A friend asked me recently, how can someone be sceptical about GM and yet also believe in climate change? This post is an attempt to answer her.

If you scream "I totally heart science, the Royal Society has teh awesomist mindz ev-er, you cannot dispute their pure and good genius" in one breath before voicing suspicion at these strange, corrupt and elitist would-be-wizards in pay of big pharma/ag/oil/ [insert your own bogey-man] in another, then yes, you are being a bit silly. But such silliness is pretty rare.

Moreover, I'm not sure we should expect a homogeneous response to something as diverse as science. When people use the term "anti-science", I want to know what definition of science they've based their concept of anti on. Who'd be simplistic enough to be "pro" the whole of science? What sort of shallow, shampoo advert "science bit" approach to the complexities of modernity are they living by?

This crude term "anti-science" is not only facile, it is all too often applied to close down debate. To steal a great line from Jack Stilgoe, it's "a privatisation of the idea of progress".

It's terribly convenient, for example, for UK environment secretary Owen Paterson to use the anti-GM stance of many greens as a sign the movement is somehow largely wrong-headed on the whole of science, because it weakens their arguments with him over climate and energy issues, when really they are quite different issues.

It's also a lot easier for the GM lobby to play a game of "you are wrong on science" rather than acknowledging that the bulk of the critique against them is economic and political. Similar points could be made for nuclear power, and even climate change, where sceptics are easily laughed off as not getting the science when all the time they are shouting economics. Fracking is a good example, as dissenters are dismissed as wrong about geological risks, somehow brushing questions of climate change and the energy market under the carpet in the process (eg last year's Royal Society report).

Green campaigners sometimes play into this. The idea that they are simply about the science can be an attractive allusion. As Mike Hulme argued in 2009, for all the Climate Campers claimed to be "armed only with peer-reviewed science", they were armed with a much larger vision of the future which connected science to a range of ethical, economic and political points. Why hide that?

I've seen people utilise "it's the economy stupid" to avoid discussing particular dimensions of environmental policy, too, though. Science isn't the only rhetorical trump card in the deck.

At this point, it might be tempting to rally against any attempts to close down debate; to celebrate the importance of constant scepticism, doubt and open debate as the lifeblood of science. Except doubt has a politics to it too, and attempts to keep debate open can be as disingenuously applied as the idea of "anti-science".

As Naomi Oreskes and Eric Conway argue in their seminal 2010 book Merchants of Doubt (if you haven't read it, do) a small number of scientists found ways to manipulate the uncertainty inherent in any scientific question as a way to disrupt or simply delay a range of health and environmental policy decisions which they (or their funders) found politically and economically uncomfortable. Doubt can be dangerous.

In his review of Merchants of Doubt (Nature paywall), Brian Wynne argues Oreskes and Conway's thesis is incomplete. They fail to examine those areas of politically sensitive science and technology where doubt is routinely downplayed, rather than amplified. I have some sympathy with this analysis, but I don't think a "complete" book on the ways science is used in society is possible. It's just too variable.

There are very different social and scientific contexts at work in GM and in climate change. Just as we shouldn't let the way certainty was overstated in BSE frame MMR, we'd do well to appreciate that the complex philosophies, communities and politics of scepticism work differently in different debates. Doubt's just different in different areas of science, for different reasons, interacting with different political, ethical and economic networks.

None of this is to deny that many people – green, red, blue or other – are regularly wrong about some area of science or another. Neither is it to ignore large social and cultural gaps between science and political activists which can lead to systemic and repeated problems. If you see a problem, call it. But call the specific problem, not some loose idea of "science".

If you want to be clever about science, ask for evidence about particular claims and be prepared to change your mind when the evidence changes. Ask questions about this evidence too, including what's missing, what the doubts are, and whom all of this serves. And question yourself, your own lack of knowledge and own motivations, including judging when scepticism is the most appropriate use of your energies.

This post is part of a series on science and the green moment.

Alice Bell is a research fellow at the Science Policy Research Unit, University of Sussex. She quite likes science, and even the odd green; at least most of the time.