Sunday, January 25, 2009

Horizontal Gene Transfer and Intelligent Design Theory

AUTHOR: Graham Lawton

SOURCE: "Why Darwin was Wrong About the Tree of Life"

COMMENTARY: Allen MacNeill

A recent article in the New Scientist trumpeted the news that "Darwin was wrong", at least insofar as his "tree of life" was concerned. To be specific, the author stated that new discoveries in the field of horizontal gene transfer had invalidated Darwin's "tree of life", as illustrated by his diagram in the Origin of Species.

Horizontal gene transfer (especially as the result of viral transduction) has been known to occur for almost half a century. In my undergraduate genetics course at Cornell (which I took in the spring of 1972) we did a lab in which we used lambda bacteriophage to transfer genetic material from one bacterial colony to another. Ergo, none of the mechanisms of HGT described in the article in New Scientist are all that new.

Indeed, I have listed at least six mechanisms of HGT in my blogpost on the “engines of variation” located here. In that list, they are numbers 28, 29, 33, 36, 40, and 41. Most of these HGT mechanisms have been known for decades and are among the best understood mechanisms of increasing both genetic and phenotypic variation.

What is relatively new is the application of the information gained about HGT to phylogenetic reconstruction. HGT is the rule among bacteria, and apparently occurs fairly frequently among eukaryotes as well. Evolutionary biologists, and especially phylogeneticists and systematists have been using HGT data for phylogenetic reconstruction for over a decade, even among eukaryotes. So, once again this is not new.

However, there is currently a tread at Uncommon Descent to the effect that
(1) the New Scientist article is pointing out that "Darwinism" is a bankrupt theory, and

(2) that HGT is more easily explained as part of "intelligent design theory" (ID).

Does the increasing recognition of HGT and its use in phylogenetic reconstruction mean that the current theory of evolution is invalid, or that ID can explain these phenomena better? On the contrary, the more we learn about HGT the more it seems to be even more random and undirected than vertical gene transfer (i.e. genetic recombination and heredity via reproduction). To be specific, the overwhelming majority of identified HGTs are of non-coding DNA sequences that have no detectable effect on the phenotypes of the organisms in which it has occurred.

That is, almost all of the DNA sequences that have been unambiguously shown to be the result of HGT are sequences that do not code for proteins nor participate in the regulation of coding sequences. Rather, they are sequences that have “gone along for the ride”, especially as the result of RNA retroviral HGT. Such sequences are so common that they are routinely used to construct and modify genetic phylogenies, as well as to determine genetic homologies.

The vast majority of HGTs are essentially neutral genetic mutations, as first described by Motoo Kimura in his neutral theory of molecular evolution. As such, they produce an immense amount of genetic variation without producing a corresponding amount of phenotypic variation. Furthermore, when such phenotypic variation does occur, it is more often deleterious than beneficial (usually mildly deleterious, as pointed out by Tomoko Ohta in her nearly neutral theory of molecular evolution). Only very rarely are such HGTs beneficial, and then only in relatively restricted ecological and evolutionary settings.

But neutral or slightly deleterious genetic changes (such as those produced by the vast majority of HGTs) are exactly the opposite of what one would expect to see as the work of an “intelligent designer”. Such an entity would (as several of the commentators in this thread have suggested) tailor HGTs to produce adaptive (i.e. beneficial) changes in the phenotypes of the recipients of its HGTs. Either that, or the “intelligent designer” doesn’t “tailor” its HGTs at all, but rather produces them randomly, rather like a dealer in a card game. But in that case, the actions of a soi dissant “intelligent designer” would be indistinguishable from Darwinian evolution, and including any reference to its actions (and/or inferring its existence) would be unnecessary (and would therefore violate Occam’s razor).

One last point: although the vast majority of HGTs produce either no phenotypic effect or slightly deleterious phenotypic effects, a relatively small number produce phenotypic effects that are correlated with increased survival and/or reproductive success. Unlike the vast majority of HGTs, these beneficial HGTs rapidly proliferate in the populations in which they arise, in exactly the way Darwin proposed in 1859. That is, they are preserved and passed on (while deleterious HGTs are eliminated), and thereby become more common over time among the populations in which they occur.

As always, comments, criticisms, and suggestions are warmly welcomed!


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At 1/26/2009 06:24:00 AM, Blogger Allopatrik said...

Thanks, Allen. What interests me about the ID take on the article is, if they took the time to see where on the tree of life the vast majority of the HGT has occurred and is occurring, they would see that the tree metaphor is as strong as ever. It just has a more complex root system than we once thought.

Dave Wisker

At 1/26/2009 07:24:00 AM, Blogger Allen MacNeill said...

Indeed, I took to calling it the "mangrove of life" several years ago, and noticed recently that this metaphor has been taken up by others. Either that or it's a typical case of convergence (yes, I know, homoplasy is bad, unless you spell it out...)

At 1/27/2009 03:06:00 AM, Blogger Rob R. said...

Off Topic: If you don't mind my asking, why have you never earned your PhD, Mr. MacNeill? I always assumed you had (you certainly seem to have the 'chops' and you work in academia, etc) but I remember you correcting somebody on some blog whom called you Dr. Anyway, is there a story behind it or is it just one of those 'never got around to its'... just curious. Please keep up the good work I really appreciate your contributions here and elsewhere on the web.


At 1/27/2009 08:08:00 AM, Anonymous Anonymous said...

Despite HGT, the tree of life seems to resolve much better than the Doolittle diagram in textbooks suggest:
Ciccarelli et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science. 311:1283–1287.
Dutil het al, 2008. Signature Genes as a Phylogenomic Tool. Mol. Biol. Evol. 25:1659–1667.

At 1/27/2009 08:24:00 AM, Blogger Allen MacNeill said...

I was hired to teach introductory biology at Cornell immediately upon finishing my masters degree (indeed, I hadn't quite finished it when I was hired). I had completed most of the course work for my PhD and had taken my A exam, but my wife (now long my ex-wife) got pregnant and was accepted into medical school, so I took a leave of absence from the graduate school. I then proceeded to raise my daughter (and her sister, who came along seven years later) and continued to teach biology. Then, about the time I was ready to reactivate my PhD program, I divorced and remarried and had four more children. As I already was teaching biology and evolution at Cornell, I simply continued to do so. As far as I know I have the longest leave of absence from the graduate school for anyone, including ABDs.

I may even go back one day and finish, just for the fun of it.

At 1/28/2009 07:00:00 AM, Anonymous Anonymous said...

When you say:
"In my undergraduate genetics course at Cornell (which I took in the spring of 1972) we did a lab in which we used lambda bacteriophage to transfer genetic material from one bacterial colony to another.", I don't think this corresponds to my understanding of horizontal gene transfer in the context of the current tree of life furore. I think this is meaning between species, not between strains of the same species.
Unless you did do transduction between bacterial species!


At 1/28/2009 08:58:00 AM, Blogger Allen MacNeill said...

This opens another can of nematodes, as I support Lynn Margulis' assertion that there are no "species" of prokaryotes (see for more on this). Either that or every single bacterial cell qualifies as its own "species". Bacteria are extremely tolerant of exchanging genetic material by a variety of mechanisms, including viral transduction. Therefore, viral transduction of one bacterium to another is exactly what most people talk about when they talk about horizontal gene transfer.

At 1/28/2009 09:13:00 AM, Blogger Allen MacNeill said...

P.S. As for my current lack of a PhD degree, I sometimes point out that the following scientists also lacked a doctoral level degree in science when they published their best known works (followed by their highest earned academic degree):

Nicolaus Copernicus (doctorate in canon law)

Galileo Galilei (ABD in medicine)

Isaac Newton (undergraduate degree in mathematics)

Albert Einstein (undergraduate degree in physics)

Charles Darwin (undergraduate degree in Anglican divinity)

Clearly, the lack of a PhD in one's chosen field is no impediment to accomplishment in science, and if the huge population of PhDs who publish nothing of note is any indication, having a PhD is no indication of genius.

At 1/28/2009 10:51:00 AM, Anonymous Anonymous said...

If I recall correctly, Einstein earned a PhD from the University of Zurich.

Dave Wisker

At 1/28/2009 01:07:00 PM, Blogger Allen MacNeill said...

According to the biographical information available online, Einstein's degree was not a doctoral level degree. Despite this, he was eventually hired to teach physics at the university level, partly because his research and publications in physics were so well known, and partly because the tradition that college and university professors were required to have a doctoral level degree had not yet become entrenched (especially in Europe).

To be specific, Einstein did not yet have a doctoral level degree when he published his three revolutionary papers on Brownian motion, the photoelectric effect, and special relativity in 1905. At the time, he was working as a patent clerk.

At 1/28/2009 01:59:00 PM, Blogger Rob R. said...

"P.S. As for my current lack of a PhD degree, I sometimes point out..."

To be clear, I wasn't trying to be disparaging or insinuate anything in asking the question. I was just curious. Honest Injun. Thanks again for your contributions to this whole culture war mess. You've become someone I seek out when I want to know something about evolution.


At 1/28/2009 03:54:00 PM, Anonymous Anonymous said...


Yes, I was worried I was opening another can of wriggly things there with mention of bacteria and species in one sentence!
What's the host range (if that's the correct terminology) of a typical phage? I'm a fly boy, not a bug boy...


At 5/06/2009 12:01:00 AM, Blogger Stargazer said...

Dear Prof.,

May I ask if the horizontal gene transfer is specific (any characteristics on the plasmids which are preferentially transferred to other bacteria) ?


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