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At Sci News: Ancient Retroviruses Make Up 8% of Human Genome, Researchers Say

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Like modern HIV, ancient human endogenous retroviruses (HERVs) had to insert their genetic material into their host’s genome to replicate.

Viruses insert their genomes into their hosts in the form of a provirus.

There are around 30 different kinds of HERVs in people today, amounting to over 60,000 proviruses in the human genome.

They demonstrate the long history of the many pandemics humanity has been subjected to over the course of evolution.

Scientists think these viruses once widely infected the population, since they have become fixed in not only the human genome but also in chimpanzee, gorilla and other primate genomes.

Research has demonstrated that HERV genes are active in diseased tissue, such as tumors, as well as during human embryonic development. But how active HERV genes are in healthy tissue was still largely unknown.

Role of HERVs in Human Health and Disease

The fact that thousands of pieces of ancient viruses still exist in the human genome and can even create protein has drawn a considerable amount of attention from researchers, particularly since related viruses still active today can cause breast cancer and AIDS-like disease in animals.

Whether the genetic remnants of human endogenous retroviruses can cause disease in people is still under study.

The new study adds a new angle to these data by showing that HERV genes are present even in healthy tissue.

This means that the presence of HERV RNA may not be enough to connect the virus to a disease.

Importantly, it also means that HERV genes or proteins may no longer be good targets for drugs.

HERVs have been explored as a target for a number of potential drugs, including antiretroviral medication, antibodies for breast cancer and T-cell therapies for melanoma.

Treatments using HERV genes as a cancer biomarker will also need to take into account their activity in healthy tissue.

On the other hand, the study also suggests that HERVs could even be beneficial to people.

The most famous HERV embedded in human and animal genomes, syncytin, is a gene derived from an ancient retrovirus that plays an important role in the formation of the placenta.

Pregnancy in all mammals is dependent on the virus-derived protein coded in this gene.

Unknowns Remain

The new study reveals a level of HERV activity in the human body that was previously unknown, raising as many questions as it answered.

There is still much to learn about the ancient viruses that linger in the human genome, including whether their presence is beneficial and what mechanism drives their activity.

Seeing if any of these genes are actually made into proteins will also be important.

Answering these questions could reveal previously unknown functions for these ancient viral genes and better help researchers understand how the human body reacts to evolution alongside these vestiges of ancient pandemics.

Full article at Sci News.

The presence of HERV’s in the human genome doesn’t necessarily demonstrate an evolutionary history of humans, just a history of humans. The relevant question to consider is where did the virus acquire the information to produce proteins in the first place?

Comments
Pater @4 let me quote from the link you posted
So, lets examine why these are such powerful evidence of common descent. As I mentioned, when retrotransposons mobilize they deposit a copy at a random location in the genome. This means that when an Alu is looking for a place to put a new copy, it has ~3 billion places to choose from -
... deposit a copy at a random location in the genome ... ... it has ~3 billion places to choose from .... Really ? What about this ? From a mainstream paper:
Retroviral Integration Site Selection The stable insertion of a copy of their genome into the host cell genome is an essential step of the life cycle of retroviruses. The site of viral DNA integration, mediated by the viral-encoded integrase enzyme, has important consequences for both the virus and the host cell. The analysis of retroviral integration site distribution was facilitated by the availability of the human genome sequence, revealing the non-random feature of integration site selection and identifying different favored and disfavored genomic locations for individual retroviruses. This review will summarize the current knowledge about retroviral differences in their integration site preferences as well as the mechanisms involved in this process.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185549/ or this one (another mainstream paper):
Retroviral integration: Site matters Mechanisms and consequences of retroviral integration site selection https://onlinelibrary.wiley.com/doi/full/10.1002/bies.201500051
martin_r
November 16, 2022
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OT: recently uploaded Dr. Meyer video lecture on "Return of the God Hypothesis"
Stephen C Meyer https://youtu.be/ApNrqJ8eloY?t=248
bornagain77
November 16, 2022
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of related note,
Jan. 2022 Fossil Record refutes human evolution https://uncommondescent.com/intelligent-design/at-fox-news-adam-and-eve-are-compatible-with-evolution/#comment-744141 Fossils and Human Evolution (full series) - Casey Luskin - Oct. 2022 https://evolutionnews.org/tag/fossils-and-human-evolution-series/ Sept: 2022 - Genetic Evidence falsifies the claim the humans evolved from apes-like creature. And falsifies it in a ‘hard’ manner. https://uncommondescent.com/intelligent-design/at-evolution-news-did-life-first-arise-by-purely-natural-means/#comment-765765 Darwinists simply have no evidence that morphology, and/or biological form, is reducible to mutations to DNA. https://uncommondescent.com/intelligent-design/evangelical-scientists-getting-it-wrong/#comment-740247 Population Genetics falsifies, instead of confirms, Darwinian claims for human evolution https://uncommondescent.com/intelligent-design/christian-darwinists-must-now-backtrack-re-adam-and-eve/#comment-741335 Human exceptionalism falsifies Darwinian claims for human evolution https://uncommondescent.com/intelligent-design/evangelical-scientists-getting-it-wrong/#comment-740249 Nov. 2022 - Darwinists, (in what makes the ‘problem’ of explaining the origin of the human species pale in comparison), have no clue whatsoever why “I” should even come into existence as a “person” with a unique individual subjective conscious experience, but are instead reduced to arguing that my sense of self, my “I”, is merely a ‘neuronal illusion’ https://uncommondescent.com/evolution/at-evolution-news-there-is-no-settled-theory-of-evolution/#comment-770111
bornagain77
November 16, 2022
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Here is a good, easy to understand, explanation for why ERVs are NOT strong evidence for evolution. https://answersingenesis.org/biology/microbiology/endogenous-retroviruses-common-ancestry/bornagain77
November 16, 2022
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A good explanation of why ERVs are strong evidence for evolution: http://www.askabiologist.org.uk/answers/viewtopic.php?id=3914Pater Kimbridge
November 16, 2022
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and one more thing ... from an engineering point of view, i was also amazed to learn, that these retroviruses don't insert into human DNA directly (as you may think) They can't. Because it is not physically possible ... Because there is AN INCOMPABILITY PROBLEM .... and now comes some engineering in ... Human genome is made of DNA molecule and retroviruses use RNA molecules. SO THE VIRUS JUST CAN'T INSERT RNA INTO DNA... THIS IS THE INCOMPATIBILITY PROBLEM ... So, in order the insertion can be even done, retroviruses' RNA molecule needs to be converted into a form of DNA ... otherwise, the virus can't insert its 'data' into 'human storage' ... a clear incompatibility problem like we see everyday when using various computers /storage media or video codecs ... For the purpose of converting retroviruses' RNA into DNA, a molecular machine called REVERSE TRANSCRIPTASE is being used - comes together with retroviruses ;-)
Reverse transcriptase (RT), also known as RNA-dependent DNA polymerase, is a DNA polymerase enzyme that transcribes single-stranded RNA into DNA. This enzyme is able to synthesize a double helix DNA once the RNA has been reverse transcribed in a first step into a single-strand DNA.
here is a short but very informative 2 mins video on this conversion procedure: https://youtu.be/eS1GODinO8w?t=95 PS: i, as an engineer, would love to understand, how a retrovirus knows, that in order to insert its 'type of data' into human 'data storage', its 'data format' has to be converted into a compatible one ... and then some biologist comes in, claiming, that blind unguided process figured it out how to create a data format conversion tool ... seriously, what is wrong with these people ???martin_r
November 16, 2022
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As to: "(Darwinists) think these (retro)viruses once widely infected the population, since they have become fixed in not only the human genome but also in chimpanzee, gorilla and other primate genomes." But alas, "retroviruses do not align with the expected evolutionary pattern", and Darwinists have had to postulate that the "human lineage must, somehow, (mysteriously),, have been purged of these endemic viruses."
The Naked Ape: An Open Letter to BioLogos on the Genetic Evidence, Cont. - Cornelius Hunter - May 28, 2016 Excerpt: Another such unique feature )of Humans) is at the genome level: the lack of endemic infectious retroviruses in humans. The problem is that these viruses are present in the other primates, and so according to evolution these viruses must be present in their common ancestor which, again according to evolution, would be an ancestor of humans as well. Therefore this lack of endemic infectious retroviruses in humans is inconsistent with evolution: "Other than the recent introductions of HIV and human T leukaemia virus (HTLV) into humans from other animals, humans seem to be devoid of species-wide endemic infectious retroviruses. By contrast, like most other mammals studied, other hominids and non-human primates (NHPs) do have such viruses. Indeed, given the remarkable corroboration between the phylogenetic trees of primates and their lineage-specific simian foamy viruses (SFVs) our common ancestors with other hominids almost certainly had SFVs. The same is probably true of the lineage-specific simian infectious retroviruses (SIVs) found in most NHPs. Assuming that the common ancestors of hominids carried multiple endemic infectious retroviruses, how did the human lineage eliminate them? Given that humans remain susceptible to re-infection with both SFVs and SIVs from other hominids, this seems unlikely to be explained solely on the basis of more efficient host restriction systems. Rather, there seems to have been an episode in which the ancestral human lineage was somehow ‘purged’ of these endemic viruses." In other words, the endemic infectious retroviruses do not align with the expected evolutionary pattern. The human lineage must, somehow, have been purged of these endemic viruses. Perhaps such a purging occurred, and future research may be able to strengthen that hypothesis. But as it stands, this evidence is not consistent with evolution. https://evolutionnews.org/2016/05/the_naked_ape_a/
Again, retroviruses do not fall into a common decent pattern
Retroviruses and Common Descent: And Why I Don’t Buy It - September 2011 Excerpt: If it is the case, as has been suggested by some, that these HERVs are an integral part of the functional genome, then one might expect to discover species-specific commonality and discontinuity. And this is indeed the case. https://uncommondescent.com/evolution/retroviruses-and-common-descent-and-why-i-dont-buy-it/ Are Endogenous Retroviruses Convincing Evidence for Primate Common Ancestry? Dr. Andrew Fabich – video (JonathanM 2017) https://www.youtube.com/watch?v=EN0eRCdW9jI
As to, "Research has demonstrated that HERV genes are active in diseased tissue, such as tumors, as well as during human embryonic development. But how active HERV genes are in healthy tissue was still largely unknown.,,, The new study adds a new angle to these data by showing that HERV genes are present even in healthy tissue." But alas, Darwinists also did not predict that ERVs would be functional in embryonic development, and in healthy tissues. In fact, retroviruses were initially deemed, by Darwinists, to be non-functional 'junk' DNA. And thus finding important functions for ERVs 'should' count as, (yet another) empirical falsification of Darwinian 'theory',
The definitive response on ERV's and Creation, with Dr. Jean Lightner and Wazooloo (5:00 minute mark - the "problem" that functional ERVs present to Darwinists) https://youtu.be/feHYEgzaGkY?t=290 Viral Genome Junk Hits the Trash - By Jeffrey P. Tomkins, Ph.D. - April 04, 2016 Excerpt: When virus-like DNA were first discovered, it was thought the majority of them would prove to be junk—until now. DNA sequences called endogenous retroviruses (ERVs) are abundant in mammalian genomes. The ERV sequences initially got their name because they showed strong sequence similarity to known viruses. Then evolutionists proclaimed the animal genomes evolved to their present state, in part by repeated infection with viruses initially deemed part of an organism's "junk" DNA. As research on ERVs progressed, it became apparent that many of these genomic features are not junk, but important for the mammal's survival, such as placental development.1 Many other ERVs were found to be specifically regulated by cell type.2 These ERVs contain special sequences that act like genetic switches in the genome by binding regulatory proteins (transcription factors) that control genes.2 Now a new study shows many other ERVs across the genome play key roles in controlling immune responses, another important process necessary for the survival of mammals.3 More specifically, this new research shows that ERVs regulate genes that produce pro-inflammatory signaling molecules released upon infection. This crucial system is called the innate immune response and genes regulated by ERVs associated with this biological network are called innate immunity factors. When ERV elements associated with these genes were inactivated in the laboratory, the production of innate immunity factors stopped—a simple but elegant experiment unequivocally demonstrating functionality. Obviously a mammal would get sick and have difficulty surviving without ERVs regulating their genome. In a recent article, I go into more detail about ERVs and why the evolutionary story is completely backwards when it comes to explaining their presence in the genome.4 https://www.icr.org/article/viral-genome-junk-hits-trash 4 - Viral Genome Junk Is Bunk - by Jeffrey P. Tomkins, Ph.D. - March 31, 2015 Excerpt: Second, the alleged process whereby these ERV sequences were supposedly stably integrated into the germlines of animals has never been documented. The process itself is an exercise in speculation. In studies where their random and uncontrolled integration has occurred in regular body cells (called somatic tissue), cancerous tumors are often the outcome.1 In reality, most modern ERV-like viruses do not readily integrate into a host’s genome; only a few, like the AIDS virus, have been found to do this. And the ones that do perform this integration type of behavior do not target germline cells that would then enable them to be passed on to the next generation. Third, important functions are now being attributed to ERV sequences in mammalian genomes. In fact, several studies in recent years have highlighted the importance of many ERV gene sequences in placenta development and maintenance—a process crucial to reproduction and life.3,4 Not only are important genes contained in these sequences, but also many different regulatory elements that function as key genetic switches.5 https://www.icr.org/article/viral-genome-junk-bunk
As to: "The most famous HERV embedded in human and animal genomes, syncytin, is a gene derived from an ancient retrovirus that plays an important role in the formation of the placenta." And yet syncytins do not support common descent.
The Placenta Problem: How Common Descent Fails - Ann Gauger - June 17, 2016 Excerpt: I'll quote a review paper on syncytins. These are the people who discovered syncytins, and they have done great work. Yet they are forced into a corner by their own work and the idea of common descent.,,, “... syncytins are 'new' genes encoding proteins derived from the envelope protein of endogenous retroviral elements that have been captured and domesticated on multiple occasions and independently in diverse mammalian species, through a process of convergent evolution. Knockout of syncytin genes in mice provided evidence for their absolute requirement for placenta development and embryo survival, via formation by cell-cell fusion of syncytial cell layers at the fetal-maternal interface. These genes of exogenous origin, acquired 'by chance' and yet still 'necessary' to carry out a basic function in placental mammals, may have been pivotal in the emergence of mammalian ancestors with a placenta from egg-laying animals via the capture of a founding retroviral env gene, subsequently replaced in the diverse mammalian lineages by new env-derived syncytin genes, each providing its host with a positive selective advantage.” Rather than postulating six independent, random capture events in placental development, they are now postulating at least one more, a founding syncytin leading to a primitive placenta, then the other syncytins to replace that one in each lineage. Each replacement must have had a clear selective advantage as time went on to make the replacement possible, and each must be the outcome of a random series of events. To say it again, the common descent prediction is that there must have been a founding syncytin in the first mammal with a placenta, or something else that functioned in syncytin's place, in order for the primitive placenta to arise and subsequently be passed to all mammalian clades. For which there is no evidence, and may never be. Can common descent explain the unexpected observation of six independent origins for the placenta? No. Could it predict it? No. Common design has an explanation, but not one that will be palatable to my interlocutors. The designer used the same idea six different times to produce the same outcome in six different "designs" (clades). http://www.evolutionnews.org/2016/06/the_placenta_pr102930.html
And again, retroviruses were initially deemed, by Darwinists, to be non-functional 'junk' DNA. So that retroviruses would now be found to be functional, even essential to embryonic development, and "that HERV genes are present even in healthy tissue", (and yet not fall into a common descent pattern), should, if Darwinism were a normal science instead of being, basically, an unfalsifiable religion for atheists, count as yet another empirical falsification of their, ahem, 'theory'.
1 Thessalonians 5:21 Test all things; hold fast what is good
bornagain77
November 16, 2022
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When i first time heard about ERVs i was amazed ... As an engineer, i was amazed .... At this moment, there are about 6000 known DNA mutations which cause serious genetic diseases. But, when retroviruses repeatedly inserted pretty significant amounts of DNA into human genome, that is alright, nothing bad happened ... What amazes me even more, allegedly, these retroviruses take random places on human DNA to insert to ... In other words,... i will randomly insert into you 8% of new data, you are still here and intact ... but few mutations known as genetic disorders kill you or will cause serious conditions ... Could some smart Darwinist explain to me, how is it possible that random ERV-insertions don't do any harm ?martin_r
November 16, 2022
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