Feb 13, 2007

what came before RNA? recent origin-of-life research heads in thermodynamic directions

In a recent article in Scientific American, Robert Shapiro explains why ">the prospects for "RNA World" OOL theory are bleak. You can be sure creationist hacks are salivating over this quote:
There is no reason to presume than an indifferent nature would not combine units at random, producing an immense variety of hybrid short, terminated chains, rather than the much longer one of uniform backbone geometry needed to support replicator and catalytic functions. Probability calculations could be made, but I prefer a variation on a much-used analogy. Picture a gorilla (very long arms are needed) at an immense keyboard connected to a word processor. The keyboard contains not only the symbols used in English and European languages but also a huge excess drawn from every other known language and all of the symbol sets stored in a typical computer. The chances for the spontaneous assembly of a replicator in the pool I described above can be compared to those of the gorilla composing, in English, a coherent recipe for the preparation of chili con carne. With similar considerations in mind Gerald F. Joyce of the Scripps Research Institute and Leslie Orgel of the Salk Institute concluded that the spontaneous appearance of RNA chains on the lifeless Earth "would have been a near miracle." I would extend this conclusion to all of the proposed RNA substitutes that I mentioned above.

Nobel Laureate Christian de Duve has called for "a rejection of improbabilities so incommensurably high that they can only be called miracles, phenomena that fall outside the scope of scientific inquiry." DNA, RNA, proteins and other elaborate large molecules must then be set aside as participants in the origin of life....
If that were the conclusion, origin-of-life researchers would have reason to throw down their beakers in despair.

But the end of one hypothesis is just the beginning of another:
Inanimate nature provides us with a variety of mixtures of small molecules, whose behavior is governed by scientific laws, rather than by human intervention.

Fortunately, an alternative group of theories that can employ these materials has existed for decades. The theories employ a thermodynamic rather than a genetic definition of life, under a scheme put forth by Carl Sagan in the Encyclopedia Britannica: A localized region which increases in order (decreases in entropy) through cycles driven by an energy flow would be considered alive. This small-molecule approach is rooted in the ideas of the Soviet biologist Alexander Oparin, and current notable spokesmen include de Duve, Freeman Dyson of the Institute for Advanced Study, Stuart Kauffman of the Santa Fe Institute, Doron Lancet of the Weizmann Institute, Harold Morowitz of George Mason University and the independent researcher Günter Wächtershäuser. I estimate that about a third of the chemists involved in the study of the origin of life subscribe to theories based on this idea....

Systems of the type I have described usually have been classified under the heading "metabolism first," which implies that they do not contain a mechanism for heredity. In other words, they contain no obvious molecule or structure that allows the information stored in them (their heredity) to be duplicated and passed on to their descendants. However a collection of small items holds the same information as a list that describes the items. For example, my wife gives me a shopping list for the supermarket; the collection of grocery items that I return with contains the same information as the list. Doron Lancet has given the name "compositional genome" to heredity stored in small molecules, rather than a list such as DNA or RNA.

The small molecule approach to the origin of life makes several demands upon nature (a compartment, an external energy supply, a driver reaction coupled to that supply, and the existence of a chemical network that contains that reaction). These requirements are general in nature, however, and are immensely more probable than the elaborate multi-step pathways needed to form a molecule that can function as a replicator.

Over the years, many theoretical papers have advanced particular metabolism first schemes, but relatively little experimental work has been presented in support of them. In those cases where experiments have been published, they have usually served to demonstrate the plausibility of individual steps in a proposed cycle. The greatest amount of new data has perhaps come from Günter Wächtershäuser and his colleagues at the Technische Universität München. They have demonstrated portions of a cycle involving the combination and separation of amino acids, in the presence of metal sulfide catalysts. The energetic driving force for the transformations is supplied by the oxidation of carbon monoxide to carbon dioxide. They have not yet demonstrated the operation of a complete cycle or its ability to sustain itself and undergo further evolution. A "smoking gun" experiment displaying those three features is needed to establish the validity of the small molecule approach.
That's the difference between science and pseudoscience: science requires experimental validity. Creationists have harped for years on the low probability of life's spontaneous emergence in the universe. Meanwhile, scientists have been fashioning, testing, junking, redeveloping, and once again fashioning more and more plausible scenarios, not content to rest in comfortable ignorance.

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