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I think given the evidence of the time, Malthus had sound reasoning. What he didn't (probably couldn't) predict was the stunning growth in technology that has increased crop yields by orders of magnitude, as well as the rise of the middle class, with its de-emphasis on having a large family. Organisms choosing not to breed given the opportunity is pretty new. But you're definitely correct that when a hypothesis is failing, its the hypothesis, and not the evidence that needs to be tweaked. That's a big problem in social science generally, I think. What's the old joke in economics? Something like, "Those data are interesting, but do they fit the theory?!"