Tuesday, April 1, 2014

Extinction by microbial methane

Dramatization on episode two of Cosmos of the volcanic eruptions
traditionally blamed for the Permian Extinction.
Credit: Fox, National Geographic Channel.
Isn't it interesting that any problems with major theories go unreported until a solution to those problems has been found?  Proponents of the Big Bang very rarely admitted to the flatness and horizon problems until their proposed fix, inflation theory, was "proved" two weeks ago.  Likewise, the greatest extinction event event ever, the Permian extinction (according to the old-earth model), has generally been attributed to violent volcanic eruptions in Siberia about 252 million years ago which resulted in massive outgassing, polluting the air and suffocating most of life on earth.  This explanation was recently presented by Neil deGrasse Tyson on the second episode of his show, Cosmos: A Spacetime Odyssey.  Yet, until a solution was published yesterday, very few people acknowledged the problem that even huge volcanic eruptions could not have produced as much methane as would be necessary to cause the Permian extinction, even though the problem was discovered twelve years ago.

In 2008, scientists from the University of Oregon proposed that the Siberian eruptions set ancient coal seams ablaze, releasing enough methane to account for the Permian extinction.  This proposal was supported two years later with evidence of coal ash in Permian rocks and was also mentioned on Cosmos.  However, this was apparently not enough to convince many scientists, even if it was presented as known fact to the public.

An alternate explanation by a group of scientists from MIT and the Chinese Academy of Sciences was published yesterday in Proceedings of the National Academy of Sciences of the United States of America.  They proposed that the Siberian eruptions were not the primary culprit in the change in earth's carbon cycle at the end of the Permian, which they say was too rapid and large to have been caused by volcanism, and that combustion of coal deposits "is difficult to reconcile with observed geochemical changes."  Rather, they claimed that the eruptions brought large amounts of nickel to the surface, which was then used by a particular strain of bacteria to produce large amounts of methane.  The methane was converted to carbon dioxide, either by chemical or biological processes, lowering the oxygen content of the atmosphere and oceans and causing the mass extinction.  The scientists offered three lines of evidence to support their conclusion:
  1. Carbon-isotope records show an extremely rapid increase in inorganic carbon within the oceans at the end of the Permian.
  2. The bacterium Methanosarcina, which uses nickel to metabolize acetate/acetic acid into methane, acquired the ability to efficiently produce methane at the end of the Permian.
  3. Sediments from the end of the Permian period in southern China show a sharp increase in nickel concentrations.
Individually, none of these points is particularly convincing, but combined they form a substantial argument.  It is difficult to write off these observations as simple coincidence.  Are these really "observations," though?  How much interpretation was involved in this study?

Unlike carbon dating, which uses radioactive isotopes to derive ages, carbon-isotope analysis uses stable isotopes to determine how carbon moved through the ecosystem and environment, reflecting characteristics such as temperature and organic content.  Indeed, there may have been a significant change in the carbon source when the upper Permian rocks were deposited, but the carbon isotopes say nothing of the age of the rocks.  Such a dramatic carbon change could also have been the result of the Flood, which would have not only disturbed the ecosystem, but likely would have involved volcanic eruptions and other major events, including the Siberian eruptions.  A similar argument could be made for the nickel concentrations found in southern China.

In my opinion, the study hinges on the date of the first acetoclastic (acetic acid-eating) Methanosarcina.  If it had been dated to any other time, the authors would have very little data on which to base their hypothesis.  The authors used small protein differences between several species of Methanosarcina, combined with measured mutation rates, to calculate how long ago their common ancestor lived.  Of course, this method assumes constant mutation rates, and the authors readily admitted this, to their credit.  Apparently, their result contradicted that of a previous study, but the authors claimed that the older study used a "less reliable" method and remained confident in their own date of 240±41 million years.  Granted, that is a fairly short interval in the context of the supposed history of bacteria, but an error of 41 million years still seems quite substantial.  At 281 million years ago, the early Permian and the earliest edge of the range, beetles were just about to appear on the earth.  The more recent edge of the range at 199 million years ago is just at the beginning of the Jurassic period, when dinosaurs were just starting to dominate the earth.  Nevertheless, the authors state in their abstract that the development of efficient acetoclasticism in Methanosarcina is "stastistically indistinguishable from the [Permian] extinction."  While that may technically be true, I find it misleading.

I also found what appears to be a contradiction in their study.  Their figure 3 (below) shows two phylogenetic (evolutionary) trees for Methanosarcina and its relatives to justify their date.

On the left is a chronogram, a type of tree that shows evolutionary splits relative to a timeline.  On the right is a different and more detailed tree developed using a specific set of genes.  Strangely, the arrangement of the species is markedly different between the two trees.  On the left, M. mazei and M. acetivorans form a sister group to M. barkeri, with M. thermophila on a distant branch.  On the right, M. thermophila and M. barkeri are in a sister group to M. mazei, and M. acetivorans is on a distant branch.  It is possible that I am speaking out of ignorance, and that there is a reason for this discrepancy due to the specific methods used, but I still find it odd.  Furthermore, the caption for this figure states that "the age of acetoclastic Methanosarcina [was] adjusted to match the combined [protein age] estimate," yet it is not clear what this age was adjusted from.  Interestingly, the sister group to the acetoclastic group was supposed to have split off and diversified around 800 million years ago, yet the acetoclasts are not shown to have diversified until 550 million years later.

Given these observations, I am not convinced that the authors truly have a rigorous argument for their position on the cause of the Permian extinction.  Indeed, I am not even convinced that the Permian extinction happened at all as it is commonly presented.  While we can observe a distinct change in fauna between Permian and Triassic rocks, it is only reasonably interpreted as a major extinction event under the assumption that the rocks represent a gradual progression of time.  Under the creationist view, the Permo-Triassic boundary represents a geographic change in ecology more than a chronologic one.  Below this boundary, rocks are dominated by marine and shoreline sediments, possibly from encroaching floodwaters from the ocean.  Above this boundary are much more terrestrial deposits, possibly from waters that traversed the continent before depositing their sediment load.  The Flood of Noah was a complex event, so there is no simple explanation for all of the variations in rocks and fossils seen in the record, but creationist scientists are gradually piecing it together bit by bit.  Admittedly, the creationist model is not quite as extensive as the naturalistic one, but that is to be expected given the disparity of researchers and resources available to each side.  Such disparity says nothing of the validity of either position, however.  Scientists of both (and other) persuasions continue to investigate the world to increase knowledge, which is good as long as facts are kept distinct from interpretations.

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