Everyday Scientist

ACS insider?

October 12, 2007 at 8:36 am | sam | news, open thread, science community

Did everyone get this email?

Subject: Time to Reform the American Chemical Society
From: Madeleine Jacobs <acs_insider@yahoo.com>
Date: Thu, 11 Oct 2007 17:24:22 -0700 (PDT)
To: [redacted]

Hello,

I’ve been an ACS employee for many, many years, but I’ve grown concerned with the direction of the organization. I’m sending this email to alert you that ACS has grown increasingly corporate in its structure and focus. Management is much more concerned with getting bonuses and growing their salaries rather than doing what is best for membership. For instance, Madeleine Jacobs is now pulling in almost $1 million in salary and bonuses… That’s almost 3X what Alan Leshner makes over at AAAS, and almost double what Drew Gilpin Faust makes to lead Harvard.

I think Madeleine is smart, but I’m not quite sure if she’s in the same category as Dr. Faust. She doesn’t even have a PhD!

What really concerns me is a move by ACS management to undermine the open-access movement. Rudy Baum has been leading the fight with several humorous editorials—one in which he referred to open-access in the pages of C&EN as “socialized science.” ACS has also spent hundreds of thousands of dollars in membership money to hire a company to lobby against open-access.

What troubles me the most is when ACS management decided to hire Dezenhall Resources to fight open-access. Nature got hold of some internal ACS emails written by Brian Crawford that discussed how Dezenhall could help us undermine open-access. Dezenhall later created a group called Partnership for Research Integrity in Science and Medicine (PRISM), which has this silly argument that open-access means “no more peer-review.”

If you’re wondering why ACS is fighting this, it’s because people like Rudy Baum, Brian Crawford and other ACS managers receive bonuses based on how much money the publishing division generates. Hurt the publishing revenue; you hurt their bonuses.

I’m hoping that sending out this email will get people to force ACS executives to become more transparent in how they act and spend membership money. Not to mention their crazy need for fatter salaries.

It’s time for some change. If you want to check out the sources for this information, there is a wiki site that has all the articles and documents outlining what I’ve just written.

You can find it here:

http://www.sourcewatch.org/index.php?title=American_Chemical_Society

Those of us inside ACS know that it’s time for things to change. But management won’t alter their behavior. The money is just too good.

Sincerely,
ACS Insider

Strange. Did this “ACS insider” send the email to all ACS members?

What do people think about this? I’m not surprised that ACS is working to fight the open-access movement, because it threatens their business (or their business model). Whether it’s appropriate for ACS to spend member fees to fight that fight is a different matter, I suppose.

I do agree that exorbitant pay rates for the top executives is a problem, and an indicator of larger issues within the organization.

All in all, it’s hard for me to care that much: My student membership fees are relatively small and I don’t have to pay for journals (although I know they are expensive for the library). And the ACS conference is well run.

What do other people think?

Let’s Be Fair to Dow

October 9, 2007 at 1:30 pm | Charles | news, science and the public, science community

[Editor’s note: This is a follow-up of a previous post. Apparently, Charles disagrees with me. -Sam]

Let’s be fair to Dow here.

The Bhopal pesticide plant explosion was a horrible incident by all accounts! The disaster caused around 8,000 immediate deaths. 12,000 deaths have been linked to the disaster, and another 100,000 or so people suffer lingering health risks.

To start with, let’s see what Union Carbide has tried to do to rectify the situation:

1. The day of the explosion (December 4th, 1984), Union Carbide sent material aid and medical experts to Bhopal to assist with treatment.
2. Carbide donated an immediate $2 million into the Indian Prime Minister’s disaster relief fund within 1 week after the incident (December 11th, 1984).
3. 3 months after the incident (February 1985), Carbide established the “Employee’s Bhopal Relief Fund” which raised more than $5 million for immediate relief.
4. 5 months after the incident (April 1985), Carbide paid for Indian medical experts to take part in training of treatment techniques.
5. Less than 3 years after the incident (August 1987), made an additional $4.6 million for humanitarian relief.
6. In 1989, Carbide settled with the Indian Government in the Indian court system for $470 million. The settlement was paid in full almost immediately. In the settlement it was agreed that the state government of Madya Pradesh would take full responsibility for the site cleanup.
7. In April 1992, Carbide sold 50.9% of it’s shares of UCIL (Union Carbide of India Limited – the subsidiary responsible for the incident) to fund a $90 million trust fund for the establishment of a Bhopal hospital treating heart, lung, and eye ailments. As of 2001, when the hospital opened it’s doors, the trust had amounted an estimated $100 million.
8. In addition, Carbide provided $2.2 million to Arizona State University to establish a vocational-technical training center in Bhopal (which was later closed) and $5 million to the Indian Red Cross.
9. Carbide developed the “Responsible Care” system with other members of the chemical community to “help prevent such an event [as Bhopal] in the future by improving community awareness, emergency preparedness, and process safety standards.”

So, over the course of the 20 years between the incident and the purchase of Union Carbide by Dow Chemical, Union Carbide had spent almost $600 million towards the cleanup and relief efforts.

Now, let’s compare the 1989 $470 million dollar settlement ($686.2 million in 2007 dollars) against other U.S. settlements by chemical companies:

The largest Superfund site in the U.S. today is the Hudson River, in which over 500 tons of polychlorinated biphenyls (PCBs) have been dumped over the course of 80 years (most by GE in the last 30 years). The estimated cost is $500 million. GE has formed an agreement with the EPA to pay a total of $7.62 million and donate scientists and manpower to the initial sampling and cleanup effort. Unknown population affected over 80 year period. PCB’s have been linked to cancer, although GE denies that there are increased cancer risks in the area.

The 2nd largest settlement in Superfund history, and the largest settlement involving a chemical company, was the Sikes Disposal Pits near Crosby, an illegal toxic waste dump used by a variety of petrochemical companies, which has affected an estimated 10,000 people. 30 chemical companies were sued successfully for an estimated $120 million in cleanup costs.

The Love Canal incident in 1953, which prompted the creation of Superfund, occurred when the Hooker Chemical Company covered area over a toxic dump with dirt and sold it the city of Love Canal for $1 an acre. Numerous houses and a school were built on the site. Unknown numbers of people were affected, but over 221 families were evacuated by 1981. People from the area suffered larger than average rates of birth defects and miscarriages. The government finally sued and won around $129 million for cleanup costs in 1995.

Of course, the scale of the disaster in the Bhopal case makes these other cases pale in comparison. That’s why criminal charges are proceeding against 6 UCIL members (including the former Chairman of UCIL, the Managing Director, the Vice-President Functioning in charge, the Works Manager, and the Production Manager). That’s also why the parent company of Union Carbide paid out so much both to the Indian Government (which it HAS to work through for environmental cleanup) and directly to the victims (around 20% of the money Carbide spent went to medical training, immediate humanitarian aid, and the establishment of hospitals and medical trust funds).

And also, granted, much of the money (specifically the $470 million) did not reach the victims families and was not spent on cleanup, but that’s due to the incompetence and/or corruption of the Indian government. In April 2005, the Indian Supreme Court ruled the government had to release remaining settlement funds to the victims and their families. After taking into account accrued interest, the remaining settlement amount is estimated at $330 million (See NYT article cited below). It is certainly NOT Union Carbide or Dow’s fault that the Indian government and sat on the money instead of using it for cleanup or victims reparations. Remember, part of the $470 million settlement was that the local government be responsible for cleanup (presumably using part of the settlement for cleanup).

Now, Union Carbide can’t take what happened back – I’m sure they would like to if they could. No one wants to be responsible for up to 20,000 deaths. But they can’t, so they spent more on the cleanup efforts than any other single U.S. corporation for a chemical spill or dumping in the short history of corporate environmental responsibility. Not only more, but almost 5 times more (6-7 times more in current dollars).

So where is the justification, legal or moral, for the Indian Government to sue Dow, who was NOT responsible for the incident, for $22 million when they are sitting on $330 million from the initial settlement? Why should Dow pay for the cleanup when Union Carbide already paid for the cleanup as part of it’s 1989 settlement, and paid more than any other single U.S. corporation in history (that I could find) for a chemical spill!

If Dow were to accept any responsibility, it would set a very dangerous precedent. Can you imagine a world where a company is sued by a government and settles: the case is closed. That company is acquired 15 years later. The government now sues the new corporation even though the previous acquisition has already fulfilled its legal and financial obligations. That’s legally and morally irresponsible, especially considering the goverment in question has 70% of the intial settlement still on-hand.

Bhopal Sources:

Wikipedia Article on Bhopal with Citations

Union Carbide Bhopal Information Center

New York Times Article from 2004: “Bhopal Victims Not Fully Paid, Rights Group Says.”

Other Sources:

EPA: Hudson River Superfund Site

EPA: Sikes Disposal Pits Superfund Site

DOJ: Fiscal Year 2001 Accomplishments (Including Sikes Disposal Pits Settlement)

EPA: Love Canal History

DOJ: Press Release on Love Canal Settlement

acs boston update 3: thursday

August 23, 2007 at 1:18 pm | sam | conferences, science community, seminars

Thursday was the last day of ACS Boston. I’m tired of trying to be entertaining (you probably can’t tell the difference), so I’m just going to summarize the talks I liked:

• Peter Lu has recently moved from PNNL to Bowling Green State University in Ohio. He talked about his fancy instrumentation that combines AFM/STM with a fluorescence/Raman microscope (with photon time-stamping and pulsed excitation, etc.).
  • First, he talked about looking at membrane-roughness changes with changes in membrane proteins: interfacial electron transfer caused changes measured by AFM and Raman.
  • Then he talked about studying LH1-LH2 FRET to probe dynamics of light-harvesting protein energy transfer. The FRET signal was rapidly fluctuating and looked like noise (not like TJ Ha’s obviously anticorrelated SM FRET time traces, for instance). Any FRET information was further obscured by Levy-flight dynamics. To glean anything from this data, he developed an analysis he called 2D cross-correlation amplitude mapping (see the new J. Phys. Chem. C paper on this analysis). He also applied this analysis to studying SM enzymatic pyrophosphorylation reaction dynamics.
• Norbert Scherer talked about chemical-perturbation spectroscopy: watching FRET fluctuations and how they are related to periodic [Mg] jumps to probe the enzymatic reaction landscape. His experimental system is RNase P RNA labeled with Cy3/Cy5. My favorite part was when called a complicated figure on one of his slides a “ridiculogram.”
• Jamie Boyce is a grad student finishing up in Sergei Sheiko’s lab, where I did my undergrad research. I went to her talk in the POLY division, and it was nice to see Jamie again and get an update on the lab’s work. She talked about a range of AFM studies of the shape, deformation, physics, and conformational changes of polymers with complex architectures, especially molecular “bottle brushes.”
• Hu Cang is a postdoc in Haw Yang’s lab. They are using a scanning stage and careful setup of the confocal pinhole and detectors to track/”trap” diffusing particles in three dimensions. To get motion in the z direction, the confocal pinhole is positions slightly off the focus, so position changes are seen as intensity changes. Changes in x and y are measured using a prism mirror placed at the focus, splitting the beam to two detectors; position changes are seen as more light going to one detector. The particle (GNP, QD, fluorescent bead, etc.) is tracked by keeping it in the focus using a feedback loop with the translation stage. For a bead, they can track something with 60-nm precision in 3D. They can also learn information about rotation and shape from a dichroic beamsplitter and two detectors: the decay of the correlation reveals information about rotational dynamics. This was demonstrated by using Ag nanorods in glycerol: we were able to see correlated fluctuations. He mentioned their J. Phys. Chem. C paper on the tracking method. Here’s their J. Phys. Chem B paper about a unbiased binning method for change-point detection.
• Peter Kapusta from PicoQuant talked about commercial implementation of Enderlein’s concept (see this ChemPhysChem paper) of using two foci to quantitatively measure the confocal spot volume for FCS.
• Adam Cohen is a former member of the Moerner lab; he just joined the faculty at Harvard. He talked about his ABEL trap, which traps single fluorescent particles/molecules using a feedback voltage applied to the solution (pushing the dot back to the target position). He talked about his early experiments, such as DNA fluctuation dynamics. Then he talked about his “hardware trap” version, which can apply a trapping voltage with each photon measured by an APD, the trapping speed limited only by photon shot noise. He also talked about measuring dynamics of individual GroEL chaperonin molecules trapped by his machine. Finally, he talked about trying to trap single Cy3 molecules in solution. All his stuff was really impressive, but I don’t want too sound biased. (He also advertised spots in his new lab for “bright, motivated” grad students interested in building and testing novel devices.)
• Michael Greene at NIST described some cool nanodroplets of sample in perfluorinated liquids. He could trap the nanodroplets, analyze the sample, and even bring two different droplets together. I wish I had more to say, but my brain is dead.

OK, that’s all on my reporting from ACS. Now I’ll get back to blogging about silly things…

acs boston update 2.5: posters

August 23, 2007 at 12:53 pm | sam | conferences, science community, seminars

I saw many cool posters at the PHYS poster session Wednesday evening. Here are my favorite:

• Charles Schroeder did his graduate work with Steve Chu and he’s finishing his postdoc with Sunney Xie; I did a summer REU with Chuck when he was at Stanford. For his work in the Xie lab, he used a custom promotor to incorporate fluorescein UTPs and anti-fluorescein QDs to study RNA and DNA polymerases. Looking at a DNAP/RNAP system on a chain extended from a magnetic bead using flow, he was able to track changes in position of the polymerases and chain length (using a similar technique to what Antoine van Oijen did—I summarized his stuff before). His conclusion was that DNAP moves past the position of RNAP (either over it or pushes it along the chain).
• Stirling Churchman is just finishing up in the Spudich lab. In a collaboration with Henrik Flyvbjerg, a theorist, she has used a better fitting method than Gaussians to fit the PSF for high-precision localization. Instead of Gaussians, they use the theoretical emission pattern of a dipole emitter (taking into account the NA of the objective and the higher rate of emission into the medium with higher index of refraction) to fit the PSF. With this more accurate fitting—and a MLE algorithm—they were able to get the same localization precision using only half the photons! They’re writing up a paper now.
• Volkan Ediz is a grad student in David Yaron’s lab. He uses QM calculations to predict some photophysical properties of a class of asymmetric cyanine dye, predicting barriers to twisting into dark states (see their JACS paper here). Their work is related to some of the work I’ve done and a previous grad student in the Moerner lab did with a different fluorophore; but their calculations are more hard-core. I met Volkan and David last year at ACS San Francisco; they’re really nice!
• Klaus Schaper is at Heinrich-Heine-University Dusseldorf and has been synthesizing rhodamine dyes with triplet quenchers covalently attached. The concept is that the quencher will make the dye brighter by both reducing the triplet lifetime and reducing the probability of photobleaching (from excitation from triplet states or from reactive oxygen produced by interactions with the dye triplet state). He used azobenzene on a sulforhodamine B, and found that he could get at 2.5-fold increase in the maximum emission rate (before saturation and bleaching) in an FCS experiment!
• Franziska Luschtinetz, from the University of Potsam, looked at the changes in the photophysics of biotinilated dyes (called DY-635B and DY-647B) upon binding to streptavadin. She found different effects on the absorption and fluorescence emission spectra, ranging from dye rigidization and H-type excimer behavior, upon the binding. Finally, she also did some time-dependent fluorescence anisotropy and FCS measurements with these dyes. I didn’t actually get to talk to Franziska, but she helpfully provided printouts of her poster!

One more day of ACS coming up!

acs boston update 2: wednesday

August 22, 2007 at 8:13 pm | sam | conferences, science community, seminars

Today started with the T Red Line turning around back toward Cambridge* two stops from my station. Then there were delays. All because of some switching problems. Or something. Well, I took a cab (slightly more expensive than the ones in San Francisco, but not bad). In the end, I actually made it to the seminar room before the first talk.

Also, I saw some wicked awesome graffiti on my walk to the convention center. I guess someone really like 2-methylpentane! And there was more than that. I saw a methylacetylene somewhere, too! And whatever this is:

Here are some highlights from the talks on Wednesday:

• Sunney Xie talked about “old stuff” (SM Michaelis-Menton kinetics and reaction theory using data from beta-gal—see the Nat. Chem. Biol. paper here) and new in vivo work looking at fluorescently labeled lac repressor binding to DNA.
  • For the first part, Sunney mentioned a new SM enzyme kinetics theory he developed (with Haw Yang and others) based on Marcus theory of electron transfer; they’ve submitted a paper to J. Phys. Chem. B (first author is Min).
  • The second “half” of his talk was so fast it was hard to follow. But he discussed using very fast imaging (5-ms frames and excitation pulses) to differentiate proteins (lac repressor) specifically bound to DNA and those that are nonspecific or diffusing (because only bound proteins are imagable as a bright spot, while diffusing spots blur out). They can also do kinetics studies of protein binding or unbinding to DNA: by finding how long it takes for spots to appear or disappear, respectively. This is reported in his recent Science paper.
• Peter Sims is a grad student in Sunney’s lab at Harvard. He talked about some molecular motor experiments in live cells. Using dark-field microscopy, he imaged the scattering of gold nanoparticles (endocytosized into vescicles, then transported by kinesin or dynein) onto a quandrant photodiode. Using this fast detector and many photons scattered by the GNPs, he was able to get 1.5-nm spatial precsion with very fast temporal resolution. In order to track the cargos throughout the cell, they used a piezo translation stage to keep the signal on the QPD. The results: “kinesin” (those dots moving consistently toward membrane) took 8-nm steps; “dynein” (dots moving toward nucleus) took steps of 8, 12, 20, 24, 32 nm and other factors of 4; and dynein also showed smaller steps when load was added. I suspect they’ll write a paper soon.
• Paul Alivisados spoke during Daniel Chiu‘s slot; I don’t know why. The must have swapped slots, but I don’t know because I missed the previous slot. Paul talked about plasmon coupling of his nanoparticle pairs and different colors of scattering from transverse vs. lateral coupling modes of the pairs (and triples and different groupings). He also talked about his nanorods in which atoms sort into dots or bands, depending on the doping. He gave a similar talk at Stanford a few weeks ago.
• Antoine van Oijen did his postdoc with Sunney I think; now he’s at Harvard Medical School. Anyway, he talked about replisomes and other replication machinery, trying to understand how lagging-strand synthesis works while the polymerases move in the other direction. He used flow cells to pull strands of DNA (attached on one end to the surface and on the other end to a bead), and watched the workings of the proteins. He used the fact that ssDNA is much shorter than dsDNA at the same flow rate (i.e. force) to convert the extension of the chain to percentage that is single-stranded. He could see replication loops being formed and move down the chain; he also saw pauses in the leading strand while primers were being synthesized, presumably allowing the lagging strand to catch up the leading strand. He also did some work on a Xenopus cell-free system to determine the distance between origins and pre-replication complexes on single DNA strands.
• Both Stephen Kowalczykowski and Chirlmin Joo (a TJ Ha student) spoke about SM imaging of RecA filaments on DNA.
  • Steve uses laminar-flow channels and optical tweezers to move DNA from a region with proteins and ATP (or other sets of components). He watched fluorescently labeled RecA nucleate and grow on stretched DNA chains. He talked not only about RecA, but also other DNA-associated proteins: RecBCD, Rad54, and Tid1 (see new paper here). He watched stretched DNA strands to learn about speed and direction of DNA motor proteins (using a fluorescent bead attached to the protein).
  • The Ha lab uses SM FRET fluctuations to learn information about nucleation and dynamics of RecA fibers. They also noted faster FRET dynamics of systems locked in lipid vesicles, concluding that fully formed filament nuclei bind and unbind to the DNA (because the filament can find the DNA again in the vesicle, and one-at-a-time monomer addition shouldn’t change the FRET signal in the vesicle). Chirlmin also mentioned that they use a hidden Markov model in finding transitions in FRET levels.
• Richard Ebright discussed careful FRET measurements of RNA polymerase movements and mechanisms. Some rigorous evidence for certain mechanisms or RNAP (and strong evidence against mechanisms). He also mentioned that he used non-natural amino acids (like Peter Schultz) to add azides to proteins and specifically label with fluorophores using the Staudinger reaction (see Bertozzi’s reviews here and here).

Tonight is the PHYS poster session, so I’ll probably write a post later about the coolest papers I saw. Stay tuned!

________________

* I’m staying with a friend in Cambridge (thanks Stephen!). It’s really convenient and free. In fact, he’s treating me like a king. Which is the appropriate treatment.

acs boston update 1: tuesday

August 21, 2007 at 5:12 pm | sam | conferences, science community, seminars

 Although I missed Sunday and Monday, I did see some cool talks today:

• Watt Webb‘s talk was a typical Webb talk: cool pictures, great voice, and a hodgepodge of info. He spoke mostly about lipid rafts in cell membranes.
• Stefan Hell had some spectacular images from his super-resolution work (STED and RESOLFT and other acronyms). His newer work on fast “PALMIRA“—stochastic single-fluorophore photoswitching imaging, like PALM/STORM—and multicolor imaging is really impressive. He added a square-root factor to the denominator of the Abbe diffraction limit: (1 + I/I_s)^1/2, where I_s is the threshold intensity above which you get sub-diffraction imaging. Hell also talked about 3D PALMIRA using slicing 2-photon excitation of new photoactivatable rhodamines they developed!
• Bo Huang is a postdoc in Xiaowei Zhuang’s lab; I know him from when he was a graduate student in Dick Zare’s lab. He showed some truly beautiful three-color PALM images of microtubules and clathrin in cells (fixed, I think). They have a brand-new paper in Science with all these great images, check it out! Viewing just the TIR image, one would conclude that some clathrin pits were associated with microtubules; the PALM image revealed that the clathrin was only near the microtubles, but not actually colocalized (see image above). As far as the mechanism of cyanine dye photoswitching, Bo said that it was triplet related (dependent on heavy-ion concentration), thiol related (BME, L-glutathione, and cysteine all worked), and not isomerization (not dependent on viscosity). Xiaowei said that Roger Tsien thinks that it is nucleophilic attack by the reductants in the oxygen scavenger.
• Michel Orrit used some sensitive interferometric and heterodyne experiments to measure the absorption of single gold nanoparticles (~10 nm) at room temperature. These particles absorb a lot of light, but are not very luminescent: so they efficiently heat the surroundings, allowing for photothermal detection. Some cool work, but hard to relate to cellular imaging.

I’ll update more tomorrow. Prepare for Sunney Xie, Daniel Chiu, Antoine van Oijen, and much more!

And you can always check out the C&E News bloggings about the Boston conference. Or Mitch. Or Paul. Or Kyle.

acs boston update 0: sunday and monday

August 21, 2007 at 4:37 pm | sam | conferences, science community, seminars

Because a bunch of my family was in town, I missed the first two days of ACS Boston. I thought it would be better to see some friends and family whom I rarely see than hear about science that I listen to everyday. After a few days, that decision starts to feel like a dumb move. (Just kidding, Dad.)

So I missed some talks I was excited about:

• Steve Quake
• Arne Gennerich
• Alice Ting (but W.E. gave me a good synopsis—some cool stuff!)
• Paul Barbara
• Jim Spudich
• Erdal Toprak

I’ve already seen recent talks by the most of the other speakers on Sunday and Monday, so I’m not as sad about missing those other great talks (e.g. Yildz, Zare, Alivisados, Dickson, etc.).

gearing up for acs boston

August 16, 2007 at 9:53 am | sam | conferences, news, science and the public, science community

I’ve been scanning the Technical Program for ACS Boston, and I’m super excited! Should be some great talks in the single-molecule biophysics field: days and days of fun!

 In all my reading of the program, this session seems the most … well, erotic? (At least the talks after the intermission, depending on what you’re into.) These talks put the “sex” in Technical Section.

acs boston

August 9, 2007 at 8:56 am | sam | blogs, conferences, science community

Is anyone going to ACS Boston? August 19-23. In Boston. Massachusetts. New England. USA. Earth. Universe. Etc.

I’ll be there, in the “Single Molecule Spectroscopy, Imaging and Manipulation of Biomolecular Systems” sessions. Paul at ChemBark thinks he’ll go.

Who wants to hang and party? Should we make a meeting time/place?

From “publish to perish” to “patent and prosper”

July 25, 2007 at 12:35 pm | ilya | everyday science, grad life, literature, news, science community

Hey folks,

I recently came across a very interesting retrospective in the Journal of Biological Chemistry written by Howard Schachman, who’s been engaged in biochemistry research in Berkeley for over 50 years.

Schachman lays out the changing nature of research and academic life as he’s observed them over the past 50+ years. I, for one, am always interested to read about how things have changed and where they’re heading. Here’s a particularly interesting quote:

In 1953, while McCarthyism was rampant, the Federal Bureau of Investigation (FBI) began screening grantees. Based on FBI reports, Oveta Culp Hobby, as Secretary of Health, Education and Welfare (HEW) in the Eisenhower administration, interceded and ordered the cancellation of grants to Linus Pauling and other prominent scientists.

Read on to find out what happened! I guess that president Rove’s clumsy meddling isn’t as bad as it can get.

what’s the point of peer review, anyway?

July 2, 2007 at 3:32 pm | sam | literature, science community

I’m pissed off.

My PI recently asked me to help him referee a manuscript (obviously the authors and journal will remain unnamed). I read the paper carefully and wrote a detailed report, requesting several changes before being appropriate for publication.

This manuscript had many major issues (including reproduced but uncited figures, inconsistent structures, poor statistics, and claims of data in the abstract that were nowhere in the paper). My referee report was friendly but asked for corrections. I was even kind enough to split the comments into major and minor.

We never heard anything back from the editors of the journal after we submitted our referee report.

So I was shocked to see the paper published recently … without any of the changes we requested! The reproduced figure—identical to an earlier publication—remains parading as original data, the structures remain inconsistent, the extraneous claims remain in the abstract, the statistics remain unjustifiable. WTF? Maybe two other referees said to publish without changes, but my comments should have been helpful to the authors and editors! I was trying to make the article better and help the authors emphasize their results. What was the point of all my work?

[Update] I think that the editors must not have sent on or looked at my referee report, because the authors didn’t even correct a wrong page number on one of their references. What jerks!

great line from a seminar

June 29, 2007 at 8:02 am | sam | science community, seminars

We had a pretty bad p-chem seminar yesterday. The opening slide had about a million slightly related topics that he was going to discuss. He must have sensed something from the audience, because he said:

“Many things, you might be confused. But my brain is clear!”

That got a good laugh.

Unfortunately, he failed to transfer that clarity to the audience…

RIP de Gennes

May 23, 2007 at 5:45 pm | sam | news, science community

We lost a great scientist this month: Pierre-Gilles de Gennes. He won the Nobel Prize for Physics in 1991 for his work to understand complex matter such as polymers. My research and studies as an undergrad involved a lot of polymer physics, so I learned to love his book Scaling Concepts in Polymer Physics.

(Thanks for the heads up, Biocurious.)

NAS

May 1, 2007 at 1:10 pm | sam | news, science community

My advisor W.E. Moerner was elected to the National Academy of Sciences this morning. Two other science faculty members at Stanford were also elected new members: Mike Fayer and Steve Block. The departement will celebrate this afternoon with an ice-cream social. That’s nice…

aqueous gel sample prep

April 18, 2007 at 4:46 pm | sam | everyday science, science community

Does anyone have any experience making samples (preferably thin-film, ~100 nm) using agarose, gelatin, or some other transparent aqueous gel/biopolymer? For my poly(methyl methacrylate) samples, I spin-coat at 2500 RPM for 30 s and get a ~30-nm film. I can experiment with conditions, but I thought I’d ask first.

I’m trying to measure fluorescence from a relatively concentrated sample (~10^-6 M fluorophore in biogel) on a glass coverslip using epi-illumination.

If I get any answers, I’ll let you know here.