Thursday, October 29, 2009

Microbes continue: pathogens and genomic islands

The ARJ microbe series continues this week with Georgia Purdom's "The role of genomic islands, mutation, and displacement in the origin of bacterial pathogenicity." Previous entries in the series:

Francis & Purdom: "More abundant than stars: an introductory overview of creaation microbiology"
HTML - PDF - My comments

Liu & Soper: "The natural history of retroviruses: exogenization vs endogenization"
HTML - PDF - My comments

Criswell: "A review of mitoribosome structure and function does not support the serial endosymbiotic theory"
HTML - PDF - My comments

Sherwin: "A possible function of Entamoeba histolytica in the creation model"
HTML - PDF - My comments

Loucks: "Fungi from the biblical perspective: design and purpose in the original creation"
HTML - PDF - My comments

This new paper is a good one. This was the first in the microbe series that made me excited to read it. To be honest, this is the first creationist paper in a long time that made me excited to read it. I hate to say that, but it's true.

What's the big deal? This paper is a synthesis of ideas that me and several of my colleagues have been playing around with for some time now. The question we're trying to answer is where do bad bacteria come from? Now we know that most bacteria are not bad. Only a small fraction cause disease, but those that do often have really fascinating mechanisms by which they cause disease. For example, the anthrax bacterium has an elaborate two-part toxin (part of which is shown in the figure). One part binds to your cells and injects the part called "lethal factor." Guess what lethal factor does.

The problem of course is that God created everything "very good" in the beginning. Death and suffering resulted from the sin of man, the Fall, and the Curse. So where do bad things come from? Where do we get diseases, especially fatal diseases like anthrax? Some creationists just attribute disease to a general notion of degeneration after the Fall, others have insisted that it's mutation, others (including me) have implicated genome decay, that is, the loss of genes. On the other hand, a couple years back I did a survey of genomes of pathogenic bacteria and found that some of them had gained genes.

The truth is that pathogenic bacteria are actually quite complicated and resist any simple explanations. Purdom emphasizes that in this article. Some pathogens originate by acquiring genes in a set called a "pathogenicity island." Others have similar genes, but they aren't pathogenic unless other cellular genes are present. Still other bacteria need a pathogenicity island and loss of certain cellular genes.

In all cases, though, Purdom argues that the genes or the phenotypes acquired by pathogenic bacteria are not intrinsically bad. Often close relatives of the pathogens have very similar sets of genes but are not pathogenic. Following Joe Francis's ideas, she suggests that pathogens originated as either symbionts of macroorganisms or less commonly from free-living ancestors. She also reminds us to examine the possibility that the bacterial host has changed by failing to relate to the symbiotic bacteria properly.

I do have one minor quibble: Purdom repeatedly states that "no intentional pathogenic mechanisms exist." By this, I think she means that pathogenic mechanisms or structures can be used for nonpathogenic purposes and therefore could be thought of as merely modifications of otherwise harmless things. This would imply that all pathogenic bacteria or pathogenic structures are modified versions of harmless bacteria or structures. Conversely, God did not make pathogens to be pathogens. I'm not sure I agree with that. I don't think we should necessarily rule out the concept of purposeful redesign at the Fall. On the other hand, I think her idea is a decent working hypothesis.

In any event, it's a masterful synthesis, and I'm eager to see more. She concludes the paper with a few suggested research projects, and I'd like to add at least one more: Could there be novel therapeutic applications of this line of thinking? That's something that's worth looking into. In the meantime, BSG is coming, and I'd love to see more work along these lines (hint, hint, Georgia).

Purdom. 2009. The role of genomic islands, mutation, and displacement in the origin of bacterial pathogenicity. ARJ 2:133-150.