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The fuel used to run the tractors can itself also be biodiesel.
Absolutely! The question are is you want to have an agricultural system with such a fragile link in the chain. And modern factory farming isn't just "a tractor", which can certainly help small scale operations. I can see a tractor being an adjunct, but probably supporting a large group of farmers, who, at any rate, probably need to keep busy anyway.
How is a thing you can do yourself in a closed loop "fragile?"
Because there are a lot of parts on the tractor that might need to be repaired and replaced. Even if you had access to everything you need, how many people are going to know how to do it?
And timing is critical in faring, so you'd have to get the tractor repaired quickly if anything goes wrong.
So if you lose one person or can't fix one part quickly enough, your entire agriculture system falls apart if its based around a tractor.
A system built around human labor or even animal labor is much more resilient.
We were talking about carbon inputs and biodiesel, not reliability. Growing biodiesel has no carbon inputs if the farm itself runs on biodiesel.
Just looking at the whole picture. Farms do not "run themselves on biodiesel," they put that biodiesel in machines.