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Author Topic:   Adding information to the genome.
Kaichos Man
Member (Idle past 4487 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 226 of 280 (535457)
11-16-2009 6:17 AM
Reply to: Message 222 by Percy
11-14-2009 9:26 AM


Re: I call!
Seriously, dude, get a clue.
And you're a moderator?

"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 222 by Percy, posted 11-14-2009 9:26 AM Percy has replied

Replies to this message:
 Message 227 by Wounded King, posted 11-16-2009 6:33 AM Kaichos Man has not replied
 Message 230 by Percy, posted 11-16-2009 8:12 AM Kaichos Man has replied

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


(1)
Message 227 of 280 (535460)
11-16-2009 6:33 AM
Reply to: Message 226 by Kaichos Man
11-16-2009 6:17 AM


I for one welcome our continuing catbert overlord ...
Percy is somewhat more than a moderator. He pretty much runs the whole kit and caboodle, down to writing the software the site operates on.
TTFN,
WK

This message is a reply to:
 Message 226 by Kaichos Man, posted 11-16-2009 6:17 AM Kaichos Man has not replied

Replies to this message:
 Message 228 by Parasomnium, posted 11-16-2009 6:38 AM Wounded King has not replied

  
Parasomnium
Member
Posts: 2224
Joined: 07-15-2003


(1)
Message 228 of 280 (535461)
11-16-2009 6:38 AM
Reply to: Message 227 by Wounded King
11-16-2009 6:33 AM


Re: I for one welcome our continuing catbert overlord ...
On top of that, if Percy participates in a thread, he leaves the moderating to others. And when he moderates a thread, he doesn't participate. Even though he is an admin, he's still entitled to an opinion.
Edited by Parasomnium, : No reason given.

This message is a reply to:
 Message 227 by Wounded King, posted 11-16-2009 6:33 AM Wounded King has not replied

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


(1)
Message 229 of 280 (535471)
11-16-2009 7:46 AM
Reply to: Message 216 by Kaichos Man
11-14-2009 4:41 AM


Drifting the night away
Your quotes in no way address anything I said, for the reasons Percy and others have already highlighted.
Needless to say, their fate is largely determined by random drift.
When any novel mutation arises de novo it is of course at very low frequency in the population. The statistical reality is that almost all such low frequency alleles will be removed by drift. In fact there is a good case to be made that drift acts as much to reduce variation within a population as it does to maintain it.
Go to any genetic dfit simulation and you can see this, take http://www.biology.arizona.edu/...ution/act/drift/frame.html as an example. Plug in a population size, up to 10, and a number of generations to follow and you will see that the majority of the variation in the population is in fact extinguished by the operation of drift.
One issue with that simulation is that the effects of drift are exacerbated due to the very small population sizes allowed. For a simulation allowing you to study larger populations,albeit for only one allele, go to http://darwin.eeb.uconn.edu/simulations/jdk1.0/drift.html . If you set the p value to 0.1, a low frequency allele, then you can see that the alleles frequently run to extinction, until you get to higher population sizes. What natural selection does is to affect these trends by giving beneficial alleles a better chance of propagating (or rather the traits we consider to be 'selected' are the ones that do this themselves). Go to http://darwin.eeb.uconn.edu/simulations/selection-drift.html to see the effect of selection on the previous drift simulation. Even with a much smaller starting frequency the alleles can reach fixation in a much shorter space of time than by drift alone. This doesn't avoid the operation of drift however, in a small population even strongly selected alleles still often run to extinction.
If you refuse to accept what Kimura said, there isn't.
The problem is that you refuse to understand or stick to what Kimura says. You keep trying to graft on your own misunderstandings and try and piggy back them through using Kimura's authority.
TTFN,
WK

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

  
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 230 of 280 (535477)
11-16-2009 8:12 AM
Reply to: Message 226 by Kaichos Man
11-16-2009 6:17 AM


Re: I call!
Kaichos Man writes:
Seriously, dude, get a clue.
And you're a moderator?
As Percy no, I'm not a moderator. Admin, my linked account, is a moderator. I'm not playing a moderator role in this thread. But if you feel like you're experiencing problems in a thread then you should raise your issues at Report discussion problems here: No.2 and devote your attention in this thread to responding to the points people make, just as we are doing for the points you make. I will describe my points again.
Kimura never uses the term "junk DNA." He instead says "functionally less important." And he's talking about variation at the molecular level, not the phenotypic level. We've told you this many times in this thread.
The other point I'll just repeat:
Percy writes:
Kaichos Man writes:
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.
In case it isn't clear, this is where instead of evasion you explain how this Kimura quote supports your point.
--Percy
Edited by Percy, : Grammar.

This message is a reply to:
 Message 226 by Kaichos Man, posted 11-16-2009 6:17 AM Kaichos Man has replied

Replies to this message:
 Message 232 by Kaichos Man, posted 11-17-2009 7:20 AM Percy has replied

  
pandion
Member (Idle past 3000 days)
Posts: 166
From: Houston
Joined: 04-06-2009


(1)
Message 231 of 280 (535489)
11-16-2009 9:44 AM
Reply to: Message 213 by Kaichos Man
11-13-2009 7:58 AM


Bio 101
Kaichos Man writes:
Kimura shows that selection can play little or no role in the generation of variation.
Nah! He doesn't show that. He echos and supports that idea from basic biology, genetics, and population genetics. Selection is one of the mechanisms of evolution that tends to eliminate variation in populations. It does this because favorable variation in light of the surrounding environment lends differential reproductive success. The idea is most definitely not original with Kimura.
(Genetic) drift, by the same token, tends to eliminate variation. As Wounded King has pointed out, the smaller the population, the more likely it is that novel variations will be eliminated. The founder effect, a special case of genetic drift, is understood to be causal in the speciation of small island populations.
There are other commonly recognized mechanisms that tend to reduce variation in populations, biased variation and non-random mating. Of course there are also mechanisms that tend to increase variation: mutation, gene flow, transposable elements, and recombination.
Others may be able to list other, less obvious, mechanisms.
Edited by pandion, : redundant statement

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 4487 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 232 of 280 (535653)
11-17-2009 7:20 AM
Reply to: Message 230 by Percy
11-16-2009 8:12 AM


Re: I call!
Kimura never uses the term "junk DNA." He instead says "functionally less important."
What would you say constitues the vast majority of "functionally less important" DNA?

"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 230 by Percy, posted 11-16-2009 8:12 AM Percy has replied

Replies to this message:
 Message 233 by Percy, posted 11-17-2009 7:41 AM Kaichos Man has not replied
 Message 234 by Percy, posted 11-17-2009 8:00 AM Kaichos Man has replied

  
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 233 of 280 (535656)
11-17-2009 7:41 AM
Reply to: Message 232 by Kaichos Man
11-17-2009 7:20 AM


Re: I call!
You've lost the thread of the conversation. What you said that I objected to was, "It therefore made sense to Kimura that the only place the variation needed by evolution could take place was in the junk DNA." This is, of course, false.
Reread my Message 218 where I describe how you were making two contradictory claims about what Kimura believed. You were claiming that he both acknowledged and rejected that evolution could occur in functionally important DNA.
There's no substitute for knowing what you're talking about, and you clearly don't. After more than 200 posts you're still making the same mistakes you started with. I again suggest you read and reread the paper you've been quoting from until you understand it: Retrospective of the last quarter century of the neutral theory. Keep a dictionary of genetics terminology close by and refer to it often.
--Percy

This message is a reply to:
 Message 232 by Kaichos Man, posted 11-17-2009 7:20 AM Kaichos Man has not replied

  
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 234 of 280 (535661)
11-17-2009 8:00 AM
Reply to: Message 232 by Kaichos Man
11-17-2009 7:20 AM


Re: I call!
Hi Kaichos Man,
Let me try to add a little clarification.
You later corrected your statement to be, in effect, that Kimura believed the *principle* [as opposed to "only"] place were evolution could take place was in junk DNA. But Kimura doesn't use the term junk DNA. He says "functionally less important," and the stress you're placing on junk DNA is another cause of your misinterpretations.
The key point that Kimura is trying to make, and you actually quote him saying it at one point, is that the less functionally important a region of DNA is the faster it can evolve. And virtually all biologists would agree with this.
What Kimura said that was controversial at the time was that evolution in functionally less important regions of DNA, termed genetic drift, was a significant contributor to evolution at the phenotypic level, and he demonstrated this mathematically.
Where you've gone completely wrong about Kimura is in claiming that he denied a role for natural selection. As I've said before, he was only trying to place another actor on the stage of evolution in the form of genetic drift. He wasn't trying to replace natural selection. No biologist would ever conclude that natural selection doesn't happen, because it is required for adaptation. Without natural selection there could be no adaptation.
--Percy

This message is a reply to:
 Message 232 by Kaichos Man, posted 11-17-2009 7:20 AM Kaichos Man has replied

Replies to this message:
 Message 240 by Kaichos Man, posted 12-08-2009 7:35 AM Percy has replied

  
LucyTheApe
Inactive Member


Message 235 of 280 (536170)
11-20-2009 8:05 AM
Reply to: Message 154 by Percy
11-06-2009 7:56 AM


Re: Willfully...
Percy writes:
Reality *is* an information system.
It's a bit metaphysical Percy! But logically:
R -> I
~I -> ~R
Entropy is imaginary.
Honestly, I think we need to do a whole new thread on information.
Edited by LucyTheApe, : l

There no doubt exist natural laws, but once this fine reason of ours was corrupted, it corrupted everything.
blz paskal

This message is a reply to:
 Message 154 by Percy, posted 11-06-2009 7:56 AM Percy has replied

Replies to this message:
 Message 236 by Wounded King, posted 11-20-2009 8:21 AM LucyTheApe has not replied
 Message 237 by Percy, posted 11-20-2009 8:48 AM LucyTheApe has replied

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


Message 236 of 280 (536171)
11-20-2009 8:21 AM
Reply to: Message 235 by LucyTheApe
11-20-2009 8:05 AM


Re: Willfully...
Honestly, I think we need to do a whole new thread on information.
Please! No! Not another one, aaaaargh!!
TTFN,
WK

This message is a reply to:
 Message 235 by LucyTheApe, posted 11-20-2009 8:05 AM LucyTheApe has not replied

  
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 237 of 280 (536173)
11-20-2009 8:48 AM
Reply to: Message 235 by LucyTheApe
11-20-2009 8:05 AM


Re: Willfully...
If you wish to continue that information discussion then thread Evolving New Information is waiting for you. My last post is Message 399, and the question in which I'm most interested is how you calculated the figures you provided in your Message 339. You said, "The shell consists of 832 bits the first bit of code consisted of another 1752 bits and the second bit of code added another 376 bits." How did you arrive at those numbers?
--Percy

This message is a reply to:
 Message 235 by LucyTheApe, posted 11-20-2009 8:05 AM LucyTheApe has replied

Replies to this message:
 Message 238 by LucyTheApe, posted 11-20-2009 9:17 AM Percy has replied

  
LucyTheApe
Inactive Member


Message 238 of 280 (536175)
11-20-2009 9:17 AM
Reply to: Message 237 by Percy
11-20-2009 8:48 AM


Re: Willfully...
one on one in a new thread.

There no doubt exist natural laws, but once this fine reason of ours was corrupted, it corrupted everything.
blz paskal

This message is a reply to:
 Message 237 by Percy, posted 11-20-2009 8:48 AM Percy has replied

Replies to this message:
 Message 239 by Percy, posted 11-20-2009 5:12 PM LucyTheApe has replied

  
Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 239 of 280 (536241)
11-20-2009 5:12 PM
Reply to: Message 238 by LucyTheApe
11-20-2009 9:17 AM


Re: Willfully...
LucyTheApe writes:
one on one in a new thread.
Screwed up the old one so bad it's irretrievable, huh!
Do what you like, but thread Evolving New Information is still waiting for a response from you about how you calculated the amount of information in your code snippet.
--Percy

This message is a reply to:
 Message 238 by LucyTheApe, posted 11-20-2009 9:17 AM LucyTheApe has replied

Replies to this message:
 Message 275 by LucyTheApe, posted 01-15-2010 8:53 AM Percy has replied

  
Kaichos Man
Member (Idle past 4487 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 240 of 280 (538607)
12-08-2009 7:35 AM
Reply to: Message 234 by Percy
11-17-2009 8:00 AM


Re: I call!
What Kimura said that was controversial at the time was that evolution in functionally less important regions of DNA, termed genetic drift, was a significant contributor to evolution at the phenotypic level, and he demonstrated this mathematically.
I assume you mean "genotypic level". This he demonstrated mathematically. With regard to the phenotypic level, he limited himself to speculation:
"I think that even at the phenotypic level,
there must be many changes that are so nearly neutral that
random drift plays a significant role, particularly with respect
to "quantitative characters.""
Where you've gone completely wrong about Kimura is in claiming that he denied a role for natural selection.
He did, in the generation of variation:
"(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.
Notice that Kimura saw "relaxed selection" as a prerequisite for the generation of variation. Once variation had been achieved through point mutation of duplicate genes, he saw renewed selection as the arbiter of adaptive value.

"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 234 by Percy, posted 11-17-2009 8:00 AM Percy has replied

Replies to this message:
 Message 241 by Kaichos Man, posted 12-08-2009 7:41 AM Kaichos Man has not replied
 Message 242 by Percy, posted 12-08-2009 8:17 AM Kaichos Man has replied
 Message 248 by RAZD, posted 12-08-2009 9:04 PM Kaichos Man has replied

  
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