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Genome Evolution | First, a Bang Then, a Shuffle
The Scientist ^ | 1/27/2003 | Ricki Lewis

Posted on 01/31/2003 4:19:03 PM PST by jennyp

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Creationists insist that evolution cannot increase biological complexity. Evolutionists point to gene duplication and the subsequent hijacking of function & refinement thru selection. This article points out just how rampant such duplication-driven complexity increase has been.
1 posted on 01/31/2003 4:19:03 PM PST by jennyp
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To: jennyp
bumppmub
2 posted on 01/31/2003 4:22:47 PM PST by aposiopetic
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To: CalConservative; balrog666; dpwiener; Buck Turgidson; Poohbah; guaguanco; Junior; VadeRetro; ...
Rampant-Biological-Complexity-Increase BUMP.
3 posted on 01/31/2003 4:23:03 PM PST by jennyp (http://crevo.bestmessageboard.com)
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To: jennyp
Chromosomes - God's fingerprints.
4 posted on 01/31/2003 4:27:03 PM PST by WriteOn
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To: aposiopetic
Man you're quick!
5 posted on 01/31/2003 4:29:42 PM PST by jennyp (http://crevo.bestmessageboard.com)
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To: jennyp
"We've known for some time that duplications are the primary force for genes and genomes to evolve over time," says Evan Eichler, director of the bioinformatics core facility at the Center for Computational Genomics, Case Western Reserve University, Cleveland.

Except, as you say, some of us are making a point of being clueless. Some of us have most definitely not "known for some time" how evolution can account for increases in complexity. You couldn't get this information into a creationist skull if you put it into a notched bullet and shot it in.

6 posted on 01/31/2003 4:41:26 PM PST by VadeRetro
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To: jennyp
Polyploidy is rarer in animals, which must sort out unmatched sex chromosomes, than in plants, which reproduce asexually as well as sexually. "But polyploidization is maintained over evolutionary time in vertebrates quite readily, although rarely. Recent examples, from the last 50 million years ago or so, include salmonids, goldfish, Xenopus [frogs], and a South American mouse," says Postlethwait.

Dumb question on my part: In general, duplication/polyploidization confers no particular advantage to sexually reproducing organisms, but may do so (or not confer disadvantage) in certain instances?

7 posted on 01/31/2003 4:44:40 PM PST by aposiopetic
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To: jennyp
Duplicate genes are the devil's plaything!
8 posted on 01/31/2003 4:46:53 PM PST by PatrickHenry
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To: jennyp
Creationists insist that evolution cannot increase biological complexity. Evolutionists point to gene duplication and the subsequent hijacking of function & refinement thru selection. This article points out just how rampant such duplication-driven complexity increase has been.

Then they won't show up on this thread.

9 posted on 01/31/2003 5:59:08 PM PST by balrog666 (If you tell the truth you don't have to remember anything - Mark Twain)
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To: aposiopetic
Dumb question on my part: In general, duplication/polyploidization confers no particular advantage to sexually reproducing organisms, but may do so (or not confer disadvantage) in certain instances?
I think it's mostly that the polyploid offspring, if they survived, would never find a compatible mate to produce offspring with. (Unlike in plants, which are more likely to find a compatible mate. See here for a good explanation of plant polyploidy.)
10 posted on 01/31/2003 6:43:17 PM PST by jennyp (http://crevo.bestmessageboard.com)
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To: jennyp
"...You don't have to be a statistician to realize that the distribution of duplications is highly nonrandom," says Eichler.

Tell us again about random mutation, natural selection.

11 posted on 01/31/2003 7:20:17 PM PST by AndrewC (Darwininian Dictionary -- anything useful for just-so stories)
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To: jennyp
Some duplications cause disease. A type of Charcot-Marie-Tooth disease, for example, arises from a duplication of 1.5 million bases in a gene on chromosome 17. The disorder causes numb hands and feet.

My eyes are glazing over - just like in college.

12 posted on 01/31/2003 7:50:36 PM PST by Mike Darancette
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To: aposiopetic
bumppmub

pum! mup! pup! mump! mubbup! pmupbmupbupppppmmmubbbpmmmuubbb!

Ah yes we can all see how this will eventually get to the Gettysburg Address. Just a matter of time and natural selection.

13 posted on 01/31/2003 9:55:59 PM PST by HiTech RedNeck
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To: HiTech RedNeck
Ah yes we can all see how this will eventually get to the Gettysburg Address. Just a matter of time and natural selection.

Nah. If you replayed life's tape, or however that Gould quote goes. But with time & natural selection you would get something meaningful. But it would probably be in a language we've never even heard of!

14 posted on 01/31/2003 10:31:19 PM PST by jennyp (http://crevo.bestmessageboard.com)
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To: jennyp
Creationists insist that evolution cannot increase biological complexity. Evolutionists point to gene duplication and the subsequent hijacking of function & refinement thru selection. This article points out just how rampant such duplication-driven complexity increase has been.

Actually, the vast amount of redundant and non-functional content in the human genome, despite these duplications, is a good indication that all this new available space in the genome has not given rise to increased complexity, just imperfect copies of pre-existing information.

Sometime, read "Science and Information Theory" by Nobelist Leon Brillouin. Information (ie design specifications) do not arise from nothing. Only by transfer from other, equivalent information or intelligence. It is called "negative entropy" and is governed by the second law. Raw energy input increases entropy in a system, not negative entropy (information).

15 posted on 01/31/2003 11:17:57 PM PST by mcsparkie
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To: jennyp
Never fails to amuse me what faith evolutionists have. For every mutation, duplication, what have you that can "find favor" so to speak with the environment there got to be how many millions of don't cares and "turkeys" produced in exactly the same manner? (Remember we got to rule out intelligent design or it ain't "science." Can't have God at the controls of the CAD system twiddling this thing ya know! So we would have to get a staggering amount of this dilapidation and noise.) Once we get to something that is significantly bigger and less prolific than insects, this whole scenario breaks down. But it's all the evolutionists have to play with.
16 posted on 02/01/2003 4:15:42 PM PST by HiTech RedNeck
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To: jennyp
His group used molecular-clock analyses to date the origins of 1,739 duplications from 749 gene families.

The problem with the above, and with the whole article is that there is no molecular clock. There are several reasons for this the most essential one is that we do not have any examples of half billion year old DNA, 100 million year old DNA or even million year old DNA to make comparisons to. Therefore all the samples we have (with a few exceptions that can be counted on the fingers of one hand) are of current DNA. So how can one tell how far current DNA is from millions of year old DNA if one does not have something to compare it to? The answer is one cannot. The second problem is that SUPPOSEDLY all organisms now living are equally far apart from the first life as all others, so to take one as an example of 'what is older' is totally fallacious. It is using the assumptions of the theory of evolution as to how species supposedly descended from each other to prove how species supposedly descended from each other. This is circular reasoning and utter nonsense. There are more problems with the molecular clock also. Since some creatures have much shorter generations than others, and mutations supposedly occur at each reproduction (how else could they happen!) the 'mutational clock' (for that is what is really being talked about here) should be going at a completely different speed for elephanst than for flys, yet evolutionists moronically claim that it goes at the same speed.

17 posted on 02/01/2003 8:10:34 PM PST by gore3000 (Evolution is whatever lie you want it to be!)
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To: jennyp
But with time & natural selection you would get something meaningful.

No you would not. There are supposedly some 10 million years of mutations separating man from chimps. Chimps and men differ by some 5% of their DNA (the evolutionist 1% has been proven wrong by the same man who originally made the statement). Since chimps and men have about 3 billion DNA base pairs that 5% represents some 150,000,000 favorable mutations in those ten million years. Since with all our science, all our billions in research on DNA for decades have not shown a single favorable mutation has ever happened, I think that your statement is absolutely wrong scientifically - just as evolution is completely wrong scientifically.

18 posted on 02/01/2003 8:18:55 PM PST by gore3000 (Evolution is whatever lie you want it to be!)
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To: jennyp
The bottom half of the geologic column (( no fossils )) formed from below . . .

and the top half formed rather quickly from above (( no intermediary fossils )) - - -

uniformism (( time )) // evolution is ==== gone // over // never happened !


19 posted on 02/01/2003 8:25:41 PM PST by f.Christian (( Orcs of the world : : : Take note and beware. ))
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To: gore3000
There are supposedly some 10 million years of mutations separating man from chimps. Chimps and men differ by some 5% of their DNA (the evolutionist 1% has been proven wrong by the same man who originally made the statement). Since chimps and men have about 3 billion DNA base pairs that 5% represents some 150,000,000 favorable mutations in those ten million years. Since with all our science, all our billions in research on DNA for decades have not shown a single favorable mutation has ever happened, I think that your statement is absolutely wrong scientifically

Stop trying to use numbers to test their ideas. It makes them furious. All other branches of science use mathematical analysis to support their conclusions, but the rules are different for evolution. For an evolutionist the standard of proof is:

"If I can imagine a way it MIGHT have happened, then you must believe the it DID happen that way, or you are a willfully ignorant bible-thumping idiot. PS- Once the way I imagined that it might have happened gets nullified by further observations, you must then believe that the next thing I imagine is the way it did happen- or else you once again are a willfully ignorant, bible thumping idiot.

20 posted on 02/01/2003 8:42:44 PM PST by Ahban
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To: jennyp
This article points out just how rampant such duplication-driven complexity increase has been.

Does it, or does it merely speculate that such has occured in animals? The duplication of genes is (according to the article) far from random. Maybe genes that get expressed the most or tend to mutate the most have the most copies. That is engineering and it does not demand a naturalistic explanation.

The article assumes that gene duplication will automatically produce an increase in complexity. There is little evidence that this is true. The reason is that there is precious little evidence that gene copies can ever become a gene with a function much different from the old gene. Because of that, all the duplications in the world won't get you from ameoba to man. It will just get you to a man with a lot of psuedogenes. We have lots of such genes, but so much "junk DNA" is conserved that some have been led to wonder if it does not have a function after all, such as steering protiens to the right part of the cell.

21 posted on 02/01/2003 8:58:56 PM PST by Ahban
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To: Ahban
All other branches of science use mathematical analysis to support their conclusions, but the rules are different for evolution.

Yup, facts are such a problem for evolutionists, one more thing for them to need to try to explain away! They also have their own math. For example, one would think that if you take away something you would end up with less not more. However in evo math when natural selection takes away from the gene pool you get more genes than you had before!

22 posted on 02/01/2003 10:22:09 PM PST by gore3000 (Evolution is whatever lie you want it to be!)
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To: PatrickHenry
Automated blue-skipping placemarker, a service of FreepScriptTM.
23 posted on 02/02/2003 4:53:30 AM PST by PatrickHenry (Preserve the purity of your precious bodily fluids!)
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To: Ahban
Maybe genes that get expressed the most or tend to mutate the most have the most copies. That is engineering and it does not demand a naturalistic explanation.

The author is not speaking to the distribution of duplication events before selection. From our POV that is still random. We don't know initial conditions, don't know a mechanism, and can't predict future events. That's as random as things get.

What it comes down to is that nobody can distinguish between a random and an "intelligent design" event.

24 posted on 02/02/2003 7:51:32 AM PST by Nebullis
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To: Nebullis
Yes, I agree with you as far as that goes (even if a random distribution randomly made genes, they would not be random after selection got done with them, except for true pseudogenes).

That was not really what I was getting at. If as you say, "we don't know initial conditions, we don't know mechanism, and we can't predict future events" then how in the world can one be so confident that it WAS random and naturalistic? Isn't it really just a choice that says more about the heart of the chooser than the voice of the evidence?

Actually, I was hoping to hear from you on this one. Weren't you the one who pointed out in another thread that much of what we call 'junk DNA' is highly conserved in humans and other critters? I think you also pointed out that if it is highly conserved, it can't be junk, it must have some function that is useful to the organism.

Maybe as you say we can't distinguish between a random and an intelligent desing event, but when with each discovery complexity and interelatedness grows, when with each discovery that which we thought was superfulous proves to be important, then I would think that at least slides the bar a little more towards the "design" rather than "random" end of the scale.

Wouldn't you agree? Is this (that is, interelated complexity could be extremely high and things thought to be junk would prove to have function.)not exactly what would be expected if the design hypothesis were correct?
25 posted on 02/02/2003 11:57:13 AM PST by Ahban
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To: Ahban
One vase vs two facing profiles . . .

opposite conclusions - - - viewpoints (( bias )) !

Metaphysics // philosophy // psychology explains all !
26 posted on 02/02/2003 12:04:40 PM PST by f.Christian (( Orcs of the world : : : Take note and beware. ))
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To: gore3000; Nebullis
There are supposedly some 10 million years of mutations separating man from chimps. Chimps and men differ by some 5% of their DNA (the evolutionist 1% has been proven wrong by the same man who originally made the statement).
BZZZZZT! It's more like 1.4% where it counts - in the genes themselves:
The new estimate could be a little misleading, said Saitou Naruya, an evolutionary geneticist at the National Institute of Genetics in Mishima, Japan. "There is no consensus about how to count numbers or proportion of nucleotide insertions and deletions," he said.

Indels are common in the non-functional sections of the genome, said Peter Oefner, a researcher at Stanford's Genome Technology Center in Palo Alto, California. Scientists estimate that up to 97 percent of DNA in the human genome has no known function. However, he added, indels are extremely rare in gene sequences.

"We haven't observed a single indel in a [gene] to date between human and chimp," said Oefner. Therefore, the revised estimate doesn't alter the amount of DNA that holds information about our species. Humans and chimps still differ by about one percent in gene sequences, he said.

Besides, IIRC his method of counting insertions & deletions would treat a 100 base pair insertion as 100 mutations. Nebullis, do you remember if this is true?
Since chimps and men have about 3 billion DNA base pairs that 5% represents some 150,000,000 favorable mutations in those ten million years. Since with all our science, all our billions in research on DNA for decades have not shown a single favorable mutation has ever happened, I think that your statement is absolutely wrong scientifically - just as evolution is completely wrong scientifically.
Plugging in the correct numbers & assumptions:
Since chimps and men have about 3 billion 90 million gene-encoding DNA base pairs that 5% 1.4% represents some 150,000,000 14,000 neutral or favorable mutations in those ten million years.

27 posted on 02/03/2003 1:55:21 AM PST by jennyp (http://crevo.bestmessageboard.com)
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To: Ahban
Stop trying to use numbers to test their ideas. It makes them furious.

Trying to use bogus numbers to defend their ideas makes us furious. :-)

28 posted on 02/03/2003 1:57:17 AM PST by jennyp (http://crevo.bestmessageboard.com)
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To: jennyp
Then post your own numerical analysis and we can debate about whose numbers are more reasonable. It is no good to just say "their numbers are bogus" with no reasons why and no counter model of your own.

Please, give us your estimates.
29 posted on 02/03/2003 2:45:05 PM PST by Ahban
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To: balrog666; Condorman; *crevo_list; donh; general_re; Godel; Gumlegs; Ichneumon; jennyp; ...
LBB's gonna be pissed.
30 posted on 02/03/2003 2:55:10 PM PST by Junior (Put tag line here =>)
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To: Ahban
Then post your own numerical analysis and we can debate about whose numbers are more reasonable. It is no good to just say "their numbers are bogus" with no reasons why and no counter model of your own.

She did, in #27.

31 posted on 02/03/2003 2:59:33 PM PST by Lurking Libertarian (Non sub homine, sed sub Deo et lege)
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To: Lurking Libertarian; jennyp
Oh, quite right you are. Thank you. And thank you jenny. I shall return to take a look at those numbers tonight.
32 posted on 02/03/2003 3:29:33 PM PST by Ahban
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To: jennyp
It's more like 1.4% where it counts - in the genes themselves:

Not quite. This 'study' is not a study at all. It is a reinterpretation of the work done by Roy Britten in comparing the sequences of human and chimp DNA. It is a reductionist view of the DNA differences between humans and chimps. It throws away most of the differences because supposedly they are unimportant because they are not in genes. Well the rest of the DNA does matter unlike what this hack has to say. Yes 97% of DNA does not code for genes, but his statement that

Scientists estimate that up to 97 percent of DNA in the human genome has no known function.

is totally false and he is not a scientist if he made it. The last half dozen years of biological research have been concerned with finding out just exactly what that 97% of DNA which evolutionists call "junk" does. What this DNA does is control what the gene does, when and how much protein it is to make, and even what specific proteins, amongst several which many genes can make, are to be made by the gene. In other words 'this junk' which this hack says scientists say 'has no known function' is what makes an organism function. In one single discovery, they have found what 10% of that DNA does - it acts as a zipper during cell division. So your article is total nonsense and National Geographic should be ashamed to publish such garbage.

So the 3.9% difference you wish to throw away is indeed important as is the 97% of DNA which your phony article claims is non-functional. What this shows is the quality of science being peddled by what were once respectable magazines in their attempt to save the totally discredited theory of evolution by discrediting the good reputation they had built up for decades.

33 posted on 02/03/2003 8:17:53 PM PST by gore3000
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To: jennyp; gore3000
As to your numbers in post 27, I have a source,
http://www.newscientist.com/news/news.jsp?id=ns99992833 that says the true difference is actually just above five percent. As for your point that indels are mostly non-coding, and thus don't count, the article above states , "The result is only based on about one million DNA bases out of the three billion which make up the human and chimp genomes, says Britten. "It's just a glance," he says.

But the differences were equally split between "junk" regions that do not have any genes, and gene-rich parts of the genome, suggesting they may be evenly distributed.
"

That seems to be at odds with what Oefner implies when he claims indels are mostly in non-functional sections of the genome.

Note that snippet from the article also mentions three billion base pairs, not the 90 million figure that you use. I know you are only counting the part of the genome that we know codes, but if a human has a billion extra base pairs that do not code, that new stuff must have come from somwhere. It counts as far as being a mutation event that somehow established itself throughout the human genome.

In short, gore3000s numbers are better, its not 14K gene changes between man and chimp in 10 million years, but rather 150K changes that have established themselves througout the population.

However that is just the numbers. I think you are right on one important part. He seems to be counting all of those mutations as favorable, when you point out that many of them, most even, could be neutral. I'd like to know what gore3000's reasoning is on that. It seems to me that there is no reason all of those changes have to be favorable.

So how fast do mutations, neutral or favorable, work their way into populations today? That should give us a measuring stick to see of 150,000 mutations can work their way into the human genome in ten million years. Perhaps it would be better to say "work their way into the genome of an isolated group like Icelanders" since human populations were much smaller during most of our history.

That would be one mutation (neutral or favorable) working its way into the whole population every 67 years. I wish someone who knows about the rate now would speak up here, but that sounds like a really, really really short time, don't you think? I mean, we don't breed like flies, it takes a while for mutations to be established, yes?

Not only that, much of the difference between us and chimps is not just in the genes, but in the degree they are expressed.

Check here... http://www.newscientist.com/news/news.jsp?id=ns99992160

It says that human brains changed five times as much as chimp brains in the same period. That sounds like some favorable mutations to me. All of those changes must be reasonably doable in the 10 million years evolution allows in order for the evolutionary hypothesis to be more reasonable than the design hypothesis.

Am I missing something here, or are gore3000s numbers better than you first realized (considering neutral mutations are included too)?
34 posted on 02/03/2003 9:10:24 PM PST by Ahban
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To: Lurking Libertarian
my #34, the analysis of the two sets of numbers, is meant for you too.
35 posted on 02/03/2003 9:12:49 PM PST by Ahban
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To: Junior
Thanks for the ping. Interesting thread.
36 posted on 02/04/2003 5:07:42 AM PST by RadioAstronomer
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To: Ahban

In short, gore3000s numbers are better, its not 14K gene changes between man and chimp in 10 million years, but rather 150K changes that have established themselves througout the population.

(Gore3000 claimed 150 million mutations.)

The point of Britten's new study is that these previously missing mutations were simple insertions & deletions. So if you have a 1000 bp duplication, it's still just one mutation. I think the "extra 3.9%" figure refers to the increased difference in sequence, not to 2 1/2 times more mutations. I couldn't find the post I was thinking of from back in September (on another board) that explained the point directly, but here's an article from CalTech that hints at what I'm saying:

To describe exactly what Britten did, it is helpful to explain the old method as it was originally used to determine genetic similarities between two species. Called hybridization, the method involved collecting tiny snips of the DNA helix from the chromosomes of the two species to be studied, then breaking the ladder-like helixes apart into strands. Strands from one species would be radioactively labeled, and then the two strands recombined.

The helix at this point would contain one strand from each species, and from there it was a fairly straightforward matter to "melt" the strands to infer the number of good base pairs. The lower the melting temperature, the less compatibility between the two species because of the lower energy required to break the bonds.

In the case of chimps and humans, numerous studies through the years have shown that there is an incidence of 1.2 to 1.76 percent base substitutions. This means that these are areas along the helix where the bases (adenine, thymine, guanine, and cytosine) do not correspond and hence do not form a bond at that point. The problem with the old studies is that the methods did not recognize differences due to events of insertion and deletion that result in parts of the DNA being absent from the strands of one or the other species. These are different from the aforementioned substitutions. Such differences, called "indels," are readily recognized by comparing sequences, if one looks beyond the missing regions for the next regions that do match.

To accomplish the more complete survey, Britten wrote a Fortran program that did custom comparisons of strands of human and chimp DNA available from GenBank. With nearly 780,000 suitable base pairs available to him, Britten was able to better infer where the mismatches would actually be seen if an extremely long strand could be studied. Thus, the computer technique allowed Britten to look at several long strands of DNA with 780,000 potential base pairings.

As expected, he found a base substitution rate of about 1.4 percent-well in keeping with earlier reported results-but also an incidence of 3.9 percent divergence attributable to the presence of indels. Thus, he came up with the revised figure of 5 percent.[emphasis mine]

That really sounds to me like what I was saying: The 5% represents the total difference in base pair sequences, but it took a number of mutations equal to 1.4% of the total length to produce those differences.

Uh-oh... I think my math was off, too. 3 billion total bps x 1.4% mutations = 42 million mutations. 90 million gene-encoding bps x 1.4% = 1.26 million mutations. That is a lot, though much less than gore3000's 150 million mutations.

However that is just the numbers. I think you are right on one important part. He seems to be counting all of those mutations as favorable, when you point out that many of them, most even, could be neutral. I'd like to know what gore3000's reasoning is on that. It seems to me that there is no reason all of those changes have to be favorable.

So how fast do mutations, neutral or favorable, work their way into populations today? That should give us a measuring stick to see of 150,000 mutations can work their way into the human genome in ten million years. Perhaps it would be better to say "work their way into the genome of an isolated group like Icelanders" since human populations were much smaller during most of our history.

That would be one mutation (neutral or favorable) working its way into the whole population every 67 years. I wish someone who knows about the rate now would speak up here, but that sounds like a really, really really short time, don't you think? I mean, we don't breed like flies, it takes a while for mutations to be established, yes?

Let's see... 10 million years divided by 42 million mutations = 1 fixation every .238 years (3 months or so). But keep in mind that there are always many mutations at different locations in the genome working in parallel to get themselves fixed at the same time. How many? I have no idea, but if there were 1000 different alleles out there in the population at the same time that would mean an average allele would have 238 years in which to fixate for the numbers to work out. If there are 100,000 alleles then the average allele has 23,800 years to acheive fixation for the numbers to work out. (Did I state that clearly?)

As for how long it takes for an individual allele to achieve fixation, I don't know the exact numbers, but they do fixate more quickly in small populations than in large ones. (If there are 10 in the population, 1 has a new neutral mutation, & every breeding pair produces 2 offspring, then the mutation could represent 0%, 10%, or 20% of the next generation's population. In the 3rd generation I think it would represent 0%, 10%, 20%, 30%, or 40%.)

Another thing to ponder is that through most of humanity's history, we were divided into many small, somewhat isolated tribes that had relatively little gene flow between them. I'll bet that genetic drift was rampant for a long time, even when the total human population number was relatively large. It wasn't until a couple thousand years ago that we truly became one big population with lots of biracial children. ("Lots" as measured over several generations.) So the total amount of genetic change was probably higher thousands of years ago than is happening today.

So even with 42 million mutations between humans & chimps, I don't think it presents any problem.

37 posted on 02/04/2003 4:21:41 PM PST by jennyp (http://crevo.bestmessageboard.com)
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To: jennyp
Some lurkers may faint. A real, numbers-based dialog without acrimony. I need to read your post another time or two in order to sort it out. Off-hand, it seems like we are getting better numbers, and coming together on the numbers.
38 posted on 02/04/2003 5:54:09 PM PST by Ahban
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To: jennyp; Ahban
The point of Britten's new study is that these previously missing mutations were simple insertions & deletions. So if you have a 1000 bp duplication, it's still just one mutation. I think the "extra 3.9%" figure refers to the increased difference in sequence, not to 2 1/2 times more mutations.

First of all, the article you cited is not a new study. All it does is rework the what Britten did and make it sound more favorable towards evolutionary theory. The person, as I pointed out is an ideological hack who continues to tell the EVOLUTIONIST LIE that 97% of the DNA is junk. The article ahban cited on the brain - about this very DNA which this EVOLUTIONIST LIAR says scientist consider nonsense, shows what he is.

In fact, what modern biology has found is that it is not the genes but what evolutionist call 'junk dna' that is the most important part of our genome, it is what makes us tick and makes the genes work properly:

Within a single bacterial cell, genes are reversibly induced and repressed by transcriptional control in order to adjust the cell’s enzymatic machinery to its immediate nutritional and physical environment. Single-celled eukaryotes, such as yeasts, also possess many genes that are controlled in response to environmental variables (e.g., nutritional status, oxygen tension, and temperature). Even in the organs of higher animals --- for example, the mammalian liver --- some genes can respond reversibly to external stimuli such as noxious chemicals. ...

The most characteristic and exacting requirement of gene control in multicellular organisms is the execution of precise developmental decisions so that the right gene is activated in the right cell at the right time during development of the many different cell types that collectively form a multicellular organism. In most cases, once a developmental step has been taken by a cell, it is not reversed. Thus these decisions are fundamentally different from bacterial induction and repression. In executing their genetic programs, many differentiated cells (e.g., skin cells, red blood cells, lens cells of the eye, and antibody-producing cells) march down a pathway to final cell death, leaving no progeny behind. The fixed patterns of gene control leading to differentiation serve the needs of the whole organism and not the survival of an individual cell.
From: Regulation of transcription initiation

So what this hack says about 'junk dna' is total unscientific nonsense. Without the mechanisms set up by this 'junk DNA' the genes would not work at all, period. The organism would not function, period. What we see here is an evolutionist lying through his teeth trying to save a totally decrepit and false theory through lies.

39 posted on 02/04/2003 7:10:17 PM PST by gore3000
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To: jennyp
here's an article from CalTech that hints at what I'm saying:

You are misreading the article you cite:

The problem with the old studies is that the methods did not recognize differences due to events of insertion and deletion that result in parts of the DNA being absent from the strands of one or the other species.

What the above means is simply that because of deletions in each species, the strands selected did not align properly, hence a simple 'alphabetic' comparison of the sequences gave a wrong number. What Britten did, and the reason he revised the figures, is he properly aligned the strands according to what was the purpose of them. In this way he came up with the more accurate 5% number.

Now as to neutral mutations, they just cannot spread throughout a species - according to studies made by evolutionists themselves when they were trying to solve the problem posed by genetics. The basis of population genetics is the Hardy-Weinberg principle which says that in a stable population the genetic mix of the population will remain stable absent any genetic advantage of a particular genetic makeup. What this means is that a neutral mutation in a population of 1 million organisms will continue to be in only 1 millionth of the population if it is neutral. In fact it will likely dissappear completely due to chance (if you play a game at odds of 2 to 1 with two dollars long enough you will lose both dollars), so neutral mutations cannot be in any way responsible for these differences in any significant way.

Due to the above, yes, the differences are 5%. Yes, you need some 150 million mutations. Yes, mostly all of them have to be favorable to have survived.

40 posted on 02/04/2003 7:26:25 PM PST by gore3000
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To: gore3000
You are misreading the article you cite:

The problem with the old studies is that the methods did not recognize differences due to events of insertion and deletion that result in parts of the DNA being absent from the strands of one or the other species.

No, you're misreading it. Britten came up with a more accurate figure for the differences in sequence. He was not trying to measure the number of mutations needed to produce those differences in sequence.

What the above means is simply that because of deletions in each species, the strands selected did not align properly, hence a simple 'alphabetic' comparison of the sequences gave a wrong number. What Britten did, and the reason he revised the figures, is he properly aligned the strands according to what was the purpose of them. In this way he came up with the more accurate 5% number.

But the DNA hybridization technique "involved collecting tiny snips of the DNA helix from the chromosomes of the two species to be studied". Now, stop & think what this would mean if you had a child that doubled its parents' chromosomes (ex.: from 10 to 20): The hybridization technique would not detect any difference between the two genomes! It would "think" it was just seeing twice as many snips of the child's DNA sample as it was "seeing" of the parent's sample, and would declare the genomes to be exactly 0% different.

In reality such a doubling of the number of chromosomes required one mutation, but the newer sequence comparison technique would correctly conclude that there was a 50% difference in total sequence between parent & child. See? The two techniques are measuring two different things.

Now as to neutral mutations, they just cannot spread throughout a species - according to studies made by evolutionists themselves when they were trying to solve the problem posed by genetics. The basis of population genetics is the Hardy-Weinberg principle which says that in a stable population the genetic mix of the population will remain stable absent any genetic advantage of a particular genetic makeup. What this means is that a neutral mutation in a population of 1 million organisms will continue to be in only 1 millionth of the population if it is neutral. In fact it will likely dissappear completely due to chance (if you play a game at odds of 2 to 1 with two dollars long enough you will lose both dollars), so neutral mutations cannot be in any way responsible for these differences in any significant way.

Please see this page from Kimball's Biology Pages. Scroll down to the section titled "When the Hardy-Weinberg Law Fails to Apply". Then find the subhead "Genetic Drift:

Genetic Drift

As we have seen, interbreeding often is limited to the members of local populations. If the population is small, Hardy-Weinberg may be violated. Chance alone may eliminate certain members out of proportion to their numbers in the population. In such cases, the frequency of an allele may begin to drift toward higher or lower values. Ultimately, the allele may represent 100% of the gene pool or, just as likely, disappear from it.

IOW, Hardy-Weinberg only helps you if you're talking about a species that does not separate into tribes, so it really is one huge interbreeding population. It might help you if we're talking about promiscuous ocean-dwelling fish, or birds that live in huge flocks, or modern humans, etc. But it does not help you with prehistoric humans.

Due to the above, yes, the differences are 5%. Yes, you need some 150 million mutations. Yes, mostly all of them have to be favorable to have survived.

In conclusion, no, no, and no.

41 posted on 02/05/2003 2:31:48 AM PST by jennyp (http://crevo.bestmessageboard.com)
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To: All
This thread won't last...
42 posted on 02/05/2003 7:02:40 AM PST by Condorman (Fact-based crevo threads have the life expectancy of a glass hammer.)
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To: Condorman; gore3000
<whistling, tapping fingers...>
43 posted on 02/06/2003 11:06:47 PM PST by jennyp (http://crevo.bestmessageboard.com)
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To: jennyp; gore3000; Condorman; RadioAstronomer
Jenny,

That is gracious of you to point out that both of our math is in error! I still am not convinced that we should multiply the base pairs by .014 rather than .05. Still, I am willing to give you that one in order to move forward with the discussion.

I am convinced that whether there are 150 million base pair differences (my and g3K's number) or only 42 million bpd (your new number) between man and chimp, it is all but impossible for those differences to accrue in the alledged 10 million years. Large, long-lived, slow reproducing, low-offspring mammals just don't get their genome rearranged that fast.

You admitted, with your 42 million, that this would be one change fixing itself in the entire human genome every three months- and that was in FUNCTIONING GENES THAT ARE EXPRESSED! This does not seem realistic at all. Can anyone out there, crevo or evo alike, give us some insight on how long it takes a mutation to establish itself in even a small population of big mammals?

I went to that link you gave to g3K. Here, from your link are two examples of a LACK of gene change that I found very interesting....

Two examples of reduced polymorphism because of genetic drift:

By 1900 hunting of the northern elephant seal off the Pacific coast had reduced its population to only 20 survivors. Since hunting ended, the population has rebounded from this population bottleneck to some 100,000 animals today. However, these animals are homozygous at every one of the gene loci that have been examined.

Cheetahs, the fastest of the land animals, seem to have passed through a similar period of small population size with its accompanying genetic drift. Examination of 52 different loci has failed to reveal any polymorphisms; that is, these animals are homozygous at all 52 loci.

The lack of genetic variability is so profound that cheetahs will accept skin grafts from each other just as identical twins (and inbred mouse strains) do. Whether a population with such little genetic diversity can continue to adapt to a changing environment remains to be seen. "




Do you see the problem? You have to assume that the entire human race has fixed gene changes every three months for 10 million years, where as when we examine small populations of similar mammals we find that NO new genes have fixed themselves in the whole population (OR EVEN SHOWED UP IN A PART OF IT!!!) for a hundred or even thousands of years.

What we see in the real world just does not seem to match up with what evolution says would have to happen. If human genes mutated that much, the human race would be long extinct.
44 posted on 02/07/2003 8:33:25 AM PST by Ahban
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To: jennyp; Ahban
Frankly, I haven't been completely convinced that measuring an x.x% difference in human and chimp DNA is a particularly meaningful calculation in the first place. It makes for a great sound/word-byte, but what does it actually tell us that makes it worthy to include in the debate? People on the creo side love to toss out these numbers as a blow to evolution, but very few on either side are well-versed enough to understand what is actually being measured, and more importantly, the conclusions indicated by that number. (Although, while we're slinging calculations around willy-nilly, don't forget that whatever ulitmate number one arrives at for total mutational differences, that must be divided in half for rate of change calculations. After all, once the populations separated each began to drift independently.)

As jennyp has pointed out, there are several different types of differences that can be measured, from direct 1:1 comparisons straight up the line, to other analyses designed to account for insertions, deletions, reversals, and partial or complete gene duplications, in addition to other more exotic mutations.

I also wonder which chimp genome is being compared with which human genome. And how does this compare with a genome comparison between an African bushman and say, an Alaskan Eskimo? Or an Australian Aborigine versus a Brazilian Wari'?

But I think the larger point is this: No one doubts the similarity of chimps and humans. The physical and behavioral similarities are reinforced by genetic analysis, which points unquestionably towards common ancestry. The mechanisms of genetic variation are still under investigation, and the creo side, instead of triumphantly crowing about how these mechanisms couldn't possibly have caused X degree of diffence in Y amount of time, need to present evidence for something that could.

45 posted on 02/07/2003 9:27:06 AM PST by Condorman (Mutation: Not just a genetic anomaly, it's a way of life!)
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To: Condorman
I also wonder which chimp genome is being compared with which human genome. And how does this compare with a genome comparison between an African bushman and say, an Alaskan Eskimo? Or an Australian Aborigine versus a Brazilian Wari'?

It hardly matters which human genome is measured, as you are closer genetically to any other human being on Earth than are two chimps living on opposite sides of the same mountain in Africa. More evidence that the human genome is slow to change.

I agree with your point that we need to keep refining numerical models so that the numbers better reflect reality- that is what we are trying to do. The answer is to keep at it, like we are trying to do, not tip over the chessboard and speculate that we can't use numbers to calculate anything meaningful. Of course we can, if we try. What scares some is that the meaningful calculations will show the vast improbability of the chimp-man common ancestor.

But I think the larger point is this: No one doubts the similarity of chimps and humans. The physical and behavioral similarities are reinforced by genetic analysis, which points unquestionably towards common ancestry.

Your bias is showing. The common ancestry is unquestionable only to a person who accepts it on faith to begin with. Common Designer is just as valid a hypothesis, unless one dogmatically rules it out in advance regardless of the evidence due to a personal choice.

The mechanisms of genetic variation are still under investigation, and the creo side, instead of triumphantly crowing about how these mechanisms couldn't possibly have caused X degree of diffence in Y amount of time, need to present evidence for something that could.

You have it backwards I am afraid. It is up to the EVO side to show that there are mechanisms which can reasonably produce these changes in the time allowed. We already have "something that could"- an intelligent designer.

The mice that scientists recently inserted jelly-fish glow genes into can now glow in the dark. Should civilization end and these critters escape into the wild I suppose some scientits 500 years from now could speculate that these genes evolved. Others could hypothysize that these genes were the results of intelligent designers manipulating genes.

I don't think the first group of scientists should demand that the second group produce the bodies of those long gone researchers as "proof" of the design hypotheis. The second group should be able to use stats to show how absurd is the idea of evolution in this case, especially within 500 years.

46 posted on 02/07/2003 10:34:31 AM PST by Ahban
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To: Ahban
you are closer genetically to any other human being on Earth than are two chimps living on opposite sides of the same mountain in Africa.

Granted. Now how much closer? The claim that chimps are 5% or 1.4% different than humans is not particularly informative without a basis for comparison.

Common Designer is just as valid a hypothesis, unless one dogmatically rules it out in advance regardless of the evidence due to a personal choice.

Common Designer implies common ancestry. I'll cop to a slight semantic stretch at this point, of course, but even assuming the existence of a common designer, it still shows that he/she/it/they made people out of monkey parts. The thing is, we have a clear time line for the emergence of primates. Work backwards in time along the fossil record and the skulls of our ancestors become increasingly ape-like.

In the meantime, the Designer Hypothesis is not rejected because of dogma, or anti-religious fervor, or because of powerful mind-control rays from hyper-intelligent, 7-dimensional guppies. It's rejected because of a lack of evidence on the one hand, and a lack of unique predictions on the other. Put together and it's hard to make much of a case.

We already have "something that could"- an intelligent designer.

But no evidence to support that hypothesis. I'm also going to contest that "intelligent" bit. A sophomore in any ME program in the country can propose a laundry list of structural and engineering improvements in the human body this "intelligent designer" fellow somehow overlooked. And this without even putting down their beer or looking up from the PS2.

The second group should be able to use stats to show how absurd is the idea of evolution in this case

Only if the second group was fully conversant with the initial conditions at the period in time when the glow-in-the-dark mice first appeared in the animal kingdom. Without that info, calculating statistical improbability it just guesswork with a slide rule.

47 posted on 02/07/2003 1:09:08 PM PST by Condorman (Life is a collection of low-probability events)
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To: Condorman
Hmmm. Your tagline on post #42 was "Fact-based crevo threads have the life expectancy of a glass hammer.)
"

That was clearly in response to our fact-based posts which immediately preceded it. Then it becomes clear (post #44) that the numbers make the evolutionary hypothesis untenable and suddenly, by post #47 (#45 even!), "calculating statistical improbability it just guesswork with a slide rule" unless intital conditions are fully known.

Within five posts you comepletly change your opinion as to the value of this debate. Why is that C-man?

Your claims that there is "no evidence" for the design hypothesis is as those who looked through Galieo's telescope and claimed they could not see the moons of Jupiter. The evidence SCREAMS design. The look at the numbers on this thread is just one tiny part of that.

Likewise with you claim that the Design Hypothesis makes no unique predictions. I posted a thread which gave a testable design model. It had lot's of predictions, but once again evos looked into the telescope and claimed to see nothing.

The EVO hypothesis has the very same problem with unique predictions as the design hypothesis. Most of the things it claims as support are really just as much evidence for common designer- shared DNA being a case in point.

As for your scoffing that any sophomore ME could suggest improvements on our design, I would say that it would be more a reflection of the ignorance and arrogance the ME rather than any weakness in the human design itself.

We are an engineering marvel unmatched by any of our works. If we knew more about how we are really put together, those presumed weaknesses would not look so weak. I saw a great example of how our 'backwards eye' was actually a brilliant innovation. I wish I could remember the details.

None of that matters though, because that is not what this thread is about. It is about the Human - Chimp gene gap and whether it is a gap that could have reasonably been crossed. Up until your tagline on #42, you thought this thread was about facts, by post #47, once it was clear the facts were not going your way, you now decide it is about "guesswork".

48 posted on 02/07/2003 1:45:23 PM PST by Ahban
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To: Ahban
Oh come on, Ahban, don't tell me you misread my post THAT badly!

Within five posts you comepletly change your opinion as to the value of this debate. Why is that C-man?

The chimp and the human genome can be directly compared for similarity. Unfortunately the comparisons are often reported as pure numbers and without the background, I don't know exactly what "5% similarity" actually means in real-world terms. Calculating statistical probabilities of events that have already occured, a popular ID/Creationist past time, is an exercise in retroactive astonishment. The odds, for example, that SOME guy wins the lottery are far greater than the odds that it's going to be THAT guy.

The evidence SCREAMS design.

Now whose bias is showing?

I posted a thread which gave a testable design model. It had lot's of predictions, but once again evos looked into the telescope and claimed to see nothing.

I recall seeing that thread in existence, but honestly don't remember actively participating. Got a link?

I would say that it would be more a reflection of the ignorance and arrogance the ME rather than any weakness in the human design itself...If we knew more about how we are really put together, those presumed weaknesses would not look so weak.

For humans, the knee, the spine, and male nipples immediately spring to mind. As do the pelvic structure of ceatceans and snakes, and the eyes of the golden mole. And I'm not even ME (Mechanical Engineer, for the lurkers). The human body exhibits sufficience; I would expect an intelligently designed organism to exhibit optimization.

Up until your tagline on #42, you thought this thread was about facts, by post #47, once it was clear the facts were not going your way, you now decide it is about "guesswork".

Again, chimp-human genome comparison studies are about fact. My comment about "guesswork" was in direct response to your statement regarding the ability of scientists 500 years from now to calculate the probability of the natural emergence of a rogue band of free-ranging, glow-in-the-dark mice. Not about chimp-human genome comparisons. My apologies if I was less than clear. (As an aside, I would be quick to point out that glow-in-the-dark mice would likely experience a significant predatory disadvantage compared to their non-luminescent brethren. A blinking, neon "Eat at Joe's" sign comes to mind for some reason... heheh...)

Regarding the "glass hammer" tagline, this thread has garnered almost 50 whole posts in a single week. Didja happen to notice that you and I are currently the only ones participating? The Russian silver fox thread suffered a similar fate. Now compare to the public policy debate threads. The Texas Tech prof thread, for example, was posted a day before this one and is almost up to 350 posts. Generally speaking, policy debates drag on forever, while the new discovery threads are subjected to a flurry of ID/Creationist drive-bys and are quickly abandoned. You are one of the few that actually stick around to hash out the facts, for which I do give you credit.

49 posted on 02/07/2003 3:19:28 PM PST by Condorman (Ignore the post; it's the TAGLINE that matters!)
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To: Condorman
Now compare to the public policy debate threads. The Texas Tech prof thread, for example, was posted a day before this one and is almost up to 350 posts.

Ahem, that's nothing; this Dini thread is up to 1142!

50 posted on 02/07/2003 4:24:43 PM PST by jennyp (http://crevo.bestmessageboard.com)
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