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I disagree ancestral and evolutionary factor are very strong... It's our genetics that determine our urges and that what a cravings are.
Remember that meat and carbs would have been seasonal and we have been hardwired to gorge on such things when they are in plentiful supply to benefit us during difficult times.
The way we put on fat for example is very different from area to area... the indian subcontinent for example historically had a famine/draught every 7 years or so. This visceral fat that would have been utilised during this time is now the cause of high rates of diabetes and heart disease much more then the wider population. The same can be said of Arabs that have replaced sheep/goat herding and fishing with wafting around airconditioned shopping malls will fast food and desert bars. Kuwait has a population that one third diabetics.
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I was agreeing with @frankenbike's point that "we evolved to eat meat" is not a justification for continuing to eat meat, since we can now do without it. What we crave is not relevant from a moral standpoint. I'm not sure what the relevance of the rest of your first post is from that perspective either. Unhealthy diets are unhealthy, obviously.
I agree with you about inbreeding in pets. That shit is fucked up. It's not relevant to responsible meat-eating though. I was referring to livestock, with the implicit caveats that have been made throughout this thread regarding animal welfare and intensive rearing.
I agree that historical or evolutionary precedent is no reason to either support or reject something. Unfortunately, everyone's life will have some impact on animals. We destroy their habitats when we build our homes, roads, shops, and factories that make the shit we buy. When we farm crops we displace or kill them to maximise yield. I'm not convinced that killing animals for food is fundamentally different from killing animals for any of the reasons above. We don't need to eat meat, but then we don't need to play golf or buy iphones (etc. etc.) either, both of which will have quite some impact on animals and their environment.
It's not unreasonable to argue that we shouldn't bring animals into the world just for the purposes of killing them later, but when we do so we make a tacit contract with the animal that we will provide it with a life that is as natural, comfortable and safe as possible and a quick stress-free death at the end of it. As a result many domesticated animals live much happier lives than their wild cousins.