Please don’t use this argument

I got briefly drawn into a twitter argument with a fellow atheist who proudly flashed this image:

badarg
The next time you get bullied by religious people on facebook, remind them that they are using hardware and software invented and built by atheists, including facebook!

That is embarassingly bad. And when I pointed out a few of the flaws in that claim (briefly, ala twitter), he just repeated the claim and then accused me of trolling.

Look, it’s a terrible argument. It annoys me in multiple ways.

  • Have you ever heard Christians claim that all of science is built on a Judeo-Christian foundation? I sure have (WARNING: Creationist video on autoplay at link!). I’ve been told many times that Newton didn’t believe in evolution. It sounds stupid when they say it, it sounds stupid when atheists say it.

  • What, do you really think there are no religious scientists and engineers? Tim Berners-Lee is a Unitarian Universalist. Guglielmo Marconi was both a Catholic and an Anglican. James Clerk Maxwell was a Baptist. I mean, seriously, you’re going to claim our modern technological world is the product of atheists, and you’re going to ignore Maxwell? Jebus. Pretty strong selection bias you’ve got there.

  • I die a little bit inside when you tell me that your paragon of techno-atheist excellence is Mark Zuckerberg and Facebook. Who thinks that Facebook was something that couldn’t possibly have been invented by a devout Christian?

  • All anyone needs to do is cite one Christian who worked on the development of the internet, and your argument dies. Is it wise to stake your claim to something all it takes is one counterexample to shoot down?

  • I notice all the exemplars in the picture are white men. Keep using this logic; let’s start bragging to everyone on the internet that they are using hardware and software invented and built by white people. It’s the same argument. Do you see the flaws yet?

  • We are living in an interesting little bubble of time in which our best educated, most economically stable people are drifting into more secular ways of thinking. Odds are that if you’re sufficiently secure economically that you can go to Harvard in a tech field, even so secure that you can drop out of Harvard, you’re also likely to be secular or liberally religious, and you’re also more likely to be white. Do not confuse cause and effect. You are succeeding because being godless and pale-skinned gives you an edge — you’re looking at people who started out on third base. It’s not because being godless gives you special science powers.

You are not going to find many people who are more adamant than I am that religion and science are incompatible — they are fundamentally different ways of determining the validity of truth claims, and one works while the other perpetuates garbage — but I am not going to confuse that with an incompatibility between religious people and science. Scientists who are religious are quite capable of setting aside supernatural beliefs to work well and succeed in the lab. Being an atheist doesn’t turn you into a scientist or engineer. Avoiding church doesn’t make you a better scientist or engineer — practicing science, no matter how silly the hobbies you practice in your spare time, does that.

I didn’t know I was signing up for a psychology experiment!

Jadehawk has an interesting post up on what psychology considers harassment — that is, when the pros assess effective harassment campaigns, what do they do?

Conclusion: Even mild interruption, ridicule, and criticism elicits stress responses, and all these mild stress-response-elicitors count as harassment in psychology. That doesn’t mean we should stop criticizing people, and it doesn’t mean that people who want to be skeptics, scientists and/or activists don’t need to learn to deal with a certain degree of both criticism and “trolling”. However, as with microaggressions, a constant barrage of aggression (some low-grade some decidedly less so) is typically more wearying/damaging than the occasional blatant, massive outburst. Consequently, telling a person who’s subjected for months to non-stop criticism, “satire”, parody, “trolling”, and plain old “as defined by every college campus everywhere” harassment* on multiple fronts that they aren’t being harassed is pure, unadulterated bullshit. Even the thickest skin will eventually be worn down** my months, or even years, of this sort of thing.

Yeah, years. But here’s the surprise from my perspective: what creationists and Christians did to me would not be considered harassment. They were not camping on my virtual doorstep greeting me first thing every morning with a flood of stupid videos and photoshopped images. They were not using twitter to masquerade as my friends under pseydonyms. They were not setting up blogs and forums with no other purpose than to malign me and a few other atheists personally. Even when I pissed off the Catholics, what would happen is that many individuals would fire off an angry letter or two, and then move on with their lives. It meant I got a deluge of email, but it wasn’t one or a few nuts going on a prolonged tear. Mabus was an exception. He isn’t anymore.

It wasn’t until I annoyed a subset of atheists that the real harassment began. Serious harassment. People who have no lives and think the most important thing to do every day is to pour out their hatred for me, or Rebecca Watson, or Ophelia Benson, or anyone on the Atheism+ forum. I’m not talking principled disagreement or even stupid disagreement: I mean commitment to do any dumbass thing they can to lash out, and being driven by hatred for a few people.

I do want to address one bizarre comment from some guy named Hunt, though, who is commenting on Jadehawk’s article.

A lot of these people deserve each other though. The Slymepit seems to be a perfect counterpart to PZ, who has trolled and harassed creationists, for instance, for a decade. He’s finally come up against people who are as willing to put the same energy into trolling back, irreverently and in a very similar way to what he’s done to others for years, and it’s pissing him off. What goes around comes around.

Nope. He doesn’t get it. I disagree strongly with creationists, and they disagree with me, but I don’t troll or harass. When I visited the Creation “Museum”, I informed them of my plans, I even signed an agreement to not cause trouble while I was there, not that I planned to; when I encourage my students to attend creationist talks, I also tell them to be polite and non-disruptive, and that the goal is to get information, not interrupt them. I don’t criticize creationists by sneering at their sexuality, defacing photographs of them, and getting up every day with cheery enthusiasm at the prospect of calling them fat, or ugly, or thinking of ways to tweak their names to make them sound like terms for genitalia.

I have a blog that ridicules creationism by dismantling their idiotic arguments, and that isn’t even obsessive about that…and definitely isn’t focused exclusively on just a few individuals.

What those jerks are doing isn’t in any way similar to what I’ve ever done. And what’s worse, it isn’t similar to what creationists have done: Eric Hovind may not be very bright, but he’s never sunk to the depths that the denizens of the Slymepit have.

But then, the false equivalence is one of the most common tools in use by the trolls. “He has criticized creationists, therefore he is fair game for me to draw him having sexual congress with a dog. It’s ‘dissent’!”

You know what’s most annoying to me, though? For years we’ve been trying to make the case to the public that you can be a decent human being while not believing in god. And then these slack-jawed, 4chan-lovin’, youtube-chatterin’ privileged gits come along and instead demonstrate that atheists can be the biggest assholes of them all.

Can you handle two polls in a day?

Here’s another one. A few Australian political leaders are taking a cue from the Americans and following a piecemeal approach to destroy abortion rights. You know how this works: the majority of the population favors those rights (and gay rights, and marijuana decriminialization, and so many other reasonable positions), so the haters get into office and start nibbling around the edges. They start choking off funding here and there, they throw money at propaganda, they make it increasingly difficult to get a basic medical procedure, and before you know it, abortion doctors are marginalized, people who get abortions are treated as pariahs, and public opinion starts to shift, because ignorance is a fairly potent lobbying group.

So the Australians have been doing the same thing. At least some people are noticing and beginning to speak up.

Should abortion laws be tightened using federal government legislation as flagged by Senator John Madigan?

Yes 43%

No 54%

Not sure 3%

There was one other little bit that I wanted to comment on.

On Wednesday, Senator Madigan will introduce a motion in the Senate aimed at stopping the public funding of abortions that are used purely to select boys or girls.

He told my colleague Lenore Taylor that he had ”seen data that abortion on the basis of gender selection is happening overseas and that means it is likely to be happening here”.

This may be an unpopular opinion, but if we’re going to be consistent and regard fetuses as undeserving of the rights of full adult humans, and if we’re going to respect the woman’s right to choose her own reproductive future, we can’t be in the business of telling women what good reasons they’re allowed to use. Elective abortions to select the sex of their child are perfectly reasonable, rational decisions. They should be allowed, and we shouldn’t be horrified if women elect to do them.

There is a problem that many people devalue girls so much that they could skew the sex ratio. But that’s a completely different issue — the institutionalizing of patriarchal values — and it isn’t addressed by dictating the choices women may make with their own bodies.

I also find it ironic that it is the same people who unthinkingly promote those patriarchal values who are horrified that they lead to women opting to abort more female fetuses. I’m not impressed that you insist on the right of girls to be brought to term so you can treat them as disposable once they reach reproductive age.

Netroots Nation offering admission by poll?

Netroots Nation is the big progressive political conference sponsored by the gang at the Daily Kos. It’s being held in San Jose this year, at the end of June. They are opening the doors to their exhibition hall and giving 6 organizations free booth space — and among those vying for a slot is American Atheists. I would have thought they’d just give AA the space because progressives and atheists are such a natural match for each other…but no. They’ve decided that the way to determine who should get this space is by…an open, public, online poll.

Oh, we’ve got this.

Go take a look at the list of candidates for the free booth space. American Atheists is a natural, but I’ve got to say…there are a lot of worthy possibilities there. Wrestle with your conscience for a bit and vote for the one you like best.

Oooh, maybe we don’t have this. You people are always exercising your brains and thinking about your choices, and you might go haring off and voting with your mind rather than your shriveled little obedience gland.

Dan Savage and I have something in common

Savage is the new Humanist of the Year! I think that means we have to give each other a hug if ever we meet.

2013humanists

He’s going to be at the American Humanist Association Annual Conference in San Diego on 30 May-3 June, along with those and many other interesting people. I wish I could be there—I’ll be landing back in the US around then, after a long week in Romania, but I think I’ll need time to recover and get back to work.

But to all of you who’ve been exasperated with the refractoriness of certain elements of the atheist movement…check out the humanists. That stuff so many fight against bitterly is simply taken for granted in the humanist community.

A Canadian poll on abortion

I thought Canadians had more sense than this: an MP, Jeff Watson, would like to know if you’d like a complete ban on all abortions. Right now, 37% of his constituency seem to think that’s just fine and dandy. Maybe he needs some global input?

Which best describes your position:.

I support fully taxpayer-funded abortion, at any time in the pregnancy, for any reason at all; 41%

I support some legal restrictions on access to abortion, for example restricting full access to abortion to the first trimester of pregnancy; 11%

I support abortion for any reason but it shouldn’t be taxpayer-funded; 2%

I support creative policy options and supports that help women with unexpected pregnancies keep the baby; or 7%

I support a complete ban on abortion. 37%

Don’t let Catholics run hospitals

Imagine if you lived in a town where the only hospital was owned by the Jehovah’s Witnesses, and you were in a car accident — you’ve got a ruptured spleen, you’re bleeding internally, and your life is at risk. The surgeon is going to go in and stitch up and cauterize everything, but you’re warned that they don’t keep any kind of blood supply in the hospital, and they refuse to do blood transfusions — they have an in-house professional ethicist (who is a Jehovah’s Witness, of course) who rejects the morality of exchanging sacred blood, and the administrators have signed an agreement with the church to never, under any circumstances, carry out blood transfusions.

If you need a blood transfusion, they say, don’t worry, the ambulance will take you to a different hospital…50 miles away. You, unfortunately, are in shock, you’ve got a gusher pouring blood into your body cavity, and this is not an option. You get to die.

We would not tolerate this situation. That hospital would have a change of ownership as fast as the public could drive it, and if anyone did die because of that kind of criminal neglect and refusal to follow standard medical procedure, a malpractice suit would be the least of their worries. Someone would be going to jail.

So why are Catholics allowed to buy up and impose Catholic dogma on hospitals? Is it because their ignorant dogma does the greatest harm to women (especially those slutty ones who have sex) and bizarre rules about reproduction don’t directly harm men?

But Catholics are buying up hospitals all over the country. They’ve got declining attendance, they’re closing churches, they’re having trouble recruiting priests, but they’ve still got buckets of money, and they’re using that money to impose control in another way — by taking over your health care.

Catholic institutions across the nation are merging with secular hospitals, clinics, and even small private practices at an unprecedented rate. Optimists explain that the consolidation and shared infrastructure help reduce costs. Pessimists point out that the aggressive mergers come at a time when Catholic bishops are exerting and expanding their authority. “I see it as a conscious effort to achieve through the private market what they failed to achieve through the courts or at the ballot box,” says Monica Harrington, a San Juan Island resident who’s spent the last year fighting a Catholic hospital in her town.

Three of the largest health-care systems in the Northwest—PeaceHealth, Providence Health & Services, and Franciscan Health System—are Catholic entities, and they’re busy making new deals in our state. According to MergerWatch, a nonprofit that tracks Catholic hospital mergers across the nation, there was a record-breaking 10 mergers announced in Washington State in 2012.

It’s a chilling story. Catholics can’t get their way in popular opinion, so they’ve followed another path, buying up and limiting health care options so that you have no choice but to follow their ancient biblical rules. The linked article is an examination of the growing move to limit your medicine to Catholic medicine in the Pacific Northwest, but it applies everywhere. They interviewed doctors who reported on their constraints.

Three physicians working in Whatcom County eventually agreed to speak with me. PeaceHealth bought out the secular hospital in 2008. Since then, PeaceHealth has systematically bought up nearly every specialty clinic in the area, from cardiologists to pediatricians, hospice to oncology. The physicians who agreed to meet me for coffee talked about the mindfuck of being raised Catholic, turning to atheism, and excelling in medicine—only to wake up one day with the church as your boss. The first physician joked grimly about the religious directives being “medieval torture porn.” He talked about the struggle of trying to balance his duty to patients with the edicts of a Catholic hospital.

These religious directives are nightmarish. They aren’t always followed — these really are rules laid down by religious fanatics who have no experience or connection to the actual practice of medicine, and conscientious doctors try to find workarounds — but what limits them now is competition. If Catholics get a monopoly on health care in an area, then the trouble really begins.

To understand Catholic health care, it’s important to know the rules that guide Catholic hospitals, otherwise known as Ethical and Religious Directives (ERDs). These directives are drafted and tweaked by the rotating cast of mostly white, mostly celibate bishops couch-surfing at the Vatican. ERDs operate like a code of conduct that medical staff in Catholic hospitals agree to abide by, regardless of whether or not a particular staffer is Catholic. For the most part, the directives aren’t suggestions—they’re prescriptive.

“Any partnership… must respect church teaching and discipline,” one directive states. The church monitors the implementation of these directives through hospital ethic committees overseen by regional bishops like our very own Archbishop Peter Sartain.

Sure, in 43 pages of Ethical and Religious Directives, there’s some common-sense guidance to be found. But they’re also flush with horrifying detail. As you’d expect, the directives pertaining to women’s fertility read like a misogynist romance novel or found art from the Middle Ages: “Catholic health institutions may not promote or condone contraceptive practices.” Emergency contraception can only be given to rape victims, and even then only “if, after appropriate testing, there is no evidence that conception has occurred already.” Vasectomies and tubal ligations are also prohibited. Egg and sperm donors are deemed “contrary to the covenant of marriage,” surrogate motherhood is prohibited because it denigrates “the dignity of the child and marriage,” and doctors at Catholic hospitals can’t help infertile couples conceive artificially—using their own eggs and sperm—because test-tube babies “separate procreation from the marital act in its unitive significance.”

Then there’s this: “Abortion… is never permitted.”

Not even when the egg attaches outside the uterus and puts a mother’s life in danger: “In case of extrauterine pregnancy, no intervention is morally licit which constitutes a direct abortion.”

The short-sighted and selfish male readers out there (and we know we have no shortage of those assholes in the atheist community) aren’t possibly quite as outraged as they should be. These rules affect women, right? I got mine, let them worry over it, it’s not my fight.

Unfortunately, Catholics also have some weird ideas about LGBT relationships. Another set of people who are going to be hurt by this Catholic takeover are those who are in any kind of relationship that doesn’t fit their narrow definition of one man, one woman…and give them the power to flex their ideological muscle, and you might find yourself snubbed if you’re divorced.

So maybe you aren’t gay and your sexual relationships are conservative and conventional. The other big problem is death, which all of us will do someday. Washington state passed a death with dignity law a few years ago, allowing physician-assisted suicide in terminal cases. Guess which hospitals ignore the law and will prolong your suffering indefinitely?

Don’t let Catholics control your hospitals. Keep the church out of your health care decisions. Make Catholic Ethical and Religious Directives (ERDs) illegal — individuals may follow them at their personal discretion, but no health care facility gets to impose them on their patients, especially when they defy the law.

I am so over the skeptical movement

I am so over Ben Radford. I thought he was obtuse before. Now I’m convinced that he’s simply an idiot. He attempts to rebut my criticisms.

Myers admits that I’m technically correct that Ensler’s statistics are not exactly right, but claims I’m being “hyperskeptical,” and states that “One billion women have been victims of ‘homicide, intimate partner abuse, psychological abuse, dating violence, same-sex violence, elder abuse, sexual assault, date rape, acquaintance rape, marital rape, stranger rape and economic abuse,’ confirmed by statistics that Radford cites. One billion women. Radford’s hyperskepticism is so fierce that he objects to Ensler using 3 general words – raped, beaten, violated – instead of 26 more specific words, but is willing to overlook the horrific truth that she is correct and one billion women will suffer for their sex in their lifetime.”

Except that I didn’t; Myers misread it. I actually didn’t write the “one billion” figure that Myers misquotes me as saying; that was Ensler’s number. What I actually wrote (check it yourself) was that “one-third of women [have been victims of] homicide, intimate partner abuse, psychological abuse, dating violence, same-sex violence, elder abuse, sexual assault, date rape, acquaintance rape, marital rape, stranger rape and economic abuse.” (One in three women is not the same as one billion if you do the math, though perhaps that’s just my hyperskepticism.)

I was not saying he was technically correct. I was saying that the figure he’s carping about is actually right, and that his complaints are empty. I did not realize that he’d respond by proudly declaring his innumeracy: I’m sorry, but 1/3 of 1/2 of 7 billion people is actually about one billion.

Worse yet, he then goes on to piously plead that people need to heed the principle of charity in their arguments (I’ve noticed that it’s usually the people who most need charity who are begging for it.) Then — get ready for it — he turns around and writes this appalling piece of ham-handed dreck. Yeah, right. Fuck the principle of charity. No charity for you, Radford.

I’m so over Harriet Hall’s t-shirt. She’s been going on and on, circling around the drain to somehow defend it. It’s simple: she wore it to spite some people she clearly doesn’t like, and to get praise from other people who don’t like Rebecca Watson and the Skepchicks. It’s really that easy. Just admit it and move on. I know it’s hard to admit that you’re that petty, but it would end all this nonsense, and it would be honest. Get over it; the wordy excuse-making is getting embarrassing. Besides, Amanda Marcotte has Hall’s number.

I’m so over Reap Paden. Dear god, he’s so obsessive he’s made another creepy video that says far more about him than me.

The one thing I’m happy to do is publicize these dumbass arguments. Why is it that people who attach themselves to a movement that prides itself on having rationality as its raison d’etre are so godawful pathetic at making a case for themselves?

ENCODE gets a public reaming

I rarely laugh out loud when reading science papers, but sometimes one comes along that triggers the response automatically. Although, in this case, it wasn’t so much a belly laugh as an evil chortle, and an occasional grim snicker. Dan Graur and his colleagues have written a rebuttal to the claims of the ENCODE research consortium — the group that claimed to have identified function in 80% of the genome, but actually discovered that a formula of 80% hype gets you the attention of the world press. It was a sad event: a huge amount of work on analyzing the genome by hundreds of labs got sidetracked by a few clueless statements made up front in the primary paper, making it look like they were led by ignoramuses who had no conception of the biology behind their project.

Now Graur and friends haven’t just poked a hole in the balloon, they’ve set it on fire (the humanity!), pissed on the ashes, and dumped them in a cesspit. At times it feels a bit…excessive, you know, but still, they make some very strong arguments. And look, you can read the whole article, On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE, for free — it’s open source. So I’ll just mention a few of the highlights.

I’d originally criticized it because the ENCODE argument was patently ridiculous. Their claim to have assigned ‘function’ to 80% (and Ewan Birney even expected it to converge on 100%) of the genome boiled down to this:

The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.

So if ever a transcription factor ever, in any cell, bound however briefly to a stretch of DNA, they declared it to be functional. That’s nonsense. The activity of the cell is biochemical: it’s stochastic. Individual proteins will adhere to any isolated stretch of DNA that might have a sequence that matches a binding pocket, but that doesn’t necessarily mean that the constellation of enhancers and promoters are present and that the whole weight of the transcriptional machinery will regularly operate there. This is a noisy system.

The Graur paper rips into the ENCODE interpretations on many other grounds, however. Here’s the abstract to give you a summary of the violations of logic and evidence that ENCODE made, and also to give you a taste of the snark level in the rest of the paper.

A recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 − 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.

You may be wondering about the curious title of the paper and its reference to immortal televisions. That comes from (1): that function has to be defined in a context, and that the only reasonable context for a gene sequence is to identify its contribution to evolutionary fitness.

The causal role concept of function can lead to bizarre outcomes in the biological sciences. For example, while the selected effect function of the heart can be stated unambiguously to be the pumping of blood, the heart may be assigned many additional causal role functions, such as adding 300 grams to body weight, producing sounds, and preventing the pericardium from deflating onto itself. As a result, most biologists use the selected effect concept of function, following the Dobzhanskyan dictum according to which biological sense can only be derived from evolutionary context.

The ENCODE group could only declare function for a sequence by ignoring all other context than the local and immediate effect of a chemical interaction — it was the work of short-sighted chemists who grind the organism into slime, or worse yet, only see it as a set of bits in a highly reduced form in a computer database.

From an evolutionary viewpoint, a function can be assigned to a DNA sequence if and only if it is possible to destroy it. All functional entities in the universe can be rendered nonfunctional by the ravages of time, entropy, mutation, and what have you. Unless a genomic functionality is actively protected by selection, it will accumulate deleterious mutations and will cease to be functional. The absurd alternative, which unfortunately was adopted by ENCODE, is to assume that no deleterious mutations can ever occur in the regions they have deemed to be functional. Such an assumption is akin to claiming that a television set left on and unattended will still be in working condition after a million years because no natural events, such as rust, erosion, static electricity, and earthquakes can affect it. The convoluted rationale for the decision to discard evolutionary conservation and constraint as the arbiters of functionality put forward by a lead ENCODE author (Stamatoyannopoulos 2012) is groundless and self-serving.

There is a lot of very useful material in the rest of the paper — in particular, if you’re not familiar with this stuff, it’s a very good primer in elementary genomics. The subtext here is that there are some dunces at ENCODE who need to be sat down and taught the basics of their field. I am not by any means a genomics expert, but I know enough to be embarrassed (and cruelly amused) at the dressing down being given.

One thing in particular leapt out at me is particularly fundamental and insightful, though. A common theme in these kinds of studies is the compromise between sensitivity and selectivity, between false positives and false negatives, between Type II and Type I errors. This isn’t just a failure to understand basic biology and biochemistry, but incomprehension about basic statistics.

At this point, we must ask ourselves, what is the aim of ENCODE: Is it to identify every possible functional element at the expense of increasing the number of elements that are falsely identified as functional? Or is it to create a list of functional elements that is as free of false positives as possible. If the former, then sensitivity should be favored over selectivity; if the latter then selectivity should be favored over sensitivity. ENCODE chose to bias its results by excessively favoring sensitivity over specificity. In fact, they could have saved millions of dollars and many thousands of research hours by ignoring selectivity altogether, and proclaiming a priori that 100% of the genome is functional. Not one functional element would have been missed by using this procedure.

This is a huge problem in ENCODE’s work. Reading Birney’s commentary on the process, you get a clear impression that they regarded it as a triumph every time they got even the slightest hint that a stretch of DNA might be bound by some protein — they were terribly uncritical and grasped at the feeblest straws to rationalize ‘function’ everywhere they looked. They wanted everything to be functional, and rather than taking the critical scientific view of trying to disprove their own claims, they went wild and accepted every feeble excuse to justify them.

The Intelligent Design creationists get a shout-out — they’ll be pleased and claim it confirms the validity of their contributions to real science. Unfortunately for the IDiots, it is not a kind mention, but a flat rejection.

We urge biologists not be afraid of junk DNA. The only people that should be afraid are those claiming that natural processes are insufficient to explain life and that evolutionary theory should be supplemented or supplanted by an intelligent designer (e.g., Dembski 1998; Wells 2004). ENCODE’s take-home message that everything has a function implies purpose, and purpose is the only thing that evolution cannot provide. Needless to say, in light of our investigation of the ENCODE publication, it is safe to state that the news concerning the death of “junk DNA” have been greatly exaggerated.

Another interesting point is the contrast between big science and small science. As a microscopically tiny science guy, getting by on a shoestring budget and undergraduate assistance, I like this summary.

The Editor-in-Chief of Science, Bruce Alberts, has recently expressed concern about the future of “small science,” given that ENCODE-style Big Science grabs the headlines that decision makers so dearly love (Alberts 2012). Actually, the main function of Big Science is to generate massive amounts of reliable and easily accessible data. The road from data to wisdom is quite long and convoluted (Royar 1994). Insight, understanding, and scientific progress are generally achieved by “small science.” The Human Genome Project is a marvelous example of “big science,” as are the Sloan Digital Sky Survey (Abazajian et al. 2009) and the Tree of Life Web Project (Maddison et al. 2007).

Probably the most controversial part of the paper, though, is that the authors conclude that ENCODE fails as a provider of Big Science.

Unfortunately, the ENCODE data are neither easily accessible nor very useful—without ENCODE, researchers would have had to examine 3.5 billion nucleotides in search of function, with ENCODE, they would have to sift through 2.7 billion nucleotides. ENCODE’s biggest scientific sin was not being satisfied with its role as data provider; it assumed the small-science role of interpreter of the data, thereby performing a kind of textual hermeneutics on a 3.5-billion-long DNA text. Unfortunately, ENCODE disregarded the rules of scientific interpretation and adopted a position common to many types of theological hermeneutics, whereby every letter in a text is assumed a priori to have a meaning.

Ouch. Did he just compare ENCODE to theology? Yes, he did. Which also explains why the Intelligent Design creationists are so happy with its bogus conclusions.