Talking about Man is not just physical being but there is another important faculties which should be give an intention to. Physical being is something we could get it through our senses. Let me simplify it, we see the stones as a physic/material and we touch it with our hand while the hand itself also refer physically. Understanding man physically and discussing about a sensible object doesn't mean anything without knowing the meaning of thing. Man has a dual nature, he is both body (jism) and soul (nafs), he is at once physical being (jism) and spirit (ruh). How does it work? let me explain briefly.
Allah has taught Adam the names (asma') of everything (Al-Baqarah (2): 31). By the "names" we infer it means the knowledge (ilm) of everthing (al-ashya'). This knowledge doesn't encompass knowledge of specific nature of the essense (ad-dhat) or the inmost ground (al-sirr) of a thing (shay'). So where is Knowledge (ilm)? because all the things in this world are the object of knowledge from God. I think we understood already the physic and the object that able to discern in this world (all of them are His sign).
The seat of knowledge in man is a spiritual substance which is variously referred to in the Holly Qur'an sometimes as his heart (al-qalb), or his soul or self (al-nafs), or his spirit (al-ruh) or his intellect (al-aql).
Thus when it is involved in Intellection and apprehension and also abstraction of object of the external world it is called "Intellect (aql)". that is why man has the power of faculties to indicate right and wrong to attain bright destiny. So, we have also the choice for better (ikhtiyar) left to some one. When it is engaged in receiving intuitive illumination it is called "Hearth (qalb)"
When it governs the body it is called "Soul (nafs)". Soul also has hierarchy there are; tranquil soul (al-nafs al-muthmainnah) is when inclines itself towards the right direction until it achieves tranquility in the remembrance of God. Secondly, the soul that censures itself (al-nasf al-lawwamah), it is the soul that sometimes his intellectual power and encounters the intelligible whereby thier their eternal truths cause it to affirm its loyalty to God; and sometimes its animal pwoers drag it down to the lowest foothills of the bestial nature. and lastly the soul that incites to evil (al-nafs al-amarah bi 'al-su'), it is bestial nature and remains captive in that condition.
when it reverts to its own world of abstract entities it is called "Spirit (Ruh)", When human is passed away it causes the death of the external senses involving that of the body as a whole. As I sad earlier, these fourth are the seat of knowledge in man that are a spiritual substance while the body as whole is used to give the conception from these spiritual substances and give the images to the other human being or man.
Analogically, I am Zakki. One day, I went to my lecturer's room for consultation then I zakki as a student. I am Zakki, when I was with my parent I must be Zakki as her kid while I was in front of my sisters, I still Zakki but I as his brother. The same person (zakki) but different names or function accordingly.
I just write down here the brief understanding the seat of knowledge. May Allah Guide us to understand His sign in the world so that we can His amanah (responsibility) in this world properly.
For further reading, you may read; Prof. Dr. Syed Muhammad Naquib Al-Attas, Prolegomena to the metaphysics of Islam.