it's a neat idea, but the code backend for that would be atrocious.
Every plant tile planted would have to keep a history of the two plants that provided it's heritage data, even after they are long since consumed, and the memory should have been freed. This means that horticulture would gobble up resources like crazy, trying to track all the geneological data needed to properly simulate genetic expressions and mutations on otherwise fungible produce.
Yeech... I wouldnt want to code it....
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Hmm.. I still dont like the idea of magic being a testable and verifiable energy source. It is just too plain hard to reconcile with mundane physics without causing a thermonuclear explosion, or causing real-manifested nightmares to spawn in children's bedrooms. (Pratchett ironically, chose to include this later effect in his disc world even!)
I prefer to look at magic as an expression of what is unknown. It is unknown how an amethyst man's biology works, therefore, his biology is clearly magical, since it defies conventional reason. (He COULD be purely photonically powered!) Same with a nethercap. For a long time, people felt pregnancy was magical, for instance. We have since learned that it is no such thing whatsoever.
If we are going to start introducing exotic physics metamaterials, then we have to seriously consider all the consequences of that, which quickly becomes head exploding.
For instance, atomic scale wormholes to another dimension with perfect thermal properties held perfectly at 0c interacting with ordinary matter to reduce temperatures, would have very unpleasant effects upon ingestion in species not adapted to that-- It would freeze their digestive tracts, and in warm blooded animals, it would cause hypothermia, because the organism would be unable to regulate internal body temperatures! It would be its own kind of illness and associated syndrome of effects, caused by being contaminated with "nether particles" through ingestion. (though I suppose it would be GREAT for embalming people!) This throws a big monkey wrench into using them as an autotroph to make the cavern ecosystem plausible.
The method I suggested with the seebeck and peltier effects, would just mean the nethercaps have shiny metal striations in them, and their natural slow decomposition is what causes the inverse effect as a slow heat fountain.
Making magic into real forces and not just an artifact of applied ignorance has many very dangerous reprocussions. you should be *VERY* careful doing that!
**Note--
Not that I think all magic should be made out to be pure ignorance though. Necromancers, Mummies that raise the dead, and the like are obviously REAL magic. However, these occurrences are "extraordinary"--
We would need an explanation for why subterene environs are so obscenely magical, but why dwarves arent natural spell casters, despite living in, and consuming, immensely magically imbued environmental products. Why dont dwarves have superpowers, and such-- for instance. We would also need an explanation for why surface areas are routinely mundane excepting in specially magically dense areas, like undead reanimating biomes, and super happy cottoncandy grassed sunshine and dewdrop infested good biomes.
This gets into cosmological explanations, which are PRNG generated-- making them off limits, and or-- not really PRNG, but actually "Selected from formula", and requiring a cogent formula to build sensible cosmologies from.
We would also need explanations for why wild magical energies dont just conjure things up into existence willy nilly.
Pratchet balanced that, by saying "Belief" is a finite resource. (See for instance, the Hogfather story.) But then again, he has power over the cosmology to say that. again, we dont-- PRNG generated worlds.
Balancing this is fundemental if you want a reasonably sensible xenosynthetic biosphere that runs on magic down there.