I get mail

Another one today? I just had to offset the lunacy of the earlier post by sending my thanks to Leo from Texas, who sent me a nice long letter telling me about all the things he liked in The Happy Atheist. Yay! Fans!

Also, the audio book is in the works, and I’ll let you know when it’s available. I didn’t read it, though: Aron Ra did the honors. So another Texan…maybe that state isn’t so bad after all.

When the phrase “out-of-touch” is too mild…

We need a measure of just how far out into space a commentator has launched themselves. I propose that we use the unit, the TomPerkins.

Last week, he sent a letter to the opinion page of the Wall Street Journal, and they published it, despite the fact that it is certifiably nuts, because Tom Perkins is an obscenely rich venture capitalist. Never mind what he says, he’s rich. Yet this letter blithely compares the fate of obscenely rich venture capitalists to that of European Jews in World War II.

Writing from the epicenter of progressive thought, San Francisco, I would call attention to the parallels of fascist Nazi Germany to its war on its "one percent," namely its Jews, to the progressive war on the American one percent, namely the "rich."

Whoa. He kind of red-lined my TomPerkins meter there.

But now you have to go read his book. Yes, he’s written a whole book, and it’s not what you think it is: he was once married to Danielle Steel, and this book is pure one-percenter porn. Go read the excerpts and gag, or you can buy your own copy on Amazon. The latter is not recommended; while the article says it’s available for 1 cent online, it doesn’t seem to be true any longer — there has been a run on Tom Perkins literature, no doubt driven by aficionados of awful writing.

Hey, look what just arrived!

That new book about lovely atheists by Chris Johnson, A Better Life. I’m supposed to be in it, but it’s been sitting in a box outside all day, and it’s frozen solid and painful to touch, so I can’t open it yet. Later. Order it now!


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.