I am unaware as to how the bonds form, so enlighten me.
Consider a room full of children, each one holding a toy. As they mill about aimlessly, a child sees another toy that he'd like to have, so he reaches for it. But the other child won't let go and he, in turn, reaches for the first child's toy. Soon all of the children are "bonded" together in pairs, held together by the toys that both children want.
The children are like protons and the toys are like electrons and the pairs of children are like hydrogen atoms, bonded together by a pair of electrons that they both want.
And it all happens naturally. The probability that the bonds will form is 100%.
Can you tell us how the protons, electrons and hydrogen atoms came into existence?
You're moving the goalposts. The topic is about making a protein out of TinkerToys, not about how to manufacture TinkerToys.
The fallacy of your argument is that you assume everything happens naturally. Do you have evidence for this natural origin?
It isn't an assumption. We're only talking about things that do happen naturally. Children fight over toys naturally. Atoms bond naturally. If you want to prevent atoms from bonding in their natural ways, you have to give them natural alternatives.
What seems more logical, a planned reason for these events, or "well stuff happens" and we don't want to speculate about how it happened.
What's more logical is processes that we know about, not speculation about some unknown "planner".