It may seem weird to call for a soft-boiled egg cooking time down to the second, but bear in mind that the temperature difference between a creamy yolk and a solid one is a mere 8°F. If you like your yolks only thickened, without any slightly set parts on the edges, boil them for 6 minutes. Egg yolks cook faster than egg whites, so we call for cold eggs; cold yolks cook slower, insulated in the shells by the whites.
Bring 2 quarts water to a boil in a medium saucepan over medium-high. Gently add eggs, straight from the fridge. The boil will halt for a moment as the water temperature drops. When boiling resumes, adjust heat as needed so the eggs don't bounce hard on the bottom of the pan, cracking the shells. Cook 6 minutes and 15 seconds for thick, creamy yolks that have just barely begun to set around the edges.
Meanwhile, fill a medium bowl with ice and water. The second the eggs are done, pull them out with a slotted spoon, and plunge them into the ice bath. Let stand 2 minutes. Cut off tops or crack eggs, and remove shells gently; soft-cooked eggs are wobbly and fragile. Sprinkle evenly with salt and pepper after cutting in so the yolks get seasoned, too.