Endogenous Retroviral Insertions: Not Proof of Man-Monkey Kindred

[Punchy]

If endogenous retroviral insertions and other non-coding DNA are functional rather than vestigial, this should be considered evidence for design rather than evolution. ERV's were once the "magic bullet" that I used in arguing for common descent. But if humans are created in the image of God, it should be expected that most, if not all, of our DNA was designed for a purpose rather than appearing by accident.

New research continues to reveal the functional importance of the junk DNA sequences known as endogenous retroviruses (ERVs). This most recent work demonstrates that ERVs play a key role in the reproduction of mammals by controlling the development of the placenta. Evolutionary biologists maintain that because junk DNA is an imperfection, it provides incontrovertible evidence for evolution. Yet once again biochemists have concluded that junk DNA actually has function. The growing recognition of the functional importance of junk DNA undermines one of evolution’s best arguments and suggests that careful planning by an intelligent Designer, rather than undirected, random biochemical events, shaped the genomes of organisms.
http://www.reasons.org/resources/tnrtb/200611.shtml

Developmental Biology
Endogenous retroviruses regulate periimplantation placental growth and differentiation

( development | placenta | sheep | trophectoderm )
Kathrin A. Dunlap *, Massimo Palmarini , Mariana Varela , Robert C. Burghardt , Kanako Hayashi *, Jennifer L. Farmer *, and Thomas E. Spencer *

*Center for Animal Biotechnology and Genomics, Department of Animal Science, and Image Analysis Laboratory, Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843; and Institute of Comparative Medicine, University of Glasgow Veterinary School, Glasgow G61 1QH, United Kingdom


Edited by George E. Seidel, Jr., Colorado State University, Fort Collins, CO, and approved August 8, 2006 (received for review May 10, 2006)

Endogenous retroviruses (ERVs) are fixed and abundant in the genomes of vertebrates. Circumstantial evidence suggests that ERVs play a role in mammalian reproduction, particularly placental morphogenesis, because intact ERV envelope genes were found to be expressed in the syncytiotrophoblasts of human and mouse placenta and to elicit fusion of cells in vitro. We report here in vivo and in vitro experiments finding that the envelope of a particular class of ERVs of sheep, endogenous Jaagsiekte sheep retroviruses (enJSRVs), regulates trophectoderm growth and differentiation in the periimplantation conceptus (embryo/fetus and associated extraembryonic membranes). The enJSRV envelope gene is expressed in the trophectoderm of the elongating ovine conceptus after day 12 of pregnancy. Loss-of-function experiments were conducted in utero by injecting morpholino antisense oligonucleotides on day 8 of pregnancy that blocked enJSRV envelope protein production in the conceptus trophectoderm. This approach retarded trophectoderm outgrowth during conceptus elongation and inhibited trophoblast giant binucleate cell differentiation as observed on day 16. Pregnancy loss was observed by day 20 in sheep receiving morpholino antisense oligonucleotides. In vitro inhibition of the enJSRV envelope reduced the proliferation of mononuclear trophectoderm cells isolated from day 15 conceptuses. Consequently, these results demonstrate that the enJSRV envelope regulates trophectoderm growth and differentiation in the periimplantation ovine conceptus. This work supports the hypothesis that ERVs play fundamental roles in placental morphogenesis and mammalian reproduction.
http://www.pnas.org/cgi/content/abstract/0603836103v1

Proceedings of the National Academy of Sciences of the United States of America

PNAS is one of the world's most-cited multidisciplinary scientific serials. Since its establishment in 1914, it continues to publish cutting-edge research reports, commentaries, reviews, perspectives, colloquium papers, and actions of the Academy. Coverage in PNAS spans the biological, physical, and social sciences.
http://www.pnas.org/misc/about.shtml

This serves as yet another example of how the presupposition of naturalism can hurt rather than help scientific research. If we were to allow for the possibility of design, we'd pay closer attention to how organs and DNA that appear to be nonfunctional actually serve a valuable purpose. In anthropology, we learned that there is no such thing as human vestigial organs, only organs that were once incorrectly understood. Today, we are beginning to realize that there is no such thing as "junk" DNA.

Evolutionary biologists maintain that the pseudogenes, SINEs, and endogenous retroviruses shared among humans and the great apes provide persuasive evidence that these primates arose from a common lineage. The crux of this argument rests on the supposition that these classes of noncoding DNA lack function and arose through random biochemical events. For evolutionary biologists, it makes little sense to attribute "junk" DNA to the Creator...

As researchers continue to uncover function for pseudogenes, it becomes apparent that the evolutionary perspective on noncoding DNA as junk has thwarted scientific advance. In spring of 2004 a research team discovered a new class of antifreeze proteins in fish. This function allows fish to live in subfreezing environments. However, researchers failed to recognize this new type of antifreeze protein for nearly 30 years because they had assumed its gene was a pseudogene. Only after researchers realized that the previously identified antifreeze proteins were insufficient for fish to survive in icy polar waters were they motivated to search for additional antifreeze molecules.

The discovery that some pseudogenes are actually functional means the evolutionary paradigm no longer offers the only viable explanation for their existence. Critical pseudogene activity in the cell makes an equally plausible case that the Creator intentionally incorporated this class of DNA into the genomes of humans, chimpanzees, and other organisms for reasons the scientific community is only beginning to grasp.

(Who Was Adam? A Creation Model Approach to the Origin of Man, Fazale Raza and Hugh Ross)

Peace.

 

[Valkhorn]

Science cannot invoke the supernatural. Invoking miracles explains nothing.

A god is also not testable.

So your point fails.

 

[Punchy]

Invoking miracles explains nothing.

Assuming that "junk" DNA is nonfunctional explains nothing. Invoking an intelligent designer is unnecessary in realizing this fact.

 

[Army of Juan]

That's just retarded.

ERVs are like scars in the DNA from attacks from viruses (viri?).

The fact that we have some of the exact same ERVs as other apes is evidence that our common ancestor had them and we inherited them.

It's kind of like how we share the same damaged vitamin C gene as other apes. Why would a designer do that?

If somepne "designed" the human body, then whoever did that was a moron because we have all kinds of poorly implemented features.

 

[Punchy]

That's just retarded.

Wouldn't it be "retarded" if our presuppositions blinded us to the functions of noncoding DNA?

 

[Punchy]

I find the possibility that there is an alternative explanation for ERV's quite liberating.

 

[Danhalen]

I hate the terminology "junk DNA." I like that you switched to "non-coding DNA." As far as claiming the function of ERV's implies the necessity of a designer to insert them, well, I think this is rather specious. It is more likely the regulatory function of ERV's continues to be passed on because they actually provided additional benefit to the pre-existing regulatory function of non-coding DNA. Now that the organism depends on the function provided by the ERV, it would be detrimental to the organism to lose it, and therefore it is continually selected for.

It would be best tested if we could reverse engineer the genome of the last common ancestor to where the ERV in question was inserted, remove the ERV, and then check the selective advantage versus the non-ERV organism. This is theoretically possible, but questionable on an ethical level (but I would do it given the opportunity).

 

[Punchy]

Are we willing to consider the possibility that the explanation for shared ERV's is not common descent?

 

[MewtwoX]

There might be a problem with your analysis.

Evolutionary Theory does not use ERVs as part of the "Junk DNA" argument.

ERVs are shown to be remnants of viral infections through DNA analysis and due to the random nature of insertions and the very low probability of separate species recieving the same insertion, they stand as evidence of common descent.

In other words, its not because they have no function (Might I note that Vestigial does NOT MEAN "NO FUNCTION"), but rather because the possibility of these viral insertions happening simultaneously in separate species with the same structure is incredibly low, the presence of common ERVs indicates Evolutionary Common Descent.

Also, I don't recall anything preventing ERVs from being functional, nor from having a positive contribution to the body from either mutation over time or at the instance of transduction.

Your analysis and points seem to be red herrings on ERVs.


EDIT: Some reinforcement...

Endogenous retrovirus insertions are short stretches of DNA that resemble active retrovirus sequences but they are usually inactive. The genome fragments can be easily recognized because they show significant sequence similarity to known retroviruses. In most cases there are so many differences that we can be confident that the integrated retrovirus cannot be functional.
There are many different types of retroviral sequences in the human genome. The most common class is called LINES (Long INterspersed Sequences). There are several subclasses. One of the common subclasses is the L1 subclass - there are about 30,000 copies of this type of LINE in the human genome.
You can view the human genome using the USCD Genome Browser selecting for a view that shows you repetitive sequences. Here's an example of an L1 LINE on Chromosome 9. If you click on the solid black bar in the middle of the image you'll see that it represents a stretch of DNA that's 6168 bp long. It resembles a retrovirus sequence but it has diverged by 3.6%.

From Laurence A. Moran

http://www.talkorigins.org/origins/feedback/may05.html

PS: Hey, he's from my University.... cool.

 

[flatworm]

If endogenous retroviral insertions and other non-coding DNA are functional rather than vestigial,

The two are not mutually exclusive. Vestiges can retain function.

The expression of some ERV genes does not in any way detract from the fact that ERVs prove common descent between humans and other primates. Claiming the viral genes were "poofed" there by an intelligent designer is just another example of Last Thursdayism, whereby a supposed creator tricks everyone by planting false clues of common descent and/or great age.

this should be considered evidence for design rather than evolution.

BS. That doesn't follow from the fact a retroviral gene can be expressed.

ERV's were once the "magic bullet" that I used in arguing for common descent. But if humans are created in the image of God, it should be expected that most, if not all, of our DNA was designed for a purpose rather than appearing by accident.

ERVs are just part of the overall nested heirarchy of genetic similarity between humans and other primates. They're still a smoking gun, one among many. So you've found an example of a retroviral gene that gets expressed. Can you say the same of all human-primate ERVs? If not, claiming they must be "designed" is just wishful thinking.

This serves as yet another example of how the presupposition of naturalism can hurt rather than help scientific research.

Oh really? A presupposition of a supernatural designer predicts absolutely jack squat. It is not falsifiable and there is no way of distinguishing between a true supernatural explanation and a false one- a presupposition of naturalism is the only game in town.

If we were to allow for the possibility of design, we'd pay closer attention to how organs and DNA that appear to be nonfunctional actually serve a valuable purpose.

Some do, many clearly don't. You can choose to believe otherwise, but that's just wishful thinking.

In anthropology, we learned that there is no such thing as human vestigial organs, only organs that were once incorrectly understood.

You've been lied to. The appendix and extensor coccigix are widely accepted to be vestigial. Vestigial doesn't necessarily mean totally devoid of function.

Today, we are beginning to realize that there is no such thing as "junk" DNA.

Meaning that some DNA previously thought to be nonfunctional has now been shown to have a function. Claiming that this somehow shows that "there is no such thing as 'junk' DNA" is, again, just wishful thinking.

 

[papadex]

Are we willing to consider the possibility that the explanation for shared ERV's is not common descent?

Of course, if you can provide a solid argument with evidence. However, the fact that ERV's serve adaptive functions in no way makes design any more probable, or universal common descent any less probable.

 

[Danhalen]

Are we willing to consider the possibility that the explanation for shared ERV's is not common descent?

If given a compelling counter argument to common descent, yes. Considering there is no argument, no.

 

[flatworm]

Are we willing to consider the possibility that the explanation for shared ERV's is not common descent?

Claiming shared ERVs were actually just magically "poofed" there by a designer is just another "Omphalos" argument. It supposes this "designer" was actively planting false clues to common descent. In fact, any evidence whatsoever can be handwaved away in this fashion, which is why ID is not scientific.

 

[Electric Skeptic]

...This serves as yet another example of how the presupposition of naturalism can hurt rather than help scientific research.

"another example"? I haven't seen the first one, yet?

Oh, and this isn't one, either.

 

[Punchy]

Of course, if you can provide a solid argument with evidence. However, the fact that ERV's serve adaptive functions in no way makes design any more probable, or universal common descent any less probable.

Given our current scientific knowledge, common descent is our best explanation for ERV's. What I simply do not like is the belief that any of our DNA is "junk."

 

[CACTUSJACKmankin]

Let's posit a scenario in which every ERV and "junk DNA" sequence were found to have specific function. Does that mean all of your DNA has fuctionality? No. There are still silent genes. These are genes that never get turned on. They have a function, or at least had one in the past, but just never contribute to the organism. These are another example of a gene sequence that have little selective pressure and act as an excellent piece of evidence for relatedness.

 

[Danhalen]

Given our current scientific knowledge, common descent is our best explanation for ERV's. What I simply do not like is the belief that any of our DNA is "junk."

Junk DNA is no longer generally accepted as a proper term by evolutionary biologists. It was once thought to be useless, but then their minds were changed upon further investigation. I don't see why you have a problem with a term that is no longer considered to have relevance.

 

[danaman5]

Work continues to be done on the function of non-coding DNA. Common descent hasn't blinded anyone to its potential functions, and research has continued to the present day. Therefore, your argument falls apart. "Junk DNA" was just a popular science buzzword.

 

[Upisoft]

Assuming that "junk" DNA is nonfunctional explains nothing. Invoking an intelligent designer is unnecessary in realizing this fact.

It's more accurate to say that science does not assume that "junk" DNA do something. Because if you assume something, you start to use it as it is true. In this aspect science tries to find what, if anything, does the "junk" DNA.
In the same way the science does not assume that "god did it", but does not dismiss that as a possibility.