OH. GOOD. GREIF.
Oh come on it's fun! Don't be mad!

Let's think about the Bible for an instant, a text which in some form or other has endured for THOUSANDS of years. And it was written by people THOUSANDS of years ago. Such people would not have had any concept of the intricate, lengthy processes by which the universe operates, whether it be by breaking down or building up. The ultimate function of Genesis is to relate that there is a form of functional order by which life as we know it came to exist.
So far so good...
This also happens to include God, whom the reader today should understand IS NOT bound to a physical universe or plane of existance as we know it (if you care to consider that God exists, of course).
And how exactly do you know this, other than by revelation?
This is exactly what I meant by special knowledge of the universe beyond "what meets the eye". How can you even know these things?
What you're arguing here is official doctrines and beleif statements, which may vary considerably in ANY broad religious group. Note how even general scientific understanding operates in this fashion, especially in regards to the "bleeding edge" of science. And just like a set of flawed data within a scientific community, if a religious group (which is NOT stagnant) finds their understanding or doctrine to be inaccurate, they will re-analyze their beliefs and make a (hopefully positive) change.
Any religion *has* a bunch of unverifiable unempirical statements about the world preached on faith. As I said previously, they can be more or less minimal about it. But like the above problem I've pointed to you about how do you know god is not bound to this universe, bla bla bla, they all have it.
Any relationship with "bleeding edge" science is flawed, since no theoretical physicist will preach their own version of the cosmos without labeling it with glaring red letters "CALCULATED AND JUSTIFIED SPECULATION", and not write any holy book about it.
Now, regarding the Pope's statement - ultimately understand that he holds to the belief that a God exists. As you noted, this can not be proved or disproved within the scope of the physical universe. Given that he also holds to the belief that human beings are accountable to this God, and that this being has an affect on thier lives, he remains as an important element within their being. So actually, no, there's really not a problem with his statement, considering that this is based around the concept that there exists a being which is not bound to the physical world, yet has an impact on human existance at some level.
He believes in "God", so far so good. He also believes that humans are accountable to him. I have no problems with it. He could believe he's Elvis. I would still have no problems with it. What is problematic in that quotation is not his beliefs on how the world is (for I couldn't care less about that), but his arbitrary ruling that X and Y are out of scope of the empirical domain because they are "Special", they are "souly", they have this extra-special metaphysical sauce(tm) that is, by the pope's definition, out of the domains of science. If this is what he preaches to people, then yes I have a problem with it and I consider it to be against science. Many young people will listen to this and will close their minds to any kind of research to these questions, because they deemed them to be "out of scope of science".
What you seem to be exercising more than anything else is your own personal doctrine,
Not doctrine, opinion. Yes, ghastly, I am opinionated

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...which seems to be one of literalism with regards to beliefs which were never bound to science to begin with. This, you argue, makes religion invalid.
No, my point is that *every* religion *lives by* a set of unfounded and unverifiable claims, and that these are mostly incompatible with the scientific attitude.
However, you fail to understand that religion IS NOT science, but rather a set of principals by which you exist within the world. Many, many accounts in a religious text are situational, written for a specific time and place, when a particular understanding endured. And they serve their purposes accordingly. Because you will not allow yourself to understand this, your misunderstanding of the point that religion and science continues. Science serves to further our understanding of the universe, while religion serves (ideally) to enrich our existance within the universe. The two are not incompatible.
Not only did I assert that religion is the traditional attempt to surpass the humean is-ought problem a page or two ago, but I also find it quite ironically sad that you yourself describe religion as "situational". That's the kind of adjectives we use in Portugal to define opportunistic politics, and that is not, incidentally, a coincidence.
Of course religion is "situational", you see it every day, everywhere. You see this kind of thinking in alternative medicine, for example, where this "living thing" (using Battuta's adjective) adapted and fitted to 21st century language, and thus we are bombarded with "Quantum Healings" and "Magnetic Rings" and sciencey-looking stuff. The point is that it doesn't matter what it does (mostly nothing), but what it
makes people feel it does, kickstarting the placebo effect.
It's the exact same phenomena with religion, with the plus bonus that with religion you get to say to most people that X and Y are "wrong" because "God said so, so there", and that ends the conversation, minimizing any danger of moral degradation, etc. People remember these things and the (unchallenged) authority that comes along with it, and so it's a powerful tool to do just that.
But one just has to look to what many theocratic countries think that their "god" tells them what is the "right" thing to do to a rational person
cringe at this line of argument for religion.