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jerrywickey

Evolution of a Single Protein

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One of my big interests is protein evolution. But still no luck on following the evolution of a protein. I have tried. No studies. No papers. No evidence it happens ever. Just flawed theories. No help from interested and knowledgeable people.

 

I wrote software to study it. The simulation gave me many things to think about which I did not expect to find. But it did not provide even a ghost of a pathway to the first protein.

 

Perhaps proteins never came into existence. Perhaps, proteins don't exist. (Just kidding. frustrating that I have to actually say that, lest some joker replies: "Proteins do exist, You're dumb." If you are this sort of member, please refrain from replying to this post.)

 

We observe 45,000 protein domains. Each of which is used over and over again throughout all proteins of all organisms.

 

There are two possible explanations for this repeated use.

 

1) There are many other peptide sequences which carry on useful chemical activities but only this set of 45,000 were selected by evolutionary processes and as such proteins for all organisms have a lineage traceable back to these domains. Or

 

2) Evolutionary processes have tried many or nearly all sequences and these 45,000 are the only ones which express useful chemistry, and therefore it is this conservation of function that dictates these same constituents for all proteins.

 

Each possibility carries important implications for evolution. Figuring out which will advance our understanding of evolution. There are many facts of which we are certain, that might make one of these possibilities more likely than the other.

 

There may already be enough information to make a confident choice. I don't have all that information but many forum members together may.

 

Express your interest and I will begin to post queries that make an attempt to organize the information in to a task resolution.

 

The first query is:

 

Do we observe splicing of protein coding genes which produce a protein coding mRNA with an incorrect splice at a point in the middle of the nucleotide sequence coding for a domain?

 

This is a crucial question. If no one is aware of any lab work or papers which document this observation, we can draw some incremental conclusions and ask the next question.

 

If there is interest, I will go further and explain further. I've already typed more than most like to read in one post.

 

Feel free to disagree with the possible reasons for the same domains being reused in all proteins. Post another possibility. That could be an important clue.

 

Jerry

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One of my big interests is protein evolution. But still no luck on following the evolution of a protein. I have tried. No studies. No papers. No evidence it happens ever. Just flawed theories. No help from interested and knowledgeable people.

 

Jerry, have you gone to PubMed and done a search using the terms "protein, evolution"? I did. There are over 74,000 references. The first one is:

Dowling DP, Costanzo LD, Gennadios HA, Christianson DW. Evolution of the arginase fold and functional diversity. Cell Mol Life Sci. 2008 Mar 24;

 

At the end of the post I have a couple of papers for you to start. I even have a book on my shelf called Protein Evolution. There are several books on the subject. Go here: http://www.amazon.com/s/ref=nb_ss_b/105-5714668-1097220?url=search-alias%3Dstripbooks&field-keywords=Protein+Evolution&x=10&y=14

 

But it did not provide even a ghost of a pathway to the first protein.

 

This is different. Now you don't want evolution of proteins That's because proteins arise by chemistry. If you heat amino acids -- either dry as in a tidal pool or at hydrothermal vents, they form proteins. There is quite an extensive literature on this. Most of the work was done prior to 1980. Start here:

http://www.siu.edu/~protocell/

http://www.theharbinger.org/articles/rel_sci/fox.html

 

and I can give you further references if you want.

 

Here is the reference list:

 

1. E Wilson-Miles and DR Davies, On the ancestry of barrels. Science 289: 1490. Sept. 1, 2000. "the structure arose from the duplication and fusion of the gene of acommon half-barrel ancestor"

2. M Buck and MK Rosen, Flipping a switch. Science 291: 2329-2330, March 23, 2001. Describes studies on the motion of proteins that are signalling molecules, including mutations that give activity in the absence of phosphorylation. (also refutes Behe because demonstrates one way to build an IC system).

3. http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0030139 Formation of gene families and protein folding

4. Science paper by Doolittle (back in 1981) http://www.sciencemag.org/cgi/reprint/214/4517/149.pdf

8. http://www.sciencemag.org/cgi/content/full/312/5770/97 JT. Bridgham, SM Carroll, J W Thornton Evolution of Hormone-Receptor Complexity by Molecular Exploitation Science 7 April 2006: Vol. 312. no. 5770, pp. 97 - 101 PDF file and other papers here: http://www.uoregon.edu/~joet/pubs.htm

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YES!!!

 

You see the obsticles. Others post that protein evolution is a simple matter that has been solved over and over again.

 

Thanks

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