Qur’an is a Book of Signs
For a Muslim, it very important to have complete belief in the 6 Pillars of Eeman (Islamic Faith) (i.e, Allah (Subhana wa Ta’ala), the Angels, the Prophets (From Adam to Muhammad (Peace be on them all)), the Revealed Books (Torah, Zaboor, Injeel and Qur’an), Pre-Destination (Qadr) and Judgment Day.
(For details on each Pillar of Islamic Faith, you can have a look at the Video Lecture of the same at www.qsep.com)
Let’s take an example. We pray 5 times Salaah with specific actions and positions. We have come to know now that the position of Prostration in Salaah is a healthy meditation position. That shouldn’t necessarily be a reason for us to offer the 5 times Salaah. The reason should be that it should be offered as it is the Order of Allah (Subhana wa Ta’ala), which is nothing but confirming the Islamic Faith. The following narrations of the Prophet (Peace be upon him) are self-explanatory in establishing the Faith and following the Order of Allah (Subhana wa Ta’ala):
Jabir reports that the Prophet (Peace be upon him) said,
“Between a person and disbelief is discarding prayer.” 
Buraidah reported that the Prophet (Peace be upon him) said,
“The pact between us and them is prayer. Whoever abandons it is a disbeliever.” 
So, if a Muslim sees the modern day scientific establishments, it should help him re-affirm his faith. But, the case should not be vice versa, that only because of the proofs or scientific establishments he has faith in Allah and the 5 pillars of Faith. This can lead him to the danger of rejecting those articles of faith, which have not been established by modern day science.
Coming back to the subject, Allah (Subhana wa Ta’ala) tells us in the Qur’an that lots of signs will be established to confirm that Islam is the Truth. And according to me, the scientific discoveries in this era are affirming what Allah (Subhana wa Ta’ala) has hinted us in the Qur’an more than 1400 years back.
“Soon We will show them our signs in the (farthest) regions (of the earth), and in their own souls, until it becomes manifest to them that this is the Truth. Is it not enough that thy Lord doth witness all things?” 
The Arabic word used is ‘AAYAAH’ which literally means ‘signs’, and which is really more to the point. The Holy Qur’an does not mention the word ‘MU’JAZAH’ (miracle). 
Dr. Zakir Naik’s elaborates on this as follows:
“Let me remind you that the Qur’an is not a book of Science, ‘S-C-I-E-N-C-E’ but a book of Signs, ‘S-I-G-N-S’ i.e. a book of ayaats. The Qur’an contains more than 6,000 ayaats, i.e. ‘signs’, out of which more than a thousand speak about Science. I am not trying to prove that the Qur’an is the word of God using scientific knowledge as a yard stick because any yardstick is supposed to be more superior than what is being checked or verified. For us Muslims, the Qur’an is the Furqan i.e. criteria to judge right from wrong and the ultimate yardstick which is more superior to scientific knowledge.”
 Related by Ahmad, Muslim, Abu Dawud, at-Tirmizhi and Ibn Majah
 Related by Ahmad, Abu Dawud, at-Tirmizhi, anNasa’i and Ibn Majah
 Al-Quran, Surah Fussilat 41:53
 From Al-Quran-Miracle of Miracles by Ahmed Deedat
 Qur’an, Surat ar-Rum 30:22