Prismattic comments on In Defense of Tone Arguments - Less Wrong Discussion
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I agree with the general thrust of this, but note that specific case of the uselessness of the appendix is controversial.
My list for this argument starts with the fact that it would be much better if the trachea and esophagus didn't intersect, with the nostrils on the side of the neck -- no one would ever choke, a circumstance of death usually associated with children (typically exemplifying the morally blameless for most religious people).
I can argue back that each of the two discrete pathways would be narrower than the one common pathway we have, so having a common pathway is not as stupid as you are making it out to be. This answer is poor because the risk of choking is much more problematic than having a narrower airway.
Earthquakes are also mildly useful in that they bring out precious metals to the surface of the earth. I am pretty sure an omnipotent god could have brought out such materials without having to kill millions of people each time he did it.
Regarding the appendix, I frankly don't care if a handful of doctors claimed the appendix had some trivial functions. The way I see it: people without an appendix are indistinguishable health-wise from people with an appendix, while until a very recent time, people with an appendix had to worry about dying when it inflames and ruptures. Humanity would have been much better off without an appendix.