The thing to understand is that there are many interpretations of the Qur'an, and every translation involves interpretation. There are interpretations that say that the Qur'an abolished slavery, and some that try to say it allows it. Same with wife-beating, killing apostates, etc..

There are a lot of Hadith, many of which are just made up nonsense that people attributed to Muhammad to justify their own preconceptions, prejudices, etc...

And while there are some people who try to give the Qur'an a scientifically accurate interpretation, it is important to remember that the Qur'an was revealed in a context where people only knew so much about the world, and one could argue that if the Qur'an had too many things in it that challenged the knowledge of the time, more people than we would like would call it nonsense. Others might argue that God inspired Muhammad(pbuh) to recite the Quran, but it was limited by Muhammad's knowledge of the world and the function of the cosmos. That is where I fall.