I just read Koen's blog post here: You are not allowed to view links.
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I would suggest that instead of spreading Hercules' deeds across all the pharma section for unknown reason (for sure, the author's intention was not to tell the story of Hercules), the Hercules story serves the mnemonical purpose of grouping plants in order to memorize the necessary ingredients of a recipe. In other words, the following chain of thought is in place: the story (Hercules) -> the members of the group (the deer, the dog, the hydra) -> the exact plants.
Several questions can be posed here:
1) How is a story associated with the particular recipe?
2) How are members of the group chosen (e.g. why these particular three feats of Hercules out of 12)?
3) How are these mnemonic markers associated with plants (perhaps via the heads/tails concept that I once proposed, with the leaves referring to the plant name, and the roots referring to the story, with the leaves-to-roots association established by the Herbal section, in which case this association can be purely formal, not meaningful for a plant taken per se)
Curiously, all three group members in the Koen's example are starting with the letter H: the hydra is Hydra, the dog is Hund, and the deer is Hirsch. In English, the same holds true, because the deer is Hind at the same time. I would doubt that this is the universal principle though, because that does not fit for the top row of the same folio. The lion would start with L, but the stables or sewage (as Koen interprets it), would not.
I would like to point the likely possibility that not all recipes allude to Hercules. For example, the top row of f89v1 would have a partial match in Samson's deeds as well. Like Hercules, Samson did slay a lion with his bare hands. The leftmost shape with seven "sub-roots" is a match for seven plaits of Samson cut off by Delilah. I'm not sure for the shape in the middle, but honestly it does not look like stables or sewage neither.