Need help with anti-vaccine woo's

[FSBlueApocalypse]

Ok, so a friend of mine sent this as a "Peer reviewed" paper on vaccines. Yeah, I know. Either way, some help with their claims, and background on the papers they site would be helpful.

http://www.vaccines.net/autoimmu.htm

[MrBogosity]

Here's what happens:

When you get ANY infection, ANYTHING that your immune system has to learn to fight, there's a small albeit real chance that your immune system will get confused. As it learns which proteins are proteins from the virus or bacteria it needs to fight, if those proteins are similar to nerve proteins your immune system might get confused and start attacking them, too.

The thing is, when they make vaccines, they're careful to exclude any proteins that have a real chance of confusing your immune system. So with any given vaccine, you have a FAR greater chance of getting the disease and THEN getting an autoimmune disorder from that, than you are getting the autoimmune disorder from the vaccine itself.

[IceSage]

I can't believe we're in the days of which the vaccines that have prevented me from getting age-old illnesses... are now being argued against.

Our society is going crazy.

[MrBogosity]

I think we should find some big plot of unused land somewhere and declare it "vaccine free living." Let all the anti-vaxxers move out there and live without any schools or whatever requiring vaccinations.

Then they'll all die of easily-preventable diseases and the human gene pool will be greatly improved.