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.

metabolic pathways made easy

September 25, 2008 at 8:05 am | | crazy figure contest, great finds

Nick was kind enough to send our lab this helpful chart of metabolism pathways (from Sigma Aldrich):

I think Nick put it best: “This really helps to put different aspects of metabolism into perspective.  Sort of.”

what is the SPF of hair?

September 23, 2008 at 5:28 pm | | crazy figure contest, literature, science@home

Hair provides about SPF 10 UV protection to the head. At least according to this recent paper: Parisi, et alSolar Ultraviolet Protection Provided by Human Head Hair. Photochem. Photobiol. 2008. The intersting thing is that long hair provide about the same or even less UV protection than short hair. The authors posit that this could be because long hair is more likely to part and expose the scalp.

Oh, that’s how they did it.

reece roth

September 18, 2008 at 10:08 am | | news, science and the public, science community

Finally, the US is prosecuting the real terrorists: University professors!

Prof. Reece Roth of University of Tennessee was found guilty of exporting secret data to China and Iran because he had some Iranian grad student and he took his laptop to China when he went on a lecture series.

This is way worse than outing a CIA operative for political purposes. I hope he gets the death penalty.

Seriously though, this makes me sad. He looks like my grandfather. The one who was a spy for the Japanese during the war. jk.

yes, but i’m the expert

September 14, 2008 at 11:33 pm | | pseudoscience, science and the public

I’ve been getting comments on my post about how crazy an idea it is to run your car on water. I thought that I was more than fair: pointing out that the thermodynamics is obviously against the idea (splitting water in order to burn it is stupid), but I left some room for the possibility that adding lighter gases might change the combustion efficiency. Still, I was skeptical. I was made more skeptical by the deceptive advertising (e.g. water4gas scam revealed). Remember the seven warning signs of bogus science.

But, despite my requests for non-anecdotal references, I just received long, rambling, confusing, and criticizing comments. For instance:

I wish to correct part of your story, Obviously you must have race through when reading and watching the videos on youtube and elsewhere.

1st of all many people err and state that water is split into H2 and O2. Water is H20. Peroxide is H2O2, Water is actually split into H2 and O. When using the term HHO it is denoting two hydrogen molecules and one oxygen molecule.

So here, I am accused of not studying the concept carefully enough. Huh? I am an expert on this: I am a chemist. I know what water splits into. I know stoichiometry. Monatomic oxygen is not bubbling out of water.

Then there’s the comment:

Your comments remind me of a story; As the first steamboat was readying for it’s maiden voyage, there was a man telling everyone who would listen: “That thing will never work”!

As the steamboat pulled out into the river, he started telling everyone: “They’ll never get that thing to stop”!!

Or, how about this expert: “Man won’t be able to breath at speeds greater than 20mph”!!

Why don’t you take your “Expert” B.S. and tell it to my 25+ very happy customers.

Again, disregarding my expert understanding of thermodynamics, replacing it with fantom customers with their anecdotal evidence.

I also had some attacks from military men:

Water can be used as a safe and powerful fuel, if it is done properly. I guess none of you were in the Navy. In boot camp we were warned not to use water on a jet fuel fire because it burns at the higher temperatures of those fires. That’s why they use foam on fires at airports.


Something I think you should know is that the AV8 Harrier jet utilizes this. Water is injected into the engine where it instataniously seperates and burns. As you surely have read, hydrogen puts out 3 time the energy as gasoline (jet fuel). The Harrier hovers many hundreds of feet in the air becuse of the hydrogen burning.

You may want to know that I was with the Marine fighter squadron VMFA-513 when it was at Beaufort, SC. and it was still manufacture by the British, before McDonnell Douglas joint up to partner in building the plane.

I presently work at Boeing in St Louis, MO. The facts I state about the Harrier is common knowledge by those of us who work for Boeing St Louis.

Weird. Kendall kindly debunked both these silly ideas (the Harrier jet uses water injection to cool the engine, and water can’t burn on a diesel fire). But where are these references to the military coming from? I think it is further anti-expert and anti-elite: If you had a little real-world experience, you’d know that … is true. All you schooling can’t help you here.

You know, I’d agree if we were talking about fixing a tank or welding an I-beam or leading groups of people or one of the many other important things in this world that require real-world experience. But this is not the case when it comes to thermodynamics! I’m sorry, but in this case, an expert’s opinion is important.

People hate experts and the “elite” until they actually need their expertise. What would the world be like if people who think free power comes from splitting water and reburning it ran automobile companies? Or where good folks who didn’t believe in the germ theory of disease were our surgeons? Or people with no interest in ever learning about international relations became President of the United States of America?

I don’t think everyone should get a PhD. (On the contrary.) I don’t think one needs an academic education to be intelligent or successful or respected. I think the “real world” gives lessons that cannot be learned in a classroom or lab. However, I also believe that experts have a place in this world, too.

This all reminds me of Richard Feynman’s story about the painter. Let’s all just throw in a little yellow…

are cows magnetic?

September 11, 2008 at 2:05 pm | | literature

Yes they are. Or at least their butts and noses are: Begall, S. et alMagnetic alignment in grazing and resting cattle and deer. PNAS 2008, 105, 13451–13455. This is what happens when I filter my RSS feeds: I miss papers like this one and read about them on blogs.

The authors looked at Google Earth images of cows and deer, finding that they tend to align themselves along Earth’s magnetic field:

We marked the cattle’s longitudinal axis by drawing a straight line with the Powerpoint drawing tools and estimated for each animal separately its direction to the nearest 5° by overlaying a circular scale with 10° steps.

Crazy. I read parts of the paper, and it looks like careful analysis. For instance, they took into account the possibility that individual cows may align themselves to others in a herd, so herds were analyzed separately.

I worry a little about using Google Earth because it is not guarenteed to be accurate: Google could have aligned those cows!

are we still here?

September 10, 2008 at 7:29 am | | nerd, news, wild web

It’s important that we all keep up with the dangerous things that are happening in the world. Fortunately, there are people out there willing to slog through the data and pass on the results to the rest of the world. Of course, there is also this, but it has an obvious liberal bias.

(Thanks, Nanoscale Views.)

chem art

September 9, 2008 at 6:10 pm | | nerd

I took a metal-casting class last spring. I made a few pieces from Epi tubes, because they were fun to manipulate and melted away in the mold. Here are my contributions to the world of Chemistry Art:

And a pipet tip stabbing a tube:

And a keychain:

I don’t actually hate Epi tubes.

Drains on Laser Tables

September 3, 2008 at 9:35 am | | hardware

If I may make a humble suggestion, how about some sort of system for conveniently removing liquids (and maybe small screws, ball bearings, and our LBO crystal) from the bottomless pit that is a laser table?

Powered by WordPress, Theme Based on "Pool" by Borja Fernandez
Entries and comments feeds. Valid XHTML and CSS.