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Author Topic:   Adding information to the genome.
Kaichos Man
Member (Idle past 4488 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 166 of 280 (534329)
11-06-2009 9:30 PM
Reply to: Message 162 by Percy
11-06-2009 9:15 AM


Re: Lactose added to genome is added information
neither I nor Coyote nor anyone else on the evolution side thinks there are two different methods of evolution, one that changes the genome and some other one that changes the phenotype.
Fine. Good. Understood. So when Kimura writes:
"The Neutral theory asserts that the great majority of evolutionary changes at the molecular level, as revealed by comparative studies of Protein and DNA sequences, are caused not by Darwinian selection but by random drift of selectively neutral or nearly neutral mutants."
...you assert that the same must be true at the phenotypic level.
Fair enough. Doesn't leave natural selection with much on its plate though, does it?

"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 162 by Percy, posted 11-06-2009 9:15 AM Percy has replied

Replies to this message:
 Message 168 by Percy, posted 11-06-2009 10:55 PM Kaichos Man has replied

  
Kaichos Man
Member (Idle past 4488 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 167 of 280 (534332)
11-06-2009 9:58 PM
Reply to: Message 158 by Huntard
11-06-2009 8:24 AM


Re: Lactose added to genome is added information
meaning he thinks they play a lesser part than hitherto thought
So our thinking was erroneous with regard to the part they played.
Yet your arguments have been delt with, the answers given, you just ignore them.
That's because the answers given did not, in my opinion, deal with my arguments, so I am well within my rights to ignore them.
Huntard, do me the honour of not considering me a complete idiot. You will know when I believe my argument has received a mortal blow (or been manoeuvred into apparent deadlock) because I'll probably stop talking about it and change the subject. In the overall battle between Creationism and evolution, this could be termed retreating and attacking on another front.
Like my mamalian jaw "slowly" evolving example (which was first mentioned by RAZD), I'm guessing you now accept that this is how it could have happened?
No, quite the reverse. Have you seen the last few exchanges between myself and Wounded King? That discussion has changed markedly...

"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 158 by Huntard, posted 11-06-2009 8:24 AM Huntard has replied

Replies to this message:
 Message 169 by Percy, posted 11-06-2009 11:06 PM Kaichos Man has replied
 Message 170 by Huntard, posted 11-07-2009 2:34 AM Kaichos Man has not replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(2)
Message 168 of 280 (534337)
11-06-2009 10:55 PM
Reply to: Message 166 by Kaichos Man
11-06-2009 9:30 PM


Re: Lactose added to genome is added information
Hi Kaichos Man,
Your misinterpretation of that Kimura quote has been explained to you how many times now? And you're still asking the exact same question instead of going back to the explanations you've already been provided and seeking clarification or more detail? In reply to the very message where this precise behavior on your part was described?
I'll try to repeat, but in a little more detail, the same explanation that Wounded King already gave you many posts ago. The four nucleotides of DNA are adenine, cytosine, guanine and thymine, abbreviated as A, C, G and T. The amino acids that are the building blocks of proteins are specified by DNA nucleotide triplets called codons, like ATC (adenine, thymine, cytosine) or TGT (thymine, guanine, thymine).
There are 64 different codons but only 20 amino acids, so there's lot's of redundancy. For example, the amino acid isoleucine is specified by ATT, ATC or ATA. The amino acid leucine is specified by CTT, CTC, CTA, CTG, TTA or TTG. Here's a nice table I found:
Just look at all the redundancy. The TCT codon creates serine, but so do TCC, TCA, TCG, AGT and AGC. That means that a mutation could change TCT into TCC or into TCA or into TCG and it would still code for the same amino acid as before the mutation, serine. Or AGT could mutate into AGC and it would still code for serine. Such mutations would cause no change at all. This high degree of redundancy is one reason why Kimura said that most change at the molecular level (i.e., in the DNA and proteins) is not caused by selection, because a mutation that causes no phenotypic change cannot be selected for (that's not quite true because some nucleotides are more easily constructed and therefore more available than others, but that's a relevant detail we need not consider in this discussion).
But there's yet another reason why Kimura said this. The amino acids that DNA codons represent are combined into proteins by the cell's internal machinery, but changing just one or a few amino acids in a protein often results in a protein that behaves identically or very similarly to the original. This means that many mutations that change the codon to program for a different amino acid still end up producing a protein that does pretty much the same thing as the original protein. Once again there is no change at the phenotypic level, only at the molecular level, and so there can be no selection. So proteins are another place where molecular change can occur without selection.
And there's still another reason why Kimura said this. Kimura's neutral theory includes both neutral and near neutral mutations. A mutation or accumulation of mutations that causes DNA to produce a protein that behaves differently than the original, thereby causing a change in the phenotype, could still be neutral if the change provides no change or nearly no change in selection. This is the random drift due to neutral or near neutral mutations that Kimura talks about.
And so it is for those three reasons, redundancy at the codon level for producing amino acids, redundancy at the amino acid level for constructing proteins, and neutral or near neutral phenotypic changes, that Kimura was able to accurately say that most change at the molecular level is not a result of Darwinian selection.
But these changes due to random drift are not adaptive like those driven by selection. Most change at the phenotypic level, which is under genetic control and results from mutations (and allele remixing in sexual species) is a result of adaptive forces driven by selection, which is why Kimura goes on to say:
Kimura writes:
The theory does not deny the role of natural selection in determining the course of adaptive evolution.
So when you see a hummingbird with a tongue long enough to reach to the base of a deep flower, that's adaptive evolution caused by selection of mutations favorable to a sufficiently long tongue. When you see a male peacock's tail on display, that's adaptive evolution caused by selection of mutations favorable to a tail that appeals to peahens, thereby increasing the probability of reproduction allowing the peacock to contribute its genes to the next generation.
Any questions that aren't just a repeat of your original question?
--Percy
Edited by Percy, : Clarify 3rd to last paragraph.

This message is a reply to:
 Message 166 by Kaichos Man, posted 11-06-2009 9:30 PM Kaichos Man has replied

Replies to this message:
 Message 171 by Kaichos Man, posted 11-07-2009 6:53 AM Percy has replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(2)
Message 169 of 280 (534339)
11-06-2009 11:06 PM
Reply to: Message 167 by Kaichos Man
11-06-2009 9:58 PM


Re: Lactose added to genome is added information
Kaichos Man writes:
Huntard, do me the honour of not considering me a complete idiot.
This would require you doing us the favor of not acting like one.
No, quite the reverse. Have you seen the last few exchanges between myself and Wounded King? That discussion has changed markedly...
We all go through phases of patient explanation. Everyone has their limit. In WK's last post (Message 161) he echoes what everyone has been telling you, that you're just repeating the same questions over and over again, or in WK's words in response to your claim that the rebuttals were ineffective, "But he [meaning you] should also explain why he doesn't find your argument effective, not merely restate his own." It's like you're trying as hard as you can to not comprehend anything. There's no explanation so carefully crafted, so studiously composed, so carefully researched, that you can't misinterpret or ignore it in a way such that, apparently, the only thing you can think to do is state your question yet again.
--Percy

This message is a reply to:
 Message 167 by Kaichos Man, posted 11-06-2009 9:58 PM Kaichos Man has replied

Replies to this message:
 Message 172 by Kaichos Man, posted 11-07-2009 7:07 AM Percy has replied

  
Huntard
Member (Idle past 2295 days)
Posts: 2870
From: Limburg, The Netherlands
Joined: 09-02-2008


(1)
Message 170 of 280 (534354)
11-07-2009 2:34 AM
Reply to: Message 167 by Kaichos Man
11-06-2009 9:58 PM


Re: Lactose added to genome is added information
Kaichos Man writes:
So our thinking was erroneous with regard to the part they played.
The large role they played in certain situations was wrong according to Kimura. Nowhere does he claim it never happened, nor that it isn't happening within his research. So there are no "erroneous tenets".
That's because the answers given did not, in my opinion, deal with my arguments, so I am well within my rights to ignore them.
Then explain why they are not, don't just repeat yout original statement.
Huntard, do me the honour of not considering me a complete idiot.
I don't. But don't act like ou don't understand anything either.
You will know when I believe my argument has received a mortal blow (or been manoeuvred into apparent deadlock) because I'll probably stop talking about it and change the subject.
Ah. Like the jaw, for example. Ok. Would be a bit clearer if you'd admit it, rather then just stop talking about it tough...
No, quite the reverse. Have you seen the last few exchanges between myself and Wounded King? That discussion has changed markedly...
Which means (as you have stated above) you now think it could've happened gradually.

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 167 by Kaichos Man, posted 11-06-2009 9:58 PM Kaichos Man has not replied

  
Kaichos Man
Member (Idle past 4488 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 171 of 280 (534360)
11-07-2009 6:53 AM
Reply to: Message 168 by Percy
11-06-2009 10:55 PM


Re: Lactose added to genome is added information
And so it is for those three reasons, redundancy at the codon level for producing amino acids, redundancy at the amino acid level for constructing proteins, and neutral or near neutral phenotypic changes, that Kimura was able to accurately say that most change at the molecular level is not a result of Darwinian selection.
Agreed. But you seem to have left out the most important reason- that the majority of variation evident at the molecular area is in the functionally less important areas, namely junk DNA. One of Kimura's 5 principles is:
"(ii) Functionally less important molecules or parts of a molecule evolve (in terms of mutant substitutions) faster than more important ones."
Kimura's take on the macroevolutionary process is illuminating:
"(i) A population is liberated from the preexisting selective constraint. (ii) 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. (iii) The latent selection potential
of some of the neutral mutants is realized. In other words, some of the accumulated neutral mutants (at the phenotypic level) turn out to be useful in a new environment, which the species then exploits. (iv) Intergroup competition and individual selection lead to extensive adaptive evolution, creating a radically different taxonomic group adapted to a newly opened ecological niche."
It's interesting that Kimura sees natural selection as an essentially conservative force, from which "liberation" is required before evolution is possible (step i). This is relevant to the parallel discussion on stasis.
But even more important is his view on variation (step ii). Notice that it requires a relaxation of selective pressure accompanied by random drift acting on gene duplication and point mutation. Natural selection's only role at this stage is to get out of the way.
Notice also that it isn't until (step iv) that selection enters the equation- after gene duplication, point mutation and random drift have created phenotypic variations able to exploit the new ecological niche.
So where does that leave us? Do the genome and phenotype evolve by different methods? Kimura asks the same question:
"Finally, I would like to discuss briefly the problem How
can we understand evolution at two levels-that is, molecular
and phenotypic-in a unified way?
And then he answers it:
" It is generally believed that, in contrast to the neutralist view of molecular evolution, evolutionary changes at the phenotypic level are almost exclusively adaptive and caused by Darwinian positive selection. However, 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"
Emphasis added. Carefully worded, but I think we can all (if you'll excuse the terrible pun) catch his drift.
Edited by Kaichos Man, : italic problems

"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 168 by Percy, posted 11-06-2009 10:55 PM Percy has replied

Replies to this message:
 Message 174 by Percy, posted 11-07-2009 9:55 AM Kaichos Man has replied
 Message 175 by RAZD, posted 11-07-2009 7:33 PM Kaichos Man has replied

  
Kaichos Man
Member (Idle past 4488 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 172 of 280 (534362)
11-07-2009 7:07 AM
Reply to: Message 169 by Percy
11-06-2009 11:06 PM


Re: Lactose added to genome is added information
No, quite the reverse. Have you seen the last few exchanges between myself and Wounded King? That discussion has changed markedly...
We all go through phases of patient explanation. Everyone has their limit. In WK's last post (Message 161) he echoes what everyone has been telling you, that you're just repeating the same questions over and over again
Huntard's question related to the evolution of the mammalian jaw. I was referring to the exchange between WK and myself regarding hox genes.

"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 169 by Percy, posted 11-06-2009 11:06 PM Percy has replied

Replies to this message:
 Message 173 by Percy, posted 11-07-2009 8:47 AM Kaichos Man has not replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 173 of 280 (534369)
11-07-2009 8:47 AM
Reply to: Message 172 by Kaichos Man
11-07-2009 7:07 AM


Re: Lactose added to genome is added information
Kaichos Man writes:
I was referring to the exchange between WK and myself regarding hox genes.
Yes, I know. But WK went to the trouble of commenting on your exchanges with others, saying the same thing that everyone else is, that you ignore rebuttals and just keep repeating your original questions. In other words, the guy with whom you're currently having a productive discussion can still see how poorly you're still handling your discussions with everyone else.
The key to understanding is learning how to ask good questions. In one of the religious threads a stupid question in a discussion about Jesus might be, "Are you saying that Jesus Christ is Santa Claus?" A better question might be, "In what tangible ways does Jesus Christ respond to prayers?"
--Percy

This message is a reply to:
 Message 172 by Kaichos Man, posted 11-07-2009 7:07 AM Kaichos Man has not replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 174 of 280 (534376)
11-07-2009 9:55 AM
Reply to: Message 171 by Kaichos Man
11-07-2009 6:53 AM


Re: Lactose added to genome is added information
Kaichos Man writes:
Agreed. But you seem to have left out the most important reason- that the majority of variation evident at the molecular area is in the functionally less important areas, namely junk DNA. One of Kimura's 5 principles is:
"(ii) Functionally less important molecules or parts of a molecule evolve (in terms of mutant substitutions) faster than more important ones."
Well, yes, the principle is true, but I wouldn't call it "the most important reason." For one thing, "functionally less important" is not a synonym for junk DNA, though it certainly includes it. For another, it is now generally believed that in the past we overestimated the proportion of DNA and proteins that were non-functional. For example, many regions of junk DNA are still transcribed into snippets of RNA, and recent work indicates that these RNA snippets play a significant role.
But while arguing that Kimura believes that natural selection plays only a minor role in evolution you seem to have quoted Kimura contradicting you:
Kaichos Man quoting Kimura writes:
  1. A population is liberated from the preexisting selective constraint.
  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.
  3. The latent selection potential of some of the neutral mutants is realized. In other words, some of the accumulated neutral mutants (at the phenotypic level) turn out to be useful in a new environment, which the species then exploits.
  4. Intergroup competition and individual selection lead to extensive adaptive evolution, creating a radically different taxonomic group adapted to a newly opened ecological niche.
Steps 3 and 4 require natural selection. This sequence of four steps is pretty much what Drosophila described to you in an earlier post.
No biologist in his right mind would ever reject the role of natural selection, and Kimura was a biologist of the highest rank. The evidence for natural selection surrounds us everywhere in every adaptive feature of every organism from bacteria to whales. Neutral theory is not why white rabbits evolve in the arctic and not in the tropics, or why fish that can crawl between ponds evolve in regions that experience frequent drought, or why new strains of flu evolve every year. These are all examples of adaptive evolution as a result of natural selection.
So you have somehow misinterpreted as supportive a passage where Kimura directly contradicts you. You know what you believe, and you apparently interpret any passage you don't understand as supporting what you believe.
If it were true that Kimura actually rejected natural selection as having a significant role in evolution then he would be an enormously controversial figure within biology, but he didn't and he's not. What he proposed is that neutral and near neutral mutations also play a significant role in evolution. He wasn't trying to replace natural selection as the main actor in evolution, he was only trying to place another actor on the stage along side natural selection.
--Percy
Edited by Percy, : Change list to Roman numerals.

This message is a reply to:
 Message 171 by Kaichos Man, posted 11-07-2009 6:53 AM Kaichos Man has replied

Replies to this message:
 Message 176 by Kaichos Man, posted 11-09-2009 6:05 AM Percy has replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 175 of 280 (534405)
11-07-2009 7:33 PM
Reply to: Message 171 by Kaichos Man
11-07-2009 6:53 AM


moving on ... Foraminifera as a confirming example
Hi Kaichos Man,
You will know when I believe my argument has received a mortal blow (or been manoeuvred into apparent deadlock) because I'll probably stop talking about it and change the subject.
Thanks for admitting that you were wrong on the lactose and jaw evolution.
In the overall battle between Creationism and evolution, this could be termed retreating and attacking on another front.
In the overall battle between learning and denial, this would be true only if the "attacking on another front" does not consist of making the same uninformed arguments that have been refuted. Curiously, my experience is that this is the "declare victory and run away" defense of creationsts, similar to the Monty Python "run away run away" scene/s. The evidence on this thread thus far shows that your ability for "attacking on another front" is limited to repeating previous statements.
Agreed. But you seem to have left out the most important reason- that the majority of variation evident at the molecular area is in the functionally less important areas, namely junk DNA. One of Kimura's 5 principles is:
"(ii) Functionally less important molecules or parts of a molecule evolve (in terms of mutant substitutions) faster than more important ones."
Kimura's take on the macroevolutionary process is illuminating:
quote:
(i) A population is liberated from the preexisting selective constraint.
(ii) 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.
(iii) The latent selection potential of some of the neutral mutants is realized. In other words, some of the accumulated neutral mutants (at the phenotypic level) turn out to be useful in a new environment, which the species then exploits.
(iv) Intergroup competition and individual selection lead to extensive adaptive evolution, creating a radically different taxonomic group adapted to a newly opened ecological niche.
(normal quote formatting added)
Now let's look at an example of that kind of situation in the fossil record and see what it shows:
Geology Dept article 3
quote:
Some scientists have theorized, but never been able to demonstrate, that in the absence of competition, an explosion of life takes place. The evolution of new species is greatly accelerated, and a profusion of body shapes and sizes bursts across the horizon, filling up vacant spaces like weeds overtaking a pristine lawn. An array of new forms fan out into these limited niches, where crowding soon forces most of the new forms to spin out into oblivion, as sparks from a flame.
...
As revealed by the ancient record left by the foram family, the story of recovery after extinction is every bit as busy and colorful as some scientists have long suspected.
"What we've found suggests that the rate of speciation increases dramatically in a biological vacuum," Parker said. "After the Cretaceous extinction, the few surviving foram species began rapidly propagating into new species, and for the first time we're able to see just how this happens, and how fast."
As foram survivors rush to occupy their new habitats, they seem to start experimenting will all sorts of body shapes, trying to find something stable, something that will work, Arnold said. Once a population in a given habitat develops a shape or other characteristic that stands up to the environment, suddenly the organisms begin to coalesce around what becomes a standardized form, the signature of a new species.
As the available niches begin to fill up with these new creatures, the speciation rate begins to slow down, and pressure from competition between species appears to bear down in earnest. The extinction rate then rises accordingly.
This scenario, Arnold says, suggests that the speciation process is sensitive to how fully packed the biosphere is with other species, not the number of individuals. Ecologists, in referring to a given environment's ability to sustain life as its carrying capacity, generally mean the natural limit, in sheer numbers, of individual organisms that any environment can support, as opposed to the number of different kinds of organisms.
"This is an intriguing concept -- a species carrying capacity, so to speak," Arnold says. "This implies that the speciation process is sensitive to how many species are already out there."
In other words, exactly what Kimura suggested is recorded in detail in this fossil record, a fossil record that is nearly complete:
quote:
Drs. Tony Arnold (Ph.D., Harvard) and Bill Parker (Ph.D., Chicago) are the developers of what reportedly is the largest, most complete set of data ever compiled on the evolutionary history of an organism. The two scientists have painstakingly pieced together a virtually unbroken fossil record that shows in stunning detail how a single-celled marine organism has evolved during the past 66 million years. Apparently, it's the only fossil record known to science that has no obvious gaps -- no "missing links."
"It's all here -- a complete record," says Arnold. "There are other good examples, but this is by far the best. We're seeing the whole picture of how this organism has changed throughout most of its existence on Earth."
It's interesting that Kimura sees natural selection as an essentially conservative force, from which "liberation" is required before evolution is possible (step i). This is relevant to the parallel discussion on stasis.
Which is, of course, your opinion about how Kimura sees natural selection and not fact based on statements from Kimura. Once again we see that your opinion is not a good predictor of reality.
Biologists talk about levels of selection pressure. This pressure always exists, but it varies from high to low, depending on the complete ecology. When selection pressure is high, the organisms are constrained by that pressure from passing on any extraneous features, but when selection pressure is low, the organisms are less constrained by the need for survival and reproduction, and thus are able to engage in some extraneous features.
The difference between this and what you said, is that evolution under high selective pressure can be actively changing a population rather than conserving it.
And then he answers it:
quote:
It is generally believed that, in contrast to the neutralist view of molecular evolution, evolutionary changes at the phenotypic level are almost exclusively adaptive and caused by Darwinian positive selection. However, 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"
Emphasis added. Carefully worded, but I think we can all (if you'll excuse the terrible pun) catch his drift.
(normal quote formatting added)
The amazing thing is that you think this is surprising or revolutionary. Selection that does not involve death or incapacity of the individual due to genetic misinformation occurs at the level of the individual, and this selection is based on the phenotype. The genotype has had it's say, now it is the job of the individual at the phenotype level to survive and reproduce, or all the selection at the genetic level is for naught.
Now the question is whether every trait expressed in the phenotype leads to selection. When you see patterns of coloration that are virtually ignored and that play no effect on survival or sexual selection, then it should be fairly obvious that traits too can be neutral (or nearly neutral) to selective pressure.
ie - evolution with natural selection adapts species to changes in habitats, while evolution with genetic drift provides variations within populations that over time can change a population into a different species.
An example of this is provided by the fossil record of Pelycodus:
A Smooth Fossil Transition: Pelycodus
quote:
The numbers down the left hand side indicate the depth (in feet) at which each group of fossils was found. As is usual in geology, the diagram gives the data for the deepest (oldest) fossils at the bottom, and the upper (youngest) fossils at the top. The diagram covers about five million years.
The numbers across the bottom are a measure of body size. Each horizontal line shows the range of sizes that were found at that depth. The dark part of each line shows the average value, and the standard deviation around the average.
The dashed lines show the overall trend. The species at the bottom is Pelycodus ralstoni, but at the top we find two species, Notharctus nunienus and Notharctus venticolus. The two species later became even more distinct, and the descendants of nunienus are now labeled as genus Smilodectes instead of genus Notharctus.
As you look from bottom to top, you will see that each group has some overlap with what came before. There are no major breaks or sudden jumps. And the form of the creatures was changing steadily.
Here you see a gradual increase in size in the population resulting in several species classifications as they move the population out of the range of the previous population. If natural selection were "conservative" as you claim, then this lineage should be vertical from P. ralstoni to N. nunienus, so you get a double whammy here: genetic drift accumulating into gradual increase in size, and lack of "conservation" by natural selection.
Natural selection would not constrain this evolution as long as each population was able to survive and mate at each level of the progression.
Enjoy.

we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
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to share.


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This message is a reply to:
 Message 171 by Kaichos Man, posted 11-07-2009 6:53 AM Kaichos Man has replied

Replies to this message:
 Message 177 by Kaichos Man, posted 11-09-2009 6:34 AM RAZD has replied
 Message 185 by Kaichos Man, posted 11-10-2009 5:29 AM RAZD has replied

  
Kaichos Man
Member (Idle past 4488 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 176 of 280 (534522)
11-09-2009 6:05 AM
Reply to: Message 174 by Percy
11-07-2009 9:55 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?
The evidence for natural selection surrounds us everywhere in every adaptive feature of every organism from bacteria to whales.
Well, not really. This is a transcript of Kimura's appearance on a BBC documentary:
"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.
And when you say:
If it were true that Kimura actually rejected natural selection as having a significant role in evolution then he would be an enormously controversial figure within biology, but he didn't and he's not.
You're half right. He didn't "actually reject natural selection", but he certainly was considered controversial:
Dobzhansky: "It took a century to show that [objections to Darwinism] are devoid of foundation. But now Dr. Kimura and his followers claim evolution to be due to changes which are neither useful nor harmful to their possessors. They are simply neutral and are established merely by chance. If that were so, evolution would have hardly any meaning, and would not be going anywhere in particular. All that we knowall that we observe both in nature and in the laboratoryseems, I believe, to contradict this contention. This is not simply a quibble among specialists. To a man looking for the meaning of his existence, evolution by natural selection makes sense."
It seems Dobzhansky was considerably less comfortable with Kimura's theory than you are, Percy.

"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 174 by Percy, posted 11-07-2009 9:55 AM Percy has replied

Replies to this message:
 Message 180 by Percy, posted 11-09-2009 9:28 AM Kaichos Man has replied
 Message 181 by Coyote, posted 11-09-2009 10:52 AM Kaichos Man has replied

  
Kaichos Man
Member (Idle past 4488 days)
Posts: 250
From: Tasmania, Australia
Joined: 10-03-2009


Message 177 of 280 (534525)
11-09-2009 6:34 AM
Reply to: Message 175 by RAZD
11-07-2009 7:33 PM


Re: moving on ... Foraminifera as a confirming example
It's interesting that Kimura sees natural selection as an essentially conservative force, from which "liberation" is required before evolution is possible (step i). This is relevant to the parallel discussion on stasis.
Which is, of course, your opinion about how Kimura sees natural selection and not fact based on statements from Kimura.
Really? Consider:
The second is the "conservative nature" of the changesi.e., functionally less important molecules, or portions of molecules, evolve faster than more important ones"
And
"As to the second feature (i.e., the conservative nature), it can easily be understood from the neutral theory, because the less drastic or more conservative the mutational change, the more likely it is to turn out to be nondeleterious, and therefore selectively neutral."
As well as:
"What I want to emphasize is that relaxation of natural selection is the prerequisite for new evolutionary progress.
Once again we see that your opinion is not a good predictor of reality.
And your opinion is not a good predictor of who's opinion is being stated.
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 175 by RAZD, posted 11-07-2009 7:33 PM RAZD has replied

Replies to this message:
 Message 178 by RAZD, posted 11-09-2009 7:58 AM Kaichos Man has replied

  
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 178 of 280 (534531)
11-09-2009 7:58 AM
Reply to: Message 177 by Kaichos Man
11-09-2009 6:34 AM


another example of dodging?
Hi Kaichos Man, nice try.
quote:
The second is the "conservative nature" of the changesi.e., functionally less important molecules, or portions of molecules, evolve faster than more important ones
Which does not make it a conservative force to maintain the population in stasis as you claimed. You have mixed two meanings of conservative, the fallacy of equivocation. You still have changes.
I notice you did not respond to the rest of my post, so you must agree with that yes?
Message 167 You will know when I believe my argument has received a mortal blow (or been manoeuvred into apparent deadlock) because I'll probably stop talking about it and change the subject. In the overall battle between Creationism and evolution, this could be termed retreating and attacking on another front.
So anytime you fail to answer we can take this as your accepting that your argument has "received a mortal blow (or been manoeuvred into apparent deadlock)" ... where the "deadlock" is that you cannot figure a way to reply that isn't already answered.
Enjoy.

we are limited in our ability to understand
by our ability to understand
Rebel American Zen Deist
... to learn ... to think ... to live ... to laugh ...
to share.


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This message is a reply to:
 Message 177 by Kaichos Man, posted 11-09-2009 6:34 AM Kaichos Man has replied

Replies to this message:
 Message 186 by Kaichos Man, posted 11-10-2009 5:44 AM RAZD has replied

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


(1)
Message 179 of 280 (534534)
11-09-2009 8:52 AM
Reply to: Message 164 by Kaichos Man
11-06-2009 8:46 PM


Re: Gene networks in development
can you explain the step-by-step causality of a new gene arising that 1) has the sole function of controlling other genes, b) knows exactly which genes to control and c) has a way of replacing or overriding their current form of regulation?
you are making a whole series of unwarranted assumptions about how such genes should arise or act, with the possible exception of point 1. The fact is that as long as there are protein domains which can promote expression either by recruiting transcriptional machinery directly or by opening up the chromosomal structure to allow transcription, then these domains can be joined to almost any one of dozens of DNA binding domains whose specificities can be highly variable. This allows a decoupling of repressing and activating activity as a domain for either can be associated with a similar binding domain.
We can see this capability in in vivo experiments when a fusion of the Engrailed-repressor protein domain to a binding domain of some other transcription factor acts to repress the direct transcriptional targets of the transcription factor, no matter what its normal activity would be. The converse experiment uses the VP16 protein domain which is from a Herpesvirus and is a potent transcriptional activator. For an example of such experiments see Li an McGinnis (1999) where they use the VP-16 domain to change the regulatory activity of specific Hox genes in Drosophila and study how they alter segment identity.
TTFN,
WK

This message is a reply to:
 Message 164 by Kaichos Man, posted 11-06-2009 8:46 PM Kaichos Man has not replied

  
Percy
Member
Posts: 22391
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


(1)
Message 180 of 280 (534539)
11-09-2009 9:28 AM
Reply to: Message 176 by Kaichos Man
11-09-2009 6:05 AM


Re: Lactose added to genome is added information
Kaichos Man writes:
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.
It's interesting to see those quotes you provided from a 1973 BBC documentary (Perspectives on Molecular Evolution), but Kimura's ideas as they developed in the years after that (the "nearly neutral" variation of the theory came after that documentary) are not considered controversial today. Kimura's neutral theory now has wide acceptance within biology and has proved particularly useful in population genetics.
You can quote mine Kimura to your heart's content trying to make him seem to consider natural selection as playing a minor role in adaptation, but as I keep telling you, no biologist in his right mind could ever believe that. The evidence for natural selection is in every adaptive feature of every organism.
Kimura's 1973 statement about hemoglobin seems crafted as an illustration to aid public understanding. It doesn't reflect any actual research findings and isn't true. In fact, just as the hemoglobin of high and low altitude creatures differs to take advantage of different oxygen levels, so does the hemoglobin of fish (subject to increasing pressure with increasing depth and a whole host of other factors) differ from that of land animals, and these differences are due to natural selection. Kimura's hemoglobin example was likely successful in getting his point across to laypeople, but biologists both then and today would role their eyes at such a naively incorrect statement.
Kimura's neutral theory makes claims about the causes of variation at the molecular level, and that hemoglobin is a well know molecule probably explains why he chose it for an example, and undoubtedly some proportion of hemoglobin variation is neutral, but just as undoubtedly a significant proportion has been driven by adaptive selection due to environmental pressure. Kimura understands this when he provides his step 4 that you cited earlier:
Kimura writes:
  1. Intergroup competition and individual selection lead to extensive adaptive evolution, creating a radically different taxonomic group adapted to a newly opened ecological niche.
Notice that Kimura says that selection is responsible for adaptive evolution. When he's talking about neutral variation dominating over selected variation he's talking about the molecular level.
When Kimura says:
Kimura writes:
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.
He was only saying what we're already telling you is true and that we all agree with. Many changes at the molecular level are neutral with regard to selection. But adaptation requires selection, Kimura knew this, and he was not saying that chance plays a greater role in adaptation than natural selection. He was saying that at the molecular level chance plays a greater role. You keep forgetting the "at the molecular level" part of what he's saying.
--Percy
Edited by Percy, : Add clarifications.
Edited by Percy, : Grammar.

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 182 by AnswersInGenitals, posted 11-09-2009 4:08 PM Percy has seen this message but not replied
 Message 183 by Kaichos Man, posted 11-10-2009 5:04 AM Percy has seen this message but not replied

  
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