Creation & EvolutionForum for the discussion of this important topic. This forum is open to non-believers. There is a Christians-only forum in the Christians-only section too.
I'll reply to other posts when I have a chance. (I'm pretty busy at the moment, and I'm typing with only nine fingers for the next couple of months, which slows everything down.)
Aw. What happened to the tenth?
Originally Posted by Zaius137
Not to confuse matters to much one aspect of the chimp human DNA comparison seems to have created a mathematical contradiction as such. The contradiction concerns the human and chimp “Y” chromosome. Now as I understand it a study from MIT came out to say that the Y-STR variation is mutating faster than expected, this could be a huge understatement. (wi.mit.edu/news/archives/2010/dp_0113.html).
Based on my skim-reading it, that paper was not about STRs. It discusses gene content and rearrangements in large-scale repeats, but STRs (a.k.a. microsatellites) are repetitions of just a few nucleotides. In case I skimmed too superficially to catch something important, I also searched the paper for "str" and "repeat", but it didn't seem to mention STRs at all.
Fine except that if the human Y-STR mutation is assumed to be high it dropes the estimate to the “Y chromosome ADAM” quote:
Age estimates vary overall between 6,530 years and 535,755! It is obvious that fast/medium mutating markers provide unbelievably small age estimates (most of them are less than 20 thousand years). However, if we limit the analysis to slow mutating markers, most age estimates are in excess of 300,000 years!
Hey as a creationist I like that first number… “6,530 years”….
You can like that number, but if you decide to go with any of the numbers at all, you missed the point of the whole post. Which is, I'll quote, that "age estimates about Y-chromosome Adam using Y-STRs are basically useless".
Thanks for the link, BTW. It was an interesting read. I hadn't known that we had such a big mess in Y-Adam age estimates.
__________________ "There is much we do not understand about the history of life, and the same will be true of our grandchildren. But, then, if we knew all there was to know, scientific interest would cease. Textbooks may portray science as a codification of facts, but it is really a disciplined way of asking about the unknown." - A.H. Knoll, Life on a Young Planet
"[G]ood and evil are names for what people do, not for what they are." Philip Pullman, The Amber Spyglass
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Since I do not have the ability to link documents directly as of yet there are some problems with my citations. I thought the article I used mentioned specifically the Y-STRs… But Could Y-DNA term be used as a more general reference covering the Y-STRs implicitly?
"You can like that number, but if you decide to go with any of the numbers at all, you missed the point of the whole post. Which is, I'll quote, that "age estimates about Y-chromosome Adam using Y-STRs are basically useless"."
Are they basically useless… It does seem that the author is trying to put some distances between him and the Y-STR (short tandem repeats) variance. From my limited understanding the full Y-DNA haplotype comes from two results of the Y-STRs and UEPs as it applies to genealogy. Now the Y-STRs are prone to mutation much more easily than UEPs. Aren’t The Y-STRs the group to look at to gage fast mutation? But isn’t the author implying that the Y-STRs are not as relevant because of the expected 200k year frame normaly accepted by evolution? But if indeed the Y-ADAM lived only 6k years ago the Y-STRs should hold more importance… maybe?
But the wider question still begs an answer. With the demand that the Y-human chromosome morph so much as to show a divergence from the chimp over 6my, how is it possible to accommodate both the slower(200k evolution assertion) and the faster(chimp/human divergence) mutation rate at the same time? If putting aside the Y-STR point for the moment is acceptable.
Last edited by Zaius137; 24th September 2011 at 09:52 PM.
Since I do not have the ability to link documents directly as of yet there are some problems with my citations. I thought the article I used mentioned specifically the Y-STRs… But Could Y-DNA term be used as a more general reference covering the Y-STRs implicitly?
Well, Y-DNA includes Y-STRs obviously, but if we are discussing STRs specifically, then using a general term like Y-DNA just confuses things.
Are they basically useless… It does seem that the author is trying to put some distances between him and the Y-STR (short tandem repeats) variance.
He does say that he doesn't believe the very low estimates. But he doesn't seem too fond of the highest numbers, either.
From my limited understanding the full Y-DNA
haplotype comes from two results of the Y-STRs and UEPs as it applies to genealogy. Now the Y-STRs are prone to mutation much more easily than UEPs.
Sorry, what does UEP stand for?
Well, yes, the haplotype is a combination of various things, but the Dienekes blog clearly discusses STR-based age estimates.
Aren’t The Y-STRs the group to look at to gage fast mutation? But isn’t the author implying that the Y-STRs are not as relevant because of the expected 200k year frame normaly accepted by evolution?
If you're talking about the blog article, no. Y-STRs were deemed useless because they do not agree with each other. That suggests that they are not reliable gauges of divergence time.
Since there is only one true Y-Adam for any given population, and this guy obviously lived at only one time, reliable markers should all give the same age. Instead, you take different ones and get wildly different age estimates. That suggests that something is wrong with at least some of your markers. Something other than their age and their estimated mutation rate is contributing to the results. Could be that the mutation rates changed over time, could be that you are getting lots of undetected back-mutations in fast-evolving STRs; I don't know all that much about the possibilities for this type of marker.
But if indeed the Y-ADAM lived only 6k years ago the Y-STRs should hold more importance… maybe?
Yeah, but based on that blog post, we just don't know when Y-Adam lived. Or didn't, at the time of writing.
But the wider question still begs an answer. With the demand that the Y-human chromosome morph so much as to show a divergence...
Every pair of sequences that differ even by a single base shows "a divergence". Did you want to say "this much divergence"?
... from the chimp over 6my, how is it possible to accommodate both the slower(200k evolution assertion) and the faster(chimp/human divergence) mutation rate at the same time? If putting aside the Y-STR point for the moment is acceptable.
They refer to different things. Large-scale rearrangements, SNPs and microsatellite variation all obey different rules, so there's no reason they should occur at the same rate. As we've seen, even within one category there is considerable variation.
(Is that chimp-human mutation rate faster when you compare STRs, anyway? Are there comparable chimp and human STRs on which it could be measured at all?)
__________________ "There is much we do not understand about the history of life, and the same will be true of our grandchildren. But, then, if we knew all there was to know, scientific interest would cease. Textbooks may portray science as a codification of facts, but it is really a disciplined way of asking about the unknown." - A.H. Knoll, Life on a Young Planet
"[G]ood and evil are names for what people do, not for what they are." Philip Pullman, The Amber Spyglass
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I know your opinion of the “Wiki” is not a favorable one but it does make a conclusion that seems to coincide with the article from "uncommondescent.com/intelligent-design/a-simple-statistical-test-for-the-alleged-99-genetic-identity-between-humans-and-chimps/" namely the prediction of a 70% found in the “Wiki” and the 62% found in that article. How could I justify your comments criticizing the article? I would like to review these supplemental materials to verify your claims. Can you give a link?
The two estimates of relatedness do not coincide; in fact, they are completely inconsistent with one another. To understand why, you have to understand what is being measured in the various estimates of genetic divergence.
In the case of the 62% value that you cited earlier, what's being measured is the fraction of 30-base-pair segments that are identical between the two species. Why exactly one would want to measure this is a good question. There might be practical reasons for calculating this, e.g. you are doing some kind of large-scale test on the genome that uses 30-base-pair primers, and you want to know how well the assay will work if you use primers you designed for human DNA on chimpanzee DNA. As a measure of genetic divergence, it's simply bizarre -- why do 30-bp identical segments matter? You'll get wildly different answers if you use 100-bp or 10-bp segments, so why choose 30-bp?
Then there are the estimates of divergence in the chimpanzee genome paper. These include: 1) 1.23% of sites have had a single bp substitution in one lineage or the other; and. 2) another 0.17% of sites have had an insertion or deletion in one of the lineages (amounting to ~1.5% unique sequence in each genome). So the combined estimate is that ~1.4% of sites should differ between the species. To compare this estimate with the 30-bp one, we just have to calculate the probability that a 30-bp stretch has zero differences if on average 1.4% of sites are different. If the differences are randomly distributed, that's (1 - 0.014)^30, or 65.5%. In other words, if the estimates in the paper are right, then the corresponding 30-bp value should be 65.5%, which looks awfully similar to the value that was found, 62%. So in fact, the chimpanzee genome divergence estimate is in good agreement with the (quite peculiar) 30-bp estimate.
Finally, there is the Wikipedia estimate of 70%. This one is impossible to assign a meaning to, since it consists largely of a series of blunders, rather than estimates of anything real. The Wikipedia article starts by noting that the chimp genome paper estimates were based on 2.4 Gb of aligned sequence. Since the human genome is 3.1 Gb long, this leads to the conclusion that only 2.4/3.1 or 77% of the genomes matched, with the rest counted as divergent. The article then adds other differences to that. This conclusion is, well, dumb. Only 2.7 Gb of chimpanzee genome was even sequenced successfully, so the maximum that could have been aligned would have been those 2.7 Gb, even if the genomes were identical. The first supplementary note (linked above) describes what happened to the remaining 0.3 Gb that didn't align. 0.24 Gb could be aligned, but the alignments were to many places in the human genome, so the sequence was discarded. This is perfectly sensible, since the bulk of this is certainly bad assembly in the chimpanzee genome, and there's no point in making a comparison using bad pieces of assembly. Some of this poorly aligning sequence might represent multiple rearrangements of one or both genomes, but even if it does, there is no reason to think that the pieces of sequence would themselves be any more diverged than the rest of the genome. Finally, there was 0.09 Gb of sequence that didn't align at all. Again, a small part of this might be real sequence that is unique to the chimpanzee genome, but it also includes all kinds of other junk, including sequence that's present in the human genome but that hasn't been assembled; given the small amount of sequence reliably found in insertions/deletions, it is unlikely that much of it is really unique chimp sequence.
So the great bulk of the divergence claimed in the Wikipedia article is fictional. Of the rest, some is the divergence reported in the paper, and some is double-counting the same differences found in the main genome paper and again in a supplementary paper. Overall, the estimate is complete garbage.
However some evolutionary researchers also suggest that other evolutionists do not know what they are talking about.
Evolutionary researchers suggest that other researchers don't know what they're talking about all the time. That's what scientists do. With extremely rare exceptions, however, they do not disagree about the basics of evolution.
Evolutionary scientists have jumped the fence eg John Sanford evolutionists turned YEC and there are plenty of them. These are appropriately qualified scientists that no longer see any sense in evolutionary theory. So any insinuation that all creationists are ignorant of science is a false and misleading line.
Sanford is not appropriately qualified as an evolutionary scientist. He was an expert in manipulating plant genomes, and has no background in evolutionary genetics. As a result, he makes pretty basic mistakes when he tries to use that field to attack evolution.
Look to all the chatter here amongst evolutionists discrediting and debating research. It is as clear as mud.
Sure, if you don't know a field, it can be hard to tell what is well established and what is controversial. So you have a few choices. You could learn about the field yourself, but that's a big job. You could find official statements of what the scientific consensus is: review articles, statements by official scientific bodies. Or you choose to believe whatever fits your religiously motivated prejudices. Which choice do you make?
"Schwartz and Grehan contend in the Journal of Biogeography that the clear physical similarities between humans and orangutans have long been overshadowed by molecular analyses that link humans to chimpanzees, but that those molecular comparisons are often flawed: There is no theory holding that molecular similarity necessarily implies an evolutionary relationship; molecular studies often exclude orangutans and focus on a limited selection of primates without an adequate "outgroup" for comparison; and molecular data that contradict the idea that genetic similarity denotes relation are often dismissed." Humans More Related To Orangutans Than Chimps, Study Suggests
Yes, I'm familiar with that paper, and with that argument. This is so far into the fringe that it's pretty much straight crackpottery. There are tens of thousands of geneticists in the world, and many thousands of other kinds of biologists. Some of them are going to hold some very odd ideas indeed. Again, do you choose to highlight the 99.9% of biologists who agree that chimpanzees are our closest relative, or the 1 in a thousand who disagrees?
Also, what does any of this have to do with the rest of the thread? Just trying to throw a lot of dust in the air is not a positive contribution.
Evolution is to blame. After a one-day retreat (i.e. a day-long meeting) of the Boston Evolutionary Genomics Supergroup, Shamil Sunyaev convinced me that I should play volleyball, since they were short of players. And volleyball is all fun and games until someone tears a tendon trying to return a shot.
Quote… “Overall, the estimate is complete garbage.”
Wow there is a lot of supplemental reading here. Just started skimming the articles but maybe you can point to one in particular that formed your opinion about the “Wiki”?
About the article that found we only were 62% not 98% the same as chimps.
I do believe that the 30bp number was to start the statistical comparison and it carried on from there. It was probably picked by reason of statistical integrity.
I know you said the “Wiki” was nonsense, if you believe that then throw in another article from “Wiki” with the same assertion…
Figures published in Natureon September 1, 2005, in an article produced by theChimpanzee Sequencing and Analysis Consortium, show that 24% of the chimpanzee genome does not align with the human genome. There are 3% further alignment gaps, 1.23% SNP differences, and 2.7% copy number variations totaling at least 30% differences between chimpanzee andHomo sapiensgenomes. wikipedia.org/wiki/Chimpanzee_genome_project
Gee you seem to know an awful lot more than most of these guys. Maybe you should run the analysis yourself. I Goggled the WGS method of comparison and seemed to find a lot of critics. I know just because some one criticizes a article or method doesn’t mean its wrong…right. Maybe you can further explain this excerpt from that original doc we talked about.
“If we restrict the analysis to older duplications (≤ 98% identity) we find fewer assembly problems: 72% of those that can be mapped to the human genome are shared as duplications in both species. These results are consistent with the described limitations of current WGS assembly for regions of segmental duplication”
Here is what icr had to say about non aligned segments…
The availability of the chimp genome sequence in 2005 has provided a more realistic comparison. It should be noted that the chimp genome was sequenced to a much less stringent level than the human genome, and when completed it initially consisted of a large set of small un-oriented and random fragments. To assemble these DNA fragments into contiguous sections that represented large regions of chromosomes, the human genome was used as a guide or framework to anchor and orient the chimp sequence. Thus, the evolutionary assumption of a supposed ape to human transition was used to assemble the otherwise random chimp genome.
I did form an opinion from the other side of the fence…
Between the three sources (Wiki and Nature 04072 paper and Chimp DNA vs Human DNA\Uncommon Descent) it is my humble opinion the Uncommon Descent analysis is the more objective since it does not require the evolution assumptions. I think I can claim that the content referred to in both the Wiki and Nature 04072 paper is strongly influenced by evolution assumptions and are therefore tied to them. The article from Uncommon Descent method is basically a pure statistical tool tasked for a direct comparison (theory of statistics dependant) and based on pure data. The data from other comparisons do hold innate assumptions that there is common ancestry and builds the comparison accordingly. It almost appears that the human DNA sequence guided the chimp/human similarity calculation in serving as a framework to assemble the chimp DNA sequence. I still hold my opinion that position is important in determining differences in DNA coding. If my opinion is true, science still knows very little how to apply innate “assumptions” to a comparison analysis. Therefore I accept the pure statistical method at this time. I never did reject the idea that a comparison can be made, but which comparison would stand up better to a Null-Hypothesis?
I do believe as others that the 95%-99% similarity is the real garbage put out by Darwinists. But I also believe that there must be innate similarities because of a common design not from a common ancestry. I just wish the Darwinists would hold themselves to a reasonable and intellectually honest number, instead of propagating a belief under the guise of objectivity by stoking up the numbers.
I know I got the opinion from the liberal Christian viewpoint just thought I could voice the conservative view….
I especially like comment 78, in which the author of the original article agrees that his own method (with the 62% 30BP matches) says the chimp human similarity is 98.75% at the base level.
Apparently the IDers estimate falls right in line with the garbage put out by Darwinists.
“probability that a 30-bp stretch has zero differences if on average 1.4% of sites are different. If the differences are randomly distributed, that's (1 - 0.014)^30, or 65.5%.”
The (1-0.014) ^ 30 will not approximate the estimate from Common decent, because from the description there I see a different algorithm with a match starting at 30-bp. "Correction: “For each pair of homologous chromosomes A and B, a PRNG (pseudo-random number generator) generates 10,000 uniformly distributed pseudo-random numbers which specify the offset, or starting point, of 10,000 30-base patterns that are contained in source chromosome A. The 30BPM test involves searching for all 10,000 of these DNA sub-strings of chromosome A in our target chromosome B.”" I did not read that part…
Did you read the paper?
“Since the human genome is 3.1 Gb long, this leads to the conclusion that only 2.4/3.1 or 77% of the genomes matched, with the rest counted as divergent.”
No this means that 77% were “comparable” leaving the 23% that did not align. Very close to the figure given in the “Wiki”.
“Some of this poorly aligning sequence might represent multiple rearrangements of one or both genomes, but even if it does, there is no reason to think that the pieces of sequence would themselves be any more diverged than the rest of the genome.”
That is assumption not fact…
Sorry but I think that the “Wiki” does make a point… even with your tap-dance.
“The first supplementary note (linked above) describes what happened to the remaining 0.3 Gb that didn't align. 0.24 Gb could be aligned, but the alignments were to many places in the human genome, so the sequence was discarded.”
This still leaves you a 2.4Gb align able…. (2.4+.3)= 2.7 (2.7Gb)
What doesn’t make sense from your statements above is I can not discern your objection. You need to clarify why the 2.4Gb/3.1Gb ratio does not show a 77% alignment.
And Blayz I looked at #78 you sure about the thread?
Last edited by Zaius137; 26th September 2011 at 04:23 PM.
“Overall, the estimate is complete garbage.”
Wow there is a lot of supplemental reading here. Just started skimming the articles but maybe you can point to one in particular that formed your opinion about the “Wiki”?
Could you please use quote tags? Following your responses is very difficult. As for the supplemental notes, I pointed out which one I was referring to -- the first. Specifically, the part about the chimp genome assembly.
I do believe that the 30bp number was to start the statistical comparison and it carried on from there. It was probably picked by reason of statistical integrity.
I'm sure you do believe that. Do you have any grounds for believing it, however, other than wanting it to be true?
I know you said the “Wiki” was nonsense, if you believe that then throw in another article from “Wiki” with the same assertion…
Figures published in Natureon September 1, 2005[/font], in an article produced by the Chimpanzee Sequencing and Analysis Consortium, show that 24% of the chimpanzee genome does not align with the human genome. There are 3% further alignment gaps, 1.23% SNP differences, and 2.7% copy number variations totaling at least 30% differences between chimpanzee andHomo sapiensgenomes.
So someone repeated the same errors in two Wiki articles. What's your point?
Gee you seem to know an awful lot more than most of these guys. Maybe you should run the analysis yourself.
Have you not been paying attention? I am one of the guys who did the analysis -- one of the members of the Chimpanzee Genome Sequencing and Analysis Consortium, who produced the chimpanzee genome paper that the Wiki article is butchering. Since I didn't work on that part of the analysis, I also checked my reactions with the guy who was in charge of the chimpanzee genome assembly (and one of the leading experts on genome assembly in the world). So, yeah, the authors of the paper do know more about this subject some unknown guy who read the paper and edited a Wikipedia article.
I Goggled the WGS method of comparison and seemed to find a lot of critics. I know just because some one criticizes a article or method doesn’t mean its wrong…right. Maybe you can further explain this excerpt from that original doc we talked about.
“If we restrict the analysis to older duplications (≤ 98% identity) we find fewer assembly problems: 72% of those that can be mapped to the human genome are shared as duplications in both species. These results are consistent with the described limitations of current WGS assembly for regions of segmental duplication”
WGS is certainly not as reliable a method for sequencing and assembling a genome as some other appoaches; that's why the public Human Genome Project didn't use it. It is, however much easier and cheaper, so it's used anyway. (And now we're using methods that are even harder to assemble, but that are vastly cheaper still.) What the quoted text means is that segmental duplications -- nearly identical pieces of sequence that appear more than once in a single genome -- are hard to assemble with WGS sequencing, since if you just have a piece of sequence, you can't be sure which copy it belongs to. When the two copies differ somewhat more, the problems are not as severe. Clear?
Here is what icr had to say about non aligned segments…
The availability of the chimp genome sequence in 2005 has provided a more realistic comparison. It should be noted that the chimp genome was sequenced to a much less stringent level than the human genome, and when completed it initially consisted of a large set of small un-oriented and random fragments. To assemble these DNA fragments into contiguous sections that represented large regions of chromosomes, the human genome was used as a guide or framework to anchor and orient the chimp sequence. Thus, the evolutionary assumption of a supposed ape to human transition was used to assemble the otherwise random chimp genome.
Actually, two assemblies were done of the chimp genome, one using the human as a reference and one done from scratch. They differ very little, and only in how the chunks of the genome are put together, not how different chunks are between species. But accuracy has never been the ICR's strong point.
Between the three sources (Wiki and Nature 04072 paper and Chimp DNA vs Human DNA\Uncommon Descent) it is my humble opinion the Uncommon Descent analysis is the more objective since it does not require the evolution assumptions. I think I can claim that the content referred to in both the Wiki and Nature 04072 paper is strongly influenced by evolution assumptions and are therefore tied to them. The article from Uncommon Descent method is basically a pure statistical tool tasked for a direct comparison (theory of statistics dependant) and based on pure data. The data from other comparisons do hold innate assumptions that there is common ancestry and builds the comparison accordingly. It almost appears that the human DNA sequence guided the chimp/human similarity calculation in serving as a framework to assemble the chimp DNA sequence. I still hold my opinion that position is important in determining differences in DNA coding. If my opinion is true, science still knows very little how to apply innate “assumptions” to a comparison analysis. Therefore I accept the pure statistical method at this time.
Your opinion is in error. Here's what happened: the chimp genome paper assembled the chimp genome, using the human as a reference. We then compared the two sequences and counted how many differences there were. Then the Uncommon Descent guy came along and used exactly the same assembled chimp genome, only instead of counting the number of differences, he counted the number of 30-base segments that differed. Could you tell me why his approach is less dependent on evolutionary assumptions than ours?
I never did reject the idea that a comparison can be made, but which comparison would stand up better to a Null-Hypothesis?
Huh?
I know I got the opinion from the liberal Christian viewpoint just thought I could voice the conservative view….
Science doesn't give a fig about your theology, and neither do I. The Wiki article's mistakes have nothing to do with theology.
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