Micro v. Macro Creationist Challenge

What does this indicate for how you view primate evolution?

I would agree with Taq, Percy and others that these were examples of gene loss in the ancestors of Chimpanzees since they branched off from a common ancestor with Humans. We can use these pattern of gene loss/gain with other primates to establish phylogenetic relationships and compare this to other features we see in the sequenced genomes to see if they concur.

But this isn't why I posted because Taq and Percy already have this well in hand. What I was looking for was your own interpretation of these patterns. For example, creationists possibly including Durston, tend to separate humans from other primates as separate kinds, possibly going further with ape and monkey kinds. But this example you've raised contradict this depending on however you would define the significance of gene gain/loss.
So how would you describe the relationships of primate species, if any, based on the distribution of shared genes?

So Percy and Taq argued that non-homologous genes between humans and chimps was due to gene loss in each. Having realised the error of their argument they are now arguing for the appearance of lineage specific genes.

I thank Percy for the chart that provides some gains and losses in number of genes. I find it particularly interesting to note the apparently high mutation rates in humans, chimps, orangotangs, mice and rats. Is this high rate of gene loss and gain observed in these populations today?

Meddle writes: I would agree with Taq, Percy and others that these were examples of gene loss in the ancestors of Chimpanzees since they branched off from a common ancestor with Humans.

Actually, I didn't say that. It seems to me that other things being equal that something more symmetric should have happened, that humans and chimps should both have acquired and lost alleles and genes since the common ancestor. Here's some information I thought significant from the paper Comparing the human and chimpanzee genomes: Searching for needles in a haystack says:

quote:

---

∼50 known or predicted human genes were found to be missing partially or entirely in the chimpanzee genome, and some of these differences were confirmed by PCR or Southern blotting (The Chimpanzee Sequencing and Analysis Consortium 2005).
...
Alu elements (duplications) are the most abundant class of SINEs in humans, making up ∼10% of the genome (Lander et al. 2001), where they apparently expanded up to three times more than in the chimpanzee genome (The Chimpanzee Sequencing and Analysis Consortium 2005).
...
However, given the relatively few protein-sequence differences between human and chimpanzees, differential regulation of gene and protein expression is a likely mechanism for explaining human:chimpanzee differences.

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In other words, chimps may have lost genes that humans did not; duplications were 10 times more common in the human genome; and gene regulation by non-coding regions is a large unexplored area. There's a lot more in the paper.

--Percy

CRR writes: So Percy and Taq argued that non-homologous genes between humans and chimps was due to gene loss in each.

That's false. I offered many different explanations, from gene loss to de novo evolution of new genes. I never said that every single non-homologous gene between humans and chimps was due to gene loss.

I find it particularly interesting to note the apparently high mutation rates in humans, chimps, orangotangs, mice and rats.

Where are you getting this from?

A single substitution mutation can produce a new gene promoter and lead to the transcription of previously non-coding region of DNA. You don't need high mutation rates for the production of new genes.

I find it particularly interesting to note the apparently high mutation rates in humans, chimps, orangotangs, mice and rats. Where are you getting this from?

From Percy in Message 223

I read that post and I can't see what you claimed anywhere in that post.

Are you telling untruths again, CRR?

You do know that people can actually read, don't you?

CRR writes: From Percy in Message 223

What are you referring to specifically?

That chart isn't measuring mutation rates, merely the rate of gene loss and gain.

Those values do not appear to be rate values since there is no indication of a time period.

I've been trying to track down more details about this chart:

I originally assumed the obvious, that the number in the right hand column is the number of genes, and that the red/blue numbers are the number of genes added/subtracted from the common ancestor. But now I'm not sure I trust this chart, for these reasons:

• For humans:

  19619+276-1439 = 18456

  For chimps:

  17811+933-274 = 18470

  That number on the right should be the number of genes for the common ancestor, and it should be the same number whether you calculate backwards from human or chimp, but it isn't. There may be a good explanation, but I don't know what that is, and I couldn't find an explanation anywhere.

• The number of genes for humans is estimated to be 19,000-20,000, but that chart places it at 19,619, which is far more precision than we currently have.

• The number of genes for chimps is estimated to be 20,000-25,000, but the chart places it at 17,811, again, too much precision, and far different than the estimate.

• We haven't studied the genomes of the other animals in the table to anywhere near the extent of humans and chimps and so could not possibly know the number of genes to the precision in the table.

• If the numbers in the chart *are* genes, then as you noted the mutation rate is very, very high. Far too high. Not possible.

• I can't find the webpage that the chart comes from.

For these reasons, I'm disavowing this chart.

But the original point made back in my Message 223 still stands. It's not valid to pay attention to "only one side of the ledger, namely losing genes."

--Percy

(a) shows the numbers of losses and gains.
(b) shows the rates

You have to backtrack to the article that Percy referenced; which I did.

I agree with Percy that the graphs require further explanation. I couldn't work out the numbers on the right either.

[edit] btw I thing the colours are reversed between the two graphs, which makes it a bit confusing.

Edited by CRR, : No reason given.

CRR writes: (a) shows the numbers of losses and gains. (b) shows the rates

Shows the rates of what? Gene loss/gain? Rate of duplication events? Indel rates? Substitution rates? Per nucleotide mutation rate?

a) shows the numbers of losses and gains. (b) shows the rates

There are no time units on graph b. I think you are making stuff up when you complain about rates being too high.

I was still thinking back to the genes CRR cited in Message 167 which were examples of loss in Chimpanzees. But the discussion has moved on since then to include gene gain, so sorry for the confusion.

Also your graph in Message 223 comes from here but it is a supplementary image not in the main body of the article.