Here's an issue that I haven't heard much about: Bereishis 30:32-43 vs. Genetics.
The process by which Yaakov arranges for lambs to look a certain way are not conventional. So what do we say?
Here are some preliminary ideas:
- Yaakov did all this 'al pi kabbalah'/magic
- Gentics is wrong. All Dor Yesharim clinics should be burned.
- Yaakov was using the best science available in his day (his 'hishtadlus'), and HKB"H made it work for him miraculously
- Good ol' 'nishtanu ha-teva'im'
- Yaakov really used genetics, but since the 'dor ha-midbar' wouldn't have understood, the Torah described the events in a way that would make more sense to them.
Of course, the notion that the male's thoughts during conception affect the nature of the offspring is common in Chazal and all the way until late medieval times. The well-known Gemara in Nedarim which describes 9 different types of flawed conception is an excellent example. Perhaps that's what Chazal meant when they opined that 'the semen originates in the head', and not that Chazal had an incipient knowledge of the human endocrine system, as RAF suggests. They were probably basing themselves on observation: it's obvious that male sexuality can be aroused by what he sees, hears, smells, etc. That, in turn, affects what goes on in other extremities. Thus, something must be 'transmitted' from the brain to the extremities, and the original circumstances of the 'seed' in the brain will determine it's nature. This is a perfectly good explanation until one employs the scientific method.
Thus, as much as I don't like to say it, option #3 above would seem to be the best reconciliation of Torah mi-Sinai with genetics in this instance. I'm all ears for a better explanation.