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There exists widespread controversy over stem cell research, especially human embryonic stem cell research. The bulk of debate has focused on issues that arise from the techniques used in the creation and usage of stem cells; the use of cloning techniques to derive stem cells is particularly controversial. Other concerns include balancing advocacy of the research against irresponsibly exaggerated predictions of cures, the affordability of any successfully developed treatments, the protection of research subjects (including women who may provide eggs for research), democratic governance of publicly funded research programs, and patenting and intellectual property rules.

The status of the human embryo and embryonic stem cells are sensitive topics. With the present state of technology, creating a human embryonic stem cell 'line' typically requires the destruction of a human embryo that was created but not used for fertility treatments. Other methods that are under investigation but have not yet proved successful are the removal of some embryonic cells from an existing embryo, and/or, more widely discussed, a technique variously known as research cloning, therapeutic cloning, or somatic cell nuclear transfer (SCNT). SCNT is particularly controversial, for reasons unrelated to differing beliefs about the status of the embryo.

The ensuing debate has prompted national and international authorities to seek suitable regulatory frameworks, and highlighted the fact that stem cell research raises a number of political, social and ethical dilemmas.