Scientists have figured out a way to farm metals from plants

And on top of the usual problems of working out long-term storage, you’d also get lots of arguments about whether your mix is right for good composting.

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Not really. And the next step would be to process the plants to concentrate the metals (which would be a lot easier that to process the soil). Then either re-use the metals or put them into proper storage.

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But we know how to make soil and water on Mars, I saw it in this great documentary film!

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I guess we are in Command & Conquer timeline.

I’d agree. Depends on the ions involved, depends on the plant, but I’d agree that plants can act as a filter, accumulating metals in higher concentrations than found in the soil. Similarly to how overfarming can deplete soil of certain nutrients, plants can deplete the ground of other compounds. Also similar to how mercury and other metals can be accumulated in bigger fish.

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Mining is “violent colonization”?

More often than not, yes.

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The meek shall inherit the earth, but not the mineral rights.
– J. Paul Getty

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