There is even documentary evidence that indicates that the Church has been aware of the existence of pedophilic priests for decades. More documentary evidence has surfaced showing that during the 1990’s, when the scope and extent of the crimes of Catholic priests were just coming to light, the head of the Vatican's office of The Congregation for the Doctrine of the Faith (in the past this office was known as the Inquisition...and in the interest of brevity I will call it the Modern Inquisition from here on), headed by none other than Cardinal Joseph Ratzinger, used the supposed spiritual and moral authority of the Church to silence victims and their families. Documents obtained from the time that Cardinal Ratzinger was in charge of the Modern Inquisition plainly shows that his primary concern was with the Church's, and its priests, reputation - not the well-being of the children entrusted to their care by parents and other adults that, believing in the religious authority and supposed benevolence of the Church, trusted that the children would be safe from harm.
So far the arguments seem to be mostly about the supposed "harm" done to the "skeptical movement" by those non-believers (like Richard Dawkins, Christopher Hitchens, PZ Myers, and in my own small way, yours truly) calling for the Pope to be taken into custody by civil authorities should he make trips outside the jurisdiction of the Vatican. Another tack that the critics of those that feel an uncompromising stance is warranted, is that, in the long run, such a stance is harmful to the cause (and I use the term "cause" advisedly) of reason. As PZ puts it, the criticisms seem more about the tone of the more outspoken rationalists than the substance of their arguments.
As bloggers and as science communicators, I admire both PZ and Phil, but they are different people, with different ways of coming at this particular issue, but I have to go with PZ on this one. I am very much in favor of, as Sam Harris has called it, "conversational intolerance" towards peoples' religious beliefs. The Bad Astronomer seems to make a distinction between holders of traditional religious beliefs1 and, say, anti-vaccination morons, holocaust deniers, and moon landing conspiracy nut-jobs. I do not make such a distinction, and it seems, rightly in my view, that PZ does not either. American citizens are free to enter into, or stay away from, whatever houses of worship they feel most resonates with, or conflicts with, respectively, their individual conscience (for a more academic treatment of this see here - my analysis of Constitutional issues surrounding religion and the U.S. Military for a Constitutional Law class I took while at university).
If gangs of (truly) militant atheists started going around boarding up houses of worship under the cover of darkness or blocking access to them (the way believers attempt to block access to the clinics of doctors that provide abortions), I would proudly defend to my death the right of my fellow human beings to spout whatever supernatural nonsense they wish within the confines of their chosen house of worship. By the same token, I would proudly defend to my death, mine, my children's, or anyone else's right to question, examine, analyze, criticize, and otherwise publicly tear to shreds any publicly stated idea or assertion, religious or not.2 Once religious beliefs, insofar as they are statements purporting to be about the way the world/universe/reality actually works, the veracity of certain historical claims, or that high levels of popular religiosity are necessary to building a prosperous, safe, and just society here on earth, leave the sanctuary (both literally and figuratively) of a "house of worship" they are as open to criticism as any idea in the arts, science, history, or economics.
At the end of Phil's piece, he says we (meaning, I suppose, the "skeptical community") "need to be human and humane" if we wish to "change the hearts and minds of people". As social animals, one of our most precious possessions are our reputations as reliably rational (and the definition of "rational" can vary greatly) beings in our relations with others. What is wrong with idea of putting people on notice that professing absolute certainty in the truth of nonsensical religious beliefs will endanger their credibility? As Sam (now Dr., as he finally finished his Ph. D.) Harris and Richard Dawkins have said repeatedly, we seem to have no problem openly laughing at, and mocking, the beliefs of those that accept the reality of the Norse and Greek pantheons, astrology, "crystal healing," and dowsing. Why is it that there is one remaining superstition that is "off limits?" The beliefs mentioned above have been successfully marginalized, due to, in no small part, the application of heaping amounts of shame and embarrassment upon those that publicly profess their certainty of the truth of the above beliefs.
We inhabit a complex and frequently dangerous world in which we must often rely on others to (hopefully) reliably inform us of the dangers around us and how to avoid them. In practical terms, we cannot all be running around testing every wild mushroom or every colorful berry to see whether it is safe to eat or not; we have to rely on the fact that our neighbors’ information about such things is accurate and well-founded.
An example of what I am talking would be a conversation I overheard between two co-workers not too long ago. Both parties are very conservative and the one speaker is a devout Christian and generally a nice fellow, but the shrapnel from my exploding irony meter would have punched through an armor-plated Humvee at 200 meters. Here is basically what he said..."Yeah, I'll believe 'global warming' is real when I feel the rising sea lapping at my ankles." I remember thinking to myself "oh sure, you accept all of the miracle stories in the Bible as completely credible accounts of actual historical events, but the idea that nearly 7 billion human beings (and all the ancillary stuff of human culture...crops, livestock, etc.-a major part of the Earth's biomass, see this) could have a deleterious effect on the planet's climate...that is simply preposterous..." His credibility as a thinking human being is completely shot as far as I am concerned.
If a student, for whatever trivial reason, failed to do their math homework the previous night and was less than forthcoming in their failure the following day (okay, they outright lied and claimed to have done it), is subsequently called upon to work one of the problems on the board, in front of the whole class, I am quite willing to wager that most people would agree that the shame and embarrassment the student felt was a deserved consequence of their prevarication. This is a reason why people do not like to get caught with their intellectual pants around their ankles. There is not a single adult human being on the planet that is entitled to not being called "on the carpet" (as it was termed during my service in the U.S. Navy) when their faith is writing checks that the evidence and their intellect cannot cash.
Going back to Sam Harris' idea of "conversational intolerance," no one is under any obligation, whatsoever, to treat religious beliefs any differently than any other kind of woo-woo. Scorn and embarrassment are absolutely legitimate weapons in the fight against those that would endanger the future of humanity by clinging to the beliefs of humanity's infancy. Nor could I care less about the hurt feelings of Catholics in all this. I was raised a believer myself (though not a Catholic) and my shame and embarrassment at the many hypocritical moral and ethical failings of my fellow believers, both collectively and as individuals, is one of the reasons I turned my back on the faith I was brought up with. As a believer, I was raised to value honesty, forthrightness, and integrity, and found, much to my family's consternation, that I held everyone to those standards.
I think the "militant" non-believers are right on this issue. For me, and from what I can tell, many other non-believers, based on what they have said and written on this subject, this is a matter of principle. For far too long have "believers" coasted though their existence believing, due in no small part to the complicity of all of us, that they are nice, decent, moral people, all the while largely crediting their religious faith for their supposed "superior" morality, and using that supposed "superior" source of morality as a bludgeon against those that do not share their views. It is high time for all believers to be told, in no uncertain terms, that the core of their supposed "superior" morality is in fact, morally bankrupt.
1I must say in the BA's defense, that he spares no pity for parents that withhold proper medical care for an ill child because of their religious beliefs, though it must be admitted that most prominent conservative Christian sects still take their kids to the doctor when they are sick, it is only the most truly nut-ball cults that deny medical care to children for religious reasons.
2 The idea that our democratic ideals are somehow connected to “Judeo-Christian” traditions is laughable. If democratic ideals were inherent within Christianity or its predecessor, Judaism, why did it take almost two millennia for democracy to rise from the ashes of Periclean Athens and the Roman Republic? In fact, Christianity cursed the west with the idea of the “divine right” of kings to rule of which Europe had to divest itself of before realizing democratic ideals. There is as little foundation for the idea of a secular, democratic republic (which is what the United States is) in the Christian scriptures as there is for Newtonian physics.