the other McLafferty rearrangement

January 28, 2008 at 9:10 pm | | science community, seminars

Fred McLafferty spoke today for our Student-Hosted Physical-Chemistry Seminar series; and I had the fortune of joining a few other grad students for dinner with this great scientist. He is a really friendly guy and he has tons of energy.

He was also very quick-witted. At one point in his talk, when he was discussing a cleavage along the backbone of a protein, a typo in one of his slides tripped him up:


He immediate came back with, “Oops, that’s from when I practiced my slides on my son’s Mac; the computer must have replaced that carbon with a nitrogen!”

pretty picture for a friday

January 25, 2008 at 3:32 pm | | cool results, everyday science

Just a picture of my nice column (thanks for the help and the hood-space, Nick):


Some photoproducts of a cool reaction that I’ll tell you about when it’s published.

wolf prize

January 22, 2008 at 9:25 am | | science community

W.E. just won the Wolf Prize in Chemistry, which is really great news! Well, for my lab, at least. Also great news because, when Dick Zare won, the department had an ice-cream party…

strange ice

January 17, 2008 at 5:35 pm | | EDSELs, everyday science, grad life

edsel.jpgToday, I became the senior graduate student in my lab. Which is scary, because who do I go to when I have questions?!?! The new students joining the lab tend to come to me with a lot of questions. I’m sure the other senior lab members get a lot of questions, too; and it’s fun to watch the now-second years get all the same questions that they asked me when they joined. I really like helping people with science questions, and I want the new members of the lab to benefit from me just as much as I benefited from my seniors when I joined. But then there are those other questions…

This EDSEL goes for the Best Question from a New Lab Member of 2007. Runner-up is “What is the phone number here in lab?” My answer: “Um, it’s written right there on the phone.” The winner goes to this conversation:

Post Doc: I just got a package that had ice in it to keep the sample cold. What do I do with the ice?

Sam: You can put ice in the sink. It’s just water, so it’s OK to go down the drain.

PD: But it’s strange ice.

Sam: What do you mean, “strange”? Is it dry ice?

PD: I dunno.

Sam: You know, dry ice: solid carbon dioxide?

PD: I dunno.

Sam: Hrumph. Is it smoking?

PD: Yes.

Sam: That’s dry ice. Just leave it in the box and it will sublime.


Now, the post doc isn’t from the US, so maybe he couldn’t remember the word for dry ice. But I thought the “frozen CO2” description would help. I guess not. I’d ask him to post his side of the story, but he’s no longer in the lab.

“Post Doc,” if you’re reading this: Congrats! You won an EDSEL.

EDSEL: coolest paper of 2008 (so far)

January 11, 2008 at 4:59 pm | | EDSELs, journal club, literature, single molecules

edsel.jpg(Or: How I Learned to Stop Worrying and Love the Awards.)

Lest EverydayScientist fall behind the other blogs (CBC’s Cornies and Kyle’s MAFAYEG), I’m now forced to award prizes for arbitrary things. Right now, I’m worried about a silly-awards gap.

So I give you the first EverydayScientist’ Extraordinary Laud (EDSEL) award for the Coolest Paper of Early January 2008:

Huang, B., Wang, W., Bates, M., Zhuang, X. Three-dimensional super-resolution imaging by stochastic optical reconstruction microscopy. Science 2008 (published online Jan 3).1


Stochastic optical reconstruction microscopy (STORM) is Xiowei’s cool super-resolution technique (Eric Betzig has a similar version called “PALM”). And I’ve already blogged about Bo’s talk at ACS Boston.

There’s not anything revolutionary in this paper: they’ve used their STORM technique, and simply added an extra lens to distort the PSF of single molecules, causing those above or below the focal plane to distort in a consistent manner. That way, they “imprinted” axial information on the image, and can generate 3D representations from the fitting data.2 But, while the technique isn’t a breakthrough, this paper is in Science because the images produced are really amazing:


You can see that the microtubules in the cell move down! Cool. And the supplemental material included this beautiful movie of some microtubules crossing over each other (the scale bar is only 200 nm, below the diffraction limit):

[local /wp-content/uploads/ View Movie]

3d-storm1_clathrin.jpgAnd I also really loved this comparison of 2D STORM (top) versus a 100-nm thick x-y cross-section in the 3D image (bottom) of some clathrin-coated pits. You can really see that they are hollow!

Now, all these images are of fixed (read: “dead”) cells. Because STORM imaging requires cycling acquisition, each frame generally takes a long time. This makes living-cell imaging and measuring dynamics difficult.3 And this is really a proof-of-principle study: the results don’t answer any biophysical questions. Nevertheless, the images are really beautiful!

I fully expect this technique—and the other super-resolution approaches—to become another tool in the biophysical toolbox (along with TIRF, FRET, FLIM, FRAP, and other acronyms). Just you wait…


1 I tried to be good and requested permission from AAAS to reprint these images and movies. But they haven’t gotten back to me. So I’ll just post them anyway. Don’t sue me, Bo. [UPDATE: Reprinted with permission from AAAS. I finally received permission to use these images. If you wish to reuse these images you can obtain permission from AAAS by following the guidelines here.]

2It is generally known that the dipole-emission pattern of single emitters contain information about axial depth. It is also straightforward to introduce an astigmatic distortion to the optical system to imbed depth information.

3 Not impossible: someday it will be done. Stefan Hell already is quite fast with his PALMIRA imaging.

what a happy lightbulb!

January 10, 2008 at 6:56 pm | | crazy figure contest, literature

Another one for the silly-figure contest:


This is the table-of-contents image for a recent JACS paper: “Solid-State Photodecarbonylation of Diphenylcyclopropenone: A Quantum Chain Process Made Possible by Ultrafast Energy Transfer“.

I suppose that this silly image is germane to the subject of the paper (especially the “chain process”). But, really?!? How old are we? Some people have fun with TOC images, I suppose.

In fact, is that the little MS guy that helps me figure out things in Excel? Microsoft should sue for copyright infringement.

Political Science Update: New Hampshire Primaries

January 9, 2008 at 3:30 pm | | news, political science, science and the public

It’s Clinton for the Dems, and McCain for the GOP.

Like I did with Huckabee, I dug around to see where McCain stood on science. I was glad to find that he opposes the politicization of science. Source. That is, he accepts that humans are contributing to global warming, and that that’s a problem. He accepts evolution. Source. He introduced the American Innovation and Competitiveness Act of 2006, which aimed to improve communication among scientists. His voting record is pro-stem cell research. I can’t figure out whether he wants to grow a budget for scientific endeavors, and his website is still nothing like Hillary Clinton’s website, but I think I’m safe in saying McCain is at least not an enemy to science.

However, he’s been pandering to the Evangelical constituency, and it’s not clear what this might lead to. On the one hand, he’s pushing for energy independence and cleaner energy—although some might buck at this because he supports funding nuclear energy—on the other, he’s hanging out with the Bob Jones crowd who accept 6-day Creationism and believe the Founding Fathers were all devout Christians. Only time will tell.

In the meantime, he would pose a formidable foe to Hillary Clinton, as evinced in the most recent polls taken in December asking who people would vote for between McCain and Clinton:

Fox News: 47% McCain / 42% Clinton
Zogby: 49% McCain / 42% Clinton
CNN: 50% McCain / 48% Clinton


With McCain mildly pro-science and Clinton avidly pro-science, I’d say this poses some risks toward science’s future, but it’d still be better than what’s come before.

Hotel Mauna Kea

January 8, 2008 at 3:51 pm | | grad life, nerd

Sent to me by my research advisor:

scifinder scholar 2007: finally online

January 7, 2008 at 3:36 pm | | everyday science, literature, software, wild web

Here at Stanford Chemistry, we just got access to Scifinder Scholar 2007 … the online version. Cool! Finally, web-access to CAS searching. I decided to try it out and give a little review.

First, I’ll say that I actually like the little stand-alone SFS program: I find it quite user friendly and versatile. But a version accessible via the web is nice (and inevitable). The online version has kept most of the same interface and function, with a web style.

Other databases, notably ISI Web of Science, are really great at finding H-index values or citation trends. But, when I really want to do a lit search on a topic or reaction, SFS is always my first choice (maybe after just typing it into Google). CAS has a nice Flash demonstration and screen shots here. Here are some on my own screen shots (click on them for full images).

A fruitless search:

And the result. Or a reaction search:


Another cool new feature in SFS (web or software version), is the “keep me posted” button: You can follow up on searches or results. Currently, I have alerts from ISI sent to my RSS reader; I’ll have to explore this new SFS feature to see if it’s better.

A couple bad things about the new web version of SFS. It can be a little slow loading the Java and Javascript pages. More importantly, it does not include the ever-so-helpful “remove duplicates” feature. (UPDATE.) I hope this latter problem can be corrected, because I hate seeing the same paper listed millions of times!

I think I’ll use SFS web, especially when I’m using a computer that doesn’t have the software installed. Overall rating: super rad cool.

Political Science Update: Iowa Caucus

January 3, 2008 at 9:16 pm | | news, political science, science and the public, science community

The Iowa Caucuses have concluded with Obama winning the Dems’ caucus, and Huckabee winning the GOP’s. What do the Iowa Caucuses mean for science? First, the caucuses are not good predictors of who will win their respective party’s nomination. Iowa gets it wrong about as often as it gets it right:

George McGovern finished second in 1972—the year the modern caucus process started—and still won the Democratic nod. When Jimmy Carter won the presidency in 1976, he finished second in the Iowa caucus to “uncommitted.” George H.W. Bush defeated Ronald Reagan in the 1980 caucus. George H.W. Bush finished third in Iowa in 1988 and won the presidency that year. Michael Dukakis finished third in the 1988 caucus and won the Democratic nomination. Bill Clinton took third place in Iowa in 1992, with 3 percent; Harkin won 76 percent. Source.

Nevertheless, Iowa is supposedly important in shaping the candidates’ platforms. It serves as America’s veritable test kitchen for candidates’ White House recipes. (Too much metaphor?) Candidates can try out what works and what doesn’t. Obama tried out the ol’ “time for a change” theme, and it seems to have worked better than Clinton’s “I’ve got the experience,” and Edwards’ “I’ve got the compassion” narratives. Huckabee won by offering up the image of a regular Conservative Christian good ol’ boy, over Romney’s “I’m Mormon, but I like to kill terrorists like the rest of you!” approach, Giuliani’s “I am 9/11” slogan, and John McCain’s “I was tortured once, but I believe in a strong….”

Specifically, as to science, as you’ll recall, Sam kindly pointed out that Obama pitched a pro-science platform, but painted that platform in broad and Monet-esque strokes. And Huckabee avoided science, more or less, aside from saying that he opposed stem cell research. To be fair, I dug around a bit more to see what Huckabee’s views were on science. I didn’t find much more. He appears to reject or withhold judgment as to evolution, claiming the question of evolution is irrelevant to the presidency. (I would disagree with Huckabee here. Acceptance of evolution might indicate an amicable view toward science, particularly in light of all the recent hostility surrounding evolution curricula in schools. And rejection of or indecisiveness toward evolution might even more strongly indicate an ignorance, apprehension, suspicion, or hostility toward science. I would say evolution is a “barometric” topic of sorts.) Also, Popular Mechanics quotes Huckabee as follows with regard to energy and climate change:

a.) “Achieve energy independence by the end of my second term.”
b.) “We have to explore, we have to conserve, and we have to pursue all avenues of alternative energy: nuclear, wind, solar, hydrogen, clean coal, biodiesel, and biomass.”
c.) “We will remove red tape that slows innovation. We will set aside a federal research and development budget that will be matched by the private sector to seek the best new products in alternative fuels. Our free market will sort out what makes the most sense economically and will reward consumer preferences.”
d.) “If we are energy independent, we will be able not just to take care of our own needs and protect our economy, we will also create jobs and grow our economy by developing technologies that we can sell to the rest of the world to meet their needs.” Source.

I’m guessing this was just a response to Evangelicals warming up to the problems surrounding global warming. It doesn’t seem terribly pro-science. That said, to the extent the caucuses have taught the candidates something about science (and it probably hasn’t), my guess is that it told the Dems that a vague science agenda is preferable; and the GOP, that de-emphasizing science in favor of faith is the smart card. For both parties, generalities are better. Some past elections would suggest as much. For instance, Gore had a very specific and detailed agenda, much like (Hillary) Clinton does now, and he lost out to (G.W.) Bush who called Gore’s approach “fuzzy math.” Similarly, Perot didn’t gain cool points against (Bill) Clinton and (not the banana) Dole when he pulled out his chart with a detailed explanation of his plan. (Nevermind whether it was a good plan).

All that aside, what if Iowa has it right this time? What if the general election is a showdown between Obama and Huckabee? So far, it looks like Obama has the lead, at least according to mid-December polls. Here’s the rundown:

Fox News’ poll (biased?): Obama 35% / Huckabee 21%

NBC survey: Obama 48% / Huckabee 36%.Gallup: Obama 53% / Huckabee 42%.

Zogby (who?): Obama 47% / Huckabee 42%.

CNN: Obama 55% / Huckabee 40%.

So if Iowa is any indication—and it isn’t—then science is on the up and up!

the only award i’ve ever cared about

January 3, 2008 at 10:07 am | | blogs, science community

I’m more than proud to say that I’ve finally won an award in grad school: MOST AWESOME FUCKING AWARD YOU’LL EVER GET.


Everyday Scientist and Carbon Based Curiosities

Sam is just as hilarious and poignant as Dylan Stiles was yet he hardly gets any comments. It’s fucking tragic. Not only is he a better blogger than me, but he’s clearly got large hands. Two things I envy. I also want to take this time to congratulate CBC for growing up and getting a real blog with WordPress. Hooray! Yet again, good blogging but at least they’re getting lots of comments, which is the only form of “payment” bloggers ever really get.

It’s a real honor to be recognized by one of the super-chemist bloggers, Kyle Finchsigmate, of The Chem Blog. Also, to be compared to Dylan Styles and CBC in the same paragraph made me pee my pants a little. That award is going over on my sidebar, somewhere!

But we should recognize the other contributers to this blog: Charles, William, Jordan, Nick, David, Kendall, and Ilya. Thanks for helping me win this award, guys. I could have done it without you, though. I mean, really, I think you guys are just holding me back from becoming great things. Or something.

what’s wrong with this picture?

January 1, 2008 at 9:35 pm | | crazy figure contest

Sorry, my site has been down for a few days. Here’s a treat for the eye:


What’s wrong with this picture?

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