The 111th Congress has a lot to do before it gives way to the 112th next year, but one thing it certainly should do is make clear where it stands on embryonic stem cell research.

Even though Congress has funded the research to the tune of $546 million over the past nine years, a federal judge has stopped it cold, throwing a promising field of medical science into chaos.

Federal Judge Royce C. Lamberth decreed last month, notwithstanding all those appropriations, that Congress was “unambiguous” when it passed legislation in 1996 banning “research in which human embryos are destroyed.”

Not only that, he imposed an immediate injunction on federally funded research and this week kept it in force despite pleas from researchers that his ruling would cause “tremendous, immediate, irreparable harm” to their work and to its “millions of potential beneficiaries.”

At the moment, stem cell scientists are in total confusion about what the state of their federal support is — and whether it will even continue.

That’s why Congress needs to act — and soon — to make clear that the so-called Dickey-Wicker amendment (passed in 1996 before stem cells were even isolated) does not apply to the research.

For years, Senate and House appropriations committee reports have declared — under Congresses and presidents of both parties — that Dickey-Wicker’s language “should not be construed to limit federal support” for human embryonic stem cell research carried out under presidential guidelines.

Under current guidelines, federally funded researchers cannot destroy embryos to obtain cell lines, but can acquire them from private entities that do.

Overwhelmingly, the days-old embryos are “left over,” frozen and destined for destruction at in-vitro fertilization clinics.

But Lamberth ruled that “the language of the statute reflects the unambiguous intent of Congress to enact a broad prohibition of funding research in which a human embryo is destroyed” and that current research “necessarily depends upon the destruction of a human embryo.”

So far, the judge has issued a formal ruling only to impose and sustain his injunction, but he has signaled strongly what his opinion is on the merits of the federal funding: it’s illegal.

When Lamberth rules, the Obama administration, university medical schools and scientific groups will appeal, but it may be months or years before the issue is finally resolved — unless Congress acts to clarify its intent.

Stem cells are the inner core of the embryo and are deemed “pluripotent,” meaning that they can be tweaked to become almost any kind of human cell — offering potential cures to a vast range of diseases.

As Francis Collins, director of the National Institutes of Health, wrote in a memorandum to the judge, “stem cell research holds great promise for the development of treatments for a wide range of serious and life-threatening diseases and conditions,” including cancer, diabetes, heart disease, spinal cord injuries and neurodegenerative diseases including Parkinson’s.

The Food and Drug Administration has approved a clinical trial using embryonic stem cells for spinal injuries, he noted.

Embryonic stem cell research has been fiercely opposed by right-to-life groups including the Roman Catholic Church and the Family Research Council, and presented a moral dilemma to former President George W. Bush.

He solved it by declaring that federal research could proceed on cell lines derived before August 2001, but not after. Congress voted to lift those limits, but Bush vetoed the bill.

President Barack Obama issued new guidelines and expanded the number of cell lines open to research. But it’s unclear whether Lamberth’s rulings will stop only Obama-approved research or Bush-approved research, too.

The injunction “will result in immeasurable loss of valuable and one-of-a-kind research resources,” Collins wrote in his memorandum.

“Experiments that may have been months or years in development will be halted prematurely … Investigators who have devoted their careers to this exciting research may have to close their laboratories or move to another country,” he added.

The plaintiffs in the case are two scientists doing research on so-called “adult” stem cells — usually, derived from skin or blood and caused to resemble “pluripotent” cells.

They argued that money spent on embryonic research would take funds from “adult” research, but Collins noted that NIH devotes nearly three times as much funding to nonembryonic research as to embryonic.

In his latest ruling, the judge implied that only new funding should be stopped and that scientists were overreacting to his injunction with a “parade of horribles.” But dozens of ongoing projects are due for re-funding at the end the fiscal year, Sept. 30.

So it’s up to Congress to straighten this out. Rep. Diana DeGette (D-Colo.) is drafting legislation to do so. But is it possible to get anything done when there’s controversy involved? Let’s hope so.