21st century science publishing will be multilevel and multimedia

I have to call your attention to this article, Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees, just published in PLoS One. It’s cool in itself; it’s about the analysis of metagenomic data, which may have exposed a fourth major branch in the tree of life, beyond the bacteria, eukaryotes, and archaea…or it may have just exposed some very weird, highly derived viruses. This is work spawned from Craig Venter’s wonderfully fascinating work of just doing shotgun sequencing of sea water, processing all of the DNA from the crazy assortment of organisms present there, and sorting them out afterwards.

But something else that’s special about it is that the author, Jonathan Eisen, has bypassed his university’s press office and not written a formal press release at all. Instead, he has provided informal commentary on the paper on his own blog, which isn’t novel, except in its conscious effort to change the game (Eisen has also been important in open publishing, as in PLoS). This is awesome, and scientists ought to get a little nervous. It maintains the formality and structured writing of a standard peer-reviewed paper, which is good — we don’t want new media to violate the discipline of well-tested, successful formats. But it also adds another layer of effort to the work, in which the author breaks out from the conventional structure and talks about the work as he or she would in a seminar or in meeting with other scientists. A paper provides the data and major interpretations, but it’s this kind of conversational interaction that can let you see the bigger picture.

I say scientists might want to be a little bit nervous about this, because I can imagine a day when this kind of presentation becomes de rigueur for everything you publish, just as it’s now understood that you could give a talk on a paper. It’s a different skill set, too, and it’s going to require a different kind of talent to be able to address fellow scientists, the lay public, and science journalists. Those are important skills to have, and this kind of thing could end up making them better appreciated in the science community.

Are any of your grad students and post-docs blogging? You might want to think about getting them trained in this brave new world now, before it’s too late. And you might want to consider getting started yourself, if you aren’t already.

The Minnesota Anti-Texan Act of 2011

I would like to propose a new law for consideration by our legislature, which I am calling The Minnesota Anti-Texan Act of 2011. I need to work on the formal language for it, but I can give the gist of it here.

If any person within the boundaries of the fine state of Minnesota exhibits any of the signifiers of a Texas origin — wearing a cowboy hat, for instance, or Big Hair, or having a drawl, or chewing tobacco — you can shoot them. You catch someone listening to Clint Black on the radio, bang, blow them away, you’ve got a justifiable defense. Someone says “sheeeeeee-it” instead of “uff-da,” you’ve got cause: kill them on the spot. It’s perfectly fair to hang out at the airport waiting for incoming flights from Houston, and following visitors outside the terminal to group hunts, too; it might even be a new source of revenue for local guides.

To be fair, after the bill is passed I support a waiting period of one year before it’s implemented, so that there’s time to spread the news and give Texans warning. They will be allowed to enter the state, as long as they respect our traditions: no leather clothing, just layers. The only hats allowed are stocking caps or tuques. They should study the movie Fargo to learn the lingo, and listening to lots of Prairie Home Companion will help them understand the local mores. We’re not so much against Texans as we are against blatant Texans, and as long as they show appropriate shame for their nature, and try hard to cover up, we’ll do our best to tolerate them.

Wait, you may be thinking, this isn’t justice: a death sentence for wearing the wrong kind of headware? No one deserves to suffer for trivial fashion choices, or because a bunch of yankees have prejudices about who someone is. But I think it’s only right that if someone takes pride in being a dumb cracker, and inflames our senses by flaunting their inherent Texish character, then they deserve what’s coming to them.

And we’re just following Texas’ lead.

A meeting Thursday night that was billed as a way to discuss concerns some have about the investigation into a series of alleged sexual assaults on an 11-year-old girl turned into a forum that many used to blame the girl police contend is the victim of heinous attacks.

Many who attended the meeting said they supported the group of men and boys who have been charged in the case. Supporters didn’t claim that the men and boys did not have sex with the young girl; instead they blamed the girl for the way she dressed or claimed she must have lied about her age — accusations that have drawn strong responses from those who note an 11-year-old cannot consent to sex and that it doesn’t matter how she was dressed.

See? My proposed Minnesota law is hallowed by good ol’ boy tradition. Texans are clearly just asking for it.

Oh, wait…there’s that remark about how lying about her age would have excused the gang rape, and this:

“She’s 11 years old. It shouldn’t have happened. That’s a child,” Oscar Carter, 56, who is related to an uncle of one 16-year-old charged in the case, said in an interview earlier in the week. “Somebody should have said what we are doing is wrong.”

So it would have been OK if the girl was 17, the age of consent in Texas? I guess I’ll have to put a clause in my law that says it’s only OK to murder Texans or people who look like Texans or people who imply they are Texan with subtle behaviors if they are over 17.

I am a just and fair person, after all.

And remember, if nobody tells you that what you are doing is wrong, it’s not your fault if you rape or murder someone. You can’t possibly detect the evil that you’re doing unless someone else reminds you. If you’re a Texan.

What does it take to be a science journalist?

Science journalists, you really piss me off…at least some of you. Here are a couple of headlines about that recent paper I summarized that make me want to slap someone.

“Eye evolution questioned.” No, it’s not. That’s just trying to stir up a non-existent controversy. The eye evolved. This was a paper exploring the details of how specific photoreceptor types with the eye evolved. (I should mention that the summary is OK, but the headline was stupid. Maybe I ought to slap the editor.)

“Ancient Origins of the Human Eye Discovered.” Aaargh, it’s a paper about brachiopods, not humans, and it’s about the evolution of protostomes as well as deuterostomes…it’s about the whole frackin’ animal kingdom, not just our self-exalted little twig.

Both of those headlines are about the very same paper, and I get the impression the reporters hadn’t even read it, but instead relied on teasing out comprehensible angles from interviews. We ought to have a rule: if you can’t read the research and comprehend it, you shouldn’t be writing about it. I know, suddenly 9/10ths of the science journalists in the world are abruptly unemployed.

Ben Goldacre offers some excellent commentary on this problem. Read it if you’re hoping to be a professional science communicator. I agree with him: you don’t need a Ph.D., but you do have to have some knowledge of the field you are reporting on, and most importantly, a passion to learn more about it.

Old fool gets attention for being ignorant

Before you say it, I know I’m giving him attention, too. Cardinal George Pell, the old fool, got lots of press for being a climate denialist, again. After a talk, he denounced the climate scientists for not being scientific, while he, the guy who believes angels and saints and great magic boojums in the sky, knew better because “‘I spend a lot of time studying this stuff.”

I suspect he’s another graduate of Google University.

But Pell is irrelevant. The real question is, why do the newspapers cover his pronouncements in any serious way? The man is comic relief, nothing more.

NPR can go die in a fire

This is unbelievable. James O’Keefe, he of the Acorn fraud, of the aborted seduction, the unimaginative weasel whose sole game is staging bogus scenarios with his ideological opponents and trying to catch them saying embarrassing things, has done it again, teasing an NPR executive into saying disparaging things about the Tea Party lunatics. I saw the recording; it was tame, I’d say stuff a thousand times more disparaging about those racist morons while knowingly on the air.

But it worked. NPR caved in, suspended the administrator, and now another one has resigned. Why? I don’t know. Because the cowards at NPR are afraid that the Republicans are going to kill all their funding, so they are running away from any confrontation with the political party that wants to destroy them, as if that will help.

Don’t think for a minute that this craven behavior will stay the budget axe, though. All it has really accomplished is to destroy any interest I have in supporting the organization. Why should I? They’ve already surrendered to the deranged right wing. Their usefulness as a non-propaganda news source is dead.

Worse, they’re giving the Breitbartian vermin a little thrill of power. This isn’t the end. How many more news organizations are going to fold in fear before these stupid bully-boys?

One movie, ruined!

In a too rare fit of quality, our local theater is showing The King’s Speech this week, which I keep hearing is wonderfully well made and a serious Oscar contender. I was thinking of going, but now Christopher Hitchens shreds its historicity — it’s about yet another royal fascist-sympathizer — and Katherine Preston explains that it’s got the neurology of the speech defect all wrong. I don’t think I can watch it at all now. I can enjoy a fiction without apology, but I find it impossible to watch a false story that pretends to be true.

The reviews are annoying, too — they all praise the quality of the movie-making and the acting, while telling me that the core premises of the story are false. How can I enjoy it when Something Is Wrong On The Screen?

The Nature of Existence

I forgot to mention that I did attend the local screening of The Nature of Existence, the new movie from Roger Nygard in which he traveled the world asking various people grand questions about the meaning of life, etc. It was entertaining, and it is subtly subversive of religious views, so I will recommend it. But I do have a few reservations that I was also able to bring up in the Q&A after the movie.

One thing that was alarmingly obvious when watching it is that almost all the gurus and authorities and religious figures that he interviewed were male. There were exceptions — the 12 year old daughter of his neighbor (who was an unrepentant atheist, and I thought the most sensible voice in the whole movie), a lesbian priest, the wife of a pastor — but otherwise, this show is one long sausage-fest. When I pointed this out, Nygard was apologetic and recognized that this is a significant omission, but explained that he simply hadn’t noticed when he was filming the material. Isn’t that the whole problem, that we’re oblivious to these omissions of half the population of the planet?

Another problem was actually a tactical decision, and I can actually understand why it was done this way. All of the interviews were friendly; Nygard made a conscious decision to be entirely non-confrontational and just allow the interviewees to speak without criticism. It’s a policy that opened doors and allowed him access, and encouraged the people to speak at length. I can’t imagine him making this movie any other way, but still…there were parts where the lack of a critical interrogation meant the subjects were able to effectively hide the more hateful parts of their beliefs. For instance, he interviewed the odious Zakir Naik, the Muslim fanatic who thinks it is a religious obligation to kill opponents of Islam (apostates should merely be imprisoned), and who also considers homosexuality grounds for execution. He also interviewed pompous ol’ Orson Scott Card, and his raving homophobia was left unexposed.

So I was left with rather mixed feelings. The movie only illuminates the middle ground of religious belief, and while it exposes the absurdity while avoiding being judgmental, it also manages to bury the worst aspects of religion. That’s tactically sensible and I consider it an overall good because it will get the movie watched by more people, but man, it’s not my style, and it sort of grated on my nerves. It was nice. I kept waiting for something to explode.

Roger Nygard in Morris

The University of Minnesota Morris has a special guest coming to town: Roger Nygard, the filmmaker best known for making the movie Trekkies, about the Star Trek culture. He’s here as a guest of our philosophy department, though, because his latest movie is The Nature of Existence, in which he asks various people about the meaning of life.

I don’t know. Wandering around the world asking strange weirdos to explain why the world was created sounds like a lousy way to do philosophy, and an even worse way to do science, but it might be a great way to do entertainment. We’ll have to see.

He’s going to be doing a marathon screening of the companion series to the film from noon to 9pm on Sunday (tomorrow!) 30 January, in Imholte 109. This event is free and open to the public.

But wait! There’s more! And all totally free!

On Monday, 31 January, you can meet with Roger Nygard from 3:30-4:30 in the McGinnis Room of the university library. And then at 7pm, in Imholte 109, there will be a screening of the movie The Nature of Existence…again, open to the public. This event is sponsored by the Midwest Philosophy Colloquium, the International Programs Committee, and the Morris Freethinkers.

I’ll be dropping in on some of the events, depending on whether I can get all caught up in my lecture prep for the coming week (with my current load, I will die if I don’t have most of the work laid out on the weekend); I’ve also got to get some preliminary work done organizing some talks for the week after, which contains Darwin Day, in case you’d forgotten. I will peel myself away for at least a little while, though, to be entertained but probably not enlightened.