Monday, January 5, 2015

A Second Miller-Urry Experiment

Article: The Origins of Life, by Helen Fields. Published by Smithsonian Magazine
http://www.smithsonianmag.com/science-nature/the-origins-of-life-60437133/?all

The Miller-Urry experiment was widely hailed as a milestone in origin of life research, for it showed a verifiable way for the generation of amino acids and other required biological building blocks to be generated by natural phenomena. However, the two assumed energy sources, ultraviolet light and lightning, only act on the surface of the planet, which, at the time life evolved, was most likely not a hospitable place. Due to the lack of free oxygen, there was no ozone layer to prevent the damaging ultraviolet rays from making it to the surface and smashing up the slowly accumulating (or so is hypothesized) fragile complex organic molecules. However, this article presents an alternative way: the building blocks of life could have been formed at the high heats and pressures around geothermal vents, deep under the ocean, protected from ultraviolet radiation (and the asteroids of the LHB) by kilometers of water. With a much less volatile environment, the complex molecules would have had a chance to form protected.
The article also gives insights into how those basic molecules could have bumped into each other enough to form the polymers of life. The prebiotic soup that was the starting point of life could not have been very concentrated, so much so that randomly floating monomers forming polymers has been described as "infinitesimally small." However, if the molecules were sliding along a surface, all of a sudden this becomes a two-dimensional instead of three-dimensional problem, making an interaction much more likely. It would also reduce the amount of space the molecules had to work in from the whole ocean to just the surface itself, reducing the search space. These researchers are investigating to see if certain rocks might have been able to do that with amino acids or other monomers. If so, that's another lot of improbability in the origin of life accounted for.
Yet, like all articles on the origin of life I have seen, it does not address the real issue with the RNA world hypothesis, the one currently accepted by most researchers. Despite there being plausible hypothesis for the generation of basic biological monomers, there remains the problem: How do we get this first replicating molecule? According to this article: http://www.nature.com/nature/journal/v515/n7527/pdf/nature13900.pdf, the best that has been done that had a limited capacity to self-replicate when given the proper starting components (those components is another moderately improbable "if"), is 83 bases in length. It requires 1 ribozyme (enzyme made of RNA) and 1 template strand, which is the same thing as the enzyme. Probability-wise, if there are 8 possible bases (U, A, G, C in both left-handed and right-handed forms http://en.wikipedia.org/wiki/Chirality), and a specific sequence of 83 bases to follow, the number of possible sequences is 8^83, which is approximately 10^75. Taking in mind that we need 2 of these, one as ribozyme and one as template, we need to multiply again for the two sequences: 10^75*10^75=10^150. This is the same as the number of actions the universe could have taken in its entire lifetime, (http://en.wikipedia.org/wiki/Universal_probability_bound) of 10^150 possible actions. In other words, if the whole universe attempted to find, by random processes, two specific sequences of 83 bases each, it could, if if every possible action it took searched one possible combination. Note that this is, of course, a wild overestimation on the probabilistic resources that could be brought to bear on the problem of the origin of life, and the estimate of 10^150 possible actions assumes a search time of about 1 billion times longer that the age of the universe. That, it seems to me, is the real problem with our current understanding of the origin of life.

4 comments:

  1. The situation becomes even more problematic when we consider that the possible bases does not just include the canonical U,A,G,C, but also other, different ones, such as Xanthine, which makes even more possible combinations.

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    1. T, the RNA version, is also possible. With A,U,G,C,T,X, in both chiralities,we have (12^83)^2=10^179, far over the estimate on the number of positions the universe can search.

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  2. We also must consider that when we have the first replicating molecule, we are not "home free," there is still a long way to go from a ribozyme that can add bases based on a template to a full cell that does not need ready-made bases (which would be, in any case, not very common).

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    1. http://www.the-scientist.com/?articles.view/articleNo/39252/title/RNA-World-2-0/'
      This is a good article on the challenges facing the origin of life. It to, however, like I said,does not come up with how the first RNA molecule was assembled.

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