The world changes, so we are not really adapting to the same conditions that our ancestors did. Let's go for a fake example.
Imagine that there is a mutation that hands a human 20 points of IQ, but then makes said human extremely near sighted. For most of human evolution, that'd be a terrible call: Being able to see well was far, far more important than those 20 points of IQ: There are diminishing returns, of both eyesight and smarts.
But today, we are smart enough to make bad eyesight be a minor annoyance, as opposed to something crippling than it was 2000 years ago. So if smarts and myopia were to be related genetically, then today we'd be selecting for more nearsighted people, because today, being nearsighted is not a big deal, but the extra smarts are valuable. A change in the world leads to a different optimal tradeoffs. The one difference is that now, it's us selecting ourselves, and using technology to account for our genetical weaknesses: We are a bit ahead of Darwin's finches.
This is what is so amazing of the world today: We have social, behavioral selection mechanisms that work far faster than any external pressures we are facing today. Think of, for instance, of AIDS: For many years, a deadly STD, with no cure and not even treatment. Social adaptation to STDs (monogamy + condoms) and our awareness of the problem made it so that we didn't lose most of the population to it. Without rationality, we'd deal with a disease like that like mosquitos deal with pesticides: A whole lot of them die, but eventually a tiny minority has the right genes that make them resistant, and you get a new population of mosquitos, with different genetics. So by adapting technologically, our evolutionary pressures change completely.
Algernon's law essentially says that biologically simple, major changes to human intelligence are very unlikely to have been strictly better in the ancestral environment, or else they would have happened already. Let's look at Wikipedia's article on the Flynn effect and go down the list of major proposed causes:
> Schooling and test familiarity / Generally more stimulating environment
This one doesn't postulate an actual improvement in intelligence, though it might explain why the test scores are rising.
> Nutrition
Better nutrition has not been easy for most of human history, so this one is fine.
> Infectious diseases
Shifting childhood metabolic effort away from fighting off diseases is one of those tradeoffs mentioned in more detailed discussions of Algernon's law -- if you happen to be in a low-disease environment then, sure, that frees up resources for other things.
