Can religion be questioned? When religion contradicts science, which side should we take?

Shri Durgaprasad asked: Paadanamaskaaram Swami,

1) In a discussion on recent supreme court rulings on homosexuality and adultery, one person commented like this:

We are not copying from the west..the west has copied from us....anyway everything depends on where you draw the line in the timescale. And adding religious tag to common moral values is harmful because the very nature of established religions do not allow questioning..and ppl get sentimentally hurt on any questioning on religion. And centuries if religious values didn’t make our countrymen honest. Societies where majority are atheists are way ahead of us in common honesty...

2) One another problem the new generation is facing is, which side to sway when the science and the religious reasoning contradict..... Should we sway towards religion or science??

Please enlighten on this. At your lotus feet, -Durgaprasad

Swami replied (for both 1&2):- Whether it is religion or science, one can find the truth only through reasoning, which involves sharp and deep analysis. Scripture is also not an exception for such analysis because we cannot be sure whether the scripture is a genuine version or an adulterated version with insertions made by ignorant people in the course of time. During the process of reasoning, we can distinguish between the genuine concepts and the adulterated concepts. Even divine preachers did the same in writing commentaries on the scriptures. The commentaries varied in their conclusions due to such adulteration of the original text. Due to this reason, we often find mutually contradicting concepts within the same scripture. You should understand the path of these divine preachers, who wrote commentaries on the scriptures. The path is that you should not accept anything without deep and sharp analysis. People, who dislike the questioning of scripture, should answer why there is a difference in the commentaries written on the same scripture.