One of the reasons Japanese food is good for you is that it uses little red meat. I had always assumed that this resulted from the scarcity of good grazing land in Japan over many centuries, given that it's an island country with a high population density and the land is mostly rugged and thickly-forested. In fact this is even more true than I realized, in a way that I didn't expect. Until 1871, it was actually illegal to eat meat from livestock (especially beef) in Japan. This law, repealed by the occidentophile Meiji emperor, dated to the Heian (Kyoto) period (eighth through twelfth centuries), but other prohibitions on beef-eating were in place even well before then; cows eat a lot and divert resources from other activities which feed people more efficiently. In an island nation subject to famines, it's easy to see the appeal of such restrictions to the controllers of Japan's medieval centrally-planned economy.
Any discussion of prohibitions on eating cow meat immediately invites comparisons to India. It's thought that the Hindu prohibition on eating beef also originated as a way to keep people from destroying their capital (i.e., their early iron age plowing and milk machines), which you might be tempted to do by eating them when times got tough. The question is this. Why did the prohibition become part of a religion in India, but not in Japan? Why in Japan did it remain merely an edict of the emperor (or the samurai junta)? Would it only have been a matter of time before the Japanese prohibition became incorporated into religion? That is to say, would a Japan unpolluted by contact with the outside world have, by the year 3000, evolved a Shinto ban on eating beef, parallel to the Hindu one? Conversely, would an Indian king entertaining a Roman ambassador have been able to repeal a ban on beef-eating, because back then the ban was still recognized as a man-made law as opposed to a god-given one?
It's intriguing to think that there's another reason, that the respective bans were part of cultural-economic complexes that affected how this taboo developed over time. If so, we should expect other differences. And to that end, another difference in the taboo system between Japan and India is that in Japan, an actual caste (the eta, or burakumin - less derogatory today) developed for the handling of beef- and cattle-related products. This caste is only now achieving re-integration with the rest of Japanese society, and reading about Japanese Buddhism's treatment of this subculture will go a long way to disabusing you of any notion that the Eastern religions are any kinder than their Middle Eastern and Western counterparts. Just like orthodox Jews made an end-run around the Torah by hiring goy children to run errands involving fire and whatnot on the Sabbath, in Japan a (disrespected) caste evolved that handled butchery and leatherworking. Orthodox Jews still had to cook food on the Sabbath and Japanese still needed leather.
But some Hindus like beef and leather just as much as anyone else (and so do foreign tourists in Hindu countries). From indirect observation I know that in the world's only remaining officially Hindu nation Nepal, cattle are killed in rural areas by such clever workarounds as "I didn't kill it; the fall off the cliff (that I pushed it off) killed it." And yet there has evolved no separate class of cattle-killers. These inane theological loop-holes produce not only cultural but technological artifacts, my favorite of which is Tibetan prayer spinners (spinning the holy maraca makes the scroll inside it go around; on the scroll is written a prayer, so apparently the Buddha is indifferent to whether your meditation is supplemented by angular momentum). At first glance, it's an admirably ingenious spiritual machine. At second and succeeding glances it becomes more and more ridiculous, but at least it's much less sinister than workarounds involving living things, as I mentioned above. But as to the question, why a religious rule in India, and not Japan; why a caste in Japan, and not in otherwise caste-heavy India - I confess I'm as fascinated as I am without an answer.
On a personal note, about ten years ago I was put to use by a Hindu scientist friend who needed mouse erythrocytes for an experiment, except his religion forbade him from killing the mice himself. He asked me to come up to his lab to turn on the gas and dispatch the mice for him. I did him the favor, but needless to say, after the fact I badly tortured him with questions about how, exactly, he could avoid karmic penalty yardage for this, considering that he was the one who recruited me for the task, and he even closed the lid of the jar. If I were Japanese I guess that would make me a nezumi-no eta.
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