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Bleh, that post I made earlier makes no sense now that I reread it. BASICALLY: Yeah, I'm not really into epigenetics, but I thought I knew enough for the very vague description I was going to put there to make sense without specifically looking into the particular mechanisms that would be at work, which I guess it didn't. Also part of what I wrote in the explanation in the fan theory guide was really weirdly worded and implied the actual sequence of the paternal genome was changed, which probably didn't help.
The earlier guestbook post sounds like I'm defending this theory on the basis that theories don't need to make sense to someone with a more intimate understanding of the field; that was meant to be a response to the final "does it matter if someone well-versed in a subject will recognize a theory as nonsensical" question, not the comments about my theory in particular. If, indeed, Pokémon inheritance can make perfect sense with normal Earth genetics, then my theory is very silly and obviously way overcomplicating things, and I'm very intrigued because genetics fascinate me and I've never heard of anything like that in real life. So if you were to throw some examples my way I'd be overjoyed.
Hope that made somewhat more sense.
Ultimately, since there is no actual reality to be discovered behind how governments/Pokéballs/genetics/etc. work in the Pokémon world (i.e. the creators almost certainly didn't have some specific educated idea in mind), and these are sufficiently complex things that any explanation posed will be pretty wildly speculative, I don't think it's especially productive to look for the explanation, or generally anything other than "well this is how *I* think it would work". When you get to that level, the best a theory can do is fit with what we observe, and there's no guarantee any possible theory could fit with what we observe while at the same time making perfect scientific (or economic, etc.) sense. It becomes a matter of trying to turn Pokémon's fantasy world into science fiction, essentially. Of course one theory can be simpler and more plausible than another, and most theories can definitely be improved by someone who knows more, but I can't help feeling just about any theory explaining the more fantastic elements of something like Pokémon is bound to be unconvincing to someone very intimately familiar with the real-world science at hand.
Or, while more research is always better than less, it strikes me as pretty futile to strive to make fan theories about something like Pokémon satisfy people with a greater education in the relevant academic fields. Because it wasn't created to make scientific sense in the first place, there's only so far anyone is likely to go in making sense of it after the fact.
All that said, I'm very interested if there are actually organisms where something like Pokémon's inheritance system actually exists. Are there examples of something like that large-scale inheritance-only-through-the-female-line in nature?
I tried to be vague on things like the mechanism by which genes are 'activated' or 'marked' as moves are learned, both because I'm not intimately familiar with epigenetics personally and because it struck me as unimportant precisely how it happens, so specifying it would just needlessly complicate an already pretty overcomplicated theory (I also didn't want to specify whether Pokémon's genetic material is DNA or something else, so talking about mechanisms specific to Earth cell chemistry would have been odd). But my admittedly cursory understanding of epigenetics was that the epigenetic processes that would be involved here could more or less be described as 'marking' particular genes, and that's also how I understand the Wikipedia article you linked. If I'm way off on that count, or if my wording is completely absurd given a more extensive knowledge of the subject, please correct me.
Commenting on: 12-29-11
I find it kind of hard to keep track of the guide without pictures, especially the step-by-step explanation of how germline cells are formed.
It's kind of hard to talk about what would be plausible or implausible about this system of inheritance without getting down to "well this is how *I* think it would work," and there are plenty of real-life organisms with systems of inheritance that get roughly this crazy. At the same time, though, there are ways similar problems have already been solved by organisms that live here on earth, so your system ends up looking pretty strange and complex by comparison. Chromatin remodeling would be a plausible explanation for the way that moves are inherited (does your system account for the fact that level-up moves can also be inherited, but only if *both* parents know them?), for example. I dunno, I don't really want to be like "go out and do a ton of research on high-level topics for your pokémon fantheories," but it would really make what you came up with ring more true, I think.
Perhaps that would be something to address in your fan theories guide? It's fun to speculate about things like how the government of the pokémon world might operate or the technology behind pokéballs, but unless you happen to know a lot about government or theoretical physics/engineering you're probably going to come up with something that would look pretty strange, if not outright wrong, to someone well-versed in those areas. Or would you say that's not important?
"dictats that it should be female"
You forgot an "e" in "dictates."
You may have been sleepy when you typed that, but as a perfectionist, I think you would appreciate having that error pointed out for you.