It appears you know everything about everything except for one detail. You don't comprehend your bible because you simply don't how to separate revelation from science.
Applying the scientific method to revelation leads to foolish statements like the "religious challenge failed". Success and failure are conclusions based on observation. There is no "religious" challenge because the bible isn't a science or history books, but the collections of books about God revealing Himself to man.
Let start with God. There are no God scientific theories because there are no God scientific facts. From Genesis 1:1 we know that God existed before He created everything we can observe. This means that God is in the unobservable as well as the observable He created. For there to be a scientific fact about, we would have to observe the unobservable.
It is clear from the first verse in Genesis that no scientific method can be applied to the bible because it can not even be applied to the first verse. As hard as mankind tries to find God with their observations, their effort are "chasing the wind."
One we realize that the bible can not be understood by science, we are left with faith/belief. “God reveals, man observes” means we need a leap of faith to believe. We quote scripture (sometimes in context, sometime not) because we have nothing else. You may think you have science (scientific method) in scripture, but you don't. We believe we have God word, you may believe otherwise. But the bible is a tool for believers, not a conversion manual for non believers.
You cite a whale that shallow Jonah. Unfortunately, there is no whale in Jonah but a great fish. What kind of great fish? We know nothing of the great fish except that Jonah was in for three days and three nights. Retelling this prophet life is not about fish but about God’s steadfastness. You can run away from doing what God asks, but you can not run from God.
Answer: We have two belief systems: Revelation and Science. What works in one system does not work in the other. There is no God in science; there is no belief without God. Religious Challenge Accepted: The right answer is God.