Italian Training Camp

NIH Funding

This is why people in biomedical field are screwed:

See that period in the 90’s, when the budget started to take off? That’s when new labs were built, programs were expanded, and lots of grad students were trained. Now, that all of those grad students have graduated, and are looking to start their own labs, the funding has plummeted. The result?

R01 grants, the foundation of research labs, are only getting funded at a rate of 20%. Sure, there are some grants don’t deserve funding, but thousands of other people doing quality work aren’t getting the money they need to make their research happen. More alarmingly, the average age of a researcher’s first R01 grant has skyrocketed to age 43. If you get out of grad school at 28, that means you’re spending 15 years stumbling from lab to lab in low-paying post-doc positions, trying to scrounge up enough money to get your work done. Gee, I went to school for 23 years for this??

How does this affect all you non-scientists out there? Well, as PZ Meyers points out simply and eloquently, biomedical research saves lives. Period. Ever known someone with cancer? Look at those survival rates and tell me that research money isn’t well spent.

We need to make it clear to our representatives in congress that science funding is a priority. Last year, the US spent 64% of it’s discretionary budget on the military - a total of over 632 billion dollars (this doesn’t even include supplemental spending on Iraq!). The irony of all this is that military dollars are supposed to be keeping Americans save and alive, but by moving even 1% of that into the NIH budget, we could ensure that a far greater number of people kept on living.

via DrugMonkey and NEJM

Origin of Species

Lotteries

A household with income under $13,000 spends, on average, $645 a year on lottery tickets, about 9 percent of all income.

If this statistic is accurate, it’s staggering. It also reinforces what most of us already know: The lottery is a tax on the stupid.

source: NYT via Kotte

Unless he proves me wrong…

Tom Delay: “Unless he proves me wrong, [Obama] is a Marxist.”

Hunter responds: “Unless he proves me wrong, Tom Delay lures children into his van with candy, gasses them to death with bug spray, and uses their powdered bones as an aphrodisiac when making love to all the animals at the San Antonio Sea World.”

Only seems fair….

23andWe

Wondering how 23andMe plans on making money off of selling SNP chip results, when so little is known about most SNPs? Well, today they unveiled part of their master plan: 23andWe. After getting your results, you can go fill out fun little surveys, all the while helping 23andMe build a massive database of genotype/phenotype information that they can mine for new genetically-influenced traits. Clever.

BuzzYeah has screenshots and more info

Getting genotyped isn’t worth it yet, from a medical standpoint, but if I had 1000 dollars that I didn’t know what to do with, I’d sure do it.

Collins stepping down

Francis Collins is stepping down as the head of the NHGRI. Sure, I don’t agree with his take on religion, but Collins did a damn fine job of heading up the Human Genome Project, and then working his butt off in Washington to secure funding and political support for genomics projects. He’s a major reason that the field has advanced so rapidly in recent years.

In addition to his bureaucratic duties, Collins’ own lab does some pretty nice work related to genetic disease, including the very interesting syndrome known as progeria. He’s also a great communicator, and if you ever get a chance to hear him speak, either on his own research or on genomics as a whole, don’t miss it.

Keep your friends close…

James Baker, Secretary of State under Bush I, explains why talking to your enemies is not appeasement:

People that we disagree with are the ones we need to be talking to the most. It’s how adults resolve their differences. This administration, and McCain, seem to have missed that lesson in grade school.

QOTD

“Progress isn’t made by early risers. It’s made by lazy men trying to find easier ways to do something. ”
Robert Heinlein

West Virginia Voters

QOTD

Sometimes people say I shouldn’t mind being searched if I have nothing to hide. I immediately accuse them of having a swastika tattooed on their genitalia — if they have nothing to hide, then surely they shouldn’t mind dropping their pants to prove me wrong.

source

Frequent Flier Follies

Heather called me today and asked if my flight, scheduled for this evening, was on time. “Let’s see”, I said, as I logged into southwest.com. Houston. . . to St. Louis . . .  loading . . .

“Hrmmm. My flight number isn’t showing up - that’s odd”. “All right. . .” goes to email, pulls up e-ticket “Nope, scheduled for 8pm, flight from St. Louis to Houuustooon…” Drop a beat. “Oh shit.”

Not only did I book my flight in the wrong direction, but I actually checked in last night and confirmed my flight itinerary without noticing the error. Thankfully, with the help of a lovely SWA agent and some frequent flier flights I had laying around, I’m getting to St. Louis tomorrow morning in plenty of time for Heather’s graduation tomorrow, and getting my money back for the incorrect reservation.

I’m pretty sure that before I started flying once a month, I would have checked my reservation a little more carefully. So beware, all ye frequent fliers, lest you make the same mistakes as I.

Little Brother

Cory Doctorow just released his newest book “Little Brother” as a free electronic book. I downloaded it the other day, and devoured it in about 2 hours that night. I don’t often recommend books, every American, especially those under the age of 25, should read this book.

The story shows how fear of terrorism and modern technology could be used to turn our society into a modern-day dystopia, straight out of the pages of Orwell’s 1984. Thankfully, the same technology enables free culture to thrive in an era where the Department of Homeland Security routinely reads your email and the government tortures its own citizens.

Although I’ve disparaged some of Cory’s earlier works for being long-winded and lacking in plot, this one doesn’t suffer from any of those flaws. It’s fast-paced, interesting, and a great read. Read it for free here, or by it at any local bookstore.

Wedding Ceremony

We got a lot of great compliments on our wedding ceremony, especially from friends who, like us, aren’t really religious. In answer to the questions we got, it was cobbled together from other ceremonies we found on the internet, and we added our own touches where we thought it was appropriate. We were really happy with how it turned out.

So that others can do the same thing, I posted the ceremony on our wedding site. Take what you want, or use the whole thing, if you’re so inclined.

Rotating One Monitor with Ubuntu

Ubuntu’s support for graphical displays has come a really long way. In Hardy 8.04, most of the configuration is handled through a GUI that works very well, in my experience. There are still a few edge cases that require a little manual configuration, though. Today I ran into one of them.

I have two monitors at work, and today I decided to rotate one of them to a vertical orientation. It’s nice for coding, because I can see many more lines of code at once. The other one I like to keep widescreen. Here’s how to accomplish this using an Nvidia dual-headed card, the nvidia proprietary driver (not nv), and two Dell flatscreen monitors.

Assuming you already have your monitors set up and working with the nvidia driver, start by backing up your xorg.conf. If something goes wrong, you can always restore this and be back where you started.

sudo cp /etc/X11/xorg.conf etc/X11/xorg.conf.bck

Then, fire up nvidia-settings from the terminal. Under “X Server Display Configuration”, make sure that you’re using “Separate X screen” and not “Twinview”. Twinview works great when the monitors are in the same orientation, and even gives slightly better performance, but didn’t allow me to rotate just one of the monitors. Check the box that says “Enable Xinerama”, and then write the changes to your X Configuration file.

Now, for the rotation:

sudo emacs /etc/X11/xorg.conf

In the appropriate “Monitor” section, add the lines:

Option "RandRRotation" "on"
Option "Rotate" "CCW"

Change “CCW” to “CW” for clockwise, instead of counter-clockwise.

Save the file, hit CTRL-ALT-Backspace to restart your Xserver, and you should be seeing the results. Great! Well, almost great…

There’s just one problem. There’s a known bug where gnome-terminal doesn’t work properly when nvidia composite drivers are enabled. The first solution in that thread (disabling the composite) didn’t work for me, so I did the following workaround that sets some environment variables every time the terminal is launched. Hit ALT-F2 and type “xterm” (since we can’t use gnome-terminal), then do the following:

sudo mv /usr/bin/gnome-terminal /usr/bin/gnome-terminal2
sudo emacs /usr/bin/gnome-terminal

In the new file you’re now editing, paste the following:

#!/bin/bash
XLIB_SKIP_ARGB_VISUALS=1 gnome-terminal2 $@

Save the file and make it executable:

chmod +x /usr/bin/gnome-terminal

Now, everything should work correctly.

QOTD

If more of us valued food and cheer and song above hoarded gold, it would be a merrier world.

–J.R.R. Tolkien

San Francisco

I’m in San Francisco until Tuesday night at a conference. I’m staying right on the bay, so I ducked outside tonight for some fresh air and to take a few pictures. After spending 6.5 hours on a plane to get here, and then the next 4 in meetings, I needed to stretch my legs. For those of you who worry that the government isn’t spending your tax dollars wisely, know that I had to stop over in Phoenix because the direct flights were too expensive for the NCI. The experience has also convinced me that if I ever take a trans-atlantic flight, I should just load up on Ny-Quil before takeoff. I get a little stir crazy after about 2 hours.

The flight in is very picturesque. After hours of dull brown wasteland, the snow-capped Sierra Nevadas shoot up out of the desert, then give way to the lush green California Valley. The landing at SFO is interesting as well, because the approach is over the bay. Out the window, the water rises closer and closer, until you’re convinced that you’re about to splash down, but at the last possible second the runway appears to meet the wheels of the plane.

Sadly, there won’t be time for much tourism because I’ll be cooped up discussing integrative analysis of cancer biology. Don’t get me wrong, I’m glad to be here and expect to learn a lot, but I’m definitely wishing I could explore the kick-ass city right outside the hotel doors. Looks like I’ll have to come back with Heather one of these days. From the little bit I’ve seen, it looks awesome.

National Day of Prayer

I try to repost this every year on this date:

In 1952, Congress passed a law establishing the National Day of Prayer as an annual religious observance.

Quick: give me another sentence that uses the words “Congress,” “law,” “establish” and “religion.”

Hint (it’s under Amendment I)

Cognitive surplus

Clay Shirky thinks we’re at a critical point in our society, where we shift away from a passive television culture and use the cognitive surplus to create a participatory culture. Here’s an excerpt, but definitely read the whole thing.

I was being interviewed by a TV producer to see whether I should be on their show, and she asked me, “What are you seeing out there that’s interesting?”

I started telling her about the Wikipedia article on Pluto. You may remember that Pluto got kicked out of the planet club a couple of years ago, so all of a sudden there was all of this activity on Wikipedia. The talk pages light up, people are editing the article like mad, and the whole community is in an ruckus–”How should we characterize this change in Pluto’s status?” And a little bit at a time they move the article–fighting offstage all the while–from, “Pluto is the ninth planet,” to “Pluto is an odd-shaped rock with an odd-shaped orbit at the edge of the solar system.”

So I tell her all this stuff, and I think, “Okay, we’re going to have a conversation about authority or social construction or whatever.” That wasn’t her question. She heard this story and she shook her head and said, “Where do people find the time?” That was her question. And I just kind of snapped. And I said, “No one who works in TV gets to ask that question. You know where the time comes from. It comes from the cognitive surplus you’ve been masking for 50 years.”

Shirky estimates that if you took all of Wikipedia as a unit of measure — that is, all 2,354,625 articles, with their billions of edits, behind the scenes discussions, and individual contributors — the US’s two hundred billion hours per year of television watching could produce the equivalent of 2,000 wikipedias. That’s a lot of untapped mental activity. He argues, pretty convincingly, that if you could harness even 1% of that time in participatory ways, you’d come up with some pretty amazing stuff. Wikipedia, Youtube, and the rest of the blogosphere agree.

While My Youtube Gently Weeps

Today’s Youtube find: two fantastic covers of George Harrison’s ‘My Guitar Gently Weeps’. The first is by Jake Shimabukuro, on ukelele:

The second is by Tom Petty, Prince, and company. Don’t miss Prince’s lengthy solo towards the end.