The best response to the New York Times' article about the autism-inflammation theory comes from Emily Willingham. She writes,

What we have here is an argument that relies on shaky and shifting hypotheses of autism and autoimmune epidemics and hygiene, built using sparse data and scientific hints, a poor understanding of basic evolution and ecology, and a paradox of calling for a return to a more infectious past to “cure” autism while blaming immune-dysregulated, occasionally infected mothers of the present for …  autism. In his closing, Velasquez-Manoff argues that evolution provided us with a roadmap of the original microbial and parasitic ecosystems we once were, one that, presumably, if we follow it, will guide us out of the “insanity” and “affliction” that is autism. If it’s possible, that’s where he’s most wrong. Evolution isn’t something that happens with a plan. To describe it in those terms is to have a profound failure of understanding of what evolution is. Where we’re going, evolutionarily speaking, there are no roads.  And it would be better for most of us if there weren’t any parasitic worms, either.