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The present conflict over the moral status of the human embryo reflects deep differences in our basic convictions and is unlikely to be resolved through deliberation or debate. While there are currently no federally legislated constraints on the use of private funds for this research, there is a consensus opinion in the scientific community that without NIH support for newly created embryonic stem cell lines, progress in this important realm of research will be severely constrained. A May, 2005, report by the President's Council on Bioethics, “Alternative Sources of Pluripotent Stem Cells,” outlines several proposals for obtaining pluripotent stem cells without the destruction of human embryos. One of these methods, Altered Nuclear Transfer, proposes to use the technology of somatic cell nuclear transfer (SCNT), but with a preemptive genetic or epigenetic alteration that precludes the integrated and coordinated organization essential for natural embryogenesis. Drawing on insights from systems biology, the distinction between totipotency (capacity to form a whole organism) and pluripotency (capacity to form all the cell types) is explored. The implications of this distinction are used to discuss the moral arguments for the inviolability of nascent human life and the moral standing of entities with only partial and unorganized developmental potential. Away forward is proposed that may open positive avenues of advance in both stem cell research and a broader arena of research in developmental biology.