Sunday, August 23, 2009

Intelligent Design Creationists and Lateral Gene Transfer

 
Some of you might recall an article in Nature Physics published a few weeks ago [Collectivist Revolution in Evolution]. In that article, Mark Buchanan, a physicist, mentioned that biologists were questioning the tree of life.

Buchanan gets so many things wrong I hardly knew where to begin. So, when I blogged about it I just mentioned one thing [Lateral Gene Transfer and the Return of Lamarckian Evolution]. I concluded with ...
This kind of hyperbole is not helpful. Shame on Nature Physics for publishing it.
As expected, the creationists—intelligent and otherwise—were delighted with this latest challenge to evolution. I doesn't matter to them whether a physicist knows what he's talking about.

One of the "otherwises" is named Denyse O'Leary. She's happy to promote the idea that evolution1 is being challenged. It's a special thrill for her to discover that biology is being questioned in a physics journal [The overthrow of Darwinism - in real life, forget the pop science media].

Denyse doesn't do any of the intellectual heavy lifting (surprise!). Instead she links to another Intelligent Design Creationist named David Tylor. Tylor is also mesmerized by the Nature Physics article. He blogged about it at: The collectivist challenge to Darwinism.

Here's part of what he said ...
Talk of unseating Darwinian evolution has not gone down well with some. Larry Moran quotes some of Buchanan's visionary words and declares: "This kind of hyperbole is not helpful. Shame on Nature Physics for publishing it." However, we could do with more substance in arguments against this essay. Darwinism is inherently reductionistic and it can devise ways of framing HGT to fit into its own mental models. But what it cannot easily do is adopt the holistic perspectives that are emerging everywhere. This is why some of us find a framework of design to be compelling. Design provides a coherent context for systems biology, for biomimetics, and for many other contemporary areas of research. Furthermore, although our understanding of HGT is imperfect and in its infancy, design thinking provides a warrant for inferring the origin of genes capable of being transferred, and for understanding the roles played by HGT in populations.
Where to begin?

Horizontal gene transfer (HGT, also known as Lateral Gene Transfer) has been studied for six decades. We have an excellent understanding of the mechanisms; namely, transformation, transduction, conjugation, fusion, and endosymbiosis. There's nothing new there.

"Darwinism" and "Darwinian evolution" are products of the nineteenth century. The only people who are stuck in that century are the creationists. Modern evolutionary biologists have been at the forefront of "holistic" approaches since the recognition that populations evolve, not individuals. For most biologists, this happened in the 1940s. To put this into perspective, that's at least sixty years ago, or 1% of the entire history of Earth!

I'm actually quite happy to promote the "unseating [of] Darwinian evolution" as anyone who reads Sandwalk will attest. David Taylor and Denyse O'Leary are completely incapable of recognizing that legitimate challenges to the old-fashioned way of thinking about evolution are now part of mainstream biology. In fairness, what can we expect from people who think that a 2500 year old book written in Hebrew, Aramaic, and Greek still contains relevant information about science?

"Design" fails to provide a coherent context for anything. I've yet to see anyone explain how and when God intervened to create modern life.

Finally, in case David Tylor is actually interested in learning about the science he criticizes, here's a list of recent postings on the topic. I'd be happy to debate him whenever he feels ready. I'd be happy to do it on The ID Update: News and Commentary Updates for the ID Community but that blog doesn't allow comments. Isn't that strange?

1. The Tree of Life
2. Perspectives on the Tree of Life: Ford Doolittle
3. Perspectives on the Tree of Life: Day One
4. Perspectives on the Tree of Life: Day Two
5. Perspectrives of the Tree of Life: Day Three
6. On the Origins of Eukaryotes


1. She calls it "Darwinism," just like all the other IDiots.

13 comments:

  1. 1% of the entire history of Earth!
    heh

    ReplyDelete
  2. "Where to begin?"

    Why do you remind me of Wile E. Coyote?

    http://www.youtube.com/watch?v=QpGHDX5KIhk

    It's over Larry. There's nothing holding you up.

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  3. "Horizontal gene transfer (HGT, also known as Lateral Gene Transfer) has been studied for six decades. We have an excellent understanding of the mechanisms; namely, transformation, transduction, conjugation, fusion, and endosymbiosis. There's nothing new there.

    This is a disingenuous statement.

    The significance of HGT in eukaryotic evolution has only emerged fairly recently.

    Nat Rev Genet. 2008 Aug;9(8):605-18.

    Horizontal gene transfer in eukaryotic evolution.
    Keeling PJ, Palmer JD.

    Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z, Canada. pkeeling@interchange.ubc.ca

    Horizontal gene transfer (HGT; also known as lateral gene transfer) has had an important role in eukaryotic genome evolution, but its importance is often overshadowed by the greater prevalence and our more advanced understanding of gene transfer in prokaryotes. Recurrent endosymbioses and the generally poor sampling of most nuclear genes from diverse lineages have also complicated the search for transferred genes. Nevertheless, the number of well-supported cases of transfer from both prokaryotes and eukaryotes, many with significant functional implications, is now expanding rapidly. Major recent trends include the important role of HGT in adaptation to certain specialized niches and the highly variable impact of HGT in different lineages.

    ReplyDelete
  4. "Horizontal gene transfer (HGT) was once thought to be virtually impossible. Now however, it is recognized as the main driver of evolution among prokaryotes. This paradigm shift should be unsettling for darwinism, because the genes that bacteria acquire by HGT generally lack observable "origins". They come from somewhere else, already formed. If they were gradually composed in the darwinian manner, clear evidence for that process should be accumulating. It isn't.

    Still, darwinists maintain that HGT is of minor importance among eukaryotes. But important examples have now been documented too often to keep count. The studied marine algae simply add to the evidence that HGT is crucial for eukaryotic evolution as well.

    As genomic databases grow, darwinists expect the number of genes without known orthologs to decrease. This is not happening. Also, darwinists expect genes for given features to be found only in organisms that exhibit those features. Otherwise, the unnecessary genes would lack the pressure of natural selection and degrade. Moreover, they would never have had the benefit of natural selection to help them form in the first place. Yet many examples of such unnecessary genes have been documented. The recent analysis also adds to that list.

    In cosmic ancestry, all genes are very old. They would naturally be sometimes found in species that don't use them. Among eukaryotes, processes like gene conversion may help to preserve the silent genes from degradation. By HGT, species that can use them may eventually acquire the genes, and an evolutionary advance may ensue. We think the evidence supports this scenario. The recent analysis of marine algae does not surprise us."
    - Brig Klyce (http://www.panspermia.org)

    ReplyDelete
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  6. Darwinist darwinist darwinist...damn that gets old quickly, but does save me the time have to read anything you might write as you've already cast yourself as a tool.

    ReplyDelete
  7. Charlie,

    HGT/symbiosis in eukaryotes was established in the late 60ies.

    ReplyDelete
  8. Lorax

    Intsead of indulging in name-calling, why don't you explain your objections to Larry's objection to the term/word "Darwinism"?

    ReplyDelete
  9. Veronica,

    I expect your question arises from a mistake in reading comprehension. If you look back, I used a "t" three times not an "m." Darwinist ≠ Darwinism. Once we agree on that, then I expect you'll see that my comment wasn't directed at Larry, who never used "Darwinist" in his post, but Charlie, who bandies is around like most IDiots as an assault weapon and little more.

    I don't have the time or energy to answer your question in regards to Charlie's unimaginative obsfucation. Part of his argument that I can understand is that if you find a pencil-drawn circle on a piece of paper, it must have been drawn by god, because it doesn't have an apparent origin.

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  10. "Darwinism" is not just a pejorative term used by creationists and ID'ers to disparage evolutionary theory.

    It is a perfectly legitimate definition of the mechanism of evolution first suggested by Darwin and Wallace and modified by their successors.

    It is a theory of biological evolution developed by Charles Darwin and others, stating that all species of organisms arise and develop through the natural selection of small, inherited variations that increase the individual's ability to compete, survive, and reproduce.

    Since "darwinism" has mostly been debunked, it's not surprising that evolutionary biologists are no longer comfortable with the term.

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  11. From the link it is David Tyler not David Taylor.

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  12. I've just had a quick read of the 2007 Nature essay by Goldenfeld and Woese:

    http://dx.doi.org/10.1038/445369a

    It seems to me Mark Buchanan reflects their views fairly well in his 2009 article, so if anyone deserves criticism...

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  13. "...inferring the origin of genes capable of being transferred..."

    Oh dear. Along with such nonsense as "front loading" to try to infer design where a parsimonious interpretation doesn't need it, we've now got the design viewpoint on HGT.

    Apparently we cannot simply say there were lots of organisms with similar biochemistry and the physical capability to do HGT, so it happened - oh no, someone had to intend that HGT take place and design genes that were capable of being interchanged.

    This reminds me more and more of the old joke about the 3 friends debating the subject of the greatest invention in history. One says fire; another says the wheel; the 3rd says the Thermos. When his amazed friends ask why, he says, "You put something hot into it, it stays hot; you put something cold into it, it stays cold." Still puzzled, his friends press him further, asking why this capability is so wonderful. He answers, in a hushed, awestruck tone: "How does it know?"

    ReplyDelete