Why should I boil pretzels in baking soda water before baking?

The pretzel originates in Germany, where it is called Laugenbrezel. It was originally prepared in a alkali solution, which is where the "Laugen" part of the word comes from; typically, lye was used, but baking soda gets you most of the way there without a trip to the pharmacy (a Mexican or Asian market may do the trick if you want culinary lye).

The alkali solution is what causes the crust to brown so deeply, and it's most of the difference between a pretzel and a bagel. A bagel would typically be boiled in a malted sugar solution instead. The flavor is also affected, but I don't know how to describe the difference; there's a very pronounced aroma difference if you skip this step. To me, you end up with nothing more than a pretty breadstick unless the dough gets that alkali bath.

If you do use culinary lye, use gloves and don't rush anything. Traditional Laugen aren't boiled, so you just need a cool 3% lye solution; no boiling step.

In Germany, the pretzel shape isn't the only option for Laugen. Little rolls calls Laugenbrötchen and longer, roughly baguette-width sticks called Laugenstangen are also popular. On my most recent trip last year, the Laugenstangen were frequently sold in the form of sandwiches, though I don't remember seeing many of those when I was first living there in the mid-90s.

ETA: Having done this a few more times since originally posting, I'd also add that the utensils you use in lye-based pretzels need to be wood, glass or plastic. Eye protection is important too. Metal will likely corrode or oxidize when it contacts food put in contact with lye, even if it's after the wash. I'd recommend setting the washed pretzels on a wooden surface after dipping if you want to minimize damage/discoloration on your baking sheet.

It's there to increase the pH (make it more basic), which gelatinizes the crust. This in turn leads to a brown one, desirable in pretzels. If you hunt up the transcript for the episode ("Pretzel Logic", which can be found here: link, Scene 8) Alton goes into some detail about why this is, and why commercial makers get a browner crust than home bakers generally get. In short, they use more hazardous ingredients in the water.

when using baking soda for pretzel making it is optional to boil (hot method) the dough shortly in the solution or simply dip the dough in a non-boiling, warm (cold method) solution.

hot vs cold depends on the texture you want in the finished bread...

-HOT METHOD: when you boil the dough it creates/cooks a deeper outside layer w the solution which leads to a more dense and heavy "bagel like" consistency. it creates more chewiness throughout the bread.

COLD METHOD: when dipping cold the pretzel taste/effect is still achieved but leads to a lighter, less chewy, texture throughout the bread. the inside of the dough isn't penetrated as much and leads to a more "white bread like" consistency.

*****baking soda used for this is less reactive than using lye. lye creates a very chewy outside w a soft fluffy interior. the hot method creates a chewiness all through the bread. the cold method isn't as chewy but creates a more fluffy texture all through the bread.

In addition to the browning, there is a distinctive taste to pretzels that are treated in an alkaline solution prior to baking. If you can't get (or don't want to work with) food grade lye, there is another option. If you place baking soda in a low oven, you can convert sodium bicarbonate into sodium carbonate, thus increasing alkalinity. Then, use that baked, baking soda in place of regular baking soda or lye to achieve good results.