Based on natural selection
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This is because a micropenis is not a simple genetic trait like blue eyes or a big nose.
Instead a micropenis will often occur because of a failure of the gonads to produce enough sex hormone for the penis to fully develop, and that in turn would be due to a problem with the pituitary gland or the hypothalamus.
So it isn’t like people with a micropenis are breeding true, instead it is simply that some people have genetics which make them somewhat more likely to have pituitary or hypothalamus problems that result in a micropenis. Those problems are very rare to occur, less than 1% of the population, and so they aren’t impactful enough to be completely eliminated through natural selection. Someone could have genetics that make them more likely to have a micropenis and yet it is overwhelmingly likely they still have normal genitalia despite that. All the equipment would work fine and until relatively recently everyone would be completely unaware there was increased risk!
A lot of things in biology are like this. For example some people have genetics which make them significantly more likely to have heart attacks than the population at large. Yet that trait isn’t completely removed from the population via natural selection because while they have significantly higher risk the actual prevalence of the issue is still very low. Even if they have three times the chance of the average person to have a heart attack, three times a slim chance is still very unlikely.
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