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Summary of question
What is meant by this saying of Imam Ali, "Do you suppose that you are only a small body, while the macrocosm is placed within you?"
There is a narration of Imam Ali (as) which says: "You think you are a small entity, but within you is enfolded the entire Universe". I don't really grasp the meaning of this saying. I assume that there is a deep significance behind these words. I would like you to enlighten me with its meaning.
Concise answer
Some mysticism and literary books have ascribed poems to Imam Ali (A.S). For instance, it has been said that Imam Ali (A.S) said: "Do you suppose that you are only a small body, while the macrocosm is placed within you?" Although this poem does not have a chain of transmission, it has a profound meaning. It pinpoints man's real position and status which he is able to achieve and attain but he is not mindful of it and therefore he continues to think that he is a useless body.
Detailed Answer
What has been put forth in the question is, in fact, referring to some poems which have been ascribed to Imam Ali (A.S). The original Arabic version of the poems are as under:
َدوَاؤُکَ فِیکَ وَ مَا تَشْعُرُ
وَ دَاؤُکَ مِنْکَ وَ مَا تَنْظُرُ
وَ تَحْسَبُ [تزعم] أَنَّکَ‏ جِرْمٌ‏ صَغِیرٌ
وَ فِیکَ انْطَوَى الْعَالَمُ الْأَکْبَرُ
وَ أَنْتَ الْکِتَابُ الْمُبِینُ الَّذِی
بِأَحْرُفِهِ یَظْهَرُ الْمُضْمَر[1]
'O man, the cure to your ailment is within you and you do not know; and your pain is also from you but you do not see.
Do you suppose that you are only a small body, while the macrocosm is placed within you?
O man, you are a clear book with whose letters every invisible thing becomes visible.
Indeed, man is the sensible world with the sensible world; and he is angelic world with the angelic world and is an angelic power with the angelic and sovereign power.[2] This power rests only with the man who has incorporated various dimensions within him and this poem only signifies this point.
Chain of Transmission of the Narration
This poetic narration has not been reported in first hand Shia sources and it is found and ascribed to Imam Ali (A.S) mostly in literary and mystical works authored in the seventh Islamic century onward. [3] Also, this poem is reported in a book titled, the Commander of the Faithful (Amir al-Mumeneen) which has been authored in the ninth hegira century.[4] It should be noted that no chain of transmission has been reported for these poems. Also, these poems can be found in the books authored by more recent scholars.[5] However, the content of these poems are acceptable and very profound and there are many books,[6] especially mystical works that have reported them.
Content of the Narration
These poems seek to state man's real position and place which is attainable by man. As well, they seek to reject the nihilist and materialistic approach and assumption which man has of his own self. There are different interpretations for this poem which shall be mentioned in brief:
A) "Do you suppose that you are only a small body, while the macrocosm is placed within you?" Although this poem has been interpreted in different ways, all of the interpretations signify man's greatness and dignity. Having said that, we shall now mention the interpretations of this poem:
1. Man might, from a simplistic view, consider himself as being purely physical and earthly whereas, in fact, this earthly body has within itself numerous miracles and divine signs. Man is a scaled version of this world incorporating all magnanimities of this world from simple to compound; from material to abstract.[7] In other words, man should take notice of this point that there is no sign in the universe except that there is the like of it in man.[8]
Thus, the interpretation of this poem can be considered as having the meaning of the following verse of the Quran:
«وَ فىِ الْأَرْضِ ءَایَاتٌ لِّلْمُوقِنِینَ * وَ فىِ أَنفُسِکمُ‏ْ  أَ فَلَا تُبْصِرُونَ»
"And in the earth there are signs for those who are sure, and in your own souls (too); will you not then see?"[9]
The following Persian poems also refer to the same meaning:
اى نسخه اسرار الهى که تویى
وى آینه جمال شاهى که تویى‏
بیرون ز تو نیست آنچه در عالم هست
در خود بطلب هر آنچه خواهى که تویى[10]
You are a copy of divine secrets; a mirror reflecting the beauty of the king. What is in the universe is in you too. You should seek from yourself what you are looking for since you are the compendium (of the universe).
2.  Man has soul in addition to the material and physical body. He possesses the power to make advancements, to go ahead and achieve higher position. There is reason or intellect even in the human physics and if we consider man's body as the criterion, we will still find him superior to other beings. All these make him superior and better than other beings and man has been reminded not to consider himself only as a material being since he has a lot of potentialities and capacity that help him achieve further perfection and higher positions which are not attainable for other beings.
Some have also made reference to man's knowledge which stems from divine knowledge.[11] Some have referred to the general soul and intelligence[12] existing in man; some to his knowledge and action[13] and some others have made mention of man's ability to learn the divine attributes and it is for these reasons that man has been considered as incorporating the greater world.[14]
و أنت الکتاب المبین الذی
بأحرفه یظهر المضمر
The fact that a perfect man[15] is called "book" has been pointed long before and it has been used for man amongst divine saints and noble men of God.[16]
In this connection, there is a narration attributed to Imam Ali and Imam Sadiq, peace be upon them who say: "The human face is the greatest of divine proofs for God's creatures and that is a book which God wrote with His (mighty) hand as well a structure which God built up with His wisdom."[17]

[1] Meibudi, Hussein bin Mu'ein al-Deen, Diwan Amir al-Mumeneen (A.S), researched and edited by Zamani, Mustafa, p. 175, Qom, Dar Nida al-Islam for Publication, first edition, 1411 A.H.
[2] Imam Khomeini, Sharh-e Dua-e Sahar, p. 7, Qom, Institution for Preparation and Publication of Imam Khomeini's Works, first edition, 1416 A.H.
[3] Sekandari (d. 709 A.H.), Ahmad bin Ataullah, Al-Lataif al-Ilahiya fi Sharh Mukhtarat min al-Hekam al-'Ataeyah, p. 16, Beirut, Dar al-Kotob al-Ilmiyah, first edition, 1424 A.H.; Qaisari (d.751 A.H.), Dawood, Sharh Fosus al-Hekam, researched and edited by Ashtiani, Sayyid Jalaluddin, An Introduction by Qaisari, p. 91, Tehran, Scientific and Cultural Publications Company, first edition, 1375 (solar), Amuli, d. after the year 794 A.H., Sayyid Haider, Tafsir al-Mohit al-A'zam, researched and corrected by Musavi Tabrizi, Sayed Mohsen, vol.1, p. 254, Tehran, Printing and Publishing Organization affiliate to Ministry of Islamic Guidance, third edition, 1422 A.H.
[4] Mawlana Shouqi, Diwan Imam Ali (A.S), researched and corrected by Rawzatian, Sayyeda Maryam, p. 62, Tehran, Anjuman Athaar wa Mafakhir Farhangi, first edition, 1383 (solar).
[5]  The First Majlisi (Majlisi Awwal), Muhammad Taqi, Rawzatul Muttaqin fi Sharh man La Yahzuruhu al-Faqih, researched and corrected by Musavi Kermani, Sayyed Hussein, Ishtihardi, Ali Panah, Tabatabai, Sayyed Fazlullah, vol.2, p. 81, Qom, Kushanpour Islamic Cultural Institute, second edition, 1406 A.H.
[6] Tafsir al-Muhi al-A'zam wa al-Bahr al-Khazm, vol.1, p. 254; Kashefi Sabzewari, Hussein bin Ali, Mawahibun Alayhi, researched by Jalali Naeni, Sayyed Muhammad Reza, p. 1080, Tehran, Iqbal, 1369 of the solar calendar.
[7]  Turaihi, Fakhr al-Deen, Majma' al-Bahrain, researched by Husseini, Sayed Ahmad, vol.4, p. 48, Tehran, Murtazawi Bookstall, third edition, 1375 (solar).
[8] Husseini, Shah Abdul Azimi, Hussein, bin Ahmad, Tafsir Ithna Ashari, vol.12, p. 261, Tehran, Miqat Publications', first edition 1363 (solar).
[9] Adh-Dhariyat, 21.
[10] Banuye Isfahani, Sayed Nusrat Amin, Makhzan al-Irfan dar Tafsir Qur'an, vol.15, p. 372, Muslim Women's Movement, Tehran, 1361 (solar).
[11] Mulla Sadra, Muhammad bin Ibrahim, Tafsir al-Qur'an al-Karim, researched by Khajawi, Muhammad, vol.4, p. 391, Qom, Beidar Publications, second edition, 1366 (solar).
[12] Khomeini, Sayed Mustafa, Tafsir al-Qur'an al-Karim, vol.1, p. 360, Institute for Preparation and Publication of Imam Khomeini's Works, first edition, 1418 A.H.
[13] Sadruddin al-Shirazi (Mulla Sadra), Sharh-e Usul-e Kafi, researched and corrected by Khajawi, Muhammad, vol.3, p. 34, Tehran, Cultural Research and Studies Institute, first edition, 1383 (solar).
[14]  Faiz Kashani, Muhammad Mohsen, Al-Wafi, vol.2, p. 319, Isfahan, Imam Amir al-Mumeneen Ali Library, first edition, 1406 A.H; Majlisi, Muhammad Baqir, Mir'at al-Uqool fi Sharh Akhbar Aal al-Rasul, researched and corrected by RAsuli, Sayyed Hashim, vol.3, p. 272, Tehran, Dar al-Kotob al-Islamiyah, second edition, 1404 A.H.
[15] Vide: Human being and Humanity in Gnosticism, question 11573; Lordship and Perfect Man, question 3416.
[16] Faiz Kashani, Mulla Mohsen, Tafsir al-Saafi, researched, A'alami, Hussein, vol.1 ,p. 92, Tehran, Al-Sadr Publications, second edition, 1415 A.H.
[17]  «الصورة الإنسانیة هی أکبر حجج اللّه على خلقه، و هی الکتاب الّذی کتبه بیده، و هی الهیکل الّذی بناه بحکمته ... » Sawari Mazandarani, Muhammad Saleh bin Ahmad, Sharh al-Kafi (Usul wa al-Rawzah), researched and corrected by Sha'arani, Abul Hasan, vol.1, p. 128, Tehran, Islamic Library, first edition, 1382 A.H; Hashemi Khoei, Mirza Habibullah, Minhaj al-Bara'ah fi Sharh Nahj al-Balaghah, researched, Mianani, Ibrahim, vol.19, p. 289, Tehran, Islamic Library, fourth edition, 1400 A.H.
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