ERVs: Supposed 'Proof' of Common Descent Bites the Dust

[ftacky]

The theory that identical ERVs aka HERVs (human endogenous retroviruses) found at a similar location in the genome is proof of an evolutionary connection has been found to be questionable at best. Newer studies now show numerous cases of multiple identical ERV sites found in COMPLETELY UNRELATED SPECIES: sheep/fox, cat/baboon, possum/chimp, bird/cat, etc. and the list keeps growing... Statistically, we can no longer conclude these are unique situations pointing to any proof whatsoever of common descent. It is most likely that initial studies were done primarily on humans and chimps rather than other mammals and this skewed the data.

The theory that ERVs are leftover retroviral elements is itself now questionable. Recent discoveries show genetic sequences labeled as ERVs are MANDATORY FOR BASIC BIOLOGICAL FUNCTIONS WITHOUT WHICH SURVIVAL IS IMPOSSIBLE:

A partial list of mandatory functions attributed to ERVs:
a) Large-scale regulation of our genome as a whole.
b) Direct support and regulation of our immune system.
c) Aid in the production of countless proteins mandatory for life.
d) Prevention of miscarriages.
e) Mutations within retrovirus-like sequences actually cause disease, thus proving their mandatory nature.
f) Etc., etc., etc..

The most parsimonious explanation for this is that retroviral-like elements are not ERVs but INTRINSIC genetic material that have always existed in our genome as a necessity for life, rather then leftover foreign pathological viruses.

1) How could humans and other animals survive at all without the genetic materials essential for life BEFORE they became infected by ERVs?
2) Why don't we see ERV insertions into germ cells today?
3) Why would such infections be preserved, even through apoptosis and unfavorable selection of infected organisms?
4) What made ERVs change from viral activities and aquire transcriptional abilities to create essential genes?
5) What made ERVs immediately turn into essential gene regulators upon insertion?
6) Why have ERVs - initially pathological - NEVER been proven to cause disease but have been proven to be favorable for life instead?
7) What made the identical ERV transcribe differently in humans and chimps?

Way too many hard questions for which the answers make no sense - without genetic fantasy scenarios - and more importantly, remain unproven and unvalidated. Ad hoc (makeshift or improvised) arguments WITHOUT POSITIVE EVIDENCE are often used in an attempt to explain away these inconsistencies and maintain an evolutionary bias.

"A clear PROOF for the existence of a HERV capable of productive replication REMAINS ELUSIVE..."
(Ref: PNAS October 5, 2004 vol. 101 no. Suppl 2 14572-14579)


“Our data reveal that the activity of endogenous retroviruses is regulated differentially and is cell type specific, SIMILAR TO NORMAL GENE REGULATION … our findings suggest that HERVs BEHAVE LIKE NORMAL CELLULAR GENES and are a permanent component of the transcriptome of a cell.” (Ref: Journal Of Virology, 1/2005)

“In short, the notion that molecules of germ cells … are in states of perpetual change is not, in our present understanding of cell biology, tenable. This doesn’t mean that “molecular change” does not occur; only that mechanisms provoking such change in germ cells are likely instantaneous and stochastic and probably OFTEN LETHAL – which WILL PRECLUDE their persistence into future generations.”
(Ref: MIT Press Journals, Fall 2006, Vol.1)

"Several ERVs appear to PROVIDE PROTECTION FROM INFECTION and are INVOLVED IN REPRODUCTION...Studies in cultured cells have shown that a protein of a HERV might have a ROLE IN THE DEVELOPMENT OF THE HUMAN PLACENTA...Miscarriage is a serious medical problem for all mammals, including humans." (Ref: "ERVs are Required for pregnancy in Sheep", Science Daily)

"We have identified two hot spots for SINE insertion within mys-9 and at each hot spot have found that two independent SINE insertions have occurred at identical sites. These results have major repercussions for phylogenetic analyses based on SINE insertions, indicating the need for caution when one concludes that the existence of a SINE at a specific locus in multiple individuals is indicative of common ancestry." (Ref: GENETICS: An Ancient Retrovirus-like Element Contains Hot Spots for SINE Insertion)

Romans 1
...they glorified him not as God, neither were thankful; but became vain in their IMAGINATIONS, and their foolish heart was darkened.

 

[sfs]

This is probably a post and run job, but still. . .

The theory that identical ERVs aka HERVs (human endogenous retroviruses) found at a similar location in the genome is proof of an evolutionary connection

... is as robust as ever.

has been found to be questionable at best. Newer studies now show numerous cases of multiple identical ERV sites found in COMPLETELY UNRELATED SPECIES: sheep/fox, cat/baboon, possum/chimp, bird/cat, etc. and the list keeps growing...

A claim for which no evidence is offered.

Sheesh -- he could have at least made an effort.

 

[imind]

Sheesh -- he could have at least made an effort.

why even bother?

 

[Resha Caner]

A claim for which no evidence is offered.

I was about to ask for citations. ERVs are always an interesting topic. But it doesn't appear the OP is going to follow up. Maybe I'll use the bread crumbs to see if it turns up anything.

[edit] Maybe the reference is to this (specifically the discussion around Figure 4).

The Discovery of Endogenous Retroviruses

It might be interesting to unpack the article. FYI, I also found the first line interesting: "If Charles Darwin reappeared today, he might be surprised to learn that humans are descended from viruses as well as from apes." That's an issue I've poked at several times.

 

[sfs]

Maybe the reference is to this (specifically the discussion around Figure 4).

The Discovery of Endogenous Retroviruses

The article does not, of course, say anything like what the OP did.

FYI, I also found the first line interesting: "If Charles Darwin reappeared today, he might be surprised to learn that humans are descended from viruses as well as from apes." That's an issue I've poked at several times.

Darwin would be surprised by many things now known to biologists.

 

[Resha Caner]

The article does not, of course, say anything like what the OP did.

It might not be what the OP was referencing. There's no way to know, and it doesn't matter. The OP was obviously trolling, yet here we are.

Further, my unaided abilities won't produce an interpretation of the article worth much of anything either. So ...

Does the article show some species (such as sheep and foxes) to have the same ERVs? In the same location? If so, what is the explanation for it?

 

[mark kennedy]

I was about to ask for citations. ERVs are always an interesting topic. But it doesn't appear the OP is going to follow up. Maybe I'll use the bread crumbs to see if it turns up anything.

[edit] Maybe the reference is to this (specifically the discussion around Figure 4).

The Discovery of Endogenous Retroviruses

It might be interesting to unpack the article. FYI, I also found the first line interesting: "If Charles Darwin reappeared today, he might be surprised to learn that humans are descended from viruses as well as from apes." That's an issue I've poked at several times.

This is the part that always left me puzzled:

Some 8% of human DNA represents fossil retroviral genomes, and that is not counting the LINE elements and other retrotransposons that are scattered so liberally across our genome. (The Discovery of Endogenous Retroviruses)
​

These ERVs are either the result of highly dangerous gernline invasions or they actually did or do something. Most of them look like broken protein coding genes to me. They average about 300 bps or so and are riddled with mutations. There is only one in the human genome that actually works and I have yet to see an example of a human ERV germline invasion cited or documented.

Electron micrographs of placental tissue from humans and a variety of other animals showed retrovirus-like particles budding from placental cells, particularly within the syncytiotrophoblast layer — the layer consisting of fused cells (Figure 2). The presence of these particles in healthy tissues of many placental mammals prompted a few brave researchers to entertain the idea that ERVs actually play an essential role in placental development. (Retroviruses, the Placenta, and the Genomic Junk Drawer)
http://schaechter.asmblog.org/schae...the-placenta-and-the-genomic-junk-drawer.html​

That's what gets me about the subject of genetics, it's always coming up with new information on a nearly constant basis. When I first started looking into this stuff genetics was part of an argument, now it's gotten to be an intellectual curiosity that never disappoints.

Grace and peace,
Mark

 

[mark kennedy]

Darwin would be surprised by many things now known to biologists.

I've often wondered if Mendel ever read Darwin. I know Darwin had an uncut copy of Mendel's paper on hybrids but couldn't read it because it was in German. I can't help wonder though if Mendel read On the Origin of Species, Darwin did spend some time on plants and horticulture. Just wonder what these two could have come up with over tea, guess that's just one of those big fat who knows.

 

[Resha Caner]

The presence of these particles in healthy tissues of many placental mammals prompted a few brave researchers to entertain the idea that ERVs actually play an essential role in placental development.

If correct, that's very cool. Paradigms are a funny thing.

 

[mark kennedy]

If correct, that's very cool. Paradigms are a funny thing.

Well they have to come from someplace and ERVs are capable of inter cellular travel. You probably know that HIV is an ERV that invades the T Cells. Infectious disease aside I wonder what these things might have originally did, or possible still do.

Grace and peace,
Mark

 

[Resha Caner]

Infectious disease aside I wonder what these things might have originally did, or possible still do.

Me too. Part of the problem is that my questions about what some of this might be about are either too anti-evolution or too removed from current research to pique anyone's interest in a serious way.

The whole R1-R2-R3 research paradigm is interesting. Though many American universities were founded by Christian organizations, less than a handful retain any ties to a church today. Moreso, many of the R1-R2 biology departments make explicit statements that they won't entertain any anti-evolution research questions. That makes the "prove it" challenge thrown at creationists difficult if they can't get access to high quality research facilities.

I fully acknowledge a lot of ignorant statements are made by creationists about biology, so that only makes it all the harder. Still "the way is shut" and so forth.

So, I approached a teaching university and offered to sponsor an undergraduate student for their senior project. I have an idea a biologist helped me with a little to get to the point where I could pose it as what (I think) is a reasonable research question. The professor I worked with seemed intrigued, but they decided the question was too advanced for an undergraduate. Stuck again. It doesn't matter anyway. Some financial setbacks have left me unable to put up the cash anymore.

At the same time, I sometimes wonder if (when I see things like what were posted here) if biology isn't slowly moving toward (somewhat) answering my question anyway. It's just that, the paradigm being what it is, I also wonder if it will be interpreted differently than what prompted me to ask in the first place.

Sorry. Just rambling ...

 

[sfs]

Does the article show some species (such as sheep and foxes) to have the same ERVs? In the same location? If so, what is the explanation for it?

It shows that they have closely related ERVs, but doesn't say anything about shared insertion points. The explanation is that ERVs start as viral infections, and viruses jump species pretty easily. HIV, which has the potential to become an ERV, jumped into humans from monkeys and chimpanzees quite recently.

 

[mark kennedy]

Me too. Part of the problem is that my questions about what some of this might be about are either too anti-evolution or too removed from current research to pique anyone's interest in a serious way.

The whole R1-R2-R3 research paradigm is interesting. Though many American universities were founded by Christian organizations, less than a handful retain any ties to a church today. Moreso, many of the R1-R2 biology departments make explicit statements that they won't entertain any anti-evolution research questions. That makes the "prove it" challenge thrown at creationists difficult if they can't get access to high quality research facilities.

I fully acknowledge a lot of ignorant statements are made by creationists about biology, so that only makes it all the harder. Still "the way is shut" and so forth.

So, I approached a teaching university and offered to sponsor an undergraduate student for their senior project. I have an idea a biologist helped me with a little to get to the point where I could pose it as what (I think) is a reasonable research question. The professor I worked with seemed intrigued, but they decided the question was too advanced for an undergraduate. Stuck again. It doesn't matter anyway. Some financial setbacks have left me unable to put up the cash anymore.

At the same time, I sometimes wonder if (when I see things like what were posted here) if biology isn't slowly moving toward (somewhat) answering my question anyway. It's just that, the paradigm being what it is, I also wonder if it will be interpreted differently than what prompted me to ask in the first place.

Sorry. Just rambling ...

I never really thought it was creation vs. evolution, I just think evolution started at creation. That's origins which is metaphysics when you think about it. Natural science only examines natural phenomenon so if a miracle is introduced to a time line science isn't really in a position to draw a conclusion that involves a miracle. So you end up backing up and considering epistemology (theories of knowledge), a much broader view of what we can know.

Breaking this down to something empirically testable would seem to come down to the time line, 6000 years vs. billions for continuous development and adaptive evolution of life. What six thousand years would suggest is an accelerated evolution and adaptive radiation in a pretty tight time frame. Either you broaden the scope to include philosophical questions are you narrow to a tedious timeline. Either way I don't think the scientific community would be receptive. Personally I think the only possible way would be to wait and see how our understanding of adaptive evolution reveals molecular mechanisms involved in those adaptations.

Grace and peace,
Mark

 

[Resha Caner]

I never really thought it was creation vs. evolution, I just think evolution started at creation.

I'm not YEC (or OEC). I don't have a label for my position, but I tend to call myself a creationist.

Further, I don't see evolution as one theory, but a collection of many theories - basically a field of study. As such, one of the flaws I see in the approach of "creation science" is a thinking that they will overturn all of evolution in one fell swoop. A similar problem among many of the evolutionists debating here is a view that since one aspect utilized in the field of evolution is well-evidenced, it means everything in the evolutionary field is true.

I think some aspects of evolution, especially UCA, constitute an underdetermined problem, and that was the essence of my research question.

 

[mark kennedy]

I'm not YEC (or OEC). I don't have a label for my position, but I tend to call myself a creationist.

Welcome to my world, I'm YEC in every way except for the age of the earth. I don't fit into the Old Earth camp because that stops at Genesis 1:2, maybe you don't fit into a category because you are still thinking about all of this. That's actually a good place to be.

Further, I don't see evolution as one theory, but a collection of many theories - basically a field of study. As such, one of the flaws I see in the approach of "creation science" is a thinking that they will overturn all of evolution in one fell swoop. A similar problem among many of the evolutionists debating here is a view that since one aspect utilized in the field of evolution is well-evidenced, it means everything in the evolutionary field is true.

Evolution is an awkward word for me since I believe adaptive radiation happened on a massive scale following the flood. This all seems so upside down to me, evolution isn't the problem, it's the answer. While the Ark was massive it housed, perhaps, 10,000 species or more and all bird, reptiles and mammals were represented and their offspring have become from 2 million to 60 million species worldwide. Logistics aside, that is adaptive radiation on a global scale no matter how you slice it up.

I think some aspects of evolution, especially UCA, constitute an underdetermined problem, and that was the essence of my research question.

I was looking at the Arctic Cod and apparently it has evolved this antifreeze gene, multiple times in the frigid waters of the northern and southern arctic. At least four different versions exist and they are all brand new genes. What I would like to know and I have had very little luck finding a clue, is what is the molecular mechanism that makes this happen. Polar Bears can still interbreed with Grizzlies, but they are obviously different species. God provided something in the genomes of every living thing that provides these adaptations. The reason I can't look away or accept some pedantic natural selection is this fact of adaptive evolution as a phenomenon in nature and the simple fact that there must be a molecular mechanism making this happen.

There is a lot of research on this, how traits can be changed in a way they are inheritable and eventually permanently fixed. I have dwelled on the subject matter for that reason because I am sure, they will eventually find it. I'm just not sure they are there yet or even close. I think when they do the wrangling of creationists and Darwinians will seem almost trite in comparison.

Grace and peace,
Mark

 

[Resha Caner]

There is a lot of research on this, how traits can be changed in a way they are inheritable and eventually permanently fixed. I have dwelled on the subject matter for that reason because I am sure, they will eventually find it. I'm just not sure they are there yet or even close. I think when they do the wrangling of creationists and Darwinians will seem almost trite in comparison.

Yes, there are many interesting emergent phenomena. For example, what triggers a tadpole to become a frog? And if that trigger didn't happen, how long would the tadpole continue to live? Is there some possible way for it to reach sexual maturity that is different than being a frog?

My lament, though, was that given the limited resources and avenues available to those for whom Christianity leads them to ask challenging questions, it is a shame that we can't be better focused and organized about it. I suppose the Discovery Institute is kind of an example, but they are just as narrowly focused on a single paradigm as research universities - one that is not profitable IMHO.

 

[mark kennedy]

Yes, there are many interesting emergent phenomena. For example, what triggers a tadpole to become a frog? And if that trigger didn't happen, how long would the tadpole continue to live? Is there some possible way for it to reach sexual maturity that is different than being a frog?

My lament, though, was that given the limited resources and avenues available to those for whom Christianity leads them to ask challenging questions, it is a shame that we can't be better focused and organized about it. I suppose the Discovery Institute is kind of an example, but they are just as narrowly focused on a single paradigm as research universities - one that is not profitable IMHO.

Let's say you and I are out for lunch, we go to a bakery and buy fresh bread and eclires

Yes, there are many interesting emergent phenomena. For example, what triggers a tadpole to become a frog? And if that trigger didn't happen, how long would the tadpole continue to live? Is there some possible way for it to reach sexual maturity that is different than being a frog?

My lament, though, was that given the limited resources and avenues available to those for whom Christianity leads them to ask challenging questions, it is a shame that we can't be better focused and organized about it. I suppose the Discovery Institute is kind of an example, but they are just as narrowly focused on a single paradigm as research universities - one that is not profitable IMHO.

I think the focus should be on hybrids rather then dramatic giant leaps. I've developed an interest in arctic wild life over the years:

The first confirmed cross between a polar bear and a grizzly bear—a white bear with brown patches—was documented in 2006; genetic analysis of a second, found in 2010, revealed that its mother was also a hybrid, suggesting that more instances are happening under scientists’ radar. In 2009, a biologist at the National Marine Mammal Laboratory photographed a probable bowhead/right whale hybrid in the Bering Sea. More hybrids are possible. Kelly and his coauthors have counted 34 opportunities for hybridization across 22 Arctic or near-Arctic species, based on the animals’ genetic compatibility and geographic range. The list includes potential hybrids of ringed and ribbon seals, Atlantic walrus and Pacific walrus, and beluga whales and narwhals. (A Strange New Gene Pool of Animals Is Brewing in the Arctic)
​

That's what Gregor Mendel was experimenting with when his famous pea plant experiments were conducted. That university in Bruno, the capitol of the Austrian Hungarian empire, it was the MIT of their day. He was recruited by CF Napp to explore how hybrids work:

"Some day the world may be as indebted as it is to Isaac Newton for physics. They may be as indebted to the City of Brno for its contributions to inheritance." (CF Napp, Brno)​

Evolution is the change of alleles (traits) in populations over time. The traits, in order to be adaptive over time have to make it past the normative screening of the genome. Hybrids have a strong tendency to revert back to the grand parent form according to Mendel and according to Darwin, infertility is the bane of horticulture. Indeed, producing adaptive traits in progeny is what has come to be known as differential selective success. However, Mendel discovered a pattern, a 3:1 ratio of dominant to recessive genes expressed as traits. Unfortunately for the Soviet Union they promoted Darwinian evolution to the exclusion of Mendelian Genetics which was a costly mistake for them in the Life Sciences:

They were not receiving Western journals. And Western ideas were considered bourgeois, erroneous and that they had to be abandoned, including - and this is what shocked Monod - 50 years of genetics. So this - there was a public announcement in the Soviet Union that Mendelian genetics, the genetics of Gregor Mendel and the chromosomal theories of genetics...It gutted Soviet biology, I would say, really, since that time; that Soviet biology never really recovered from this long episode of genetics being suppressed in the Soviet Union. ( 'Brave Genius': A Tale of Two Nobelists NPR)​

The Human Genome Project in their landmark paper tell us about the history of their science:

The rediscovery of Mendel's laws of heredity in the opening weeks of the 20th century sparked a scientific quest to understand the nature and content of genetic information that has propelled biology for the last hundred years. The scientific progress made falls naturally into four main phases, corresponding roughly to the four quarters of the century.

• The first established the cellular basis of heredity: the chromosomes.
• The second defined the molecular basis of heredity: the DNA double helix.
• The third unlocked the informational basis of heredity, with the discovery of the biological mechanism by which cells read the information contained in genes and with the invention of the recombinant DNA technologies of cloning and sequencing by which scientists can do the same.
• The last quarter of a century has been marked by a relentless drive to decipher first genes and then entire genomes, spawning the field of genomics. (Initial sequencing and analysis of the human genome. Nature, 15 Feb 2001)

There's another way to look at this, the issues are not religion and science but how traits become inheritable and thus change over time. Darwinism while offering some nomenclature has yielded little in understanding how evolution actually works.

Grace and peace,
Mark

 

[Resha Caner]

I think the focus should be on hybrids rather then dramatic giant leaps.

Is that just a personal interest or do you see a broader purpose in it?

There's another way to look at this, the issues are not religion and science but how traits become inheritable and thus change over time.

Is this because your interests don't impinge upon the theological? Or are you saying biology, properly framed, would never impinge upon the theological? Or is it just an attempt to calm the storm?

 

[sfs]

Yes, there are many interesting emergent phenomena. For example, what triggers a tadpole to become a frog?

Thyroid hormone.

And if that trigger didn't happen, how long would the tadpole continue to live?

Two years. (At least for the frogs that have been studied.)

Is there some possible way for it to reach sexual maturity that is different than being a frog?

In principle? Sure. Developmental programs can change triggers. I don't know whether such a change is possible in practice in frogs.

 

[mark kennedy]

Is that just a personal interest or do you see a broader purpose in it?

There's a lot to be gained from an understanding of the life sciences, it's important to understand how hybrids develop and the difference between that and genetic engineering.

Is this because your interests don't impinge upon the theological? Or are you saying biology, properly framed, would never impinge upon the theological? Or is it just an attempt to calm the storm?

I spent a lot of time exploring this strange conflict between religion and science. Pope Urban and Galileo, Thomas Henry Huxley and Bishop Samuel Wilberforce, Lord Kelvin vs. the Geologists and Biologists of his day. Some strange facts start to emerge unexplained really, Kepler was excommunicated, Francis Bacon and Galileo were put under house arrest. The conflicts between secular academics and Christian thinking has ripe with controversy and a long standing animosity. In spite of the Catholic churches treatment of Galileo they are still prolific star gazers and spend the largest slice of their budget on education. Wilberforce's father was the key person involved in abolishing slavery in England in 1833, he didn't do well in that famous debate but his legacy comes down to an ill advised joke.

This is an attempt to understand our history, which as a civilization started no more then ten thousand years ago. Egypt was the first to undertake enormous building projects and humans have been making a name for themselves by doing it ever since. Am I just supposed to idly accept that our ancestors sat around Africa for millions of years and then ten thousand years ago finally decided to get up and build something?

This is about how we know, that we know, what we know. I've seen nothing in science to discourage a literal understanding of the historical narratives of Scripture. What I have seen science do is produce a natural history that has all the marks of epic imaginative fancy.

Grace and peace,
Mark