President Obama’s decision to allow federally funded scientists to work with hundreds of new embryonic stem cell lines continued to fuel media debate this week about the proper relationship between science and politics.

As U.S. News & World Report pointed out the day after last Monday’s announcement, the change in policy has received mostly “glowing” coverage. At least half a dozen editorials, from San Francisco to St. Louis to New York, praised Obama’s order, as well as a memo he signed to “guarantee scientific integrity” and protect researchers from political coercion. Hard news articles characterized both measures as a boon for science and a rebuke of the Bush administration, which had limited federally funded scientists to twenty-one stem cell lines created before mid-2001 and tampered with climate change research on multiple occasions.

For all their support, however, many outlets have suggested that Obama is going too far with his rhetoric about making decisions based on science, not political ideology. Indeed, the best pieces have acknowledged that science offers options rather than answers and that decisions about stem cell research necessarily involve ethical considerations. That is important because Obama left “the thorniest question in the debate” wide open: federally funded scientists are now free to work with many more existing stem cell lines, but will Congress rescind its ban on them destroying embryos to create new ones?

Wondering just that, The Washington Post and The New York Times, published their second editorials about the new stem cell policy on Sunday and Monday, respectively. Both papers argued that scientists have a strong case for the need to create new stem cells lines themselves, but the Times basically left it at that, concluding that the “main criterion [for such decisions] should be whether a proposal has high scientific merit.” The Post, on other hand, took its argument a step farther:

Mr. Obama is right to turn to scientists for advice on the matter, but he should not hide behind them in making the ultimate decision … [I]t’s not the job of the scientist to decide whether those reasons outweigh concerns about such a practice. That’s the president’s job. He should listen to the scientists’ arguments, make his decision and — as Mr. Bush did in 2001 — explain it to the American people.

That is a much more complete and appropriate assessment of the proper relationship between politics and science. On Sunday, Boston Globe columnist Jeff Jacoby put it another way:

[S]cience is not an unqualified good … Like most Americans, I don’t believe that microscopic human embryos deserve all the legal protections of personhood. But whether it is right to destroy such embryos for the sake of medical research is not just a question about science; it is also a question of moral and political judgment.

To be fair, Obama is clearly not going to let scientists make his decisions for him. Last week, in the immediate wake of his announcement, The New York Times published an excellent analysis by Sheryl Gay Stolberg that attempted to make clear that Obama’s policy changes, “will not divorce science from politics, or strip ideology from presidential decisions.” Harold Varmus, president of the Memorial Sloan-Kettering Cancer Center and one of Obama’s science advisors, told Stolberg that “Scientists should have no illusions about whether they make policy — they don’t.”

Yet Obama’s opacity on that point has led to overreaction in other parts of the press. Last week, for example, The Washington Post published an op-ed by Yuval Levin, a fellow at the Ethics and Public Policy Center and executive director of the President’s Council on Bioethics from 2003 to 2005. In it Levin argued that, “The executive order Obama signed omits any mention of ethical debate.” That is not true, however, and it obscures a key point about how Obama’s take on science differs from the Bush administration.

That difference has to do with what American University professor Matthew Nisbet calls the “first and second premises” of science. The first premise is essentially the options that science lays out for politicians, and the second is the decision that a politician makes based on that evidence, plus his or her own ideological values. Obama clearly stated that his “faith” endows him a feeling of responsibility to pursue an area of research that could, one day, lead to treatments or cures for a number of debilitating diseases. For him, that sense of responsibility outweighs other ethical concerns about embryos and sanctity of life. According to Nisbet, “In stating the moral and religious reasoning behind his decision, Obama is no different than Bush, who was equally open about his normative framework; it’s just that Bush’s framework led to a very different policy outcome.”

Where the Bush administration found trouble, on the other hand, was in tampering with the first premise (i.e. the primary research) in areas such as climate change. Obama’s memorandum was designed to preclude such interference, but has, obviously, been taken to bear on the way his administration will deal with the second premise (i.e. decision-making).

It’s a critical that journalists sort out and explain such nuances. Doing so will lead to a better public understanding of where Obama is succeeding and failing with regard to science. The Christian Science Monitor and The Swamp, for instance, both pointed out that Obama has bucked scientists’ advice about acting more quickly on global warming and returning the western gray wolf to the endangered species list. And, as many outlets have already pointed out, there are still controversial decisions to be made about stem cells.

All said, it seems clear that Obama is trying to right by science in a way that his predecessor did not. But it is even clearer that, to succeed, the media must keep pressing him for more clarity about how science and values – combined – influence his decisions.

Curtis Brainard is the editor of The Observatory, CJR's online critique of science and environment reporting. Follow him on Twitter @cbrainard.