The Incomplete Map of the Cosmic Genome

If you’re one of those privileged people who has an iPad, and if you’re also one of those quality people who appreciates the brilliant Robin Ince, take a look at the The Incomplete Map of the Cosmic Genome for iPad on the iTunes App Store.

Now you might be wondering what it is. I’ve got it, and I still am. It’s one of those thingumabobs that fits words like “eclectic” and “ooooh” and “oh, what a colossal time sink”. It’s a…well, it’s a…OK, it’s a miscellany of enthusiastic science presentations.

It’s also kind of like a good science programming channel (you know how those have vanished from cable) with Infrequent/Mild Profanity or Crude Humour. If that helps. Download it yourself and try it and explain it to me.

They keep stuffing things in there, and you open it up and tap on something and there’s Brian Cox telling you how wonderful the universe is, or Steve Jones talking about Alfred Russel Wallace, or…ooh, an appreciation of Jacob Bronowski. I didn’t see that last time I browsed it. Excuse me, I have to vanish for a little while.

ENCODE has its defenders!

You know I was really pissed off at the crap ENCODE was promoting, that the genome was at least 80% functional and that there was no such thing as junk DNA. And there have been a number of better qualified scientists (like W. Ford Doolittle and Dan Graur and many others) who have stood up and registered their vehement disagreement with that nonsense. But there are some who agree that the genome must be largely functional, like John Mattick. Larry Moran reminds me that Mattick is the author of this infamous chart, however, which is best known as the original Dog’s Ass Plot.

Worst evolution diagram ever

That is so misleadingly dishonest it takes my breath away — Mattick cherry-picked genome sizes to fit his curve. One of my cell biology labs involves teaching students how to properly construct a simple graph, and I think I’m going to include this figure as a bad example.

Well, Mattick has done it again. He has published a paper (how do these things get through peer review?) disputing the existence of large quantities of non-functional DNA, which is largely an attempted rebuttal of Graur’s paper. It’s a short paper, but painful in its contortions and extraordinarily poor arguments. Larry Moran has done an excellent job of tearing it apart — I think he needs to polish it up and get that published.

The worst part of the paper, though, is the concluding paragraph — you know, where most of us try to put the most important message of the work.

There may also be another factor motivating the Graur et al. and related articles (van Bakel et al. 2010; Scanlan 2012), which is suggested by the sources and selection of quotations used at the beginning of the article, as well as in the use of the phrase “evolution-free gospel” in its title (Graur et al. 2013): the argument of a largely non-functional genome is invoked by some evolutionary theorists in the debate against the proposition of intelligent design of life on earth, particularly with respect to the origin of humanity. In essence, the argument posits that the presence of non-protein-coding or so-called ‘junk DNA’ that comprises >90% of the human genome is evidence for the accumulation of evolutionary debris by blind Darwinian evolution, and argues against intelligent design, as an intelligent designer would presumably not fill the human genetic instruction set with meaningless information (Dawkins 1986; Collins 2006). This argument is threatened in the face of growing functional indices of noncoding regions of the genome, with the latter reciprocally used in support of the notion of intelligent design and to challenge the conception that natural selection accounts for the existence of complex organisms (Behe 2003; Wells 2011).

I’m sure the Discovery Institute staff are dancing in pirouettes of joy at getting a neutral or possibly favorable mention in a legitimate journal. It’s not clear exactly what Mattick is trying to do here (lack of clarity is also a sin in science writing, let me remind you): either he’s trying to pre-emptively slander his critics by impugning them with an ideological motive, or he’s granting credence to Intelligent Design creationism. I’m inclined to think it’s both; he’s clearly trying to argue with the motives of Graur and others, but also, he’s claiming, as the creationists do, that evidence of function for the highly variable component of our genome is a de facto argument for a purpose for that variation, and that evolutionary theory does not support the idea of a functional purpose for variation in the sequence of most satellite DNA, for instance.

But I would not argue that ubiquitious functionality is unlikely because it has consequences for our theories; it’s wrong because of all the evidence that has been marshaled that most DNA is not there to serve a specific, selectable purpose for us humans.

Prime snide kookrant

I was surprised when I read the excerpt from the sneering letter to the editor-in-chief of Science magazine — it’s someone patronizingly chiding the little woman with the big job at a science journal in decline. It’s bad enough that it’s so condescendingly goofy, but it’s also complaining that Science has foolishly jumped into the “debate” about global climate change. There is no debate; it’s happening, there is a substantial anthropogenic component, and the science is rather firmly settled, so what would be then inappropriate is refusing to address an important environmental issue.

But then I read the full letter, and learned two things that made it even more laughable: 1) it’s an open letter published on the wacky denialist website, What’s Up With That, which means it’s going to be instantly ignored by any credible scientist, as Marcia McNutt is, and 2) it goes on and on and on and on. It’s absurdly preachy and unprofessional, and tells me that the author has no idea what kind of letter would be published by the magazine.

Further, McNutt is a professor of marine geophysics at Stanford, and what impresses the kook who wrote that letter?

McNutt is a NAUI-certified scuba diver and she trained in underwater demolition and explosives handling with the U.S. Navy UDT and SEAL Team.

The comments are also delusional. People are opining that Science is a dying journal. Really?

Climate change denialists are just about as out-of-touch and clownish as evolution denialists.

Although…I would endorse “Christ Hunting”

Yesterday, I was sent a link to an appalling photograph: one of those standard trophy shots of a group of grinning idiots standing over the corpse of an elephant they’d sportingly murdered with their great big manly guns. There’s a whole gallery of cheerful assassins, if you want to see; I don’t recommend it. It’s basically a lot of rich white people who have paid to be coddled for a week while they safely point a high-powered rifle at a large, relatively rare and fragile creature and destroy it.

provider_for_christ_banner

But one thing caught my eye. It is a small thing, but it added an additional frisson of disgust to the page. It was this banner:

Yep, it’s the Provider for Christ Hunting Adventure. They’ve taken a revolting act of senseless destruction and made it even more repugnant by justifying it with Jesus. For the low price of $2395 you get to fulfill this goal:

Goal: To Support the creation of new and more energized Providers for Christ, and the families of men and women based on Biblical principals [sic].

Oh. Biblical principles. So they hunt wildebeest and Cape Buffalo with bows and spears, possibly from the deck of a chariot? That would be a fair fight, and I would encourage more Christians to demonstrate their courage and battle lions with an assegai.

Wait, no, that’s not what it is: they’re still using great big guns to execute the local wildlife. What makes it Christian is that they get doped up on sanctimony by including local ministers who harangue the participants in seminars, and then they give the meat from the animals they kill to orphans at a squatter’s camp. Which does lead me to wonder what’s done with the meat on non-Jesusy safaris; it’s left to rot?

I have a suggestion: camera safaris. Support conservation organizations. Promote economic fairness and political stability, rather than palliation by numbing people with god. Don’t give more money to rich people with helicopters who are exploiting the environment.

How about putting the Christ Hunting Adventure out of business? I know, that won’t happen — there are far too many Christian assholes out there.

The Great Troll War of 2013

The internet is taking an interesting tack: there’s increasing concern about doing something about trolls. I think it’s a bit of backlash, because really, they’ve gone far, far overboard — the volume of raw hate and stupidity in some of the worst places on the net is appalling — and I also think internet culture is changing as it expands beyond its early population of nerds.

We’re all still trying to figure out what to do about the troll infestations, though. Lindy West has her personal answer: don’t ignore them, feed them ’til their idiocy is a matter of public mockery. And it’s all because the trolls are reaching new lows in their efforts to silence people, especially women.

Cumulatively, the sheer volume of hate that we’re expected to shoulder, in silence, every day, is wearing a lot of people out and shutting down rational discourse. Female bloggers are being hounded off the internet. Teenage girls are being hounded off the earth. There’s no good solution, but we have to do what we can to stop these people—unmask them, shame them, mock them, cement their status as social pariahs—for our own sanity and for those whose armor isn’t so thick (upgrade yo greaves, son).

Unmasking trolls, as we’ve seen, can produce some tangible and satisfying results. And I don’t mean just in a punitive way, I mean in a changing-the-larger-culture kind of way. People need to understand and internalize that online harassment, violent hate speech, rape threats, slut-shaming little girls until they hang themselves, and so on, are express violations of the social contract. They will not be tolerated and they will result in real-life consequences. That’s a long way off, and probably a bit of a pipe dream, but it might be our only hope for cleaning up this shitshow.

Here’s another example of the troll blight: Amanda Berry, the woman who’d been kidnapped and held prisoner in Cleveland for ten years, went to a concert and danced last weekend. Normal people can appreciate how great that must have felt, to be free at last and to be able to just have fun for an evening.

Not the trolls.

On CNN over the weekend, Nelly told Erin Burnett, “What stuck with me most was that she had a smile on her face. That’s one of the most impressive things to me, considering everything she had been through … I thought, wow, that was special.” But Burnett was too busy being amazed that “She looked totally normal.”

Burnett’s concerned astonishment was charitable compared to what the lowest form of opinion generators – Internet commenters – had to say about Berry’s newly reignited social life. “It’s just odd given the years of abuse she suffered. Normally she would not have that kind of trust or comfort. I’m sorry, but it doesn’t make sense,” wrote one concerned ABC News commenter, while another more bluntly decided, “It seems to me she was enjoying it and is gonna use her ordeal to cash in.” Many were concerned that she appeared with a man who stood behind her and warmly put his arm around her and kissed her neck while she was onstage. Or, as some of the ABC commenters decided, he was a “dirt bag hanging all over her,” who “groped” and “pawed” her. A CBS News commenter more generously decided she looked “pretty hot.” And 645 comments later on NBC, Berry had plenty of well-wishers but also comments about her eyebrow piercing, and how she doesn’t look like “a real victim….lol.” And of course, if you want to plumb the absolute bottom of the barrel, there’s YouTube, where Berry is being accused of “milking everything she’s getting.”

You don’t expect much beyond a gaping, misspelled void when you stare into the cold dark place that is Internet comments. But what’s appalling – if not entirely surprising – is realizing that the judging and shaming that rots the soul of online community goes that deep. It goes all the way down to picking on a woman who spent a decade being abused, because she had the nerve to go outside and be happy.

Yeah, it’s time to fight back.

Whoa. A commenter linked to a tumblr where a game developer dumps the hate mail he got after changing the stats on a gun in Call of Duty. You can’t read that without realizing there is a deep sociological problem here.

You know, if I’d known about that behavior back when I had kids at home who were playing those games and others online, there are a few things I would have done. I would not have told them they don’t get to play; nor would I have taken their internet connection away. But I definitely would have sat them down to read that site and I would have told them, “Don’t be that asshole. I would be ashamed if you had such a poor sense of perspective.”

I think that’s where it has to begin. Don’t engage in such behavior yourself, but also tell your friends, your relatives, and the people you encounter in those games that they are being terrible people. Don’t spare your boyfriend or your daughter or your mother, either, it shouldn’t matter how close they are to you…except maybe that the closer they are, the more you should care about their behavior. If you find yourself playing against people who say such things, report them, block them if the game allows you, and just stop playing with them.

You are not more manly when you lose an online game and think you can recoup some honor by threatening to rape your opponent. You are more pathetic.

Creationists are history denialists

My upcoming visit to Houston to join Aron and others in protesting Texas creationism is smoking all kinds of interesting characters out of the woodwork. Meet Dr. David Shormann (the “Dr.” must be his first name, he sure flings the title about), who has apparently been a person of some influence in shaping the Texas Board of Education policy. He’s also a flaming young earth creationist who has drunk deeply of the Answers in Genesis kool-aid, and is very, very angry at the vicious, intolerant atheists who are coming to his city to argue against his nonsense.

The freethoughts activists are protesting the freedom of Americans to trust God’s word as true in every aspect, including historically true. For some reason, they are particularly concerned about dinosaurs. They are upset with how Christians like myself interpret dinosaur history!And historical interpretation is what they are protesting, not testable, repeatable science.

Note the insistence that we differ only in “interpretation” and that history isn’t science, which is the most common argument you’ll get from acolytes of AiG and Ken Ham. His argument against historical sciences is complete nonsense: of course you can test historical inferences, and while you can’t repeat singular events, if you’re studying processes and principles, you certainly can do experiments and repeat them. For instance, the science of taphonomy is all about making observations and doing experiments to test mechanisms of preservation that allow us to then interpret fossils on the basis of a body of scientific evidence (evidence that creationists pointedly ignore).

But for sheer hilarity, you have to savor a creationist’s attempt to understand what biologists are thinking. Here’s Shormann’s argument for humans and dinosaurs living together:

The fossil record shows many things lived at the same time as extinct dinosaurs, including extant (meaning still alive) starfish and coelacanths. Apparently, the so-called freethoughts activists say we’re lying about the human-dino coexistence thing because we have yet to uncover a fossil of a human riding a dinosaur while holding a coelacanth that ate a starfish. Unless this fossil grouping is found, then atheists will claim the Bible is a book of lies and Christians who believe it are liars. Therefore, since freethoughts activists apparently never lie, and possess a perfect understanding of history, we can trust them over God’s word! And if we don’t buy into their belief that freethoughts activists are the source of historical truth instead of God, they will make laws to suppress our skepticism. Of course, I’m joking here, but are the atheists? Unfortunately, I don’t think so.

His first premise is false: there are no species of Mesozoic starfish or coelacanths still extant. Ancient coelacanths were different animals from the ones now dredged up from the sea around Madagascar!

We don’t regard the absence of a particular fossil grouping for evidence that those particular species existed concurrently. What we do have is an understanding that species exist in an environmental context, and that those environments change over time. There is a basic principle called “faunal succession” that was worked out in the 19th century: it was the discovery that fossils weren’t a hodge-podge, but that a particular stratum was associated with a community or whole eco-system of organisms, and that that community would change its constitution over time in the fossil record.

We’ve worked out the big picture of many species’ evolution — we are relying on positive evidence about the distribution of that species in time, not simply its absence. We know, for instance, that hominins evolved over the last few millions of years; we have the molecular evidence that shows the timing of divergence from other apes, we have the fossil evidence that shows their emergence in East Africa, and we can also see in the fossils that hominins of 3 million years ago were different from hominins of 1 million years ago.

Dinosaurs, on the other hand, are a very diverse group that were found in a broad range of time, over almost 200 million years, and we can find many different ecosystems represented — and the Triassic has different fossil assemblages than the Jurassic than the Cretaceous. Again, not a jumble: there’s a pattern to their distribution. And one thing we know is that there was a major faunal transition at the KT boundary, about 65 million years ago.

So we have two (well, many more than two, actually) coherent groups that don’t overlap — and they don’t overlap by more than 70 million years. It’s not simply that we don’t find dinosaurs and humans coexisting, it’s that we have found patterns and contexts for the two groups, whole vast collections of concordant data, that support the idea of a wide temporal difference between them…data that the creationists deny exists.

As for the Bible, it’s a book of self-serving legends and stories that an ancient people used to identify themselves. I wouldn’t consider it a book of lies if people accepted it for what it is: a collection of myths, poetry, metaphor, and garbled history. It’s when they try to promote it as something more, a detailed and perfectly accurate history of the world, in defiance of all of the evidence, that it becomes a tool for spreading lies.

Freethinkers don’t consider themselves perfect. We are open to the evidence, and we’re willing to use all of the evidence, not just the bits that reinforce our preconceptions. Meanwhile, believers like Shormann hide behind the claim that their knowledge is perfect because it comes from a perfect omniscient being — but I say that that has not been demonstrated. The totality of the evidence, including the ever-shifting and contradictory claims of the faithful, shows that their “knowledge” always seems to be an echo of their biases and ignorance.

Shormann goes on into ever more ridiculous claims — here’s his judgment on biology textbooks.

Also, in the 21st century, high school and college biology textbooks are becoming bloated monsters. Something has to go to make room for teaching 21st Century advances in biology, including epigenetics and bioinformatics. Many chapters have way too many pages devoted to speculative historical claims about origins, dogmatically asserting only one interpretation (evolutionism). A pro-science person would want to reduce or remove the history to make room for 21st Century science. An anti-science person would reject the 21st Century science in favor of page after page about origins. Ask the atheist which they would choose to include in an already oversized biology textbook, new science or history? If they would rather keep the history, then they are anti-science, which contradicts their claims of being pro-science.

Yes, the biology texts are huge…but that’s because we have so much information to share. I am amused, though, that he wants to throw out evolution to make room for bioinformatics. Bioinformatics makes no sense at all without evolution — I can’t even imagine the subject being taught without an understanding of the concept that genes and genomes change over time. In epigenetics, the primary focus is going to be on developmental change, but even there — does he realize that human epigenetics is analyzed in the context of experimental information done in mice and other animals?

That closing babble is pretty damned offensive, too. Everything is the way it is because of how it got that way: you can’t do biology by treating it as static and fixed. Everything in biology is a dynamic process. Denying history is denying science.