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James L. Sherley has filed the first brief of his formal appeal in his battle to stop government funding of human embryonic stem cell research.

Sherley is the adult stem cell researcher who left MIT under a cloud in 2006. He was denied tenure in the Department of Biological Engineering in 2004, and then alleged the denial was racially motivated. After repeated appeals of his tenure decision, he staged a hunger strike in the spring term of 2006 and subsequently left the Institute. He is now a researcher at the Boston Biomedical Research Institute in Watertown, Mass.

Sherley has been battling the National Institutes of Health in federal courts in Washington D.C. over the legality of their funding since August 2009.

The core issue is that federal law prohibits government funding of “research in which a human embryo or embryos are destroyed,” which is known as the Dickey-Wicker amendment. Does use of existing human embryonic stem cell (hESC) lines constitute research where embryos are destroyed, or is the prior destruction of embryos separate research?

Sherley and his co-plaintiff, Theresa A. Deisher, argue that it is the same research, and thus barred by Dickey-Wicker. The NIH, of course, disagrees. The court briefs have spent many pages debating the definition of the word “research” with countless citations to dictionary definitions and the like.

Sherley’s 96-page brief renews much of the same arguments as before: first, that present-day research is the same research that destroyed embryos; and second, that the NIH promulgated its guidelines for hESC research in violation of the Administrative Procedure Act.

Sherley’s first case, in 2009, was before the D.C. district court. The court dismissed the case, saying that Sherley and Deisher lacked standing to sue, because they were not actually harmed by the NIH’s policy. Sherley appealed that decision to the D.C. Court of Appeals, which supported him, saying that his potential loss of grant funding was sufficient to merit the suit, and sent the case back to the District Court. This was in June 2010.

The district court then issued a preliminary injunction in favor of Sherley, momentarily causing researchers, at MIT and elsewhere, to wonder whether they could continue to do their work. The injunction also disrupted the NIH grant process, preventing the NIH from making funding decisions on upcoming hESC research proposals.

The NIH appealed the preliminary injunction to the same appeals court, but to a different randomly-assigned three-judge panel. That panel ruled in favor of the NIH, by a two-to-one vote, vacating the preliminary injunction and once again sending the case back to the district court.

Finally, in September of 2011, the district court ruled against Sherley and in favor of the NIH.

What’s different this time?

Sherley’s appeal before the appeals court will be heard by yet another randomly-selected three-judge panel, the third to hear the case. This panel includes Karen L. Henderson, who was the dissenting vote in favor of Sherley when the injunction was vacated, and Janice R. Brown, who was on the first panel that unanimously concluded that Sherley had standing.

The district court’s decision in favor of the NIH gave strong deference to the appeals court’s decision vacating the earlier injunction. In that decision, the appeal’s court concluded that the word “research” in Dickey-Wicker was sufficiently flexible as to permit the NIH’s judgement. Sherley will be arguing against that prior decision by the appeals court.

Administrative Procedures Act

The second prong of Sherley’s argument is that the NIH violated the Administrative Procedures Act when it distributed guidelines on the funding of hESC research. The NIH, Sherley said, “was required to consider and respond to relevant comments, including 30,000 comments addressing whether human embryonic stem-cell research meets the criteria for federal funding.”

At the district court phase, the NIH argued that they were not required to consider comments about whether to fund hESC research, merely comments about how to fund it. The court agreed.

Remaining schedule

The NIH will file its brief on Feb. 27, Sherley may file a reply brief by March 12, and the case will be argued on March 23. The court is likely to decide the case this calendar year.