HERE’S A PARADOX: Science is our best way of deciphering the complexities of the natural world. It is useful, consistent and, despite the claims of fundamentalists — religious or postmodern — true. Yet the insights of science are often counterintuitive, frequently lacking what Stephen Colbert called “truthiness.”

When Colbert coined that term, during the inaugural episode of his satirical show, “The Colbert Report,” he applied it to things that people in general (and George W. Bush in particular) know to be true “from the gut,” as opposed to from the head. Truthiness trumps dry logic, dull evidence and mere facts. It disdains or simply bypasses laborious intellectual examination in favor of what feels right. The word has taken on a life of its own, and Colbert stuck it scathingly to Bush’s political decisions, including the rationale for invading Iraq and his claim to have looked into Vladimir Putin’s eyes and seen “his soul.”

But such gut thinking poses another set of dangers to science. All too often, it bumps into scientific truth, and when it does, it tends to win — at least in the short term. Ironically, much of the time, scientific findings don’t seem immediately logical; if they were, we probably wouldn’t need its laborious “method” of theory building and empirical hypothesis testing for confirmation. We’d simply know.

After all, the sun moves through our sky, but it is the Earth that is going around the sun. Our planet is round, even though it sure feels flat under our feet as we walk. The microbial theory of disease only prevailed because Louis Pasteur, Robert Koch and other scientists finally marshaled enough irrefutable evidence to overwhelm the alternative perspective: that things too small to be seen with the naked eye couldn’t possibly exist or have any effect on us.

This conflict was foreshadowed by Francis Bacon in his 1620 treatise, “Novum Organum,” the founding document of the scientific method. Bacon warned: “The human understanding resembles not a dry light, but admits a tincture of the will and passions, which generate their own system accordingly: for man always believes more readily that which he prefers . In short, his feelings imbue and corrupt his understanding in innumerable and sometimes imperceptible ways.”

Nor is the battle over. Indeed, there is a constant tension between science and its truthy alternatives, from “quantum weirdness” to the irrefutable (but readily resisted) reality that a brick wall consists of far more empty space than solid matter. Evolution by natural selection, for example, is as close to truth as biological science is likely to get, and yet (even notwithstanding its conflict with biblical literalists) the notion that lineages change very slowly over vast amounts of time is less common-sensical than the observation that living things remain pretty much the same from one generation to the next.

Similarly, each of us is so small and the world so big that it simply isn’t truthy that we are literally using up certain resources, driving species extinct, polluting even the seemingly infinite oceans and modifying the climate.

The good news is that over time, actual truth wins out. Only scientifically illiterate troglodytes deny the microbial theory of disease, or the reality of atoms, or of evolution. Still, scientists face a constant struggle, a kind of Red Queen dilemma. Recall the scene in Lewis Carroll’s “Through the Looking Glass,” in which Alice and the Queen run vigorously but get nowhere. The Queen explains, “Here, you see, it takes all the running you can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that.”

Science, bless its innovative soul, constantly reveals new realities. Many of them — global warming, nuclear weapons, overpopulation, threats to biodiversity — are pregnant with immense risk. Others, like genomics or stem cell research, offer great opportunity. But nearly all are freighted with a lack of truthiness.

And so our intellectual race with the Red Queen continues. Evolution did not equip Homo sapiens with ready access to insights that transcend our personal experience. But somehow, we’d better get over our stubborn bias toward “thinking” with our gut, which is to say, not thinking at all. And that’s the truth.