Marshi

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I just read up on the technique of decoction mash, and I am a little confused: as part of decoction mash you have to boil part of your mash, but when you boil your mash, aren't you activating certain enzymes that create nasty flavors?

I'm not really interested in doing it at home, but I'm curious how some breweries (i.e. Sam Adams) does it and why it works.

Yooper

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Tannin extraction would probably be what you're thinking of (not certain enzymes) that can happen with grains are boiled. The thing is, tannin extraction is also a function of pH. In a decoction, you pull a very thick decoction, mostly grain and little liquid, so that the pH is low and that takes away the risk of tannin extraction.

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BrewerinBR

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+1 to what Yooper says ...
Further decoction mashing, like step mashing, you raise the temperature of the mash through a series of steps and rests at different temperatures. Unlike step mashing instead of adding boiling water, a small amount of thick mash is extracted and heated to a boil then returned to the mash (the amount is based on your grain bill, grain/water ratio and the temperature increase). Different rests at different temperatures produce different results. For example an IPA may be started at 122F for a protein rest for 30 minutes, then a decoction is used to bring the mash to 140F for 40 minutes and then another decoction used to go to 156F for 20 minutes. This will produce a dryer beer with a higher alcohol. Where as a Stout would be mashed starting at 122F for 30 minutes and decoction to 140F for 20 minutes and then decoction to 156 for 40F, which will produce a maltier lower alcohol beer.

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TyTanium

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...and by pulling a thick mash, you leave plenty of enzymes behind in the liquid to fully convert your starches.