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coevolution of the genetic code

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coevolution of the genetic code

Postby Roland Pohlmeyer » Mon Sep 03, 2007 8:01 pm

The genetic code, i.e. the way information is translated from DNA/ RNA into proteins is well known. However, current graphs and tables of the code emphasise order on the nucleic acid level at the expense of amino acids. Changing the way the code is represented by placing the second base at the centre of the codon wheel of the codon sun, followed by bases 1 and 3 shows up an interesiting new perspective. This simple change in perspective is in line with Wong's theory of coevolution of the code.
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Postby AstusAleator » Tue Sep 04, 2007 3:30 pm

I'm a little rusty on my molecular genetics. would you mind explaining this a little please?
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Postby Darby » Wed Sep 05, 2007 1:52 pm

Coevolution of what with what?

And I agree - I only sort of understand the wheel - a little explanation would be nice.
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Some explaining...

Postby Roland Pohlmeyer » Mon Sep 24, 2007 2:59 pm

Sorry to leave you confused for so long, but I will try to do my best to explain what the wheel is meant to show.

An old dogma in biology states DNA makes RNA makes protein. Previous depictions of the code have focussed on the DNA/ RNA level, with a rigid order of bases. The result of that approach was that codons for some amino acids fell apart and groups of amino acids were separated. The code is degenerate, meaning that sometimes an amino acid has more than one codon, some even have as many as six. When you have a rigid order of bases in a matrix-like table or in the circular form it is not possible to unite all the codons for leucine (L), serine (S), arginine (R) or stop. I tried to unite all those codons in one graph and realised that you could only do it when using the circular representation, placed the second base at the centre and allowed for some variation in the way the bases are listed. The codons unite and it is possible to group codons according to chemical properties of the respective amino acids: (u) non-polar, (p) polar, (+) basic/ positive charge, (-) acidic/ negative charge, (*) special features, (r) aromatic ring structure/ pi electrons, OH alcoholic group.

The result is that you see that an interplay between nucleic and amino acids has shaped the code, with similar amino acids occupying neighbouring codons (coevolution). Previously people had emphasized the role of nucleic acids over that of amino acids. If you try to do away with this hierarchy you start to see the bigger picture. The code gets simpler even though it may look confusing at first. Some creationists have argued that the code is simply too complex to have evolved without the interference from an intelligent designer, seen from this perspective, the code looks shockingly simple.

I stumbled across this serendipitously and only submitted my manuscript to a scientific journal last week. I hope this clears up some of your confusion. Thank you for your interest and feedback. If you have any further questions, please don't hesitate to ask. I'll check on the post from time to time.

Kind regards,
Roland Pohlmeyer
Last edited by Roland Pohlmeyer on Mon Sep 24, 2007 3:12 pm, edited 2 times in total.
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Postby MrMistery » Mon Sep 24, 2007 3:05 pm

Well I'll be damned. You might be onto something there...
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Postby Roland Pohlmeyer » Mon Sep 24, 2007 3:11 pm

Oh by the way, there are two more rare amino acids selenocysteine (codon: UGA) and pyrrolysine (codon: UAG) that fit ever-so-neatly into the scheme. It's massive! But it takes a while to get used to it.
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Postby alextemplet » Mon Sep 24, 2007 4:36 pm

Yeah, now that you've explained it a little, I agree, you might be on to something. I'm impressed.
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More stuff

Postby Roland Pohlmeyer » Mon Sep 24, 2007 6:55 pm

If you want some more information about this topic, I put some results down on http://www.rna-game.org and http://livescience.blogspot.com. But I really enjoy the contributions on this topic, so please feel free to post more questions here.
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Postby Darby » Mon Sep 24, 2007 7:20 pm

I had read some stuff last year of a 2-base codon preceding the 3-base codons, and this fits with that. You are using coevolution in a way I've never seen it used, though, and it doesn't seem to fit here. It just seems a divergence from a simpler to a more complex, redundancy -capable code.
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Reply to Darby

Postby Roland Pohlmeyer » Mon Sep 24, 2007 10:59 pm

Dear Darby,

I'm trying to take your criticism on board but I'm not sure whether or not we are talking about the same thing here. I'm just trying to put my observation that the code seems quite logical into a larger context and am quoting Jeffrey Wong's theory of coevolution of the genetic code (e.g.: Wong JT. Question 6: coevolution theory of the genetic code: a proven theory. Orig Life Evol Biosph. 2007 Oct;37(4-5):403-8. Epub 2007 Jul 5.) as a possible explanation of how the code came to be as it is. Of course coevolution usually refers to whole organisms, say insects and flowers, but I believe that Darwinian mechanisms can be applied up to the very start of biological evolution.

Concerning the theory of a two base code I remain somewhat sceptical. Maybe there was one, maybe there wasn't. All life on earth, at least as far as I know, uses the three base code and I am not aware of any direct proof that a two base code preceeded our current genetic code. I just tried to simplify the genetic code as it exists today, what came before remains to some degree speculation about which I simply don't know enough to comment.

Thank you for your message. I hope I understood you correctly.
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Postby Darby » Tue Sep 25, 2007 4:32 pm

It wasn't really meant as a criticism (although it still seems a beyond-the-border distortion of a perfectly serviceable term, but not by you); I was just trying to understand. Your resource presents an interesting idea, but anyone who would use the phrase "proven theory," especially in this field, has immediately thrown their own credentials into question. Again, not a criticism of you.

Now that I've had a chance to look at it, I realize that the 2 ideas - development of a code based upon available amino acids, with expansion later, and an expansion from a 2- to 3-base codon, are complementary.

But what's explained isn't coevolution, it's adaptation - there isn't a second participant in the dance. The additional amino acids wouldn't have evolved on their own in response to the codons, only the reverse.
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nucleic acid + amino acid -> genetic code

Postby Roland Pohlmeyer » Tue Sep 25, 2007 10:16 pm

Hi Darby,

Gosh, this is getting a bit technical. First of all, I am really thankful for any kind of criticism, be it positive or negative, the important thing here is dialogue where trying to understand you makes me better in arguing my case. I'm an immunologist by training so I'm a bit rusty on Darwinian terminology. I believe that like the term genetic code can be used for two different things, coevolution can mean different things to different people.

Whilst I agree that a nucleic acid did not directly change the molecular structure of an amino acid or vice versa, the cooperation between the two led to certain rules of life to be established and maintained: primarily the triplet nature of the code and the number of amino acids found in proteins. It is reasonable to assume that if the two classes of molecules had not been able to interact in such a way, life would look very differently today if there would have ever been life at all. The kind of nucleic acids we find in living organisms today might not be there in the absence of amino acids or vice versa. I meant to express this kind of interdepency when I was talking about coevolution. Do you have a better suggestion?

Kind regards
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