Thermodynamics

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Thermodynamics prevents one from having every atom at the place we want it - wrong for practical scales

If one just looks at the atom displacements from thermal movement at room temperature alone big macroscopic slabs of stiff diamondoid materials stay atomically precise for long periods of time from a human perspective. More serious are effects from hard ionizing radiation that can't be shielded effective against with. Reliability and redundancy make things work practically nevertheless. Self repair can extend lifespans to uncalculable ranges.

There are many materials that do not keep their atoms at a constant place due to thermal motion. They do not preserve their bond topology. Many metals behave that way especially on their surface. Even water does not keep its atoms at its fixed at its molecules. It swaps around hydrogen atoms due to its molecular auto-ionization pH7 H3O+ OH-.

But there are also many materials (among them e.g. diamond) with bonds strong enough such that the constituent atoms for all practical purposes do not leave their lattice places due to thermal motion (radiation is a different story). Even when there are macroscopic amounts of material sitting around for decades at room temperature.

Biological systems (e.g. Proteins, DNA, RNA, ...) feature strong bonds. But almost all the involved molecules are chain molecules. And (oversimplifying a bit) with chains only one link needs to break for the whole chain to break. Biological systems also tend to be embedded in a potentially aggressive chemical environments (aggressive relative to a vacuum). Thus although biological systems feature strong bonds they need (and have) some active repair mechanisms to keep everything roughly where it is.

Having crystolecules with a dense mesh of redundant polycyclic bonds in a vacuum makes the time it takes for them to incur destructive damage long enough for them to be extensively used even without any repair. Self repair in advanced nanosystems (in the sense of part replacement) is an available but not unconditionally necessary option.

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