Cook the Wheat Berries: In a medium saucepan, combine the wheat berries and water.
Bring to a boil, then reduce the heat to low and simmer gently for 2 to 3 hours, until the berries are very tender and have burst open.
Drain thoroughly and set aside to cool.
Activate the Yeast: In a large bowl, combine the warm beer, yeast, and 1 tablespoon (15 ml / 0.5 fl oz) of the molasses.
Let the mixture stand for about 10 minutes, or until it becomes foamy and active.
Create the Sponge: To the foamy yeast mixture, stir in the remaining molasses and the all-purpose white flour.
Beat vigorously with a wooden spoon until the mixture is smooth.
Cover the bowl with a tea towel and leave it in a warm place for about 40 minutes to let this sponge rise. It should be bubbly and doubled in size.
Mix and Knead the Dough: Stir down the risen sponge, then mix in the salt and crushed fennel seeds. Gradually add 2¾ cups of the rye flour, stirring until the dough becomes too stiff to mix with a spoon.
Turn the dough out onto a lightly floured surface and begin to knead for at least 10 minutes, adding more rye flour as necessary to prevent sticking, until the dough is smooth and elastic.
First Rise: Form the dough into a ball and place it in a buttered bowl, turning it over once to coat the entire surface with butter.
Cover the bowl with a towel and let it rise in a warm, draft-free place for 1 hour, or until the dough has doubled in size.
Incorporate Berries and Shape: Punch down the dough and turn it out onto your floured board. Flatten it slightly, spread some of the drained wheat berries on top, fold the dough over, and knead them in.
Continue this process until all the wheat berries are incorporated.
Form the dough into a smooth, round loaf, pinching the seams together securely at the bottom.
Final Rise: Place the loaf, seam-side down, on a buttered baking sheet. Lightly brush the top with melted butter and use a sharp knife to cut a shallow cross in the top.
Cover with a tea towel and let it rise in a warm, draft-free place until it has nearly doubled in size, about 45-60 minutes.
Bake and Cool: Preheat your oven to 425°F / 220°C.
Bake the loaf for 10 minutes, then reduce the heat to 375°F / 190°C and bake for another 55 to 60 minutes. The loaf is done when it's a deep brown color and sounds hollow when tapped on the bottom.
Brush the hot loaf again with butter and transfer it to a wire rack to cool completely before slicing.
Don't rush the rising times! This dense, rye-heavy dough needs the full time to develop its rich flavor and structure. Under-proofing will result in a dense, brick-like loaf.
Patience is a virtue when cooling. For the best flavor and texture, allow the loaf to cool completely on a wire rack for at least 2-3 hours before slicing. Slicing into a warm rye loaf can result in a gummy interior.
