Well said. There is so much to be learned when science is an unhindered exploration of the world.
Well laid out argument as well. To keep this thread on track the OP made these points:
HAR1F: Vital regulatory gene involved in brain development, 300 million years it has only 2 subsitutions, then 2 million years ago it allows 18, no explanation how.
There is no explanation.
For now. Which is not surprising, as HARs - Human Accelerated Regions - have only been known about for a decade.
Does this mean that no explanation is possible in the future?
If no explanation in the future is possible, does that make supernatural explanations any more likely?
SRGAP2: One single amino-acid change between human and mouse and no changes among nonhuman primates. accumulated as many as seven amino-acid replacements compared to one synonymous change. 6 known alleles, all resulting in sever neural disorder.
Full text from this paper:
Human-specific evolution of novel SRGAP2 genes by incomplete segmental duplication
The ancestral SRGAP2 protein sequence is highly constrained based on our analysis of 10 mammalian lineages. We find only a single amino-acid change between human and mouse and no changes among nonhuman primates within the first nine exons of the SRGAP2 orthologs. This is in stark contrast to the duplicate copies, which diverged from ancestral SRGAP2A less than 4 mya, but have accumulated as many as seven amino-acid replacements (five for SRGAP2C and two for SRGAP2B) compared to one synonymous change.
...SNIP....
SRGAP2 copy-number variation
Since SRGAP2 has been shown to play an important role in brain development .... We identified six large (>1 Mbp) copy-number variants (CNVs), including three deletions of the ancestral 1q32.1 region ... with no similar large CNVs observed among 10,123 controls tested using the qPCR assay and 8,329 individuals from the Cooper et al. (2011) study. Since the CNVs are large and encompass multiple candidate genes, this observation does not prove pathogenicity of dosage imbalance of SRGAP2A. We note, however, that in one patient the proximal breakpoint maps within the first intron of SRGAP2A potentially disrupting the gene. The patient is a ten-year-old child with a history of seizures, attention deficit disorder, and learning disabilities. An MRI of this patient also indicates several brain malformations, including hypoplasia of the posterior body of the corpus callosum. Recently, a de novo balanced translocation breaking within intron 6 of SRGAP2A was reported in a five-year-old girl diagnosed with West syndrome and exhibiting epileptic seizures, intellectual disability, cortical atrophy, and a thin corpus callosum (Saitsu et al., 2011).
While much more work needs to be done, the neurological phenotypes observed in these two cases are consistent with neuronal migration deficits implicated in forms of developmental delay and epileptic encephalopathies (Saitsu et al., 2011).
The paper that this is cribbed from also states:
"SRGAP2 has been highly conserved over mammalian evolution and human is the only lineage wherein gene duplications have occurred. Our analysis indicates that the duplications spread across 80 Mbp of chromosome 1 at a time corresponding to the transition from Australopithecus to Homo"
Seem like the conclusion is that SRGAP2 changes occurred during the Australopithecus to Homo transition.
60 de novo (brand new) brain related genes with no known molecular mechanism to produce them.
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From this paper:
De Novo Origin of Human Protein-Coding Genes
...we discovered 60 genes that originated de novo on the human lineage, with 59 of them being fixed in the human population. This number of genes implies a rate of de novo generation of ∼9.83–11.8 genes per million years, a rate much higher than previously proposed rates. Despite this high rate, when the rate is expressed in terms of per gene, ∼0.00033–0.00039 per gene per million years, it is still a lower rate than the rate of new gene origin by gene duplication.
From the Author Summary of the same paper:
Here we identify 60 new protein-coding genes that originated de novo on the human lineage since divergence from the chimpanzee, supported by both transcriptional and proteomic evidence. It is inconsistent with the traditional view that the de novo origin of new genes is rare. RNA–seq data indicate that these de novo originated genes have their highest expression in the cerebral cortex and testes, suggesting these genes may contribute to phenotypic traits that are unique to humans, such as development of cognitive ability. Therefore, the importance of de novo origination needs greater appreciation.
Seem to me that the authors are arguing that their findings are "inconsistent with the traditional view that the de novo origin of new genes is rare" and may need more examination in future, including revising our views about their rarity.
