The same old bad argument against gay marriage

Riley Balling, patent attorney, is certain that gay marriage will affect his marriage. Why? Well, he splutters on in a long op-ed in the Star Tribune, but all he manages to say is the children, because…the children, that’s why.

For many of us who favor traditional marriage, marriage is about raising children in a healthy environment. Thus, any change to the definition of marriage affects our marriage. Our “traditional” marriages and the children they produce are our greatest source of happiness, and we desire that our children will live in a world that will promote their ability to make the same choices that brought us happiness.

Shorter Riley: “I have defined marriage, and marriage is defined this way, and therefore changing the definition of marriage changes marriage by definition. Oh, and my marriage is all about pooping out kids, therefore your marriage damn well better be too.”

[Read more…]

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.

[Read more…]

Friday Cephalopod: That’s a freakin’ huge tag

Poor cuttlefish: they’re getting tracked, their camouflage to no avail. But man, that’s a big tag.

Get Adobe Flash player


Oops. That was annoying — I can’t get that BBC player to work on my machine at all. It’s annoying, too, because their archaic embed code is frickin’ ginormous. Here, if you can’t see it either, is a completely different cuttlefish video.

Who was it that was supposed to be committing voter fraud again?

Here’s some news on a representative bit of Republican Party slime from Riverside County, California, home to some of the slimiest Republicans in known space. From California Watch:

In a complaint filed last week with the county registrar of voters, the Democrats presented affidavits from 133 Democratic voters who said they had been re-registered as Republicans without their consent after they encountered petition circulators outside welfare offices and stores.

One voter complained that his registration was changed to Republican after he signed what he thought was a petition to legalize marijuana. Another said he was told he was signing a petition to lower the price of gasoline, according to the affidavits.

Others said they were offered free cigarettes or a “job at the polls” if they signed some paperwork.

Also among the Democrats who said they were involuntarily re-registered as Republicans: two aides to retired U.S. Air Force Maj. Gen. Richard Roth, a Democrat locked in a tight race with Republican Assemblyman Jeff Miller for a state Senate seat.

According to Democratic Party spokespeople, thousands of people might have been fraudulently re-registered with a Republican Party affiliation. Riverside County is getting slightly more liberal each year for a number of demographic reasons, and yet the county’s Republican Party reported an upswing of 35,000 new Republican voters in the county.

Oh, and here’s a shocker from the California Watch report:

Many of the complainants were Latino or African American.

 

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.

A polarized poll

It seems a shame we can’t tip it even more strongly in a sensible direction. Or can we?

How do you feel about allowing same-sex marriage?

Strongly in favour of it 57%

Don’t feel strongly but lean towards supporting it 4%

Don’t feel strongly but lean towards opposing it 1%

Strongly opposed to it 38%

I’ve noticed lately that people sending me polls are sending me ones that are already pre-skewed in the right direction. Are atheists just automatically bombing polls even without my suggestion?

Cactus wren

I just had about a fifteen minute conversation with this bird. I was sitting on the couch on our back porch, drinking coffee: my daily routine. The bird came up to investigate me, puzzled over me for a minute or so, and then went off to terrorize the finches who’d gathered around the pile of sunflower seeds I put out every morning. This is a cactus wren, Campylorhynchus brunneicapillus, the largest wren in North America and a common bird in the desert. Even if you don’t see them, you hear them:

I’ve stuck to gender-indeterminate pronouns throughout because I’m not expert enough to determine its sex, given that cactus wrens have little sexual dimorphism. Males sing to announce their territory. They make excellent alarm clocks when you’re camping, and they start about 5:45 a.m. in the summer. This one didn’t sing at me, so I have absence of evidence.

As I typed that last sentence, a cactus wren out in the yard sang for about 10 seconds. Not sure it’s the same one.

Cactus wrens are pretty engaging. They’re nervy and unafraid, inquisitive, even aggressive at times. This wren is the only one in the yard who’ll challenge the resident scrub jays over territory. That’s just attitude: the jays are there for the sunflower seed, and the wren doesn’t care for them much. Smaller seeds, insects, and occasional beaksful of fruit make up its diet. Our landlord planted a peach tree some years ago, and there were cactus wrens among the birds that attacked the ripening fruit.

The cactus wren’s song says “home” to me, the way Stellers’ jays’ squawk did when I lived in the Bay Area, and I smile when I notice it. It’s not my favorite wren song, though. The one I like best is that of the cactus wren’s smaller, shyer cousin the canyon wren Catherpes mexicanus:

I hear that song and no matter where I am, it’s the most beautiful place in the world.