In which I say something nice about George W. Bush

Today, President Bush is expected to designate several huge areas to be marine national monuments. This will limit commercial activity in the regions and protect a large number of endangered and threatened species. While his general record on the environment hasn’t been stellar (to put it mildly), this is great news. So here it is: Thanks, GWB. This is a good thing you’ve done.

2008 recap

A few of the things I did this year:

Lincoln Memorial
- Went to Washington DC for a TCGA meeting

- Saw Barack Obama and Bill Clinton campaign in Texas.

- Started a Texas politics blog (now largely abandoned)

- Got hitched

Roatan, Honduras
- Cruised to Central America on a fantastic honeymoon

- Revisited my old loathing of pre-meds

- Got briefly fascinated by elevator mishaps

Slope
- Attended a meeting in San Francisco

- “Hunkered down” during Hurricane Ike, then survived for four days without power

- Was published in Nature

Pac-man heads
- Made Pac-man heads for Halloween

- Elected a leader who gives me hope, and blogged about the demise of the GOP


- Traveled to Hawaii

- Was published again in Genome Research. That article was then written up in the New York Times

All in all, a pretty good year. Here’s to an even better 2009.

The Chaos Inside a Cancer Cell

Our lab’s latest paper was featured in the New York Times today!

A few quick notes:

  • All props go to Oliver Hampton, who did the lion’s share of the work to get this paper out. (I’m the third author on the paper).
  • I realize that to scientists, the NYT isn’t as exciting as getting published in a big-name journal, but it sure seems to mean a lot more to my non-scientist friends and family!
  • The featured picture was generated using the Circos software package. (open source, GPLed)
  • The paper is open-access and available as an advance publication here.

uTorrent and Ubuntu

RSS feeds plus bittorrent makes auto-downloading video content from the web easy, and keeps our library full of shows to watch through the Xbox. I struggled for a while to find a bittorrent client that was simple and had the features I wanted, though.

Azureus is a bloated mess, Transmission is far too simple, Deluge made feeds a pain in the ass . . . you get the idea. Finally, I found that uTorrent had all the features I wanted in a lightweight, easy to use client. The only problem is, it doesn’t run natively on linux. Thankfully, it runs almost perfectly through Wine, with a taskbar icon and everything.

The only problem I had was that when I clicked on a torrent in my browser, I couldn’t get it to auto-launch in uTorrent. The extra layers added by wine complicated things. I finally solved the problem by writing this little bash script:

#!/bin/bash
cd ~/.wine/drive_c/Program\ Files/uTorrent
echo ""
if [ "$1" != "" ]; then
    dt=`date +%s%N`
    cp “$1″ /tmp/$dt.torrent
    var=”Z:\\tmp\\”$dt”.torrent”
    wine utorrent.exe “$var”
else
    wine utorrent.exe
fi

It takes the torrent file given as an argument, saves it to an accessible location, then opens it using uTorrent. Save the script, make it executable, and then set firefox so that it uses the script to open any torrent files. Problem solved.

Linkdump for December 19th through December 21st

The Third Stooge

iraq shoe throwing

found here.

Finally, a president who respects science

It’s time we once again put science at the top of our agenda and worked to restore America’s place as the world leader in science and technology.

- President-elect Barack Obama in his weekly address

It’s about time we heard that from Washington DC, and it’s great to see that he’s backing it up by appointing several well known and respected scientists to key positions. From my perspective, it’s especially exciting to have Eric Lander on the President’s Council of Advisors on Science and Technology. He’s one of the biggest names in genomics and should do a great job of informing this White House about the power and potential of personalized medicine.

Update: How did I miss Harold Varmus? He’s a Nobel-laureate cancer researcher. As someone working on cancer genomics, this lineup makes me very happy.

The BBC gets it wrong

Wow, this BBC article about breast cancer and embryo screening gets it wrong big-time.

[H]e said that, in this case, not carrying the BRCA1 gene would not guarantee any daughter born to the couple would be unaffected by breast cancer because there are other genetic and environmental causes.

Bzzzzzzzt. Sorry. This science reporter fails the test, and does so repeatedly throughout the article.

Everyone has the BRCA1 gene, and it actually helps prevent cancer! See, BRCA1 is involved in the process of DNA damage repair, which reduces the number of mutations in the genome. A properly functioning BRCA1 protein helps stop cancer before it starts.

What confused the reporter was that only some people have BRCA1 genes with mutations. When one or a few base pairs in the BRCA1 gene are altered, it can change the resulting protein and cause it to malfunction. These mutations are what confer a higher risk of breast cancer.

At least one scientist interviewed in the article gets it right:

Dr Alan Thornhill, scientific director of the London Bridge Fertility, Gynaecology and Genetics Centre, said: “While the technology and approach used in this case is fairly routine, it is the first time in the UK that a family has successfully eliminated a mutant breast cancer gene for their child.

It probably could have been more clearly said, but he does state that it’s the mutant copy of the gene that’s being eliminated, not the gene itself.

You may say that I’m playing semantics here, but this is crucially important stuff, as the article makes very clear. People are going to have to begin making serious decisions about risk factors affecting themselves and their children. It’s hard enough to convey this information when we get the facts right. Muddying the waters with bad reporting only makes the job tougher.

Update: Props to the BBC for changing the article. I don’t know if it was my contact form submission or someone else’s, but they’ve updated the article to make it more correct. That said, shouldn’t they acknowledge the change somewhere on the page? A footnoted erratum would go a long way towards improving transparency.

Linkdump for December 18th through December 19th

QOTD

It’s a cliché that too little American talent goes into science, and that too many people go into banking, and that our education system is said to be failing because of those effects. To some substantial effects it must be true.

I found myself on a business trip to Europe and lucky for me I was sitting in business class. Seated not far from me in business class was a young woman who had graduated from Harvard 14 months before and who was working for a major financial institution and she was traveling to Europe and when people travel for that major financial institution they travel in business class. I like to walk when I’m on a plane, so I wandered. I walked back to coach and on that airplane in coach was a distinguished physicist who I had known when I was president of Harvard who I think probably is close to even money to win a Nobel Prize one day. He was going to a conference like professors of physics do and he was going like professors of physics like him go, which is in coach. And I didn’t say anything to either of them, but I thought to myself there was something odd about the reward structure of our society.

–Lawrence Summers

quoted from here, via adaptive complexity

Linkdump for December 17th

Linkdump for December 16th through December 17th

Programming note

I’m now using postalicious to pull in my del.icio.us links, so you’ll be seeing linkdump posts every now and then. They’ll be a little more frequent over the next few days, as I clean out my bookmarks and old to-do lists from the year.

Linkdump for December 15th

Where are your priorities?

What makes you feel less bored soon makes you into an addict. What makes you feel less vulnerable can easily turn you into a dick. And the things that are meant to make you feel more connected today often turn out to be insubstantial time sinks — empty, programmatic encouragements to groom and refine your personality while sitting alone at a screen.

– Merlin Mann, in Better

QOTD

“The nuclear arms race is like two sworn enemies standing waist deep in gasoline, one with three matches, the other with five.”
–Carl Sagan

Taken to School

PLoS Genetics: Taken to School: An Interview with the Honorable Judge John E. Jones, III.

Really interesting interview with the judge from the Dover intelligent design case.

Missing Methods

Daniel Shriner nails it in last week’s Science.

Some journals have opted for placing the Materials and Methods section after the Results and the Discussion sections. Other journals have almost completely moved the Materials and Methods section from the main text to online supplements. These journals are conveying the message, however inadvertent, that the sine qua non of the scientific method, the Materials and Methods, is the least important part of a scientific publication.

Reproducing results from another group has become downright impossible in the modern era, and the journals aren’t helping matters by marginalizing the section. Besides sending the message that methods aren’t important, they’re allowing authors to get away with not reporting half of the steps they take.

I mean, have you ever tried to recreate another group’s computational analysis, based on a paper alone? Even with the extra info from the Supplementary Materials, it’s generally impossible. They leave out key parameters, or neglect to mention entire steps. I’d love to see a simple schema for representing computational methods become widely used. Preferably, it’d be machine-readable, so that the analysis could be recreated semi-autonomously.

At the very least, let’s require authors to create batch scripts that run the specified tools with the correct parameters, so that reproducibility is no longer a myth.

Happiness in pixellated form

Snow

I walked out of work today to find it snowing. To put this in perspective, this is only the second time this decade that it’s snowed in Houston.

And man, was it ever snowing. Big, fat white flakes were dropping - the kind that swirl in the wind and cling to your hair long after you’ve come in from the cold. People were gathered on the steps, laughing and taking pictures. A 6 year old girl was running around trying to catch snowflakes on her tongue, almost certainly for the first time ever. It made me sad to think that she’ll never get a snow day, and won’t ever know the childhood joy of making a snow angel.

It made me remember coming in from sledding in the backyard and having hot chocolate with marshmallows in front of a crackling fire. It made me remember how beautiful Truman’s campus is after a fresh snow, and how much fun we had sledding down the hill in Red Barn Park wearing trash bag ponchos. As much as I bitched about the cold then, this snow has me missing it now.

So enjoy your snow, Houston. It’s probably going to be another long while before you see it again.

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