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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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To: Ahban
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.
No, 1 fixation every 3 months was for all types of mutation:
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.

10 million years / 1.26 million coding base pair differences = 1 coding fixation every 8 years. Then multiply that by how many coding differences are working towards fixation at any one time. 10 mutations simultaneously working their way means each mutation has 80 years available to fixate, 100 mutations = 800 years per mutation, etc.

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....

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.

Which link is that? Could you provide the url? I couldn't find any reference to cheetahs at the Hardy-Weinberg page from Kimball.

That's an interesting finding, but I want to see more information about how exactly they were comparing these 52 loci. Were they using gel electrophoresis, or did they do actual letter-by-letter sequencing of 52 genes? It doesn't seem too surprising that an inbred population would all look the same if you don't sequence the DNA letter by letter. IOW, I think there are lots of sequence differences among cheetahs that are under the radar of that study - cheetahs are not all exact clones of each other.

Here's something interesting I found at another cheetah page:

There are seven recognized subspecies of cheetah, distinguished by subtle differences in their coats. The most striking is the king cheetah with spots that have been modified into wide discontinuous bars.

How can there be 7 recognizable subspecies if they're all exactly the same? (aHA!)

Also on that page, it describes the cheetah's habits. It seems they're very mobile - in fact cheetahs can't be housebroken because they don't stay in one place in the wild, so they have no real "home territory" to keep clean. I suspect that African cheetahs (the only population that survived after the bottleneck 10,000 ya) were one of those species I described to g3k, where they were one big population instead of tribes that were securely isolated over time. So maybe cheetahs are an example of Hardy-Weinberg forcing stasis. (Unlike humans & chimps, who both stayed in relatively small, isolated groups where gene drift could work.)

51 posted on 02/07/2003 5:29:48 PM PST by jennyp (http://crevo.bestmessageboard.com)
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To: gore3000
#51 was meant for you, too. (As was #41, which I'm not going to let you ignore.)
52 posted on 02/07/2003 5:32:01 PM PST by jennyp (http://crevo.bestmessageboard.com)
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To: Condorman
(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.)

I'm assuming we're using 10 million years in our calculations instead of the more correct 5 million, for that reason.

53 posted on 02/07/2003 5:34:47 PM PST by jennyp (http://crevo.bestmessageboard.com)
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To: jennyp; Condorman
Which link is that? Could you provide the url? I couldn't find any reference to cheetahs at the Hardy-Weinberg page from Kimball.

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Polymorphisms.html#GeneticDrift

Condorman, I will take any credit you are willing to give. I am glad to hear that you do want to move forward with a mathematical model. The mouse thing was meant to be a tight analogy with our discussion of evolution vs. intellignet design. I was only trying to show that it is not necessary to reproduce the Creator in a laboratory in order to infer that non-random forces had been at work.

Since you have said that I misinterpreted and you DO think this thought experiment of ours has some value, it does not matter about the analogy. (Also as an aside, I thought the very same thing. Where could such critters prosper? Perhaps in the block crawl space under my house, where they could attract bugs to eat and no large predators can enter (well, maybe a snake.))

So I am being very generous here- whenever the numbers are in doubt, I am conceding the numbers to you two. Whenever there is doubt about how much of the genome is functional (i.e. is 'junk DNA really 'junk'', I think most of it is not, you think it is) I am conceding it to you. I am bending every step of the way and using your own numbers at every point.

So here it is : we are agreed that the minimum differences in mutations would require one fixation in the population's overall genome every three months, with one fixation in the coding regions every 8 years? Yea or Nay?

54 posted on 02/08/2003 8:02:17 AM PST by Ahban
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To: Ahban
So here it is : we are agreed that the minimum differences in mutations would require one fixation in the population's overall genome every three months, with one fixation in the coding regions every 8 years? Yea or Nay?

That works for me. In fact, since the whole "problem" is how to account for whatever differences there are, it doesn't really matter to me about the coding genes. So for me the supposed problem is in accounting for all the differences. (See? I'm generous too! :-)

55 posted on 02/08/2003 3:20:42 PM PST by jennyp (http://crevo.bestmessageboard.com)
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To: Ahban
we are agreed that the minimum differences in mutations would require one fixation in the population's overall genome every three months, with one fixation in the coding regions every 8 years? Yea or Nay?

If that's what it works out to be then sure.

The next step, I suppose, is to identify possible mechanisms for the change.

56 posted on 02/08/2003 3:33:40 PM PST by Condorman (Changes aren't permanent, but change is.)
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To: jennyp; Condorman
I wish every crevo thread had this spirit about it. This was no trap- I do not know what the answer to the next key question is either. Clearly, we need to know how long it takes for a mutation to spread throughout a population of humans and or chimps (with a reasonable estimate of population size for both groups during the time in question).

Note this is not quite the same thing as the cheetah question. I will grant you that the King Cheetah is a recent addition to the type, I suspect some of those others with more subtle coat differences are just the result of alleles that were already present in the one or two breeding pairs left during the bottleneck. Still- We don't need to know how long it takes for novel mutations to BEGIN in a population, we need to know how long it takes that gene to spread throughout the ENTIRE population.

In other words, if we could capture 100 cheetahs and look at their genes right now, the odds are that ZERO would have the allele for King Cheetah coating. That new mutation is only in a tiny part of the population. In this exercise, we are talking about 1.6 million coding and 42 million possible non-useful genes that are DIFFERENT in chimps and humans. Not different as in "some humans have a gene difference that every chimp lacks" but different in the sense that "EVERY human has this gene difference that every chimp lacks".

Let's start with population size. As a creationist, my position is that humans are introduced < 45K years ago, so I do not want to put words in your mouth on this. Please ping some evo help on this if you feel it is warrented to get a good estimate.

1) How big was the early population of humans and 2) How many population bottlenecks did humans go through (times when they were reduced to less than a 20 breeding members.

We need reasonable estimates for those two, then we can (I hope) wrap it up.
57 posted on 02/08/2003 4:41:29 PM PST by Ahban
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To: jennyp
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.

No. Let's look at how the original one was done:

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.

As can be seen, this was a base for base comparison. No adjustments at all being made. Let's continue with the article YOU cited:

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.

As can be seen, the original method did not take account of deletions which would put the DNA bases 'out of sync' after a while. This is why with greater knowledge of the genomes of both species (the complete sequencing of the human genome and some partial sequencing of chimps) Britten re-did his work. This time he took account of the deletions to more accurately match the genomes. That he 'refuted' his own work shows to me at least that there was good reason for him using this way of comparison as more accurate. (as to the article by John Pickerel whom I showed to be an evo hack with no credibility in post# 37 the less said the better).

As we have seen, interbreeding often is limited to the members of local populations. If the population is small, Hardy-Weinberg may be violated.

I am well aware of such statements being made by numerous evolutionists. I reject them because they contain numerous half truths. The first half truth (and a half truth is really a complete lie that because it contains and element of truth makes it more believable and thus a better sounding lie) is the implication that while Hardy-Weinberg can be violated in a small population, this makes it likely that a neutral mutation will take over the whole species from that blast off point is false.

Let's continue with the example of the population of a million in the species and let's say that the 'tribe' of 100 gets a neutral mutation and it spreads through it. Well, if the 'tribe' gets mixed into the general population (somehow, sometime, somewhere) then Hardy-Weinberg will be in effect again and those carrying the neutral mutation will be only 1/10,000 of the species and will remain so BECAUSE THIS MUTATION IS NEUTRAL. So again this neutral mutation will not take over the population or even become a significant part of the overall genome pool of the species. So this argument is bunk.

There is an even bigger problem though with these mutations becoming through a small inbred group a part of the genome pool of the whole species. It is a scientific fact that harmful mutations far exceed all other mutations. It is a scientific fact that inbreeding is harmful for the tightly inbred group. What this means is that the inbred group will become much less viable due to the inbreeding and that any neutral mutations within it will (if the group does not die off due to the harmful mutations) will dissappear when (or if) it joins the larger group and those harmful mutations show that the inbred group is less viable and less 'fit' than the main group.

What all the above amounts to is that you do need pretty close to 150,000,000 favorable mutations between man and chimp in just some 10,000,000 years of divergence (according to evolutionists). Problem is that we have not been able to find, in decades of experimentation a single such mutation creating the greater complexity needed to account for the differences between man and chimp.

58 posted on 02/09/2003 4:56:13 PM PST by gore3000
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To: jennyp
whistling, tapping fingers..

Sorry I have been kind of busy the last few days and was unable to respond sooner. I hope you enjoy my response just above. :)

59 posted on 02/09/2003 4:59:01 PM PST by gore3000
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To: jennyp; Condorman
Are you two busy, or do you just have no estimates? To determine if the differences between man and chimp are reasonably due to chance we need defensable estimates on two things:

1) How big was the early population of humans and 2) How many population bottlenecks did humans go through (times when they were reduced to less than a 20 breeding members.

We are having a good thread here. Let's move it to a conclusion.
60 posted on 02/10/2003 3:08:59 PM PST by Ahban (he who picks the terms wins the debate)
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To: gore3000
Thanks for the reply. (I'm busy too...)

No. Let's look at how the original one was done:

I thought my explanation in #41 was quite clear, and I can't make it any clearer: Britten's original study, by its nature, would never be able to detect sequence differences due to insertion or deletion mutations. The new technique can, and found an extra 3.9% difference in the sequences. But since a single insertion or deletion mutation can affect hundreds or thousands of base pairs with a single mutation, the extra sequence differences add a miniscule amount to the number of mutations necessary to account for them.

Which is why there are 42 million mutations separating us from the chimps, which caused 150 million base-pair differences.

As we have seen, interbreeding often is limited to the members of local populations. If the population is small, Hardy-Weinberg may be violated.

I am well aware of such statements being made by numerous evolutionists. I reject them because they contain numerous half truths. The first half truth (and a half truth is really a complete lie that because it contains and element of truth makes it more believable and thus a better sounding lie) is the implication that while Hardy-Weinberg can be violated in a small population, this makes it likely that a neutral mutation will take over the whole species from that blast off point is false.

You know, I'll bet that Hardy-Weinberg were two evolutionists! In fact, I'll bet they knew quite well that their equations were only valid for large populations.

Let's continue with the example of the population of a million in the species and let's say that the 'tribe' of 100 gets a neutral mutation and it spreads through it. Well, if the 'tribe' gets mixed into the general population (somehow, sometime, somewhere) then Hardy-Weinberg will be in effect again and those carrying the neutral mutation will be only 1/10,000 of the species and will remain so BECAUSE THIS MUTATION IS NEUTRAL. So again this neutral mutation will not take over the population or even become a significant part of the overall genome pool of the species. So this argument is bunk.

No, you're assuming the population of 1 million consists of 1 semi-isolated tribe of 100 and another mass of 999,900. I'm talking about a species that tends to live in tribes in the first place. So we're talking about a species of 1 million individuals who are split up into 10,000 tribes of 100 each. Every time the mutation gets introduced into a new tribe, it has just as good a chance of fixating within that tribe as it did in the first tribe.

There is an even bigger problem though with these mutations becoming through a small inbred group a part of the genome pool of the whole species. It is a scientific fact that harmful mutations far exceed all other mutations. It is a scientific fact that inbreeding is harmful for the tightly inbred group. What this means is that the inbred group will become much less viable due to the inbreeding and that any neutral mutations within it will (if the group does not die off due to the harmful mutations) will dissappear when (or if) it joins the larger group and those harmful mutations show that the inbred group is less viable and less 'fit' than the main group.

No, the scientific fact is that most mutations are neutral. You're thinking of the mutations that have some effect on the organism - they are mostly harmful. But virtually all of the harmful mutations aren't counted among the 42 million mutations that separate us from chimps anyway, since the proto-chimps & proto-humans who carried those mutations quickly died out. I think we can safely assume all those 42 million mutations were either neutral or beneficial. (Almost all of them neutral.)

As for inbreeding, you're now forcing yourself to argue that any species that habitually lives in tribes will die out! That's just absurd.

61 posted on 02/11/2003 12:46:56 AM PST by jennyp (http://crevo.bestmessageboard.com)
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To: Ahban
Are you two busy, or do you just have no estimates? To determine if the differences between man and chimp are reasonably due to chance we need defensable estimates on two things:

1) How big was the early population of humans and 2) How many population bottlenecks did humans go through (times when they were reduced to less than a 20 breeding members.

Hmmmm... I don't think they'll ever know something like that with any degree of specificity. How could they?
62 posted on 02/11/2003 12:48:41 AM PST by jennyp (http://crevo.bestmessageboard.com)
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To: Ahban
To determine if the differences between man and chimp are reasonably due to chance we need defensable estimates on two things:

See, here is where we start to disagree. There are several theories for population bottlenecks, none of them definitive yet. For example, see here for the theorized European bottleneck, or the recent FR thread on the Asian descendents of Ghengis Kahn, and I would tend to doubt (a prejudice, I grant) a 20-count human population anywhere but at the very beginning of the species.

The "Out of Africa" theory is, from what I've gathered, just a start to human population history. If we base this exercise on human population bottlenecks for gene fixation, then we are necessarily limited on the conclusions we can draw. I propose a different strategy: We KNOW that chimps and humans are different. The question we are trying to answer, I think, is how did that happen?

I think it would be more informative to identify, investigate, and expand upon the mechanisms of genetic variation. To claim that the chimp-human differences are due to chance is, IMO, to miss an investigative opportunity. "Chance" is not a mechanism. For that matter, neither is "Designer." Gene duplication and replication errors during meiosis and mitosis-- THOSE are mechanisms. The recent work on the role of virii in altering the genetic code is reported to be extremely interesting. For your side, if a Designer did the work, HOW did he do it, are we be able to distinguish "Designed" genetic change from that which occurs naturally, and if so, how would we go about doing that?

63 posted on 02/11/2003 3:16:28 PM PST by Condorman (You should enjoy seeing the population increase; it means you are superior to more people.)
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To: jennyp
I thought my explanation in #41 was quite clear, and I can't make it any clearer:

I did not say it was not clear, I said it was wrong. As I said, the proof of the pudding that the 5% is indeed the real genetic difference between man and chimp is that Britten, who had done the original study claiming the 1.5% or so, refuted himself. The question has always been about the genetic difference between the two. As I showed you also, the person who wrote the article you are following is a hack with no credibility. No legitimate scientist can say any longer that non-coding DNA is junk like that guy said.

You know, I'll bet that Hardy-Weinberg were two evolutionists! In fact, I'll bet they knew quite well that their equations were only valid for large populations.

Yup, Hardy, Weinberg, Fisher and Wright, the most famous figures in population genetics were all evolutionists. They worked for decades trying to figure out a way to get out of the problems posed by Mendelian genetics to the theory of evolution. They were pretty good mathematicians, but since they were lacking the scientific basis to apply their mathematical ideas they were very wrong. Specifically the problem came about with the discovery of DNA. The problem DNA posed was quite simple and quite awesome. It disproved for good the idea that one single mutation could effect a great change in function. With a single base pair being the result of a mutation, new species from one mutation became totally impossible. Evolution had always assumed that just one change could effect a large change in a species. The population geneticists, working on that assumption believed that a single mutation could have a large enough change in the selectivity to overcome the stasis of Hardy-Weinberg. However, with DNA showing that you would need numerous favorable mutations to achieve any significant change. These mutations would be first of all be subject to being unfavorable and kill the organism, secondly be neutral and be very likely to die off soon after arising, and the few, few favorable ones, because they had such a low or non-existent selective value until many more mutations would be added to it, would also face a high degree of chance of being lost.

What all the above means in essence is that since mutations start in a single organism:
1. Hardy-Weinberg makes the spread of mutations very unlikely to the whole population.
2. Neutral and slightly favorable mutations (those with a low selection coefficient) are likely to not only not spread, but to die off completely within a few generations.
3. And here's the kicker - because due to DNA insuring that a single mutation cannot have any large effect on an organism, all mutations are essentially neutral mutations and likely to die within a few generations.

The only 'out' from the above problem proposed by evolutionists (like you are doing here), is the small inbred population. There is a good scientific reason why calling someone an 'inbred' is an insult. Inbreeding causes harmful mutations to thoroughly make the inbred population less viable. That's a scientific fact and there is no talking their way out of it for evolutionists.

64 posted on 02/11/2003 6:50:18 PM PST by gore3000
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To: Condorman; jennyp; gore3000
Dog-gone it, there you go again. Both of you side stepped any attempt to put this thing to numbers, even a reasonable estimate. C-man, you are now apealing to speculation about virii making monkies into men, at least that is what I get from your vauge response. Well, you at least said you doubted there was ever a bottleneck down to 20 breeders except at the start. That was better than our friend jenny, who did not hazard a guess.

Since you guys seem relectant, by default the crevo will put some numbers in. As I have been doing this whole thread, I will be outrageously generous to you in my assumptions.....

I will say there have been ten, no TWENTY OCCASIONS where the human population has super-bottle necked. A small group survied and ALL the rest died off. Each time, this group has had a hundred, no wait, a thousand, ok, as long as I am going crazy here, TEN THOUSAND mutations that were not present in any of their ancestors fixated throughout their whole population.

I must be insane. There is no way the population bottlenecked that much, and the number of mutations fixated is far too high. Even with a small population being a POSSIBLE exception to the Hardy -Weis. Law there is not REQUIREMENT that the mutations take hold, yet here I am saying TEN THOUSAND of them took hold at all 20 bottlenecks. Tell you what, just to get plain silly about it I will say it was TWENTY THOUSAND mutations that got fixated. Way too high of course.

If we total that up we get 20 X 20,000 = 400,000 mutations. That is a lot, but it pales before the 1.42 million we need in the coding regions alone. Add to that the fact that this is not for the coding regions, but the whole genome. Another words, we must compare the 400,000 mutations likely (and that only with fantastically pro-evo assumptions) to the minumum of 42 million observed (using your numbers again).

I can see why you guys are reluctant to give numbers. gore3000 points out that certain conditions are needed before neutral mutations can spread in a population. When you try to model human-chimp differences based on the laws of genetics that we know, the gene differences fall far outside what would be expected.

C-man is forced to appeal to some mystery virus. Is that really any more rational than appealing to a Designer? Is saying "I don't know" but I know evolution did it any less a faith based statement than what I hold true?

We have a lot in common, we are all men and women of faith. I invite you to have faith in the God of the Bible. It may not be the choice you make, but the reason for that choice will have nothing to do with its rationality.
65 posted on 02/11/2003 8:05:40 PM PST by Ahban (he who picks the terms wins the debate)
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To: Ahban; Sentis; Nebullis; jennyp
When you try to model human-chimp differences based on the laws of genetics that we know, the gene differences fall far outside what would be expected.

And all that tells us is that we probably don't know everything about the mechanisms of genetic variation yet. This in no way strengthens any other particular hypothesis.

C-man is forced to appeal to some mystery virus.

You are appealing to incredulty to make your case. I bring up viral action as a mechanism of variation. "Mystery" is YOUR addition. Sentis is the one who originally referenced the recent work in virus-induced variation, so I am pinging him to the thread. I believe Nebullis may also be able provide some information on the topic.

Chimps and humans are genetically different. I'm saying let's try to figure out how it happened. 42 million differences? Great! First, are we sure, and second, how do we get there from here (or, how did we get here from there)? I read your posts as suggesting that a natural explanation is impossible.

66 posted on 02/11/2003 9:01:45 PM PST by Condorman (Everything is transitory, including the state of being transitory.)
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To: Condorman; jennyp; Ahban
You've laid out reasonable facts. I'll add a few more.

The mutational burden, so to speak, of the human-chimp difference doesn't rest on the human branch alone. The chimp branch also diverged from a common ancester. So, the numbers shrink further.

Are those numbers reasonable from what we know about mutation rates in humans, today? Yes. Researchers studied the mutation rate at a number of different loci and found that these rates agree with the rates implied by the human-chimp genetic difference.

67 posted on 02/12/2003 7:26:57 AM PST by Nebullis
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To: Nebullis
Thank you for the info. Do you happen to have off-hand any specifics (a link would suffice) on the mutation rate research you mentioned?
68 posted on 02/12/2003 10:43:24 AM PST by Condorman (I'm not lazy. I'm researching inertia. The buzzards are observers.)
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To: Condorman
While i do know a bit about viruses and their role in evolution I am no longer discussing this topic with crevos. If they are so prone to Lying to make their point I see no reason to waste my time explaining how evolution works just to be insulted over and over because I don't call on their imaginary Gods to explain away everything.
69 posted on 02/12/2003 1:49:04 PM PST by Sentis
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To: Sentis
I understand your frustration. While I would generally tend to agree with you, Ahban appears genuinely interested in the subject. In that spirit, am inclined to engage him.

Regarding the role of viruses in alteration of the genome, I referenced the recent research your brought up on a previous thread. Ahban referred to my comment (rather disparagingly, I'm sad to say) as an appeal to a "mystery virus." As I originally gleaned the reference from you, I was hoping you might be willing to provide more information than I was able.
70 posted on 02/12/2003 3:28:05 PM PST by Condorman (Error reading DNA.SYS! (A)bort, (R)etry, (M)utate?)
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To: Condorman
The mystery virus isn't much of a mystery as it is still in existence in our own genetic code. These viruses attach themselves to our DNA and actually become part of our own DNA code. This creates even more variability in the code than is possible through selection alone.
71 posted on 02/12/2003 3:37:49 PM PST by Sentis
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To: Nebullis; Condorman
The mutational burden, so to speak, of the human-chimp difference doesn't rest on the human branch alone. The chimp branch also diverged from a common ancester.

True, and Condorman pointed that out. jennyp already had that one covered though, she is using 10 million year divergence instead of five million to take into account that you have two groups that are diverging. All of these estimates that we are making have that factored in.

Along with "C", I will be glad to take a look at any link you have on human mutation rates. I would especially like to know about the FIXATION of such mutations in the population.

I don't mean the fixation of some existing Alelle in some sub population, but a truly novel mutation establishing itself in a group. That is what we need to know, not just the mutation rate, but the novel mutation rate, and not just the novel mutation rate, but the fixation rate.

72 posted on 02/12/2003 4:47:06 PM PST by Ahban (he who picks the terms wins the debate)
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To: Condorman; Sentis
I will be delighted to look at any information on viral corruption of gametes that Sentis can provide. If the case can be made that this can close the apparent DNA gap then let's get out with it.

If I can appeal to a Designer to explain the gene gap I guess its only fair that you can appeal to a virus. Still, it should be a lot easier to test whether virii are up to the job than a Desinger who is outside the three'D plus time universe.
73 posted on 02/12/2003 7:36:33 PM PST by Ahban (he who picks the terms wins the debate)
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To: Ahban
here are a few web sites to peruse about the viruses role in evolution.

http://www.microbeworld.org/htm/aboutmicro/microbes/types/virus.htm

http://www.discover.com/nov_02/breakvirus.html

and here is one about the role of testosterone in human evolution which has little to do with what we are talking about but is interesting as i ran into it while researching this topic.

http://www.naples.net/~nfn03605/dheaandr.htm




The amazing thing about viruses and evolution is that they may even be the key player in evolution among related species. They can encode the hosts dna into their own and transpose that dna to other cells or even into other animals. This means that for example a virus could take the dna information that expresses for blue eyes from one human and infect another human without that info encoding some of his cells with that information. Does this mean that the second host will express blue eyes in his offspring?probably not. What it does mean is that the virus has transposed that info into another being and may become active one generation or a hundred generations later.

In the Human/Chimp case something else is probably active in our differences in species. Human's have a linked chromosome and chimps do not. Which accounts for a massive difference in Humans and chimps. The linked chromosomes in Human's can be possible because a virus at some point linked the two creating a single chromosome in one family of organisms that evolved into humans. The Creatures without the linked chromosomes became chimps.

74 posted on 02/12/2003 8:38:35 PM PST by Sentis
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To: Ahban
All of these estimates that we are making have that factored in.

Molecular clock estimates range from 5-8 million years from the human-chimp ancestor. A conservative estimate of 5 million years ignores the recent circa 7 million yo hominid find. It doesn't change much regarding the estimates of about 1% difference in coding regions between chimps and humans. That difference is perfectly reasonable with what we know about mutation rates.

I would especially like to know about the FIXATION of such mutations in the population.

I invite you to do your own homework. You might not be aware, but within that percentage difference, neutral substitutions, that is, mutations that are not fixed, are included.

75 posted on 02/13/2003 6:27:43 AM PST by Nebullis
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To: Nebullis
Thanks for the info!

I figured you would be the one to know.
76 posted on 02/13/2003 8:03:59 AM PST by Condorman (Tagline contributions may be tax deductable.)
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To: Condorman
I should add that variation in the human gene coding regions is estimated at 0.1%. It may be similar for chimps. The polymorphisms accounting for this variation are not fixed and aren't restricted to neutral mutations.
77 posted on 02/13/2003 9:26:30 AM PST by Nebullis
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To: balrog666
"Then they won't show up on this thread."

Here I am. :)

It all boils down to what one chooses to believe. Some scientists claim they have always 'known' something, then when questioned, you find out they only assumed it.

78 posted on 02/13/2003 10:25:22 AM PST by MEGoody
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To: Nebullis
Molecular clock estimates range from 5-8 million years from the human-chimp ancestor. A conservative estimate of 5 million years ignores the recent circa 7 million yo hominid find

That is a lot to hang on one find that may or may not have that age. I am using numbers provided by jennyp and agreed to by Condorman. They will attest I'm sure that I have been more than fair on the numbers, giving in to their own numbers at every turn.

It doesn't change much regarding the estimates of about 1% difference in coding regions between chimps and humans. That difference is perfectly reasonable with what we know about mutation rates.

I don't see where it is reasonable. I know some mtDNA regions are hyper mutational, but not chromosomal DNA. I don't see how the observed difference squares with the H-W laws we have been discussing on this thread. Even the outrageous pro-evo assumptions I made generate a differece of less than 1% of the observed differences (400K vs. 42 million). And its not 1%, its AT LEAST 1.4% (a 40% difference) in useful genes alone even if all of the non-coding genes are true junk, which is unlikely.

I invite you to do your own homework

Since when is supporting evolution MY homework? The assignment falls to those who proclaim evolution. My homework has convinced me that the scenarios needed to close the gene gap by known natural causes in the time allowed are unreasonable. You were invited to this thread by C-man in hopes that you had some hard data that indicated otherwise.

If you in fact have such data, you might as well present it. If not, I think it is fair for thread participants and observors to conclude that the chimp-man common ancestor hypothesis is unlikley.

within that percentage difference, neutral substitutions, that is, mutations that are not fixed, are included

OK, let's make sure we are meaning the same thing by our terms. I consider a gene pattern "fixed" when it is found throughout a population, regardless of whether it is neutral or helpful.

If you are arguing that all 1.42 million fixed differences are favorable rather than neutral then you are arguing gore3000's original position. It was one of the things that I gave in on, as jennyp argued that the 1.42 million represented fixed neutral as well as favorable mutations.

If there are that many FAVORABLE mutations fixed, then there must have been thousands of times that many neutral ones. That makes the chimp-man scenario even more unlikely.

79 posted on 02/13/2003 6:15:46 PM PST by Ahban (he who picks the terms wins the debate)
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To: Sentis
The testosterone thread was the best of those three. I did not find much besides speculation that second one. The first was a primer that did not much speak to our issues.

I see in theory how viral transfer, if done to gametes, could speed evolution by reshuffling what is already there. That does not speed up the mutation rate though. Presumably, whatever virii were doing five million years ago is what they are doing now. If they changed our genome fast then, they should change it fast now.

If we know the rate mutations (from radiation, chemicals, virii or whatever source) are being fixed into the entire human population then we can bounce that against number of known differences to get a prediction of the rate of change required.
80 posted on 02/13/2003 7:03:02 PM PST by Ahban (he who picks the terms wins the debate)
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To: Ahban
If you are arguing that all 1.42 million fixed differences are favorable rather than neutral ...

The mutations include favorable, neutral, and unfavorable ones. What's more, they include polymorphisms, or unfixed mutations. Those polymorphisms include favorable, neutral, and unfavorable mutations.

81 posted on 02/13/2003 7:26:23 PM PST by Nebullis
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To: Ahban
The problem is we don't know the rate of mutation in any species as it isn't set . It is a random variable and its speed is set by a variety of factors. A virus, a random mutation, or a cancer can cause all sorts of mutations but when all factors act in a short time (several generations) then mutations occur at a higher rate. You also miss a main point Viruses not only reshuffle what is already there they can add genetic material from their own DNA or carry DNA from other creatures.They can also link genes in different ways.

In fact I would even go so far as to suggest if Christians are hunting for GOD they look toward the lowly virus as the architect of most higher lifeforms today. :)

Again rate of mutation is due to environmental factors that cause mutation when all the factors are working at once mutation occurs quickly but when a person says quickly it could mean hundreds or thousands of years.

As you can see no rate of change can be set. If we know all variables that may be possible. I however doubt we as scientists know all factors that can cause mutation yet. The Viral factor in evolution is brand new and there are even more cutting edge hypothesis that may or may not change what we already know.


What kind of links are you looking for I placed links that are easy to understand rather than technospeak that the average reader would fall asleep over?
82 posted on 02/14/2003 6:35:58 AM PST by Sentis
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To: Sentis; jennyp; gore3000; Condorman; Nebullis
I agree that we have a lot more to learn about what virii have done to the genome, but that also means it is not reasonable to attribute what many regard as God-like powers to them.

Let's approach this another way. I have gone with ya'lls numbers every step of the way to make it fit. I have not asked any of you to budge a bit even though gore3000 makes a good case that your numbers are suspect.

If we look at the total number amount of difference in the humane genome then maybe we can find the average human mutation rate REGARDLESS if it was caused by radiation, virii, or whatever. It then does not matter how the mutation occured- it takes virus and every other kind of mutation into account. We can then compare that to human-chimp differences and see how likely it is that they split.


Let me show you what I mean: I will not do your homework for you, as some have suggested, but I will do a sample problem for you. I will pretend like I am on your side, and generate some numbers that supports your case.....

A study by Doritz found eight base pair differences out of 397 studied from mtDNA from ethnic groups around the world. Using this study, we can calculate that there is about 2 percent variablity in this hyper-mutational region of mtDNA (8 /397= .02).

Does all of the human genome vary by this amount? IF the mutation rate of this region were applied to all CHROMOSOMAL DNA then a 42 million bpd divided by .02 equals an expected humane genome size of 2.1 billion base pairs. That number of base pairs and higher means that variablity in the human genome can account for it. As one goes lower than that number, the idea that natural factors alone are responsible goes down.

Compared to the actual count of 3 billion bp, you are well within the ballpark of saying the differences can happen as a result of naturalistic mechanisms.

OK, end of Darwins-advocate mode.

The only catch in the above is DOES TOTAL CHROMOSOMAL variability in humans equal or exceed that 2% figure I cited? NO. I don't know what the real difference is though. How much % wise do we all differ from one another in our total CHROMOSOMAL DNA? How do our 42 million (or 150 million using g3ks calculations) bpd's from chimps compare to the number of pbd we have from one another?

If we evolved, shouldn't that calculation give us the average chimp-human mutation rate? Conversely, if we are super-similar to one another compared to our differences with chimps, wouldn't that imply that WE DON'T mutate fast enough to explain the difference?

Do any of you have this information? I invite any of you to plug the real number (not the 2% figure I used, but the real abount of %bp difference in the human genome) into the process I have outlined above and let's see what the numbers show us. Any takers?

If not, does my brainstorm example lead you into any ideas as to how you could model mathematically the reasonableness of the man-chimp connection?
83 posted on 02/15/2003 12:36:28 PM PST by Ahban
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To: Ahban
How much % wise do we all differ from one another in our total CHROMOSOMAL DNA?

Isn't this identical to the point I made way back in post 45?

84 posted on 02/15/2003 12:46:00 PM PST by Condorman (Never send a monster to do the work of an evil scientist.)
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To: jennyp
Interesting, polyploidy events could explain how mutations which would normally express themselves in a deletrious manner, because of two chromosomes, would not show up because of the extra copies of the gene. So this could allow for a rare beneficial mutation while still maintaining what you still had. You wouldn't go backwards in this scenario, but rather always upward, to more and more complexity, always maintaining what you had gained before because of the extra copies a polypoloidy event would give. Fascinating!
85 posted on 02/15/2003 12:53:36 PM PST by realpatriot71 (legalize freedom!)
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To: Condorman
Not at all. At 45 I thought you were running away from trying to get meaningful numbers, even though you had commented that the original post was "fact based" when you thought those man-chimp numbers were in your favor. I understood your sudden reluctance to acknowledge the value of mathematical models as the result of your foresight that taken to their reasonable conclusion, the numbers don't support the evolution of man.

A couple of posts later you said I had misread you on that, and I took you at your word.

I hope you are not going to the position that I presumably mistakenly attributed to you back on #44. If the post does represent a "fact based" study, then number estimates on man-chimp genomes are fair game.

I am trying to take these numbers to their logical conclusion, practically begging any and all of you to present your models as I have mine. Rather than attempt to refute my numbers based on fact- which you cannot do since I have used your own numbers at every step of the process, I see a desire to move away from any attempts at measurement. Is that "science"?

I hope I am "misreading" you again. You don't expect us to accept the "science without numbers" mind-set that resists any attempt at quantification?

That can't be your position. It is not a rational one. It is PURE FAITH beyond that of my position that God made man. I am offering mathematical models to support my contentions, whilst I have been offered nothing in return but hypotheticals that are to be accepted on faith.

If my models are flawed, point out the flaws- I have been very reasonable throughout this entire thread about accepting numbers from your side. Don't just side-step the whole issue of quantifying the probability of the evolutionary hypothesis, offer your model in return.
86 posted on 02/15/2003 1:55:24 PM PST by Ahban
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To: Ahban
At 45 I thought you were running away from trying to get meaningful numbers, even though you had commented that the original post was "fact based" when you thought those man-chimp numbers were in your favor.

Which thread are you reading, man?

I understood your sudden reluctance to acknowledge the value of mathematical models as the result of your foresight that taken to their reasonable conclusion, the numbers don't support the evolution of man.

Never said that. I wanted to establish a baseline. If chimps are 95% the same a man, what does that mean? How does that compare to intra-human genome comparisons? How close are humans to, say, goldfish? Without any kind of reference point, 5% is a meaningless figure.

I understood your sudden reluctance to acknowledge the value of mathematical models as the result of your foresight that taken to their reasonable conclusion, the numbers don't support the evolution of man. A couple of posts later you said I had misread you on that, and I took you at your word.

Once again, here is the context of that remark.

I am trying to take these numbers to their logical conclusion, practically begging any and all of you to present your models as I have mine.

Where have you been? We have! Sexual reproduction, gene duplication, transposition, and viral action have all been presented and identified as mechanisms for genetic modification. You sought to dismiss virii by referring to my remarks as "C-man's mystery virus" until Sentis expounded on the concept, but have since been content to let the matter drop. Nebullis appeared and made note of the fact that mutation rates appear to be consistent with the observed genetic differences between chimps and man given the time frame.

But here's the rub, even if those mechanisms are shown to be inadequate, this IN NO WAY provides support for a designer. Your only argument at the point appears to be "What we know can't account for the changes, it must have been the Designer." What you forget is that unless we have evidence to the contrary, we have to exhaust all the possible natural alternatives before a Designer might be considered.

I made the same point in post 63 and concluded with this question: If a Designer is responsible for the chimp-human divergence, how did he do it, and would we humans be able to distinguish Designer-induced genetic changes from those occuring naturally? You claimed that I'm attempting to sidestep the issue.

I'm sorry, but I think I'm starting to lose interest in this thread. I do appreciate your efforts, but your responses indicate that you don't appear to be comprehending the points I'm trying to make. Maybe I'm not being clear, maybe you don't understand, maybe it's a combination of the two. Whatever the case, I seem to be spending more time regurgitating our conversations than making any progress forward.

87 posted on 02/16/2003 3:05:20 PM PST by Condorman (I get my monkeys for nothing and my chimps for free.)
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To: Condorman
From this thread:


88 posted on 02/16/2003 3:10:14 PM PST by Condorman
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To: Condorman
I agree that it is time for this thread to come to an end. It is clear that I am not going to get what I have been asking for. Good luck in the future.
89 posted on 02/16/2003 7:29:45 PM PST by Ahban
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Human Ancestors Went Out Of Africa And Then Came Back... [1998]
ScienceDaily | Friday, August 7, 1998 | adapted from New York University materials
Posted on 12/17/2007 8:37:11 PM EST by SunkenCiv
http://www.freerepublic.com/focus/f-chat/1940963/posts


90 posted on 12/17/2007 6:14:04 PM PST by SunkenCiv (Profile updated Monday, December 10, 2007____________________https://secure.freerepublic.com/donate/)
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