The judge ruled that the Obama administration’s policy was illegal because the administration’s distinction between work that leads to the destruction of embryos — which cannot be financed by the federal government under the current policy — and the financing of work using stem cells created through embryonic destruction was meaningless. In his ruling, he referred to embryonic stem cell research as E.S.C.“If one step or ‘piece of research’ of an E.S.C. research project results in the destruction of an embryo, the entire project is precluded from receiving federal funding,” wrote Judge Lamberth, who was appointed to the federal bench in 1987 by President Ronald Reagan.
I have to say, the reasoning there seems pretty solid to me. If Congressional intent was to prevent the funding the destruction of embryos, then making a distinction between "paying to destroy embryos" and "paying for processes that involve destroying embryos" is a pretty stupid one.
For scientists, the problem with the judge’s reasoning is that it may render all scientific work regarding embryonic stem cells illegal — including work allowed under the more restrictive policy adopted by President George W. Bush in 2001.
If it's the case that all embryonic stem cell research involves the destruction of embryos, than clearly the Judiciary is right that both executive orders are over-reaches.
Bottom line: The real culprits here are Congress. Blame Bart Stupak and the pro-life Democrats.