>Whose livelihood is destroying the engineer that design better protein folding software?

Hasn’t homology modeling essentially been abandoned by researchers at this point? Maybe their livelihood wasn’t completely ruined but if you had specialized in that technology, you were probably materially harmed by the introduction of AlphaFold. That harm doesn’t outweigh the obvious benefits, but I would be very surprised if the harm doesn’t exist.

>Even the humble startup shipping yet another calendar tool isn’t harming anyone or being the direct cause of layoffs of other workers.

If they’re undercutting and outcompeting an existing calendar tool, they very well could be contributing to layoffs at their competitors.