Any theory can undergo healthy skepticism, and it should. However when the public at large receives conflicting information, it is very hard for them to distinguish what they know and what they believe. Thus, most people resort to what they believe, or what they feel is right without delving into deeper research and actually finding out things for themselves, or at least forming opinions for themselves. They mindlessly copy of off their sources, creating a polarization on some of these controversial topics - topics that need to be discussed and that few are willing to discuss.

Actually, they tend to revert to the side of the story that was told to them by the most (a) handsome, (b) charismatic, or © popular source

Agreed. That was my "not able to think for themselves" spew.

I don't often come across any truly skeptical arguments against scientific hypotheses and theories that are not at least somehow related to Religion and/or Politics. It's usually those two "camps" of thinking that are used as grounds for disproving anything, regardless of how rationally or logically sound it may or may not be.

I admit to not being very scientifically literate (yet), but I love trying to understand how and why other people have the viewpoints and opinions that they do, even if I don't agree with them.

I've seen some abnormally strong scepticism on the part of laymen towards the HIV-AIDS link, the efficacy of vaccination, and the notion of abiogenesis. At the same time, I also see assumptions on the part of laymen that science has already fully solved the hard problem of consciousness, and that science has completely figured out genetic contributions towards cognitive processes and personality development, and the question of psychometric measures of "intelligence" and personality.

I think a lot of the skepticism is simply due to people tend not to believe what they don't understand. Gravity and evolution are both theories, but an apple falling from a tree is infinitely easier to comprehend than a monkey seemingly magically transforming into a human over thousands of years. People feel compelled to argue against what scientists have established to be nearly facts simply because they can and because the number of people who understand science is far fewer than the number who understand it, so the ignorant voice is a loud and powerful one.

"What about some theories that the scientific community considers naive, but the public seems to believe that scientists have already resolved the problem? An example I can think of is probably our poor understanding of 'dark matter'."

An example in the field I specialise in would be bee decline, colony collapse disorder, etc.

The public seems to be convinced already that pesticides are the sole or primary driver of problems like the general decline of bees, and more specifically, Colony Collapse Disorder. The media and public also seem to conflate CCD with bee decline generally. While CCD is a component of bee decline, it's more or less confined to North America, and the jury is currently out as to whether it's caused by pesticides or something else.

While the media harps on about CCD, even in countries like the UK where we have no CCD (Greenpeace are particularly bad at this), they completely ignore other known problems driving bee decline like parasites and disease, which we do have a good understanding of, but need more research on to develop better ways to prevent and mitigate.

Pesticides almost certainly do play a role, but scientists and beekeepers (many of whom are essentially trained to be bee biology scientists (mellitologists) in their own right) have been warning since at least the late 80s/early 90s that a major crisis was ahead because of a particular parasite, varroa destructor, which spreads disease, in particular. The crisis we're seeing now is merely exacerbated by pesticides, but the media still harp on about them as though they're the only problem.

I saw that one the discovery channel, lots of biologists are suspecting a bee pandemic, I don't know enough to go into more insight, but it seems more likely than that of isolated colony destructions.

I think a lot of skepticism should be applied to many of the fields theoretical physics, especially ones that try to interpret quantum mechanics. While many of the theories about it have mathematical backing, the problem is, is that it's very hard to actually test the conclusions in the reality that these equations allude to. An example of skepticism towards the interpretations is the well known Schrodinger's cat, which criticizes the Copenhagen interpretation. A couple theories that are shady to me is the holographic principle and string theory. The former is that there's no way as of now to formally test it, and the latter due to inconclusiveness, but interesting nonetheless.

However, quantum mechanics is still incredibly exciting as it is aggravating, the fact that the events during radioactive decay and hawking radiation occur without any cause at all is confusing but exhilarating, it shows we have much to learn. And hopefully the large hadron collider can provide more insight to the nature of particles and contribute to the quantum world. Like I said, certain parts of physics are really hard to test, but it can be done. As with the discovery of the Higgs boson. Gotta love science.

Like LibertyRedFox said, healthy skepticism is a very good thing, but I do understand that what we're talking about is general public ignorance. I have found evolution and gravity to be the big ones, of course, and you've already said those. And, like chubby9302 said, theoretical and particle physics seem to get a fairly bad wrap from the public eye. I'd think this would be mostly due to a lack of understanding, as the subjects are quite difficult to comprehend, as I have personally found, but that is no excuse to blatantly deny those theories. Jonouchi also has a very good point, as to most of the skepticism is in relation to religion and politics. I don't think mine quite fits as a ... theory, but I've seen disbelief and ignorance over animal behaviour, and how animals behave. People seem to believe that all predators are blood thirsty killers, and that they have nothing ... no other brain function other than that, which is quite sad. This is, obviously, just a lack of understanding and a lack of wanting to understand.

There's a whole essay to be written about, say, the different ways that The Public and Science evaluate evidence (The Public respond best to emotional stories told 'from the heart' regardless of factual content, and prefer anecdotes to evidence; Science, of course, simply pursues the statistical and mechanical links to ensure unbiased accuracy). Those are points well worth making, even in brief, because startlingly few career scientists whom I know, seem to be aware of how this works. Many, faced with a topic about which they know a good deal but which is publicly controversial, simply keep repeating old facts and finding new ones, even though this usually comes across as arrogance to an emotionally-motivated skeptic.

But that said, I'll gloss over it a little to point out an elephant in the room... okay, maybe a poor phrase to use on a furry site, but you know what I mean!

When I see popular controversy over scientific topics, I invariably see that it's not a debate about the science - it's a debate about something bigger, for which the science has become a proxy, a socially acceptable way of talking about topics that would otherwise seem to be fringe issues.

Evolution wasn't challenged because it was wrong; it was challenged because it contradicted deeply held minority beliefs about a literal divine creation. Fighting evolution became a tale of fighting atheist scientists who'd been seduced by Satan (why else would they refuse to accept God's testament, etc etc?)

Climate change isn't controversial because the evidence is uncertain or fabricated; it's controversial because most of the obvious ways to stop it involve government intervention, which is politically convenient to left-wing politicians and politically anathaema to right-wing politicians. The former used it to justify increasingly outlandish political proposals; the latter wrote the whole theory off as a political exaggeration at best, an outright fabrication by would-be communist dictators at worst. Fighting climate change became about standing up for freedom and liberty in the face of dark plotters who wanted to destroy all those nice things; obviously or why else would they lie about it?

Likewise, most of these popularly controversial topics have an underlying political or ideological battle underpinning them, so the facts are little more than a convenient cover. Witness how the loudest anti-GM arguments are actually about rolling back industrial agriculture and returning to a more 'traditional' and 'wholesome' lifestyle; witness how the loudest anti-nuclear voices are about governments wanting weapons or big scary evil corporations wanting money, and both presumably willing to kill you to get it; witness how pro-homeopathy and pro-herbalism positions are usually about bashing an ivory-tower elite of medical doctors who hate everything that's not modern and new, even if it cheats their patients out of cures.

Popular skepticism arises because there are two powerful competing narratives; one is factual and logical, but the other is loud and motivated by a thrilling sense that being skeptical is somehow 'standing up to Them', although the Them varies widely - but They are always shady, powerful, unaccountable, wicked, and generally want to hurt you and your kids for their own benefit, and you're a Hero for not believing Their lies! If enough people say that, it stops sounding crazy, and starts sounding pretty persuasive; and maybe those other guys who sounded really logical and knowledgeable really are a mixture of charlatans and gullible fools...

In such situations, accepting 'the facts' isn't 'becoming more informed', it's capitulation; it means accepting the truth of a whole host of unrelated quasi-factoids that are simply unthinkable to the loudest skeptics (e.g. accepting evolution, to a creationist, means denying God - so no amount of facts will shake their belief that there 'must' be something wrong with evolution, it simply can't be true - in turn, other people see how certain the diehard skeptics are, and assume they've done their research). Conspiracy theories are at the heart of a distressing number of popular science 'debates'.

It's at this point I'd love to include a simple solution; but sadly, I don't have one. Better education helps; but with any highly specialised but controversial topic, eventually it will always come down to a choice of either dedicating one's self to a LOT of extra learning and verification of facts, or simply asking, "Whose version of the Truth do I believe more?"