Happy Blasphemy Day!

I hope you’ve been spending your Blasphemy Day thinking irreverent thoughts and committing sacrilegious acts. I’ve been at a humanist conference where we damned religion to heck, and I’m about to board an airplane where I will spend the flight putting finishing touches on a profane pro-science and anti-religion (anti-moderate religion, even) column for Free Inquiry, and I’ll try to find a few minutes to cuss out the non-existent angels who are not holding my airplane up in the sky.

But also, this is serious business. Consider the young Greek man who has been arrested for mocking a cleric; Alexander Aan, arrested in Indonesia for denying the existence of god; Alber Saber, arrested in Egypt for linking to a stupid movie that mocked Mohammed; Rimsah Masih, accused of desecrating the Quran and facing hateful death threats; Asia Bibi, sentenced to death for blasphemy in Pakistan; and too many others to list. Consider that the European Union has just called for “full respect of religion” and “the importance of respecting all prophets” — blasphemy laws are spreading.

So blaspheme today! Assert your right to deny bullshit loudly and honestly!

I guess the Secular Coalition for America will let just anyone volunteer

Come on, SCA. Exercise some care and vet your volunteers better. After Edwina Rogers, we need some confidence-builders in the organization, and learning that they’ve made this awfully stupid appointment does NOT fill me with confidence. Why would you want a guy who posted an op-ed on AVoiceForMen, a hate site, and who posts the home addresses of a woman he dislikes on another hate site, as a candidate to represent a state organization?

Of course, it could just be that the organization is so desperate for volunteer help that they’ll take the dregs. That’s not a confidence builder, either.

There’s a petition. Unfortunately, it’s already full of trolls using fake names — change.org really needs to tighten up their procedures. These petitions already reek of uselessness, and the fact that they’re so easily gamed makes them totally pointless.

Why I am an atheist – MD

I had been an atheist for over a decade but hadn’t realized it. It took a child to make me see that. My own child. He asked me one day why I didn’t go to church like others in our family. All these reasons flew through my head in a matter of seconds, but they all boiled down to one. “Because I don’t believe in it,” I answered him. “Me neither,” he said.

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Jonathan Wells talks about history

Oh, boy. Jonathan Wells explains why some of us reject the outrageous interpretations made from the ENCODE work claiming 80%+ functionality of the genome. It was really an effort to get past this sentence.

Some historical context might help.

Bwahahahahaha! First sentence, he makes a joke. Wells is a creationist clown notorious for his tortured abuse of the history of science. He doesn’t have a merely whiggish view of history — it’s more of a Burke&Hareish perspective, where if History isn’t conveniently dead to permit him to commit ghoulish atrocities on it, he’s willing to take a cosh to it’s skull and batter it into extinction. When Wells announces that he’s going to provide “historical context”, brace yourself for a graceless exercise in ugly alternative histories.

After James Watson and Francis Crick discovered the molecular structure of DNA in 1953, Crick announced that they had found "the secret of life," a popular formulation of which became "DNA makes RNA makes protein makes us."

What? I don’t even…OK, second sentence is wrong. That looks like a mangled version of the Central Dogma of molecular biology, with a weird appendage tacked on to claim that it “makes us”. Crick did not discover the secret of life. What the Central Dogma is about is the irreversibility of information flow: nucleotide sequence specifies the order of amino acids in a protein, but there is no mechanism to translate a sequence of amino acids back into a sequence of nucleotides in RNA/DNA. It’s an important concept, but not the secret of life.

But biologists discovered that about 98% of our DNA does not code for protein, and in 1972 Susumu Ohno and David Comings independently used the term "junk" to refer to non-protein-coding DNA (though neither man excluded the possibility that some of it might turn out to be functional).

More garbage. NO. No one equated non-protein-coding DNA with junk. Unless it was a creationist. In 1972, we knew about lots of non-coding DNA that wasn’t just functional, it was essential — genes for tRNAs and regulatory sequences, for instance. The term “Junk DNA” was initally coined to describe pseudogenes — gene duplicates that had been rendered nonfunctional by mutation. We knew that gene duplication was common, but that successful gene duplications, that is events that resulted in a copy with novel functions that would be maintained by natural selection, were going to be rare. So Ohno expected large quantities of such relics to be found in the genome.

Why didn’t biologists simply call non-protein-coding sequences "DNA of unknown function" rather than "junk DNA?" For some, it was because "junk DNA" seemed more suited to the defense of Darwinism and survival of the fittest.

No, because the term was initially applied to a specific class of sequences that were recognized as failed duplications. They weren’t of unknown function…they were the debris left over from unsuccessful natural experiments.

Now we know of other mechanisms that produce repetitive, non-functional sequences. There are transposable elements that have no purpose but to replicate themselves over and over in the genome, there are viral insertions, for instance. We know how they get there, and it’s not because their existence confers greater fitness on the bearer, or because they make active contributions to the phenotype. They’re just splatters of DNA.

The term “Junk DNA” is perfectly reasonable to apply to such mostly-useless sequences. I think the only legitimate argument against the term is that we have so many different classes of the material that more specific labels would be more useful…but the argument that these sequences are functional is a nonstarter.

In 1976, Richard Dawkins wrote in The Selfish Gene that "the true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus [i.e., non-protein-coding] DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA."

Hey, Wells gets something mostly right! Yes, that’s correct, and it’s the explanation born out by observations of things such as LINEs and SINEs, which code for enzymes (or sequences recognized by such enzymes) that insert copies of themselves back into the genome. This isn’t just a supposition, we know how this works.

He gets the motivation behind the dispute completely wrong, however. We aren’t calling some sequences “junk” because we don’t know what they do: to the contrary, it’s because we know where those sequences come from and what they do. It’s also not because, somehow, it is a Darwinian prerequisite that “junk” exist in the genome. Again, to the contrary, there was initially resistance to the idea of junk because of a Darwinian bias towards seeing adaptedness in everything. The idea of non-functional DNA sequences that don’t contribute significantly to the phenotype emerged from observations of what we actually found when we started taking apart the components of the genome.

That’s why a lot of us are irritated with the ENCODE interpretation that the whole genome is ‘functional’. It’s not because of a philosophical predisposition, or because we apply the label by default to sequences we don’t understand, but because that conclusion rides roughshod over a lot of well-established evidence.

Oh. Right. In addition to history, evidence is another of those esoteric concepts that Jonathan Wells can’t comprehend.

Why I am an atheist – Steve

It’s probably a sign that you’re doomed to be a heathen when your initial conception of God was not the Gandalf-looking dude from the “Creation of Adam”, but the Fairy Godmother from “Cinderella.” It was easy for me as a child to buy into fictional characters being real. The brief time that I did go to church, and claim to feel something there like angels in the rafters or whatever, was also at about the same time that I was looking for the Teenage Mutant Ninja Turtles in sewer grates. Yep, The Almighty, and four mutated terrapins named after renaissance artists were equally plausible to me.

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I don’t care, just GIVE ME A CHOICE

A blogger recently posed this question.

If I had to vote for one of two hypothetical candidates, would I be more likely to vote for a liberal Christian or a conservative atheist?

My first, immediate response was to just answer the question: yes, of course I’d vote for the liberal Christian. All you have to do is realize that Karl Rove is an atheist to know that the label “atheist” is not an automatic marker for a good person (just as we know “Christian” isn’t either, with more examples than I can count.)

But then I thought about it a moment more, and realized it is a goddamned stupid question.

I have never, in my entire life, been given an opportunity to vote for an openly atheist candidate for any office. Not once. This is a radically hypothetical question postulating an unthinkable world (to an American, at least) in which atheists can run for office without the bigoted Christian majority making it an exercise in futility, where we actually get a choice. In that reality, I think actually I might seriously consider voting for a non-odious conservative atheist (not Karl Rove, not a Randian asshole) just for the novelty of it all and to see someone, anyone representing my irreligious views in office.

Because isn’t that really the issue, that atheists are virtually locked out of most offices?

Then there are some weird assumptions in the question itself. What if a conservative atheist were answering it? There’d be no conflict of values at all. Notice how it simply assumes that nearly all atheist readers would be politically liberal — which I think is mostly true, despite the strong strain of Libertarianism within atheism.

But doesn’t that imply that if we had an atheist candidate representative of most atheists’ political leanings, the question ought to be:

If I had to vote for one of two hypothetical candidates, would I be more likely to vote for a liberal Christian or a liberal atheist?

O Glorious Imaginary Universe of Delightful Choices! Can you imagine going into the voting booth and finding yourself confronted with a decision between two reasonable, intelligent, thoughtful candidates, rather than Dumb Thug vs. the person the other party decided to run against it? Or, as I often find when voting for local offices, Dumb Thug vs. Dumb Thug.

But of course what reality tells us is that the candidate who clothes himself in religious garb and makes their faith an issue in a political campaign is almost always conservative — religion tends to side with stupid, archaic, and authoritarian on social issues. What that means is that if we ever did get an opportunity to make that choice at the ballot box, it would look like this:

If I had to vote for one of two hypothetical candidates, would I be more likely to vote for a conservative Christian or a liberal atheist?

And now it’s no question at all.

The drugs don’t work!

Ben Goldacre has a new book coming out, Bad Pharma: How Drug Companies Mislead Doctors and Harm Patients, which will be available this week in the UK and January in the US. From this excerpt in the Guardian, it’s going to be phenomenal…and phenomenally depressing. Once again, money poisons good science — the pharmaceutical industry is so awash in profits and greedy for more that they skew the results of clinical trials to get favorable statistics.

In any sensible world, when researchers are conducting trials on a new tablet for a drug company, for example, we’d expect universal contracts, making it clear that all researchers are obliged to publish their results, and that industry sponsors – which have a huge interest in positive results – must have no control over the data. But, despite everything we know about industry-funded research being systematically biased, this does not happen. In fact, the opposite is true: it is entirely normal for researchers and academics conducting industry-funded trials to sign contracts subjecting them to gagging clauses that forbid them to publish, discuss or analyse data from their trials without the permission of the funder.

This is such a secretive and shameful situation that even trying to document it in public can be a fraught business. In 2006, a paper was published in the Journal of the American Medical Association (Jama), one of the biggest medical journals in the world, describing how common it was for researchers doing industry-funded trials to have these kinds of constraints placed on their right to publish the results. The study was conducted by the Nordic Cochrane Centre and it looked at all the trials given approval to go ahead in Copenhagen and Frederiksberg. (If you’re wondering why these two cities were chosen, it was simply a matter of practicality: the researchers applied elsewhere without success, and were specifically refused access to data in the UK.) These trials were overwhelmingly sponsored by the pharmaceutical industry (98%) and the rules governing the management of the results tell a story that walks the now familiar line between frightening and absurd.

Drugs that don’t work, dangerous side-effects concealed by legalistic loopholes, blatant biases in drug testing…and the data are hidden away from the conscientious doctors who try to give informed recommendations. It’s all scary stuff.