Anomalous Genome Rearrangement Preceded the Modern Human Brain

[9] - New Genomic Data Disputes Random Mutation & Natural Selection

The complex modern human brain emerged gradually over millions of years through random mutations and natural selection. That’s the familiar story we all learnt, but today we can officially cast it into the rubbish bin of history.

After my last article on this theme, I was planning to follow up by discussing various extraordinary genes involved in brain formation. Unfortunately, the ups and downs of my personal life and well—being, stress and depression, temporarily derailed me. Perhaps it was for the best, at least with respect to the forced delay, as you will perhaps agree.

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The Zoonomia Project

The Zoonomia Project is an international collaboration to discover the genomic basis of shared and specialized traits in mammals.

“By sequencing and comparing the genomes of hundreds of diverse mammals, Zoonomia is identifying segments unchanged across all species, as well as segments changed in just a few. We are discovering both the genomic basis of traits essential for all animals and changes that underlie the unique traits of individual species.

Data from the Zoonomia project are enabling us to assess every position in the genome for variation across 240 different mammalian species. Positions that have stayed the same across most or all of the mammalian species sampled — spanning roughly 100 million years of evolutionary time —  likely serve some important function, and hence could cause disease if changed by mutation.”

Please, just cast your mind back to our previous discussions of Human Accelerated Regions (HARs) and Human Conserved Deletions (hCONDELs). It turns out that our timing there was rather prescient as we now have an update to this research story. Dr Pollard and her team over at the Gladstone Institute are among the scientists making use of the Zoonomia Project data.

The findings are nothing short of startling. Well, they would be if you had not already been hearing about a mind-bending revised story of human origins that involves genetic intervention.

Before we get into the specifics, I strongly suggest that you watch this powerful presentation just given at the SALT conference by Dr Garry Nolan, a Stanford Geneticist.

Alex Klokus - “I'm curious do you believe that extraterrestrial intelligence has visited planet Earth?”

Dr Garry Nolan - “I think you can go a step further it hasn't just visited it's been here a long time and it's still here.”

[snip]

Dr Garry Nolan - “…they don't have to land on the White House lawn we can only think the joke about is there intelligence in DC at all right you, you just need to show yourself to enough to acculturate. Yeah, now, if you've been around for a long time, and this is something that I do think has been going on, they've been around for a long time, they are affecting our culture, right? It's actually often thought that many of the religions that we think of as the most important have been part of this process.”

“The idea I really like is ‘genomic SETI’. We search right here on Earth for artefacts in the genomes of terrestrial organisms.” – Professor Paul Davies

Consider just how far along we have come in the last few years. Professor Avi Loeb, the senior Harvard astronomer, founded a project that is looking for alien probes in our solar system and possibly hidden among the UFO reports here on Earth.

Now we have a respected Stanford geneticist stating that he is 100% certain an extraterrestrial intelligence is here alongside us and has been for a very long time.

Meanwhile, the US government has founded a new department, AARO, to examine anomalous phenomena in our atmosphere and instructed NASA to explore related efforts.

We are definitely not in Kansas anymore.

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One Giant Leap for Mankind

According to the findings of the new Gladstone Institute study, unexpected strangeness occurred in our ancestral lineage around one million years ago. Suddenly and inexplicably, large segments of the human genome went through profound rearrangement.

The results are observable deletions, duplications and reversal of sections of DNA. Once these structural variations occurred they would have initiated ongoing exponential rapid changes in human DNA associated with features unique to humans. Most notably, much of the reconfiguration impacted brain development.

This major change did not happen in a drawn-out series of copy errors, or random mutations, but instead emerged in the development of a single foetus. Possibly, occurring in a singular egg or sperm as it formed, but certainly in a single hominin infant.

Keep in mind we are not talking about a readily comprehensible genetic change here, oh no, no, no. This child had a significant number of significantly changed highly conserved regions. Recall here that the HARs had been stable for tens or even hundreds of millions of years.

Indeed, thanks to the latest research work we now know that across 240 mammalian species, there are no signs of a similar evolutionary leap. Their highly conserved regions remained highly conserved, rarely even exhibiting singular point mutations.

Only in humans does a smorgasbord of acceleration, deletion and rearrangement suddenly occur. The bulk of which played a role in giving us our astonishing cognitive abilities. By all the known laws of chance, so many changes in crucial conserved regions should have killed that child (if it really was only one not multiple children).

These regions are stable for good reason, their functions are crucial for life. That a random event would change hundreds of these regions and it not only be survivable but actually beneficial, is nothing short of magical.

“Any sufficiently advanced technology is indistinguishable from magic.”

- Arthur C. Clark

Scrambled Structure

While I am less interested in the technical details of the anomalous evolutionary changes than the mere fact this occurred, for your possible interest I will share some of the specifics.

As touched on, large segments of the DNA building blocks have undergone insertions, deletions, or rearrangements in the human genome. These modifications cause human DNA to fold differently in the nucleus when compared with our closest living primate relatives.

Many genes within HARs are linked to other genes, acting as enhancers that increase the transcription of their linked genes. Of 312 HARS of particular interest, almost 30 per cent are in the regions of DNA where structural variations cause the genome to fold differently in humans.

These same regions of interest were replete with a large number of the genes that differentiate humans from closely related primates like chimpanzees. Experimental investigation revealed that one-third of identified HARs were transcribed specifically during the development of the human neocortex.

The human neocortex is the most recent, and arguably most beneficial, brain region in human beings. It makes up 75% of our total brain mass and is involved with most of our uniquely human behavioural traits.

Additionally, many of the HARs play roles in embryo development. Among the processes, these HARs are involved in are the formation of neural pathways associated with intelligence.

Many of the skills that differentiate humans from other creatures, reading, social skills, memory, attention and focus are linked to these significantly modified highly conserved regions. It would not be wrong to suggest they actually made us into Homo sapiens.

I will let the rest of the paper speak for itself. Should you wish to explore the research in its full depth check it out here, Three-dimensional genome rewiring in loci with human accelerated regions.

The biggest takeaway for me is that far more unexpected changes occurred than previously known and they were even more anomalous and rapid than previous studies had recognised. As research continues in this field we are seeing the signal for manipulation grow ever stronger, rather than weakening, suggesting we are on the correct track.

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Weird Genes

Having tackled the breaking news, I do still want to address some of the most intriguing genes involved in our brain’s evolutionary development.

The first peculiar gene of note is ARHGAP11B, a gene discovered to be highly active within the human neural progenitor cells but entirely absent from examined mouse cells. Marta Florio, a molecular and cellular biologist at the Max Planck Institute, explains that this tiny snippet of DNA, just 804 letters long, is a short segment snipped out from another longer gene.

The observed appearance is that ARHGAP11B has been chopped up and then a select fragment duplicated and reinserted into the human genome. This is something scientists are doing today with so-called CRISPR/Cas9 gene editing technologies — but not something we would expect to see occurring hundreds of thousands of years ago.

The same gene, ARHGAP11B, seems to be uniquely human, it has not been found even in our primate relatives. Very notably, this crucial sliver of code is there in the genome of both Neanderthals and Denisovans. This tells us the replication and insertion happened before the now well-dated split between these human populations (approx 750 - 800kya).

The gene ARHGAP11B prompts the neocortex to produce many additional neurons. The neocortex is the most recently evolved section of the brain (hence the prefix neo-, meaning “new”). Some scientists suspect this tiny snippet of DNA laid the foundation for the human brain’s massive expansion.

The human neocortex has distinctive folds that allow for far greater information processing than possible with a large but smooth brain. Many genes are unique to humans, further separating us from primates. Most of these relate to our complex brain structure.

In 2020, scientists inserted ARHGAP11B into the fetus of a common marmoset monkey, causing the enlargement of its brain’s neocortex.

Plans are afoot for more monkeying around with human brain genes, indeed Chinese scientists inserted MCPH1 in macaque monkeys and found that it improved memory skills. They are looking to run similar trials with SRGAP2C, a gene suspected to have given Homo erectus the intellectual edge over Australopithecus, and the language-associated gene, FOXP2.

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Planet of the Apes

Another intriguing gene which plays a crucial role in human brain development is miR-941. This gene is highly active in brain regions controlling decision-making and enabling language abilities.

The study of miR-941 has caused researchers to speculate that its involvement in advanced higher brain functions is fundamental to making us human.

This gene, miR-941, seems to have inexplicably suddenly emerged fully functional from noncoding DNA regions. The emergence date has been suggested as perhaps around one million years ago, it certainly preceded the divergence of Denisovans, as they also carry the gene.

Listening to the opinions of one member of the miR-941 research project, Martin Taylor of the University of Edinburgh, we get the impression he suspects that it appeared around the time of the sudden rapid brain growth observed in the fossil record from 800,000 years ago. Taylor explains that the gene “sprang from nowhere at a time when our species was undergoing dramatic changes.”

Perhaps one of the best-known human genes is the aforementioned FOXP2, implicated in the emergence of human language abilities. Researchers from MIT and several European universities have shown that the human version of the gene makes it easier to transform new experiences into routine procedures.

The FOXP2 protein sequence is very strongly conserved in mammalian evolution. Human FOXP2 differs by two amino acids from that of chimpanzees, gorillas, and macaques, all of which have identical sequences. These two amino acid fixations are rather unlikely to manifest by chance random mutation alone.

The initial changes in the FOXP2 transcriptional factor occurred after the split from our primate relatives but before the divergence of Neanderthals and Denisovans.

Neuroscientists have found that further mutations occurred in this gene about two hundred thousand years ago. These changes enhanced synaptic connectivity and adaptability in neural circuitry. It is widely believed to play a significant role in our ability to produce and understand speech.

Stanford’s Professor Garry Nolan has been exploring links between human intuition and cases of unusual enlargement of the caudate-putamen structures in the basal ganglion of the brain. FOXP2 is found to express in the development of the caudate and putamen.

Nolan has found a reason to suspect that the size of these structures impacts intuitive abilities. Could it be that our extraterrestrial benefactors wanted us to be able to effectively communicate through both speech and some form of higher psychical exchange?

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Hobbits, Dwarfs and Elves

Today we have indications that the rapid brain size increase did not occur for all lineages of early humans that lived ~800kya. Two diminutive hominins from Southeast Asia, Homo luzonensis (Philippines) and Homo floresiensis (Indonesia) retained fairly small brains. The same is true for at least one African hominin, Homo naledi.

While all of these smaller human cousins exhibit a mixture of archaic and more modern physiological and morphological traits, it is still unclear whether their ancestors were actually larger and had bigger brains. Certainly, in the case of both H. luzonensis and H. floresiensis it is possible the phenomena of island dwarfism came into play.

When a large mammal becomes isolated on a relatively small island, if free from predators, evolution tends to favour an overall decrease in body size. Brains are especially calorie hungry and if there is a struggle for sufficient calorie intake that is not aided by greater intelligence, evolutionary forces will select for smaller brain size.

Without DNA it is going to be hard to resolve the relationships between these other hominins and modern humans. They may represent hybrids between descendants of Homo erectus, Australopithecines and early Homo erectus. There are indications H. floresiensis had brain structures indicative of more modern human-like intellect, an asymmetrical brain for example.

Unlike the other two dwarf human types, Homo naledi was not limited to an island environment. It is therefore assumed it represents a population which simply remained more ape-like in size, rather than undergoing any process of isolation dwarfism. Ongoing research suggests that this hominin also had an asymmetrical brain and a frontal cortex reminiscent of modern humans.

There are growing suspicions that Homo naledi had some level of complex culture, involving the burial of the dead, intentional use of fire and perhaps symbolic representation. Might they even have used language?

What we really need to know is whether these hominins shared ancestry with us after ~800kya, interbred with our ancestors, or remained completely divergent from us. Could any of these beings represent a stream of humans that did not inherit the profound genomic changes we have been exploring?

To fully answer these evolutionary questions, we will need to find viable genetic material in their fossils.

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Conclusion

The greater the number of highly unexpected evolutionary events that geneticists uncover, the greater the likelihood that the conventional model of human evolution is wrong. The more anomalies that cluster around the start of the Homo sapiens lineage, the stronger the signal for genomic intervention becomes.

We not only have a lengthy list of counter-intuitive leaps in evolution, unique to humans but clustering in time. The fusion of chromosome-2, accelerated changes in highly conserved regions, deletion of large chunks of stable regulatory DNA, reconfiguration of structural folding and new brain genes appearing almost from nowhere.

It is not only notable that all of this weirdness is fundamental to modern humans, but we have to consider the necessity for these changes to spread across the entire species from a singular individual. Natural evolution would infer each of these astonishingly problematic events happened just once, in a single individual, then somehow spread across the global population.

This prevalence of the various mutations seemingly runs counter to the expectation that such severe mutations would be recessive, vanishing back into the normal population after breeding occurred. Would the carriers even look like viable mates, or instead appear visibly different, almost freakish?

In the intervention model not only do we expect overnight radical changes to be observed, as they now have been, but they would be present in multiple breeding pairs. The changes would therefore quickly stabilize within the new population. Offspring of the second generation, isolated from their unaltered relatives, could mate only with each other, ensuring the beneficial new traits were carried forwards in time.

Rather than all of these changes beating the evolutionary odds by millions to one, the reality would be that an intelligently guided process was at work. It is also likely a number of initial experiments failed, as inferred in our original source material.

Even with expert guidance for the engineering process, some of the fetuses would not survive manipulation of their critical regulatory DNA regions. These dead-ends are just not seen in our fossil records because they all died either during gestation or shortly after birth.

That modern human ancestors survived so many radical changes to their genome has no connection to the wheel of fortune, they were simply the only successful batch of modified embryos. Who knows how many times the experiments had to be run before the desired results were attained?

Reading between the lines, with all of the scientists expressing such shock at our many genomic anomalies, I imagine a significant number of engineered embryos failed to thrive. The alien engineers accelerated our evolution, ramping up survival of the fittest and genetic selection to break-neck speeds.

As I have explained in previous discussions, this can’t be proven. Science is not about proof, only evidence. Our starting hypothesis is that the Churinga artefact is providing an accurate download of lost history, including details of deliberate genomic engineering to create Homo sapiens. What we are finding in the real-world data is anomalies indicative of exactly the type of genomic engineering the Churinga download detailed.

No matter how strong the evidence for intervention gets, even if it becomes overwhelming, you must decide for yourself whether the account reflects reality. Even the most seemingly obvious truths can be countered and rejected. We see this phenomenon with respect to the shape of our Earth and NASA’s moon landings.

Our reality is based as much on the limits of our personal cognitive filters and preferences as it is on objective evidence. Some truths may not even be possible for us to believe.

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