Instead, we got a fake dilemma based on pseudoscientific nonsense by writers that love to throw around the word "evolution" but don't have the science knowledge of a bright high school junior.
Actually the science presented in the episode is consistent with that shown in other episodes.
The episode The Chase put forward that much of the intelligent life in the galaxy was designed to occur. By a early species (sometimes) called the Progenitors.
Phlox might not have known the whole story, but he did seem to understand that intelligent life doesn't just happen (in the Star Trek universe) naturally, but is "preprogrammed' to be the result of the development of certain humanoid lifeforms.
Random selection plays no part.
Phlox's decisions are based upon his knowledge of how things are, observation of other species. Again, Phlox might not have all the pieces, but he does know that evolution of intelligence is something that is predetermined and built into a beings genetic structure. In his examination of the second species (I forget their name) Phlox might
have seen the genetic markers of a future highly intelligent species, more so than with the first species.
well, we don't get an indication that Phlox seems to think that there's an intelligence behind the genetic disease, just that it's "evolutionarily determined" or something. Again, I don't have a problem with Star Trek's pseudoscience in most cases, but I DO have a problem with it when it's getting uncomfortably close to the "biological racism/social darwinism" of the 19th century, and when it's being used to justify ethically monstrous decisions, like in "dear doctor." Further, Phlox' ideology is simply inconsistent with being a doctor. Why doesn't he just tell people who are near-sighted that "nature intends them to see poorly" rather than giving them eyeglasses or corrective surgery? Doctors "interfere" with the course of nature all the time, so his attitude is just ludicrous.