Tuesday, May 06, 2014

Analysis of one scientific journal article

Very recently in April this year, a group of scientists have published a paper entitled Non-enzymatic glycolysis and pentose-phosphate pathway-like reactions in a plausible Archean ocean in the journal Molecular Systems Biology. The paper depicts the interconversion of metabolic intermediates found in the glyocolytic and pentose phosphate pathways, when some of the intermediates are placed in an environment that seeks to mimic the primordial ocean, which it seems is called the Archean ocean. The paper is interesting on many levels, but I would like to analyze it on one aspect only. Does it prove anything with regard to abiogenesis or make it more plausible? I would suggest not.

For the sake of argument and charity, I assume that all observations reported in the paper are true. That said, note here that what essentially happened is that interconversion of intermediates in those pathways occur when those chemicals are placed in the reaction environment. The whole experiment is fascinating in terms of biochemistry, but how exactly does it prove abiogenesis? It could conceivably show that the pathways are not too difficult to evolve, although it must be noted that the entire experiment happened in a controlled environment. The entire experiment occur with fixed concentrations of various compounds, and it is effectively closed. Out in nature however, do such conditions actually occur?

So firstly, the problem here is that, in order for the experiment to approximate the supposed primordial conditions, either of two possibilities must happen. One, the concentration especially of metabolites must be found in the entire Archean ocean around the world. That is unlikely since the ocean is big and thus to have a concentration at even that low level of 100┬ÁM would require a lot of those organic chemicals to be present. Alternatively, two, the metabolites must be localized in a part of the ocean, i.e. a warm pond or sorts, which must somehow act as a closed system effectively towards the outside. But can such a closed system be formed naturally outside the lab?

Secondly, we are not told whether other chemicals were found besides the ones they were looking for. While this is a minor issue, it is significant only because in nature, all of this feeds into the supposed chemical soup of newly formed amino acids and other organic compounds. This brings us to the issue here of how the understandably narrow focus of the project makes it not possible to actually stimulate a real environment of the Archean ocean. If abiogenesis were true, then not only should we include the salts and metals thought to be in that ocean, but also amino acids of all kinds including the wrong D- isomers, free nucleotides and nucleosides and everything else in between. That would certainly be more realistic, and probably we would not have the results of this paper then.

Thirdly, we note that the intermediates were purchased from companies like Sigma-Aldrich in pure form to be used for the experiment. The question is: how does that correspond to the supposed natural conditions in the Archean ocean? There is not a Sigma-Aldrich chemical plant in the primordial earth producing those chemicals they have purchased, and dumping it into the ocean in order to start the development of both metabolic pathways! In the primordial oceans, these intermediates themselves have to be produced from something simpler, like for example ammonia, hydrogen and water. Stating that interconversion is possible does not address the issue of how any one of the intermediates was formed naturally in the first place!

As I have said, this paper is fascinating, but only in terms of biochemistry. The whole paper is no help at all for answering the question whether abiogenesis has or has not actually occurred. According to the abstract, "these results therefore favour a hypothesis that abundant ions of the Archean ocean could have served as catalysts for the first forms of metabolism." In actual fact, it proves nothing of that sort. Rather, it only proves that ions thought to be in the Archean ocean could serve as independent catalysts for metabolic reactions. But then it would be less sensational.

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