Last month, three of the leading proponents of biomedical research in the US Congress levelled an unlikely charge at President Barack Obama's proposal to focus health research on cancer and autism: they said the plan amounted to the 'politicization' of science. The first response to such a claim might be to marvel that any member of Congress could even pretend to take umbrage that a politician was involved in allocating money to the National Institutes of Health (NIH). It's even more surprising that the critique should come from three leaders on congressional spending committees: Representative David Obey of Wisconsin and Senators Tom Harkin of Iowa and Arlen Specter of Pennsylvania, all Democrats although Specter was, until recently, a Republican. After all, every year, in the documents that accompany spending legislation, Congress directs the NIH to focus on specific diseases and even specific populations. If targeting spending on cancer is illegitimate politicization, then what would one call urging the NIH to "increase research that is focused on understanding heart disease and cerebrovascular disease among Native Hawaiians", as the Senate did, not atypically, in 2007?

But the fundamental problem with the politicization charge is not its disingenuousness or its lack of perspective. Rather the almost reflexive resort to that word is a sign that it has been drained of all genuine meaning, and that, in turn, reflects fundamental misunderstandings about how decisions concerning science have to get made.

Decisions about how to allocate taxpayer funds among scientific fields or diseases cannot be politicized because they are inherently political. Apportioning public monies is a matter of making policy choices, of applying values and setting priorities; it is not some cold, mathematical exercise to be solved for the 'right' answer. (There can turn out to be wrong answers, but only measured against whatever politically selected criteria were used to make the original allocation.)

Congress could decide to delegate the NIH budget decisions to NIH officials, or to a group of scientists or selected lay people, all of whom would certainly have their own politics. But the delegation itself would be a political choice about whose priorities and what kinds of politics should determine funding.

Alternatively, Congress could devise some methodology for choosing priorities, based on, say, the number of citizens suffering from a disease, its seriousness, the likelihood of finding a cure, the cost of treatment and even the fear the disease engendered. But just beginning to list such factors underscores the political nature of the decision. What factors should be included and how should they be weighed? Would diseases of the young or the old get higher priority? Research on men or women? What about illnesses that primarily affect just one ethnic group? Evaluating each factor would require judgment calls, and Congress would have to decide who would make those calls.

This is more than an academic point, and tossing around the word politicization is more than harmless sloganeering. The term is often used, consciously or not, as a way to obscure or shut down debate on issues that ought to engage the public and their representatives. Indeed, it's hard to know exactly why Obey, Harkin or Specter (who has very publicly battled his own cancer in recent years) object to the Obama plan because of the way they've framed the issue.

One possibility is that they're concerned that dollars that go to cancer and autism research will be unavailable to be spent on diseases that they see as equal or higher priorities. Or they may be worried that Obama will use his initiatives to parry their efforts to increase total NIH spending. Or they may fear that the proposal will unravel the unwritten pact that increases the budget of every NIH institute by about the same percentage, uniting NIH constituencies to fight for the agency's bottom line.

Those concerns are all worth discussing. The president's proposed budget for the fiscal year that begins on 1 October includes a 5% increase for cancer research and a 16% rise for autism, while proposing that overall NIH spending grow by only 1.4%, to about $31 billion.

But if congressional appropriators think the president has picked the wrong priorities or is stinting on overall research funding, then there ought to be a full debate about the proposals, their rationale and any alternatives. Crying "politicization" is a strategy for circumventing all that by making the proposals seem illegitimate and unworthy of discussion. That can distract attention long enough to smuggle one's own favoured approaches into legislation.

That is bad enough, but the profligate use of the word politicization has other detrimental consequences. There are times when the charge is warranted — when, for example, politicians try to manipulate a scientific conclusion — and the term will gradually lose its bite if it comes to mean nothing more than "you made a choice I don't like". Crying politicization should not become a case of crying wolf.

Perhaps worse still, constant talk of politicization can erode public faith in the political system and deepen the misconception that there is something automatically suspect about political decision-making, when it is ultimately the only tool a democracy has. One might think that politicians would be more worried than anybody about demonizing the process that is the very reason their jobs exist, but instead they try to gain favour by posing as being 'above' politics. This is an old strategy — politician has long been synonymous with rascal and worse in the American lexicon — but it can gradually delegitimize the entire system.

It's rare to have a direct debate on the role of politics in making decisions about science. Scientists and their patrons have long tried to perpetuate the myth that the allocation of science funds is somehow more pure (not just better done) than the mad scramble for funding in every other policy area. Perhaps the last time the issue was fully argued was when President Harry Truman vetoed an early version of the National Science Foundation in the late 1940s because a panel of scientists, rather than the president, was to select the agency's director. But the myth becomes pernicious when it enables politicians to try to shut down debate by playing on the sense that science spending decisions can or should be apolitical.

Obama's cancer and autism proposals may or may not be a good idea. But that's for politicians to decide; there is no higher authority.