If we're talking about designer babies, I can think of four reasons that this might be a bad idea.
1) The technology will probably not be readily available to poor people. This creates potential for the wealthiest families/countries to produce smarter, stronger, healthier children than the poor families/countries, creating a self-perpetuating cycle of eugenic disparity between the rich and the poor. This could lead to a new form of feudalism, except now the aristocrats really are superior. Call this the 'genetic aristocracy' effect.
2) Society and the market may decide that babies should be designed as a matter of moral principle. It would start with society demanding that all babies are screened for disease genes, but then they may demand that babies are as smart as possible, or strong, etc. This may lead to genetic discrimination. Call this the Gattaca effect.
Interestingly, a law was recently passed in the US outlawing genetic discrimination. However, this should be taken more as a sign that it will happen and congress knows it, rather than a sign that it won't.
3) If the technology is developed, governments may use it to produce (probably covertly) a generation of children better suited to serving their own ends, which would be children that are healthier, stronger, dumber, and more prone to indoctrination. Over time, using a combination of eugenics and aggressive indoctrination, it may be possible to create a lower class of humans, barely conscious, bred only to fight war and keep the peace (and trust God/the government). Call this the 'anti-aristocracy' effect.
4) Evolution works best when you don't interfere. Humans may think they know nature's tricks, but no one is cleverer than evolution when it comes to survival. By creating a generation of designer babies, we may inadvertently select out a key gene the immune system uses to fight off viruses. Because of this, humans may not be able to fight off the next plague, and this would make humanity more vulnerable to extinction.
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