Should Atheists Applaud a Religious Leader's Endorsement of Science?

There have been many articles and discussions in the media about Pope Francis encyclical supporting protection of the environment. One such post caught my  attention because of its gushing title "Pope Francis just took a huge step to uniting religion with science".  Here was my response to that essay: 

"Sorry. Science and religion still don't mix. One is based on rational inquiry, the other on subjective faith. As for the Pope's stand on the environment, even a stopped clock is right twice a day. In this case however, Francis is only half right. For as long as the Church continues to oppose the right to artificial contraception and family planning, then overpopulation and poverty will continue to degrade the environment."

A cousin of mine who had also read about the Pope's pronouncement  reminded me that the relationship  between religion and science is more complex than meets the eye, and he mentioned that there have been many individuals  in various fields of science who also had ties to religious institutions, e.g. Roger Bacon, a monk who innovated the scientific method. This was my reply:

Yes I know about the blurring of lines between the members of the clergy and scientists. Gregor Mendel was a botanist and a monk. The founder of the astronomical observatory here in Metro-Manila, Federico Faura, was a  priest. But usually these "hybrids" as I call them credit God as the ultimate force of nature which it seems to me would inhibit their scientific objectivity e.g. in cosmological issues , e.g .involving the cause  of the Big Bang or what it means to say that not even time existed before then.

Also I wonder how would theistic physicists deal with the uncertainties in quantum mechanics or the theory that the universe does not have an eternal shelf life: It will eventually end in either in the Big Crunch or in an ever expanding universe wherein the galaxies themselves will unravel and all the stars and living things will eventually die out, leaving "God's creation" as a lifeless entity.

On the other hand, if the universe collapses back to a singularity in the Big Crunch, a subsequent Big Bang could the start the cycle of a new universe all over again. And maybe the universe  we're living in now is not the first one. There could be an infinite sequence of Big Bangs and Big Crunches. But in each such collapse,  life is snuffed out. {"The Lord giveth  and the Lord taketh away"–repeatedly? That's quite an obsessiveness-compulsive complex).. Oh, and what about the existence of a multiverse or parallel universes which some cosmologists hypothesize is a distinct possibility. In these scenarios, is there one god per universe, else why would a supreme being need to create more than one such entity?

And how does a God-believing biologist deal with the fact that as the result of evolution by natural selection and catastrophic occurrences, 99.9% of all  beings since the beginning life on this planet have gone extinct?. What kind of supreme being makes that much trial and error and has to just about start over from scratch each time?  Then there is the brutal fight for survival among many of "the good Lord's" creatures "Nature red in tooth and claw" as Tennyson put it which conflicts with the religious belief of God's love for all living things. 

Probably the easiest way for"hybrids" to deal with these contradictions between theism and science is compartmentalization, i.e.in this case the mental division of religious faith and systematically acquired knowledge into separate methods of thought processing.. Another tack, which is the one that I took  when I was a theist but still also pro-science,  is to consider  God as the ultimate source of  scientific explanations, e.g. God created evolution. This is akin to the attributing God as the first cause of nature as discussed above but refining it to accommodate scientific theory as well. .

But in the end these ruses  are mere denial of the elephants of reality and logic in the middle of the room. In the matter of natural selection for example why would God go through all that time and trouble to develop man when he could have created all life forms that now exist including humans on the spot instead of over billions of years?

In short no matter how religious believers including theistic scientists may try to assert that a supreme being  is the final cause of the universe's existence, they have no evidence to support their claim. And  although religious leaders may make scientific sounding statements that are really only half-hearted and half informed, there's no substitution for critical thinking, and the application of the scientific method in understanding the natural world. To date this objective procedure has found absolutely no evidence of a heavenly creator, and  it's highly unlikely that it ever will.