New genes

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Postby marcsurtees » Tue Oct 27, 2009 5:28 pm

Roger Stanyard wrote:
marcsurtees wrote:
Yes I believe that human beings were specially created, for non-scientific reasons.

Even when all the available data pointed to 99% similarity I believed this. After all we are more than our DNA and there are plenty of phenotypic differences that set us apart from apes.



In that case, mankind will have long been whiped out by cancer. Not much of a predictive tool you have. In fact it doesn't stack up.


Sorry, why should that be the case if we are not apes?
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Postby Steve660 » Tue Oct 27, 2009 5:47 pm

the chimp genome sequence work still shows a difference of about 6% to 7% made up of the following:
single nucleotide polymorphisms ~1%
indels ~3 % difference
variation in copy number 2 to 3% difference


As was pointed out earlier, the 3% contribution from indels is misleading because indels involve many base pairs. Instead indels should be counted as one difference per indel, not one difference per each base pair involved. As indels are about 7 times less common than single nucleotide substitutions that 3% should actually be seen as 3/7 = 0.4 %. I suspect something similar will apply to copy number. It is becoming obvious to all, but yourself, that you are starting with your conclusion (humans and chimps are separate creations) and are trying to twist the figures on DNA differences to support your predetermined conclusion, just like a typical creationist.

Yes I believe that human beings were specially created, for non-scientific reasons.

Well, at least you are honest about it. The only rational reason to believe something is on the basis of evidence. Any other reason is irrational. You are being irrational.
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Postby marcsurtees » Tue Oct 27, 2009 7:19 pm

Steve660 wrote:As was pointed out earlier, the 3% contribution from indels is misleading because indels involve many base pairs. Instead indels should be counted as one difference per indel, not one difference per each base pair involved. As indels are about 7 times less common than single nucleotide substitutions that 3% should actually be seen as 3/7 = 0.4 %. I suspect something similar will apply to copy number. It is becoming obvious to all, but yourself, that you are starting with your conclusion (humans and chimps are separate creations) and are trying to twist the figures on DNA differences to support your predetermined conclusion, just like a typical creationist.


The 3% figure comes straight out of the Nature article. And dividing by 7 because indels are 7 times less common seems like "twisting the figure"!
By the way starting with a hypothesis and testing it is perfectly good methodology. And most scientists will be just as tenacious when defending an hypothesis.
But more to the point, as I have already pointed out, if the genetic difference is 1% or 30% its all the same to me.

The reasons why I am pushing this are twofold:
Firstly, if the true difference is greater than 1% it will be another useful argument for creationists to add that to all other differences.
Secondly (and I think much more interestingly) are the issues surrounding "the myth of 1%" and how it has been used by evolutionists.

And by the way Wikipedia still says the difference could be as much as 30%!
See:http://en.wikipedia.org/wiki/Human_evolutionary_genetics and the section with the title: Sequence divergence between humans and apes
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Postby Brian Jordan » Wed Oct 28, 2009 1:37 am

marcsurtees wrote:Yes I believe that human beings were specially created, for non-scientific reasons.
Are you saying that you have non-scientific reasons for your belief, or do you believe that there were non-scientific reasons for our "creation"?
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Postby Steve660 » Wed Oct 28, 2009 6:03 pm

The 3% figure comes straight out of the Nature article. And dividing by 7 because indels are 7 times less common seems like "twisting the figure"!

No, it is not twisting anything, it is common sense. An indel that inserts or deletes, say, 100 base pairs, should be counted as one difference, not 100. If you are comparing two editions of a book and most of the differences are single letter misprints you could simply add up the misprinted letters as a % of the whole and get an answer. Now suppose a whole chapter in one edition has been duplicated. Following your creationist "logic" you would count every letter in that duplicated chapter as a difference, thus ramping up the differences by many thousands. I would count the duplicated chapter as one more difference. A more realistic, and less misleading, approach.


if the genetic difference is 1% or 30% its all the same to me.

Yet you seem very anxious to make the number as large as you can get it. I might also add that, in isolation, it is limited in what it tells us. More revealing is how much we differ from other creatures. Whatever counting method you employ, what is the % difference between us and armadillos, us and earwigs, us and carrots? OK, these may not have been sequenced yet, but here's a prediction: the further away from us the species is taxonomically, the more different it will be genetically. That is a prediction of evolution that, doubtless, will be tested in years to come. As I understand it, what data is already available for other species is (so far) bearing it out. One might expect a few instances of convergent evolution fooling the taxonomists, but most of the time this what we should see, and are seeing. What would creationism predict?


And by the way Wikipedia still says the difference could be as much as 30%!
See:http://en.wikipedia.org/wiki/Human_evolutionary_genetics and the section with the title: Sequence divergence between humans and apes

Oh well, if Wikipedia says it then it must be true! In fact it seems the author there has simply made the same mistake you initially did, and which sfs so eloquently corrected. The 24 % not aligned is that which was not sequenced well enough to permit meaningful comparison.
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Postby sfs » Wed Oct 28, 2009 9:06 pm

marcsurtees wrote:The really interesting thing is that the new evidence is consistent with a greater difference than 1%, at least 6% and possibly more.
First there is the 6% difference reported by Demuth et al, and the posts from sfs not withstanding, the chimp genome sequence work still shows a difference of about 6% to 7% made up of the following:
single nucleotide polymorphisms ~1%
indels ~3 % difference
variation in copy number 2 to 3% difference

I don't know where you got those numbers. According to the chimp sequence paper, the single-nucleotide substitution rate (they're not polymorphisms -- a polymorphism is a variant within a species) is 1.2%, indels represent ~1.5% of sequence present in chimp but not in human and another 1.5% present in human but not in chimp, and that's it. CNVs aren't mentioned, because they are a subset of indels, basically just large duplications or deletions. So no double counting, please.

This is clearly a significant departure from the 1% myth that for so long was promoted by evolutionists to support the claim that we are related to chimps.
But, as has been pointed out, there is no debate about evolution so the dogma that we are apes is never challenged.

[Note: I've tried to be polite and respond to your posts civilly, but that isn't very easy when you make such tendentious and insulting comments as you do here. Given how little you obviously know about the subject, don't you think even a hint of humility or tentativeness might be in order?]

Two points: First, the 1% was not a "myth"; it was an estimate of the divergence, made when it was thought that single-base mutations were the dominant source of genetic variation. We know now that insertions and deletions, while rarer than substitutions, can be large enough that they actually affect more DNA than single-base substitutions. This is true both within and between species. Thus, when the 1% human/chimp divergence estimate was made, it was also estimated that individual human genomes differed by 0.1%; it is now known that both numbers should actually be several times larger, thanks to indels.

Second, the particular value (whether 1% or 5%) has very little to say about whether we're related to chimpanzees. What actually provides evidence for their relatedness is the many detailed patterns we see in the genetic similarities and differences. The reason that common ancestry between humans and chimpanzees is never challenged (well, almost never -- there is that one guy who thinks we're more closely related to orangutans, but he's something of a crackpot) is not because it's dogma, but because it's so well established. Common ancestry explains and predicts the patterns we see very well, and no other explanation (including special creation) does remotely as good a job. So we stick with the model that works. When someone comes along with a model that works better, we'll listen. Until then, expect to be ignored.

What the 1% difference does matter for is determining which other species we are most closely related to. For that purpose, we can ignore indels altogether; as long as we are looking at the same metric throughout, comparing the single-base human/chimp difference to the human/gorilla and chimp/gorilla differences tells us which species pair is most closely related. It turns out that humans and chimpanzees are most similar to one another genetically.

A couple of other points to consider: First, the evolutionary model tells us that humans and chimpanzees, being the most closely related, should each be equally diverged from gorilla (assuming reasonably similar reproduction rates, which is the case). I.e., the genetic difference between human and gorilla should be nearly identical to the genetic difference between chimpanzee and gorilla. Does special creation make any prediction about this relationship? Would you care to guess what the empirically measured value is?

The second point follows from the fact that gorillas are only slightly more diverged from humans than chimps are (i.e. the split between the gorilla lineage and the human/chimp lineage occurred shortly before the human and chimp lineages split, in the evolutionary model). Under these circumstances, according to evolutionary theory, the close relationship between humans and chimps will only be true on average; for some fraction of the genome, humans and gorillas will be more closely related, and for some fraction chimps and gorillas will be most closely related(*). In fact, we are only most closely related to chimpanzees in ~2/3rds of our genome. Does special creation predict this? What does special creation predict about how the different sets of relatedness will be distributed? Evolution says they should occur in chunks, with the entire chunk showing, e.g., humans and gorillas most closely related, and it gives a rough estimate of the size of the chunks. What predictions does special creation make in this area?

(*) This occurs because there was variation in the ancestral human/chimp/gorilla population, which survived through the species splits. Thus, the gorilla, human and chimp ancestors all had two versions, A and B, of some genes. In some cases, A happened to survive in humans and gorillas while B survived in chimps, making humans and gorillas more closely related, and so on. This process is known as lineage sorting.
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Postby Steve660 » Wed Oct 28, 2009 10:11 pm

Yet another eloquent response from sfs. Science 3 : Creationism 0. When will Marc give up?
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Postby marcsurtees » Fri Oct 30, 2009 9:35 pm

sfs wrote: I don't know where you got those numbers. According to the chimp sequence paper, the single-nucleotide substitution rate (they're not polymorphisms -- a polymorphism is a variant within a species) is 1.2%, indels represent ~1.5% of sequence present in chimp but not in human and another 1.5% present in human but not in chimp, and that's it. CNVs aren't mentioned, because they are a subset of indels, basically just large duplications or deletions. So no double counting, please.

OK lets see if I can get the terms and numbers right.
I have gone back to the original articles from Nature Vol 437 and the supplemental data.
From these it seems that we have the following sources of variation:
Single-nucleotide substitution 1.2% (Nature 437:69-87, 2005)
Indels 3.2% (Nature 437:69-87, 2005, supplemental information S2)
Segmental duplications 2.7% (Nature 437:88-93, 2005)

Now I am not sure if I can add all these up but we can add up the first 2, therefore at the very least we have 4.4% difference. Therefore, the true difference between chimps and humans obtained by comparing the genome sequence data is at least 4.4% .':D'
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Postby Roger Stanyard » Sat Oct 31, 2009 1:31 pm

marcsurtees wrote:
sfs wrote: I don't know where you got those numbers. According to the chimp sequence paper, the single-nucleotide substitution rate (they're not polymorphisms -- a polymorphism is a variant within a species) is 1.2%, indels represent ~1.5% of sequence present in chimp but not in human and another 1.5% present in human but not in chimp, and that's it. CNVs aren't mentioned, because they are a subset of indels, basically just large duplications or deletions. So no double counting, please.

OK lets see if I can get the terms and numbers right.
I have gone back to the original articles from Nature Vol 437 and the supplemental data.
From these it seems that we have the following sources of variation:
Single-nucleotide substitution 1.2% (Nature 437:69-87, 2005)
Indels 3.2% (Nature 437:69-87, 2005, supplemental information S2)
Segmental duplications 2.7% (Nature 437:88-93, 2005)

Now I am not sure if I can add all these up but we can add up the first 2, therefore at the very least we have 4.4% difference. Therefore, the true difference between chimps and humans obtained by comparing the genome sequence data is at least 4.4% .':D'


So how is that "evidence" thst we don't share a common ancestor with chimps?

It strikes me as strong evidence that we share a common ancestor.
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Postby Roger Stanyard » Sat Oct 31, 2009 2:23 pm

marcsurtees wrote:
Roger Stanyard wrote:
marcsurtees wrote:
Yes I believe that human beings were specially created, for non-scientific reasons.

Even when all the available data pointed to 99% similarity I believed this. After all we are more than our DNA and there are plenty of phenotypic differences that set us apart from apes.



In that case, mankind will have long been whiped out by cancer. Not much of a predictive tool you have. In fact it doesn't stack up.


Sorry, why should that be the case if we are not apes?


Well, let's have a look at your own “explanation” of the differences between species to see the problem.

According to your “explanation” homo sapiens are not “apes” despite the huge genetic similarities (consistent with morphological similarities) which you now appear to agree exist with chimps..

Instead, according to your source of science, your literal interpretation of Bible, the eenes of homo sapiens were created, 6,000 years ago, by a spirit breathing into a lump of mud. (Perhaps you would like to show us , as a scientist, how to replicate this.) A completely separate process was used to create all other “kinds” at the time. We would therefore expect there to be no genetic similarities between humans and any other species.

Wait a minute, though, there's another problem with you position in that, with one exception, all but two members of species of ape were subsequently killed by God because he didn't like mankind. That was around 4,400 years ago, according to you.

So only four alleles of each species of ape, mankind excluded, survived the flood. It is therefore reasonable to predict that there would be massive evidence of genetic bottlenecks in all species that were on the ark, in contrast to these that survived that weren't (fish, dolphins. wales, birds, etc, I guess).

We would also reasonable expect that descendents of “kinds” that were on the ark would show evidence of far fewer alleles than those that weren't, given that there could have been only a maximum of 4 for (or 10) for each such kind at the end of the flood but no such limitation for kinds/species that were not on the ark.

Your evidence is where?

However, the problem with this gets worse, because you claim that there were only a maximum of 16 human alleles at each genetic loci which could have been present at the end of the food.

Let me present the position of our associate, Lenny Flank, on this issue:

See, according to the creationists, all humans alive today are descended from 8 people who got off a Really Big Boat. Anyone who understands junior high genetics will know that 8 people have between them a maximum possible of 16 different alleles for each genetic locus (in reality, the 8 people on the Big Boat would have had even FEWER, since some of them were descended from others and thus shared alleles, but for the sake of argument we will give the creationists every possible benefit of the doubt and assume that they were ALL heterozygous and shared no alleles at all in common). That means, if the creationists are correct that "most mutations are deleterious" and that "no new genetic information can appear through mutation", there can not be any human genetic locus anywhere today with more than 16 alleles, since that is the MAXIMUM that could have gotten off the Big Boat.

But wait ----------

Today we find human genetic loci (such as hemoglobin or the HLA complex) that have well over *400* different alleles (indeed some have over *700* different alleles). Hmmmm. Since there could have only been 16 possible on the Big Boat, and since there are over 400 now, and since 400 is more than 16, that means that somehow the GENETIC INFORMATION INCREASED from the time they got off the Big Boat until now.

That raises a few questions -----

1.if genetic mutations always produce a LOSS in information, like the creationists keep telling us, then how did we go from 16 alleles to over 400 alleles (perhaps in creationist mathematics, 400 is not larger than 16)?

2.if these new alleles did not appear through mutations, then how DID they get here?

But wait -- there's more:

Not only, according to creationists, must these new alleles have appeared after the Big Boat, but, according to their, uh, "theory", all of these mutations must have appeared in the space of just *4,000 years* -- the period of time since the Big Flood. That gives a rate of BENEFICIAL MUTATIONS, which add NEW GENETIC INFORMATION, of one every 10 years, or roughly two every generation ------- a much higher rate of beneficial mutation than has ever been recorded anywhere in nature. Nowhere today do we see such a rate anywhere near so high. So not only would I like to know

1.what produced this extraordinarily high rate of non-deleterious mutations, but
2.what stopped it (indeed, what stopped it conveniently right before the very time when we first developed the technological means to study it)?

But wait --- we're not done YET . . . . . .

Since less than 1% of observed mutations are beneficial (the vast majority of mutations are indeed deleterious or neutral and have no effect), that means for every beneficial mutation which added a new allele, there should have been roughly 99 others which did not. So to give us roughly 400 beneficial mutations would require somewhere around 40,000 total mutations, a rate of approximately 100 mutations in each locus EVERY YEAR, or 2,000 mutations per locus for EACH GENERATION. Do you know what we call people who experience mutation rates that high? We call them "cancer victims".
But wait, we're STILL not finished . . . . . .

In order for any of those mutations to be passed on to the next generation to produce new alleles, they MUST occur in the germ cells -- sperm or egg. And since any such high rate of mutation in a somatic cell (non-sperm or egg) would have quickly produced a fatal case of cancer, if the creationists are right this mutation rate could ONLY have occurred in the germ cells and could NOT have occurred in any of the somatic cells.


If one of our creationists can propose a mechanism for me which produces a hugely high rate of mutation in the germ cells while excluding it from any other cells, a Nobel Prize in medicine surely awaits --- such information would be critically valuable to cancer researchers. But alas, no such mechanism exists. The rate of mutations made necessary by creationist "arguments" would certainly have killed all of Noah's children before they even had time to have any kids of their own. In order to produce 400 beneficial alleles in just 4,000 years, humanity would have been beset with cancers at a rate that would have wiped them all out millenia ago.

Explain, please . . . .
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Postby Steve660 » Sat Oct 31, 2009 7:04 pm

Another devasting debunking, this time from Roger. Science 4 : Creationism 0. When will Marc give up, or could it be that, like a typical creationist, he just can't tell when he is well and truly beaten?
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Postby marcsurtees » Sat Oct 31, 2009 9:42 pm

Steve660 wrote:Another devasting debunking, this time from Roger. Science 4 : Creationism 0. When will Marc give up, or could it be that, like a typical creationist, he just can't tell when he is well and truly beaten?


Well, considering that we have established that the genomic difference between chimps and humans in fact at least 4.4%, I think I have good reason not to give up. Indeed the fact that the chimp genome is larger than ours by about 7 to 8% means the difference is greater than 4.4%.

As for the article posted by Roger; it is a little hard to respond to that considering that no refs are cited and each point could take a while.

But in any case (as I have mentioned before on this forum) my position on genetic diversity in on the web for all to read if they want to.
But the basic problem is that you assume that I believe that all mutations are harmful, which I don't. There are at least 8 mechanisms for producting genetic variation and it can happen very quickly. Even last week there was a report in Nature showing that genome evolution can be very rapid.
See Naito et al (Nature 461, 1130-1134, 2009) Unexpected consequences of a sudden and massive transposon amplification on rice gene expression.
But please note that it is still rice!
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Postby psiloiordinary » Sun Nov 01, 2009 2:11 am

Ah!

You believe in stairs but not staircases!

Regards,

Psi
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Postby Steve660 » Sun Nov 01, 2009 12:26 pm

Well, considering that we have established that the genomic difference between chimps and humans in fact at least 4.4%, I think I have good reason not to give up. Indeed the fact that the chimp genome is larger than ours by about 7 to 8% means the difference is greater than 4.4%.


Have we established this? Just like a short while ago "we" (for which read "you", and add on the qualifier "think") had "established" that it was, in fact, a 30 % difference?
As I pointed out earlier the indels should be considered 0.4 %. i.e. one difference per indel, not one difference for every base pair affected by the indel. Adding this on to the single nucleotide substitutions (1.2 %) makes 1.6 %. There, we've established the genomic difference to be 1.6 %. See also www.talkorigins.org/indexcc/CB/CB144.html which addresses the same issue and makes the exact same point. (I arrived at the same conclusion myself, before I read that item, by the way). One wonders how many times this has to be explained to you before it will penetrate your creationist skull? If you can give me an indication, please, I can perhaps then copy and paste it the required number of times.

I note you also continue to ignore my point about how this difference compares to differences between humans and other species. You also have yet to answer my question about what creationism would predict?
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Postby sfs » Mon Nov 02, 2009 2:30 am

marcsurtees wrote:OK lets see if I can get the terms and numbers right.
I have gone back to the original articles from Nature Vol 437 and the supplemental data.
From these it seems that we have the following sources of variation:
Single-nucleotide substitution 1.2% (Nature 437:69-87, 2005)
Indels 3.2% (Nature 437:69-87, 2005, supplemental information S2)
Segmental duplications 2.7% (Nature 437:88-93, 2005)

Now I am not sure if I can add all these up but we can add up the first 2, therefore at the very least we have 4.4% difference. Therefore, the true difference between chimps and humans obtained by comparing the genome sequence data is at least 4.4% .':D'

You're right to be cautious about just adding them. Yes, the first two can be added, at least for some purposes. The third category should be a subset of the 2nd (if you duplicate a segment of DNA, it is an insertion of DNA, and hence an indel), and in theory could be completely ignored. In practice, the 2nd and 3rd numbers were estimated in different ways, and the two methods found different numbers specifically for segmental duplications (8.3 Mb vs 26.5 Mb). If the larger number is more accurate, than the total difference should be 1.2% + 2.8% = 6.0%. Or not, if the smaller number is more accurate -- this is not an area where the answer is known with great precision. Roughly 5% is a good ballpark estimate.
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