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Stem cell research at MIT and throughout the country seems sure to be strongly impacted by a federal court ruling Monday prohibiting the use of federal funds to support human embryonic stem cell research.

While the precise meaning of Monday’s preliminary injunction is not fully clear, it appears to prohibit not only the research permitted under the Obama administration, but also the limited stem cell lines available under President George W. Bush’s policies that took effect on August 9, 2001.

National Institutes of Health Director Francis S. Collins said on Tuesday that the NIH believes “grantees that already have awards from NIH are permitted to continue their research, and need not stop in place.” Grant renewals and grants currently in the pipeline will be suspended, however, Collins said.

Institute Professor Robert S. Langer ScD ’74 said “I think its disappointing — it sets progress back.” Langer works with human embryonic stem cells approved under the Bush administration.

Biology professor Richard A. Young said “there is a huge cost today to being in an environment where we’re deciding to shut down experiments. These experiments are involved in understanding the fundamentals in human genome control.”

At MIT, affected scientists include Langer and Young, as well as professors Rudolph Jaenisch and Daniel G. Anderson, all of whom have NIH funding for stem cell work. While their current work may proceed, they operate under multi-year grants that are subject to yearly renewals, and those renewals cannot happen while the injunction remains in force.

“The whole thing is really unfortunate,” Anderson said. “There are so many important problems in the world, why would you spend your time trying to stop research that’s trying to help people? I understand there are religious motivations … I think if people really understood what these cells were — it’s not like any embryos are going to be destroyed on an ongoing basis.” Anderson noted that human embryos are destroyed on a regular basis as part of in vitro fertilization.

“Is their mission to stop people from doing important research?” Anderson asked.

Monday’s injunction was issued by Chief Judge Royce C. Lamberth of United States District Court for the District of Columbia, in James Sherley, et al, v. Kathleen Sebelius, et al.

James L. Sherley, a former MIT professor, and Theresa Deisher, as well as several non-scientist plaintiffs sued the NIH and the Department of Health and Human Services in August 2009, alleging that the use of federal funds to support research where embryos are destroyed was illegal.

The suit was originally dismissed by the judge in October, when he ruled that the plaintiffs lacked standing to sue, because they were not injured by the NIH policy.

Sherley and the other plaintiffs appealed and in June, the appeals court ruled that Sherley and Deisher did have standing to sue (though the other plaintiffs did not), and remanded the case back to the district court for further proceedings.

Sherley and his counsel did not respond to calls for comment. According to court documents, Sherley argues that he is harmed by being forced to compete with other scientists for limited federal funding dollars.

“The funding should go to the best research,” Anderson said. “Those decisions are hard. They ought to be made through peer review.”

Sherley was an associate professor at MIT until he was denied tenure in spring 2007. He alleged that racism was a factor, and staged a hunger strike in protest. Sherley is now a senior scientist at the Boston Biomedical Research Institute.

At MIT, while individual researchers working with stem cells uniformly condemned the situation, there was been no similar response from MIT’s senior administration.

Claude R. Canizares, vice president for research and associate provost, was travelling, but said in an e-mail this morning that MIT was waiting for details and would review them.

MIT’s immediate response appears to be coordinated by the MIT Washington DC office, which did not respond to a message left Wednesday afternoon. The Washington office e-mailed a group of NIH researchers on Tuesday, summarizing Monday’s ruling and indicating they were waiting to hear from the NIH as well as the Association of American Universities. Another e-mail was sent out after NIH Director Collins spoke to reporters, indicating existing grants could continue their research.

Scientists are still waiting to hear from the NIH. Collins indicated Tuesday that direction would be issued in the NIH Guide, probably late Tuesday, but as of Wednesday night, that has not yet happened.

On Tuesday, White House Deputy Press Secretary Bill Burton said “from what we can tell, this would also stop the research that President Bush had allowed to go forward early in his presidency. So we’re exploring all possible avenues to make sure that we can continue to do this critical lifesaving research.” Both legislative and judicial remedies appear to be on the table.

The Department of Justice plans to appeal the preliminary injunction and to move for a stay, and that will likely be filed this week, according to DOJ spokeswoman Tracy Schmaler.

Lamberth could rule on a motion for a stay as early as hours or days after its filing, said Court spokeswoman Jenna Gatski.