Frankenvirus

| 9 Comments

It was All Hallows Eve when the paper came out in Genome Research, and although there wasn’t the crackle of lightning bolts or a hunchbacked assistant called Igor, the announcement that researchers had resurrected an ancient human endogenous retrovirus (HERV) brought enough of the “how dare you resurrect an unknown virus” kind of response to warm the heart of Frankenstein devotees everywhere. I won’t discuss these aspects of Frakenvirus, it’s done better elsewhere. However, the whole HERV resurrection issue has interesting implications for Intelligent Design advocates.

Retroviruses are viruses that can insert copies of their own genetic material into our DNA. Sometimes mutations inactivate the virus, and the broken virus, now a HERV, gets passed along to our offspring. HERV’s litter the human genome. Astoundingly about 8% of our genome is broken viruses. We have roughly 5 times the number of broken viruses in our genome as we have protein coding genes. You would think this alone would give ID advocates pause, what kind of Intelligent Designer would leave chunks of broken virus throughout their creation[1]? But ID advocates say we can’t speculate about the nature of the Designer, maybe having more broken viral DNA than protein coding genes is a way of “Making An Artistic Statement” at the All Universe Gene Design Convention (best Carbon-based lifeform category), who knows?

More interestingly, the HERV-K family, which is the family of viruses the resurrected virus came from, is only found in primate genomes. When phylogeny studies are carried out, the phyogeny of broken viruses mirrors that of other phylogenies. Specifically humans and chimps are shown as sharing the most recent common ancestor. The ID advocates can’t claim this is an essential gene, that any Designer must incorporate into the genome, it’s a broken virus. As the only way to get the same broken viral DNA in the genomes of chimps and humans is common descent, this sort of looks bad for ID advocates. But then again, we are not allowed to speculate on the nature of the designer, perhaps the Designer was running late with their entry in the All Universe Gene Design Convention, and decided to snaffle some primates from Sol III for a quick and dirty bodge job (or again, maybe it was “Making An Artistic Statement”).

There are about 30 broken copies of the particular HERV-K resurrected by the researchers in our genome. The researchers took dozens of these, then used alignment to build a “consensus” virus. The resulting Frankenvirus was viable, infected human cell lines and did all the things a good retrovirus does. Resurrecting ancient proteins isn’t new, researchers have resurrected ancestral photopigments, and receptors using phylogenetic alignments, but this was the first time so many were resurrected at the same time, and shown to form a functional system. This is another big problem for ID advocates, Dembski in particular has been pushing the concept that enzymes are extremely functionally isolated, and that even slight perturbations of structure would inactivate them. If this were true, researchers would not be able to generate the Frakenvirus, or any other of the resurrected proteins, as you can never generate an exact structure from these alignments. Thus proteins cannot be extremely functionally isolated, as Dembski claims.

The Frankenvirus is a astounding piece of science, it is causing headaches for those people worried about resurrecting ancient plagues, but it is already a plague on some of the fundamental arguments of ID advocates.

Researchers Website: http://www.igr.fr/brochure_recherch[…]ence-1.shtml

[1] Okay, The Sirius Cybernetic Corporation, for one.

Dewannieux M, Harper F, Richaud A, Letzelter C, Ribet D, Pierron G, Heidmann T. Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Res. 2006 Oct 31

Reus, K HERV-K(OLD): the ancestor sequences of the human endogenous retrovirus family HERV-K(HML-2). J. Virol. 75 (2001), 8917–8926.

Johnson WE, Coffin JM. Constructing primate phylogenies from ancient retrovirus sequences. Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10254-60.

9 Comments

maybe having more broken viral DNA than protein coding genes is a way of “Making An Artistic Statement” at the All Universe Gene Design Convention (best Carbon-based lifeform category)

You might be on to something here. Homo sapiens - winner of the genetic Turner Prize!

I can’t think of a creationist come-back for our genome being littered with old viruses, but I’m sure they’ll come up with something.

A creationist commented to me that only the protein-coding part of our genome was almost a perfect match with chimps, but what about the rest of it? Isn’t the entire thing a 98% match though? I was under that impression. If such a small segment of our DNA codes for protein, it would be even more strongly revealing that our entire genome matches so closely with that of another primate.

If creationists are willing to accept forensic DNA evidence to check for relatedness among human families, (DNA fingerprinting, which is done with noncoding DNA, is one method) why is it such a leap to accept it to check for relatedness among species?

It is interesting to note that Wells and Dembski don’t seem to mention HERVs or any other molecular vestiges in the appalling first chapter of their upcoming college level ID textbook “The Design of Life”(1st chapter online here) In this chapter they discuss human origins and, surprise surprise, they “forgot” to mention these important pieces of evidence.

Syntax Error: not well-formed (invalid token) at line 8, column 120, byte 1176 at /usr/local/lib/perl5/site_perl/5.16/mach/XML/Parser.pm line 187.

It does make good evolutionary sense that the protein coding region remains highly conserved. Thanks for the clarification - I will relate the info to my creationist friend.

Got bored at TT, so I thought I would see what you guys are up to. Yes, I think the broken virus argument lends considerable evidence to common ancestry, which ID advocates Behe and Mike Gene accept (as do I). But I’m wondering: do we know for sure that broken viruses (viri?) have no functional role?

Also, you lost me on that “enzymes are extremely functionally isolated” counter-argument.

Katarina Wrote:

I can’t think of a creationist come-back for our genome being littered with old viruses, but I’m sure they’ll come up with something.

The usual response when I bring it up is… ignore me and complain that nobody is presenting evidence for evolution.

Michael Suttkus: “The usual response when I bring it up is… ignore me.…”

Yeah, I know exactly how you feel.

Michael Suttkus: “The usual response when I bring it up is… ignore me.…”

Yeah, I know just how you feel.

About this Entry

This page contains a single entry by Ian Musgrave published on November 4, 2006 3:08 AM.

IRS claims Kent Hovind’s $250,000 challenge; all mysteries of life now solved was the previous entry in this blog.

Stand Up for Science this Tuesday is the next entry in this blog.

Find recent content on the main index or look in the archives to find all content.

Categories

Archives

Author Archives

Powered by Movable Type 4.381

Site Meter