Science Culture
sporte | June 24, 2008or is it just an idea that's ahead of the curve?
Last week, I was stunned to discover at least 31 papers in an NCBI Gene database entry that were in the entry for the wrong gene. I wrote about this here, here, here, and here.
Now, an oversight like this is a little understandable. The titles of the entries do include the name of the wrong gene (DRD2 - the dopamine D2 receptor). And it was only four years ago that people figured out that the marker in the title of the articles mapped somewhere else.
If computers were responsible for the annotation, well, this would be understandable.…
sporte | June 21, 2008Are you curious about Second Life?
Next week you can satisfy your curiosity and learn about the personal genomics frontier at the same time.
Bertalan Meskó announced that Erin Davis (science writer) and Joyce Tung (human geneticist) from 23andMe will be giving a presentation next week in Second Life on personalized genetics.
As travel costs rise and traveling becomes harder, I think we'll see many more things happening in alternative places like Second Life. Virtual environments like this can make on-line communication entertaining in ways that conference calls and webinars can't. I may…
sporte | June 20, 2008It's pretty common these days to pick up an issue of Science or Nature and see people ranting about GenBank (1). Many of the rants are triggered, at least in part, by a wide-spread misunderstanding of what GenBank is and how it works. Perhaps this can be solved through education, but I don't think that's likely. People from the NCBI can explain over and over again that some of the sequence databases in GenBank are meant to be an archival resource (2), and define the term "archive," but that's not going to help.
Confusion about database content and oversight is widespread in this…
sporte | June 14, 2008A few months ago, I made a new page for a more complete blogroll. Now, that my class is over and I have a break from traveling around leading workshops, I'm ready to add some links.
Other bloggers; Bora, Mike the Mad, PZ, Janet, DM, and Abel; use a nice technique called "blogroll amnesty" where they offer other writers a chance to be on their blogroll. I like that.
So, to paraphrase Mike:
If you link to me and you're not a creep, let me know and I'll return the favor (instructions below). For those you who've written to me and asked me to add you to the list, here's your chance.
Add a…
sporte | June 1, 2008This month's edition of Medicine 2.0 focuses on connections. You'll learn how new technologies are empowering patients by connecting them with their own health records, connecting patients and paramedics with doctors, and connecting doctors with each other.
Nothing connects like Web 2.0.
Let's hit the Midway!
Many submissions to this carnival certainly captured the carnival spirit. I had just become resigned to the notion of scouring the internet myself, looking for posts that would fit today's collection, when a couple of days ago, I was inundated with email submissions.
Great! I thought,…
greengabbro | May 28, 2008Quick background: Paul Erdös was a prolific mathematician. If you co-authored a paper with him, you have an Erdös number of 1. If you co-author a paper with someone with an Erdös number of 1, you have an Erdös number of 2. It's like playing Six Degrees of Kevin Bacon if you're a gigantic dork.
Now that one of my papers has been officially accepted, I officially have an Erdös number of no greater than 6 - which fact I discovered using this handy-dandy search engine*. Though sadly, one of the papers that links me to Erdös is an obituary, not actual research.
As far as I can tell, this is not…
sporte | May 28, 2008Where have all the flowers gone?
Long time passing
Where do all the flowers gone?
Long time ago
Where do all the flowers gone?
Young girls picked them everyone,
When will they ever learn? When will they ever learn?
-Pete Seeger
Where do graduate students and post-docs go when they decide it's time to leave the pipeline? And, if they're thinking about going, how do they find a path into something new?
These questions are especially timely given all the current NIH funding issues. It's odd, too, that we probably have the data, that is, I think we can count the number of people who've gotten…
sporte | May 22, 2008On June 1st, I'll be hosting the next edition of Medicine 2.0, a carnival devoted to exploring the impacts of web 2.0 technologies on medicine and medical practice.
All topics that consider the impacts of web 2.0 on medicine and healthcare are fair game.
Are you talking with doctors about sexually transmitted diseases in Second Life?
Have you had your genome sequenced? Do your doctors send you e-mail?
Are you using web technologies to measure your food consumption and calorie burning?
If you have an article that you think fits the description, feel free to submit it to me, either via e-…
sporte | April 24, 2008Bill Gates, Eric Lander, Maynard Olson, Leena Peltonen, and George Church fielded questions last night at a fascinating panel discussion on personal genomics at the University of Washington.
We were fortunate to be in the audience. I'll share some of the questions and answers, in some cases shortened and paraphrased.
The room in Kane Hall at the UW was already warm when we arrived last night (yes, I do go to evening seminars). A student handed us cards and cute little pencils for writing our questions and we sat down. We fought the impulse to write "What's the air speed velocity of a coconut-…
hrynyshyn | April 20, 2008This three-part series on radical skepticism and the rise of conspiratorial thinking about science, by Daniel Engber, in Slate, is required reading for anyone interested in the role of skepticism in science and society. It's called "The Paranoid Style in American Science."
Here's the concluding paragraph to the second of the three parts. But it's not the money quote. For that, you'll have to read the whole thing.
It's no surprise that suspicion of science has grown distended in recent years and now looks a bit like paranoia. Each new uncertainty campaign further degrades our faith in science…
hrynyshyn | April 8, 2008Could it be that all this talk about how best to frame argument is pointless? It would if our capacity to change our minds in the face of new information was genetically determined.
If evolutionary psychology doesn't turn your crank, give this post a miss. I'm not convinced myself that there's a lot of merit to this particularly line of inquiry. But just in case...
In a comment posted to one Chris "Intersection" Mooney's recent efforts to explain his support for "framing" science, PZ "Pharygula" Myers gets to the nub of the problem:
Science educators need to get people to accept new ideas,…
greengabbro | April 5, 2008I have been slowly wading through A Social History of Truth, Steven Shapin's study of how early modern English gentleman's etiquette was appropriated for scientific purposes - primarily to help decide who to trust, and to handle disagreements about the nature of the world. While Shapin doesn't move beyond the context of early modern England or speculate about what modern scientific culture might have inherited from the founders of the Royal Society (doing so properly would be an awful lot of work), he discusses several concepts which I have very much enjoyed comparing to the interactions I…
sporte | March 16, 2008Things move off of our entry page pretty quick sometimes. If you missed this post from Bioephemera, go take a look.
She has great pictures and a fascinating story about one Seattle's favorite places.
sporte | February 25, 2008Bora had an enjoyable post yesterday on obsolete lab skills. I can empathize because I have a pretty good collection of obsolete lab skills myself. These days I'm rarely (okay, never) called upon to do rocket immunoelectrophoresis, take blood from a rat's tail, culture tumor cells in the anterior eye chamber of a frog, locate obscure parasites in solutions of liquid nitrogen, or inoculate Kalanchoe leaves with pathogenic bacteria.
(Wow! It sounds like I worked for the three witches in MacBeth! Fire burn and cauldron bubble!)
I don't entirely think that my lab skills are "obsolete." I…
sporte | February 23, 2008Long ago, I worked in a large lab that was divided into several small rooms. For part of that time, I shared one of the small rooms with a graduate student from Taiwan. She was a wonderful person who taught me that many cultural norms are not normal in other cultures.
One moment stands out.
She sneezed.
"Gesundheit" I replied.
She stared at me, clearly puzzled. "What?"
"You know, it's a word we say when people sneeze. It keeps demons from running up your nose"
If she looked puzzled before, now, she was clearly alarmed. I could see her sneaking furtive glances towards the door. Was she…
greengabbro | February 14, 2008I'm a proud member of the United Auto Workers.
The entertainment value of people's broken socioeconomic assumptions when I say this is not to be underestimated, but I don't feel that I'm personally much better off with the UAW than without. The sciences as a whole are much better funded than, say, comparative literature. Graduate students in the earth sciences typically have the option to get a "real" job without leaving the field, which makes school almost like part of a competitive labor market - even without collective bargaining I would probably still be paid okay. I don't have…
hrynyshyn | February 13, 2008Some folks are pushing for the US Postal Service to issue a stamp or two bearing the image of the late great Carl Sagan. I say, if they can put out a Star Wars series, they can bloody well do the same for a real galactic hero.
hrynyshyn | January 31, 2008An editorial in the current edition of the journal Nature suggests we science types take advantage of the writers' strike. It does this under the headline "A quantum of solace," stolen from the next Bond flick. The headline's a stretch, and so is the editorial itself, but hey...
Here's the essential bit:
Scientists often complain that they can never change the way that science is portrayed in films, which seems as if the screenplays are written on a planet with different laws of physics. But, to quote an earlier Bond film, never say never. Indeed, today is a propitious time for such…
hrynyshyn | January 25, 2008CBC reports that Canada's "national science adviser Arthur Carty would be retiring on March 31, and that the position and office would be phased out." To which I could only say: "Who would want the job anyway? You'd just be ignored and made to feel small and insignificant."
John Smol, a leading ecology professor and researcher with Queen's University, said he found the news "troubling and worrisome."
"Having someone in a position to advise the prime minister or a cabinet minister gave me more confidence in the process," Smol said. "There's so little of this contact between the scientific…
sporte | January 14, 2008is coming home and flying into Seattle. I took these pictures with my phone (in Airplane Mode, of course).
In the first shot, you get to see Mt. St. Helen's and all the interesting geology around it.
Can you tell which way the volcano blew?
Mt. Rainier is in the background
The second shot is downtown Seattle.