Let’s reverse the quest what is the moral status of an anencephalic human (i.e. a human with underdeveloped cortex)?
You have to realize that your problem only arises because you have tied soul to species membership. But if you think of a soul as product of a sufficiently advanced brain (or, more generally, sufficiently advanced cognitive functions), then your problem disappears.
And tying soul to specied membership is a very dumb thing to do. Consider the following thought experiment: you are evil overlord and you want to do some evil thing (obviously).
You know that humans are ensouled, but chimps are not. Genetic difference between a human and a chimp is 30 million DNA base pairs. So you make 30 million hybrids like that:
- hybrid #0 – (reference) chimp
- hybrid #1 – chimp + 1 base pair modifed in human direction
- hybrid #2 – chimp + 2 base pairs modifed in human direction
…
- hybrid #29’999’998 – human -2 base pairs
- hybrid #29’999’999 – human -1 base pairs
- hybrid #30’000’000 – (reference) human
The concept that soul is tied to species membership dicates that at some point, hybrid #N is already ensouled, by hybrid #N-1 is not. Let’s say that you have a “soul test” which allows you to find what N is.
But! We know what base pair was changed between hybrids #N and #N+1. So we know that changing this specific base pair, call it base pair #P, triggers ensoulment. So we now make two more hybrids:
- hybrid A: human, base pair #P from chimp. Result: human, unensouled.
- hybrid B: human, base pair #P from humen. Result: chimp, ensouled.
You run your “soul test” to validate the above.
And! You now have a genetic test to see if humans are ensouled. So, you now take DNA swabs of all your subjects and identify those who have the base pair #P flipped.
And you declare that they are, both legally and morally, animals.
Then, you get a better idea. You genetically engineer a virus which flips base pair #P. So the person infected loses his/her soul and becomes an animal.