Blogs / The Loom

Why don’t I blog more? In part because I’m busy reading other blogs. I finally got around to adding some of my favorite science blogs outside the scienceblogs.com empire to the blogroll over on the left side. Allow me to take a moment to introduce you to them.

The Anti-Toxo: A blog about every new paper or article on Toxoplasma, the resident parasite here at the Loom. If you want to understand our parasitic overlords, this is a must read.

Center for Science Writings Blog. John Horgan, veteran science writer, now runs the Center for Science Writing at Stevens Institute of Technology. Lots of good stuff on the blog.

El Gentraso: British science writer John Whitfield, who has been wandering the weird fields where thermodynamics meet life.

Evilutionary Biologist: Biologist John Dennehy is not actually evil. I particularly like his homages to classic papers. Get your history of science!

Genomicron: T. Ryan Gregory, Canadian biologist who works on genome size evolution.

Greg Laden: U Minnesota anthropologist and battler against creationists.

Heliophage: Science writer Oliver Morton’s latest blog, tied to his new book on photosynthesis.

hpb etc.: History and Philosophy of Biology. Those who don’t know history in science are doomed to erroneously claim they thought of things first.

John Hawks Anthropology: University of Wisconsin anthropologist’s blog. Plenty of news on human evolution, plus potent takedowns.

Knight Science Journalism Tracker: The Knight Science Journalism Foundation’s Charles Petit funnels all the good science journalism (at least the stuff that appears in newspapers) into one place, along with commentary from time to time.

Panda’s Thumb. One-stop shopping for antidotes to creationism.

RealClimate. A paragon of scientist-written blogs. Delivers science on climate change.

Red State Rabble. News from Kansas.

Sandwalk. Canadian biochemist Larry Moran.

Science Made Cool. Diane Kelly first made a name as the world expert on the biomechanics of penises. Seeking new fields of conquest, she’s starting up a company called Zygote Games to develop smart science games for kids. The one I’m looking forward to is, of course, Parasites Unleashed.

Sex Genes and Evolution: John Lodgson, a biologist who studies exactly those three things.

Small Things Considered. I first met Moselio Schaechter through a common interest in obscene mushrooms. Schaechter is also an authority on Escherichia coli, and he kindly looked over the manuscript of my new book on that subject. Now he’s blogging on all things microbial.

Steven Johnson: Author of The Ghost Map and other books on the meeting of science with culture.

synthesis: Rob Carlson, synthetic biology visionary. Sporadic but always interesting.

This Week In Evolution: Does the University of Minnesota actually require their biologists to blog? Because there are an awful lot of them that do. Anyway–R. Ford Denison, who studies how fungi bacteria and plants interact, takes thoughtful looks at new evolutionary research.

The Tree of Life. UC Irvine Davis genome guru Jonathan Eisen blogs on his passions–metagenomics, phylogeny, and open access.

That’s all for now. I’m too lazy to add the links in the post–just scroll down to the blogroll to check them out. And please don’t forget to come back to the Loom!

(Title stolen from Marshall Crenshaw)

I just wanted to take a moment to reiterate my longstanding policy on comments. I reserve the right to delete comments that are slanderous, obscene, or glaringly off-topic. I also reserve the right to ban commenters who do not follow these rules even after being reminded of them. Anyone who accepts these simple rules is welcome to tell me why I am utterly wrong about the topic at hand, even if you think the world is six thousand years old. (And I am entitled to comment on why you are wrong, too.) But this is not the place for spam-like manifestos.

Let the conversation resume.

It’s getting harder and harder to remember what it was like to write about science in the pre-Web 2.0 days. Back then (i.e., 2004), I’d come across an intriguing paper, I’d interview the authors, I’d get comments–supportive or nasty–from other experts in the field, and then publish an article distilling everything I’d learned. It would take months or years for the authors to follow up on their work or for other scientists to publish their own papers attacking or supporting the original research.

How quaint. Let’s take a look at an experience I had yesterday. I was reading a blog called The Evilutionary Biologist. It’s written by John Dennehy, a scientist who works on bacteria and viruses. A couple weeks ago, I only knew Dennehy as one of the co-authors of a paper on trapping viruses I wrote about for the New York Times. (I’ve met him, too, and he’s actually not the least bit evil.) But then Dennehy got the blog fever, and he is now posting great stuff–new research and classic papers. So here I am finding out about important new papers from the blog of someone who was once, for me, the sort of person I’d write about.

Yesterday Dennehy wrote about a new paper on the evolution of the flagellum, the spinning filament that microbes use to swim. This is a topic of some interest to me, because I’m writing a book about E. coli, and much of what scientists know about the flagellum they’ve gotten from studying E. coli. Some fascinating new work is emerging on how the flagellum evolved, based on surveys of flagellum genes and related genes that build other structures. I wrote about some of this work in November in National Geographic. (E. coli’s flagellum was also a star at the Dover intelligent design trial, because intelligent design advocates claim that it must be the work of a designer.) In the new paper, scientists at Arizona State University the University of Arizona report on searches they’ve made for flagellum genes in the genomes of 41 different species of microbes. They identify a core of genes found in all groups of microbes with flagella, and argue that it was present in their common ancestor. They also argue that these genes are the products of a series of gene duplications, descending from a single ancestral flagellum gene.

So, I do what any science writer does. I read the new paper and looked for some comments. I email Nick Matzke, a co-author of an earlier paper on this topic. He wasn’t impressed. To register his displeasure, he wasn’t content just to send me a grousing email. He blogged at length on Panda’s Thumb. Commenters threw in their own two cents. Meanwhile, another source-turned-blogger, Ryan Gregory (whom I wrote about in an article on dinosaur genomes), wrote about the study as well, to which Larry Moran, himself a blogger as well as University of Toronto biochemist, responded harshly in the comments, saying that the paper should never have been published. (Moran, Matzke, and others complain about the methods the ASU scientists used to identify related genes.)

Now, in the pre-Web 2.0 era, all this to-ing and fro-ing happened all the time. At a packed presentation at a scientific conference, people would stand up during the question period and have at it, or head out to the hallways to continue the arguments. But most of this sort of debate didn’t get far beyond the walls of the conference hall. Science writers like me would try to offer a glimpse into the arguments, but there’s a hard limit to how much we can convey in a thousand-word piece. Any other debate had to get channeled into the glacial flow of scientific publications. Now, as this flagellum exchange makes clear, freewheeling scientific debates can reach a wider audience.

This can potentially be a good thing. It may drive the scientific process forward more efficiently, and it may let non-scientists better understand a crucial part of science. But as it stands, this open debate has some big problems. For one thing, it’s incredibly diffuse–a post here, a comment there. It’s not even really a debate. The authors of the paper itself have not, to my knowledge, responded anywhere to all this. (Admittedly, this has all unfolded in about 24 hours, so perhaps I need to lay off the coffee and wait a while.) Obviously, the blogosphere gets a lot of its strength from its decentralized structure, but it seems to me that productive debate is a lot like life. If you pack a lot of enzymes and DNA and other molecules in a tight package, you get life. Disperse them, and you get a few random reactions. Pack comments about a particular paper in one place, and a real debate can emerge. Disperse them across the blogosphere, and you encourage cheap shots and irrelevant tangents, while good observations go unappreciated.

It’s not as if there hasn’t been a lot of talk about how to make this sort of conversation possible. Science papers could be published in an open-access format and readers could post comments directly to the paper. And in fact, there is such a system in place, called PLOS One. In case you’re not familiar with PLOS (short for Public Library of Science), it’s now a real powerhouse in the world of scientific literature, with a number of high-impact journals. (Full disclosure: I was asked to write an essay for one of their journals.) PLOS One, started in January, takes their philosophy a step further.

What I find striking, however, is how quiet it is over at PLOS One. Check out a few for yourself. My search turned up a lot of papers with no discussion attached. Many others had a few comments such as, “This is a neat paper.” There’s nothing like the tough criticism coming out about the new flagellum paper to be found at PLOS One.

I suspect this situation has come about because scientists as a group are only just becoming comfortable in the blogging environment. (Moran, Gregory and Dennehy are all pretty new to it, for example.) It’s one thing to air your complaints in a small room at the annual meeting of the International Society of Helminthologists. It’s another to post them in a place where all of your colleagues–and anyone else with an Internet connection–can read them. So perhaps in a couple years I’ll revisit this issue and see if indeed the debate really has crossed over into a new incarnation.

And if it does, I’ll have to give some serious thought to what a science writer is supposed to do in such a Brave New World…

Update 4.18: I’ve struck Moran from the newbie list. His blog Sandwalk is relatively new, but he’s been online at talk.origins, etc., for many years. My mistake.