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we don't know how plants will do when subjected to the conditions of another planet, or outer space. there may not be enough sunlight, or there may be far to much. if we use artificial light, then much of it will be wasted.
hydroponics on the scale nececary for a life suport system become bulky and complex, due to the sheer volume of plants required.
by definition, if it nds up in space, then it was part of your launch mass. the conservation of mass alone tells us that. no launch mass is saved by making food in-situ, apart from posbliy storage.
not just bacteria, several kinds of bacteria, all at the right lebels and depths within the soil. keeping these bacteria is a big problem for farmers here on earth, it's an even bigger problem in a totaly controlled system, where nature isn't doing most of the work for you.
organic processes brings a level of guess work into the system. you can never be sure jsut how they'll grow, or how much oxygen they'll produce, or if they'll all mysteriously die a week into the flight.
in contrast, we are in complete control of artifical systems. we know exactly what is going on, and can easily analyse and rectify any faults.
Say for instance a fungal infection is brought on board. for starters, you would have to find it. in an artificial system, problems can be seen imediately, as the entire system can be monitored, and you know exactly how it will behave. but to find something like a fungus, you would have to check every plant. then you must race the clock to eradicate the fugus before it destroys the entire crop. with an artificial system, you would shut it down to prevent further damage, and then fix the problem at relative lesiure.
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