i hope this isn’t faked….

October 4, 2010 at 7:25 am | | EDSELs, literature, single molecules

… because it’s so beautiful! Schaller et al. have used the Sheetz-Spudich sliding assay to watch collective motion of moving biomolecules. Like watching flocks of birds:

Or crazy swirling patterns:

For these awesome results, I’m awarding the authors an EDSEL for “Coolest paper (if it isn’t faked) of little filaments spinning around in circles of 2010.”

Not that I have any reason to think that these results are faked. They just seem so crazy and beautiful. Animated, even.

2009 EDSEL-Nobels

September 16, 2009 at 9:27 am | | EDSELs, science community

edsel_nobelTime for the 2009 EDSEL-Nobels. Just to clarify, these are not predictions for the real Nobel. Instead, they are relatively arbitrary awards given to great scientists.

This year’s criteria include: how many papers/books I’ve read from the scientists, whether I’ve seen them give a talk, and how they’ve contributed to a field I am interested in.

The 2009 EDSEL-Nobel Prizes go to Nicholas J. Turro (Columbia) and Josef Michl (Colorado) for their research and literary contributions to photochemistry.

I have used both their books (here and here) extensively in my own research. I had the pleasure of seeing an interesting talk by Turro last year and look forward to seeing Michl in a couple weeks at Stanford’s Johnson Symposium.

room for moms

November 10, 2008 at 11:48 am | | EDSELs, grad life

A few years ago, our Department Chair (Dick Zare) extended the maternaty leave for students. That was nice. But the Chemistry Department doesn’t have any lactation rooms, so students were forced to go to the biology building (gross).

Now Zare has found a room. Therefore, I award Richard N. Zare an EDSEL Award for his current and previous efforts for pregnant students in the Stanford Department of Chemistry.

I really do think that Stanford Chemistry treats its graduate students quite well. I suggest all you undergrads out there apply to Stanford. It’s a wonderful place (most of the time).

2008 EDSEL-Nobel in Chemistry

October 1, 2008 at 11:07 am | | EDSELs, nobel, science community

Well, its that time of year again. Nobels will be rolling out soon! Carbon-Based Curiosities has already awarded their CBC Nobel to Krzysztof Matyjasewski of CMU. I endorse this choice, because I have a scientific connection to Kris: My undergrad lab collaborated with him very closely. I even have a paper with both our names on it! So I’d be happy if he won.

But I’ll award the EDSEL-Nobel to someone else, if just to be a contrarian. One thing I promise: I’m not going to put much thought into this.

A few people are unjustly disqualified from this competition: Roger Tsien (too obvious); W.E. Moerner (my PI, wouldn’t be fair); Barry Trost (who?); and myself (because the truths I have revealed in my research would just rip open everybody’s minds!). Some of the criteria I used to judge included: the person’s name size on my CUL author cloud; their index (which is my new citation index, defined as the person’s h index divided by 2π in order to account for self-referencing); and the extent to which I actually believe their reported results.

This year’s EDSEL-Nobel goes jointly to Peter Schultz (Scripps) and Carolyn Bertozzi (Berkeley) for “their applications of click chemistry to something practical: totally messing with cells and making them glow and stuff.”

Schultz has introduced azide/alkyne (and many other) unnatural amino acids into the genetic machinery, thus inserting a specific site for labeling with fluorphores or other probes. Here’s a good Schultz review paper. Bertozzi feeds cells unnatural sugars that have “bioorthogonal” reactive groups (click or otherwise). Here’s a good Bertozzi review paper. Other labs have actually applied these techniques for successful labeling and biophysics experiments. And I suspect their techniques will become streamlined and more broadly accessible in the future. Or maybe not and I awarded this prize prematurely.

i guess this is how you comment on a JACS comm

September 29, 2008 at 11:15 am | | crazy figure contest, EDSELs, literature, science community, scientific integrity

So I guess there’s not really an official way to get a comment published in JACS. So I’ll be a jerk and complain to everyone on the AEthernet. I saw a paper in JACS which really caught my eye, an interesting title for me, who designs fluorophores:

Yamaguchi, Y.; Matsubara, Y.; Ochi, T.; Wakamiya, T.;  Yoshida, Z.-I. How the pi Conjugation Length Affects the Fluorescence Emission Efficiency. J. Am. Chem. Soc. 2008 (ASAP).

And, of course this amazing fit to data in the TOC image (scroll down to see what this plot should look like):

My first thought was, Whoa! Then I immediately thought, Wait, why do all the points fall exactly on the theory line? That’s unusual. Still, I read the paper with much interest. By the time I got to the end, I earnestly thought it might be an April Fools edition JACS.

I followed the basic theory (Marcus-Hush theory) and the mathematical manipulations. Their result was fascinating: the length of the pi conjugation should directly influence the deexcitation rates: , where Aπ is the length of the conjugation, Β is a constant (approximately 1 Å-1), c is the speed of light, ν is the emission frequency, h is Planck’s constant, and kr and knr are the radiative and nonradiative deexcitation rates, respectively. This is interesting, because fluorescence quantum yield (Φf) is defined by those same rates: . So inserting an equation that depends on conjugation length should be a simple and interesting result.

But, for some reason, the authors normalize out the leading factor. I didn’t really understand why. Anyway, the final result is a little different than I would have figured: . Now, somehow Aπ can be negative, and the authors justify that with the fact that it had become a logarithm in their mathematical gymnastics. I won’t really argue that that’s wrong, because I don’t understand why they did it in the first place.

And here comes the central problem with the paper. In order to confirm this theoretical relationship between quantum yield and pi length, they plot the theoretical equation along with data they have measured (plot above). But they never measure Aπ, they calculate it from the measured rates listed in the table; those same rates were calculated from the measured quantum yield. This is circular logic. So there’s no “correlation between absolute fluorescence quantum yield (Φf) and magnitude (Aπ) of π conjugation length,” as they claim. Instead, they simply plot the ratio of rates versus a different ratio of those same rates. The real axes of the plot are  on the ordinate and  on the abscissa. That’s totally unfair and misleading!

They claim that other independent measures of pi length also work, and that is shown in (of course) the Supporting Information. There, they do give some analysis using Δν1/2a3/2 as a value for Aπ, where Δν is the Stokes shift in a given solvent, and a is the Onsager radius of the molecule in a continuous dielectric medium (taking the relevant factors of the Lippert-Mataga equation). The authors chose not to plot this analysis—they offer only a table—so I’ll plot the real results for you:

That’s sad. Note also that the calculated values cannot be less than 0.5, because size is always positive and even zero for this Lippert-Mataga value of Aπ means that the exponential goes to 1 and the denominator of the new theoretical quantum-yield equation goes to 2.

How does Aπ scale with the Onsager radius or the Lippert-Mataga measure of size?

Well, there is a trend. Not a great trend, but a trend nonetheless. This paper would have been a lot better if they had explored these relationships more, finding a better measure or estimator of size or Aπ. Instead, the authors decided to deceive us with their beautiful plot.

Assumptions in this paper:

  1. That all the nonradiative pathways come from intramolecular charge transfer.
  2. That the emission wavelength does not change with increasing pi conjugation.
  3. For the independent test, that the charge transfer in all cases is unity, so that the change in dipole moment from ground to excited state equals the distance over which the charge transfer occurs.

Assumption 1 is fair, but not entirely applicable in the real world. Assumption 2 is patently false, which they even demonstrate in one of their figures; however, that may not be this paper’s fatal flaw. Assumption 3 is, well, fine … whatever. The real problem is that the authors do not independently test the theoretical prediction, and use circular logic to make a dazzling plot (dazzling to the reviewers, at least).

The biggest disappointment is that the approach and the concept is really interesting, but the authors fail to follow through. I think this could have been an great paper (or at an least acceptable one) if they had been able to demonstrate that the deexcitation rates (and thus the quantum yield) did depend on the size of the pi conjugation. For instance, if the authors had been able to accurately predict pi-conjugation length using the experimental deexcitation rates, then they could have then flipped that and predicted quanum yield from the size. Instead, there’s just a stupid plot that doesn’t make any sense.

So this paper wins an EDSEL Award for the worst paper I’ve read in JACS. I have no idea how that even got past the editors, saying nothing of the reviewers! That said, I am willing to admit my ability to be totally wrong. If so, I apologize to everyone. Please let me know if I made any mistakes.

best podcast … ever

June 23, 2008 at 12:35 pm | | EDSELs, literature, science community, wild web

JACSβ is ACS’s attempt at going Web2.0, but I’m not too impressed, yet. The strangest thing is the JACS podcasts, which is nothing more than someone reading a JACS Comm word-for-word … literally! Seriously, they even read the submission date and describe the figures.

You can’t really get the full effect of a scientific article unless it’s narrated. Back in my day, we had all papers read to us out loud; I’ve never picked up a journal or read a paper on a computer screen. I’ve just hired someone to read anything I hand to him.

Seriously, though, I challenge you to go listen to the two podcasts they have at the JACSβ website. See if you can listen to and understand the articles all the way through.


UPDATE: My labmate pointed out the following: “The best thing is that according to the website, the JACS podcast is ‘Free for a limited time.’ Limited!?! Like we’ll pay for it after?” Ha!

UPDATE 2: This should have received an EDSEL in Literature.

coffee physics

March 4, 2008 at 10:38 am | | EDSELs, great finds, literature

OK, is this a joke? Or is the author simply a bullshit artist?


Source: (Buffo, R. A.; Cardelli-Freire, C. Flavour and Fragrance Journal 2004,19, 99-104.)

I can forgive the εR-equals-zero-instead-of-unity mistake, but what does that have to do with CO2 release? And the glass-transition temperature? Seriously? Of a coffee bean?

edsel.jpgMy favorite part is that neither of those two ridiculous statements is cited.

OK, this wins an EDSEL for “Most creatively incorrect physical analysis of food chemistries.”

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/3d-storm_movie.mov 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.

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