A Lorelei Verthandi

[Note: This was originally published in two parts in December 2007. It has been lightly edited for style and formatting, while remaining true to the original content.]

Earlier last week, GilDodgen of Uncommon Descent wrote about his plans to revolutionize medicine and save us all from antibiotic-resistant bacteria. He exhibits some spectacularly bad logic, even for a cdesign proponentsist. I don’t want to go into Dodgen’s points and claims specifically; those have already been torn to ribbons by such fine bloggers as these: Humble Monkey, Sandwalk, Respectful Insolence, and Panda’s Thumb.

Instead, I want to address the more general trend of creationist denial regarding antibiotic-resistant bacteria. Resistance to antibiotics (henceforth just “resistance”) is one of the starkest examples we have of the power of evolution by natural selection of random mutation. So it only stands to reason that creationists will fall over each other to deny that resistance has anything to do with evolution. To do so, they employ two main talking points lies (which we can see embodied in this Answers in Genesis article):

1) “The genes for resistance are not the result of random mutation; they’ve been there all along, we just didn’t notice them.”

2) “Even if resistance does occasionally result from random mutation, it doesn’t count as evolution, because there’s always a price to be paid for gaining resistance.”

Regarding the first point, even if the creationist grudgingly admits the importance of natural selection to the growth of a resistant population, they vehemently deny that what’s being selected is the result of random mutation. Instead, they say that either there were a handful of resistant bacteria around to begin with, or they inherited the genes for resistance from a different kind of bacteria via lateral gene transfer. Dodgen’s post falls into this camp, sort of, since he’s downplaying the power of random mutation. Another, perhaps clearer, example would be a recent UD post by idnet.com.au discussing divergence of E. coli in the human gut versus that of the baboon. Although resistance is not specifically addressed, it is claimed that any new genes found in either population of bacteria must be the result of lateral gene transfer. (Note that lateral gene transfer is in fact a primary mechanism of bacterial evolution, but it doesn’t explain the origin of the genes being transferred.)

Real science, of course, is chock full of examples of the power of random mutation. Let’s look at just one example: Pseudomonas aeruginosa infections in patients with cystic fibrosis, from a paper published by Antonio Oliver et. al. in the journal Science in 2000.

Cystic fibrosis (CF) is a genetic disorder resulting from a mutation in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR). Normally, CFTR adjusts ion concentrations in order to make water flow out of the cell via osmosis. In the lung, this source of water is what keeps your mucus nice and wet and fluid. But if CFTR is broken, the mucus in the lung (and elsewhere, such as the GI tract) becomes dry and super-thick, causing all kinds of hell for the CF patient’s body.

P. aeruginosa is an opportunistic bacteria; it can’t and won’t infect a healthy adult. It can, however, cause serious infection in certain scenarios if exposure is high and the host’s defenses are already down. Two major targets for serious acute (short-term) infection are mechanically ventilated patients and victims of serious burn wounds. But for patients with CF, P. aeruginosa instead causes chronic (long-term) infection. For most such patients, it’s not the CF that kills you, it’s the Pseudomonas.

As it turns out, P. aeruginosa infections from CF lungs show a lot more colony diversity than colonies grown from patients with acute infections. Oliver’s group hypothesized that this diversity was due to the conditions within the CF lung, which as a result of hyperosmolar viscous mucus is highly compartmentalized and continually changing. Such an environment would favor the growth of bacteria that could keep on their toes, so to speak, quickly and readily adapting to changing environmental niches within the lung. And evolutionary biology predicts that, in order to adapt to that kind of environment, you have to be really good at mutating.

So the experimenters collected a whole bunch of P. aeruginosa samples from 30 CF patients, and a whole bunch of P. aeruginosa samples from 75 patients with acute infections, and compared the mutation frequencies of those isolates. Both the CF and non-CF patients had a whole bunch of P. aeruginosa isolates with low mutation frequencies. But in addition, the CF patients had a whole bunch of isolates with mutation frequencies 100 times as great! Genetic analysis of these mutator isolates over several years indicated that they were all different and persistent; these were bacteria that evolved into mutators within the host and stuck around, and not mutators transmitted between patients. Further investigation demonstrated that, for several of the mutator isolates, one or more error-avoidance genes were mutated or deleted altogether, explaining their high mutation rate.

This is the point in the presentation when a creationist might say, “Aha! Nothing new was created; mutation was only capable of breaking genes that were already there!” But this is only the first half of the story; as we’ll see, the mutator phenotype opens the doors to further beneficial mutations.

You see, cells normally keep those error-avoidance genes around for a reason. If the mutator phenotype is so prevalent in CF patients, it must be conferring some advantage in that environment. That is, given the conditions of the CF lung, it’s apparently more important to be able to get beneficial mutations than to prevent detrimental ones.

Patients with P. aeruginosa infections, especially those with CF, are subject to extensive treatment with a broad range of antibiotics. So the experimenters took a look at whether the mutator phenotype had any effect on the evolution of antibiotic resistance:

This is the key figure for our discussion. Black bars are mutator strains from CF patients, grey bars are non-mutator strains from CF patients, and white bars are strains from non-CF patients (all non-mutator). For a broad range of antibiotics, mutator strains showed a much higher frequency of antibiotic resistance compared to non-mutator strains.

The only way this makes sense is if antibiotic resistance is the result of naturally-selected random mutation. Mutator strains have higher mutation rates, and are therefore more likely to acquire the mutations necessary for resistance. The non-CF non-mutators serve as a control. The important comparison is between CF mutators and CF non-mutators, because they had everything in common except their mutation rate. They were derived from the same ancestral strains that first infected the patient. They were subject to the same antibiotic therapies. They grew in the same environment, shared space with the same other species of bacteria, and therefore had the same potential for lateral gene transfer. If resistance were the result of anything other than mutation, then we should see no statistical difference between the black and grey bars. But we do see a difference.

That’s evolution. The CF lung is a dynamic environment with different selective pressures than sites of other, acute infections. CF lungs favor selection of bacteria that can mutate rapidly. This increased rate of mutation results in other selectable beneficent mutations, such as resistance to antibiotics.

It’s important to note that Oliver and company weren’t trying to convince anyone that bacteria evolve; real scientists understood that already. They were trying to use that understanding to save people’s lives. Their insight into how a Pseudomonas infection behaves within the lung is the first step to fighting that infection. Armchair physicians who don’t understand antibiotics and deny the power of random mutation are of no help.

Now that we’ve addressed (at least in a small way) the origin of these resistance genes, we can take a look at their greater role in evolution and what random mutation can do to bacteria that are already resistant to antibiotics.

At the end of the day, evolution is about change, plain and simple. Creationists don’t seem to realize this, as evidenced by their second objection to resistance as evidence of evolution: “If resistance DOES result from random mutation, it doesn’t count as evolution, because there’s always a price to be paid for gaining resistance.”

This is the sort of approach taken by Michael Behe, who likens the development of resistance genes to “trench warfare” and genome degradation, as opposed to an “arms race” of increasing buildup. Like many things that Behe believes, this is baloney.

First of all, it misses the point of evolution, which (as I said before) is change. Whether or not these changes meet Behe’s mystical criteria for “increasing complexity” doesn’t matter. It’s still evolution.

But more importantly, it’s short-sighted. As we’ll see, evolution of resistance means more than just having a resistance gene.

One thing is true about the creationists’ claim: in the majority of cases, resistance comes with a cost. Antibiotics work by disrupting some normal process within the cell. Resistance genes can operate by two different mechanisms: they can either disrupt the normal cellular process so the antibiotic can’t target it anymore, or they can create new proteins that actively do something to inhibit the antibiotic (like export it or degrade it). The latter is typically a plasmid-bound resistance gene, the former more typical of chromosomal mutations. But in the absence of antibiotic, these resistance mechanisms tend to lead to decreased growth. Mutations that disrupt antibiotic activity also decrease the efficiency of the targeted cellular process; proteins synthesized from plasmid might have a side effect on normal cell function; even just copying an unused plasmid is a waste of energy. From a medical perspective, this suggests that when antibiotic resistance crops up, we can just take away the antibiotic for a little while and the antibiotic-sensitive bacteria will eventually outbreed the resistant bacteria, and we can start over.

Behe and other creationists quit there and call it a day. But the problem is that all these studies of the cost of resistance were performed in naïve bacteria. That is, one minute the bacteria didn’t have the resistance gene, the next minute they did, and we looked at the difference.

What would happen if we let the bacteria and their new resistance genes get accustomed to each other for a while? Evolution would predict that, in the absence of antibiotics, there would be pressure to ameliorate the cost of resistance through mutation. Either you get rid of the resistance gene causing the problem, or you keep the resistance gene but acquire new cost-compensatory mutations that reduce its side effects.

Several studies were performed to test that hypothesis. Richard Lenski published a great review article in 1998 covering several of them. I’ll do my best to summarize some of the major findings.

Cost-compensation of plasmid-bound resistance

A strain of E. coli was transformed with a plasmid carrying resistance to the antibiotics tetracycline and chloramphenicol. For this generation of bacteria, the cells with the plasmid were slightly less fit than those without (in the absence of antibiotics).

The researchers then grew the plasmid-carrying bacteria for 500 generations (75 days) in a culture containing chloramphenicol, to make sure the cells didn’t just ditch the plasmid. They then took those bacteria out of the chloramphenicol and isolated a colony of cells without the plasmid. For this generation of bacteria, the cells with the plasmid were slightly more fit than those without!

Further study showed that it was the bacterial chromosome that had changed, not the plasmid. Over just five hundred generations, enough cost-compensatory mutations had accumulated on the bacterial genome to make the resistance plasmid a boon rather than a bane, even in the absence of antibiotic.

Cost-compensation of chromosomal resistance mutations

Here, researchers started with mutations of rpsL, a gene that encodes part of the bacterial ribosome (a little blob that synthesizes protein), that result in streptomycin resistance in E. coli. Streptomycin is a type of antibiotic called an aminoglycoside; it binds to the ribosome, preventing protein synthesis and killing the cell. Certain rpsL mutations prevent streptomycin from binding to the ribosome, thus making the cell streptomycin-resistant. However, this change to the ribosome also slows the rate of peptide (protein) elongation.

The researchers grew streptomycin-resistant bacteria in the absence of streptomycin (since it’s on the chromosome, not a plasmid, they don’t have to worry about the gene just being lost), and after a mere 180 generations they found that the rate of peptide elongation was back up to what it had been in wild-type cells. What’s more, they found that the bacteria still had the mutation conferring streptomycin resistance. Rather than mutating back to wild-type, the cells had acquired cost-compensatory mutations elsewhere in the chromosome.

These two studies indicate that fighting antibiotic resistance would be a LOT harder than was previously thought. It isn’t as easy as just taking away the antibiotic and letting the resistant bacteria fade into obscurity. Rather than ditch their costly genes for resistance, the bacteria are evolving cost-compensatory mutations so they can have their cake and eat it, too.

Hm… multiple naturally-selected mutations leading to a benefit with little or no noticeable cost? Sounds like evolution to me.