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A few examples:
-Librarian can apparently plan the course of evolution over many generations. There is in fact no roadmap to evolution, and no way for there to be one without invoking divine power. Populations of organisms change over time in response to their environment, with characteristics that improve survival being more likely to be passed down. But since populations are adapted for their specific environmental circumstances, there is no such thing as being higher or lower evolved. There is only ideal adaptation to a particular environment, and environments change all the time. So unless Librarian is manipulating climate conditions on Earth or something, her guiding of evolution is nonsensical. I certainly don't see how "guiding" evolution would let her plant the idea to invent Mjolnir and Cortana, which she implies in Halo 4.
-Librarian can "accelerate" the Chief's evolutionary journey. I don't know what an evolutionary journey is, but evolutionary changes do not occur on the level of an individual within their lifetime...incremental changes that prove beneficial are passed on to offspring. Changing something in the Chief instantly to make him immune to the Composer isn't biology, it's magic.
-All the ancestral humans are white dudes, both in Legends and the Halo 4 terminals. The archaeological record clearly shows that humans originated in Africa, and that for most of the species' history, all humans would have looked like people of African origin. Lighter skin and fuzzy faces are relatively recent adaptations of populations that migrated to northern Europe. Portraying ancestral/original humans as white doesn't just raise all sorts of problematic social concerns, it's straight-up historically wrong.
-Halsey calls spartans "humanity's next step, our destiny as a species." This nearly ruins the otherwise awesome opening scene to Halo 4 for me, because it means absolutely nothing and makes Halsey sound like a crazy Dr. Science. The spartans were augmented, but if Halsey is implying they could somehow pass that augmentation to offspring, she's fallen off the Lamarckian cliff. Or does she think that all humans in the future should be augmented? Her attitude toward the Spartan IVs later on would suggest otherwise. Basically, this line is dumb.
Evolution is a well-established fact of nature, but politicization and misrepresentation mean that less than half of Americans accept that it exists, and fewer understand how it works. And understanding evolution is important not only to understand ourselves and world around us, but to understand important issues like medicine, disease, genetically-modified food, etc. So when we have popular entertainment throwing around the term "evolution" in a wanton way that has no bearing on the real biological process, it only confounds the problem. *Full disclosure: I'm a science teacher, and it's important to me that people have some basic science literacy.*
343, I beg of you, if you want these plot contrivances to happen, please call them magic, not evolution. But I think you can do better, regardless.