The prophet Mohammad is not between us [not in the way we can understand in physical word] [And also we cant access Imam Mahdi (Aj)]
so we cant say our understanding from Islam, is the real Islam. because we cant ask prophet and fix our mistakes!
Science is not complete. Number of open questions in Science is too much. and every day may one scientist find something that shows previous concepts that was accepted was false.
like Einstein that showed Quantum physic. and Showed relation between material and energy! which was unbelievable 10 years before him.
Sometimes two things have no conflicts but we think there is one.
for example looking at a cross from two Dimensional perspective shows a cross but looking in three Dimensional area may show a space between them.
the other famous example of this is the elephant in the dark room, 5 men are in the room. each one touch a different part of the elephant and says what it is! one say it is a barrel ( who touched elephants legs) the other says it is a Sweep ( who touched tails) and so on...
the Conclusion of 1,2 and 3 is we are not forced to judge! its not possible for us to know everything so when we reach "Doubt" we don't have to judge!
There is a Hadith from prophet Mohammad in Al-Kafi book (its one of the 4 main hadith books of Shia) 
فمن ترك الشبهات نجا من المحرمات ومن أخذ بالشبهات ارتكب المحرمات وهلك
من حيث لا يعلم.
So Who leave doubts will be saved form Harams(Sins) and who take
doubts will do haram and will perish from something he can't think
so next time we reach a point that we think there is a conflict between our religion and science, we simply do following:
we ask Allah to help us, then we Search on the topic, research and ask professionals and if we don't satisfied and conflict didn't solved, we just leave it! and simply say I don't know! may God show me the truth...
Description & References:
in Shia (My) and part of Sunni believe Imam Mahdi is alive but we don't know where is he.
The Other Sunni's (Most of today's) believe is he is not born yet.
الكافي - الشيخ الكليني - ج ١ - الصفحة ٦٨