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Author Topic:   Please explain evolution.
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 16 of 23 (153384)
10-27-2004 12:41 PM
Reply to: Message 12 by Wounded King
10-27-2004 6:10 AM


Come on Crash, thats clearly not true! Just look at your figure, a change of 1 base pair probably won't be a problem provided that it is the third base of the codon, but even a 1 bp change in the 1st or 2nd base will almost always produce a non-synonymous substitution.
There's a fair number of amino acids that have codons with two or even three differing bases. But you're right that that isn't most of them. And for most of them, the first codon nucelotide has to be the same.
But for most of them, the second and third can be changed. (Maybe you missed that some of them are listed twice?) I would offer that 2 out of 3 is large enough to be described as "probable."
70% of residues may well survive changing and allow a protein to function, although a reference would be nice to know exactly what research you are drawing from
Fair enough:
CB150: Functional genetic sequences changing
quote:
The analogy with language is flawed. Proteins are far more flexible. They can differ greatly in their sequence similarity, even 70-80% or more, and still have the same function.
The bibliography is at the bottom; the page does not make it clear which reference supports which claim, specifically.
but I doubt that if you changed 70% of the hydrophilic residues in a protein to hydrophobic residues you would get a functioning protein.
That may be. The page does not say.
Perhaps I overstated my claim. Nonetheless it's fairly clear that there is much resistance to mutation in the protein generation mechanism.

This message is a reply to:
 Message 12 by Wounded King, posted 10-27-2004 6:10 AM Wounded King has replied

Replies to this message:
 Message 17 by Wounded King, posted 10-27-2004 2:06 PM crashfrog has replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 17 of 23 (153404)
10-27-2004 2:06 PM
Reply to: Message 16 by crashfrog
10-27-2004 12:41 PM


There's a fair number of amino acids that have codons with two or even three differing bases. But you're right that that isn't most of them. And for most of them, the first codon nucelotide has to be the same.
But for most of them, the second and third can be changed. (Maybe you missed that some of them are listed twice?) I would offer that 2 out of 3 is large enough to be described as "probable."
Look at the figure Crash, where are you getting this stuff from?!!!
Apart from the stop codons a change in the 2nd base position is always non-synonymous. Only Leucine and Arginine have 6 codons and can support changes at the 1st position. Given that third base wobble is not always effective, in many cases there are only 2 codons for a particular residue, we arrive at the figure I previously mentioned ~30% of substitutions will cause synonymous mutations. 30% is certainly a large enough probability to ensure frequent occurence, but certainly not enough to merit being described as the probable outcome.
Your quote from the Talk.Origins site suggests that 70-80% is the extreme range which some proteins can tolerate rather than that most can, as you claim. Going by any normal system of referencing it seems likely that they cite no reference for this figure as the nine references are all from points 1, 2 and 4.
Nonetheless it's fairly clear that there is much resistance to mutation in the protein generation mechanism.
I wouldn't say resistance as such, but there is certainly a fairly high tolerance for mutations, contrary to what many creationists claim.
TTFN,
WK
This message has been edited by Wounded King, 10-27-2004 01:09 PM

This message is a reply to:
 Message 16 by crashfrog, posted 10-27-2004 12:41 PM crashfrog has replied

Replies to this message:
 Message 18 by Loudmouth, posted 10-27-2004 2:16 PM Wounded King has replied
 Message 21 by crashfrog, posted 10-27-2004 7:49 PM Wounded King has replied

Loudmouth
Inactive Member


Message 18 of 23 (153407)
10-27-2004 2:16 PM
Reply to: Message 17 by Wounded King
10-27-2004 2:06 PM


quote:
Your quote from the Talk.Origins site suggests that 70-80% is the extreme range which some proteins can tolerate rather than that most can, as you claim. Going by any normal system of referencing it seems likely that they cite no reference for this figure as the nine references are all from points 1, 2 and 4.
On the flip side, convergent evolution can create functionaly similar enzymes that differ greatly. That is, there is more than one way to skin a cat, if you get my drift. The interesting part is that these analogous but non-homologous proteins often share a common active site but can differ greatly outside of the active site. I will agree that 70-80% change in the SAME protein is rare, but 70-80% dissimilarity between proteins with similar enzymatic activity is not uncalled for.

This message is a reply to:
 Message 17 by Wounded King, posted 10-27-2004 2:06 PM Wounded King has replied

Replies to this message:
 Message 19 by Wounded King, posted 10-27-2004 5:57 PM Loudmouth has replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 19 of 23 (153459)
10-27-2004 5:57 PM
Reply to: Message 18 by Loudmouth
10-27-2004 2:16 PM


Certainly! I wonder how far that goes in terms of higher conformational structure rather than amino acid sequence?
Are analogous proteins frequently more alike structurally than one might expect or do they also come up with radically different solutions to the same problem. I appreciate that the same active site may develop more than once but how disimilar structurally are such enzymes in other respects.
TTFN,
WK

This message is a reply to:
 Message 18 by Loudmouth, posted 10-27-2004 2:16 PM Loudmouth has replied

Replies to this message:
 Message 20 by Loudmouth, posted 10-27-2004 6:20 PM Wounded King has not replied

Loudmouth
Inactive Member


Message 20 of 23 (153462)
10-27-2004 6:20 PM
Reply to: Message 19 by Wounded King
10-27-2004 5:57 PM


quote:
Certainly! I wonder how far that goes in terms of higher conformational structure rather than amino acid sequence?
That is a good question. The only way to confirm conformation is through protein crystal formation, which is a tough to come by since some condensations/crystalizations take up to a year and require large quantities. I'll do some digging when I have a chance.

This message is a reply to:
 Message 19 by Wounded King, posted 10-27-2004 5:57 PM Wounded King has not replied

crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 21 of 23 (153482)
10-27-2004 7:49 PM
Reply to: Message 17 by Wounded King
10-27-2004 2:06 PM


Apart from the stop codons a change in the 2nd base position is always non-synonymous.
What? Serine's second base has synonymous substitutions. As does it's first base.
But now that I look closer, I see that you're right - its not nearly as common as I had thought. Fair enough.
Aren't we getting just a bit pedantic?

This message is a reply to:
 Message 17 by Wounded King, posted 10-27-2004 2:06 PM Wounded King has replied

Replies to this message:
 Message 22 by Wounded King, posted 10-28-2004 6:18 AM crashfrog has not replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 22 of 23 (153594)
10-28-2004 6:18 AM
Reply to: Message 21 by crashfrog
10-27-2004 7:49 PM


Quite right Crash, I missed Serine mea culpa, but that and the stop codon seem to be the only ones.
As you suggest, we might be getting a bit into the realms of nit-picking.
TTFN,
WK
This message has been edited by Wounded King, 10-28-2004 05:18 AM

This message is a reply to:
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Adminnemooseus
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Posts: 3974
Joined: 09-26-2002


Message 23 of 23 (156631)
11-06-2004 11:49 AM


Closing down relic "Great Debate" topic
This topic most likely would not have passed the "Proposed New Topic" review process now in place. Also, it would no longer be a topic for the "Great Debate" forum.
The recent content probably better belongs elsewhere.
Adminnemooseus

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