There's a reasonable argument that we're fairly clueless
    about how most natural systems actually work.

That's kind of my point. To a certain extent you are right that everybody, including scientists, are "clueless". BUT there's a huge difference in attitude between a scientist and Random Joe. That difference is politics. The scientist looks at the data, formulates hypotheses, asks tough questions, etc. Random Joe reads one article and his mind's made up.