscopic fossils, carbonaceous matter, isotopic compositions) preserved in the ancient rock record -- the observationalist strategy of using the known record of life's past to infer the path of evolution.
Each of the three strategies has contributed measurably to current understanding, but the first two -- the "top-down" and "bottom-up" approaches -- form the heart of ISSOLian "Origin-of-Lifeology." Nevertheless, all know that because both of these strategies are laden with model-dependent assumptions, neither is fully satisfying. Given a choice, all would prefer firm, unquestionable evidence of the what, when, and how of life's beginnings.
To me, it seems not at all surprising that results yielded by the two favored approaches are enshrouded in a degree of uncertainty. Given our current state of knowledge, how could it be otherwise? The "top-down" approach is pegged to microbes living today, yet their very existence tells us that they are well adapted, successful, and highly evolved -- microorganisms that are only distantly related to their primitive ancestors and that, in toto, represent a evolutionarily highly filtered and infinitesimally small fraction of the microbial biota of the evolutionary past. Similarly, the "bottom-up" approach is fraught with problems. The notion it embodies that life on Earth was built from small-to-large, simple-to-complex, seems certain to be correct -- even if Earthlife is a product of some sort of panspermia -- but the problem is how the pieces came into place. Which pieces? How were they formed? In what sequence did they come into order? What constitutes a plausible answer?
[As an aside, and even though insights garnered from these two approaches have not, I think, proven as definitive as one might hope, the future is by no means bleak. The popular press has dubbed the 2000s as the "Century of Bioengineering," and in this they are probably right. But what they, and the public, and even a number of our colleagues seem not to appreciate is that simply because of bioengineering -- and genomics, and cloning, and designer babies, and the rest -- this century appears likely to become, also, the "CENTURY OF EVOLUTION." More will be learned, in more detail, than has ever been known before. And the genomes of all organisms do contain -- in an evolutionarily filtered, abbreviated, "short-circuited" format -- a wealth of information about life's evolutionary history.]
So -- given the current state-of-the-science -- we are left with the third of the three traditional strategies: fossils, carbonaceous matter, and isotopic data sequestered in the rock record. Can such direct evidence solve our problem of the what, when, and how of life's emergence? Unfortunately, no. Here, the difficulties are least four-fold:
- The fossil record can yield only a minimum age for life's existence. [The oldest known evidence reflects only what has been detected, not when life first existed.]
- Evidence of pre-cellular life is not, even in principle, preservable in ancient rock units. [The oldest reliably detected nucleic acids, for example, date only from thousands -- not millions, certainly not billions -- of years ago. And organic structures even as robust as intracellular membranes are unknown from all but a very few, exceptionally well preserved and geologically relatively young, Precambrian-age fossils.]
- Almost all truly ancient carbonaceous matter -- that older, say, than three billion years -- has been geochemically "pressure-cooked" to such an extent that identification of its source (whether biological or nonbiological) cannot be determined on the basis of its inherent molecular structure. [Geochemical conditions drive all organics, regardless of source, toward the same end product, graphite; and as graphitization proceeds, biogenic and abiogenic organic matter converge to produce the same set of geochemically stable intermediates, polycyclic aromatic hydrocarbons, PAHs.]
- The evidence from stable isotopes -- of carbon, in particular -- is more robust than that based solely on molecular structure, since such isotopic compositions remain essentially unaltered until graphitization has produced PAHs having H/C ratios of ~0.2 or below. But such evidence is strong only for that part of the rock record -- back to ~3.5 billion years ago -- from which there is a sufficiently large body of data to define confidently the isotopic compositions of the relevant geological reservoirs. [Interpretation of carbon isotopic records older than ~3.5 billion years has thus been open to question (as will be, for the foreseeable future, inferences drawn from any such measurements on samples from Mars), due both to the effects of metamorphism and a lack of data on the isotopic compositions of the relevant reservoirs.]
Where does this leave us? Perhaps, just possibly, the "CENTURY OF EVOLUTION" will solve our problems. But even if it does, the answers generated will still be model-dependent and, thus, to my mind, less than fully satisfying.
As for future advances in studies of the early fossil record, the first big problem will be to correlate -- in three dimensions, at a micron-level scale -- cellular morphology and chemical composition in individual microscopic fossils. Due to use of Raman imagery, a technique only recently introduced to paleobiology, such correlation in three dimensions seems easily within reach. What next will be needed is the correlation, in individual fossils, of cellular morphology-chemical composition with isotopic composition and the nanometer-scale fine structure of their carbonaceous components. These, too, are attainable by techniques already on hand, as shown by recent proof-of-concept studies using ion microprobe spectrometry to determine isotopic compositions, and atomic force microscopy to visualize fine-structural morphology. And to avoid the pitfall of viewing morphology as an "ambiguous indicator of biogencity" -- the title of a recent paper that errs by focusing on single specimens rather than populations of microorganisms -- there is a continuing need for in-depth population-based studies of fossil communities and the products of their degradation, a matter of carrying out the same sorts of morphometric and taphonomic studies on fossil assemblages as those used to analyze living microbial communities and the organic detritus in which they occur. (In essence, the identification of bona fide microscopic fossils is a signal-to-noise problem for which one must have good understanding of the associated "noise" in order to properly evaluate the biologic "signal.")
But an additional arrow needed to fill this quiver may not be so easily obtained. As more and more workers enter the field -- spurred largely by interest in (and funding from) Astrobiology -- there is a pressing need for interdisciplinary education. Here, our institutions have failed us. Each of us, I think, suffers from our educational backgrounds. None of us knows all the relevant disciplines. Indeed, none of us even knows all the telling questions. Our greatest task, it seems to me, is to do the best we can to help those who come after us to be better, and brighter, and more insightful, and far more interdisciplinary than are we.
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