New genes

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Postby Roger Stanyard » Sun Oct 18, 2009 7:58 pm

marcsurtees wrote:
This is a question that is not possible to answer with the currently available data, and rather tends to obscure the significance of the facts.



It's central to your argument because it has been "worked out" with currentlly available data.
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Postby psiloiordinary » Sun Oct 18, 2009 8:43 pm

Thank you sfs,

That makes you 1 for 1 in posts versus creationist arguments shot down!

Surely the best signal to noise ratio ever seen on the forum!

Best regards,

Psi
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Postby marcsurtees » Mon Oct 19, 2009 12:58 pm

psiloiordinary wrote:Thank you sfs,

That makes you 1 for 1 in posts versus creationist arguments shot down!

Surely the best signal to noise ratio ever seen on the forum!

Best regards,

Psi


I have to agree that sfs has provided a convincing response and I will have to fall back on my previous position which is 6% difference based on the following:

The Evolution of Mammalian Gene Families Jeffery P. Demuth, Tijl De Bie, Jason E. Stajich, Nello Cristianini, Matthew W. Hahn
In the December 2006 issue of PLoS ONE,
From the abstract:
Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic “revolving door” of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives.

google "The Evolution of Mammalian Gene Families" to find the article on line.
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Postby psiloiordinary » Mon Oct 19, 2009 3:43 pm

Hi Marc,

Can we just step a moment and look at it from this angle;

You want to make a claim that Chimps are X% different from people.

Why?

I don't think you are meaning to imply that the TOE suggests they are in fact identical, so what are you trying to say?

Regards,

Psi
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Postby Steve660 » Mon Oct 19, 2009 5:43 pm

I have to agree that sfs has provided a convincing response and I will have to fall back on my previous position which is 6% difference based on the following:


A creationist backing down? A rare event indeed.

The Evolution of Mammalian Gene Families Jeffery P. Demuth, Tijl De Bie, Jason E. Stajich, Nello Cristianini, Matthew W. Hahn
In the December 2006 issue of PLoS ONE,
From the abstract:
Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic “revolving door” of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives.

google "The Evolution of Mammalian Gene Families" to find the article on line.


So they are using a different way of counting and got a different number. So what? The number you get depends on how you count the differences. As I said before you are trying to ramp up the differences to suit your desired conclusion - that humans and chimps are unrelated. Starting with the conclusion you want and searching for evidence to fit it is not science.
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Postby Brian Jordan » Tue Oct 20, 2009 1:38 pm

It seems our friends at Lying for Genesis have had something to say about this recently. This article from Answers in Genesis http://www.evolutionnews.org/2009/10/ke ... _conf.html promotes this TiS article: http://www.truthinscience.org.uk/site/c ... ew/277/65/ Quite what this has to do with TiS's Intelligent Design smokescreen I've no idea.
"PPSIMMONS is an amorphous mass of stupid" - Rationalwiki
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Postby Roger Stanyard » Tue Oct 20, 2009 4:57 pm

marcsurtees wrote:The Evolution of Mammalian Gene Families Jeffery P. Demuth, Tijl De Bie, Jason E. Stajich, Nello Cristianini, Matthew W. Hahn
In the December 2006 issue of PLoS ONE,
From the abstract:
Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic “revolving door” of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives.

google "The Evolution of Mammalian Gene Families" to find the article on line.


So? It still doesn't make your "creation science" a valid explanation of the differences between species. Nor does it make the world 6,000 years old or Noah's Ark story true.
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Postby sfs » Fri Oct 23, 2009 6:38 am

marcsurtees wrote:I have to agree that sfs has provided a convincing response and I will have to fall back on my previous position which is 6% difference based on the following:

The Evolution of Mammalian Gene Families Jeffery P. Demuth, Tijl De Bie, Jason E. Stajich, Nello Cristianini, Matthew W. Hahn
In the December 2006 issue of PLoS ONE,
From the abstract:
Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic “revolving door” of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives.

google "The Evolution of Mammalian Gene Families" to find the article on line.

That's considerably better than your previous position, since this one correctly represents the contents of the paper. Thank you for withdrawing the other claim.

Your newer position is not without its own problems, however. If you want to accurately represent the state of knowledge on this question (rather than simply winning a debating point), you really should do more than just cite this paper. One reason for doing more is that other estimates of the same quantities estimated have been all over the map. The chimpanzee genome paper (2005) refused to attempt an estimate of the number of genes lost in humans, because of the poor quality of the annotation of chimpanzee genes, but they did identify 36 entirely and 17 partially deleted genes in chimpanzees. Then the paper you cite (2006) found 729 genes deleted in chimp, along with 86 deleted in human, while a third and still later paper (Journal of Computational Biology 16:1419–1427 (2009)) initially found only 6 genes deleted in humans; this number increased to 28 when they used updated gene annotations. Thus we have estimates that vary quite a lot, depending on how the study was done and which set of gene annotations was used, indicating that this is not something that is known with any kind of precision at this point. (In fact, this kind of study is really very difficult. Comparing two pieces of similar DNA is easy; deciding whether a piece of DNA is missing from a genome is hard, since you're never sure which parts of the genome are missing because of experimental artifacts. The difficulty is compounded here because the human sequence was used in assembling the chimpanzee genome, which could bias things in the comparison considerably.) Simply citing the result from a single paper, under these circumstances, is not legitimate.

There are indications even within the Demuth paper itself that one should assess the results cautiously. One is the asymmetry between events in humans and chimpanzees. According to the study, humans gained 689 genes and lost 86, while chimpanzees gained 26 and lost 729, in both cases compared to the putative genes in their common ancestor. Now it is certainly possible that the gains and losses in each species are so lopsided, and in opposite directions, because things really happened that way, but the difference does suggest that there may be systematic errors taking place. The most likely error is missing sequence in the chimpanzee genome, which is much cruder than the human assembly; such missing sequence would, in fact, contribute both to spurious losses in chimp and spurious gains in human. Making this possibility more likely is a second point: the authors of the paper note that they originally found 2382 unique genes in humans (human gain + chimp loss), but that improved sequencing coverage of the chimp genome (6x rather than 4x) reduced this to the 1418 they report here; i.e. moderately better data reduced their estimate by 40%. So there is strong reason to think that the gene complement in chimps was not well understood, and no obvious reason to think that the number of differences won't continue to go down as the chimpanzee genome improves. (There is also a third reason to be suspicious of the paper, namely the fact that it was published in PLoS ONE, rather than in a more conventional and respected journal. PLoS ONE is a bit of a catchall for papers that couldn't get, or weren't worth trying to get, publishing elsewhere. But that is not exactly scientific evidence.)

I don't think anyone really knows at this point how many genes differ between humans and chimpanzees.
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Postby marcsurtees » Sat Oct 24, 2009 10:03 am

sfs wrote: I don't think anyone really knows at this point how many genes differ between humans and chimpanzees.


Thanks for your comments, which I will bear in mind. I always try to make the point that science does not give certainity and your final remark illustrates this very well. Which is why I get annoyed with some representatives of the scientific community when they say there is no debate about evolution.

This thread within a thread started when I pointed out that some evidence seems to point to the fact that the genetic difference is greater than the 0.5 to 1.5% difference that has been used for many years as evidence for relatedness. Last time I checked even Wikipedia still states that the difference is more like 30%. The 6% figure that Demuth et al provide shows that what one counts has an impact on the answer one gets. And as you point out there is still a significant amount of uncertainity about the real difference.
I think we can both agree that there is a lot more to learn about the differences and similarities between apes and humans. And even when we know there will be much debate about what that actually means.
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Postby Michael » Sat Oct 24, 2009 3:32 pm

marcsurtees wrote:
sfs wrote: I don't think anyone really knows at this point how many genes differ between humans and chimpanzees.


Thanks for your comments, which I will bear in mind. I always try to make the point that science does not give certainity and your final remark illustrates this very well. Which is why I get annoyed with some representatives of the scientific community when they say there is no debate about evolution.

This thread within a thread started when I pointed out that some evidence seems to point to the fact that the genetic difference is greater than the 0.5 to 1.5% difference that has been used for many years as evidence for relatedness. Last time I checked even Wikipedia still states that the difference is more like 30%. The 6% figure that Demuth et al provide shows that what one counts has an impact on the answer one gets. And as you point out there is still a significant amount of uncertainity about the real difference.
I think we can both agree that there is a lot more to learn about the differences and similarities between apes and humans. And even when we know there will be much debate about what that actually means.


Marc

Check out your basic biolgy. Humans are apes and have been seen as such fro 250 years
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Postby psiloiordinary » Sun Oct 25, 2009 7:31 am

marcsurtees wrote:
sfs wrote: I don't think anyone really knows at this point how many genes differ between humans and chimpanzees.


Thanks for your comments, which I will bear in mind. I always try to make the point that science does not give certainity and your final remark illustrates this very well. Which is why I get annoyed with some representatives of the scientific community when they say there is no debate about evolution.

This thread within a thread started when I pointed out that some evidence seems to point to the fact that the genetic difference is greater than the 0.5 to 1.5% difference that has been used for many years as evidence for relatedness. Last time I checked even Wikipedia still states that the difference is more like 30%. The 6% figure that Demuth et al provide shows that what one counts has an impact on the answer one gets. And as you point out there is still a significant amount of uncertainity about the real difference.
I think we can both agree that there is a lot more to learn about the differences and similarities between apes and humans. And even when we know there will be much debate about what that actually means.


Marc,

You leap from; I don't think anyone really knows at this point how many genes differ between humans and chimpanzees.

To; Which is why I get annoyed with some representatives of the scientific community when they say there is no debate about evolution.

This is a large unsupported leap and far from honest.

Why don't you ask sfs if they think that evolution (i.e. if it happens) is debated in scientific circles?

Regards,

Psi
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Postby Malcolm Stein » Sun Oct 25, 2009 9:33 am

psiloiordinary wrote:
Marc,

You leap from; I don't think anyone really knows at this point how many genes differ between humans and chimpanzees.

To; Which is why I get annoyed with some representatives of the scientific community when they say there is no debate about evolution.

This is a large unsupported leap and far from honest.

Why don't you ask sfs if they think that evolution (i.e. if it happens) is debated in scientific circles?

Regards,

Psi

Marc - or, better still, ask sfs if there is a debate in scientific circles as to whether or not human beings and chimps had a common ancestor. That after all is the thing that really bothers you isn't it?

Let me get this straight. You believe that human beings were specially created about 6000 years ago, and that a 30% difference (i.e 70% similarity) between humans and chimps supports your view? How? And when that is shown to be around 6% or probably rather less than that, you concede it (ok, with caveats), but still hold onto your belief? You said in an earlier post that you follow the evidence. It certainly doesn't look like it.
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Postby Steve660 » Mon Oct 26, 2009 6:07 pm

Another excellent post from sfs. Science 2 : Creationism 0. Marc, ditch that slide!
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Postby marcsurtees » Mon Oct 26, 2009 8:27 pm

Psi
Let me get this straight. You believe that human beings were specially created about 6000 years ago, and that a 30% difference (i.e 70% similarity) between humans and chimps supports your view? How? And when that is shown to be around 6% or probably rather less than that, you concede it (ok, with caveats), but still hold onto your belief? You said in an earlier post that you follow the evidence. It certainly doesn't look like it.


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.

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

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.

So yes I hold on to my belief because there is good reason to believe that the science is far from conclusive. And we have not even started to talk about the phenotype!
Last edited by marcsurtees on Tue Oct 27, 2009 5:25 pm, edited 1 time in total.
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Postby Roger Stanyard » Tue Oct 27, 2009 1:32 pm

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.
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