Question: Maulana you had once said: 'Every program has a programmer.' Who would then be the programmer of God, according to this theory?
This question has been debated since a very long time. I have read a lot about it and thought considerably on the subject. The only answer to this question is that we human beings must accept our limitations. There is no other answer to this question.
A human being cannot look directly at the sun. If we do so, we will lose our eyes. We humans have no knowledge about 95% of the stuff of the universe. We can only see and have knowledge of 5% of the contents of the universe. We cannot even see gravity. 
Newton had said that the earth has gravitational pull. But to this day, the subject of gravity has not been completely settled and debate is still going on about it. There are billions of such things which we cannot see or cannot know. Then how can we comprehend God? Those who ask this question are, in other words, proclaiming: "My capacity is so vast that I can comprehend God. I can encompass God in my knowledge." But this is impossible for a person to achieve. So, the answer to this question is given in the Quran in these words: "You have been granted but little knowledge." (17:85)

Science has for the first time acknowledged that science gives us but a partial knowledge of reality. What is the meaning of science? The human capacity of observation is such that we can only know very few things. Science is the utilization of human capacity to observe and perform experiments. I believe that science has established a very important truth. There is a book titled, 'The Limitations of Science' by science writer J.W.N. Sullivan. He explains in the book that science gives us but a partial knowledge of reality. This statement is applicable to the entire scientific community. For the first time it has been academically established that we humans can attain only partial knowledge based on our senses and the instruments we have developed. 
We must, therefore, reflect that when a creature can see and understand the creation only in a partial way, how can this creature completely comprehend the Creator of all things? We cannot do so. 
According to me, we must accept that science gives us only a partial knowledge of reality. We have reached a stage which gives us only partial knowledge, then how can we comprehend total knowledge?

All scientific developments have made us arrive at a stage which has informed us that we can only attain partial knowledge. If we seek to possess total knowledge, then this would be an incorrect question to pursue.