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Author Topic:   Adding information to the genome.
Coyote
Member (Idle past 2105 days)
Posts: 6117
Joined: 01-12-2008


(1)
Message 181 of 280 (534553)
11-09-2009 10:52 AM
Reply to: Message 176 by Kaichos Man
11-09-2009 6:05 AM


You just refuse to get it!
"Kimura [standing beside a pond of colored carp]: As between the carp and me, there are many [genetic differences], but the surprising fact is that most of these mutations do nothing to help establish the differences between a human being and a fish. The carp and I both need hemoglobin to do exactly the same job of carrying oxygen around the body. Yet one half of all the chemical units in my hemoglobin molecules are different from the carp's. That unnecessary sort of evolution, and my studies of its rate and pattern, suggest to me that natural selection has had no reason for preferring one variant of the molecule over another. I think chance plays a much greater part in evolution, and natural selection a lesser part, than biologists supposed a few years ago."
So according to Kimura, the evidence for Natural Selection is non-existent in the evolution of hemoglobin.
NO! NO! NO!
Some variants of hemoglobin work, and some don't. Natural selection weeds out those that don't. That doesn't mean that all successful variants have to be the same!
There are often many solutions to a given problem genetic. This is well illustrated in an on-line lecture that I have cited several times:
Making Genetic Networks Operate Robustly: Unintelligent Non-design Suffices, by Professor Garrett Odell (online lecture)
Researchchannel.org
Description: Mathematical computer models of two ancient and famous genetic networks act early in embryos of many different species to determine the body plan. Models revealed these networks to be astonishingly robust, despite their 'unintelligent design.' This examines the use of mathematical models to shed light on how biological, pattern-forming gene networks operate and how thoughtless, haphazard, non-design produces networks whose robustness seems inspired, begging the question what else unintelligent non-design might be capable of.

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.

This message is a reply to:
 Message 176 by Kaichos Man, posted 11-09-2009 6:05 AM Kaichos Man has replied

Replies to this message:
 Message 193 by Kaichos Man, posted 11-11-2009 6:57 AM Coyote has not replied

  
AnswersInGenitals
Member (Idle past 150 days)
Posts: 673
Joined: 07-20-2006


(1)
Message 182 of 280 (534588)
11-09-2009 4:08 PM
Reply to: Message 180 by Percy
11-09-2009 9:28 AM


Another example of genetic drift.
I find the following example to be a good illustration of how you can have random variation at the "molecular" level (letters in this case) while retaining "phenotypical" morphology and function (word and sentence meaning in this case):
Aoccdrnig to a rscheearch at an Elingsh uinervtisy, it deosn't mttaer in waht oredr the ltteers in a wrod are, the olny iprmoetnt tihng is taht frist and lsat ltteer is at the rghit pclae. The rset can be a toatl mses and you can sitll raed it wouthit porbelm. Tihs is bcuseae we do not raed ervey lteter by itslef but the wrod as a wlohe.'
This can be seen as genetic drift of the less significant letters, like the evolution of 'ye olde shoppe' to 'this old shop'.
http://www.lerfjhax.com/scrambler>Here is a site that will scramble a sentence in the above manner. In case I screwed up the hyper-tags, the site is: http://www.lerfjhax.com/scrambler.
As another example, we note that Kaicchos Man is phenotypically indistinguishable from a troll, but genetically is much lower on the Great Ladder of Being.

This message is a reply to:
 Message 180 by Percy, posted 11-09-2009 9:28 AM Percy has seen this message but not replied

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


Message 183 of 280 (534649)
11-10-2009 5:04 AM
Reply to: Message 180 by Percy
11-09-2009 9:28 AM


Re: Lactose added to genome is added information
Steps 3 and 4 require natural selection.
I fail to see how selection can play two roles in the process. Perhaps you can?
What two roles for selection do you think you see? This might be key to your misunderstanding.
I don't see two, hence the question. You have pointed out that steps 3 and 4 both require natural selection. How so?

"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 180 by Percy, posted 11-09-2009 9:28 AM Percy has seen this message but not replied

Replies to this message:
 Message 184 by Huntard, posted 11-10-2009 5:26 AM Kaichos Man has replied

  
Huntard
Member (Idle past 2294 days)
Posts: 2870
From: Limburg, The Netherlands
Joined: 09-02-2008


(1)
Message 184 of 280 (534651)
11-10-2009 5:26 AM
Reply to: Message 183 by Kaichos Man
11-10-2009 5:04 AM


Re: Lactose added to genome is added information
Kaichos Man writes:
I don't see two, hence the question. You have pointed out that steps 3 and 4 both require natural selection. How so?
They do. Why do you think this means it fills two roles? It does exactly the same in both steps. Selecting favoured stuff, and discarding unfavoured stuff, so to say.

I hunt for the truth
I am the one Orgasmatron, the outstretched grasping hand
My image is of agony, my servants rape the land
Obsequious and arrogant, clandestine and vain
Two thousand years of misery, of torture in my name
Hypocrisy made paramount, paranoia the law
My name is called religion, sadistic, sacred whore.
-Lyrics by Lemmy Kilmister of Motorhead

This message is a reply to:
 Message 183 by Kaichos Man, posted 11-10-2009 5:04 AM Kaichos Man has replied

Replies to this message:
 Message 187 by Kaichos Man, posted 11-10-2009 5:56 AM Huntard has replied

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


Message 185 of 280 (534655)
11-10-2009 5:29 AM
Reply to: Message 175 by RAZD
11-07-2009 7:33 PM


Re: moving on ... Foraminifera as a confirming example
Thanks for admitting that you were wrong on the lactose and jaw evolution.
I have changed my position on mammalian jaw evolution, as a result of my own research into hox genes Dlx5&6. You can claim some credit for forcing me to undertake this research. I no longer believe that simultaneous and compensatory mutations are needed, and that these are impossible by evolutionary mechanisms. I now believe that the creation of hox genes and their subordinate genes are impossible by evolutionary mechanisms.
As for lactation, that remains one of the worst examples of an evolutionary "just so" story I've ever come across. Some guy points at a fossil and says "I think those bones and teeth are too well developed for a creature that I don't think was old enough to feed itself". Next thing you know we've got a permeable egg being clasped to a hair follicle. Viola! Lactation has evolved.
Any self-respecting science-fiction writer would screw that one up and toss it at the waste paper basket with a sigh and "No-one's going to buy that". And yet this rubbish is probably just a heartbeat away from finding it's way into the next high school biology textbook. As a "fact", no doubt.
It's not good science, RAZD.
It's not even good fiction.

"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 175 by RAZD, posted 11-07-2009 7:33 PM RAZD has replied

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


Message 186 of 280 (534656)
11-10-2009 5:44 AM
Reply to: Message 178 by RAZD
11-09-2009 7:58 AM


Re: another example of dodging?
Which does not make it a conservative force to maintain the population in stasis as you claimed.
Kimura wrote:"What I want to emphasize is that relaxation of natural selection is the prerequisite for new evolutionary progress'.
-ergo-
If natural selection is not relaxed, evolution will not progress.
-ergo-
Stasis.

"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 178 by RAZD, posted 11-09-2009 7:58 AM RAZD has replied

Replies to this message:
 Message 202 by RAZD, posted 11-11-2009 9:43 PM Kaichos Man has replied

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


Message 187 of 280 (534660)
11-10-2009 5:56 AM
Reply to: Message 184 by Huntard
11-10-2009 5:26 AM


Re: Lactose added to genome is added information
It does exactly the same in both steps. Selecting favoured stuff, and discarding unfavoured stuff, so to say.
Well, that's one explanation, though it could be argued that it's the same process viewed from different angles. Personally, I think that when he says "latent selective potential is realised", he actually means that something useful emerges, and the actual "selection" take splace in step iv.
No matter. What is important from the point of view of "Adding information to the genome" is that Kimura clearly saw no significant role for selection in the creation of variation. He attributes that to gene duplication and random drift.

"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 184 by Huntard, posted 11-10-2009 5:26 AM Huntard has replied

Replies to this message:
 Message 188 by Wounded King, posted 11-10-2009 6:15 AM Kaichos Man has replied
 Message 189 by Percy, posted 11-10-2009 8:57 AM Kaichos Man has replied
 Message 190 by Huntard, posted 11-10-2009 9:09 AM Kaichos Man has seen this message but not replied

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


(1)
Message 188 of 280 (534662)
11-10-2009 6:15 AM
Reply to: Message 187 by Kaichos Man
11-10-2009 5:56 AM


Kimura and mainstream evolution marching in accord once more.
What is important from the point of view of "Adding information to the genome" is that Kimura clearly saw no significant role for selection in the creation of variation.
I think that except for discussions of systems of 'evolvability' you will find this to be the case for almost all evolutionary biologists. The creation of variation is by various mutational processes, and it is generally the case that these variations are considered to arise in a stochastic manner essentially insensitive to any selective pressures the organism may be experiencing. This is one reason why even if mutations are not truly random, in terms of being equiprobable, in their distribution through the genome they remain random in terms of their effects on the fitness of the organism.
It is this random mutation that is the very basis of virtually all genetic variability. The difference between Kimura's neutral evolution and adaptive evolution is simply in the way that the patterns of genetic variability are captured from one generation to the next. In neutral evolution the patterns are influenced by stochastic effects and random sampling, in adaptive evolution benefifical alleles/mutations tend to increase in frequency due to improved reproductive success of the organisms carrying them. These processes are not mutually exclusive, non-adaptive variation can be carried to fixation on the back of a nearby beneficial mutation and even the strongest beneficial mutation with a huge selective advantage may be extinguished from the gene pool by some random factor.
You seem to be arguing against a straw man version of evolution where natural selection is the source of variation as well as the mechanism/force which acts to maintain adaptive variation. Kimura's focus is on Random mutation/ Random selection, the 'Darwinian' model's on Random mutation/ non-random selection. They may argue the exact extent to which particular regions of the genome are ascribable to either factor, but they believe in the same source of variation.
Surely what Kimura's theories are truly antithetical to is a belief that the genome was purposefully created? If junk DNA is all really functional and we just don't appreciate it, which a number of ID proponents suggest, then why does it look like the product of mere randomness?
TTFN,
WK

This message is a reply to:
 Message 187 by Kaichos Man, posted 11-10-2009 5:56 AM Kaichos Man has replied

Replies to this message:
 Message 192 by Kaichos Man, posted 11-11-2009 6:54 AM Wounded King has not replied

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


(1)
Message 189 of 280 (534676)
11-10-2009 8:57 AM
Reply to: Message 187 by Kaichos Man
11-10-2009 5:56 AM


Re: Lactose added to genome is added information
Kaichos Man writes:
No matter. What is important from the point of view of "Adding information to the genome" is that Kimura clearly saw no significant role for selection in the creation of variation. He attributes that to gene duplication and random drift.
Well, duh! No biologist sees natural selection as a source of variation. Random mutation is the source of variation.
Every year thousands of aspiring artists put their wares before the public. The artists are the source of variation. Which artists succeed and which eventually decide that maybe some other line of work might be more remunerative is decided by the public, who performs selection. Artists provide the variation, the public performs selection.
In an analogous way, variation in the genome is supplied by random mutation, and selection is performed by constraints imposed by the environment that control whether any particular combination of random mutations is passed on to the next generation, otherwise known as natural selection.
--Percy
Edited by Percy, : Improve phrasing.

This message is a reply to:
 Message 187 by Kaichos Man, posted 11-10-2009 5:56 AM Kaichos Man has replied

Replies to this message:
 Message 191 by Kaichos Man, posted 11-11-2009 6:41 AM Percy has replied

  
Huntard
Member (Idle past 2294 days)
Posts: 2870
From: Limburg, The Netherlands
Joined: 09-02-2008


(1)
Message 190 of 280 (534679)
11-10-2009 9:09 AM
Reply to: Message 187 by Kaichos Man
11-10-2009 5:56 AM


Re: Lactose added to genome is added information
Kaichos Man writes:
Well, that's one explanation, though it could be argued that it's the same process viewed from different angles.
Yes, it is. Natural selection is one proces, and it fulfills one role. Selecting.
No matter. What is important from the point of view of "Adding information to the genome" is that Kimura clearly saw no significant role for selection in the creation of variation. He attributes that to gene duplication and random drift.
As does every other biologist. At least, I haven't seen one that thinks natural selection is responsible for variation. That's what mutation is for.

I hunt for the truth
I am the one Orgasmatron, the outstretched grasping hand
My image is of agony, my servants rape the land
Obsequious and arrogant, clandestine and vain
Two thousand years of misery, of torture in my name
Hypocrisy made paramount, paranoia the law
My name is called religion, sadistic, sacred whore.
-Lyrics by Lemmy Kilmister of Motorhead

This message is a reply to:
 Message 187 by Kaichos Man, posted 11-10-2009 5:56 AM Kaichos Man has seen this message but not replied

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


Message 191 of 280 (534807)
11-11-2009 6:41 AM
Reply to: Message 189 by Percy
11-10-2009 8:57 AM


Re: Lactose added to genome is added information
Well, duh! No biologist sees natural selection as a source of variation. Random mutation is the source of variation.
So you agree with Kimura that variation results from random drift operating on duplicated genes, and selection plays no part in this process? No step-by-step, slow-and-gradual, each-mutation-must-confer-a-survival-advantage process?
Good. At least that's logical. Natural selection can't play a role until it can "see" the variation, and that's going to need at least a new gene, unless it's merely a modification of existing information.
So we have new genes being crafted from duplicated genes by random drift. Genetic structures of highly specified complexity being formed by purely random forces.
I'm feeling better all ready.

"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 189 by Percy, posted 11-10-2009 8:57 AM Percy has replied

Replies to this message:
 Message 195 by Wounded King, posted 11-11-2009 7:04 AM Kaichos Man has replied
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Kaichos Man
Member (Idle past 4487 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 192 of 280 (534808)
11-11-2009 6:54 AM
Reply to: Message 188 by Wounded King
11-10-2009 6:15 AM


Re: Kimura and mainstream evolution marching in accord once more.
Kimura's focus is on Random mutation/ Random selection, the 'Darwinian' model's on Random mutation/ non-random selection.
Never looked at it that way, WK. Can you explain "random selection" a bit more?

"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 188 by Wounded King, posted 11-10-2009 6:15 AM Wounded King has not replied

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


Message 193 of 280 (534809)
11-11-2009 6:57 AM
Reply to: Message 181 by Coyote
11-09-2009 10:52 AM


Re: You just refuse to get it!
Some variants of hemoglobin work, and some don't. Natural selection weeds out those that don't. That doesn't mean that all successful variants have to be the same!
You're missing the point here, Coyote. Kimura is saying that hemoglobin didn't have to vary at all. That's why he calls it "unnecessary evolution".
Edited by Kaichos Man, : typo

"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 181 by Coyote, posted 11-09-2009 10:52 AM Coyote has not replied

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Huntard
Member (Idle past 2294 days)
Posts: 2870
From: Limburg, The Netherlands
Joined: 09-02-2008


(1)
Message 194 of 280 (534811)
11-11-2009 7:00 AM
Reply to: Message 193 by Kaichos Man
11-11-2009 6:57 AM


Re: You just refuse to get it!
Kaichos Man writes:
You're missing the point here, Coyote. Kimura is saying that hemoglobin didn't have to vary at all. That's why he calls it "unnecessary evolution".
So? What's your point with this?

I hunt for the truth
I am the one Orgasmatron, the outstretched grasping hand
My image is of agony, my servants rape the land
Obsequious and arrogant, clandestine and vain
Two thousand years of misery, of torture in my name
Hypocrisy made paramount, paranoia the law
My name is called religion, sadistic, sacred whore.
-Lyrics by Lemmy Kilmister of Motorhead

This message is a reply to:
 Message 193 by Kaichos Man, posted 11-11-2009 6:57 AM Kaichos Man has not replied

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


(1)
Message 195 of 280 (534812)
11-11-2009 7:04 AM
Reply to: Message 191 by Kaichos Man
11-11-2009 6:41 AM


Back to square one
So you agree with Kimura that variation results from random drift operating on duplicated genes, and selection plays no part in this process?
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAARGH!!!
How can you still not understand something no matter how many people tell it to you in how many ways. Variation is no more the result of drift than it is of natural selection! Variation is a result of mutation. Some of the patterns of variation we see in the diverse genomes of organisms are best explained by neutral drift, others are better explained by selection. Also please stop appealing to Kimura, it seems pretty clear by now that your understanding of what he says is tenuous at best. Why not just give us your own thoughts on neutral theory? We probably all actually agree with Kimura, the person we don't agree with is you.
each-mutation-must-confer-a-survival-advantage process?
This is in fact the crux of the matter, and the constraint that Kimura objected to, this sort of hyper-adaptationist view that every evolved feature should be adaptive. It is also a view of evolution that virtually no evolutionary biologist holds anymore, certainly not in terms of molecular evolution.
Natural selection can't play a role until it can "see" the variation, and that's going to need at least a new gene, unless it's merely a modification of existing information.
And now you are back to the same totally unsupported claim you were making in the first post! You are again using 'information' in a completely vague and useless way. Why can changes below the level of a whole de novo gene not consitute increases in information? Or are you allowing modification to encompass increases in information, because if you are then you seem to have no argument at all.
Genetic structures of highly specified complexity being formed by purely random forces.
Again, this is disingenuous to the point of dishonesty. It is selection that allows the construction of the specified complexity by maintaining functional variation. It is the initial variation that is generated by random forces.
Why can you only talk about one part of the adaptive evolutionary process at a time? You only seem to be able to think of random mutation or natural selection in mutually exclusive terms. Why can't you understand that it is principally the interaction of the two that leads to the adaptive evolution of the specified and complex functional sequences we see today?
TTFN,
WK

This message is a reply to:
 Message 191 by Kaichos Man, posted 11-11-2009 6:41 AM Kaichos Man has replied

Replies to this message:
 Message 197 by Kaichos Man, posted 11-11-2009 7:26 AM Wounded King has replied

  
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