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Shaykh al-Islam Ibn Taymiyyah writes:
As for the saying of the one who said, "Where does it (the soul) reside in the body?" Then there is no specification of any particular part of body for the soul, rather it flows through the body (as a whole), just as life, which is a temporal attribute ('arad), flows through the entire body. For life is conditioned by the soul, if the soul is in the body, it will have life, and if the soul departs from it, then life departs from it. Comment
In light of these words we can say the following: The faculty of reason, intellect (عقل) is not isolated and specificied to just one organ in the body exclusively, rather it is ascribed to the soul and body combined and then in turn, as it relates to the body, it is "connected" (متعلق) to the heart and brain. Note also that (عقل) is not an independent entity but an attribute that can be absent or present and can have strength and weakness, abundance and scarcity in a person. Further, we should also bear in mind the definition of reason (عقل), which Ibn Taymiyyah explains on numerous occasions and the essence of that can be explained by the following summarization, "Reason is collectively: knowledge by which what is beneficial is distinguished from what is harmful and then acting upon the dictates of that knowledge, as in, what this knowledge necessitates of action, hence a person traverses the ways to attain what is beneficial and traverse the ways by which harm is avoided." Thus reason incorporates both knowledge (ilm) and action (amal), and underlying action is desire (iraadah). And because imagination and conception is required by the heart (for it to desire what it desires), then the brain plays that role since reflection, thought (fikr) and observation (thought) is processed through the brain, so that begins with the brain (from sensory input) and then that goes to the heart which then "desires" on account of what is brought to it and when that is completed in the heart it raises back to the brain again. The brain then implements what the heart desires since the brain is a delegated control system for the activities of the limbs and organs (hands, feet, vision, speech, thought). However, the seat of all of that is the heart, since it is the heart that is ultimately desiring and the brain is delegated to the implementation. The heart drives and the body follows. And in this processs, the brain contributes to the element of thought and imagination that is then input to the heart and when processed by the heart for the formulation of the desire (iraadah) the matter is sent back to the brain and the brain is the delegated control mechanism for verbal speech and physical action. With this, any confusion or doubts should be settled inshaa'Allaah, and it is clear that reason (عقل) is an attribute of the body as a whole inclusive of the soul, the heart and the body. However since the heart desires (iraadah) as a result of which chosen action arises, it is the seat and the driver. Because reason is defined as acting upon what one knows to benefit and refraining from what one knows to harm, then the heart, from this perspective, is clearly the seat of reason. Ibn Taymiyyah says in al-Majmoo' (16/36): "However, that which is praised is the beneficial knowledge whose possessor acts upon, for if the one possessing it does not act upon it, then he does not have aql (reason, intellect)." And Sufyan bin Uyainah (d. 198H) said (as relayed by Ibn Abi al-Dunya): "The one who knows good from evil is (not the one who is intelligent) but the intelligent is the one who knows good and follows it and knows evil and avoids it." In these quotes we understand that it is chosen action that defines true reason, and the foundation of that is the iraadah (desire) of the heart.
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Imam al-Dhahabi's Biography for Ibn Taymiyyah in the unpublished volume of Siyar A'laam al-Nubulaa
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