Improving Wikipedia, One Article at a Time

In a discussion over on AtBC, a YEC antievolutionist, David Hawkins, was asserting that observed genetic diversity could be the result of ordinary evolutionary processes in the ~4K years since Noah’s flood. He proposed using domestic breeds of dogs as Exhibit 1 in his argument that variation and diversification could be made to fit into the Procrustean bed of a young-earth chronology.

All of this would concern me far less if there hadn’t been a discussion of genetic mechanisms contributing to genetic diversity along with that. There was some stuff about mutation as opposed to recombination as a source of novel alleles, with Hawkins opining that recombination never produced novel alleles. I got involved at that point, saying that of course recombination could produce novel alleles. Hawkins’s riposte? A quote from the Wikipedia article on “genetic recombination” that said that recombination only shuffled existing alleles and did not produce genetic novelty. That was that, so far as Hawkins was concerned. But it was just the start of the story for me.

So I did a little searching via Google scholar (See? One of the many things Google gets right.), found a research article supporting the production of novel alleles via recombination, and added a comment to the Wikipedia “genetic recombination” talk page noting the problem in the article. I came back a little later and suggested a replacement wording for the affected area of the main article. I noted that I had made the suggestion for Wikipedia back on the AtBC thread.

Here’s what I wrote there:

Recombination does not respect reading frame boundaries, and therefore can produce novel alleles. One research article describing this says:

The asymmetric patterns of polymorphism and the absence of simple dinucleotide variation in 23 kb of sequence are compatible with recombination or sister chromatid exchange, but not polymerase slippage. By inference, recombination should underlie the polymorphisms at (GT)n/(AC)n since they are a subset of (RY)n and they commonly occur in the context of longer (RY)n.

Which means that the introductory statement in the main article here:

Recombination therefore only shuffles already existing genetic variation and does not create new variation at the involved loci.

is completely incorrect. Recombination is sufficient to produce novel alleles. It does not necessarily produce novel alleles, though, which is why a misunderstanding such as the quoted statement from the article can become widespread as a meme.

Can somebody fix the main article, please? –Wesley R. Elsberry 22:05, 3 January 2007 (UTC)

Suggested rephrasing of the bad sentence… Was:

Recombination therefore only shuffles already existing genetic variation and does not create new variation at the involved loci.

should become…

Because coding regions are relatively uncommon, in most cases recombination breaks and rejoins genetic material outside those regions, with the effect of “shuffling” already-existing loci. But since recombination does not respect reading frame boundaries, from time to time it will bring together parts of differing alleles, resulting in the production of a novel allele.

How’s that sound? –Wesley R. Elsberry 22:20, 3 January 2007 (UTC)

I usually suggest changes in talk pages rather than directly editing articles. This allows those people who watch over particular articles a chance to discuss a change before it gets made, which all-in-all works better, I think.

Hawkins went over to the Wikipedia talk page and had his say there.

I emphatically disagree with Dr. Elsberry. The sentence should remain unchanged. This article is based on one of the leading cell biology textbooks in the world, co-authored by no less an authority than the late president of the National Academy of Sciences, Bruce Alberts.

And a good deal more besides that, all to the point of having my suggested change rejected by the Wikipedia community.

David J. Phippard, a pathobiologist at the University of Washington, had this to say about the exchange:

The most likely reason Mr. Hawkins is unaware of research demonstrating that recombination can produce new alleles is that he has not taken the time to research the subject. Allelic recombination is well represented in the scientific literature. For example from PNAS | December 10, 2002 | vol. 99 | no. 25 | 16348-16353 we have:

“Meiotic recombination in the anopheline mosquito is the major mechanism for allelic variation of PfMsp-1 (8); thus, intragenic recombination between unlike alleles generates new alleles in the progeny (10). Recombination sites are confined to the 5′ and 3′ regions of the gene.”

Dr. Elsberry’s rewrite is concise, accurate, and easy to understand, and should thus be adopted. The references from the quote are (8) Tanabe, K., Mackay, M., Goman, M. & Scaife, J. (1987) J. Mol. Biol. 195, 273-287 and (10) Kerr, P. J., Ranford-Cartwright, L. C. & Walliker, D. (1994) Mol. Biochem. Parasitol. 66, 241-248. David J. Phippard 17:14, 4 January 2007 (UTC) David J. Phippard

Last time I checked, Dr. Mr. Phippard had incorporated my suggested change into the main article.

I think that went well.

Wesley R. Elsberry

Falconer. Interdisciplinary researcher: biology and computer science. Photographer. Husband. Christian. Activist.

11 thoughts on “Improving Wikipedia, One Article at a Time

  • 2007/01/04 at 2:10 pm
    Permalink

    Nicely done! Thanks, Wesley.

  • 2007/01/05 at 9:13 am
    Permalink

    Wesley, thanks for clearing that up. I’d read conflicting reports on this, and Larry Moran told me on his blog that “biological crossover was not destructive”. But it actually does resemble GA’s. And in GA/GP models, destructive crossover + a variable length genome leads to junk dna (to mitigate the effects of destructive crossover – which can also separate gene families). Larry didn’t want to believe that.

  • 2007/01/05 at 6:55 pm
    Permalink

    I think it depends a lot on what one means by “destructive”. Larry does know the genetics backwards and forwards; that is in his specialization. Mine is organismal biology. So I would be open to correction that takes account of the research articles that Phippard and I referred to. The basis for what I have said is, so far as I can tell, reflected in current genetics research.

  • 2007/01/05 at 10:38 pm
    Permalink

    It is a nice example why wikipedia does not work. The faulty information was there for over a year, and unless people who know where they talk about babysit the article, it gets messed up slowly.

  • 2007/01/06 at 12:41 pm
    Permalink

    Hmmm. Nature did some comparisons of Wikipedia and Encyclopedia Britannica, sending out technical articles from each to domain experts, asking them to find any errors. The average error rate was 4 errors per Wikipedia article, and 3 errors per Encyclopedia Britannica article, IIRC. I think it was the same group that tried deliberately inserting errors into Wikipedia; they found an average residence time of something like fifteen minutes. That would put the affected article on the far end of the distribution.

  • 2007/01/08 at 12:44 pm
    Permalink

    Hmmm … here are the rest of the comments I made at Wikipedia.

    In spite of Dr. Phippard’s comments, the sentence, as it stands …

    “Recombination therefore only shuffles already existing genetic variation and does not create new variation at the involved loci.”

    is a correct statement. Dr. Elsberry is wrong when he states that it is completely incorrect. Note the following quotes from …

    Annu. Rev. Genet. 2002. 36:75–97 doi: 10.1146/annurev.genet.36.040202.111115 Copyright c° 2002 by Annual Reviews. All rights reserved RECOMBINATION IN EVOLUTIONARY GENOMICS David Posada1,2, Keith A. Crandall3,4, and Edward C. Holmes5 1Variagenics Inc. Cambridge, Massachusetts 02139, 2Center for Cancer Research,Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, 3Department of Integrative Biology, 4Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah 84602, and 5Department of Zoology, University of Oxford,Oxford OX1 3PS, United Kingdom

    “Recombination can play a dominant role in the generation of novel genetic variants through the rearrangement of existing genetic variation generated through mutation.” (p.81)”

    So while novel alleles can arise through recombination (it is true that I was not aware of this), it turns out that these novel alleles are simply the rearrangement of existing genetic material which, the above authors believe, was originally created through mutation.

    This article also says …

    “Although both [homologous and non-homologous recombination] conform to a broad definition of recombination—[that is,]an evolutionary event that has as a consequence the horizontal exchange of genetic material…” (p.76)

    “Horizontal exchange of genetic material” is not a phrase which gives the impression of anything truly novel being created.

    Dr. Elsberry’s proposed wording …

    “Because coding regions are relatively uncommon, in most cases recombination breaks and rejoins genetic material outside those regions, with the effect of “shuffling” already-existing loci. But since recombination does not respect reading frame boundaries, from time to time it will bring together parts of differing alleles, resulting in the production of a novel allele.”

    would lead readers to believe that new genetic information is being created, when in reality, previously existing information blocks are being reshuffled in a way that is not yet completely understood.

    I would be interested to see what Albert’s most recent textbook (2002 version) has to say about this, since this article was based on the earlier version of his textbook. I will comment on that when I can obtain a copy. –David W. Hawkins 11:05, 4 January 2007 (UTC)

    I also stated that …

    Readers should be aware that this change proposed by Dr. Elsberry was precipitated by a discussion on the “After the Bar Closes” Forum at Panda’s Thumb. It appears that evolutionary biologists such as Dr. Elsberry are keen to propose new mechanisms for the generation of novel alleles in the face of accumulating evidence that RM + NS (Random Mutation + Natural Selection) is insufficient to explain all the biological innovations seen in nature. One participant in the discussion–a microbiology professor–even proposed that recombination is a “kind” of mutation. Of course, this would be a significant departure from all previous understandings of the word “mutation.”

    To make the change proposed by Dr. Elsberry would be misleading to readers and in my opinion would serve to discredit the good name of Wikipedia. –David W. Hawkins 12:15, 4 January 2007 (UTC)

    I became aware of the failure of RM + NS from a new book, Genetic Entropy and the Mystery of the Genome (2005) written by Dr. John Sanford, a Cornell geneticist, who recently has repudiated neo-Darwinism and become a YEC.

  • 2007/01/08 at 10:54 pm
    Permalink

    Might as well have “become aware” via a toy in a Cracker Jack box; the evidence is against you, which apparently has resulted in your campaign to make yourself excessively annoying everywhere. I treat this weblog as an extension of my living room, so don’t expect to cast aspersions about me elsewhere and visit here as well.

  • 2007/01/09 at 10:20 am
    Permalink

    Wesley,

    I’m afraid I cannot claim doctoral status, as I’m but I second year grad student. Therefore, I suggest that you change “Dr. Phippard” to “Mr. Phippard,” “David,” or “Phipps phippymcphipperson.” Thanks!

  • 2007/01/09 at 10:25 am
    Permalink

    Ah, and I suppose it would also be an exaggeration to call me a pathobiologist, though that is the program I’m in.

  • 2007/01/27 at 2:34 pm
    Permalink

    Off-topic, but (I hope) excusably so.
    You may find it astonishing, but an interested reader can Google repeatedly for “AtBC” and never find the phrase spelled out at a forum devoted to discussion of evolutionary biology.

    I assume it is not “After the Bar Closes”, although that has a certain poetic charm.

    Nor do I take it to be the Association for Tropical Biology and Conservation (among other things, the lower-case “t” does not fit).

    So what is it? If it is a forum at http://www.antievolution.org/, what do those pesky initials stand for? Pardon my ignorance, but I need to know.

  • 2007/01/28 at 10:14 am
    Permalink

    Belay that request! A more careful reading of this very thread has already answered my question. So David Hawkins has made a contribution to someone’s knowledge, though I find that idea a little bizarre and disturbing.

    And I’ll not be so quick to reject the poetic hypothesis next time.

Comments are closed.