Last Friday the Obama administration published its new guidelines for federal funding of embryonic stem-cell research, ending the Bush-era restrictions on that work.

Except they didn’t end all of the restrictions. The new rules do not allow for work on cells made via research cloning (somatic cell nuclear transfer), and they require an informed consent process that may exclude some cell lines already derived with different consent procedures. Advocates at both antipodes of the stem-cell debate found something to criticize in the Obama rules. Researcher Irv Weissman of Stanford said the rules maintain an “ideological barrier” that will hinder progress, while Douglas Johnson of the National Right to Life Committee said the guidelines herald “an incremental strategy to desensitize the public to the concept of killing human embryos for research purposes.”

For now Obama seems to have struck an ideological balance, and some conservatives are giving him credit for it. Yuval Levin, a former Bush bioethics adviser who recently appeared on this blog, wrote on Friday that the new guidelines “certainly could have been worse” from a conservative’s perspective.

At the same time, the new rules mean that federally funded research can move beyond 2001-era technology. Bush’s guidelines, which restricted funds to lines derived before August 2001, allowed researchers to work with just 21 cell lines. Obama’s rules open the door to hundreds of additional lines created since 2001, many of them with genetic defects that can help scientists understand how diseases develop.

In moral terms this may even be a clearer approach than Bush’s policy, which claimed to protect nascent life but did allow some funding of research that required the destruction of human embryos. Those rules allowed fewer stem-cell lines to qualify for funding, yet the restriction was based on an arbitrary cut-off date. Why was it moral to allow funding of research on stem cells taken before August 8, 2001, but beyond the pale to allow funds for cells taken after that date?

Levin, who also served as executive director of the President’s Council on Bioethics, wrote that by keeping some limits on stem-cell research funding, Obama’s NIH has conceded “that the destruction of embryos for research is not an innocent and unproblematic practice, but must be constrained for ethical reasons.” So far, so good. As the bioethicist Art Caplan once told me in an interview, “A human embryo may not be a legally protected person, but it’s also not just any old stuff.” Levin then goes further: “These rules raise the question of why limits are necessary, and any serious answer to that question would lead us to conclude that these rules are inadequate. ”

That’s not at all clear to me. Under Bush’s old rules, an embryo’s fate might depend solely on the date when it was created. Under Obama’s new rules, the embryo’s fate is governed by something far less arbitrary - the parents’ intentions, informed by all the options available to them. It seems reasonable to trust that whatever parents decide, they will see their embryos as something more than raw material.

[Note: This post originally contained a quotation from a private classroom setting, which has been removed at the speaker's request.]

This was a long but exhilarating day for Janet Rowley, who was at President Obama’s side as he signed the executive order creating a new stem-cell policy. I caught up with her by phone in D.C. this afternoon as she waited for her plane back to Chicago. Rowley said the day’s events made her think back to the first meeting of President Bush’s Council on Bioethics, where her views in favor of embryonic stem cell research put her at odds with the administration.

“To be there today at the White House and see this signing, for me it was like coming full circle,” Rowley said. “When you saw the enthusiasm of the scientists who were there, the people from Congress, the patient advocates who were so important in keeping this issue alive during the dark years, if you will. It was just an unbelievable experience.”

For Rowley and other researchers, one of the most welcome themes of the day was what Rowley called “the de-linking of science and politics.” In fact, despite the historic nature of the stem-cell policy change, the other document Obama signed may have more far-reaching effects - a presidential memorandum on scientific integrity. That directive calls for more transparency in science and technology issues before the government, without suppression of findings for political reasons.

Although the Bush administration is over, the Council on Bioethics is slated to last until at least November of this year, and Rowley continues to serve on it. She said she believes some of the group’s reports have made an impact, if only to reflect how divided the country was on many issues in bioethics. Such groups can continue to address legitimate moral concerns; as Rowley said, “It’s very important because scientists have to reassure the rest of the country that we’re not out to make a bunch of clones or zombies.”

Another note: Friday’s analysis of the next steps for the NIH is up at the Huffington Post’s Chicago site; you can see it here.

The Washington Post reported this afternoon that President Obama plans to lift the Bush-era restrictions on stem-cell research funding via executive order on Monday. Now comes the hard part - implementing a stem-cell policy that’s meaningful, has full ethical protections and unlocks the scientific talent that’s been held back the last eight years.

One insider point to watch on Monday is whether someone from the National Institutes of Health will help explain the new funding channels for this research. It’s a question of some urgency. Just this week, the NIH released a set of “challenge grant” topics that are eligible for a pool of $200 million as part of the new federal economic stimulus act. The NIH site describes the qualifying projects as those which “address specific scientific and health research challenges in biomedical and behavioral research that will benefit from significant 2-year jumpstart funds.” Embryonic stem-cell research would seem a natural fit - especially since the Bush administration held it back for years - but it’s not clear yet that Obama’s rule change has come in time for stem-cell grant seekers to get a share of the stimulus money. That’s one reason why Obama’s delay in announcing changes to the stem-cell policy was a bit puzzling. Many observers - including me - expected him to lift the restrictions his first week in office.

Around research centers like the University of Chicago, stem-cell scientists are poring over such details. I just spoke with John Cunningham, M.D., a specialist in pediatric stem-cell transplantation, who directed me to the brand-new NIH list of “Highest Priority Challenge Topics.” (You can see a more researcher-oriented application guide here.) Stem-cell research is on the list, but not specifically the embryonic stem-cell research that’s been subject to Bush’s limits. I count five topics that relate to iPS cells - short for induced pluripotent stem cells - which were discovered in 2007 and seem to have many of the properties of embryonic stem cells but are derived from adult cells. That’s fantastic because iPS cells deserve more study. But embryonic stem-cell research never appears by name, except to say that “iPS cells act like embryonic stem cells.”

This is an important point because as Cunningham said, “One of the things that lifting the current ban should allow us to do is really test whether iPS cells and embryonic stem cells have similar properties.” In theory the current challenge grant list could include work with embryonic stem cells, since some of the topics are broad enough to encompass work with several different cell types. For example, Topic 11, “Regenerative Medicine,” contains a broad opportunity to “Develop cell-based therapies for cardiovascular, lung, and blood diseases.” That could cover some work with embryonic stem cells, as could some of the items under the general category of stem cells.

But none of this is set in stone. What the president says on Monday may signal whether broader embryonic stem-cell funding will begin with the stimulus package, or whether scientists - and patients - will have to wait longer to start seeing more progress. Stay tuned.

UPDATE: Here’s a take on the news in an e-mail from embryonic stem-cell researcher and friend of the blog George Q. Daley, M.D., of the Harvard Stem Cell Institute and Children’s Hospital Boston: “I am brimful of hope and excitement about the announcement on Monday. I’ll be there, and I expect Obama to lift the restrictions and usher in a whole new era of scientific openness and opportunity for stem cell research. The future looks bright indeed for stem cell research.”

Suddenly George W. Bush is no longer the easiest target for anyone frustrated at the pace of scientific progress.

He started to occupy that position at 9 p.m. Eastern time on Aug. 9, 2001, when he went on national television to outline restrictions on federal funding for the new field of embryonic stem cell research. It seemed an arbitrary and even arrogant policy. No federal funds could be used for research on cell lines derived after the moment Bush began his speech - exactly 9:00:00 p.m. He portrayed the decision as a compromise - the original intention was to give no funds at all - but many researchers saw it as a fiat that would stifle a promising field and send a message that scientists served at the pleasure of the president. Science-related decisions in subsequent years tended to bear out that early impression.

Now there’s no obvious scapegoat for the obstacles facing researchers and patients eager for new treatments. President Obama has pledged to lift Bush’s restrictions on stem cell research, and to “put science back in its rightful place.” But we still don’t have a good sense of what that means.

This could be a rare opportunity to make a new strategy for American biomedical research. It would be a massive undertaking, centered on the sprawling National Institutes of Health, which currently lacks a permanent director. The $28 billion NIH budget supports 27 centers and institutes, and an army of researchers around the country.

A blog post last week by Stanford researcher Stephen Quake suggested that this is “the time to rethink the basic foundations of how science is funded.”  He proposed more long-term grants to scientists and better incentives to pursue creative projects. The current system has some incentives for researchers to follow the agencies’ institutional priorities, rather than give reign to their best ideas.

My op-ed last Monday in the Chicago Tribune suggested creating a new NIH institute devoted to stem cell research. Yet some of the response to that piece reflected a widespread wariness of doing anything to complicate the federal research bureaucracy. My e-mail friend Yuval Levin, a National Review writer who worked in Bush’s domestic policy office, said that if anything the NIH needs a simpler management structure, not more institutes. He echoed Quake’s point that the current system doesn’t do enough to support younger investigators or new ideas.

In the short run, how Obama handles the NIH may be a better test of his managerial success than the outcome of the stimulus plan. It’s one thing to sign a piece of paper and reverse Bush’s stem-cell policy; it would be a much greater feat to free the awesome creativity of America’s scientists.