F Rosa Rubicondior: Creationism in Crisis - How An Ancient Retrovirus Evolved To Create The Vertebrate Brain

Tuesday 20 February 2024

Creationism in Crisis - How An Ancient Retrovirus Evolved To Create The Vertebrate Brain

Ancient retroviruses played a key role in the evolution of vertebrate brains | ScienceDaily
Schematic diagram of a neuron show the myelin sheath as the electrical insulator of the axon.

Extinct Late Devonian placoderm Bothriolepis canadensis. Myelin first appeared in these primitive early fish

Credit: Nobumichi Tamura / Stocktrek Images / Getty.
Creationists generally hate endogenous retrovirus (ERV's) because:
  1. They are one of the strongest pieces of evidence of common descent appearing in the same locations in the genome of all organisms in a clade, forming nested hierarchies exactly as the Theory of Evolution predicts. The probability of the same viral DNA appearing in the same locus in all species in a clade by chance is, of course, so small it can be dismissed as an explanation.
  2. They form a large part of the 'junk' DNA carried by all organisms, which, although a small proportion of it is transcribed into RNA, the RNA doesn't get translated into proteins and most of it doesn't serve any purpose. Some, but by no means all of it may have some regulatory functions.
  3. Occasionally, an ancient ERV may have become exapted for some useful purpose unrelated to the original virus, so showing how new genetic information can enter a genome, flatly contradicting creationist's claims that no new information can arise within a genome because the second law of thermodynamics [sic] and Shannon Information Theory somehow forbids it.
  4. An ERV serving a useful purpose also contradicts creationist claims that, while their favourite creator god is responsible for all the good stuff, another creator, called 'Sin', is responsible for the harmful stuff like parasites and viruses. Yet in those exapted ERVs we have viruses providing something that is beneficial and therefore, according to creationist dogma, must have been provided by their god!
  5. Lastly, the examples of where ancient ERVs have mutated and provided some additional ability or function, such as enabling the formation of the myeline sheath in vertebrates, can't be regarded as detrimental mutations, yet creationist dogma, courtesy of the hapless Micheal J. Behe, is that all mutations are 'devolutionary'[sic].
Tell me all about endogenous retroviruses; how they got into our genome and how they are evidence for evolution, please. Endogenous retroviruses (ERVs) are remnants of ancient retroviral infections that have become integrated into the genomes of their host organisms. Retroviruses are a type of RNA virus that can reverse transcribe their RNA genomes into DNA, which can then be integrated into the host cell's genome. When retroviruses infect germ cells (sperm or egg cells), the viral DNA can be passed on to subsequent generations, becoming a permanent part of the host's genetic material. Over time, these integrated viral sequences may accumulate mutations and become inactive, but they are still recognizable as remnants of past viral infections.

The presence of ERVs in the genomes of various species is compelling evidence for evolution, supporting the theory of common descent. Here's how ERVs provide evidence for evolution:
  1. Shared ERVs between related species: ERVs can be found in the genomes of diverse organisms, including humans, other mammals, birds, reptiles, and more. The presence of similar or identical ERVs in the genomes of closely related species provides evidence of common ancestry. For example, humans and other primates share many ERVs, indicating a common evolutionary ancestor.
  2. ERVs at the same genomic locations: ERVs that are found at the same genomic locations in different species suggest that these sequences were present in the common ancestor of those species and were inherited through descent with modification. The likelihood of ERVs inserting into exactly the same genomic location independently in different species is extremely low, providing convincing evidence for common ancestry. For instance, a specific ERV found at the same location in the genomes of humans and chimpanzees supports the hypothesis of a shared evolutionary history.
  3. Functional remnants of ERVs: While many ERVs have accumulated mutations over time and are no longer functional, some ERVs retain functional elements that can influence gene regulation and expression. For example, certain ERVs contain regulatory sequences that control the expression of nearby genes. The presence of functional remnants of ERVs in the genomes of various species underscores their evolutionary significance and their potential to contribute to genetic diversity and adaptation.
  4. Comparative genomics: Comparative genomic analyses, which involve comparing the genomes of different species, reveal patterns of ERV distribution and evolution that are consistent with the evolutionary relationships inferred from other types of data, such as morphological and molecular similarities. These analyses provide additional evidence supporting the evolutionary relatedness of different species.
Overall, the presence of endogenous retroviruses in the genomes of diverse organisms, their shared distribution patterns, and their evolutionary implications provide compelling evidence for common descent and the evolutionary history of life on Earth.


Certainly! Here are a few examples of endogenous retroviruses (ERVs) and their significance in providing evidence for evolution:
  1. HERV-W and human evolution: Human endogenous retrovirus type W (HERV-W) is a family of ERVs found in the human genome. One particular HERV-W insertion, called ERVWE1 or Syncytin-1, has been co-opted for a functional role in human biology. Syncytin-1 is involved in placental development and is essential for the formation of the syncytiotrophoblast layer, which plays a crucial role in the exchange of nutrients between the mother and fetus during pregnancy. The presence of HERV-W elements in the human genome, including functional elements like Syncytin-1, provides evidence of past retroviral infections and their subsequent integration into the human lineage. This integration and subsequent co-option of viral elements for a beneficial function illustrate how ERVs can shape the evolution of their host organisms.
  2. Fossil ERVs in the primate lineage: Comparative genomic analyses have revealed shared ERV insertions among various primate species, including humans, chimpanzees, gorillas, and orangutans. One notable example is the presence of a specific ERV insertion called HERV-K111 in the genomes of humans and African apes (chimpanzees, gorillas). This shared ERV insertion at the same genomic location provides compelling evidence for a common evolutionary ancestor of humans and African apes. Additionally, the absence of this ERV insertion in the genomes of orangutans, which diverged from the human-chimpanzee lineage earlier, supports the evolutionary relatedness of humans and African apes.
  3. ERV-derived regulatory elements in mammalian genomes: Some ERVs contain regulatory sequences that can influence the expression of nearby genes. For example, certain ERV-derived sequences act as enhancers or promoters, modulating the expression of adjacent genes during development or in response to environmental stimuli. The presence of these ERV-derived regulatory elements in the genomes of diverse mammalian species, with variations in their activity and effects on gene expression, provides evidence for their evolutionary conservation and functional significance across different lineages.
These examples highlight how the study of ERVs in the genomes of various organisms can shed light on their evolutionary history, including shared ancestry, genetic adaptation, and the co-option of viral elements for beneficial functions.
And now we have another example of an ancient ERV which mutated in the early evolutionary history of the vertebrates, and played an essential part on the evolution of the myelin sheath that surrounds the axon of a nerve cell and so allowed the vertebrate brain to evolve into its present form.

Although it has to be said that this example is not quite so compelling evidence of evolution as some ERVs since the suggestion is that the mutations occurred independently in mammals, amphibians and fish. This may be because the same virus infected these taxons at different times, in which case we would expect to see it at different loci in the genomes of the respective classes, but it's not clear whether this was the case, or whether the retrovirus was exapted at different times in each order, by a process of convergent evolution.
The team that discovered this, led by Tanay Ghosh, a computational biologist and geneticist in neuroscientist Robin Franklin's lab in Altos Labs-Cambridge Institute of Science, Cambridge, UK, have published the findings in the Cell Press journal Cell. It is also the subject of a press release from Cell Press, cited in Science Daily:
Researchers report February 15 in the journal Cell that ancient viruses may be to thank for myelin -- and, by extension, our large, complex brains. The team found that a retrovirus-derived genetic element or "retrotransposon" is essential for myelin production in mammals, amphibians, and fish. The gene sequence, which they dubbed "RetroMyelin," is likely a result of ancient viral infection, and comparisons of RetroMyelin in mammals, amphibians, and fish suggest that retroviral infection and genome-invasion events occurred separately in each of these groups.

Retroviruses were required for vertebrate evolution to take off. If we didn't have retroviruses sticking their sequences into the vertebrate genome, then myelination wouldn't have happened, and without myelination, the whole diversity of vertebrates as we know it would never have happened.

Robin Franklin, senior author
Altos Labs-Cambridge Institute of Science, Cambridge, UK.
It enables rapid impulse conduction without needing to increase axonal diameter, which means nerves can be packed closer together.

It also provides metabolic support to nerves, which means nerves can be longer.

Myelin first appeared in the tree of life around the same time as jaws, and its importance in vertebrate evolution has long been recognized, but until now, it was unclear what molecular mechanisms triggered its appearance.

The researchers noticed RetroMyelin's role in myelin production when they were examining the gene networks utilized by oligodendrocytes, the cells that produce myelin in the central nervous system.

Specifically, the team was investigating the role of noncoding regions including retrotransposons in these gene networks -- something that hasn't previously been explored in the context of myelin biology.

Myelin is a complex, fatty tissue that ensheathes vertebrate nerve axons.

Retrotransposons compose about 40% of our genomes, but nothing is known about how they might have helped animals acquire specific characteristics during evolution. Our motivation was to know how these molecules are helping evolutionary processes, specifically in the context of myelination.

Tanay Ghosh, first author
Computational biologist
Altos Labs-Cambridge Institute of Science, Cambridge, UK.
In rodents, the researchers found that the RNA transcript of RetroMyelin regulates the expression of myelin basic protein, one of the key components of myelin.

When they experimentally inhibited RetroMyelin in oligodendrocytes and oligodendrocyte progenitor cells (the stem cells from which oligodendrocytes are derived), the cells could no longer produce myelin basic protein.

To examine whether RetroMyelin is present in other vertebrate species, the team searched for similar sequences within the genomes of jawed vertebrates, jawless vertebrates, and several invertebrate species.

They identified analogous sequences in all other classes of jawed vertebrates (birds, fish, reptiles, and amphibians) but did not find a similar sequence in jawless vertebrates or invertebrates.

There's been an evolutionary drive to make impulse conduction of our axons quicker because having quicker impulse conduction means you can catch things or flee from things more rapidly.

Robin Franklin
Next, the researchers wanted to know whether RetroMyelin was incorporated once into the ancestor of all jawed vertebrates or whether there were separate retroviral invasions in the different branches.

To answer these questions, they constructed a phylogenetic tree from 22 jawed vertebrate species and compared their RetroMyelin sequences.

The analysis revealed that RetroMyelin sequences were more similar within than between species, which suggests that RetroMyelin was acquired multiple times through the process of convergent evolution.

The team also showed that RetroMyelin plays a functional role in myelination in fish and amphibians.

When they experimentally disrupted the RetroMyelin gene sequence in the fertilized eggs of zebrafish and frogs, they found that the developing fish and tadpoles produced significantly less myelin than usual.

The study highlights the importance of non-coding regions of the genome for physiology and evolution, the researchers say.

Our findings open up a new avenue of research to explore how retroviruses are more generally involved in directing evolution.

Tanay Ghosh.
Technical details are provided in the team's paper in Cell, which, although freely available is not published open access, so I can only quote the Abstract here:
Graphical abstract
  • RNA expression of retroviral element RNLTR12-int is crucial for myelination
  • RNLTR12-int binds to SOX10 to regulate Mbp expression
  • RNLTR12-int-like sequences (RetroMyelin) were identified in all jawed vertebrates
  • Convergent evolution likely led to RetroMyelin acquisition, adapted for myelination

Myelin, the insulating sheath that surrounds neuronal axons, is produced by oligodendrocytes in the central nervous system (CNS). This evolutionary innovation, which first appears in jawed vertebrates, enabled rapid transmission of nerve impulses, more complex brains, and greater morphological diversity. Here, we report that RNA-level expression of RNLTR12-int, a retrotransposon of retroviral origin, is essential for myelination. We show that RNLTR12-int-encoded RNA binds to the transcription factor SOX10 to regulate transcription of myelin basic protein (Mbp, the major constituent of myelin) in rodents. RNLTR12-int-like sequences (which we name RetroMyelin) are found in all jawed vertebrates, and we further demonstrate their function in regulating myelination in two different vertebrate classes (zebrafish and frogs). Our study therefore suggests that retroviral endogenization played a prominent role in the emergence of vertebrate myelin.

In the introduction to their paper, the authors point out:
Myelination, the process by which axons are invested with a myelin sheath, had a profound impact on vertebrate evolution.1,2,3 By conferring the ability to transmit by rapid saltatory conduction and assisting neuronal viability by providing local metabolic support, the myelin sheath allowed axons to function over much greater lengths and hence vertebrates to attain a larger size and diversity than would have occurred in the absence of myelination. Myelination also allowed rapid conduction without needing to increase axonal diameter, enabling the packing of larger numbers of axons necessary for the evolution of complex central nervous system (CNS). Phylogenetically, compacted myelin and genes critical to myelination, such as myelin basic protein (Mbp),2,3,4,5 likely appeared concurrently with the emergence of jaws in vertebrates, with myelin found in the most ancient living vertebrate, the Chondrichthyes (cartilaginous fish), but not in the Agnatha (jawless fish).1,2,3,6 Despite the significant functional advantages associated with myelination, a molecular explanation of what triggered this critical event in vertebrate evolution remains elusive.
The scientists never set out with the express intention of refuting so many basic creationists dogmas and claims, yet they did so quite casually by simply revealing the facts.

Creationists claim viruses, like other parasites, are evidence of 'The Fall' allowing 'Sin' to enter the world, and somehow compete with the creator god on an equal footing, yet here we have the remnant of a virus being used for the sort of function for which creationists traditionally credit their god. We also have the unarguable evidence of mutations being beneficial and so being naturally selected for, in contradiction of creationist claims that all mutations are detrimental and even fatal, or at least 'devolutionary'.

Then, as with all ERVs, this one is compelling evidence for common descent, mapping onto other evidence of the evolutionary relationships withing the vertebrates.

And, lastly, as with all research by biomedical scientists, no hint of doubt that the TOE is inadequate for explaining the facts or that the childish creationist fairy tale is about to replace it in mainstream science.

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