Thanks, M.D. Anderson, for adding another confounding variable

I’ve been talking to my class this week (and it’s going to be a theme next week) about the difficulty of analyzing epidemiological data on cancer — that there are so many steps to cancer progression and so many environmental and genetic inputs to the disease that sorting them all out is extremely complex. What I haven’t mentioned yet, but definitely will now, is the factor big money plays in encouraging statistical fraud.

The University of Texas MD Anderson Cancer Center in Houston has been the top-ranked cancer center on US News & World Report’s best-of list for the past 7 years. But that top ranking was aided by a massive error in data used to evaluate its care.

The error in M.D. Anderson’s favor was made by–M.D. Anderson! Avery Comarow, who assembles the rankings at U.S. News, told The Cancer Letter that this was a huge "screw-up." The hospital systematically misclassified emergency patients, which led to the exclusion of nearly 40 percent of admissions, Paul Goldberg, The Cancer Letter’s editor, reported. He said the error was discovered in 2009, but no way could be found to correct it. "Since U.S. News averages data over three years, the results of the M.D. Anderson top rating by the magazine released July 16 are still partially based on tainted data," he wrote.

Is “error” actually the right word to use?

Atheists should have good rules for behavior

It has come to my attention that certain people — certain thuggish, stupid people — are objecting to the Code of Conduct for the American Atheists 2014 convention. In addition to complaining that it shouldn’t bother to address the needs of trans people (WTF?), they object to this section.

American Atheists does not tolerate harassment of or by conference participants in any form. Prohibited conduct may include but is not limited to harassment related to gender, gender identity, sexual orientation, disability, physical appearance, body size, race, age, religion, sexual images in public spaces (not related to convention sessions or materials), deliberate intimidation, stalking, harassing photography or recording, sustained disruption of talks or other events, inappropriate physical contact, and unwelcome sexual attention. Racist, sexist, homophobic, or transphobic conduct will not be tolerated.

That all sounds good and reasonable to me. But some people are complaining that at an atheist convention, it is far too PC to say you may not harass people for their religion, and then they point to David Silverman, who is known for his confrontational style and his willingness to openly disagree with religious convention.

These objectors are obtuse and wrong. This does not say you may not disagree with someone; it does not say you may not publicly express a different opinion; it does not say you have to be kind and gentle to bad ideas.

It says you may not harass someone.

Harassment is persistent, aggressive behavior with the purpose of intimidating or silencing someone. The code of conduct even goes into detail: “deliberate intimidation, stalking, harassing photography or recording, sustained disruption of talks or other events, inappropriate physical contact, and unwelcome sexual attention.” To say that you may not do that to a religious person is not a violation of the purpose of American Atheists; I’d say it’s actually a damn good idea if atheists don’t harass religious people and make respectful behavior towards other human beings a part of their policy…while still continuing aggressive campaigns against bad ideas.

So if Thomas Monson, president of the LDS church, shows up at AACON2014, you can argue with him, you can tell him how much you dislike his church, but if he asks you to step aside and leave him alone, you will do so. David Silverman can give a talk in which he castigates the Mormons for their hypocrisy and the absurdity of their religion, and if Thomas Monson raises his hand to ask a question afterwards, the audience will not heckle him and shout him down. And when he starts walking up the aisle to leave afterwards, you will not grab him, block him, spit on him, shout obscenities at him, or interfere with him in any way, because that would be harassment, and that would put you in violation of the code of conduct. Well, and also put you in violation of many norms of civilized behavior.

I have no objection at all to the American Atheists code of conduct, and think it is a fine document fully in accord with the aims of the movement. If you disagree, you shouldn’t go anywhere where you might find yourself in groups of people. Perhaps you’d be better off living in a small cave in the middle of nowhere? Or perhaps confining yourself to the company of trolls on youtube?

I was pointed to the commitments and code of conduct for an anarchist book fair. They’re rather progressive. It doesn’t matter who you are, when people gather, there will be rules to regulate your behavior.

I am so tempted to visit Fargo Grand Forks next week

I’ve been informed that there will be a lecture at UND next Tuesday. I might be able to find time to dart up and come right back home that night…it’s only about a two hour drive.

BoysFlyer

I’ve heard of Boys before. It’s going to be ugly. There he is, not only attacking atheism, but doing so as a young earth creationist who rejects evolution. But also because Boys had his moment of infamy about 5 years ago. Anyone else remember this? He’s the guy who urged Bush to nuke Mecca and Medina.

Do we sit on our fat bottoms, wring our hands, and wait for Muslim terrorists to strike? What good will that do? What good will result in doing nothing until one or two major cities are in rubble? My suggestion is take offensive action. The only possible way I can see that we might, I say might, escape another Muslim attack upon our nation is for President Bush to issue the following declaration to the world:

“My fellow Americans, as your President my primary responsibility is to protect and defend the U.S. I am not interested in world opinion or in playing games at the UN. Our intelligence reveals that Muslim terrorists are planning to hit us again; furthermore, terrorist leaders have promised that our cities will be in ruins. I believe them so I have been authorized by the Congress to make the following promise: Within 24 hours following an attack upon the U.S., our Air Force will bomb Mecca and Medina into the “Stone Age.” Innocent Saudi Arabian civilians will have 24 hours from the attack on us to flee the two cities that will be razed.

“Let no one be deceived as to our motive. We don’t want to harm any person nor do we desire any territory, and there is no reason for anyone to be killed—as long as there is no attack against our nation. This decision was made to protect U.S. citizens; however, if there is a choice between us and them, it will be them who die. Moreover, Muslim leaders will be the ones who pull the trigger on their own people. If Muslim leaders want to destroy their two holy cities, then they will do so by attacking us. We will respond in 24 hours. May God protect and bless America.”

Stupid to the point of evil, that’s Don Boys. And he’s being sponsored by Baptist Campus Ministries, which claims to be bringing “honor and glory to the Lord Jesus Christ through Bible-based thoughts, words, and actions”.

Honor and glory.

Fuck your honor and glory, Christians.

My New Atheist agenda is to murder fewer people, not more.

What do you get when a creationist visits the Galapagos?

I think it’s an anti-Darwin: instead of observations, you get pretty pictures; instead of insights, you get a cloud of murk and lies. Georgia Purdom of Answers in Genesis visited the Galapagos, and now she’s coming out with a book of religious apologetics.

After my return, I started thinking about writing a book on the Galápagos Islands. I wanted people to see that what we think about how and when the Galápagos Islands formed and how the wildlife changed over time has to do with a person’s starting point or worldview. The Galápagos Islands both past and present are a display of God’s majesty in His creation and His mercy in preserving life in a fallen world instead of an “icon of evolution.” I also wanted people to appreciate the diversity and beauty of the wildlife and landscape that is unique to the Galápagos through the 2000-plus photos I had taken.

If you should ever see this book, think about Purdom going to the Galapagos on a sight-seeing trip and learning absolutely nothing, and compare it to Rosemary and Peter Grant who spent decades there, documenting patterns of change in the bird populations of Daphne Minor. I learn something from the Grant’s work, while Purdom’s delusions will just make the world a stupider place.

Give the Purdom book a pass. Get the Grants’ How and Why Species Multiply: The Radiation of Darwin’s Finches instead.

Quote war! We win!

A new billboard has gone up in South Dakota in reply to Coalition of Reason’s recent sign.

"When I saw the sign I thought of it as a direct attack on my God. I thought that it would be good for people to know that God is alive and that He has something to say," Kreider said to The Christian Post.

So, Mr Kreider, what does your god have to say?

The fool hath said in his heart, there is no god.

The fool hath said in his heart, there is no god.

Oh. The same damned quote you kooks always drag out. You know the authority of your bible is about the same as the authority of a Pokemon manual to me, so flinging quotes at me does you no good.

I can give you quotes, too — quotes from people who actually existed.

So much blood has been shed by the Church because of an omission from the Gospel: “Ye shall be indifferent as to what your neighbor’s religion is.” Not merely tolerant of it, but indifferent to it. Divinity is claimed for many religions; but no religion is great enough or divine enough to add that new law to its code.

Mark Twain

We despise all reverences and all the objects of reverence which are outside the pale of our own list of sacred things. And yet, with strange inconsistency, we are shocked when other people despise and defile the things which are holy to us.

Mark Twain

The World is my country, all mankind are my brethren, and to do good is my religion.

Thomas Paine

Religion has convinced people that there’s an invisible man … living in the sky. Who watches everything you do every minute of every day. And the invisible man has a list of ten specific things he doesn’t want you to do. And if you do any of these things, he will send you to a special place, of burning and fire and smoke and torture and anguish for you to live forever, and suffer, and suffer, and burn, and scream, until the end of time. But he loves you. He loves you. He loves you and he needs money.

George Carlin

Ask yourself this: if there is a god, why are the atheists so much more creative and witty?

Don’t be that guy

There are really bad, dogmatic ways to defend evolution, and every once in a while I run into them. And because I’m a wicked jerk, I criticize the people who do that, even when they announce that they are atheists. So this morning I ran into this nonsense on Twitter:

@DrewJPS ‘Evolved from mokeys’ is theist bollocks. As is ‘Macro/micro evo’. Never been uttered in by scientists. Ever. Ignore.

And with that, mine eyes looked up, and beheld Steven Stanley’s Macroevolution: Pattern and Process on my bookshelf before me, and I did query @DrewJPS.

Damn. So all my books about macro/micro don’t exist?

And I listed a few well known authors who have written books on this topic. Not creationists, but respected scientists and science journalists. And @DrewJPS doubted me.

@DrewJPS .@pzmyers So you’re willing to defend macro/micro evo’? Show me peer-reviewed papers. Not yours.

And therefore did I drop the PubMed bomb upon him. And I waited, expecting retraction and apology, and new learning to dawn in the brain of @DrewJPS. Instead, I got an abrupt change of subject.

@DrewJPS @pzmyers Ok, read it. How, as a a free-thinker, did you get rapped up in this ‘RadFem’ bullshit? Atheismplus is bullshit.

I think I can regard his authoritative contempt for feminism with the same low esteem I hold his opinion on evolution. Bye. Blocked.

Fellow atheists, don’t be that guy. Please. It’s embarrassing.

It just gets funnier. Now his friends are joining in the act.

@Brazen_Thinks
@DrewJPS clearly he’s a creation scientist. No main stream scientist recognises that term. Francis Collins is a theist and rejects that term

@DrewJPS
@Brazen_Thinks Also a witch-hunting twat that will send you to prison with no evidence #AtheismPlus

@DrewJPS
@DFCW It’s an group of ‘RadFem’ that call themselves Altheists. Mental. Not in my name http://rationalwiki.org/wiki/Atheism_Plus …

@DFCW
@DrewJPS militant feminists are really annoying.

Clearly, the only possible reason that I would point out their ignorance of a body of thought about evolution is that I’m an annoying militant feminist.

Magic RNA editing!

One of those wacky Intelligent Design creationists (Jonathan McLatchie, an arrogant ignoramus I’ve actually met in Scotland) has a theory, which is his, to get around that obnoxious problem of pseudogenes. Pseudogenes are relics, broken copies of genes that litter the genome, and when you’ve got a gang of ideologues who are morally committed to the idea that every scrap of the genome is designed and functional, they put an obvious crimp in their claims.

So here’s this shattered gene littered with stop codons and with whole exons deleted and gone; how are you gonna call that “functional”, creationist? McLatchie’s solution: declare that it must still be functional, it’s just edited back into functionality. He uses the example of GULOP, a gene responsible for vitamin C synthesis, which is pretty much wrecked in us. Nonfunctional. Missing big bits. Scrambled. With missing regulatory elements, so it isn’t even transcribed. No problem: it’s just edited.

As I mentioned previously, the GULO gene in humans is rendered inactive by multiple stop codons and indel mutations. These prevent the mRNA transcript of the gene from being translated into a functional protein. If the GULO gene really is functional in utero, therefore, presumably it would require that the gene’s mRNA transcript undergo editing so that it can produce a functional protein. It’s not at all difficult to understand how this could occur.

Yes, RNA editing is a real thing. RNA does get processed before it’s translated into protein. McLatchie has a teeny-tiny bit of knowledge and is abusing it flagrantly.

I’ve hammered out dents in a car, and I’ve touched up rust spots with a little steel wool and a can of spray paint. My father was also an auto mechanic and could do wonders with a wrench. Auto repair exists, therefore…

old-wrecked-car-outback-australia-14466708

…patching up that vehicle should be no problem at all, right? I expect to see it cruisin’ down the highway any time now.

Maybe two cans of spray paint this time…?

Just in time for my cancer class

In a few weeks, we’ll be having a discussion of the ethics of cancer research: what is a reasonable intervention in the case of a patient who has no hope of survival? And look at the interesting case that just appeared on my radar: two cancer surgeons who treated brain tumors by deliberately infecting them with bacteria.

Two UC Davis neurosurgeons who intentionally infected three brain-cancer patients with bowel bacteria have resigned their posts after the university found they had "deliberately circumvented" internal policies, "defied directives" from top leaders and sidestepped federal regulations, according to newly released university documents.

Dr. J. Paul Muizelaar, 66, the former head of the neurosurgery department, and his colleague, Dr. Rudolph J. Schrot, violated the university’s faculty code of conduct with their experimental work, one internal investigation concluded.

All three patients consented to the procedures in 2010 and 2011. Two of the patients died within weeks of their surgeries, while the other survived more than a year after being infected.

The premise behind their experimental procedure is probiotics, which immediately throws a warning on the play: there’s a lot of abuse of the concept out there.

Muizelaar and Schrot called their novel approach “probiotic intracranial therapy,” or the introduction of live bowel bacteria, Enterobacter aerogenes, directly into their patients’ brains or bone flaps. The doctors theorized that an infection might stimulate the patients’ immune systems and prolong their lives.

But there are some serious problems here. They didn’t have institutional review and approval of their procedure! That’s not a warning flag, it immediately calls the entire research into question and brings the ethics of the doctors under the microscope. You don’t get to do that.

And then there’s their logic. This is a disease with a median survival of 15 months. Their first patient died less than 6 weeks after the surgery, while the second lived for a year, which the report says “buoyed the doctors and seemed to bolster their theory”. That makes no sense at all — with so few trials they can’t possibly make that kind of assessment. Furthermore, their third patient died of sepsis.

At least it sounds like we’ll have something to talk about. That seems a paltry reward for three people’s deaths.

(via The Tree of Life)