Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology
The evolution of antibiotic resistance is typically the result of small changes allowing for survival in a microbe or other organism under special circumstances where the organism faces extremely strong selection pressure due to the presence of some antibiotic drug. In other cases, it is the result of the transfer of pre-existing antibiotic resistance genes from one microbe to another, and the selection of such microbes in an environment containing antibiotics. Even in the first example, evolution does not produce a truly new function. In fact the change produced often makes the microbe less fit when the antibiotic is removed--it reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution.
Fitness costs are real, and biological realities like fitness cost and other limits to evolution play a vital role in shaping strategies used to combat antibiotic resistance, antiviral resistance, and pesticide resistance. In fact, were it not for the existence of fitness cost, in many cases antibiotic resistant bacteria would proliferate and resistant strains would soon replace non-resistant strains. Because of fitness costs, resistant strains are outcompeted by non-resistant bacteria once selection pressure is relaxed, allowing doctors to combat antibiotic resistance through various drug usage strategies.
Yet under the approach adopted by the National Center for Science Education (NCSE) in its critique of Explore Evolution (EE), organisms are treated as if they are nearly infinitely-plastic; evolution is viewed as if it can do anything. If the NCSE were right--which thankfully it isn't--then medical researchers would have little hope in the fight against antibiotic resistant microbes.
Not only is the NCSE's mindset challenged by the evidence , but if it were true, the implications for medicine would be drastic: If biological realities like fitness cost and other limits to evolution did not exist, it would be pointless for medical doctors to try to combat antibiotic resistance or antiviral drug resistance, because evolution could always produce an adaptation such that bacteria would become resistant without incurring a fitness cost. Thankfully, Explore Evolution informs students about the realities of limits to bacterial evolution that give doctors and scientists empirically-based hope in the fight against antibiotic resistance.
The NCSE wrongly implies that fitness costs are a minor issue for those trying to fight antibiotic resistance and other forms of resistance, stating, "Mutations do not necessarily impair a protein's normal functioning nor impose a fitness cost." After complaining that "Explore Evolution ... says mutations do confer resistance but with a 'fitness cost,'" the NCSE then claims that "Explore Evolution significantly misrepresents how antibiotic resistance arises in this description." Unfortunately, it appears that the NCSE misunderstands both EE and the importance of fitness costs to evolutionary biologists.
Many scientific papers discuss the stark reality of fitness costs, supporting the emphasis that EE places on this topic. In fact, one paper cited by the NCSE acknowledges that the reality of fitness costs is vital to help scientists predict whether resistance will spread: "biological cost of resistance might be a more relevant predictor of the risk for resistance development."  Another paper published in Environmental Toxicology and Chemistry found that "[t]he topic of fitness costs is a central theme in evolutionary biology" because "fitness costs constrain the evolution of resistance to environmental stress."  Yet another paper observed that "[i]t is generally established that drug resistance mutations reduce viral fitness."  Regarding the specific case of antibiotic resistance, one study in the Journal of Antimicrobial Chemotherapy observed that "[t]he biological fitness cost of antibiotic resistance is a key parameter in determining the rate of appearance and spread of antibiotic-resistant bacteria."  Indeed, science journals are replete with documented examples of fitness costs, as the following selections amply demonstrate:
An article published in the journal Genetics in 2007 by Marciano et al. titled "A Fitness Cost Associated With the Antibiotic Resistance Enzyme SME-1 β -Lactamase" found that blaSME-1 β-lactamase gene, which confers antibiotic resistance to the use of carbapenems, has a fitness cost associated with mutations in its signal sequence. Only by artificially swapping the gene's signal sequence with the signal sequence from a different gene could this fitness cost be alleviated; there was no natural evolutionary elimination of this fitness cost. The article found that identifying this fitness cost barrier to evolution helped them prevent the spread of antibiotic resistant bacteria: "The identification of a SME-1-mediated fitness cost allows the direct application of genetic techniques that have been utilized to understand structural features of β-lactamase function and evolution." See David C. Marciano, Omid Y. Karkouti and Timothy Palzkill, "A Fitness Cost Associated With the Antibiotic Resistance Enzyme SME-1 β-Lactamase," Genetics, Vol. 176: 2381--2392 (August, 2007). A paper in BiomedCentral's journal Evolutionary Biology titled "Acetylcholinesterase alterations reveal the fitness cost of mutations conferring insecticide resistance" found that some insects exposed to insecticides which target acetylcholinesterase, an important enzyme involved in the nervous system of insects, evolve resistance that comes only at a fitness cost. According to the article, "Our findings suggest that the alteration of activity and stability of acetylcholinesterase are at the origin of the fitness cost associated with mutations providing resistance." As the paper put it, "higher the number of [resistance-conferring] mutations, the lower the stability of the mutant" enzyme. When seeking mutations that compensated for loss of stability in the mutant enzymes, the study found that "no mutation increased the stability of the enzyme, all combinations resulted in proteins still less stable." In other words, there was a clear fitness cost faced by insecticide-resistant mutant insects. See David C. Marciano, Omid Y. Karkouti and Timothy Palzkill, "A Fitness Cost Associated With the Antibiotic Resistance Enzyme SME-1 β-Lactamase," Genetics, Vol. 176: 2381--2392 (August, 2007). A paper in the Journal of Antimicrobial Chemotherapy, titled "Nitrofurantoin resistance mechanism and fitness cost in Escherichia coli," observes the reality of fitness cost, stating: "The biological fitness cost of antibiotic resistance is a key parameter in determining the rate of appearance and spread of antibiotic-resistant bacteria." The paper found that because of the fitness cost associated with E. coli that are resistant to Nitrofurantoin, "even though resistant mutants will appear in the bacterial population in the bladder, they will be unable to become enriched and establish an infection because of their impaired growth at these therapeutic antibiotic concentrations." The article further observes, "Resistance to antibiotics is most often accompanied by a biological cost, observed as a decrease in fitness, i.e. a reduced growth rate or virulence." Ironically, the paper cited by this study to bolster this claim--a claim that corroborates EE's statements about fitness cost--is Andersson (2006) [see below], the same paper that the NCSE cites to back its claim that "not all mutations produce fitness costs!" It seems that research scientists have interpreted Andersson (2006) differently than the NCSE. See Linus Sandegren, Anton Lindqvist, Gunnar Kahlmeter, and Dan I. Andersson, "Nitrofurantoin resistance mechanism and fitness cost in Escherichia coli," Journal of Antimicrobial Chemotherapy, Vol. 62, 495--503 (2008). Andersson (2006) explicitly observes that fitness cost is important to understanding whether resistant populations will persist after selection is relaxed:A key parameter influencing the rate and trajectory of the evolution of antibiotic resistance is the fitness cost of resistance. Recent studies have demonstrated that antibiotic resistance, whether caused by target alteration or by other mechanisms, generally confers a reduction in fitness expressed as reduced growth, virulence or transmission. These findings imply that resistance might be reversible, provided antibiotic use is reduced. However, several processes act to stabilize resistance, including compensatory evolution where the fitness cost is ameliorated by additional mutation without loss of resistance, the rare occurrence of cost-free resistance mechanisms and genetic linkage or co-selection between the resistance markers and other selected markers. Conceivably we can use this knowledge to rationally choose and design targets and drugs where the costs of resistance are the highest, and where the likelihood of compensation is the lowest.
Thus, Andersson (2006) observes that "cost-free resistance mechanisms" are "rare" and that fitness cost is a very common phenomenon, stating that antibiotic resistance "generally confers a reduction in fitness." EE thus properly discusses this common phenomenon, and Andersson (2006) actually bolsters the points of EE. We find it unfortunate that the NCSE has misused this paper in its attempt to downplay the importance and reality of fitness costs. Additionally, Andersson (2006) states, "A rational antibiotic design strategy is therefore to identify targets for which the resistance mechanism has the most negative effect on fitness." This is a good strategy, but it would be pointless if bacteria didn't face evolutionary limits and could essentially always evolve to avoid fitness costs, as the NCSE implies. Again, we see that fitness cost is a real phenomenon and is vitally important to understand as microbiologists seek to slow the spread of antibiotic resistant bacteria. EE is justified in discussing it. See Dan I Andersson, "The biological cost of mutational antibiotic resistance: any practical conclusions?," Current Opinion in Microbiology, Vol. 9:461--465 (2006).
Many similar examples could be cited. Given the scientific literature, how can the NCSE seriously maintain that fitness cost is not an important issue in microbiology or that EE is mistaken by highlighting its importance to evolutionary processes? The NCSE asserts that EE "significantly misrepresents how antibiotic resistance arises" when EE states that "[e]xperiments show that once antibiotics are removed from the environment, the original (non-resistant) strain 'out-competes' the resistant strain, which dies off within a few generations." But studies like those discussed here directly corroborate this claim of EE. And the existence of fitness costs are vital to helping biologists to fight antibiotic resistance, antiviral resistance, and pesticide resistance. For the sake of medical progress, thank goodness the NCSE is wrong.
[Note: This post was adapted from Antibiotic Resistance Revisited, a response to the NCSE, which was originally co-authored with Explore Evolution co-author Ralph Seelke, Professor of Biology at University of Wisconsin-Superior.]
 National Center for Science Education. 2008. Section on "Bacteria" in the NCSE critique of Explore Evolution. Available at http://ncseweb.org/creationism/analysis/bacteria as of January 16, 2009.
 See R. Seelke and S. Ebnet. "An unexpectedly low evolutionary potential for a trpA 49V,D60N double mutant In Escherichia coli.," Presented at the 107th Annual Meeting, Abstract R-055, American Society for Microbiology, Toronto, Canada, May 21-25, 2007; R. P. Mortlock (ed.), Microorganisms as Model Systems for Studying Evolution (Plenum Press, New York, 1984). Note: This book contains seven examples of situations in which evolution fails to produce a new function.
 Dan I Andersson, "The biological cost of mutational antibiotic resistance: any practical conclusions?," Current Opinion in Microbiology, Vol. 9:461--465 (2006).
 Lingtian Xie and Paul L. Klerks, "Fitness costs constrain the evolution of resistance to environmental stress in populations," Environmental Toxicology and Chemistry, Vol. 23(6):1499--1503 (2004).
 M. Cong, D.E. Bennett, W, Heneine and J.G. García-Lerma, "Fitness Cost of Drug Resistance Mutations is Relative and is Modulated by Other Resistance Mutations: Implications for Persistance of Transmitted Resistance," Antiviral Therapy, Vol. 10, Suppl 1:S169 (June 7-11, 2005).
 Linus Sandegren, Anton Lindqvist, Gunnar Kahlmeter, and Dan I. Andersson, "Nitrofurantoin resistance mechanism and fitness cost in Escherichia coli," Journal of Antimicrobial Chemotherapy, Vol. 62, 495--503 (2008).