Everyday Scientist

please repeat the question

I always appreciate when a speaker repeats the questions before answering. It can really enhance the Q&A. But I understand how easy it is to forget to repeat the questions, even if you had the intention to before you stood up in front of everybody.

I’m at a little conference on campus today. It’s being filmed for a video archive, so the moderators regularly remind speakers to repeat the questions (lest the context be lost in the video). One speaker forgot to repeat each and every question, and the moderator was very persistent at reminding the speaker. It was all in good spirits, and people chuckled each time the moderator needed to remind the speaker.

An hour or so later, the previous moderator gave a talk. After his presentation, he proceeded to forget to repeat each and every question, and the audience and new moderator were quick to gently remind him! Very cute.

what to do about supporting information

I met with David Martinsen from ACS Pubs today to discuss the interface between publishing and technology (internet, Kindle, Facebook, CiteULike, etc.). Interesting discussion. One topic that came up a few times was the supporting information (SI) for articles.

Page limits as well as increasingly complex experimental methods have caused SIs to balloon to sometimes ridiculous lengths. Combine this with the fact that SIs are often barely readable, marginally refereed (if at all), and crammed with unexplained figures, and SIs become ridiculous. Sometime, “see the SI” is a ploy to lull readers and referees into feeling that a statement is supported by data, even when the data is total crap. I’ve seen spectra in SIs that wouldn’t pass muster an undergrad lab, much less a peer-reviewed journal, but they were the primary data of the letter. Nevertheless, much of the core scientific information is often buried in these monstrosities.

Authors need to be encouraged to compile their SIs to be coherent, clean, correct, and scientific supplements to their papers. I have some suggestions. I start with simple suggestions, and move to more fundamental ones:

1. Offer a single-PDF option. Have an option to download a single PDF that contains all the content for the articles (i.e. the main text as well as the SI). Because the SI often contains vital information to interpret or repeat the results, it’s important to have this data (or synthesis) along with the main text. ACS already has two PDF options (hi-res PDF and PDF with links), so it would be as simple as adding a third link to the page.
2. Format SIs. This can be as simple as providing a Word template just like there is available for the main text and figures of the article. This shouldn’t increase the editors’ responsibilities, but would make SIs more readable.
3. Referee SIs. Encourage referees to carefully read and scrutinize the SI, just as they do the main text. If something is unscientific, sloppy, or wrong in the SI, it should not be included. Referees should be encouraged to request SI data or methods be clarified, tested, eliminated, or repeated if necessary as a condition for publication.
4. Include raw data. Provide space for authors to present raw data if they wish (e.g. structure, NMR, crystallographic, spectral, etc.) in the SI. I personally don’t think this is as important as careful writing, editing, and refereeing of the SI; however, providing raw data could be another level of evidence for the authors’ claims. I don’t think this should be a requirement, because we should be able to trust researchers and not spend all our time redoing someone else’s analysis.
5. Offer full articles online. Putting 1-3 together, there could be a “full” article form of any paper, which includes all information from the SI, but formatted and organized like a lengthy paper. That way, the paper form of the journal could stay short, while online forms could be complete, yet still professional, readable, and cogent. However, this would add some burden to editors, referees, authors, copy-editors, etc. Paper journals could become more of a collection of executive summaries, with the full scientific data online. (I believe that some Nature journals do this to some extent: having a short Methods section added to the PDF form but not in the paper journal. But there’s still an SI in addition.)

I think #5 is where journals should be going. True, it will add expense to publishers, but that will help them justify the subscription fees when no one receives paper journals anymore.

Other ideas?

UPDATE: Here are some other ideas, which I’ll update as needed:

• Allow authors to republish. Make it easier for authors to republish the data and figures that are in a SI again in the main text of a subsequent paper. This would permit the SI data to someday be published in a fully refereed form in a follow-up paper. Otherwise, data and figures in the SI will never be properly reported. Of course, there may be a lot of complications with copyright and getting all authors to agree.

no one wants to collaborate with Mitch?

No one wants to write an easy book with Mitch? I’m writing a page. Just choose a name reaction and draw it, yo!

fight!

Whoa. Djerassi is pissed at Trost.

[Trost’s] demeaning treatment of the key work of earlier investigators in the field of natural products by chemists who then undertake the total synthesis of the molecule in question is unfortunately all too common—either because of sloppiness or as a discreet attempt to eliminate any reference to the initial discoverers. (C&E News)

I don’t know the whole story here—does this go back to previous battles between the two Stanford profs? does Trost have something against Pettit?—but it’s certainly entertaining!

I agree with Djerassi that citing original work is important. However, at some point, we should be able to move on and cite reviews of an entire field. Also, I’m not sure C&E News is an appropriate forum to call out one individual: Trost’s paper is not the only example of inadequate citation.

UPDATE: I’m also a little confused, because the Trost paper does cite Pettit … at least three times. Maybe they aren’t the original papers, so it doesn’t look like Pettit worked with bryostatin first?

jobs anyone?

I need to start looking for a job.

W. E. Moerner, a chemistry professor at Stanford University, says he has a couple of Ph.D. students aiming to graduate later this year, and he is worried about their ability to find positions. “This is only a concern right now, as they have most of the year to finish,” he says. (C&E News)

Oh.

JACSes’s new cover!

Holy crap! JACS has decided to put art on its covers!!!!1!!

I think that’s a terrible idea. JACS was the only major chemistry journal not to frill up its cover with some bullshit pictures of some pseudosciencey research. Now it’ll probably go the way of Angewandte and have penguins and shit on its covers.

JACS used to be the classy journal of chemistry—a real gentleman’s journal. Now it’s just another noisy mag on the shelf. I encourage ACS to reverse their decision to deflower their flagship journal.

All the JACSβ stuff on the website is cool. If you want to make a JACS Facebook page and have podcasts where someone reads an entire paper word-for-word, that’s fine with me. Even the image challenges are cool (even though I get 90% of them wrong because I don’t have the patience to read all the options). But stay away from the beautiful, clean cover.

Maybe Google should change their homepage to look like Excite?

The Importance of Stupidity in Scientific Research

I came across an interesting essay about the scientific process.  I agree with the author that students are generally shielded from the  difficulty of doing research until graduate school.  I think that the reality of lab work can be made clear if modern lab classes were less “cook book” and more research-like.  Your thoughts?

chemistry dictionary for Word

This is pretty cool. Check out this chemistry dictionary for Word that contains thousands of chemistry words for the spell checker. That should reduce the little red squiggles all over the documents! Thanks azmanam over at Chemistry-Blog.

I’m using it. It knows what an azepine is!

It’s very easy to install and it doesn’t overwrite your own custom dictionary. The README file is helpful, but I suggest you store the chemistry.dic file here instead of My Documents:
C:\Documents and Settings\USER\Application Data\Microsoft\Proof

khemistry klassics

I want to start collecting the great (humorous) chemistry papers. Below are some that I can think of. Please comment with more!

• One of the best quotes in a chemistry paper is the following: “This work will be continued and I wish to reserve the field for myself.” (Gomberg, M. An Instance of Trivalent Carbon: Triphenylmethyl. J. Am. Chem. Soc. 1900, 22(11), 757–771.)
• A good April-fool’s article is Dick Zare’s (Wayne Knox’s) zero-fs pulse. (Knox, Knox, Hoose, Zare. Observation of the 0-fs pulse. Optics and Photonics News, April 1990.) This one also has a great quote at the end: “We are investigating possible violations of thermodynamics. Somebody’s pulses must be getting longer.”
• The Alpher, Bethe, Gamow paper has it’s own Wikipedia entry! (Alpher, Bethe, Gammow. The Origin of Chemical Elements. Physical Review, 1948, 73(7), 803-804.) Gammow, a jokester, added Bethe without his knowledge in order to have the names sound like the first three Greek letters. I guess Alpher—the grad student on the paper—was very reluctant to add Bethe, and has always worried that it took away some of his credit. Bethe did see the paper before it was published.
• This is a new “classic,” but the TOC art really got a lot of internet press. (Toma, et al. Inorg. Chem. 2004, 43, 3521-3527.) Was it intentional? Also funny: the TOC image is missing from ACS right now!

• I really want to find that paper with the man fishing in the glassware. Anyone remember the citation?

Anyway, please let me know if you think any other papers should be included in this humorous group.

intrasellular

I just sat through one of those “sales-pitch” type science talks. You know the kind: some amazing nanoshit is going to save the world and make investors a trillion dollars—nevermind if/how/why/when it works.

Anyway, my favorite part was when the title on one slide had the word “Intrasellular” by mistake. Great Freudian slip.

late referee reports

I just recieved two referee reports with my proof. Strange, that seems sorta late for me to be editing the content of my paper. Thank goodness the comments are generally positive.

First, we received only one referee’s report, with very little to change. That’s actually not very helpful, because I don’t know what parts of the paper need changing. And then we received a late referee report, right when we were about to submit our revision. Now we’re getting two more reports at the proof stage.

Of course, I’m happy that the editors sent us these referee comments, so I can fix things. (I wish the editors of another journal had sent my referee notes to the authors!) Nevertheless, maybe the editors should have waited an extra few weeks before telling us to start making revisions (it was a very fast turn-around). But it could be my own fault, for submitting an invited paper a couple weeks later than the editors asked. That’ll teach me.

new citation index: the h-bar value

I commented a while ago about the Hirsch h index. In fact, it was one of my first posts 2.5 years ago. Since then, the h index has become the standard in reporting the extent of an author citations. ISI and ResearcherID report h index along with total citations, and scientists have started to include their h value on their CVs and resumés.

But there’s still the problem of self-citation: citing ones own papers in later papers or reviews can increase ones own h index.

PI	h
Pande	28	4.5
Moerner	43	6.8
Andersen	48	7.6
Fayer	51	8.1
Boxer	52	8.3
Zare	94	15.0

I now introduce a modification of the Hirsch h index to solve the self-citation problem. The “h-bar index.” The math is very simple: because each researcher cites himself or herself multiple times in each paper, total citations must be divided by a normalizing constant to account for these self-citations. Therefore an author’s  index is his or her h index divided by 2π.

The table above compares the Hirsch h index and the Lord  index of the same scientists I listed in my original post. I argue that the Lord  index is a more accurate measure of an individual’s true citation record.

Prasher and the end of America

There’s a lot of buzz about Doug Prasher not winning the 2008 Nobel in Chemistry with Tsien, Chalfie, and Shimomura. Prasher was the first to discover and clone the gene for GFP, which made most of the subsequent work possible. Here’s an NPR story about Doug Prasher and his story.

In my view, the main story is not that Prasher didn’t win the prize (the Nobel committee had to make a decision), but that he is now a bus driver because he cannot get a job in science! What country is this!?! The country that funded great scientific and technological advances (from the atomic bomb to the internet, from the semiconductor transistor to the Hubble telescope).

Where is America going when we don’t fund our best scientists (to say nothing of the mediocre ones like me)?

2008 EDSEL-Nobel in Chemistry

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

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 k_r and k_nr are the radiative and nonradiative deexcitation rates, respectively. This is interesting, because fluorescence quantum yield (Φ_f) 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 (Φ_f) 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 Δν^1/2a^3/2 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.