The Militant Atheist:

The Catholic Church is one of the vilest religious organizations in existence.

The main reason people cite is protecting child rapists, which is definitely way up there in terms of what makes the organization vile. But here's some other ones I feel are sometimes overlooked:

Prohibiting euthanasia/death with dignity. I can think of nothing more wicked than forcing a terminally-ill person to suffer in agony, humiliation, and terror until their heart stops. We don't let animals suffer like this.

Perpetuating poverty. One of the main causes of poverty in the world is the disempowerment of women. When you deprive women of contraception and reproductive rights, you make her a slave to her reproductive system and she's liable to have more children than she can afford to keep. She's also less likely to be able to economically participate and be dependent on the man (that church tradition and scripture places her in a subservient role to).

Opposing minority rights. For a start: gay marriage, gay adoption, etc. They've all been vehemently fought against by this bigoted church. Even though we seem to be winning against them, it cannot be denied that a significant part of the world are firmly against the rights of LGBT individuals for nothing more than religious pablums as a result indoctrination. It should also be mentioned that the church has cast aspersions against atheists since time immemorial (sadly for them, they cannot torture and kill us anymore).

Bodily autonomy. Catholics want to reign over the uteruses of women and make decisions regarding their bodies. They do this by throwing money and propaganda at the issue and try to have abortions banned. But let's say, for argument's sake, that a fetus has the right to live... it has a right to live, but it does not have a right to use another person's body in order to live. The Catholic church wants to undermine the most fundamental human right there can be: the right to do with your own body as you please.

Stifling scientific and medical research. Trying to ban embryonic stem cell research comes immediately to my mind. It's an area of study that could possibly come up with treatments and even cures to a variety of horrendous diseases and chronic medical conditions. The church has always been opposed to this. They're also causing sexually-transmitted diseases like HIV to spread by preaching against condoms in uneducated, disease-ridden, and poverty-stricken parts of Africa. As well as this, they oppose research into fertility treatments, sterlization, tubal ligation, etc. As sad as this is, it's nothing new: the church has a track record of causing or contributing to technological stagnation throughout history -- particularly during the Middle Ages.

Making a saint of Mother Teresa. Mother Teresa was one of the most wicked women who ever lived. She loved poverty and the suffering it brought, because she believed it allowed people to share in the passion of Christ. This motivated her to run homes for the sick and dying in which poor, desperate people were brought to and then deprived of pain relief, medication, and proper medical treatment despite the fact the charity had more than enough funds to do so. The funds that were earmarked for such purposes, some laundered criminally and obtained from dictators, were used for building nunneries and other useless facilities. For more on this subject, see Christopher's Hitchens' "The Missionary Position" and "Hell's Angel".

Breeding a culture of ignorance and scientific illiteracy. This isn't to say that there aren't brilliant Catholic scientists, but it is to raise the point of how much intellectual capital the world has lost through teaching that superstition and faith has more value than reason and critical thinking. It also follows that if you already have an answer to pressing questions like "how was the universe formed?", "what is consciousness", etc. and it's "god" or some religious stopgap, then why would anyone feel compelled to look any further? The same can be said with miracles. By calling something a "miracle", you stop trying to exhaust all natural explanations. It's intellectually lazy to say the least. Now I'm sure at this point a Catholic might respond with "Oh, but we are motivated by this because we want to know the mechanisms through which God did it. It allows us to understand him!"... which proves my point beautifully: working backwards from an assumed conclusion is as anti-science as you can get and an incredibly skewed epistemology that can only serve to hold us back.

Undermining the value of human life. The Catholic church is big into the afterlife. Imagine going through your life thinking that there's an eternal existence that awaits you. Rather than believing this is the only life you're guaranteed to have, and as such viewing it as something infinitely precious, you're more likely to treat it as a preamble -- a doormat to wipe your feet on before the real life. What's 80 years on earth compared to an eternity in paradise or hellfire? At the same time, if you believe that human beings are born wicked and depraved sinners who are nothing but ash compared to some divine spirit(s), you're not going to have the healthiest of outlooks in what they can achieve and what they deserve. You may even spend your entire life in existential dread at the prospect of burning forever when you die or how this may happen to your friends and family. While literal hell is a doctrine that was somewhat retired by the church, its legacy still continues causing immense psychological damage in the world.

Etc.

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