The Slifkin controversy got me thinking about the issue of science and Torah and how they relate. Until this came up, I never gave these issues much thought, they were theoretical issues with little or no practical relevancy. In truth there are other issues that bother me more.
For example, the portrayal of certain characters in Tanach. When you read chumash, Yehuda sees a prostitute and sleeps with her, yes the Maharal says he was mekadesh her, others give other explanations but the bottom line is can you imagine whatever gadol (fill in whoever you want, the Chofetz Chaim, R' Shlomo Zalman, R' Moshe, etc.) doing that? I can't and yet Yehuda did. Something has to give here. The same with David, fine he didn't sin, but he clearly did something wrong there. What about Yitzchak and Rivka "m'tzachakim" where Avimelech could see them? Yaakov being attracted to Rachel (beauty) more then Leah? There is no end to these kinds of questions on the characters in Tanach. The Haredi world certainly doesn't deal with these questions, but I grew up in the MO world, went to YU, semicha, and never in my education were these issues dealt with either.
Another example is when we have a machlokes in halacha that is very relevant that seems to either raise questions as to the mesora or is based on a misunderstanding of science. How can we have a machlokes Rashi and Rabbeinu Tam as to what parshiyos go in tefillin. Haven't Jews been wearing tefillin for thousands of years? What were people wearing before Rabbenu Tam? When the gemara in Berachos (22b) talks about takkanos ezra, the Gemara asks why don't we check what exactly Ezra was m'taken. Tosafos points out that because it was a very common everyday occurence it was known to everyone, so too I would think is the mitzva of tefillin.
The machlokes about when tzeis hakochavim is a machlokes where the position of most of the Rishonim is very difficult. As the Gra states "hachuch makchish", well before 72 minutes after sunset it is pitch black out. And yet, most of the Rishonim hold this way, and the shulchan aruch paskens this way.
These questions relate to our every day practice and are not just theoretical and bother me a great deal.