dvunkannon
Posts: 1377
Joined: June 2008
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http://onlinelibrary.wiley.com/doi....pdf
And now for something completely different...
One of the common OOL related arguments you hear from creationists is about how everything has to be 100-150 units in length before anything interesting happens, and such long sequences are soooo specific and soooo improbable to be built by chance processes, that, therefore, Jimbo. Or Jebus. Or something.
Another argument you'll hear (as in Signature in the Cell) is that the entire protein-mRNA-DNA transcription/translation system is waaay too complex to have sprung up by chance, see the argument above.
So one of the points I like to make about the RNA world is that there was plenty of opportunity for proteins and RNA polymers to work together even when both were short, randomly assembled sequences. As this relates to the formation of the genetic code, the idea is called the stereochemical hypothesis. Nakashima regularly flogged the work of Michael Yarus when discussing this on UD.
I bring the paper above to your attention because it can be read as addressing the same set of issues, from a slightly different perspective.
One of the questions we might ask about protein-RNA interaction is how hard is it to find? Modern gene regulatory networks often work through transcription factors, which are proteins that bind to the DNA. The DNA binding domain of these proteins is actually rather small, common domains are less than 25 AA in length. They also have a fairly 'generic' architecture, such as helix-turn-helix. As we saw this past week with the announcement of the creation of functional proteins by simply stringing 4 helices together, functional helix-turn-helix shouldn't be that hard for a random process to make.
The referenced paper shows that is true for proteins binding to RNA, which is more directly relevant OOL and RNA World discussions. The RNA recognition motif, RRM, is one of several common ways for proteins and RNA to interact in our cells today. The AA sequences that are conserved across many uses and species of eukaryote, prokaryote, and virus are short, only 6 and 8 AA long. Even these are variable in content.
These variable but conserved sequences can then be embedded in a wide variety of larger proteins to be more or less specific in modern cells. Read the paper for all the goodness.
What this says to me, relavent to OOL, is that protein binding to RNA is easy to accomplish, even from random starting points. If these small binding domains are further attached to sequences with enzymatic function, then the RNA World is not going to limp along relying on the self catalytic properties of RNA for very long. Once amino acids and RNA are in the same pot, they will start to interact in a process of molecular co-evolution.
In summary, this paper shows how short and variable sequences of amina acids can have important function, creating interactions directly with strands of RNA. These findings contradict creationist arguments that rely on the length and specificity of proteins to argue that functional proteins could not arise naturally, through normal chemical processes.
PS - Just one quote:
| Quote | To date, more than 30 RRM structures have been
determined either by NMR or X-ray crystallography
and reveal unexpected variations as shown in Fig. 2.
The loops between the secondary structure elements
(loops 1–5 as indicated in Figs 1 and 2) can have
different lengths and are often disordered in the free
form. |
While it is easy, in the context of the argument I am making above, to focus on the variability mentioned in this quote, I am drawn to the mention of 'disordered'. To me, proteins that work even when they haven't folded right are important clues to some very old process. The recent NASA virtual conference had an example of this in discussing a protein in the ribosome. The newer end of the protein, on the outside of the ribosome was folded normally, the end on the interior, the most ancient part of the ribosome, was not folded.
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I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima
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