Thursday, June 29, 2006

Debunking Arguments for Life's Origins

Comments on an article accessed at the referenced URL involved the possibility of an exchange between an individual identified as Timothy Chase and me. Unfortunately the opportunity to post a response was closed off before I could respond (it seems to occur frequently) so I'll post a blog response. The authors and the referenced paper are identified for clarity. The URL brings one to an article entitled 'Scientific world unites over origins of life' which was authored by Eben Harrell. Comments follow the article.

http://tinyurl.com/kdtg3

Timothy Chase wrote:
It is grounded in a fair amount of circumstantial evidence -- and to some extent, a general understanding of the scientific method. For example, the boundary between life and non-life has borderline cases. Viruses are a good example. We know, for example, that an enzyme and nutrients are all that are required to form a self-replicating RNA virus. (See #41 above -- which includes technical references and links to the original articles.)

[Bradford]: You neglected to point out that a "self-replicating" RNA virus is dependent on transcription mechanisms of its host for replication. The host transcription function is highly complex and as necessary to successful replication as the viral nucleotide sequence. As stated in the article that you referenced "New viroids and virusoids are synthesized by the host cell as long precursors in which the viroid structure is tandemly repeated."

Chase: Likewise, we know that natural processes form amino acids under circumstances which evidently existed on the early earth with its reductive atmosphere -- prior to the continual production of corrosive oxygen through photosynthesis. Likewise, we know that stable ribose can be formed under natural conditions.

[Bradford]: Spark discharge experiments producing amino acids show why functional proteins would not form as a result of lightning storms. Experiments show that amino acids are found in a larger mixture containing other biochemically useless organic compounds. The amino acid mixtures are of equal amounts of left- and right-handed stereoisomers and sets of 20 varieties are not produced. Lacking are experimental reasons to believe that an extracellular chemical process exists leading to the separation of L amino acids from the much larger organic mix. Most importantly there is no empirical basis for believing amino acids would form polymers leading to functional proteins. Functionality is sequence dependent.

Formation of ribose, like other biomolecules, may be found to occur naturally under limted conditions. But this does not address the primary issue confronting OOL advocates. Nucleic acids, useful to living cells, are distinguished by the specificity of their nucleotide sequences. It is the identity and order of codons that confers selective value. Chemistry can explain why ribose might be part of reaction x that leads to bonds with nitrogenous bases and phosphate groups but this does nothing to explain why particular sequences useful to protein synthesis and replication functions would arise. Also lacking is a means of genetic expression. OOLers typically issue promissory notes at this juncture indicating their faith in future expermental results. However this ignores a problem that goes deeper than results. Natural selection, a crtical component of Darwinian models, is powerless to provide any predictive insight as to why we should expect a narrow subset of sequence specificity within a much broader range of possibilities when a cell whose existence is dependent on that specificity has yet to evolve. This defect pierces the heart of Darwinian theory.

Chase: As #41 demonstrates, self-replication doesn't require a cell per se -- and doesn't even require a genome to arrive at a self-replicating genome. Likewise, a metabolism is essentially an autocatalytic chemical reaction and wouldn't necessarily require any genome at all, or for that matter, an enzyme. Likewise, a cell is essentially a semi-permeable compartment, and some geological formations could act as a primitive "cell" of sorts. There are of course other problems, smaller missing pieces. More importantly, putting all of the pieces together into a coherent theory which fits the evidence we have so far as to what conditions existed on the primitive earth, and which is capable of making specific, testable predictions.

[Bradford]: Let's take a look at one of the papers indicated by a URL you provided. From the paper entitled 'An Extracellular Darwinian Experiment with a Self-Duplicating Nucleic Acid Molecule':

http://www.pnas.org/cgi/reprint/58/1/217

"Experiments were performed to explore the evolutionary consequences for a self-duplicating nucleic acid molecule put under selection pressure for fast growth. As the experiment progressed, the rate of RNA synthesis increased and the product became smaller. By the 74th transfer the replicating molecule had eliminated 83 per cent of its original genome, becoming the smallest known self-duplicating entity."

[Bradford]: Two points of note here. The biomolecules relevant to the experiment are sourced from existing biological entities. The RNA in question did not evolve in a prebiotic soup and the replicase noted in the paper (a protein) also was not the product of a prebiotic process. Second, the replication was a downsizing process whose significance will be the subject of further comments.

More from the paper:
"...Further, the sequences involved in the recognition mechanism between template and enzyme are enriched in the smaller molecules which evolve."

[Bradford]: It is expected that RNA would change as it is unstable and for this reason unsuitable as a long term carrier of genetic information; a task handled by DNA.

"Finally, these abbreviated molecules have a very high affinity for the replicase but are no longer able to direct the synthesis of virus particles. This feature opens up a novel pathway toward a highly specific device for interfering with viral replication."

[Bradford]: Loss of a function does not support an assumption that RNA would then acquire a new distinct function. The affinity for replicase results from some very specific amino acid sequences in the enzyme active site as well as the secondary structure of the enzyme to say nothing of its very existence which is a given to begin with. Evolution of a functional genome on prebiotic earth would require the evolution of larger not smaller molecules.

The last sentence is interesting in that it points to some state of the art application of truncated RNA. RNAi has already shown promise as an anti-viral agent. On that point we can agree.

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