The "biologists don't use evolution" argument is I think, one of the sillier ones out there. Do geologists "use" geologic plates?
You mention one instance where our knowledge of evolution illumates a given situation, and without it, we'd be fumbling in the dark trying to figure out what to do. In another example, Carl Zimmer, in a recent post, talks about a group of scientists who use common descent and the predictions of natural selection to isolate SNP fragments from the genome. Scroll down to "Evolutionary biology also helps guide medical research ..."
A review of ID arguments can lead one to believe that all ID arguments are fatuous. Logically, one can't just claim that all these arguments are weak without looking at them all. However, I recently looked at an astronomy slide show on answersingenisis. It attacked modern astronomy from at least a hundred different ways. One of the slides quoted noted astronomer Fred Whipple, in 1985, as saying that solar system evolution had not, as yet, been witnessed. Dr. Whipple had said this in order to give the reader a hint at what might be coming soon. Solar systems form from dust clouds, which obscure the process. Also, they are really quite far away. Its difficult, and hadn't yet be done. The Spitzer space telescope has done this. Infrared light passes through dust pretty well, and the Spitzer is large enough to get reasonable resoultion for 'nearby' stellar nurseries. Given that the original statement wasn't meant to mean that science couldn't obtain this evidence, and given that science has, in fact obtained this evidence, the ID argument falls down. But many of the arguments were of this type. Though one is tempted to conclude that all the arguments are worthless, it is clear from a sampling of arguments that it is likely that looking at them is a waste of time.
Getting back to the non-ID part of the article, does this mean that because bacteria will eventually evolve resistance to any chemicals that we throw at them, we are essentially engaged in an arms race with them?
Is our best bet to keep churning out new compounds as bacteria develop resistance to old ones, even if it might make us more vulnerable in the future, or are there other options...maybe looking at ways to boost the immune system through hormones or genetic engineering, or by finding a way to simply make our tissues resistant to the toxins that the bacteria excrete?
Getting back to the non-ID part of the article, does this mean that because bacteria will eventually evolve resistance to any chemicals that we throw at them, we are essentially engaged in an arms race with them?
I don't know that they'll be able to evolve resistance to *any* chemicals. There has been a lot of concern about antiseptic resistance--resistance to biocides such as bleach, lysol, etc. (A good review came out in the June issue of Clinical Infectious Diseases, 40:1650). We don't know if they'll evolve resistance to these or not, but I think it's best to err on the side of caution and assume it's at least possible.
Is our best bet to keep churning out new compounds as bacteria develop resistance to old ones, even if it might make us more vulnerable in the future, or are there other options...maybe looking at ways to boost the immune system through hormones or genetic engineering, or by finding a way to simply make our tissues resistant to the toxins that the bacteria excrete?
I think a combination approach is always best. Despite all our knowledge, we still really have an elementary understanding of our immune system; I'm sure there are ways we could make it more effective, in addition to combatting bacteria with various chemicals. And, of course, more vaccines to prevent what infections we can.
Yes, we are engaged in an arms race with bacteria. We always have been. In the past, it was just our immune system vs. the bugs. Now it is our immune system plus our technology vs. the bugs. But it's really no different. The bugs evolve, and the author is quite correct that without an understanding of that we would be fumbling in the dark.
As far as the ultimate strategy: yes, we do need to keep making new weapons against bacteria. However, we could also "rotate" our weapons. Keep in mind that genes that are not subject to positive selection eventually become less common in the population due to mutations accumulating and not being selected out. This is why there are blind fish in caves; they lost eyesight because they didn't need it and it wasn't selected for. If we were to-- say-- stop using penicillin for a long time, then chances are we could reintroduce it and the bugs would have lost most of their resistance to it. If we had a lot of different chemicals, we could rotate them with a very long period (say 20 years or so) and probably keep the war going for quite some time.
Hi Tara, just a minor point: Vince Fischetti works at the Rockefeller Univeristy. The Rockefeller Inistitute turned into a University in 1955. 
I agree phage is promising. I've followed it for awhile and I'm actually working on a piece about it. I think the next question, though, is how easily it will hurdle the FDA. Mark Plotkin in his book, The Killers Within, notes that FDA procedures are designed to test stable compounds that don't change over time. Getting them to clear live viruses, whose very strength is that they mutate to keep up with their bacterial prey, will require a bit of a rethink in an institution known for nasty bureaucracy. Plus, since phages feed on human bacteria, the Soviets used to find them in unsavory places - sewage, storm drains, etc. So some may have a visceral, if unwarranted, reaction against the critters. Of course, antibiotics come from mold and dirt. Beggars can't be choosers.
Even before this experiment, evidence suggested that bacterial resistance to antimicrobial peptides was likely. Comparisons among related antimicrobial peptide genes show that natural selection often favors new variants, and this is probaby because germs become resistant to variants that have been around for a while. Thus, merely observing patterns in nature that were laid down long ago, and interpreting them in the light of evolutionary theory, can have practical application. Creationists sometimes dismiss experiments on populations in the lab, saying that such research says nothing about how we actually got here. But evolution is a unified theory: differences at antimicrobial peptide genes among distinct species, that accumulated as they evolved naturally, is intimately related to bacteria evolving artificially in a lab.
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