Stem cells are very controversial for several reasons. Mainly, because stem cells need to be harvested from Embryos, which raises a huge ethical debate as to weather the (scientifically speaking, alive) embryo harvesting is not cruel and twisted, as these are human beings that are being used. Another ethical issue is that it is related to human cloning, and often times stem cells are mislabeled. Not to mention that there is an argument for the idea of cloning humans to be used for limb replacement, throwing everybody in a tizzy. Overall, one of the greatest medical acheivements of recent years has lots of issues that haunt it.
