One of the things I used to think about a lot was the Church's relationship to the natural world. More or less alone among the expressions of Christianity, Catholicism is bound up with certain concrete metaphysical claims about the order, intelligiblity, and nature of created things. Most people don't realize this, but if one rejects metaphysical thinking wholesale, one ends up directly contradicting a great deal of the Catholic dogmatic tradition, especially as expressed at various ecumenical councils. The understanding of nature is important to Catholics. From the first chapter of Genesis onward the discernment of natural order is seen as framing the proper disposition of man toward God, creatures, and fellow men. There is a "great chain of being", celestial hierarchies, degrees of perfection, degrees of excellence among species and genera of living and inanimate things. There is a natural hierarchy of dispositions and ends in human faculties and actions. Order is central to the Catholic conception of things, both in terms of theological doctrine and morals.
As one explores the Catholic picture of the order of the world from Genesis onward, there are certain disturbing problems. How is it, for example, that the revealed cosmology of the Old Testament is so totally wrong? The modern answer, given in Dei Verbum, goes something like this: revelation was authored by both God and man, and is expressed using the limited expressions, ideas, and images of the human author's time and place. This development guarantees to the Catholic biblical scholar the right to employ modern hermeneutical techniques in analyzing and interpreting the text of the bible. But as an explanation for the peculiar errors and misconceptions in scripture, it largely falls flat.
Scripture is chock full of visions and divine utterances that fall totally outside the expressions, ideas, etc. that were available to the people of the day (unless we accept that these things were all the invention of the authors). If God is going to speak to Moses to disclose to him the destiny of Israel, why not give him a cosmological picture that isn't totally false? The real picture of the universe, at least so far as we know it today, is not substantially more complex, after all.
It is odd that the Bible wouldn't get the order of the universe more factually correct, when order is so important to the whole religion. And this fits into a larger point, which is: the Church gets nature wrong more often than it gets it right, and it is historically very bad at recognizing this or reconciling factual discoveries about nature with the basic moral and metaphysical claims it makes.
Consider the case of Darwin. The emergence of species, the existence of indeterminate kinds, the fundamental role of competition and natural selection in the story of life on earth—all of this stuff is basically indisputable. You can show the principles in action in a laboratory, you can observe their consequences in a million phylogenic comparisons or genetic analyses. These things fly in the face of the picture traditionally subscribed to by Christians. God created all the species in Genesis. Adam named them. Noah preserved them in the ark.
One can scoff today and say "oh but this is all metaphor", but it was not traditionally believed to be pure metaphor. One can read Basil the Great on the Hexaemeron scoffing aggressively at people who do not subscribe to the historical truth of those chapters, or the unequivocal response of the Pontifical Biblical Commission in 1909 firmly rejecting the view that these stories are part historical, part myth, and designed for instruction and edification. The Church has, in the main, always believed this picture of the order and origin of the natural world. It has now adjusted its exegetical framework in order to retreat from that belief, but it has never bothered to cope with the implications of that failure in a systematic way.
The Church has much more important things to do nowadays than fret over the metaphysical implications of Darwinism (e.g. turning heresies into human rights), so in a way the failure to intellectually integrate the modern scientific world-picture into Catholic theology is less disturbing than the fact that it was so wrong about nature for so long, and wrong on the basis of what were more or less universally believed to be revealed truths.
Much more personally, though, this error about the natural world touches on how wrong the Church has always been about an aspect of human nature: homosexuality and the experience of being gay. Consider as a primary and readily available example the text of the first chapter of Paul's Letter to the Romans (ESV):
For the wrath of God is revealed from heaven against all ungodliness and unrighteousness of men, who by their unrighteousness suppress the truth. For what can be known about God is plain to them, because God has shown it to them. For his invisible attributes, namely, his eternal power and divine nature, have been clearly perceived, ever since the creation of the world, in the things that have been made. So they are without excuse. For although they knew God, they did not honor him as God or give thanks to him, but they became futile in their thinking, and their foolish hearts were darkened. Claiming to be wise, they became fools, and exchanged the glory of the immortal God for images resembling mortal man and birds and animals and creeping things.Therefore God gave them up in the lusts of their hearts to impurity, to the dishonoring of their bodies among themselves, because they exchanged the truth about God for a lie and worshiped and served the creature rather than the Creator, who is blessed forever! Amen.For this reason God gave them up to dishonorable passions. For their women exchanged natural relations for those that are contrary to nature; and the men likewise gave up natural relations with women and were consumed with passion for one another, men committing shameless acts with men and receiving in themselves the due penalty for their error.And since they did not see fit to acknowledge God, God gave them up to a debased mind to do what ought not to be done. They were filled with all manner of unrighteousness, evil, covetousness, malice. They are full of envy, murder, strife, deceit, maliciousness. They are gossips, slanderers, haters of God, insolent, haughty, boastful, inventors of evil, disobedient to parents, foolish, faithless, heartless, ruthless. Though they know God’s righteous decree that those who practice such things deserve to die, they not only do them but give approval to those who practice them.
Modern biblical exegetes will try to limit the scope of this passage to a specific unmentioned group in the audience of Paul's letter, in order to sweep under the rug the implication of what he is saying here, just as in the other New Testament passages the intent of the Greek will be read so as to conveniently mean "only pederasts" or "only promiscuous homosexuals" instead of simply every man who sexually desires men. However, the intent of the passage as received is abundantly clear. Homosexuality is a perversion that follows as a consequence of the intellectual and moral darkening of the soul when men are proud and reject God. It is contrary to nature. It is vile, and merits punishment with death, and begets innumerable other vices. It is a symptom of idolatry and total social decline. These beliefs are, because of their place in the New Testament and the subsequent development of the patristic moral tradition, fundamental to Christianity, and remain widespread among Christians even today.
In official Church doctrine this has been the line more or less forever. The notion that some men and women are born homosexual, while no doubt believed by many people over the centuries, has never to my knowledge been officially entertained until the past few decades. The inclination toward sexual intimacy with members of the same sex is in itself considered execrable, dishonorable, vile, shameless.
Now, leaving aside the question "Why would God make me this way, or implant in me an inescapable desire to commit acts plainly taught to be abominable?", we can ask a more basic question: How is it that the Church, which is ostensibly an infallible authority on human nature and the moral life, could have missed the fact that so many of us are inescapably given this set of inclinations from childhood?
I used to puzzle over this a great deal: What sin had I committed? What hidden pride of my heart was God punishing me for? What hidden defect of character or missed petition was the lynchpin which, when removed, would take away this unspeakably shameful longing? But the reality is that there is no such thing. I had done nothing especially wrong to merit being gay. It was and is simply a part of my nature, like it is a part of the nature of millions of other men and women, just like it is a surprisingly well-documented phenomenon across many biological species the world over.
What I mean to point out here is not an objection to the Church's "natural law" position on which sorts of sexual acts are licit, but the absurdity and cruelty of its misdiagnosis of the nature of homosexuality, from the time of Paul onward. The Church's radical error of perceiving that people like me have these inclinations because we are extraordinarily wicked or perverse, that our existence is a symptom of idolatry or depravity, that accepting us is an invitation to societal collapse.
Ultimately, for me, it is impossible to believe both that my inclinations are not gravely evil and debased, and that Christianity is in some way true. The needle is unthreadable. No religion with a falsehood baked so deeply into its moral vision of humanity could possibly be of divine origin. Whether Paul meant to condemn only Tim and Dismas who'd been sacrificing to Isis, or only had in mind a hypothetical extreme case of pederastic orgies really makes no difference. Christianity has always read the condemnation generically. In this matter as in so many others the Church has shown itself over time to be an untrustworthy guide to both human nature and the nature of the world at large.