The cabinet of Japan's prime minister, Junichiro Koizumi, is “burying its head in its hands” in frustration, in the words of one popular Japanese weekly, over a news article that appeared in Nature last month.

At issue is whether Megumi Yokota, a Japanese woman kidnapped by North Korea in 1977 at the age of 13, is still alive. In 2002, North Korea admitted to abducting 13 Japanese nationals, several of them taken from beaches while on dates. Since then, North Korea's half-hearted efforts to account for the victims have caused turmoil in the relationship between the two countries (see Nature 433, 445; 2005).

Claims that most of the victims, including Yokota, have died are unconvincing. North Korea says the remains that it passed to Japan last year are hers. But Japan's tests show that the DNA is someone else's — raising the spectre that the North Korean military is still using her to train spies.

Japan is right to doubt North Korea's every statement. But its interpretation of the DNA tests has crossed the boundary of science's freedom from political interference. Nature's interview with the scientist who carried out the tests raised the possibility that the remains were merely contaminated, making the DNA tests inconclusive. This suggestion is uncomfortable for a Japanese government that wants to have North Korea seen as unambiguously fraudulent.

The government has responded sharply to the article. At a press conference, Japan's chief cabinet secretary, Hiroyuki Hosoda, reportedly alleged that Nature's article contained “inadequate expressions” and that it misrepresented the scientist's statements. The opinions expressed in the article were “general knowledge” but were not meant to apply to the case at hand, Hosoda said, adding that his statements were checked with the scientist. The scientist himself, meanwhile, is apparently no longer available for interviews.

The inescapable fact is that the bones may have been contaminated. Who knows what they have been through during this hellish episode? According to North Korea, the body was buried for two years before being dug up and cremated at 1,200 °C, and then kept at the woman's husband's home, before a small sample was passed to Japan. It is also entirely possible that North Korea is lying. But the DNA tests that Japan is counting on won't resolve the issue.

The problem is not in the science but in the fact that the government is meddling in scientific matters at all. Science runs on the premise that experiments, and all the uncertainty involved in them, should be open for scrutiny. Arguments made by other Japanese scientists that the tests should have been carried out by a larger team are convincing. Why did Japan entrust them to one scientist working alone — one who no longer seems to be free to talk about them?

Japan's policy seems a desperate effort to make up for what has been a diplomatic failure — or more precisely, a failure of the security alliance between Japan and the United States. The alliance gives the United States rights to place unpopular bases in Japan in exchange for its role in contributing “to the security of Japan and the maintenance of international peace and security in the Far East”.

Could Japan, with US backing, have pulled other levers with North Korea? The answer is not clear, but the question can be put another way. If a totalitarian country had abducted US citizens from a beach and carried them back to teach language to potential spies for 25 years, would George Bush or any other US president be standing there with a bag of ashes haggling over DNA test results?

Part of the burden for Japan's political and diplomatic failure is being shifted to a scientist for doing his job — deriving conclusions from experiments and presenting reasonable doubts about them. But the friction between North Korea and Japan will not be decided by a DNA test. Likewise, the interpretation of DNA test results cannot be decided by the government of either country. Dealing with North Korea is no fun, but it doesn't justify breaking the rules of separation between science and politics.