"Stem Cell Research is morally equivalent to Abortion." Discuss

This came up in a recent forum thread* I was involved with; a young college kid is a biology major and is having his world turned upside-down, finding out  - apparently for the first time (which is concerning, but I digress) - that Natural Selection is not random that there are transitional fossils and so on.

And so he is making the steady but gradual shift from Southern Baptist to Atheist by being exposed to rational science.

Now in the course of that discussion - I briefly alluded to the ban of stem cell research -and following this a theist interjected the following:

I don't mind stem cell research, however, I do have a problem with using a partial birth abortion to harvest the stem cells.  It may just be me, but the idea of intentionally delivering a viable baby breach so that you can leave the head in the mother long enough to kill it and suck out its brain should be wrong absent an absolute moral code instituted by a god.  They have to be very careful, if the head accidentally pops out the baby gets to live

I identified all the falsehoods regarding stem cells, but then the college kid replied with this - and making quiet plain that he no longer accepts this and want to learn more about embryo development so he can have an informed opinion, said:

I know.  stem cell research is not the same as abortion, yet there are people who say the two are the exact same thing, morally.

I'm satisfied I did a good job correcting the theist about harvesting stem cells from aborted babies, but I wanted to put some feelers out for addressing the case of moral equivalency in case that rears up again.

Thanks.

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If anyone's been following my discussion "Help my friend: America is a Christian Nation"  - same thread but different person: Pete is an ex-pentecostal who joined in with questions about America's founding, Cam is the biology major who started the thread asking for book recommendations on evolution and atheism.