Saturday, 1 May 2021

Evolution News - Filling More of Creationism's God-Shaped Gaps With Science

Researchers performed a more detailed comparison of the genomes of modern and archaic humans and found that the way genes turned on and off could have resulted in changes in the brain and vocal tract.
Image: Getty Images
Stanford study dives deeper into genetic differences between modern and archaic humans

I've just posted an article about how advances in techniques for DNA recovery and analysis are closing Creationism's god-shaped gaps by the dozen and finding no gods and no place for gods in them. Now here is another example from Stanford University, where researchers have developed a technique for analysing not only the DNA sequence of ancient hominins but also the likely way they were activated.

This opens up the prospect of a far greater depth of analysis of ancient DNA than simply sequencing it, and so discovering finer details not only of DNA changes but changes in the way particular genes were activated. Changes in the sequence and duration of activation of genes during embryonic development can have a profound effect on the resulting genotype with little or no change in the genes themselves.

The Stanford group have used the technique to show how the brain and vocal tract evolved as our ability to vocalise developed.

The Stanford News Service article by Taylor Kubota explains how this was done:
A genome by itself is like a recipe without a chef – full of important information, but in need of interpretation. So, even though we have sequenced genomes of our nearest extinct relatives – the Neanderthals and the Denisovans – there remain many unknowns regarding how differences in our genomes actually lead to differences in physical traits.

When we’re looking at archaic genomes, we don’t have all the layers and marks that we usually have in samples from present-day individuals that help us interpret regulation in the genome, like RNA or cell structure, we just have the naked DNA sequence, and all we can really do is stare at it and hope one day we’d be able to understand what it means.

Dr. David Gokhman, Senior author
Department of Biology,
Stanford University, Stanford, USA.
“When we’re looking at archaic genomes, we don’t have all the layers and marks that we usually have in samples from present-day individuals that help us interpret regulation in the genome, like RNA or cell structure,” said David Gokhman, a postdoctoral fellow in biology at Stanford University.

“We just have the naked DNA sequence, and all we can really do is stare at it and hope one day we’d be able to understand what it means,” he said.

Motivated by such hopes, a team of researchers at Stanford and the University of California, San Francisco (UCSF), have devised a new method to harvest more information from the genomes of archaic humans to potentially reveal the physical consequences of genomic differences between us and them.

Their work, published April 22 in eLife, focused on sequences related to gene expression – the process by which genes are activated or silenced, which determines when, how and where DNA’s instructions are followed. Gene expression tends to be the genetic detail that determines physical differences between closely related groups.

It just seems so implausible that you could make a call like, ‘I think the voice box evolved,’ from the information we have. The predictions are almost science fiction. If five years ago, somebody told me that this would be possible, I would not have put much money on it.

This goes beyond the sequencing of the DNA from the Neanderthal and Denisovan bones. This begins to put meaning on those differences. It’s an important conceptual step from just the sequence – no tissue, no cells – to biological information and will enable many future studies.

Dmitri Petrov, Senior Co-author
Michelle and Kevin Douglas Professor
School of Humanities and Sciences Stanford University, Stanford, USA
Starting with 14,042 genetic variants unique to modern humans, the researchers found 407 that specifically contribute to differences in gene expression between modern and archaic humans. In further analysis, they determined that the differences were more likely to be associated with the vocal tract and the cerebellum, which is the part of our brain that receives sensory information and controls voluntary movement, including walking, coordination, balance and speech.

“It just seems so implausible that you could make a call like, ‘I think the voice box evolved,’ from the information we have,” said Dmitri Petrov, the Michelle and Kevin Douglas Professor in the School of Humanities and Sciences, who is co-senior author of the paper with Gokhman and Nadav Ahituv, a professor of bioengineering at UCSF. “The predictions are almost science fiction. If five years ago, somebody told me that this would be possible, I would not have put much money on it.”

The path to modern humans


With such a large number of variants to examine, the researchers relied on a technique called a “massively parallel reporter assay” to test which sequences actually affect gene regulation. Their version of this technique, which was developed by Ahituv, involves packaging the DNA sequence variant into a “reporter gene” inside a virus. That virus is then put into a cell. If that variant affects gene expression, the reporter gene produces a barcoded molecule that identifies what DNA sequence it came from. The barcode allows the researchers to scan the products of a large number of variants at once.

This would suggest some kind of rapid evolution of those organs or some kind of a path that is specific to modern humans.

Dr. David Gokhman
Essentially, the whole process imitates an abridged version of how each variant would play out in a cell in real life and reports the results.

Lana Harshman, a graduate student at UCSF and co-lead author of the paper, infected three types of cells with the team’s variant packages. These cells were related to the brain, skeleton and early development – subjects that are most likely to reveal evolutionary differences between us and our most recent ancestors. Carly Weiss, a postdoctoral scholar in the Petrov lab and co-lead author of the paper, analyzed the results of these experiments.

In total, the researchers found 407 sequences that represented a change in expression in modern humans compared to our predecessors. Among that list, genes that affect the cerebellum and genes that affect the voice box, pharynx, larynx and vocal cords seem to be overrepresented.

“This would suggest some kind of rapid evolution of those organs or some kind of a path that is specific to modern humans,” said Gokhman. The next step, he added, would be trying to understand more about these sequences and the roles they played in the evolution of modern humans.

Even with those unknowns, this technique by itself is a significant advance for evolutionary research, said Petrov.

“This goes beyond the sequencing of the DNA from the Neanderthal and Denisovan bones. This begins to put meaning on those differences,” said Petrov. “It’s an important conceptual step from just the sequence – no tissue, no cells – to biological information and will enable many future studies.”
Using lentivirus-based MPRA (lentiMPRA) to identify variants driving differential expression in modern humans.
The Stanford team's results can be read in their open access paper in eLife.

Abstract


The Neanderthal and Denisovan genomes enabled the discovery of sequences that differ between modern and archaic humans, the majority of which are noncoding. However, our understanding of the regulatory consequences of these differences remains limited, in part due to the decay of regulatory marks in ancient samples. Here, we used a massively parallel reporter assay in embryonic stem cells, neural progenitor cells, and bone osteoblasts to investigate the regulatory effects of the 14,042 single-nucleotide modern human-specific variants. Overall, 1791 (13%) of sequences containing these variants showed active regulatory activity, and 407 (23%) of these drove differential expression between human groups. Differentially active sequences were associated with divergent transcription factor binding motifs, and with genes enriched for vocal tract and brain anatomy and function. This work provides insight into the regulatory function of variants that emerged along the modern human lineage and the recent evolution of human gene expression.

Imagine being a Creationist fraud like Ken Ham, Ray Comfort or Kent Hovind discovering that yet another scientific thread supporting the TOE and in particular showing how humans evolved over millions of years from ape ancestors via archaic hominins, just got lot stronger. That's exactly what's just happened with the genetic evidence for the TOE which shows the relationships between these ancient hominin fossils, so closing any gaps there may have been.

Imagine being gullible enough to fall for the lie that the TOE is a theory in crisis with evidence like this now piling up daily, thanks to these sorts of advances in scientific techniques!

And yet, 40% of Americans still believe the childish story of magic creation they inherited from their parents is the best explanation for what we can observe, and Talibangelical Christians are still trying to fool courts into allowing them to teach children that myth as real science at public expense as a prelude to installing a Taliban-style Christian fundamentalist theocracy in the USA.


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