I discovered this forum while searching the very same subject for answers. I guess I've been reading those who tell you how great it is to do it because that is what they sell, and it was only the "permaculture" thinking that kept telling me I am doing something wrong if I do what they say. There was something missing from the well painted picture.
My thoughts align with some of the claims of the early posts on this thread of insufficient nutrients in the cycle, I am still not convinced that the system in overall design doesn't work but the cycle needs completion to resemble as close as possible the mechanics of nature. Still, the thought of a zero sum game (inputs-outputs) may be correct in physics terms but in terms of life and ours in specific it is not. There is light energy being transformed, together with oxygen, carbon, hydrogen, water, nitrogen, into more and more life. But what is missing from the remaining elements in nature in the cycle of "life eating life" and vegetation to produce more life?
Fungi, mold, .... Natural cycles include those in decomposing and producing nutrients composed of metal and non-metal based substances, organic and inorganic. Here we have a system where land/air based vegetation and its relation to fungi and molds is blocked. As far as I know and from what I have read it is next to a miracle that is happening at all. The conditions of collaborating fungi to any root system are disrupted by too much water when the bed floods, and too much air when it drains.
Most soil based fungi will not work. No compost no nutrients. There may be nutrients of plants to grow and survive but not the living beings dependent on them. Not healthy anyway.
How do you add organic composting into the system (fungi will eat screws and produce chelated iron for example, if you put steel wool on your bed all you might get is rust) is something I am experimenting with. The reason why is that I live in a very dry part of the world and food production and water supply is hard to come by, and permaculture despite of how wonderful of an idea it is, it is more oriented to life conducive geographies. As we are going towards 8bil and to less than 1acre/0.4hectares/person of fertile land we need solutions fast. We need to retake the dessert into the forest and we need to it with the least mechanical, energy,industrial method possible. We need to undo much of the forest destruction before the imbalance destroys us. We are the pest, we are the reason life systems are failing everywhere. We are the reason biodiversity has gone so low it is amazing we are still on a living planet.
Whether we are talking about raising fish, mushrooms, aquaponic vegetables, ... there seems to be some magic of 20' C/70'F 60% humidity sunlight and forest shade, that seems to be accelerating all life. The more you deviate from such conditions the harder life becomes. The physics equation we need to solve is maximize life and well being while minimizing pain and hardship.
And aquaponics seem to have been designed with very hostile intentions against fungi, the root of all life according to some.