Micro v. Macro Creationist Challenge

CRR writes: I guess I just took the word of geneticists on that one, such as http://journals.plos.org/plosgenetics/article?id=10.1371/... where the authors claim to have identified 634 human-specific genes and 780 chimpanzee-specific genes.

Genes are determined by RNA sequence, not DNA sequence. By their definition, a gene is a stretch of DNA that is transcribed into RNA. If a stretch of DNA is not transcribed, then it is not a gene. When they say that it is a human specific gene, they are saying that the same RNA sequence is not found among chimp RNA. They are NOT saying that the same DNA sequence is not found in the chimp genome.

Do you understand the distinction?

Let's go to the paper you cited, specifically to Table 2. In that table they compare human and hominoid specific genes and compare the DNA sequence to the syntenic regions in the macaque genome. What do they find? They see about 70 substitutions per 1,000 bases. This means that for hominoid and human specific genes, those genomic regions still share 93% DNA homology to the macaque genome. There is still DNA homology to the macaque genome for human and hominoid specific genes, even though the macaque does not have those homologous genes.

Added in much later edit:

Just for gits and shiggles, I looked up one of the human specific genes to see if there is homologous DNA in the chimp genome. I looked at ENSG00000236197 from Table 2 of the aforementioned paper. I did a BLAT search using the first 700 bp of the gene (upstream region and first exon) through Ensembl's web page and wouldn't you know it, found a match with the chimp genome in the very same region of chromosome 7 where the human gene is found. There's about a 98% match. The link below gets you to the BLAT search which includes a search against the human and chimp genome. The human to human search is to establish where in the genome the human gene is found.

http://www.ensembl.org/Homo_sapiens/Tools/Blast/Ticket?tl...

Here is a link to the Ensembl page for the human gene, in case anyone is interested.

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Try these ones.
Homo sapiens genes vs Pan troglodytes
PLCXD1 (ENSG00000182378) No homologues
GTPBP6 (ENSG00000178605) No homologues
PPP2R3B (ENSG00000167393) No homologues
SHOX (ENSG00000185960) No homologues
CRLF2 (ENSG00000205755) No homologues
IL3RA (ENSG00000185291) No homologues
SLC25A6 (ENSG00000169100) No homologues
AKAP17A (ENSG00000197976) No homologues
ASMT (ENSG00000196433) No homologues
ZBED1 (ENSG00000214717) No homologues
http://asia.ensembl.org/Homo_sapiens/Location/Synteny?db=...

CRR writes: Human-chimp non homologues Try these ones. Homo sapiens genes vs Pan troglodytes PLCXD1 (ENSG00000182378) No homologues

I searched for the first one on your list and found a homologue (first 960 bases of gene covering the first exon) in the chimp genome.

http://www.ensembl.org/Pan_troglodytes/Tools/Blast/Ticket

If you are wrong about the very first one, I see little reason to go through the rest.

PLCXD1 is also NOT a human specific gene. It is found in many vertebrate species, from frogs to mice to dogs to humans.

https://www.ncbi.nlm.nih.gov/homologene/?term=PLCXD1+human

In looking at a handful of other genes on your list, none of those are human specific either. You seem to be running a bait and switch.

You are just wrong about those human specific genes. You mistakenly conflated "gene" with "DNA sequence". People make mistakes. The key is to recognize when you make mistakes and stop making them.

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They were all listed as "no homologue" on the Encode website. Sorry, but I trust Encode more than you.

CRR writes: They were all listed as "no homologue" on the Encode website. Sorry, but I trust Encode more than you.

Did ENCODE list them as human specific genes? If not, then your point is meaningless. All you are doing is using a bait and switch.

You claimed that evolution of humans was impossible because there were all of these human specific genes that could not evolve. I proved you wrong by pointing out the fact that chimps have homologous DNA in those same regions. To try and save face, you try to find genes that were lost in the chimp lineage and found in other primate genomes to counter the argument, forgetting that your argument started with human specific genes.

What is it about loss of genes in the chimp lineage that you think argues against evolution?

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Taq writes: You haven't demonstrated that the new genes in the human lineage lack homologous sequence in the chimp genome.

Do you accept that there are genes in humans that have no homologue in chimps?

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Taq writes: Did ENCODE list them as human specific genes?

The link I provided compared them to the chimp genome only. Some of them would be human specific genes.

How many human specific genes are there? I don't know and neither does anyone else, however there ARE human specific genes as an internet search will show you. Such as Human-specific gene ARHGAP11B.

According to this Nature paper, every evolutionary lineage harbours orphan genes that lack homologues in other lineages and whose evolutionary origin is only poorly understood

Do you accept that there are genes in humans that have no homologue in chimps?

Do you accept that you are using a bait and switch?

CRR writes: The link I provided compared them to the chimp genome only. Some of them would be human specific genes.

Baloney. Until you show that any of them are human specific genes you are simply using a bait and switch.

How many human specific genes are there? I don't know and neither does anyone else, however there ARE human specific genes as an internet search will show you. Such as Human-specific gene ARHGAP11B.

As I have already shown, those genes are transcribed from DNA shared with other primate species. You can find the Ensembl page for the human specific gene ARHGAP11B here. I did a BLAT search using the first two exons and the upstream region (~1,000 bp) against the human and chimp genomes, which you can view here. As expected, there is homologous DNA (~98% identity) in the chimp genome associated with the human specific gene. They are both found on the same region of chromosome 15.

How many times do we need to repeat this process?

According to this Nature paper, every evolutionary lineage harbours orphan genes that lack homologues in other lineages and whose evolutionary origin is only poorly understood

Yes, they lack homologous RNA, but they share homologous DNA. Do we need to go over this again?

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Strangely I put more weight on the papers published in Science and Nature than on your BLAT experiments. No doubt there is a lot more work to be done in this area and I might yet be disappointed but for now I will go with the scientific consensus. Hang in there, the scientific consensus has often been wrong. You might be able to publish your own paper showing how those other authors got it wrong.

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Strangely I put more weight on the papers published in Science and Nature than on your BLAT experiments.

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Now that is just not true.

The abstract of the Nature paper at The evolutionary origin of orphan genes agrees with Taq

...however, de novo evolution out of non-coding genomic regions is emerging as an important additional mechanism. This process appears to provide raw material continuously for the evolution of new gene functions, which can become relevant for lineage-specific adaptations.

And the abstract of the Science paper Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion

states

ARHGAP11B arose from partial duplication of ARHGAP11A (which encodes a Rho guanosine triphosphatase–activating protein) on the human lineage after separation from the chimpanzee lineage

So you are disagreeing with both papers, and quite obviously so.

CRR writes: Strangely I put more weight on the papers published in Science and Nature than on your BLAT experiments.

That's strange since the Science and Nature papers are also saying that there is homologous and paralogous DNA in other primate species for human specific genes.

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In this scenario, randomly occurring sequence combinations would form cryptic functional sites (for example, transcription initiation regions, splice sites and polyadenylation sites) and would come under a regulatory control to produce a distinct processed RNA transcript (Fig. 3). This RNA could initially function as an antisense or structural RNA39 and would eventually acquire a functional ORF from which a completely new protein could evolve. The most stringent criterion for indicating the involvement of this mechanism requires that the corresponding genomic region of the gene is present in outgroup organisms, but as a non-coding stretch that is neither transcribed nor translated.
http://www.nature.com/nrg/journal/v12/n10/full/nrg3053.html

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That is from the paper that you referenced. It says exactly what I have been telling you. I would suggest reading the papers instead of projecting your wrongly held beliefs onto the papers.

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Let's go back a bit.
Are there non homologous genes when comparing humans to chimps?
Ensemble website here shows many human genes as having no homologue anywhere in the chimp genome. (And many chimp genes that have no homologue in humans).

What does Ensemble mean when it says "no homologue"?

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CRR writes: Let's go back a bit. Are there non homologous genes when comparing humans to chimps?

I have no doubt that there could have been gene loss in either the chimp or human lineages. Do you think gene loss is an impediment to macroevolution? If not, then why mention it?

"The chimpanzee MSY [Y-chromosome] contains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor."
http://www.nature.com/...al/v463/n7280/full/nature08700.html

A BLAT search also finds homologous DNA (first 1,000 bp) on the chimp X-chromosome for PLCXD1, the first gene on your Ensembl list below.

http://www.ensembl.org/Pan_troglodytes/Tools/Blast/Ticket

Ensemble website here shows many human genes as having no homologue anywhere in the chimp genome. (And many chimp genes that have no homologue in humans).

When you click on the orthologue button it finds homologous DNA in macaques, gorillas, and orangutans, to name a few. The orthologous DNA is found on the X-chromosome of those species. These genes are not human specific.

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CRR writes: Let's go back a bit. Are there non homologous genes when comparing humans to chimps? I have no doubt that there could have been gene loss in either the chimp or human lineages. Do you think gene loss is an impediment to macroevolution? If not, then why mention it? "The chimpanzee MSY [Y-chromosome] contains twice as many massive palindromes as the human MSY, yet it has lost large fractions of the MSY protein-coding genes and gene families present in the last common ancestor."

Ok I will take that as agreement that there are non homologous genes when comparing humans to chimps.
The explanation you seem to be advancing is that the non-homologous genes are explained by gene loss in both species. That is a possibility I have raised in the past. This would mean that the common ancestor had all those non-homologous genes from both species. But don't stop there. The common ancestor of all the great apes would have had all the genes of all the great apes. You can extend this as far back down the phylogenetic tree as you like.

What we see then is evolution by genetic loss. Then I guess it means that Microevolution is loss of genetic information in a population over time; and Macroevolution is when genetic loss results in morphological change and separation into new species, genera, etc.

However if you go back to my past posts you will find that I disagree with equating macroevolution to speciation. I have said that speciation could be the result of either microevolution or macroevolution; where the critical difference is whether the mutation adds a significant amount of new genetic information.

A BLAT search also finds homologous DNA (first 1,000 bp) on the chimp X-chromosome for PLCXD1, the first gene on your Ensembl list below.

I think that's about 4% of PLCXD1. As I've said before I think I will put more weight on the Ensemble assessment of whether genes are homologous or not.