Genome Evolution | First, a Bang Then, a Shuffle

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.

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.

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.

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.

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.

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.

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".

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.

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.)

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?

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.

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.

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