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Star Trek fans have held the national stereotype of being way too rabid about things for decades but they’re probably the nicest fan base in all of science fiction and the one least likely to have a large faction of them absolutely lose it over a torpedo being fired by a woman or dumb shit like that
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Knowing how chemicals and carbon compounds are recycled in Earth’s ecosystem and taking into account factory farming, I would wager the line between poop to serving of hot steak is much a much less connected line on a ship that turns matter into its constituent energy patterns.
Meanwhile on Earth we routinely have meat recalls because of e-coli contamination. Which is poop. Everyone is eating animal poop to some degree, it just becomes a problem when enough of it is in one spot to become contamination.
The replicators are also used to “recycle”, converting matter into energy, to be used for future replication.
I doubt they were hauling poop through space rather than converting it to poop energy for their next earl grey.
This is the whole premise behind Star Trek, and one form a post-scarcity civilization could take.
As a tangent, Star Trek’s technology is both magical and primitive, in that they can harness and focus energy levels that match stars routinely, they can literally form matter from raw energy and influence the fabric of time and space itself and even break causality if they really try, but despite this have almost no difference in how they are born, grow up and die.
I get the show is trying to make a relatable universe, but if we reach that level, we will also have reached so many other advancements in every other facet of existing as a human that our species itself would be utterly unrecognizable and we probably wouldn’t be worried about how real our steaks taste.
If we’re sticking with the lore, the only limitation should be what they have stored in the replicator database. No reason your poop steak couldn’t taste like an A5 wagyu or a $2 steak, depending on your personal preference.