Desert or ancient lake?

I'm watching a show on the History Channel about scientists who believe that the Sahara desert was once full of "mega" lakes. They discovered this via satellite images and followed it up when they discovered shells from fresh water lakes. Now they say that every 20,000 years the Sahara floods. And it goes on and on.

I'm not sure about all that but, if the entire earth was covered with water when it began to subside water would pool in every low lying place and for awhile, even deserts would be full of water and you'd find animal bones, etc. So, is it easier to believe that 90,000 - millions of years ago deserts were once huge lakes? Or that a world wide catastrophe, like a flood with hurricanes, tornadoes, etc. deposited water in places where it didn't exist before and wouldn't exist after.

My opinion is that science, without philosophy, only points to what the Bible already says. It is when Science tries to "theologize" it's findings that you get to the point where anything can happen given millions and billions of years - even rocks turning into monkey's turning into people.

Huh. Interesting.