In this episode, the Enterprise NX-01 encounters a planet inhabited by two distinct humanoid species, one more cognitively and technologically advanced than the other (the suggestion is that the distinction is analogous to Homo sapiens and Homo neanderthalensis). In this case, the more advanced of the two species is suffering from a pandemic genetic disease that will eventually wipe them out, while the more primitive of the two is completely unaffected.
Eventually a cure is found. Dr. Phlox administers it to the populace, and saves billions of lives. The end.
Oh, wait: that's not quite what happened. To quote the episode recap from TV.com:
Phlox meets with Archer and says that he doesn't think that it would be ethical to give the Valakians a cure because it would interfere with an evolutionary process that has been going on for thousands of years. Based on his genome studies, Phlox sees increasing skills and intelligence in the Menk that quite possibly would leave them the dominant species -- provided the Valakians died off. He suggests that Archer simply let nature take its course.
So rather than save billions of lives, the doctor (yes, we're talking about a real medical doctor, here; not some quack homeopath or nutritionist) suggests that they allow the total extinction of an entire sentient species on the grounds that it might clear the way for some other species to take over. The best part is, Captain Archer is persuaded by this argument. He even goes so far as to suggest that to provide the cure would be playing God.
As an interested layperson, I have a bone or two to pick with this.
First of all, let's face it: if you have a cure for a disease that you could dispense at effectively no expense, and you fail to do so, you are responsible for any deaths that result. We can quibble about whether situations might arise where this would be the more ethical thing to do, but if you you push the fat guy in front of the bus to prevent it from running over a kindergarten class, you're still responsible for the fat guy's death.
Secondly, we have a glaring logical fallacy: we ought to let nature take its course. This is the naturalistic fallacy (in most cases a subset of Hume's is-ought problem), which conflates "natural" with "good" (modern examples include statements such as: "Vegetarianism is wrong because humans evolved to be omnivorous" and "Organic food is better for you because it's all natural"). The fact that noninterference would lead to the extinction of a sentient species take a backseat to the idea that "nature has a plan".
Speaking of nature's plan, the writer of this episode (and therefore his mouthpiece, the doctor) seems to be terribly misinformed about how evolution works. He's not alone, of course. I'm no evolutionary biologist (if you want one of those, look here), but even I understand that there is no "natural plan". We're not evolving toward anything (intelligence, for example), nor are we higher on some form of scala natura (which seems to be the implication in this episode): we are adapting to our environment (although this may be a thing of the past, as we have long since been adapting our environment—and, more recently, ourselves—to our every whim). If intelligence is advantageous for procreation, then that will be the general trend. If sharp eyes or sharper talons were advantageous, then the organism in question would be steered in that direction, instead. For Dr. Phlox to suggest that he could predict the evolution of this species, especially given the complete environmental upheaval that would result from the death of the dominant species on the planet, is nothing short of ludicrous.
And where does "playing God" come from? Is this simply a statement of scale? Archer presumably has no problem with the good doctor curing one patient, or two... But an entire species? That, apparently, is beyond the pale! I've had problems with the Prime Directive before (and I'm not alone: defying the Prime Directive has been a pastime of starship captains since the beginning), but to apply it so poorly before it's even invented? That's simply insane.
I know that there is much more to this issue than what I've discussed here, but I'm tired, so I'll end with this. As Perry DeAngelis might have said: "He's a dick."