Give me something to look forward to!

Yeah, I’m still neck-deep in grading. My cell biology course is pretty well in hand — I’m all caught up there, I’ve posted preliminary grades so students know about where they are, and I’m fielding questions from them all day long — but I also give them a final tomorrow, which I aim to have graded by the next day. I’m still wading through my backlog of essays in cancer biology, and they turned in more yesterday, but once I’m done with those, I’m done. So my goal is to wrap up the whole semester by Friday.

Then early Saturday morning, before the dawn, I get on a plane and zip off to Christmas in Boulder, Colorado for a few days. I am going to turn my brain off during that flight, so I want recommendations for a good book to download into my iPad — the kind of thing a science fiction and fantasy fan would enjoy. Or whatever; the last novel I read, oh these many days long gone, was one of Lindsey Davis’s Falco books. So I’m not entirely bounded by one genre.

Also to discuss: people say that you should judge a book by its contents, and not the author’s political views. But I’ve found so often that the author’s views bleed into the pages — an author so pure in their craft that their personal ideals do not inform their writing is probably an author who treats writing as an abstract exercise, and isn’t particularly interesting to read — that I cannot enjoy as much books by people who are less than humanist and progressive. Mark Twain, for instance, is one of the greatest American authors because his personality suffuses his work and the author is inseparable from the stories he tells.

So maybe you can also tell me about writers who you know to be good human beings. Or maybe you know of an author of worth who completely contradicts my general principle.

A tragedy in Morris

The Happy Atheist

I have learned that the university bookstore in Morris has completely sold out of all copies of The Happy Atheist. I know, rural residents of western Minnesota, you were hoping to pick up a few pallet loads to give out as Christmas presents this year, and you were planning to drive in to town with your pickup trucks to get them today, on Black Friday. I’m sorry to disappoint you.

Like much of the rest of the world, you’ll have to order them online. They do make entirely appropriate gifts, especially if you’ve got one of those annoying relatives who always gives out religiously-themed presents.

Remedial reading for big-time scienticians

I don’t understand how this happens. You’ve got a good academic position. You’re bringing in reasonable amounts of grant money. You’re publishing in Nature Genetics and Nature Structural and Molecular Biology. And you don’t even understand the basic concepts in your field of study.

For instance, here’s a press release titled “Cause of genetic disorder found in 'dark matter' of DNA”.

For the first time, scientists have used new technology which analyses the whole genome to find the cause of a genetic disease in what was previously referred to as "junk DNA". Pancreatic agenesis results in babies being born without a pancreas, leaving them with a lifetime of diabetes and problems digesting food. In a breakthrough for genetic research, teams led by the University of Exeter Medical School and Imperial College London found that the condition is most commonly caused by mutations in a newly identified gene regulatory element in a remote part of the genome, which can now be explored thanks to advances in genetic sequencing.

Regulatory elements are not and have never been considered junk DNA. The researchers have identified a regulatory region called PTF1A that has allelic variations that cause a failure of the pancreas to form. That’s really interesting! But then you read what they have to say about it, and they are completely oblivious to the literature on genetic structure and gene regulation. Isn’t that something you’d expect them to have studied thoroughly before even proposing this project?

Or how about this press release, “Un-junking junk DNA”. It’s gotten to the point where I just cringe when I see the phrase “junk DNA” in a press release, because it is a sure sign of flamboyant ignorance to come.

"This study provides answers for a decade-old question in biology," explained principal investigator Gene Yeo, PhD, assistant professor of Cellular and Molecular Medicine, member of the Stem Cell Research Program and Institute for Genomic Medicine at UC San Diego, as well as with National University of Singapore. "When the sequence of the human genome was fully assembled, under a decade ago, we learned that less than 3 percent of the entire genome contains information that encodes for proteins. This posed a difficult problem for genome scientists – what is the other 97 percent doing?"

The role of the rest of the genome was largely a mystery and was thus referred to as "junk DNA." Since then sequencing of other, non-human, genomes has allowed scientists to delineate the sequences in the genome that are remarkably preserved across hundreds of millions of years of evolution. It is widely accepted that this evidence of evolutionary constraint implies that, even without coding for protein, certain segments of the genome are vital for life and development.

So many misconceptions. No, noncoding DNA is not synonymous with junk DNA; junk DNA was not so called because its function was mysterious; it is absolutely no surprise that some regions of the genome are vital, even without coding for proteins — haven’t they heard of tRNA or miRNA? Developmental biologists have been yapping for decades about the importance of the switches that control gene regulation…are we just ignored?

I worry that this is a symptom of a serious rot in science education — that we’re turning out great technicians and masters of the arcane art of grant writing who don’t actually understand biology, and in particular have no perspective on what the questions actually are. They may be excellent middle managers, but the comprehension and vision are lacking.

I have a suggestion. If you’re going to do research that leads you to say anything about junk DNA, I urge you to read carefully one or all of the following books: The Origins of Genome Architecture by Michael Lynch; Fundamentals of Molecular Evolution by Dan Graur and Wen-Hsiung Li; or The Logic of Chance: The Nature and Origin of Biological Evolution by Eugene Koonin. Those aren’t lightweight texts — I wouldn’t assign them to your average undergraduate — but hey, you’re a big-time professional scientist. There’s no excuse for not knowing this stuff.

The descent of Xanth

I have never cared for Piers Anthony — I’ve always considered him a cheesy hack with some repulsive ideas — so I’ve never been tempted to go back and read his old juveniles. They were tremendously popular, though. I used to get annoyed when I’d go to the second-hand book store and discover that all they had in genre fiction was a mountain of Piers Anthony crap.

But someone who had fond memories of reading the books as an adolescent did go back and read some of the Xanth series. It turns out they’re also twisted misogynistic pieces of shit.

This is the sad crux of Chameleon’s cheerful hatred of women. Bink leers at women, and it’s presented as not only okay, but as the way things should be. In a different part of the Slashdot Q&A above—where another reader asks Anthony about the poor treatment of women characters in Xanth—the author tries to prove how much he appreciates and understands women by extolling their virtues as “thinking, feeling creatures.” Not people. Creatures. You know, like basilisks. And not only that, but creatures whose thoughts and feelings apparently require the validation of someone with Anthony’s authority—that is, someone with a dick. Ultimately, Anthony is the worst kind of misogynist: one who defends his offensive views by saying, in essence, how could he possibly hate women if he’s drooling over them all the time?

A lot of us grew up reading science fiction and fantasy that glorified a particular attitude — the ultra-competent nerd engineer who conquers all of his problems with a high-tech gadget in one hand and the adoring, pretty girl in his other arm. Is it any wonder so many of us are screwed up?

Of course, maybe the reason those second-hand book stores were flooded with Xanth was that they were marketed heavily, lots of people read one, and then immediately dumped it so they could buy some LeGuin, instead.

The best review of The Happy Atheist yet

The Happy Atheist

It’s good to see The Happy Atheist getting great reviews. This one is from…the Discovery Institute! And even better, they put their top man on it, the inimitable Casey Luskin!

Go ahead, you can read the whole Luskinish thing, but here’s the shorter version of Casey Luskin:

PZ Myers can’t be happy, because he’s angry and kinda mean.

Thank you, Casey! I’m glad you were able to discern my true character there, unlike all these other people I meet who keep insulting me with phrases like “teddy bear.” But I should point out that “happy,” “angry,” and “mean” aren’t necessarily incompatible. Maybe he’s used to the Christian version of “happy,” which is synonymous with sheeply and oblivious bliss-ninny idiocy.

I like my joy ferocious.

Sean B. Carroll talking to atheists

This morning, in 45 minutes, I’ll be tuning in to AM950 to listen to Sean B. Carroll on Atheists Talk radio. He’s going to be talking about his new book, Brave Genius: A Scientist, a Philosopher, and Their Daring Adventures from the French Resistance to the Nobel Prize, the story of Jacques Monod and Albert Camus. Bringing the Two Cultures together!

Darwinian bookery

We’re doomed. Evolution is an ineluctable process; once it gets started, it’s not just an optional alternative, it becomes unstoppable, short of nuking the planet from orbit (and even then, all it takes is one surviving bacterium for it to begin again). Charlie Stross has noticed that books have crossed the threshold and are now poised for an adaptive radiation.

An epub ebook file is essentially an HTML5 file, encapsulated with descriptive metadata and an optional DRM layer. The latest draft standard includes support for all aspects of HTML5 including JavaScript. Code implodes into text, and it is only a matter of time before we see books that incorporate software for collaborative reading. Not only will your ebook save your bookmarks and annotations; it’ll let you share bookmarks and annotations with other readers. It’s only logical, no? And the next step is to let readers start discussions with one another, with some sort of tagging mechanism to link the discussions to books, or chapters, or individual scenes, or a named character or footnote.

We already share highlighting — I get a little annoyed when I’m reading on my kindle and suddenly there’s a block of text with a dotted underline — other people thought that section worthy of notice and have shared their emphasis with the world.

I’ve also noticed that the books I’ve bought through Amazon suddenly pop up with a ranking and suggestions page when I reach the end. It used to be you’d finish a book and close it satisfyingly and put it back on the shelf…but no, now it yells at you “Did you like me? Buy more of me!”

As Stross points out, the next dreadful steps, since a book has become code, will be the incorporation of malware and agents to sabotage competing books in your library and insert new ads around the place, or even replicate more of the authors’ works. I’ve downloaded some of those cheap or even free books into my epub library, and some of them are so bad that I suspect they are already intrinsically malware.

Our future:

Books are going to be like cockroaches, hiding and breeding in dark corners and keeping you awake at night with their chittering. There’s no need for you to go in search of them: rather, the problem will be how to keep them from overwhelming you.

Doomed, I tells you. I am squinting at my iPad right now. I think it’s plotting to get me.

I don’t care where you shelve it, as long as it’s not next to that one

Larry Moran has noticed a curious arrangement of books in his local bookstore.


He asks whether those are appropriately categorized, and where they should go.

The Happy Atheist has some sciencey bits and is colored by a scientific attitude, but I’d openly agree it is not a science book. It’s an atheist book. It belongs in a more philosophical section.

Larry likes to argue that the creationists are at least trying to do science, even if they are doing it incredibly badly and dishonestly; the Meyer book refers to more science than does mine, so should it be more deserving of its place in the science section? If we’re calling it bad science, we’re still calling it science, you know. Maybe bookstores need a pseudoscience section to cope with this filing problem (unfortunately, the pseudoscience section might be larger and more popular than the science section.)

I have a simple solution for right now, though. File my book in philosophy/lifestyle, maybe even the religion section (it is anti-religious, in the same way Meyer is anti-science).

File Meyer’s book in the dumpster out back.