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Author Topic:   Adding information to the genome.
Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


(1)
Message 211 of 280 (535138)
11-13-2009 4:28 AM
Reply to: Message 205 by Kaichos Man
11-12-2009 8:00 PM


I call!
Okay, two different processes, granted. But it could be said that variation is the result of both mutation and drift.
Indeed, in fact that was exactly the point I was making that you thought was contradictory. The other point is that using this interpretation natural selection is also one of the processes resulting in variation we see since it also 'decides' what variation remains.
To take your poker analogy further lets say you just keep your original hand while I keep my best cards but draw the rest again, doesn't being able to keep good cards and be able to redraw increase my chances of having a good hand? And doesn't it, more importantly to our discussion, also affect the 'variation' of the hands we have at the end of the game?
The ongoing discussion in evolutionary circles is how much of the variation we see in the genome is determined by which process, drift or natural selection. No-one, other than you apparently, believes that only one of them is in operation. That is why Kimura says that the fate is largely rather than solely determined by drift.
Indeed most bioinformatic approaches to finding 'information' in the genome consist of identifying sequences, or specific nucleotides, whose patterns of variation have been reduced by selection.
TTFN,
WK

This message is a reply to:
 Message 205 by Kaichos Man, posted 11-12-2009 8:00 PM Kaichos Man has replied

Replies to this message:
 Message 213 by Kaichos Man, posted 11-13-2009 7:58 AM Wounded King has replied

  
Kaichos Man
Member (Idle past 4489 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 212 of 280 (535150)
11-13-2009 6:56 AM
Reply to: Message 210 by RAZD
11-12-2009 11:20 PM


Re: The information on Australopithicus > Lucy
More evidence will only serve to "flesh-out" the skeleton further.
Maybe that should read "flush-out":
"Furthermore, synapomorphy aside, even if the presence of similar ramal morphology in Au. afarensis and Au. robustus did, indeed, represent homoplasy, the Au. afarensis ramal anatomy would still exclude this taxon from our ancestry". (Rak et al, 2007)

"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

This message is a reply to:
 Message 210 by RAZD, posted 11-12-2009 11:20 PM RAZD has seen this message but not replied

  
Kaichos Man
Member (Idle past 4489 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


(1)
Message 213 of 280 (535159)
11-13-2009 7:58 AM
Reply to: Message 211 by Wounded King
11-13-2009 4:28 AM


Re: I call!
The ongoing discussion in evolutionary circles is how much of the variation we see in the genome is determined by which process, drift or natural selection. No-one, other than you apparently, believes that only one of them is in operation. That is why Kimura says that the fate is largely rather than solely determined by drift.
It is the "largely" I am interested in.
Let me explain my interest in the work of Kimura. It has been claimed that I have attempted to portray Kimura as anti-evolution. We all know that isn't true. He may have been anti-modern-synthesis, but he was an evolutionist to the bootstraps. So why would I, and other Creationists, be so interested in his theory?
The answer lies in why Kimura formed his theory. He observed that "functionally less important molecules, or portions of molecules, evolve faster than more important ones". Functionally important parts of the genome show very little variation. Purifying selection keeps things very quiet. Just the odd synonymous mutation. The real party is going on in the "junk DNA", where an absence of selection means mutations can proliferate.
It therefore made sense to Kimura that the only place the variation needed by evolution could take place was in the junk DNA. Selection couldn't play a role until some form of useful variation had been created. Kimura decided the easiest way this could be achieved was through the neofunctionalisation of duplicated genes.
Obviously, this scenario is attractive to Creationists for two reasons. Firstly, the theory uses hard data to establish that evolution of the functionally important parts of the genome is severely constrained. That really gives evolution an uphill battle, for a start. And secondly, Kimura shows that selection can play little or no role in the generation of variation. In fact, he insists on a "relaxation of selection" as a prerequisite for evolution to proceed!
This means the highly-complex genetic structures required as new genomic information have to be built by random mutation alone. And all the breath-taking improbabilities we Creationists like to deal in are suddenly operative.
Indeed most bioinformatic approaches to finding 'information' in the genome consist of identifying sequences, or specific nucleotides, whose patterns of variation have been reduced by selection.
Exactly right. Kimura even wryly observed that most modern biochemists use this method to identify functionally important parts of the genome, though many of them don't realise it originated from the Neutral Theory.

"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

This message is a reply to:
 Message 211 by Wounded King, posted 11-13-2009 4:28 AM Wounded King has replied

Replies to this message:
 Message 214 by Wounded King, posted 11-13-2009 8:52 AM Kaichos Man has replied
 Message 215 by Dr Adequate, posted 11-14-2009 1:18 AM Kaichos Man has not replied
 Message 218 by Percy, posted 11-14-2009 8:27 AM Kaichos Man has replied
 Message 231 by pandion, posted 11-16-2009 9:44 AM Kaichos Man has not replied

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


(1)
Message 214 of 280 (535161)
11-13-2009 8:52 AM
Reply to: Message 213 by Kaichos Man
11-13-2009 7:58 AM


And back we go again.
I'm really beginning to doubt there is any point continuing this dialogue.
You just keep on reiterating the same stupid assertions, fail to acknowledge the many substantial rebuttals and then proceed to talk more nonsense about what biologists believe.
Kimura decided the easiest way this could be achieved was through the neofunctionalisation of duplicated genes.
These aren't junk DNA, your entire argument seems to be based on wilfully misunderstanding almost any piece of biology you encounter. Pseudogenes, the nonfunctional remnants of duplicated genes, are definitely considered junk DNA for the most part but still functional duplicates certainly aren't. Being subject to a "relaxation of selection" is not the same as being junk DNA.
Firstly, the theory uses hard data to establish that evolution of the functionally important parts of the genome is severely constrained.
That is a claim so vague that it might well be true, but it is an astronomical leap from 'severely constrained' to effectively impossible to arive at naturally.
secondly, Kimura shows that selection can play little or no role in the generation of variation.
Yes, but that is in variation as a whole, if you actually look at elements with functional variation then that role shoots up.
This means the highly-complex genetic structures required as new genomic information have to be built by random mutation alone.
No it doesn't, and no matter how much you put your fingers in your ears and go 'LA LA LA' you aren't going to change the fact. If you really think Kimura says that then you are incapable of reading properly.
TTFN,
WK
Edited by Wounded King, : No reason given.

This message is a reply to:
 Message 213 by Kaichos Man, posted 11-13-2009 7:58 AM Kaichos Man has replied

Replies to this message:
 Message 216 by Kaichos Man, posted 11-14-2009 4:41 AM Wounded King has replied

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 215 of 280 (535249)
11-14-2009 1:18 AM
Reply to: Message 213 by Kaichos Man
11-13-2009 7:58 AM


Re: I call!
It therefore made sense to Kimura that the only place the variation needed by evolution could take place was in the junk DNA.
But of course he said no such thing, as you would know if you'd ever read what he wrote instead of making up crazy shit about it.
This means the highly-complex genetic structures required as new genomic information have to be built by random mutation alone. And all the breath-taking improbabilities we Creationists like to deal in are suddenly operative.
A simpler lie would have sufficed just as well as a starting point for the standard fatuous creationist drivel about "breath-taking improbabilities". Why weave Kimura into your web of deceit?
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 213 by Kaichos Man, posted 11-13-2009 7:58 AM Kaichos Man has not replied

  
Kaichos Man
Member (Idle past 4489 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 216 of 280 (535255)
11-14-2009 4:41 AM
Reply to: Message 214 by Wounded King
11-13-2009 8:52 AM


Re: And back we go again.
Kimura decided the easiest way this could be achieved was through the neofunctionalisation of duplicated genes.
These aren't junk DNA, your entire argument seems to be based on wilfully misunderstanding almost any piece of biology you encounter. Pseudogenes, the nonfunctional remnants of duplicated genes, are definitely considered junk DNA for the most part but still functional duplicates certainly aren't.
Kimura:
"(2) Thereis a sudden increase or boom of neutral variations under
relaxed selection. In this stage, gene duplication in addition
to point mutation must play a very important role in producing
genetic variations. Needless to say, their fate is largely
determined by random drift".
secondly, Kimura shows that selection can play little or no role in the generation of variation.
Yes, but that is in variation as a whole, if you actually look at elements with functional variation then that role shoots up.
Perhaps you don't understand Kimura's problem with functional variation. I'll allow him to elaborate:
"Functionally less important molecules or parts of a molecule evolve (in terms of mutant substitutions) faster than more important ones."
This means the highly-complex genetic structures required as new genomic information have to be built by random mutation alone.
No it doesn't, and no matter how much you put your fingers in your ears and go 'LA LA LA' you aren't going to change the fact. If you really think Kimura says that then you are incapable of reading properly.
Kimura:
"(2) There is a sudden increase or boom of neutral variations under relaxed selection. In this stage, gene duplication in addition
to point mutation must play a very important role in producing
genetic variations. Needless to say, their fate is largely
determined by random drift."
As we agreed earlier. Caused by random mutation. Chosen by random drift. Both random processes.
I'm really beginning to doubt there is any point continuing this dialogue.
If you refuse to accept what Kimura said, there isn't.
Edited by Kaichos Man, : No reason given.

"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

This message is a reply to:
 Message 214 by Wounded King, posted 11-13-2009 8:52 AM Wounded King has replied

Replies to this message:
 Message 217 by Percy, posted 11-14-2009 8:17 AM Kaichos Man has replied
 Message 225 by Dr Adequate, posted 11-14-2009 11:10 PM Kaichos Man has not replied
 Message 229 by Wounded King, posted 11-16-2009 7:46 AM Kaichos Man has not replied

  
Percy
Member
Posts: 22394
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 217 of 280 (535269)
11-14-2009 8:17 AM
Reply to: Message 216 by Kaichos Man
11-14-2009 4:41 AM


Re: And back we go again.
No one here who doesn't have your reading comprehension problems sees any significant conflict between Kimura's views and evolutionary theory.
--Percy

This message is a reply to:
 Message 216 by Kaichos Man, posted 11-14-2009 4:41 AM Kaichos Man has replied

Replies to this message:
 Message 219 by Kaichos Man, posted 11-14-2009 8:36 AM Percy has replied

  
Percy
Member
Posts: 22394
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 218 of 280 (535271)
11-14-2009 8:27 AM
Reply to: Message 213 by Kaichos Man
11-13-2009 7:58 AM


Re: I call!
Hi Kaichos Man,
In case it helps you figure out where you're going wrong, here's a couple problems in the way you're looking at things.
First, the phrase "functionally less important molecules" is not a synonym for junk DNA.
Second, here's a significant contradiction in your views. First you make a statement that acknowledges that what Kimura would term "functionally important molecules" do evolve, just not as fast as "functionally less important molecules."
Kaichos Man writes:
The answer lies in why Kimura formed his theory. He observed that "functionally less important molecules, or portions of molecules, evolve faster than more important ones".
Then you contradict yourself by claiming that Kimura thought that evolution could only take place in junk DNA:
It therefore made sense to Kimura that the only place the variation needed by evolution could take place was in the junk DNA.
So your understanding of Kimura's views is contradictory. You have him knowing that evolution could take place in both functionally important and functionally less important molecules, but at different rates. And you also have him knowing that evolution could only take place in functionally irrelevant molecules, what you're calling junk DNA. I think if you work to resolve this contradiction in your understanding that it will help you discover what Kimura was really saying.
--Percy

This message is a reply to:
 Message 213 by Kaichos Man, posted 11-13-2009 7:58 AM Kaichos Man has replied

Replies to this message:
 Message 221 by Kaichos Man, posted 11-14-2009 9:03 AM Percy has replied

  
Kaichos Man
Member (Idle past 4489 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 219 of 280 (535273)
11-14-2009 8:36 AM
Reply to: Message 217 by Percy
11-14-2009 8:17 AM


Re: And back we go again.
No one here who doesn't have your reading comprehension problems sees any significant conflict between Kimura's views and evolutionary theory.
Left yourself with a nice little out with the word "significant", haven't you, Percy? That makes it all highly subjective. Who is going to decide what's significant and what isn't? For example:
"Advantageous mutations may occur, but the neutral theory
assumes that they are so rare that they may be neglected in
our quantitative consideration".
Significant?

"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

This message is a reply to:
 Message 217 by Percy, posted 11-14-2009 8:17 AM Percy has replied

Replies to this message:
 Message 220 by Percy, posted 11-14-2009 9:01 AM Kaichos Man has not replied
 Message 224 by Dr Adequate, posted 11-14-2009 11:06 PM Kaichos Man has not replied

  
Percy
Member
Posts: 22394
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 220 of 280 (535276)
11-14-2009 9:01 AM
Reply to: Message 219 by Kaichos Man
11-14-2009 8:36 AM


Re: And back we go again.
As we've told you many times, everyone agrees that advantageous mutations are rare.
In the passage you quote (which is from Retrospective of the last quarter century of the neutral theory on page 522) Kimura takes advantage of that fact to make an approximation in the math for neutral mutations that ignores advantageous mutations. Certainly if some small number like one out of a million mutations are advantageous then this is a valid approximation.
But however rare advantageous mutations might be, they do occur, and they are selected for, regardless where they occur on the scale from functionally important down through functionally less important to functionally irrelevant.
In other words, your reading comprehension problems are still showing. The perversity of explaining with the written word where your problems comprehending the written word are leading you astray is apparent to me.
--Percy
Edited by Percy, : Typos.

This message is a reply to:
 Message 219 by Kaichos Man, posted 11-14-2009 8:36 AM Kaichos Man has not replied

  
Kaichos Man
Member (Idle past 4489 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 221 of 280 (535277)
11-14-2009 9:03 AM
Reply to: Message 218 by Percy
11-14-2009 8:27 AM


Re: I call!
Then you contradict yourself by claiming that Kimura thought that evolution could only take place in junk DNA:
It therefore made sense to Kimura that the only place the variation needed by evolution could take place was in the junk DNA.
Guilty. I should have said "principal" rather than "only".
Kimura:
"It is now a routine practice to search for various signals by comparing a relevant region of homologous DNA sequences of diverse organisms and to pick out a constant or "consensus" pattern, but to disregard variable parts as unimportant"
So an important region of DNA sequence is identified by its lack of variation.

"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a fantasy." Charles Darwin

This message is a reply to:
 Message 218 by Percy, posted 11-14-2009 8:27 AM Percy has replied

Replies to this message:
 Message 222 by Percy, posted 11-14-2009 9:26 AM Kaichos Man has replied
 Message 223 by Dr Adequate, posted 11-14-2009 11:05 PM Kaichos Man has not replied

  
Percy
Member
Posts: 22394
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 222 of 280 (535279)
11-14-2009 9:26 AM
Reply to: Message 221 by Kaichos Man
11-14-2009 9:03 AM


Re: I call!
Kaichos Man writes:
Guilty. I should have said "principal" rather than "only".
And you should have said "functionally less important," because that's what Kimura said. Kimura did not use the term "junk DNA." And once you say things right it doesn't support your position at all.
Kimura:
"It is now a routine practice to search for various signals by comparing a relevant region of homologous DNA sequences of diverse organisms and to pick out a constant or "consensus" pattern, but to disregard variable parts as unimportant"
So an important region of DNA sequence is identified by its lack of variation.
I can tell that you're under the impression that this Kimura quote somehow advances your position, but not being able to misinterpret Kimura with your flair and panache I have no idea why.
Seriously, dude, get a clue. Why don't you read and reread and reread again that Kimura paper you're quoting from in its entirety until you actually understand him, being careful to note when he's talking about evolution at the molecular versus phenotypic level, and trying to avoid making mistaken misinterpretations about passages that mention advantageous mutations. Here's the link again: Retrospective of the last quarter century of the neutral theory
Of course it will take you longer to understand the paper than other people. You're in same position as Linus from the Peanuts strip. One night Charlie Brown sees Lucy and Linus looking up at the stars, and Lucy is telling Linus all kinds of nonsense. Charlie Brown comments, "Poor Linus. He's going to have to go to school twice as long as everyone else because he has to unlearn everything Lucy tells him."
--Percy

This message is a reply to:
 Message 221 by Kaichos Man, posted 11-14-2009 9:03 AM Kaichos Man has replied

Replies to this message:
 Message 226 by Kaichos Man, posted 11-16-2009 6:17 AM Percy has replied

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 223 of 280 (535342)
11-14-2009 11:05 PM
Reply to: Message 221 by Kaichos Man
11-14-2009 9:03 AM


Re: I call!
Guilty. I should have said "principal" rather than "only".
No, you'd still have been lying about Kimura's views. It would have been a smaller lie, but a lie nonetheless.

This message is a reply to:
 Message 221 by Kaichos Man, posted 11-14-2009 9:03 AM Kaichos Man has not replied

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 224 of 280 (535343)
11-14-2009 11:06 PM
Reply to: Message 219 by Kaichos Man
11-14-2009 8:36 AM


Re: And back we go again.
Significant?
Nonexistent.

This message is a reply to:
 Message 219 by Kaichos Man, posted 11-14-2009 8:36 AM Kaichos Man has not replied

  
Dr Adequate
Member (Idle past 285 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 225 of 280 (535344)
11-14-2009 11:10 PM
Reply to: Message 216 by Kaichos Man
11-14-2009 4:41 AM


Re: And back we go again.
Kimura:
"(2) Thereis a sudden increase or boom of neutral variations under
relaxed selection. In this stage, gene duplication in addition
to point mutation must play a very important role in producing
genetic variations. Needless to say, their fate is largely
determined by random drift".
You notice how this does not answer the point to which you are pretending to reply, i.e. that functional duplicates are not junk DNA?
Perhaps you don't understand Kimura's problem with functional variation.
And nor, apparently, does he, since he seems to be utterly unaware that anything that he said supports creationist drivel in any way.
Either that, or he does understand what he wrote and you don't.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 216 by Kaichos Man, posted 11-14-2009 4:41 AM Kaichos Man has not replied

  
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