Take the three as searches rather than questions, and the first thing they share is how much careful looking has gone into them. Underground detectors have run for decades at rising sensitivity without registering the leading dark matter candidate. Experiments hunting electric dipole moments have pushed below where new CP-violating physics was expected and found nothing waiting there. A reanalysis took the strongest single case for a heavy black hole seed down from 4.2–4.4 sigma to 2.3–2.9, and the most sensitive instrument aimed there saw nothing at all. Three long searches; nothing found.
Those three nulls are not the same object, though, and the differences carry more than the shared shape. The dark matter search has an end built into it: as detectors improve they approach the neutrino floor, where the universe's own background of neutrinos produces recoils very nearly indistinguishable from the signal. That is a search with a horizon: either the particle turns up before it, or the technique all but runs out of room.
The antimatter nulls are stranger, because each agrees with the Standard Model, and the Standard Model is precisely the account known to fall ten orders of magnitude short here. Confirmation from a theory already known to be insufficient is not reassurance. It says only that whatever supplies the missing factor stays hidden at the precision reached so far.
The black hole nulls are the least stable of the three, because they are absences inside a record of roughly twenty photons. Evidence that thin can weaken under scrutiny without the object ever having been absent, and can firm up again. UHZ1 has already moved once. Bounded, ambiguous, provisional — three grades of not having found something, and only the first knows in advance where its own looking must stop.
The answers rank by something less obvious than difficulty: whether more evidence can be made, or only gathered. A substance is the generous case — the detector runs again tomorrow, and whatever is out there keeps passing through it. The asymmetry cannot be re-run, but the bias that caused it, if it survives at all, survives in matter now, so precision can be bought with patience. The early black holes allow neither. Each object arrived with its photons already counted, and no later instrument adds to that object's supply; the only route is more objects. Make it, buy it, or go find more of it.
There is also a pattern in how all three were noticed, and it is about measurement rather than about the universe. In each case the confident number is the total and the uncertain part is the itemization. Gravity gives the mass of a cluster without saying what carries it. The microwave background and the light elements give the surviving ratio of matter to antimatter without saying what set it. A quasar's output gives the mass of the black hole powering it without saying how that mass was assembled. We are better at measuring sums than at naming terms, which is why these three read as discrepancies in an account rather than as blank spaces. A missing entry is only visible when the total can be trusted.
There is a reason for the lopsidedness. Each of those totals comes from long-range, aggregate physics — gravity acting across a cluster, an entire plasma cooling, radiation escaping a whole accreting system — and aggregates are what such physics reports well. The itemization would have to come from somewhere else: a particular interaction, a specific mechanism, one chain of events that happened once. The instruments that work here are the ones that sum.
That trust is what makes the second chapter's arithmetic worth returning to. The prediction there is not a marginal one, and near-total annihilation is not a hypothesis still waiting to be overturned. The microwave background records it. The light elements left by Big Bang nucleosynthesis record it. Matter and antimatter did meet in the early universe, and the meeting did consume very nearly all of both. What has never been explained is the remainder.
The remainder is the reader. Every atom in a body is built from particles that had no partner left when the annihilation finished — one part in a billion carried over from a ledger that the physics says should have closed at zero. It is a strange inheritance to hold. Dark matter is elsewhere, mapped across billions of light-years and never once handled. The first black holes are long ago, their light more than thirteen billion years in transit and arriving in counts of about twenty photons. This third thing is neither distant nor ancient in the way those are. It is the material the looking is being done with.
None of which makes the three gaps smaller. It changes where they sit relative to the person considering them. Two of these mysteries concern the contents of the universe — what the mass is, how the earliest giants were built. The third concerns why there are any contents at all, and the only sample of it anyone has ever had is already in the room.