I was revisiting this question and found @Valorum's comment interesting.

That's covered in the excellent (and fully canon) Star Trek: The Next Generation Technical Manual. I quote; "These units are primarily designed for operation at molecular (non-lifeform) resolution for cargo use, but can be set to quantum (lifeform) resolution if desired, although such usage would entail a signification reduction in payload mass capacity". For the record, the cargo Tranporter on the original Enterprise is rated to carry 22 crewmembers (1.6 metric tonnes?) in an emergency. – Valorum

It makes me wonder if inanimate cargo transported at molecular resolution degrades during the relocation process. What does canon say?

Is inanimate mass transported between point A and point B in some way lesser than it was prior to beaming? If not, then why do they need a Quantum Resolution setting to beam lifeforms?

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    It's a question of scanning resolution. While it's acceptable to only scan every few hundred molecules of an inanimate object, it's much less acceptable in a life-form – Valorum Jun 20 '16 at 20:13
  • C'mon. I'd give you checkmarks for that answer. – Major Stackings Jun 20 '16 at 20:16
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    I'm on the lookout for a reference. I'm somewhat impeded by the fact that I'm also trying to watch Terminator TSCC and it's a rather good episode. – Valorum Jun 20 '16 at 20:21

Although it relates to transporter-based replicators rather than transporters per se, we learn from the Star Trek: The Next Generation Technical Manual that when non-living matter is transported, minor errors can creep in due to the software compression techniques used to limit the data required.

Because of the massive amount of computer memory required to store even the simplest object, it is impossible to record each molecule individually. Instead, extensive data compression and averaging techniques are used. Such techniques reduce memory storage required for molecular patterns by factors approaching 2.7 x 109. The resulting single-bit inaccuracies do not significantly impact the quality of most reproduced objects, but preclude the use of replicator technology to re-create living objects. Single-bit molecular errors could have severely detrimental effects on living DNA molecules and neural activity. Cumulative effects have been shown to closely resemble radiation-induced damage.

You might also want to note that switching the transporters to HD mode requires a dramatic increase in energy utilisation.

Cargo transporters are generally optimized at the more energy-efficient molecular resolution, but can also be set at quantum resolution if necessary.

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    As we learn on DSN, it isn't the physical form of a living organism that takes so much computer memory, but the neural patterns instead. – Xantec Jun 20 '16 at 22:21
  • @Xantec - I'm guessing that even in a structure as complex as a person's body, 99.99% of molecules are identical to the ones on either side of it. – Valorum Jun 24 '16 at 15:28
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    From the TNG tech manual: "...certain types of Altarian spices have shown a tendency to become mildly toxic when replicated, so their use is avoided in replicated dishes." – pleurocoelus Jun 25 '16 at 12:51

The phrase 'reduction in payload mass capacity' does NOT mean mass is lost during transport; it means the total mass -to be transported- has to be smaller from the start. In this case because a fixed number of bits is being used to describe the transported object at a much higher resolution (in bits-per-unit-volume).

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