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Mixing and Kneading
In a large bowl, combine bread flour and salt (and whole-wheat flour, if using), and make a well in the center. Pour in yeast mixture and the remaining 1¾ cups/420 milliliters lukewarm water, and mix, using the flexible spatula or wooden spoon, until the dough is shaggy.
Knead the mixture in the bowl several times, continuously folding it over and onto itself and pressing down firmly to bring it together in a solid mass, then turn it out onto a clean work surface. Continue kneading until there are no dry spots, then, adding more flour only if needed to prevent stubborn sticking, until you have a stiff but very smooth dough that is still slightly tacky, 15 to 20 minutes. Tip: This amount of kneading, necessary to develop the gluten for a chewy bagel, is best done by hand, since the motor of the average stand mixer would strain against the very stiff dough.
Gather the dough into a ball, dust it lightly with flour, and place it in a large, clean bowl, seam-side down. Cover with a damp towel and let the dough rise at room temperature until it has doubled in size, 1½ to 2 hours.
Preshaping
Before you form the bagels, preshape the pieces into tight balls. Working one ball at a time, gather all the irregular edges and pinch them together firmly to make a teardrop shape (above). Place the dough seam-side down on the surface and cup your hand down and over top of the dough in a loose grip (like a claw, or like you’re playing the piano).
Move your hand in a rapid circular motion, dragging the dough across the surface until it has a high, tight dome. Repeat with all the pieces, then cover them with the damp towel and let rest for 5 minutes.
Shaping & Proofing
Roll the dough under your hand back and forth several times to seal together the ends, then slip the ring of dough off your hand and stretch it to even out the thickness all the way around until you have a ring that measures about 4 inches across (above). As you form each ring, place it on a parchment-lined sheet, arranging six to a sheet and spacing evenly. Tip: You can also poke a thumb through the ball of dough to make the hole and then widen and stretch with your hands into a ring, but the wrapping and rolling method tends to give more of a classic bagel look.
When you’ve formed all the bagels, cover each baking sheet with a piece of plastic, followed by a damp towel to create a sealed, moist environment for the bagels to proof slowly. Transfer the baking sheets to the refrigerator and chill at least 4 hours and up to 24.
Boiling
Remove one baking sheet from the refrigerator. Fill a small bowl with room temperature water, then carefully peel one ring of dough off the parchment paper and transfer it to the bowl. It should float, indicating that the bagels are ready to boil and bake. Remove the ring from the water, pat it dry on a towel and place back on the baking sheet. Remove the other baking sheet from the refrigerator. Tip: The dough sank? That’s OK! Let both sheets sit at room temperature, covered, to finish rising, and test if the dough floats every 10 minutes after the first 30 minutes or so.
Set the Dutch oven over high heat and bring to a boil. Whisk in the baking soda and ¼ cup barley malt syrup. You want the water to look like strong black tea, so add more barley malt syrup by the tablespoon until it does. Bring everything back to a boil, reduce the heat if necessary to maintain a gentle boil, and skim any foam from the surface. Uncover one baking sheet and carefully transfer as many bagels as will comfortably fit in one layer to the Dutch oven, leaving some room for them to bob around. Boil for 1 minute, turning halfway through. Tip: If the ¼ cup barley malt syrup made the liquid very dark, more like black coffee, add a little water to dilute.
Use a spider or slotted spoon to transfer the bagels to the wire rack and repeat with the remaining bagels on the first sheet. The bagels will swell in the water, then deflate when removed, but they will puff up again in the oven. Discard the piece of parchment that was underneath the bagels but reserve the baking sheet.
Baking
Transfer the baking sheet to the oven and bake until the bagels are deeply brown, 20 to 25 minutes, rotating the baking sheet 180 degrees after 12 minutes.
While the first sheet of bagels is in the oven, repeat the boiling and coating process with the second sheet, adding more toppings to the plates as needed. Transfer the second sheet to the oven when the first is finished. Let the bagels cool completely on a wire rack before slicing with a serrated knife. Tip: Bagels are best eaten the day they’re baked, but they also freeze well. Place the bagels in a resealable plastic freezer bag and freeze up to one month.