of interest to TB (?)

This was cited on another board:White SH, Jacobs RE. (1993) The evolution of proteins from random amino acid sequences. I. Evidence from the lengthwise distribution of amino acids in modern protein sequences. J. Mol. Evol. 36: 79-95We examine in this paper one of the expected consequences of the hypothesis that modern proteins evolved from random heteropeptide sequences. Specifically, we investigate the lengthwise distributions of amino acids in a set of 1,789 protein sequences with little sequence identify using the run test statistic (ro) of Mood (1940, Ann. Math. Stat. 11, 367-392). The probability density of ro for a collection of random sequences has mean = 0 and variance = 1 [the N(0,1) distribution] and can be used to measure the tendency of amino acids of a given type to cluster together in a sequence relative to that of a random sequence. We implement the run test using binary representations of protein sequences in which the amino acids of interest are assigned a value of 1 and all others a value of 0. We consider individual amino acids and sets of various combinations of them based upon hydrophobicity (4 sets), charge (3 sets), volume (4 sets), and secondary structure propensity (3 sets). We find that any sequence chosen randomly has a 90% or greater chance of having a lengthwise distribution of amino acids that is indistinguishable from the random expectation regardless of amino acid type. We regard this as strong support for the random-origin hypothesis. However, we do observe significant deviations from the random expectation as might be expected after billions years of evolution. Two important global trends are found: (1) Amino acids with a strong alpha-helix propensity show a strong tendency to cluster whereas those with beta-sheet or reverse-turn propensity do not. (2) Clustered rather than evenly distributed patterns tend to be preferred by the individual amino acids and this is particularly so for methionine. Finally, we consider the problem of reconciling the random nature of protein sequences with structurally meaningful periodic "patterns" that can be detected by sliding-window, autocorrelation, and Fourier analyses. Two examples, rhodopsin and bacteriorhodopsin, show that such patterns are a natural feature of random sequences.

Interesting stuff SLPx. It doesn't change the fact that only 1 in 10,000 random sequences will fold. What it does suggest is that if evolution were true you guys should probably assume the protein coding genes came from the junk DNA gaps rather than existing genes.If this was really true one should be able to analyse the junk DNA and discover emerging genes (no funciton yet but fulfil some foldability criteria like having stretches of secondary structre in PHD/PROF SS predicitons). Maybe that will be my new grad student's project? But I think I should leave that to someone less biased . Do you want to do it as a collaboration SPLx? I'm almost serious. What's your bioinformatics like? - I lecture on it but mainly do 3D structural simulations. Maybe Mokenstick and I should do it?

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Originally posted by Tranquility Base:
Interesting stuff SLPx. It doesn't change the fact that only 1 in 10,000 random sequences will fold.

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I do wonder how many random sequences might have existed....

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What it does suggest is that if evolution were true you guys should probably assume the protein coding genes came from the junk DNA gaps rather than existing genes.

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Or both, as is certainly the case with duplicated genes.

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Do you want to do it as a collaboration SPLx? I'm almost serious. What's your bioinformatics like? - I lecture on it but mainly do 3D structural simulations. Maybe Mokenstick and I should do it?

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LOL! I appreciate the offer, and I would take you up on it if I had: the facilities, the funding, and the time! I am MONTHS behind in what little projects I do have going....