It would be appropriate to present an example for showing the method of deliberation over the Qur'an and understanding its meaning. For example, someone who recites the following verse:
"Have you observed the water which ye drink?"
- Holy Qur'an (56:68).
Should not limit himself only to think about the phrase water and its apparent meanings and taste, rather should ponder about it from various dimensions. For example: He should pause and think all the plants of various colours, different species of animals which are found in this world all have been created by this water. He must think about the human being who has been created with water; in addition to his having apparent visible capabilities such as eyes, ears, and tongue also possesses inner-self and strange inner-power so much astonishing that it could help ascend him towards the most higher sublime spiritual stations.
He must ponder that this same man created by water possesses an
inner-self so marvellous, astonishing, and vast as though the entire world of creation has been miniatured in his inner-self; it is from this consideration that he is regarded as a separate entity called a smaller-world (jahan-e-asghar) as compared to the world of creation which is called the greater-world (jahan-e-akbar). And in accordance to a more delicate and sophisticated interpretation a human being represents a greater-world as compared to the world of creation being a smaller-world.
Then he must ponder that the water which is needed by all the plants, animals, and human beings, in itself, as told in the Holy Qur'an is a manifestation of Allah's blessing. Further he should think that Allah's blessing is His characteristic which cannot be separated from His Holy Essence, which would make him aware that Allah is the fountain-head and source of all things. Such deliberations are the basis and background of attaining spiritual contemplation (shahud)[21] and I believe that whoever will deliberate about every thing in this manner, would be able to test the following tradition narrated by Imam al-Sadiq [a] and its truth would become explicitly clear.
"I never saw a thing but saw Allah, before, after, and with it."
Another method which should be mentioned is that: it would be appropriate if the reciter of the holy scripture should deliberate and pause more and more in order to comprehend the meanings and objectives of this great heavenly book more profoundly as follows:
A. One of the method is to deliberate about the lifestyles of prophets. We know that those noble ones in spite of possessing all those sublime spiritual positions and Allah's nearness were inflicted with severe hardships and difficulties in their personal lives. On the one hand they were inflicted with hardships like poverty and sicknesses, while on the other hand they were confronted with severe enmity and assaults from their enemies, who not only persecuted them through cursing, slandering, and impeaching but also tortured and even executed. And in this manner Allah (the Glorious, the Exalted), trained them through infliction of different types of calamities, to the extent that their leader who was the beloved and most dearest of Allah had to say:
"None of the prophet was tortured and suffered like me."
If, the reciter of the Holy Qur'an ponders about the suffering and torture of the divine prophets, he will discover the following constructive points:
that the Majesty, Splendour, and Magnanimity of Allah are so great that noble personalities of prophets in spite of their possessing all that dignity and grandeur are humbled before the divine will and wisdom and no one could dare to criticise Him.
that because of obedience and worship (offered by him) should not expect that Allah (the Glorious, the Exalted), will do things according to his desire, or worst than that he might expect such a thing compulsory upon Allah (the Glorious, the Exalted).
that if he is inflicted with poverty, diseases, and other hardships in his life, he should never feel hopeless from receiving Allah's blessings and favours.
that one should never reprimand a believer because of being inflicted with calamities.
that one should never regard a believer as insignificant, because, of his being in a state of poverty and possessing nothing; may be his poverty and destitution could be an indication of his greatness (karamat).
that the world is quite insignificant and worthless before Allah (the Glorious, the Exalted), and accordingly he too should not regard the world as great and should never feel sorry and unhappy from loosing it.
that inclination of world towards a person will be indication of his being distant from the privileged spiritual station of Allah's nearness, and world's disinclination towards a person would be an indication of his righteousness and salvation, as it was revealed to Prophet Moses [a]:
"Whenever poverty comes to you say: O' the indication of righteous ones welcome! And whenever wealth approaches you say: the penalty of sins has arrived before their commitment."
B. The other examples upon which he must deliberate are the penalties, punishment, and divine limits which have been prescribed in the holy scripture and shari'a for the sinners. For example, he must ponder that the divine punishment for theft of even one fourth Dinar - which apparently is an insignificant sin - is cutting of hand. Therefore, he will realize how much Allah's wrath and punishments, transgression against Allah's commands through indulgence into major sins would bring. And therefore, this deliberation would become the basis for causing his heart fearful of divine wrath and severe punishments, thus, in order to keep himself immune from them would be mindful of his speaking and other actions; will try to abstain himself from the heart's and tongue's sins which are committed by human beings every day.
C. Another example which must be pondered by reader of the holy scripture is the life histories and deeds of past generations, who were destroyed because of divine wrath. Prophet Jesus [a] asked one of them:
"For which of your deed you have been tormented with such horrible punishment? He replied: 'we loved the world like a child who loves his mother, followed the sinners, had little fear and lot of big desires and spent our lives negligently by indulging into worldly amusements.' Prophet Jesus asked: 'What was their punishment and destruction?' 'In the evening they went to their comfortable beds and were struck by divine wrath', he replied. 'What was it?' the Prophet asked. 'The fountains of Hell-Fire which engulfed us till the Day of Judgement.' He replied. Prophet Jesus [a] asked: 'What did you say and hear?' 'We said, if you return us to the world, we will become righteous and pious and were told that you are liars', was the reply. When asked: 'How come no one else except you respond to me?' 'The angels of divine wrath and punishment closed their mouths with Hell-Fire, and therefore they were not in a position to open their mouths; and the reason that I am in a position to speak is - that I did not belong to them and was not with them, but since I was among them when divine torment struck them, it also engulfed me; right now, I am sitting at the brink of Hell and don't know what would happen? Whether I will fall inside it or would be rescued?' he replied."
Therefore, we must ponder about their affairs and must learn a lesson from them. For example, one of the past nation (ummah) whose fate is a warning are the "Saturday (sabbath)" companions (Ashab-e-Sabt) whose faces, were changed as pigs and monkeys, and were destroyed on account of divine wrath and punishment. The one who recites their story in the Holy Qur'an after pondering about their fate must pause and think about his own affairs, lest his own actions and deeds might be similar to theirs.
Yes! Such deliberations and pondering were responsible for taking away comfort and sleep from the eyes of gnostics and righteous ones, and caused them to recite the following slogan:
"How can one who is not immune from his tomorrow, sleep comfortably; one who does not know about his condition the very next morning". These thoughts forced them to look into the mirror repeatedly every day, lest their face might have became blackened, or metamorphosed due to their sins.
[21] shahud: the witnessing of Allah (the Glorious, the Exalted), that excludes any awareness of self and that takes place through the agency of Allah (the Glorious, the Exalted), himself, not by means of any organ or vision, whether outer or inner [Tr.].
source : http://www.al-islam.org