The ENCODE project has definitely dominated the news this week. I’ve had various reactions to my mega-post from “one of your best” to “you blew it”. I do want to note, as in this set of tweets, that getting in all the nuances and caveats, capturing both the enthusiasm and scepticism about the project, and making it all make sense for both a general and scientific audience, to a deadline, was not easy. It was more like the opposite of easy.
I’ve mulled over the post in the ensuing days. I knew not to use the “long dismissed as junk” trope. I mentioned that the types of elements that were identified were not a surprise, and ENCODE’s value was as a comprehensive catalogue. I tried to point out where the 80% figure came from, the uncertainty around it, and what “functional” meant. One of the hardest things about a story like this is that even if you have a mental list of points and caveats to tick off, and even if you think you get them in the piece, you never know if readers will pick up on them, or what message they’ll end up taking away. Are those points visible, or just there?
Anyway, I eventually decided that what was in the post was reasonable, but it needed more. I still think it’s important to get across what the ENCODE researchers think about their work, it is an exciting project, and it’s a lot more than junk-or-no-junk. But given the widespread commentary – critical, sceptical and thoughtful – it needed an update. You’ll find that update in the main post itself, time- and date-stamped, and an explanation about why I decided to edit rather than post a follow-up.
I’ve also been collecting links to other commentary, specifically about the science of the project. They’re there in the post itself, but repeated here to draw attention to them. The list in the post will continue to be updated. This list will not.
- [If you read one thing, read this] The best summary of the reactions yet: Fighting about ENCODE and junk by Brendan Maher. Graceful, measured stuff.
- ENCODE: the human encyclopedia, a long-read feature also by Brendan Maher, laying out more of the results beyond the junk DNA angle.
- This 100,000 word post on the ENCODE media bonanza will cure cancer, by Michael Eisen, heavily critical of the PR, and some of the claims (but see also: Michael Eisen’s take on ENCODE by T. Ryan Gregory).
- Mike White at The Finch and Pea is one of the few to delve into the papers for interesting angles not covered by the media coverage. Some interesting stuff here.
- Michael Eisen again on the neutral theory of molecular function.
- The ENCODE project: lessons for scientific publication, by Daniel Macarthur
- T. Ryan Gregory’s various pieces, including this one comparing ENCODE’s claims to a 1972 paper, and two others.
And finally: I love this tweet from Oliver Morton: “Genomes are like genome metaphors: messy, slowly accreted, self contradictory, more complex than anyone would think reasonable”.
Cave fish dare to originate in Gondwana, evolve & speciate, confounding young earth creationists. By Kimberly Gerson.
Strapped for funding, medical researchers pitch to the crowd. By Virginia Hughes. With crowd-funded med research like this, I wonder how much donors understand about possibility of failure in science?
Video of massive explosion on the Sun
Do birds hold “funerals”? A paper said so. The media said so. Barbara King explains.
Recently, I committed on Twitter to stop using words like “crazy”, “insane”, “deranged” — or other terms to do with a person’s mental health – in a perjorative way. I think it exacerbates stigma against mental illness by associating such conditions with behaviour that’s variously incorrect, irrational, ridiculous, or just plain hard-to-understand. This post, by David Steele, on the language of mental illness stigma, perfectly explains why I’m doing this.
Totally briliant Alexis Madrigal story on how Google is building the world’s best maps with its Ground-Truth project
Meanwhile, Becca Rosen considers what it is about an elephant’s tusks that makes them so valuable?
Naomi Wolf has a new book out – Vagina. The feminism has been eviscerated by Mumsnet, Suzanne Moore, Laurie Penny and Ariel Levy. The bad science has been corrected by Neuroskeptic (including an epic last line).
Apparently you can die from drinking a bucket of DEET. Drinking, you say? Well maybe. By Deborah Blum.
Dancing woolly aphids will probably stab you. By Bec Crew
Kerri Smith profiles Xing Xu, China’s premier dinosaur hunter
How to make an octopus – a wonderful tale of dissection and model-making.
Maryn McKenna on that new tick-borne “Heartland” disease, the latest in a rapidly appearing line of new diseases
Paralysed people with broken spines get feeling back in stem cell world first
Making people sign their forms at the top leads to more honest answers. Cool real-world experiment
Brushing your teeth in space is hard.
Found this unfeasibly cute: Curiosity’s tracks, as seen from space
What’s in a (disease) name? How multiple, complex names for a disease harms patients.
Mitt Romney believes in basic science, such as cold fusion. Wait, what?
New network encourages scientists to spend just 5 mins/wk speaking out against misinformation on animal research
An interview with conservation writer David Quammen.
The Japanese river otter is extinct, its memory preserved in a truly awful piece of taxidermy
Pentagon’s Robot Cheetah outruns Usain Bolt and heads towards your house as we speak
Another study fails to replicate an old Bargh priming study, and my blog post is Ref #12. <beams>
Spermy llamarama with Kate Clancy.
How A $440,000 Drug Is Turning Alexion Into Biotech’s New Innovation Powerhouse
The abyss is also in recession. Craig McClain on his new PNAS paper on the energy budget of the deep sea
Fungi shoot salt into the air and make clouds over the Amazon. Which is awesome.
Species can now be named online. “The very fact that we’re discussing this in 2012 seems sort of silly” – Mike Taylor.
Obama and Romney tackle 14 top science questions
While many people struggle to find jobs, this disgraced fraudster gets a new home at a cancer centre.
Tigers take night shift to dodge humans
As Silent Spring turns 50, Rachel Carson’s biographer looks at five decades of attacks on her book
Why Big Nature need not be the only nature you experience. Excellent testimonial to urban ecology.
NO. WAI. Beaches more popular when it’s sunny, study finds
1/5 of invertebrate species at risk of extinction. Poor spineless things (Insert lame political commentary.)
Species multiply as Earth heats up. Before you say anything: RATES.
Tear-jerking comic about the tragic life of one of the Space Invaders invaders
Poignant: ‘A great silence is spreading over the natural world’
Drawing dinosaurs: how is palaeoart produced? With intense collaboration, it seems.
“*Is this science?” Hilarity from Sophie Scott.
The TB test you can do at home
Why is there an increasing number of tick-borne diseases? An uptick, if you will
Makes scents: Whale-scat-sniffing dog helps conservation efforts
Earlier this week, someone on Twitter asked for my qualifications and the university I went to, so she could decide whether to read one of my pieces or not. To forestall such bulls**t in the future, here is a copy of my degree.
Ha! Genius. A poem made from slides at Jeff Bezos’ Kindle presentation
What an absolutely gorgeous photo of a giant Pacific octopus.
I made a T-shirt for Xeni Jardin to cheer her up during radiotherapy. It says: “With great power comes great radiotherapy”. Here’s the jpg. You can make your own at Cafepress.
In a mass knife fight to the death between every American president, who would win and why?
Really evocative. Composite photos merge scenes from 1906 San Francisco quake w/ present day
XKCD: What would the world be like if the land masses were rotated by an angle of 90 degrees?
Best protest sign ever
“The one job we asked Canada to do (“make—and do not lose track of—all the maple syrup”), Canada was unable to do.”
Blogger and microbiologist Jim Caryl has a photography website, and it’s fantastic.
Timelapse video of man drawing the Manhattan skyline freehand
Excellent Robin Ince post on maintaining your humanity on Twitter. He’s right to call out passive-aggressive @-cc’ing
John Pavlus is making films about the people behind mundane but completely ubiquitous objects, like those plastic cups you get. Go support it.
Bill Clinton’s speech, with edits in-line showing where he went off-script. Man should give all my talks.
Which of these is not like the others? GQ Men of the Year Covers
Misogynist hate mail from the “skeptic” “community” drives Jen McCreight to stop blogging. Awful. Just awful.
She just wanted to read her book & be left alone.
Woman stung by scorpion, charged nearly $40,000 for antivenom at an Arizona hospital. “It’s our nature,” said the US.
Words David Foster Wallace’s Mom Invented