I hate to wade into Intelligent Design but I'm feeling grumpy tonight so what the hell.
First, I do not believe in some mythical deity who created the world 7 thousand years ago. Or even last week. I'm agnostic. Those things I do not know about, I do not know about. It is not logical to waste energy either believing or disbelieving in them.
Having said that, we had a great piece on HN a year or two ago from a mathematician showing that we are most likely living in a simulated universe. I don't have the academic chops to comment on it, but I know that it's entirely possible that all of our sensory inputs are being manipulated in ways that mimic the universe we think we live in. When you think of billions of years of intelligence evolving all over the place, we're fairly simple creatures. Just like we could fool an ant into thinking his queen lives somewhere else, I don't think it'd be very difficult at all for some external entity to control us. Maybe as a game. Who knows.
The point is: the idea that our sensory perceptions are fabricated and false in some way is a perfectly self-consistent and logical thing to believe in. Of course, it's a really stupid thing to believe in if you're a scientist, because if you can't trust empirical evidence, science kind of goes out the window. So yes, scientists can't believe that and have any kind of career at all, but there's nothing wrong with Joe SixPack believing it.
I bring that up because of something good the author mentions: This means that science education is not simply a matter of learning new theories. Rather, it also requires that students unlearn their instincts
This is true. Much like pilots have to learn not to trust their inner ear when flying, students of science have to unlearn many things they may consider "common sense".
But you end up coming full circle. Even accepting science as the only light mankind has in the darkness, eventually you end back up wondering if the models we have are not just more fancy versions of the Ptolemy's Celestial Spheres[1]. You can take models that don't fit and do all sorts of magic with them to make them work. For a long time.
I am concerned that we are "diagnosing" people as somehow in need of re-education, medication, or intervention simply because they think in a different manner from the rest of us. If my neighbor wants to believe he's living in a Matrix, more power to him. He's not going to be a rocket scientist any time soon. And even if he is, plenty of people manage to have deeply trans-rational beliefs about the way things work and they function just fine in the world in all sorts of intricate, complicated scientific endeavors. We are drawing distinctions where none may be needed.
Science is provisional. In my opinion we should always approach it with humility. What I am seeing more and more is people who somehow feel elevated by science to be better than their peers. That's pretty cool when you're 20 and figure out how awesome it is that calculus and physics go together, but it's a really screwed up way to live your life or influence public policy.