This is going to build a bit more on my previous post "Naturalism and Human Equality". Naturalism demands that all living entities be ascribed equal value.
This includes bugs and plants. Why should we ascribe greater value to humans? Why not whales, because of their size, or certain trees, because of their long life-spans? If evolution is to be used as a guide, then we must conclude that survivability is the ultimate ascription for value. We could look at survivability of an individual or of an entire species, and we still would not conclude that humans are on top, though.
It doesn't seem to me that this challenge is on the top of a naturalist's list of challenges to answer; not because they believe it to be a mischaracterization or strawman of their view, but because no other self-conscious species exists that they would have to answer to. I know that many naturalists are hoping with everything they have to find extra-terrestrial intelligence. If their hopes are realized, how will they justify their position to the aliens (assuming they still believe that humans hold superior value); how will they justify their position to their own species (assuming they believe the aliens hold superior value)?
Of course, the easiest way around this whole challenge is to deny that one holds ANY species to have higher value than another. But then we have to look at how they act to see if this is actually true. Do they eat meat? Do they eat plants? Are they fighting for equal legal rights for insects? How about plant-life? It seems that value is assigned completely by emotional attachment, in naturalism. Unfortunately, emotional attachment is subjective to the individual (relative to a culture if you can get everyone on the same emotional attachment). However, it will never reach a level of objectivity, so the value based on it will never be objective either.
Since value is not assigned based on any objective value in naturalism, it only allows for the assigning of value based on arbitrary traits, such as size, weight, age, skin (hair and eye) color, sex, place on the evolutionary tree, physical location,...I could keep going. Ultimately, naturalism allows for all the "isms" that we know are wrong (including sexism and racism). Granted, it doesn't say that they are right, but that's only because there is no way to objectively identify "right" and "wrong" in naturalism. Since neither can be objectively defined, neither objectively exist in relation to the other. What one person or culture says is "right", can be disputed on the same grounds by another person or culture.
Even though we know that racism and sexism is wrong, we must watch idle as other cultures murder people based on these things, because there is no definitive way to demonstrate that they are wrong, and we are right. This is the same even within a culture, on the individual level. One individual must watch idle as a neighbor beats his wife to a pulp, because there is no definitive way to demonstrate that he is right, while the "abusive" husband is wrong.
Other "isms" that culture has been dealing with or will deal with in the future are "specie-ism", "age-ism", and "health-ism". Due to need to survive, naturalism promotes all these cultural "isms". The only "ism" that naturalism discourages is sexism. But that only stands until reproduction has been completed, then sexism is just as encouraged as the other "isms".
With the lack of objective morality, there is no foundation to stand against the natural order that promotes cold, hard survival at any cost. If our culture allows naturalism to continue to pervade our worldview, we will accept that survival of our own genes is the ultimate purpose, and since morality is subjective, nothing stands in the way of single bloodline rising up and exterminating all "lesser" human beings.