Tuesday, September 2, 2008

Biological Big Bang

It is an exciting time in biology. Last year, several articles about origin of life (OOL) and evolution were published by Eugene Koonin from the National Center f0r Biotechnology Information, National Institutes of Health, Bethesda, MD. Though I don't agree with his theories, Koonin does the best job in summarizing the state of OOL and evolution that I have seen. One article was called "The Biological Big Bang model for the major transitions in evolution." It discusses the areas in biology that show "the sudden emergence of diverse forms at a new level of complexity." These areas typically co-exist with the old forms rather than replace them as is predicted in Darwin's theory.

Koonin lists six areas of transition that are unexplained: Origin of protein folds; Origin of Viruses; Origin of cells; Origin of the major branches (phyla) of bacteria and archaea; Origin of the major branches (supergroups) of eukaryotes (true cells); Origin of animal phyla.

Several very interesting facts emerge from the text. One is that two of the principle cell types that exits, bacteria and archaea (one-celled organisms) have, among other things, "non-homologous core DNA replication enzymes." This means that the proteins of bacteria are distinctly different from another group of simple cells, the archaea (to see examples, scroll down or hit DNA label below or on right under topics). Some scientists had expected the archaea to be the evolutionary precursors of the bacteria, but they are not. The DNA polymerase molecule of the Cyanobacteria which has over 900 amino acids is different than the molecule that replicates DNA in one of the archaea species which has 882 amino acids as reported in Uniprot (Q2JWV2 and P26811).

Now, this does show that different molecules can do the same thing. But, as Koonin says, "This severely complicates the reconstruction of a cellular ancestor of archaea and bacteria..." Two different molecules with the same specific job came from a tremendously large pool of possible combinations. After all, I've shown you molecules that do very different jobs within the cells, so the amino acid sequence is crucial to function. Koonin proposes alternate solutions, still hoping for that common ancestor. But let's look at the numbers. For Cyanobacteria, just one protein, the DNA polymerase, has about 10^1200 combinations of 20 specific amino acids. The number of events (including chemical reactions) in the universe, if it is about 14 billion years old, has been less than 10^150. This discrepency is obvious.

Hubert Yockey used Information Theory to estimate that in a protein of 100 amino acids, only about 1 in 10^65 are functional for a specific job. I can imagine that a longer protein would have even less chance to be functional enough to replicate DNA in conjunction with other equally complex molecules. To determine the exact proportion of functional combinations would be a great project for proponents of Intelligent Design (it has not yet been done that I know). That area of study is being stifled in universities, as reported in various places such as Discovery Institute (link on right column of this blog). It is the subject of the movie "Expelled" with Ben Stein that was shown over the summer.

Assuming reactions between potential proteins, with 1 in 10^65 proteins being specifically functional, the probability that 3 functional ones would meet together would be about 1 in 10^195. Less than one chance in all the events of the universe for the combination of 3 proteins to function as they need. And even 3 specific, functional proteins are not enough for DNA replication for one organism.

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