I’ve always been fascinated that, the more you delve into science, the more it appears to rely on faith. You know, when they start to speak about the universe they say, well, actually, most of the universe is antimatter. Oh, really, where’s that? Well, you can’t see it. [Robinson: "Yes, exactly."] Well, where is it? It’s there. Can you measure it? We’re working on it. And it’s a very similar argument to someone who would say God created everything. Well where is he? He’s there. And I’m always struck by the similarity of the arguments at their core.Carroll takes Stewart to have meant "dark matter," not antimatter, and he's upset that Jon doesn't appreciate the great deal of evidence that supports the existence of dark matter, which makes it a direct contrast to a hypothesis like Deism, for example. And indeed the evidence for dark matter is pretty good. There are gravitational fields in the Bullet Cluster, for example, where regular baryonic matter used to reside until it was pushed away by a collision with another cluster. Dark matter, being non-interactive with normal matter, would not be pushed away by the collision, which would explain the gravitational fields in the cluster's old location. Not a slam dunk, but compelling evidence all the same.
But what if Stewart wasn't referring to dark matter--what if he meant dark energy instead? The names are similar, and both dark matter and dark energy have an influence on cosmic gravitation, so it's easy for a layperson to confuse them. Almost 3/4 of the universe is postulated to be "made of" dark energy, and we don't know anything about it, except that it "must" be there, to explain the expansion rate of the universe. We don't even know what properties dark energy might have. It might be something called "quintessence," about which all we can say is that it acts as a kind of anti-gravity, pushing the universe away from itself.
If we take Jon Stewart's comparison at its most basic, replacing "God" with some kind of generic First Cause, it's not really so far fetched. The first cause is a logical construct that would explain the existence of the universe (though it does raise new logical problems, like what caused the first cause). And at present dark energy is not much more than a logical construct, either, the explanandum in this case being the slightly less sexy expansion, rather than creation, of the universe. Unlike someone like Bill O'Reilly, who ignorantly claimed that science can't explain the tides, or magnets, Stewart is essentially correct here. We don't know why the universe is speeding up, and the words "dark energy" comprise the name we give that ignorance.
Faith is often taken to mean something like "dogmatism." In this sense it has not much value for either science or religion, but is present in each. Even in the best science, humans being what they are, it is never possible to apply the null hypothesis to all our tacit assumptions and motivations. We don't dwell on these excesses, but historically they are many. Behaviorism, for one, which promoted a near-complete lack of affection in child-rearing. The prevalence of pre-frontal lobotomies, for another, in the mid-20th century.
A common response to this line is that what is incidental to science is essential to religion, which is centered upon acts of faith. This is where I think we need to introduce complementary meanings of the word, connoting something more like dedication in the face of the unknown. Anyone who has read Marilynne Robinson knows she was not on the Daily Show to encourage religious dogmatism.
This kind of faith is essential to science. (It is also not unrelated to curiosity and play, though the stakes can be much higher in scientific contexts.) This is the kind of faith a scientist might have in thinking she might redeem the work of prior scientists, or in believing there is a rational explanation for an unexpected observation. These proceed without any certainty regarding the results whatsoever. The greatest discoveries must have required immense faith (in this second sense), so upsetting were they to our common understanding of things. Galileo's discovery of moons around Jupiter, Darwin's discovery of common descent. These required an incredible commitment and dedication to see their work through, and both suffered terribly for it.
It is attractive to believe, perhaps, that religion has room only for the first, dogmatic type of faith, and I cannot and will not argue with the menacing prevalence of it. But to pretend that all of religion is just unreasoned adherences and appeals to authority, while all of science is merely evidentiary, betrays no understanding of how much we know about the sociology of science, and the varieties of religious experience. The "conflict thesis" was once compelling, but given all the data we've been able to accumulate over the 150 years since White and Draper, there's no reason for any educated person to believe it.