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Unfortunately for my mental health my thesis was exactly about converting arxiv papers to modern looking html, and there's so much more broken, unjust and ugly things in academia then using pdfs...

Regarding your question, I'd say that it is a natural continuation of centuries long tradition of writing on the actual paper. The invention of TeX actually made it easier to produce more papers, then came PDF, and you could produce virtual papers. Also science journals pretty much have monopoly on scientific knowledge distribution, and they are mostly paper too




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