A child is not a notch on the bedpost

Them folk are not like us folk. I really had to twist my brain to read this article from Touchstone on “contradeception”, because I’m finding it hard to imagine how screwed up in the head you have to be to think that way.

It’s an article against contraception. When these quiverful zealots argue that they love kids, I can sympathize; when they say they are trying to outbreed non-Christians, I can sort of understand the logic, even though I think they’re wrong; but this story…children are like an afterthought. The reason you shouldn’t use contraception is because getting pregnant is public evidence that you are fulfilling your marital duties.

It’s a kind of busybody’s idea of heaven and earth…or perhaps a very monkey-like one. Everyone is supposed to monitor everyone else’s sexual behavior, and the purpose of marriage is to make it easy for everyone to track who is screwing who.

Sexual relationships, while enacted privately, are public property. The lover declares, “I am my beloved’s and my beloved is mine.” This protects the relationship from internal and external breach. Those within the relation-ship are bound to each other by their promise of troth, held in trust by the neutral third parties who witness the promise. Those outside the relationship know that this new unit of their community is being rightly founded, and also that any attempt to besiege the promise is illicit.

And shunning contraception means everyone will be able to tell who is sneaking around, and who is getting the job done in the bedroom. Well, at least it’ll make it easier to monitor the women, but then, that’s what this is all about…making sure that female fidelity is evident.

And in former times, when the married couple fulf lled their vows to God and each other and their witnesses, they produced, at God’s favor, babies to prove it. The lack of a baby indicated either a broken body or a broken vow. While both called for the community’s prayer, the latter also called for the community’s assistance in healing the marriage for the benefit of everyone, for a broken vow means broken people. When a baby gave evidence of a union where no vow had been made, it was similarly in the interest of the community to correct the situation in the way that would most benefit all the parties involved.

Again, it’s all about letting everyone know that the woman is having sex, by making sure she’s pregnant all the time. If you have sex outside of marriage, you are “damaged goods” and must be prominently labeled as such.

In marriage, a couple gives over supervision of their marital health to those who approved their avowal. A sexual relationship between people who made no vows would normally not remain a secret for long. But contraception blinds the community by concealing the sexual act outside of marriage, or its absence within marriage, and by leaving goods damaged in various ways unmarked as such.

It really is the public notch on the bedpost model of the purpose of pregnancy!

Why must we have physical, public evidence of the faithful fulfillment of even those marital vows most of us can’t imagine neglecting, at least at first? Who would lie about such things? Well, who would talk about them? Allowing nature to manifest our faithfulness is certainly more graceful than a verbal report.

Except…Mrs Murphy could be knocking boots with the mailman every morning, in which case her swelling belly is not a testimony to faithfulness, and Mr Murphy could be making regular visits to the bordello out on county road 6. Pregnancy is not a good evidence of fidelity, but only of the fact that a woman is getting inseminated.

The whole article is this bizarre. Not rushing to have children, practicing family planning, implies that maybe you aren’t having sex as often as you should.

This is also why the Church perceives discord in the decision of a newly married couple to take a few years to “enjoy being married” before ending marital enjoyment with children. Apparently, we are expected to take them at their word that they are fulfilling the vows made before us, although they refuse to tender the token. In those storied former times, we’d have worried that perhaps the sweet things weren’t quite sure how things worked. For now, charity ordains that we fill in the child-shaped marital deficiency with the sad assumption of trouble conceiving, except in the great majority of cases, where bride and groom make no secret of being confirmed window shoppers at the baby mall. If you’re going to be married, be smart, after all. Be ever copulating but never conceiving. Their debt to their witnesses (to say nothing of each other) goes quite unacknowledged.

I married at 23, and we waited 3 years to have our first child. I swear that we were not celibate for that period of time, nor would any sane person have assumed we were. I did not feel a need to get her pregnant instantly as a way of staking a claim on my ownership of her uterus.

And yeah, we were copulating all the time — I thought we were paying a debt to each other in building a bond. We owe no debt to witnesses outside of the marriage. I suppose if they’d insisted, we could have gone at it on the picnic table at a family reunion, but seriously — it was none of their business. Apparently, by abstaining from flaunting our fertility we were treating everyone else disrespectfully.

So also is the public treated disrespectfully by the couple who, 2.1 children later, give no sign of continued faithfulness to their vow. Is he so disgusted by the sight of his wife’s birth-changed body that he will no longer suffer its embrace? Is she using her maternal exhaustion as an excuse to withhold herself from him? Can this marriage survive? The only way we know a marriage to be sexless is when it comes out in therapy, on the golf course, at play dates, on the pages of The Atlantic.

This whole thing is very disturbing. We stopped with 3 children, by intent — we love kids, but we wanted to give each one the attention they deserved, and we had to plan ahead for that expensive business of making sure each one got a good education. The good of the children, however, is not part of the equation with these people.

So we stopped having babies almost 20 years ago…and apparently, this blue-nosed wowser would think from that that I’m now disgusted with my wife’s body, or that my wife is withholding sex now that the tiring business of making children is done. You know, it’s none of your business what any two people’s private sex life is like, but anyone can note that despite the fact that she’s had a flat belly empty of embryos for a score of years, my wife is still with me and we’re still happy together.

Who’d have thought that you don’t need to be in a state of constant pregnancy to have a good and productive relationship? It’s sad to think that there are women out there who feel the measure of their worth is determined by the diameter of their abdomens.

The worst job in the world

Are the fundies imploding? Look at this summary of their own assessment of the status of the evangelical priesthood:

Another article reveals even more telling statistics based on a survey of 1,050 evangelical Pastors (note these are evangelical pastors not liberal pastors):

  • 89% considered leaving the ministry at one time.
  • 57% said they would leave if they had a better place to go—including secular work.
  • 77% felt they did not have a good marriage!
  • 75% felt they were unqualified and/or poorly trained by their seminaries to lead and manage the church or to counsel others. This left them disheartened in their ability to pastor. 
  • 71% stated they were burned out, and they battle depression beyond fatigue on a weekly and even a daily basis. 
  • 38%  said they were divorced or currently in a divorce process.
  • 30% either has an ongoing affair or a one-time sexual encounter with a parishioner.
  • 23% said they felt happy and content on a regular basis with who they are in Christ, in their church, and in their home!

The same article also gives the following research distilled from Barna, Focus on the Family, and Fuller Seminary.

  • 1500 pastors leave the ministry each month due to moral failure, spiritual burnout, or contention in their churches.
  • 50% of pastors’ marriages will end in divorce.
  • 80 percent of pastors feel unqualified and discouraged in their role as pastor.
  • 50% of pastors are so discouraged that they would leave the ministry if they could, but have no other way of making a living.
  • 80% of seminary and Bible school graduates who enter the ministry will leave the ministry within the first five years.
  • 70% of pastors constantly fight depression.
  • 40% of pastors polled said they have had an extra-marital affair since beginning their ministry.

I imagine it’s a high-stress job. These people are actually intelligent, and relatively well-educated…and their job requires standing up in front of crowds every week, and dealing one-on-one with others frequently, and telling them a line of foolishness.

It’s an interesting complement to Dan Dennett’s work on priests who don’t believe — the statistics tell us something about the frequency of doubt, while Dennett’s stories tell us what’s going on in their heads.

Junk DNA is still junk

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The ENCODE project made a big splash a couple of years ago — it is a huge project to not only ask what the sequence of a strand of human DNA was, but to analyzed and annotate and try to figure out what it was doing. One of the very surprising results was that in the sections of DNA analyzed, almost all of the DNA was transcribed into RNA, which sent the creationists and the popular press into unwarranted flutters of excitement that maybe all that junk DNA wasn’t junk at all, if enzymes were busy copying it into RNA. This was an erroneous assumption; as John Timmer pointed out, the genome is a noisy place, and coupled with the observations that the transcripts were not evolutionarily conserved, it suggested that these were non-functional transcripts.

Personally, I fall into the “it’s all junk” end of the spectrum. If almost all of these sequences are not conserved by evolution, and we haven’t found a function for any of them yet, it’s hard to see how the “none of it’s junk” view can be maintained. There’s also an absence of support for the intervening view, again because of a lack of evidence for actual utility. The genomes of closely related species have revealed very few genes added from non-coding DNA, and all of the structural RNA we’ve found has very specific sequence requirements. The all-junk view, in contrast, is consistent with current data.

Larry Moran was dubious, too — the transcripts could easily by artifactual.

The most widely publicized result is that most of the human genome is transcribed. It might be more correct to say that the ENCODE Project detected RNA’s that are either complimentary to much of the human genome or lead to the inference that much of it is transcribed.

This is not news. We’ve known about this kind of data for 15 years and it’s one of the reasons why many scientists over-estimated the number of humans genes in the decade leading up to the publication of the human genome sequence. The importance of the ENCODE project is that a significant fraction of the human genome has been analyzed in detail (1%) and that the group made some serious attempts to find out whether the transcripts really represent functional RNAs.

My initial impression is that they have failed to demonstrate that the rare transcripts of junk DNA are anything other than artifacts or accidents. It’s still an open question as far as I’m concerned.

I felt the same way. ENCODE was spitting up an anomalous result, one that didn’t fit with any of the other data about junk DNA. I suspected a technical artifact, or an inability of the methods used to properly categorize low frequency accidental transcription in the genome.

Creationists thought it was wonderful. They detest the idea of junk DNA — that the gods would scatter wasteful garbage throughout our precious genome by intent was unthinkable, so any hint that it might actually do something useful is enthusiastically siezed upon as evidence of purposeful design.

Well, score one for the more cautious scientists, and give the creationists another big fat zero (I think the score is somewhere in the neighborhood of a big number requiring scientific notation to be expressed for the scientists, against a nice, clean, simple zero for the creationists). A new paper has come out that analyzes transcripts from the human genome using a new technique, and, uh-oh, it looks like most of the early reports of ubiquitous transcription were wrong.

Here’s the author’s summary:

The human genome was sequenced a decade ago, but its exact gene composition remains a subject of debate. The number of protein-coding genes is much lower than initially expected, and the number of distinct transcripts is much larger than the number of protein-coding genes. Moreover, the proportion of the genome that is transcribed in any given cell type remains an open question: results from “tiling” microarray analyses suggest that transcription is pervasive and that most of the genome is transcribed, whereas new deep sequencing-based methods suggest that most transcripts originate from known genes. We have addressed this discrepancy by comparing samples from the same tissues using both technologies. Our analyses indicate that RNA sequencing appears more reliable for transcripts with low expression levels, that most transcripts correspond to known genes or are near known genes, and that many transcripts may represent new exons or aberrant products of the transcription process. We also identify several thousand small transcripts that map outside known genes; their sequences are often conserved and are often encoded in regions of open chromatin. We propose that most of these transcripts may be by-products of the activity of enhancers, which associate with promoters as part of their role as long-range gene regulatory sites. Overall, however, we find that most of the genome is not appreciably transcribed.

So, basically, they directly compared the technique used in the ENCODE analysis (the “tiling” microarray analysis) to more modern deep sequencing methods, and found that the old results were mostly artifacts of the protocol. They also directly examined the pool of transcripts produced in specific tissues, and asked what proportion of them came from known genes, and what part came from what has been called the “dark matter” of the genome, or what has usually been called junk DNA. The cell’s machinery to transcribe genes turns out to be reasonably precise!

To assess the proportion of unique sequence-mapping reads accounted for by dark matter transcripts in RNA-Seq data, we compared the mapped sequencing data to the combined set of known gene annotations from the three major genome databases (UCSC, NCBI, and ENSEMBL, together referred to here as “annotated” or “known” genes). When considering uniquely mapped reads in all human and mouse samples, the vast majority of reads (88%) originate from exonic regions of known genes. These figures are consistent with previously reported fractions of exonic reads of between 75% and 96% for unique reads, including those of the original studies from which some of the RNA-Seq data in this study were derived. When including introns, as much as 92%-93% of all reads can be accounted for by annotated gene regions. A further 4%-5% of reads map to unannotated genomic regions that can be aligned to spliced ESTs and mRNAs from high-throughput cDNA sequencing efforts, and only 2.2%-2.5% of reads cannot be explained by any of the aforementioned categories.

Furthermore, when they looked at where the mysterious transcripts are coming from, they are most frequently from regions of DNA near known genes, not just out of deep intergenic regions. This also suggests that they’re an artifact, like an extended transcription of a gene, or from other possibly regulatory bits, like pasRNA (promoter-associated small RNAs — there’s a growing cloud of xxxRNA acronyms growing out there, but while they may be extremely useful, like siRNA, they’re still tiny as a fraction of the total genome. Don’t look for demolition of the concept of junk DNA here).

There clearly are still mysteries in there — they do identify a few novel transcripts that come up out of the intergenic regions — but they are small and rare, and the fact of their existence does not imply a functional role, since they could simply be byproducts of other processes. The only way to demonstrate that they actually do something will require experiments in genetic perturbation.

The bottom line, though, is the genome is mostly dead, transcriptionally. The junk is still junk.

van Bakel H, Nislow C, Blencowe BJ, Hughes TR (2010) Most “Dark Matter” Transcripts Are Associated With Known Genes. PLoS Biology 8(5):1-21.

We can’t cure the disease by praising the symptoms

Karl Giberson, who I’ve bashed once or twice, has a fresh new pile of nonsense on the Huffington Post. Jerry Coyne has already tackled it, but it pushes a few of my buttons, so I’ve got to say my piece, too.

To summarize the Giberson nonsense briefly, he claims that Intelligent Design creationism is not dead, but is thriving, and in order to defeat it, we need to shut the atheists up who are making people choose between gods and science. I disagree with every bit of it.

ID is not only dead, it was stillborn. No one believes in it; it is a sterile abstraction with no evidence that was cobbled up entirely to pass the church/state separation tests in the courts. Phil Johnson, the fellow who invented it, has plainly stated that he is a born-again Christian lawyer, and his goal with the development of ID was to create a legal construct that could not be excluded from the schools, because it left out any mention of gods. Yet all the major players on the ID side are devout: Dembski is a crazy evangelical, Behe is a Catholic, and if you go through the roster at the Discovery Institute, you’ll find similar religious/ideological leanings throughout (except, maybe, Berlinski — but he’s his own unique brand of supercilious lunacy).

The Dover trial laid it bare. ID was simply the façade a troop of fervent Christian creationists used to conceal their true motivations. ID isn’t the problem. The problem is wide-spread sectarian Christian beliefs that want to masquerade as science — they finally realized after three quarters of a century of courtroom failure that going about with bare-faced Jesus freakiness was going to get them nowhere, so they’ve pulled down ID as a handy mask. It doesn’t work. Everyone can see right through it, and the cdesign proponentsists rely on a lot of wink-wink you-know-I-love-god-even-in-my-labcoat games to get support.

ID is dead, except as a political tool, which is all it ever was anyway. The only people who use it are plain old creationists; strip away ID, and they’ll just grope for a new guise.

Giberson drags out 4 bad arguments for why Intelligent Design is still vital.

1) The complex designs of many natural structures that have not yet been explained by science. As long as there are ingenious devices and intricate phenomena in nature (origin of life, anyone?) that we cannot understand, there will be ID arguments.

2) The remarkable, finely-tuned structure of the cosmos in which the laws of physics collaborate to make life possible. Many agnostics have had their faith in unguided materialism shaken by this, most recently Anthony Flew.

3) The widespread belief that God — an intelligent agent — created the universe. The claim that an intelligent God created an unintelligent universe seems peculiar, to say the least.

4) The enthusiastic insistence by the New Atheists that evolution is incompatible with belief in God. Most people think more highly of their religion than their science. Imagine trying to get 100 million Americans to dress up for a science lecture every Sunday morning — and then voluntarily pay for the privilege.

Hang on, wait a minute. I’ve heard all of that from the Intelligent Design creationists, but I’ve also heard it somewhere else…where could that be…hmmm. Hey, I know! Those are the same arguments that the theistic evolutionists use on the Biologos website!

As long as we don’t understand every detail of how life originated, the theistic evolutionists will be claiming a role for gods in it. As long as they’re preaching about souls, they’re rooting beliefs in ignorance about how minds work.

The theistic evolutionists make a big deal of fine-tuning arguments. I fail every time to be surprised that life like ours exists in a universe where the physical constants allow the formation of stars. Oh, and please, Antony Flew’s late-life fame seems to derive entirely from the fact that he tepidly embraced ID when he was fading into senility and was being coached by a sympathetic advocate for creationism.

Theistic evolutionists believe a god or gods created the universe!

Theistic evolutionists get really peevish at all those atheists pointing out that their belief in magical beings is very, very silly. They now use that as a recruiting tool, trying to convince people that they can have their science and still believe in ghosts and spirits and demons and angels. You know, Ken Ham tries the same thing, coupling dinosaurs to biblical literalism. It’s awfully hard to distinguish the principles and tactics of Biologos from those of the Creation “Museum”.

Weird, isn’t it? It’s as if Giberson doesn’t realize that demolishing the foundations of Intelligent Design creationism would also undermine theistic evolution…and that maybe the atheists he is complaining about are aware of this, realizing that creationism, intelligent design, and theism all share precisely the same faulty construction — we can’t get rid of one without shattering all the others.

I do agree with Giberson on one thing. Most Americans do think more highly of their religion than science. But there’s a significant difference: I think that having a citizenry that worships irrational, fact-free thinking and zombie gods and believes in a coming apocalypse — which they consider an event to be greatly desired — is a bad thing. Giberson regards it as a virtue. That difference dictates that we’ll have different strategies: I want to break people’s habits of gullibility and supernatural delusions; Giberson wants to prop them up. If you really want to defeat ID, the way to do it is to defeat religious thinking.

Giberson wants to claim that a godless scientific approach is a failure, and as an example, he uses the persistence of astrology.

Consider astrology. A 2009 Pew Poll showed that some 25 percent of Americans “believe” in astrology. President Reagan “believed” in astrology. Twenty million astrology books are sold each year. What is going on here? Didn’t science thoroughly discredit astrology at roughly the same time it was establishing the motion of the earth? How can an idea so thoroughly refuted be so popular?

If the scientific community cannot successfully convince Americans to abandon belief in astrology — which is not tied to any powerful religious tradition or even to belief in God — what hope is there to refute an idea like Intelligent Design, which is so much more complex than astrology?

What an odd argument. The Bible condemns astrology; Jehovah wants his chosen people to have no truck with divination, sorcery, omens, witchcrafte, necromancy, or any attempt to contact the dead. Yet still 25% of Americans, many of whom must be Christians, still persist in it! What hope is there of refuting bogus ideas like astrology or ID with an Abrahamic religion, which has a 3,000 year record of failure?

I’ve looked into both ID and astrology, and again, Giberson is completely wrong. Astrology is much more complicated. It has accreted many centuries of rationalizations and anecdotes and weird thefts of bits and pieces of mathematics and astronomy. There’s virtually nothing to ID but hot air in comparison.

Of course, I don’t accept one bit of astrology. However, it does have widespread appeal because it can provide a long history of tradition and dogma, scholarly works that go back to the Middle Ages, an endearing habit of claiming that the entire universe is all about you, and thousands of sects and variants that one can fall back on if a prediction in one schema fails. It has all the properties of religion!

I would argue that one reason that astrology (and religion) haven’t gone away is that people like the answers they provide, even if they’re wrong, and that celebration of wishful thinking is an epidemic in the populace. And one reason it persists is that we have a significant number of our citizens dutifully trotting into churches every Sunday, where they are told by solemn authorities that the universe loves them personally, and look, here’s an old book reassuring us that it is so. Religion is a cultural parasite that weakens our intellectual immune system, and opens the door to lots of other opportunistic infections. Jesus cults and astrology and scientology and snake oil and the Secret and quantum woo are the Kaposi’s sarcoma of a deeper disease—faith.

We’re just now beginning the process of rooting out the causal agents of that disease, and what we need to do is promote more intellectual hygiene, like skepticism, which is the rational equivalent of washing your hands. The wishy-washy, ridiculous theism that Giberson promotes echoes the medieval scholars who tried to argue that bathing was a nasty habit.

Giberson doesn’t want that. We’re supposed to endorse one version of humbuggery, religion, while deploring another, ID, all in the name of keeping everyone comfortable in their prejudices, no matter how erroneous.

If the scientific community wants to dislodge ID, they need to start by admitting that their efforts have been an abysmal failure so far. And then they need to turn their considerable analytical skills on the problem of explaining that failure. If they do this, they might discover that enthusiastic pronouncements like “ID is dead” or “science has proven God does not exist” or “religion is stupid” or “creationists are insane” are not effective. They might discover that affirming that the universe is wonderful, despite our bad backs and the nonsense in our genomes, makes it easier for people to accept the bad design in nature.

And above all, they need to decide that it is OK for people to believe in God. For millions of Americans belief in ID is tied to belief in God. Unless people can find a way to separate them — and not be told by agnostic bloggers this is impossible — ID’s coffin will remain empty.

Yes, we godless scientists are often affirming the wonderful qualities of the universe. But, and this is an important distinction, we do so by discussing what is real, not the awesomeness of some imaginary phantasm that the theists want us to worship. We are not going to succeed at getting people to embrace reality if some dufus in a clerical collar keeps trying to insert some ridiculous proxy he calls a god into our understanding, and further, insists that we can really only appreciate physics and chemistry and biology if we deeply adore a particular dead prophet.

ID and a belief in gods are all tangled together, and they are inseparable. Killing one requires killing the other, and it seems to me that only the atheists are recommending the practical approach of tossing out the whole religious package with its attendant absurdities, and rebuilding an ethical, rational vision of the world that does not require any supernatural bullshit at all.

Ken Ham snubbed again

Poor Ken. He so wants to be respectable.

He’s complaining now that the Creation “Museum” tried to get in on some marketing deal with an outfit called Groupon, that advertises discount coupons or something, and he got turned down. They thought his “museum” was too controversial. So Ken Ham must whine.

Some of the businesses they feature for our area are attractions such as laser tag, spas, lawn care, etc. However, in other markets (such as Atlanta) they have featured the local natural history museum–which of course is totally evolutionary and teaches children that man is an evolved animal–but I guess that is not controversial!

That is correct. Evolution is not controversial at all in the real world. It is only controversial in the wacky fantasy land of fundamentalist superstition.

Apparently, because the Creation Museum is a Christian facility with a walk through the Bible, that is “controversial!”

No, I only wish the Bible and Christianity were regarded as controversial, but they aren’t — they’re pretty much widely accepted here in Idiot America. The problem with the Creation “Museum” is that it is brain-dead soul-sucking stupid, and while Americans love wallowing in piety, they hate being associated with obvious inanity.

Argonauts float!

Argonauts are odd animals. They rather resemble a nautilus, but they aren’t particularly closely related to them; their closest cephalopod relatives are the octopuses. Females have a thin shell and scoot about in the water column, but the poor males are all dwarfs, rarely seen, with no shell.

What is the shell for? It seems to be a chamber for holding a bubble of air that the animals use to maintain neutral buoyancy. I’m a little surprised that this was a surprise, though — the analogy to the chambered nautilus is obvious, and all the photos and videos I’ve seen of them suspended in midwater suggested that they were maintaining neutral buoyancy somehow.