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Author Topic:   Degenerate codes
judge
Member (Idle past 4854 days)
Posts: 216
From: australia
Joined: 11-11-2002


Message 1 of 6 (69624)
11-27-2003 5:19 PM


I have been reading chapter 3 of Darwin in the Genome.

www.evcforum.net/cgi-bin/dm.cgi?action=page&f=16&t=14&p=16 -->www.evcforum.net/cgi-bin/dm.cgi?action=page&f=16&t=14&p=16">http://www.evcforum.net/cgi-bin/dm.cgi?action=page&f=16&t=14&p=16

and am wondering about the following ......

Becauase of the degeneracy of the genetic code , there are nearly 200 DNA sequences that could have been used to encode the the five amino acids EGIAK . But the 15 DNA letters that encode EGIAK in the repeated patch of the spirochete coat are always part of an identical sequence of 17 letters TGAGGGGGCTATTAAGG, that is found on both sides of the repeat and in all samples of sirochete DNA tested. We never see TGAAGGAGCTATAAAAG TGAGGGCGCCATCAAGG or any of the nearly 200 other ways to encode the very same amino acids.
If these really are synonymous codons, why is it that time after time, spirochete after spirochete, it is always the same TGAGGGGGCTATTAAGG? The other 192 synonyms for EGIAK are not acting as synonyms should.
You and I could make a plan: If you say "I'll call you tonight, it means you'll call me at 8p.m. but if you say "I'll phoneyou tonight.",it means you'll call me at 9 P.M. with two different ways of saying the same thing we can cretae another code tha sends more information underneath the message

Darwin in the Genome p.33

How much is known about this kind of thing?
Might it be relevant to creo/evo in view of the fact that common sequences are part of the argument in favor of common descent? particulary that common synonomous sequences are one of the really difficult things for creo s to explain.
I mean if there is a hidden message under sequences which code for the same proteins then they are'nt really equal are they.

cleaned up some formatting, large amounts of bold print make a post hard to read. May I suggest using the quote tags instead? - The Queen

[This message has been edited by judge, 11-27-2003]

[This message has been edited by AdminAsgara, 11-27-2003]


Replies to this message:
 Message 2 by PaulK, posted 11-27-2003 5:46 PM judge has responded

  
PaulK
Member
Posts: 15907
Joined: 01-10-2003
Member Rating: 2.4


Message 2 of 6 (69625)
11-27-2003 5:46 PM
Reply to: Message 1 by judge
11-27-2003 5:19 PM


If you read on you'll see Dr. Caporale's explanation of this case. But in general synonymous sequences really are synonymous - there is no "hidden message" in most DNA and synonymous substitutions are quite common.

And it has no real relevance to common descent - after all the reproductive machinery which "understands" the "hidden meaning" is just as much a product of evolution and the same sequence might be nothing special in species which are not closely related.


This message is a reply to:
 Message 1 by judge, posted 11-27-2003 5:19 PM judge has responded

Replies to this message:
 Message 3 by judge, posted 11-27-2003 6:32 PM PaulK has responded

  
judge
Member (Idle past 4854 days)
Posts: 216
From: australia
Joined: 11-11-2002


Message 3 of 6 (69628)
11-27-2003 6:32 PM
Reply to: Message 2 by PaulK
11-27-2003 5:46 PM


But in general synonymous sequences really are synonymous - there is no "hidden message" in most DNA and synonymous substitutions are quite common.

Ok so sometimes there is a hidden message and other times there is no hidden message. How do we know when there is nothing hidden. I suppose what I am saying is how do you know that any sequence is the same just because it produces the same protein.
Has this theory been tested?

And it has no real relevance to common descent - after all the reproductive machinery which "understands" the "hidden meaning" is just as much a product of evolution and the same sequence might be nothing special in species which are not closely related.

If you are saying "might be nothing special" then surely it "might be relevant."


This message is a reply to:
 Message 2 by PaulK, posted 11-27-2003 5:46 PM PaulK has responded

Replies to this message:
 Message 4 by PaulK, posted 11-27-2003 6:41 PM judge has responded

  
PaulK
Member
Posts: 15907
Joined: 01-10-2003
Member Rating: 2.4


Message 4 of 6 (69629)
11-27-2003 6:41 PM
Reply to: Message 3 by judge
11-27-2003 6:32 PM


Well finding synonymous substitutions - as we do - is a good sign that there is no "hidden message".

So if you want to use them to explain genetic similarities you need to find evidence that there really is a"hidden message" - in both species.

And the way to do that is to find an ABSENCE of synonymous mutations.


This message is a reply to:
 Message 3 by judge, posted 11-27-2003 6:32 PM judge has responded

Replies to this message:
 Message 5 by judge, posted 11-27-2003 6:54 PM PaulK has responded

  
judge
Member (Idle past 4854 days)
Posts: 216
From: australia
Joined: 11-11-2002


Message 5 of 6 (69634)
11-27-2003 6:54 PM
Reply to: Message 4 by PaulK
11-27-2003 6:41 PM


Well finding synonymous substitutions - as we do - is a good sign that there is no "hidden message".
So if you want to use them to explain genetic similarities you need to find evidence that there really is a"hidden message" - in both species.

And the way to do that is to find an ABSENCE of synonymous mutations

But isn't the fact that humans and chimps share exactly the same mutations (when synonomous ones would do) evidence of common descent?


This message is a reply to:
 Message 4 by PaulK, posted 11-27-2003 6:41 PM PaulK has responded

Replies to this message:
 Message 6 by PaulK, posted 11-28-2003 2:43 AM judge has not yet responded

  
PaulK
Member
Posts: 15907
Joined: 01-10-2003
Member Rating: 2.4


Message 6 of 6 (69669)
11-28-2003 2:43 AM
Reply to: Message 5 by judge
11-27-2003 6:54 PM


Using the "same mutatiosn where synonymous ones would do" would help establish that the chimps are closer to humans than other apes. But it wouldn't be a major evidence for common descent on the grounds that synonymous mutations do tend to accumulate anyway - thats why the absence is significant. And they do that because these "hidden messages" are rare.

In fact the earliest studies (about 30 years ago) used proteins rather than genes and couldn't even detect synonymous mutations.


This message is a reply to:
 Message 5 by judge, posted 11-27-2003 6:54 PM judge has not yet responded

  
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