Irreducible complexity

I was very much a subscriber to irreducible complexity as a Christian. There are many creatures, appendages, and organs which i could see no logical path for their evolution like the long neck of the giraffe and its small heart-like organs used to keep its blood flowing properly or the bombardier beetle and its explosive concoction of chemicals it uses for defense.
For anyone who is unfamiliar with the concept, irreducible complexity basically a concept that systems could not have evolved because each piece is needed in order for any part to be functional and all parts cannot be functional throughout the evolutionary process meaning it would not be selected for.
I subscribed fully to this idea.
I used to describe it to others like this:
The wing of the bat works great as a whole, but in the evolutionary process it doesn't function and works against its survivability.
Imagine it's a mouse-like critter with long fingers and webbing, at some point it wouldn't yet be a wing and would impede the animals movement and it would reduce its survivability and we would have no bats.
Enter Wallace's flying frog.
It's pretty incredible amphibian that can glide up to 50 ft. And amazingly enough it's in that sweet spot of webbing to wing process. Isn't it crazy that a little further down the evolutionary tree we might have a full fledged flying amphibian?
As you can tell, it's not that a bats wing couldn't evolve, it's just that i lacked the imagination to understand how it might have happened. It probably didn't help i had a pretty strong confirmation bias against it.
Now I don't know if anyone else is using the bat's wing as an argument for irreducible complexity but christian scientists use a lot of other animal features such as the unusual aspects of woodpecker physiology.
In the same way the story I assumed spoke to the concept against evolution, the entire concept is flawed by a lack of imagination.
The truth can be just as strange as the fiction and our search for it shouldn't stop at our lack of evidence for the specifics of the how. Where we don't have evidence lies the starting point for truth, not the end of a path to a deity.

If creation story is false, can Bible be true?

The Pope announced that evolution and the big bang are fact and that God is not a wizard.
I think it's pretty interesting I haven't seen much ado about it since the week the story broke in the news. Is that because Catholics in general had already conceded that the creation story was false?
Seriously? Did he even consider the implications of it? It negates biblical faith. Period.
If there is no first man to create original sin, then what is the whole story about? Why would God need to send his son to die for us if we are just the way he created us, through evolution, to be. It means God created us all bound for hell and it wasn't the result of Adam and Eve's disobedience.
That doesn't jive with the Biblical story at all. In fact it's completely opposite (with the exception of a few passages which say God created people for hell, deceived them or gave them bad laws.)
Luke 3:23-38 lists the genealogy from Jesus to God through Adam. Does the Pope consider that false as well?
It's not as if Adam and Eve are confined to the creation account. They are mentioned and referenced throughout the bible.
If other authors of the Bible believed their story to be true, could they possibly have been inspired by God?
This is exactly how I came to a position of unbelief.
Part of me thinks this could spur a division in the catholic church and even an exodus from the faith. This may open the eyes of many that while existence itself is an argument for god, it does not necessitate the God of the Bible.
I have my doubts about that happening though. So much can be justified through interpretation and faith that those that believe can make up the gaps themselves to fabricate a cohesive vision of a Bible that is still "God breathed."
That's why it's so hard to break the circular reasoning of the Bible verifying the Bible through the interpretation of the reader.
For me it took overwhelming evidence to break free of it. The creation story proving false, or at best a lie, started me down a path of discovery of truth, but it was only the beginning. As people become better informed, less will believe in the superstitions of past civilizations, because they will be knowledgeable enough. I could have known all this during high school if I hadn't believed the lies of prominent creationists at the time.
I have to applaud Pope Francis for recognizing truth, even if just partially, in spite of theology. I know how tough that battle is, trying to reconcile reality with faith. The two will always be at odds.
Our imaginations are capable of nearly anything. It brings us to such wondrous heights and such ugly depths. It is egregious by both definitions. 
The Bible and evolution in the end are not compatible, regardless of the theological gymnastics of the imaginative mind. So if one is true, the other is false.

Have I been wrong all along?

I believed the Bible was absolute truth. As the word of God it should be perfect. What was i supposed to think when the evidence showed something contrary to the words i trusted implicitly?
The real turn in this story came from whales ability to smell, or lack there of.
Evolutionary biology shows the direct genetic link between animals. The theory of evolution predicts that the genes of ancestors will be present in some form in the DNA of creatures today.
The evolution of whales comes from land mammals which came from some aquatic critters further down the line (these aren't exactly the most technical terms but you get the idea.)
While I dint have time to discuss the entire lineage, and as far as fossils are concerned, there are some large gaps, but you can fill those gaps with whale DNA.
Because land animals evolved from a distant ancestor they have the genes for olfactory receptors which function under water only, but the genes are switched off in most terrestrial creatures. But what about whales? If they evolved from sea to land to sea again what do you think their genes would say?
Toothy whales have both genes for aquatic and airborne olfactory receptors, but they're all turned off.
I believed that God made everything. Why would he add junk genes to a creature? Genes it didn't need or use and indicated quite specifically the lineage of a creature's evolutionary process.
When I didn't know too much about genes, I assumed they all did something whether we knew it or not, but that's not the case. Organisms do not need every gene. Pseudogenes are abundant in organisms. This idea brought up an image of God sitting at a computer hitting "copy" and "paste" like a maniac as he created.
So if God presents the truth in a way that indicates a lie, is He lying?
Is it a lie for God to create every organism as if it had evolved even though it didn't?
Let me warn you now, from here I only find more lies that creationists shift their theories and stance on quite often to keep the position that their faith is grounded in truth. The reason this is such a hot topic to Christians is because the entire Bible must be true in order for the whole belief to not fall apart.
How can we inherit sin from Adam, if there was no Adam? If the creation story is false, why would Jesus, being God in flesh, mention it? I know that the domino effect is quite over used, but it applies overwhelmingly here.
Deep time is a term to describe the massive expanses of time, which are so mind-boggling large that they are difficult to truly comprehend, that make up the history of the universe.
I had never believed the universe to be older than 6,000 years, so how can we see stars billions of light years away?
Some of the creationist answers were as archaic as the Bible itself, such as the light-in-transit model which postulated that everything beyond 6,000 light years from us was played out like a movie on a galactic screen.
I immediately doubted the veracity of the claims of the distance of stars... until I studied how we find those distances through magnitude, parralax, and redshift. These methods give us an approximation which creationist argue with shifts in light travel fluctuations, but the theories are completely unfounded in reality, and it still leads to the same problem of "appearance of age."
Did God just make it appear old? Why would he form the cosmos in a way that alludes to an old universe? Maybe it wasn't in his plan for us to be able to measure those distances, but then why are we still here if it's not in his plan?
Over a period of months, which I am recounting in a single post, my faith was falling apart like a Jenga tower. I was pulling blocks to fill holes, but I was only creating new holes in my faith and my worldview.
The moment I realized that what I had been taught was untrue was the most profoundly lonely moment I have ever experienced.
Up until then I had imagined that we were all spiritually connected in a way that transcends belief or faith. That the souls of humanity existed on a plane indiscriminate of time or place.
What made it so profound for me was that for the first time ever I was alone in my mind. It was the first time I had ever conceived that God was not watching everything that went on in my mind like a continuous facebook feed filled with pictures, statuses and videos.
I was alone.
There were people nearby, but I was truly alone. It was frightening and liberating at the same time.
Even after all this I still felt the need to be sure. What if I was wrong? We're talking about ETERNAL consequences here. This goes well beyond the idea of deep time and was truly a concern. Had I been deceived? Was I lured away from my faith by the devil? What if the reason I felt so alone was actually separation from God? Am i just to dumb to see the message God has for me? Had i fallen into the same trap as my uncle and was i failing in my mission to win him back for Christ? Is the Bible absolute truth?
To answer these questions I had to turn back to the scriptures.

The quest for answers and my uncle's soul

I should preface this post by saying when I began my search for the reasonable answers I was a young earth creationist. Part of why I believed this was because the Bible said so. By tracing the lineage of the age of the lives recorded in the Bible you could estimate the earths age at over 6,000 years. With that knowledge I filtered the information I learned about geology, biology and evolution through that lens.
Some might say I was naive, but I was quite knowledgeable about the theories Christian scientists presented to support the young earth claim. Such as reptiles growing for the entirety of their lives. If people lived to 600 years old, it makes sense that lizards could grow to dinosaur sizes with that kind of life span. I was aware that DNA breaks down over time and of these discoveries of soft tissue in dinosaur bones which, to me, proved they were younger than 10,000 years (the theory at the time for how long it takes dna to break down but i cant find a reference for at the moment.) I looked at examples of the rapid developement of layers in the earth's surface as examples of how they could be formed on the timeline I believed to be true. I considered the Bible to be absolutely historical fact, inspired by God, the Word of God, perfect, and that evolution was only brought about as an alternative to the creation story.
I remember watching a documentary where a scientist said he loved digging up fossils and seeing how the evidence supported his theories. I thought to myself that it's the same process for Christian scientists, just a different theory, and that it was logical that secular scientists would look for the evidence to refute God's creation and highlight it.
I started my search to give my uncle logical understanding for faith by listening to debates about creationism vs. evolution on youtube. I know men much more intelligent than myself who believe the creation story so i needed to take the time to study and gather the information they had to offer as proof for its validity. There are a lot of videos though and they range from absurd to thought provoking, the most recent of which that I listened to was Bill Nye vs. Ken Ham.
These type of talks brought me down rabbit holes so deep Cpt. Nemo would envy me, but they pointed out some very serious flaws with my theory. How did Noah fit all those animals on the ark? Ken Ham talked a lot about "kinds", a word I cant find a solid definition for anywhere as far as taxonomy is concerned and is pretty vague on creationist websites, but thats not what I believed. All he was saying was that evolution was true, just on a much shorter time scale. I refuted any evidence of "microevolution" because I knew it was just evolution on a shorter time scale. It's important to add that with a "God" variable, there are an infinite number of possibilities. (I have a book at home about geocentric theory published by a Christian group.) So maybe God didn't stop creating. Maybe coyotes "evolved" more teeth through breeding with wild dogs.
I also was quick to point out that examples of evolution like the peppered moth only showed animals switching to a trait which they already had. They were black sometimes at the start, why should we be surprised when we still have a black moth at the end? It's not like it developed a turbine engine on its tail or a telepathy sensor or even a third antenna.
I also listened to talks surrounding theology, philosophy, and atheism to be able to approach my uncle in a well rounded way with understanding of where he was coming from. In the end I knew it would be God who turned things around for him though.
Sometimes these talks were infuriating. Most atheists doing any sort of interaction with christians were borderline rude, and to be fair a lot of christians they spoke with believed on the word of the Bible alone or because of the words of others which were blatantly untrue, which even aggravated me. If the Bible is truth it should match up undeniably with reality no matter how far fetched it may seem.
A little more than a year ago, i watched a show called the Athiest Experience. The host mentioned a website of outdated or false creation arguments. They were specifically talking about moon dust on the show if I remember correctly.
I had personally used many of the arguments on this site as they had been taught to me. Seeing them now on a "not to use" list was.... dissapointing and confusing. It meant that I had unknowingly lied to others in support of my beliefs which didnt sit well with me at all. Did anything I knew about creationism apply at all any longer?
Even more troublesome to me was that the christian theories had changed many times even in the last decade. My mom once told me one of the things that made the Bible so special was it's relevance and timelessness,  but this was not timeless. The christian theories evolved as quickly as science was making discoveries because it had to. For every new evidence against creationism, there must be an answer. Even recently at the discovery of gravity waves predicted by the big bang theory, the next day I read an article saying scripture predicted it first.
The more I studied the more problems I encountered and that lead to an ever changing stance as to how existence came to be through creation, but I didnt like it.
I felt like a child trying to explain a crime scene formed of liquid paint to a police officer, but I was both the child and the officer. Everything I believed seemed fuzzy and formless and my faith was at war with my mind.
Its hard to explain how difficult it was for me. I hadnt told anyone, not even my wife, that I was studying all these facets of the creation story with the intent to reinvigorate the faith of my lost uncle and I felt like I couldnt share it because I would never want to shake anyone elses faith. That was the complete opposite of my intended goal. All I had at this point was that my most of what I thought I knew was false, and there were no good answers to my questions.
My faith held but was what I believed evident beyond the pages of the Bible?
Then came evolutionary biology...