In an earlier post, I discussed the references in Tenach about the kidneys giving advice. Ibn Ezra explains it as a metaphor, due to his rationalist acceptance of science, and due to his seeing that as license to take the initiative of interpreting Scripture non-literally, even against Chazal (as we shall see). But I gave it as an example of dibra Torah k'lashon bnei adam, as explained by later authorities - that God packages His messages according to the intellectual framework of the people who hear them. Rambam, as explained by Rav Shlomo Fisher, gives a similar explanation in a different context:
Rambam wrote that Ezekiel’s vision of the Divine Chariot was presented to him in a manner that accorded with the view that the heavenly spheres make sounds, and that Mercury and Venus are above the sun, even though the truth is that the spheres make no sound, and Mercury and Venus are below the sun. For prophecy presents itself to the prophet in accordance with his own conception of the world. (R. Shlomo Fisher, Derashos Beis Yishai, Ma’amar Hamo’ach Vehalev, fn. 4)
In the Gemara, it's abundantly clear that Chazal viewed the kidneys as functioning to give us advice:
The Rabbis taught: The kidneys advise, the heart considers, the tongue articulates, the mouth finishes, the esophagus brings in all kinds of food, the windpipe gives sound, the lungs absorb all kinds of fluids, the liver causes anger, the gallbladder secretes a drop into it and calms it, the spleen laughs, the gizzard grinds, the stomach [causes] sleep, the nose [causes] wakefulness. (Berachos 61a)
The anonymous blogger "Not Brisk" refers to my "chutzpah" in saying that Chazal had an incorrect view of the function of the kidneys, and notes that I "don't grasp" that Chazal can have a hidden meaning. Of course, it's not a matter of "not grasping" the possibility of a deeper meaning - there are many sayings of Chazal that are obviously not intended to be understood at face value - but rather, that it is clear that this statement was meant literally, both from context and mesorah.
In this passage of the Gemara, the descriptions of the functions of the tongue, mouth, esophagus, windpipe, lungs, stomach and nose are all clearly literal, scientific descriptions. This is not an aggadic legend intended to be understood metaphorically, like the stories of Rabbah bar bar Chana. Thus, the account of the function of the kidneys is also clearly intended to be a literal description. This is entirely consistent with standard belief in the ancient world (as are the accounts of the functions of the other organs).
Not surprisingly, the mesorah is also that the kidneys literally give advice. There is no Rishon who explains the Gemara metaphorically. Ramban, Rashbash and Rabbeinu Bachya explain the kidneys as having cognitive functions. R. Yehudah HaLevi, R. Yehoshua Ibn Shuib, R. Yaakov b. Chananel Skili (a talmid of Rashba), R. Moshe ben Avraham Provençal and R. Yitzchak Lampronti all address the claim that this is scientifically disproved and rebut it sharply on the basis that our mesorah from Chazal trumps science. Chida claims scientific evidence that the kidneys really do have cognitive functions.
Of course, this position is more difficult to uphold today, when we have dialysis and kidney transplants. Still, the most faithful nevertheless uphold this mesorah. Thus, Rav Ovadiah Yosef advises kidney recipients to choose (where possible) to receive kidneys from Jewish donors, due to the role that the Gemara ascribes to them.
It is thus deliciously humorous that Not Brisk, who declares himself to be defending the view of "the most loyal and faithful among us," takes the approach of out-Slifkining Slifkin. He goes against the straightforward meaning in the pasuk, the clear meaning of Chazal, and the mesorah from the Rishonim and Acharonim, because due to his acceptance of science, he chooses to follow the decidedly non-mainstream opinion of Ibn Ezra (certainly not part of the charedi mesorah!) who himself, due to his knowledge of science, learns the pesukim allegorically and rejects Chazal! What will he accept next - evolution? Oh, the irony!
 See Guide for the Perplexed II:8-9, with the commentaries of Efodi, Shem Tov, Narvoni, and Abarbanel in Ta’anos, 4. For further discussion, see Warren Zev Harvey, “How to Begin to Study Moreh Nevuchim,” Da'at 21 (1988) 5-23 pp. 21-23 (in Hebrew).
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