Dear Atheist,

[DrKvothe]

Additionally, we've identified the molecular solutions that microorganisms have developed to protect themselves against antibiotics. In some cases, general xenobiotic enzymes are mutated to accept these new molecules as substrates, allowing them to catalyze chemical reactions which inactivate the antibiotics by changing their molecular structures and interrupting their function as potent protein inhibitors. In other cases general efflux pumpes are mutated to remove the antibiotic from the cell, keeping it below the working concentration. In other cases, the protein targets of the antibiotics have mutated, and the antibiotic no longer properly inhibits them. In other cases, horizontal gene transfer appears to be the culprit. The vast majority of antibiotics are natural compounds or semi synthetic derivatives of natural compounds. The biosynthetic machinery of these compounds evolved as weapons factories in a molecular arms race between microbes competing for nutrients. The microbial host that produces the antibiotic has to have its own resistance mechanism, and the theft of the genetic code for this resistance (horizontal gene transfer) allows a previously susceptible organism to gain resistance.

All of these mechanisms are genetically encoded, and their appearance represents a chance in the genetic code which is subsequently heritable. That's fucking evolution.