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To What Extent are Humans Optimized?

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The human body below the neck has remained largely unchanged since the evolution of Australopithecus four million years ago. One may conclude from this that the body is well optimized. The human body above the neck has changed continuously since that time and only converged on its present form 250,000 years ago. One may surmise from this that the brain is in some ways less optimized than the body.

Everything in evolution is well optimized, though, how do we know it's not either a 'local minima' or just 'less important than other things evolution acts on'? Bellybuttons haven't changed for a while, and even though they are suboptimal (see skin, generally, not having random holes or bumps), they're not important enough to change.

The left recurrent laryngeal nerve and the vas deferens are classic examples of suboptimal anatomical features. One might imagine there are structures in the brain that are suboptimal in a way that is analogous to the left recurrent laryngeal nerve and the vas deferens. Perhaps there are some we have yet to recognize as such because we don't understand how the brain works.

minimizing how many instructions you need to add to the genome in order to make something happen

This is the mechanism for why the body isn't fully optimized: it has to be backwards compatible and build iteratively off of previous DNA. That tech debt is exactly what an artificial engineered brain/body could re-design.

That makes sense, direct editing is going to cause a lot of indirect problems. Similar to immune system or dietary supplements.