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I am not really certain that you comprehend the approacch that Slifkin calls “Rational Judaisim”.
Slifkin takes the approach that every word that Chazal said they meant literally and since there are certain things Chazal said that do not hold up to modern day science we therefore can disprove them and state Chazal only Knew the Science of their times.
The traditional Mesorah has been that Chazal knew far more then the science of their times both from a Mesorah on certain things from Sinai as well as a deep Kabbilistic understanding that taught them about the makeup of the world.
That is the discussion.
Did Chazal know a great deal more then what the scientists of their day knew?
The traditional opinion is yes.
Slifkin disputes it, The Rambam that I qouted you from Chelek states that anyone who thinks Chazal were limited to the knowledge of their day is a fool.
Now a consequenc of this is as follows.
If one feels Chazal knew more then the Science of their days then when they say things that have been proven wrong the question is whether or not we simply dismiss it by stating that they were wrong ch”v.
Or rather do we state that Chazal knew the truth and were trying to conceal sodos (The Ramchal, and Vilna Gaon’s approach amongst others).
Slifkin says Chazal thought what they thought we know they were wrong.
The Rambam says Slifkin is a fool. (Again I provided the translation).
Now what was the intention of Chazal at times was? Well at times it was not to be taken literally, according to us.
According to Slifkin;.
Well he thinks it was to be taken literally.
This is just one area of dispute.
There are many.