A gene that sets primates (apes and humans) apart from other mammals

_{Denyse O'Leary

December 10, 2018

Genomics, Human evolution, Intelligent Design}

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University of Otago researchers have discovered information about a gene that sets primates — great apes and humans — apart from other mammals, through the study of a rare developmental brain disorder.

…

Dr O’Neill and research collaborators from Max Planck Institute of Psychiatry, Germany, then set forth to test the point that the gene drives aspects of brain development that are unique to primates. Some amazing data was found using a novel approach through studying human “mini-brains” in culture. It is now possible to take a skin cell and transform it using a set of genetic tricks, so that it can be triggered to form a tiny brain-like structure in culture in the lab.

Their results showed that the particular genetic change that disabled a component of this gene (PLEKHG6) altered its ability to support the growth and proliferation of specialised stem cells in the developing brain. In addition, some of these cells also failed to migrate to their correct position in the growing “mini-brain” during the first few weeks of brain development.

Professor Robertson says it has been known for a while that these stem cells behave differently between primates/humans and other animals, but understanding what genes regulate these differences has been a mystery.

“Adam’s achievement has been to show that this particular component of the PLEKHG6 gene is one such regulator that humans have ‘acquired’ very recently in their evolution to make their brains ‘exceptional’.”

Dr O’Neill says there are very few genetic elements that are primate specific in our genome, so this discovery adds to a very short list of genetic factors that, at least in one sense, make us human. – Material provided by the University of Otago More.

Here’s the paper. (open access) Summary:

The mammalian neocortex has undergone remarkable changes through evolution. A consequence of
such rapid evolutionary events could be a trade-off that has rendered the brain susceptible to certain neurodevelopmental and neuropsychiatric conditions. We analyzed the exomes of 65 patients with the structural brain malformation periventricular nodular heterotopia (PH). De novo coding variants were observed in excess in genes defining a transcriptomic signature of basal radial glia, a cell type linked to brain evolution. In addition, we located two variants in human isoforms of two genes that have no ortholog in mice. Modulating the levels of one of these isoforms for the gene PLEKHG6 demonstrated its role in regulating neuroprogenitor differentiation and neuronal migration via RhoA, with phenotypic recapitulation of PH in human cerebral organoids. This suggests that this PLEKHG6 isoform is an example of a primate-specific genomic element supporting brain development.

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See also: Researchers: Primates vary in speech capability. (But none speak.)

and

Study: Humans are the only primates that show kindness?

Comments

Is PavelU ever going to make the case that the evidence supports Darwinian evolution?ET_{December 11, 2018
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bornagain77 at 4, you relate: Kangaroo genes close to humans – 2008 Excerpt: Australia’s kangaroos are genetically similar to humans,,, “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order,” ,,,”We thought they’d be completely scrambled, but they’re not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,” http://www.reuters.com/article.....P020081118 Well, it that (the chunks) does not at least excite curiosity about whether what we have been told about origins is correct, I can't think what would.News_{December 11, 2018
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PLEKHG6 pleckstrin homology and RhoGEF domain containing G6 [ Lipotes vexillifer (Yangtze River dolphin) ] https://www.ncbi.nlm.nih.gov/gene/103072727
bornagain77_{December 10, 2018
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Of related interest, the supposed 98.5% genetic similarity was recently, by two different studies, revised downwards to approx. 85%:
Geneticist: On (Supposed 99%) Human-Chimp Genome Similarity, There Are “Predictions” Not “Established Fact” - July 31, 2018 Excerpt: To come up with the most accurate current assessment that I could of the similarity of the human and chimpanzee genome, I downloaded from the UCSC genomics website the latest alignments (made using the LASTZ software) between the human and chimpanzee genome assemblies, hg38 and pantro6.,,, The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38% In order to assess how improvements in genome assemblies can change these figures, I did the same analyses on the alignment of the older PanTro4 assembly against Hg38 (see discussion post #40).,,, The percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 82.34%. - Richard Buggs https://evolutionnews.org/2018/07/geneticist-on-human-chimp-genome-similarity-there-are-predictions-not-established-fact/ New Chimp Genome Confirms Creationist Research BY JEFFREY P. TOMKINS, PH.D. * | FRIDAY, SEPTEMBER 28, 2018 Excerpt: The first time they constructed a chimp genome and compared it to humans, they claimed 98.5% DNA similarity based on cherry-picked regions that were highly similar to human. However, an extensive DNA comparison study I published in 2016 revealed two major flaws in their construction of the chimp genome.1 First, many chimp DNA data sets were likely contaminated with human DNA, especially those produced in the first half of the chimpanzee genome project from 2002 to 2005. Second, the chimpanzee genome was deliberately constructed to be more human-like than it really is.2 Scientists assembled the small snippets of chimp DNA onto the human genome, using it as a scaffold or reference. It’s much like putting together a jigsaw puzzle by looking at the picture on the box as a guide. Since many chimpanzee data sets likely suffered from human DNA contamination, the level of humanness was amplified. I studied the 2005–2010 data sets that showed less human DNA data contamination and found they were only 85% similar to human at best.1 Just this year, scientists published a new version of the chimpanzee genome.3 This new version incorporated an advanced type of DNA sequencing technology that produces much longer snippets of DNA sequence than earlier technologies. It also involved better protocols that greatly reduce human DNA contamination. And most importantly, the authors report that the DNA sequences have been assembled without using the human genome as a scaffold. They also acknowledged the flawed nature of previous versions of the chimp genome: The higher-quality human genome assemblies have often been used to guide the final stages of nonhuman genome projects, including the order and orientation of sequence contigs and, perhaps more importantly, the annotation of genes. This bias has effectively “humanized” other ape genome assemblies.3 This confirms what many creationists have been pointing out for years. Curiously, the authors of the new chimp genome paper said very little about the overall DNA similarity between humans and chimpanzees. However, the University of London’s specialist in evolutionary genomics, Dr. Richard Buggs, evaluated the results of an analysis that compared this new chimp version to the human genome and discovered some shocking anti-evolutionary findings. Dr. Buggs reported on his website that “the percentage of nucleotides in the human genome that had one-to-one exact matches in the chimpanzee genome was 84.38%” and “4.06% had no alignment to the chimp assembly.”?4 Assuming the chimpanzee and human genomes are about the same size, this translates to an overall similarity of only about 80%! This outcome is way outside the nearly identical level of 98 to 99% similarity required for human evolution to seem plausible. http://www.icr.org/article/new-chimp-genome-confirms-creationist-research
Where you find the greatest differences between humans, chimps, kangaroos, dolphins, etc.. etc.. is not in the DNA sequences but is in the 'alternative splicing patterns' between different species. Species specific regulatory patterns that tell the genes how to get used within a species:
Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012 Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,, A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species. On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,, http://www.the-scientist.com/?articles.view%2FarticleNo%2F33782%2Ftitle%2FEvolution-by-Splicing%2F
Moreover, Alternatively spliced isoforms of proteins exhibit strikingly different interaction profiles and thus, in the context of global interactome networks, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,, and,,, As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes.
Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing - 2016 In Brief Alternatively spliced isoforms of proteins exhibit strikingly different interaction profiles and thus, in the context of global interactome networks, appear to behave as if encoded by distinct genes rather than as minor variants of each other.,,, Page 806 excerpt: As many as 100,000 distinct isoform transcripts could be produced from the 20,000 human protein-coding genes (Pan et al., 2008), collectively leading to perhaps over a million distinct polypeptides obtained by post-translational modification of products of all possible transcript isoforms (Smith and Kelleher, 2013). http://iakouchevalab.ucsd.edu/publications/Yang_Cell_OMIM_2016.pdf
To say alternative splicing patterns that are unique to each species is a problem for Darwinian claims is an understatement. 'Species specific' alternative splicing patterns, since they are part of the developmental Gene Regulatory Network (dGRN), and since they are extremely intolerant to 'adjustments', straight-up falsify Darwinian claims.
A Listener's Guide to the Meyer-Marshall Debate: Focus on the Origin of Information Question - Casey Luskin - December 4, 2013 Excerpt: "There is always an observable consequence if a dGRN (developmental gene regulatory network) subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way." - Eric Davidson - developmental biologist - per ENV
Like everything else that goes against their theory, unique alternative splicing patterns within species falsifies Darwinian claims, but Darwinists simply ignore any and all falsifying evidence of their claims:
,,,Alternative splicing,,, may contribute to species differences - December 21, 2012 Excerpt: After analyzing vast amounts of genetic data, the researchers found that the same genes are expressed in the same tissue types, such as liver or heart, across mammalian species. However, alternative splicing patterns—which determine the segments of those genes included or excluded—vary from species to species.,,, The results from the alternative splicing pattern comparison were very different. Instead of clustering by tissue, the patterns clustered mostly by species. "Different tissues from the cow look more like the other cow tissues, in terms of splicing, than they do like the corresponding tissue in mouse or rat or rhesus," Burge says. Because splicing patterns are more specific to each species, it appears that splicing may contribute preferentially to differences between those species, Burge says,,, Excerpt of Abstract: To assess tissue-specific transcriptome variation across mammals, we sequenced complementary DNA from nine tissues from four mammals and one bird in biological triplicate, at unprecedented depth. We find that while tissue-specific gene expression programs are largely conserved, alternative splicing is well conserved in only a subset of tissues and is frequently lineage-specific. Thousands of previously unknown, lineage-specific, and conserved alternative exons were identified; http://phys.org/news/2012-12-evolution-alternative-splicing-rna-rewires.html
Moreover, it doesn't matter how genetically similar two different species may be. Body plans simply are not reducible to mutations to DNA (as was presupposed in Darwinian thought). As Dr. Stephen Meyer puts it, "you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan."
‘Now one more problem as far as the generation of information. It turns out that you don’t only need information to build genes and proteins, it turns out to build Body-Plans you need higher levels of information; Higher order assembly instructions. DNA codes for the building of proteins, but proteins must be arranged into distinctive circuitry to form distinctive cell types. Cell types have to be arranged into tissues. Tissues have to be arranged into organs. Organs and tissues must be specifically arranged to generate whole new Body-Plans, distinctive arrangements of those body parts. We now know that DNA alone is not responsible for those higher orders of organization. DNA codes for proteins, but by itself it does not insure that proteins, cell types, tissues, organs, will all be arranged in the body-plan. And what that means is that the Body-Plan morphogenesis, as it is called, depends upon information that is not encoded on DNA. Which means you can mutate DNA indefinitely. 80 million years, 100 million years, til the cows come home. It doesn’t matter, because in the best case you are just going to find a new protein some place out there in that vast combinatorial sequence space. You are not, by mutating DNA alone, going to generate higher order structures that are necessary to building a body plan. So what we can conclude from that is that the neo-Darwinian mechanism is grossly inadequate to explain the origin of information necessary to build new genes and proteins, and it is also grossly inadequate to explain the origination of novel biological form.’ - Stephen Meyer – Functional Proteins and Information for Body Plans – video https://youtu.be/hs4y4XLGQ-Y
Actually, via Godel's incompleteness theorem being extended to physics, the problem of biological form, for any reductive materialistic explanation of Darwinian evolution is found to go much deeper than just mutations to DNA itself In the following article entitled 'Quantum physics problem proved unsolvable: Gödel and Turing enter quantum physics', which studied the derivation of macroscopic properties from a complete microscopic description, the researchers remark that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,, The researchers further commented that their findings challenge the reductionists' point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description."
Quantum physics problem proved unsolvable: Gödel and Turing enter quantum physics - December 9, 2015 Excerpt: A mathematical problem underlying fundamental questions in particle and quantum physics is provably unsolvable,,, It is the first major problem in physics for which such a fundamental limitation could be proven. The findings are important because they show that even a perfect and complete description of the microscopic properties of a material is not enough to predict its macroscopic behaviour.,,, "We knew about the possibility of problems that are undecidable in principle since the works of Turing and Gödel in the 1930s," added Co-author Professor Michael Wolf from Technical University of Munich. "So far, however, this only concerned the very abstract corners of theoretical computer science and mathematical logic. No one had seriously contemplated this as a possibility right in the heart of theoretical physics before. But our results change this picture. From a more philosophical perspective, they also challenge the reductionists' point of view, as the insurmountable difficulty lies precisely in the derivation of macroscopic properties from a microscopic description." - per physorg
Here are a few more notes to drive this point home:
Darwinism vs Biological Form – video https://www.youtube.com/watch?v=JyNzNPgjM4w
To state what should be glaringly obvious, since neo-Darwinian (reductive materialistic) explanations are grossly inadequate for explaining how any particular organism might achieve its basic form, then neo-Darwinian speculations for how one type of organism might transform into another type of organism are based on pure fantasy and have no discernible experimental basis in reality. Whereas, on the other hand, Theism, especially with these recent breakthroughs in quantum biology,,,
Darwinian Materialism vs Quantum Biology - video https://www.youtube.com/watch?v=LHdD2Am1g5Y
,,,is found to be very well supported in its claim that God has formed each of us in our mother’s womb. Verses:
Psalm 139:13-14 For You formed my inward parts; You covered me in my mother’s womb. I will praise You, for I am fearfully and wonderfully made; Marvelous are Your works, And that my soul knows very well. Jeremiah 1:5 “Before I formed you in the womb I knew you, before you were born I set you apart; I appointed you as a prophet to the nations.” Psalm 139:13 For you created my inmost being; you knit me together in my mother's womb.
bornagain77_{December 10, 2018
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Something tells me that this gene that supposedly sets "primates — great apes and humans — apart from other mammals" will probably be found in kangaroos and dolphins as well:
Kangaroo genes close to humans - 2008 Excerpt: Australia's kangaroos are genetically similar to humans,,, "There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order," ,,,"We thought they'd be completely scrambled, but they're not. There is great chunks of the human genome which is sitting right there in the kangaroo genome," http://www.reuters.com/article/science%20News/idUSTRE4AH1P020081118 Dolphin DNA very close to human, - 2010 Excerpt: They’re closer to us than cows, horses, or pigs, despite the fact that they live in the water.,,, “The extent of the genetic similarity came as a real surprise to us,” ,,, “Dolphins are marine mammals that swim in the ocean and it was astonishing to learn that we had more in common with the dolphin than with land mammals,” says geneticist Horst Hameister.,,, “We started looking at these and it became very obvious to us that every human chromosome had a corollary chromosome in the dolphin,” Busbee said. “We’ve found that the dolphin genome and the human genome basically are the same. It’s just that there’s a few chromosomal rearrangements that have changed the way the genetic material is put together.” http://www.reefrelieffounders.com/science/2010/10/21/articlesafari-dolphin-dna-very-close-to-human/ Kolber, J., 2010, Dolphin DNA very close to human, Kumar, S., 2010, Human genes closer to dolphin’s than any land animal, Discovery Channel Online, Richard Sternberg PhD – podcast – On Human Origins: Is Our Genome Full of Junk DNA? Part 2. (Major Differences in higher level chromosome spatial organization) 5:30 minute mark quote: “Basically the dolphin genome is almost wholly identical to the human genome,, yet no one would argue that bottle-nose dolphins are our sister species”,,, http://www.discovery.org/multimedia/audio/2014/11/on-human-origins-is-our-genome-full-of-junk-dna-pt-2/
While Darwinists often appeal to genetic similarity to try to argue for common descent, Darwinists will completely ignore genetic similarity when it falsifies their theory of common descent. For instance, identical forms of echolocation show up in widely divergent species. This finding is unexpected from an evolutionary perspective, yet this finding is exactly what we would expect to find from presupposing a Creator to reuse optimal designs:
Common Design in Bat and Whale Echolocation Genes? - January 2011 Excerpt: two new studies in the January 26th issue of Current Biology, a Cell Press publication, show that bats' and whales' remarkable ability and the high-frequency hearing it depends on are shared at a much deeper level than anyone would have anticipated -- all the way down to the molecular level. http://www.evolutionnews.org/2011/01/common_design_in_bat_and_whale042291.html
In fact, "convergent evolution", i.e. unexpectedly similar designs showing up in widely divergent species, is far more widespread of a problem for Darwinists than they will ever honestly admit:
Bothersome Bats and Other Pests Disturb the "Tree of Life" - Casey Luskin - December 5, 2012 Excerpt: But this is hardly the only known example of molecular convergent evolution. In his book The Cell's Design, chemist and Darwin-skeptic Fazale Rana reviewed the technical literature and documented over 100 reported cases of convergent genetic evolution. Each case shows an example where biological similarity -- even at the genetic level -- is not the result of inheritance from a common ancestor. http://www.evolutionnews.org/2012/12/bothersome_bats067121.html Simon Conway Morris: “Fossil evidence demands a radical rewriting of evolution.” – March 2012 Excerpt: “The idea is this: that convergence – the tendency of very different organisms to evolve similar solutions to biological problems – is not just part of evolution, but a driving force. To say this is an unconventional view would be something of an understatement.” https://uncommondescent.com/evolution/simon-conway-morris-fossil-evidence-demands-a-radical-rewriting-of-evolution/
In fact, Simon Conway Morris has a website documenting hundreds, if not thousands, of examples of unexpected and unexplained 'convergent evolution':
Map Of Life – Simon Conway Morris http://www.mapoflife.org/browse/
"Convergent Evolution", in reality, is actually another shining example that Darwinian evolution is a unfalsifiable pseudoscience instead of a real, i.e. testable, science.
Darwinist: Aha you see, genetic similarity, just what Darwinism would expect! Darwin skeptic: But what about all these examples of genetic similarity in widely divergent species that falsify your claim for common descent? Darwinist: It evolved in those species too you idiot. Don't you see they stuck the word evolution behind the word convergent? Darwin skeptic: (bangs head on desk)
Here are a few more in depth notes on the unfalsifiable nature of the pseudoscience of Darwinian evolution:
Darwin’s Theory vs Falsification – video https://www.youtube.com/watch?v=8rzw0JkuKuQ
bornagain77_{December 10, 2018
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No, PavelU. This in no way supports Darwinian evolution. Darwinian evolution can't even account for the existence of eukaryotes and it has to be given starting populations of prokaryotes.ET_{December 10, 2018
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This seems like bad news for the ID fans. More evidence supporting Darwinian evolution. I don't expect any reaction from the ID side, though. Just silence.PavelU_{December 10, 2018
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Looking forward to my upcoming brain transplant!Mung_{December 10, 2018
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