Peer review and the new media

I attended a Macintosh Users Group recently. (Yes, I am a Mac user.) This meeting was unusual. Natali Del Conte, a tech writer for CNet and CBS, was the featured speaker. She talked about being authentic, social networking, and how technology has changed how we get information. She argued that gone are the days that information is simply pushed to us and that Walter Cronkite is the most trusted name in news.

A detail I have come to think more about is what we know. I remember that stomach acid was thought to cause ulcers, but Marshall and Warren have received a Nobel prize for their discovery of the role of Heliobacter pylori and its role in peptic ulcers.

Mitch (Feb 08) and azmanam (Feb 02) have posted on congressional misunderstanding of science and false or poor science reporting, respectively, but I don’t think chemists are as cognizant of the accuracy or correctness of textbooks or peer reviewed papers. There have been a few cases in which errors have entered the chemistry world.

I wrote the the archivist at the Oregon State University Library inquiring about whether there was any correspondence regarding a paper Pauling published (there wasn’t). I wondered what the referees may have said.  Now, I have been thinking how this is like the comments to a blog post. One of the really interesting things about the new media, is errors can be pointed out. They can be argued and open to everyone.

I have been thinking about how our ideas of atomic theory have evolved. In doing so, I have been reading a fascinating series of transcripts from recordings deposited at the Center for History of Physics of the American Institute of Physics.

It was interesting that some people thought Niels Bohr had confused the literature with his papers. However, overall, what I liked was how these transcripts contained the personalities of the scientists, their interests, and in some cases their ideas (or biases) about topics being discussed. I felt these transcripts from leading scientists were like our modern internet (although generally without the details of the science).

Our modern internet has no rules. It can be difficult to sort out the wheat from the chaff. We need to learn who to follow and who to ignore. Peer reviewed journals only give the filtered result. The referees reports are confidential. Comments are not published except in blogs. Now that science is moving toward electronic publication, would a new model for scientific publication improve the scientific world?

Just to note that this is not unusual in chemistry. Organic Synthesis has long provided a kind of review for a select set of procedures. I don’t foresee H.C. Brown’s papers becoming ignored, but independent reports could prove useful. Similarly, critical steps to improving yields  would be helpful. You can find examples of this in the Organic Chemistry Forums.

Should online journals allow comments? Would it be useful? How could it be done? Would it be science?

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TheChemBlog Closes Shop

Kyle Finchsigmate

One of the pioneering chemistry blogs closed their doors earlier this month. As a brethren to the class of 2006 [1], I feel the need to pay homage to the great Kyle Finchsigmate’s influential chemical blog. TheChemBlog came online in June of ‘06 and with his anonymity still intact he was able to get away with his potty-mouth antics in a way to be informative, cutting, and always entertaining.

All good chemistry blogs have a mix of literature reviews, opinion, and funny life as chemists posts. If you examine his early writing they focused mainly on dissecting the chemical literature. The blog served as a vehicle for his wry sense of humor and to develop his capacity to analyze literature and communicate his insights to the chemical community. I mention this only because an examination of his final posts at the blog reveals a complete lack of the literature reviews, and I think this switch is telling for why he closed the doors.

All that being said, I am sure we will hear from Kyle again. As Web 2.0 platforms continue to expand and evolve everywhere in our lives, it will only be a matter of time until Kyle finds a new one to his liking. With the recent very promising blogs Chemical Crystallinity and Chiral Jones he leaves a chemical blogosphere that I believe is in good hands.

Mitch

[1] In 2006 this blog was started and known as the ChemicalForums Blog; it was January 2008 when we moved to this domain.

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On the subject of safety goggles

As azmanam pointed out, Chemjobber’s post about Lab Essentials made it onto the most recent issue of Nature Chemistry–hooray! Well, kind of. One of my comments about comfy eyewears somehow got a mention as well. Now, I didn’t imagine my debut in the Nature publications quite this way. But if I have to be known as the Asian girl with the flat nose, I might as well use this chance to elaborate on the cause that is dear to my heart.

I’ve worn glasses for as long as I could remembered, but my journey to finding a pair to wear in lab has been a rocky one. I must not be alone in this: it’s so hard to find a pair of safety glasses that fits well! My problems are:

1. The plastic part that is supposed to sit on the bridge of my nose isn’t really long enough to touch it; instead, the goggles sit suspended above my face. I have a flat nose; I’ve learned there are more important things in life to be upset about.
2. Since the goggles can’t sit on my nose, the bottom edge of the lenses digs into my cheeks for support. I get the most awful imprint on my face and it starts to hurt after a couple hours
3. Because they are ill-fitted, they fall off all the time when I’m in the middle of doing something

Do I get your attention now, PPE manufacturer? (hint)

When I first started taking chemistry as an undergrad, I was told to fish out a pair of safety goggles from the big box my TA provided. Over the next few years, I had tried on my fair share of safety goggles. Some of them were rocking the retro vibe like this, some others were the more simple style like this, and the others were the nice adjustable length like the one shown above.

The variety was nice. But I never liked any of them. I hated wearing safety goggles/glasses because none of them actually fits me. I don’t know how long it would take PPE companies to figure out that chemistry students with flat nose everywhere (including, but not exclusively, the Asian kids) are resenting wearing goggles!

I think we can agree that safety goggles are among the most important part of personal protection equipments. It’s a must for novice and experienced chemists alike. I would think that fit and comfort are significant factors in designing these because of their proximity to your face. As an undergrad, I didn’t have much of a choice of the types of goggles I could wear, so I just went with whatever that was provided to me. Let me assure you the fun of my chemistry experience was greatly diminished because of the discomfort of wearing one of these.

We’ve always had problems with freshmen (even older students) not wearing their goggles in teaching lab. Aside from laziness and carelessness, I think a big factor of it is comfort. We can promote better safety habit simply by showing students that in the same way we select glove sizes that fit us, it is possible and important to do the same for safety goggles.

And really, we have nitiles gloves in 5 sizes and like 20 different colors; I think it’s possible to add supportive nosepiece to safety goggles.

Noel

Note: I currently use a pair of AOS goggles with rubber nosepiece that I am reasonably happy with. It still falls my cheeks sometimes (as the rubber nosepiece is still quite shallow) but is a significant improvement from previous experience.

Note #2:  Nature Chemistry–if you need guest writers, you know where to find me.

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Nobel Prize in Chemistry 2009 Analyzed

Ada Yonath

Thomas Steitz

Venkatraman Ramakrishnan

As already announced biologists walked away with this year’s Nobel prize in chemistry once again, this time for work in determining the structure of Ribosomes. Read here for more and more information. We at Chemistry Blog like to quantitate and analyze like any good chemist. But how do we quantitate how badly chemists were denied? Easily, we have ChemFeeds.

ChemFeeds is my little graphical abstracts portal. It tracks 39 chemistry journals. It isn’t an all inclusive list of all chemistry journals, but it is a good representative cross-section: ChemComm, JACS, CrystEngComm, DaltonTrans, JOC, JNatProd, InorgChem, Macromolecules, OrgBiomolChem, OrgLett, Organometallics, JChemInfComSci, JOPCA, JOPCB, JOPCC, PhysChemChemPhys, Analyst, JAAS, ACS NANO, AdvFunctMater, AdvMater, ChemMater, JMaterChem, Langmuir, NanoLett, Small, Biochemistry, Biomacromolecules, ChemResToxicol, IntergrBiol, JCombChem, JMedChem, JProteomeRes, MolPharm, EnergyEnvironSci, GreenChem, JEnvironMonit, NewJChem, SoftMatter.

The database for ChemFeeds is a little shy of a year old. If we search the ChemFeeds database for the occurrence of ribosome we get 7 abstracts in the last year. If we search for GFP we get 2 hits (subtracting the Nobel lectures). What about if we search for other topics most chemists thought deserved a Nobel nod and make a table (chemists love tables).

The analysis shows that although chemists do not concern themselves with GFP or ribosomes, they are still well represented in Google and on some level deserve recognition for their reach. Dye-sensitized solar cells are the new in thing in chemistry, but from an energy perspective they make up a very small percentage of what we as humanity derive our energy (i.e. oil, nuclear, hydrothermal), but it almost makes it past 1,000,000 in Google hits. Radical polymerization, an important reaction used everywhere, but perhaps too established to get a Nobel but then again CCD cameras got the nod. Cross coupling, the most popular subject amongst chemists and can only be ignored by the Nobel committee for so long. Single molecule studies obviously strongly represented in the current literature and is more far reaching in Google than cross-coupling reactions, so that field will be ripe for a Nobel.

As chemists we would like to see the Nobel chemistry prize go to a chemist. Our Nobel hopefuls may be a measurable magnitude more chemically interesting, as measured by ChemFeeds, but there is more work for them to do until these topics become world renowned (which seems to be the dominant prerequisite these days).

Update: You can finally MySQL query the ChemFeeds database yourself: Search ChemFeeds

Mitch

P.S. I get 215,000 Google hits searching for my name exactly, Mitch Andre Garcia, but it doesn’t mean I’m winning a Nobel; although it probably does mean I should spend less time online.

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Electroneutrality is dead?

Gerald Pollack

That is the highly controversial claim made by Kate Ovchinnikova and Gerald Pollack in Langmuir earlier this year.^[Langmuir] Electroneutrality is a guiding principal in electrochemistry and is a method to understanding electrolytic cells (Pt electrodes in dilute aqueous NaCl solutions). It stipulates that any charge imbalance across an electrochemical system is quickly (~ns) balanced by the salt present in the water being driven by the electric field in such a way to neutralize that charge imbalance. Thus the need for salt bridges and all that wonderful G-chem stuff we have learned. There is even a cool little applet you can play with electroneutrality by the Harvey Project. When I tried to sit down with electrochemists to discuss the claims by O&P they quickly dismissed them out of hand after reading the beginning of their paper. So the big question is, did O&P stumble across something amazing or did they spectacularly overstate the results of their experiment.

I can summarize their paper succinctly:

1. Insert electrodes into electrolytic cell
2. Turn on power supply
3. Disconnect the electrodes from the circuit
4. Remove the bridge between beakers
5. Reconnect electrodes to measure residual charge in the two beakers.

The design seems thoughtful enough, but before I get into the merits of their results I need to take time to mention a few gems in their paper. Here is a quote from them.

Bubble formation occurred in all experiments (n > 20), although position and growth rate were inconsistent. In most cases, formation began during the charging phase and continued through discharge. Characteristics of bubble formation were not pursued in any detail, but may warrant future study.

But it doesn’t warrant further study,  all chemists know where their bubbles came from.

An other eye catcher is that they didn’t use a standard electrochemical setup. They used my trusty NI USB-6009, I know that product well as a chunk of my thesis was acquired with it. It doesn’t make the experiment invalid, but why use crap when you are trying to disprove such a time honored concept as electroneutrality. Maz and I know from experience that the USB-6009 floats if their isn’t a sufficient load on it or if their isn’t an appreciable external voltage.

Here is a quote from them contemplating that HCl solutions have an overall positive charge.

One might speculate, for example, whether ordinary acidic solutions, which have low pH, might contain net positive charge, while ordinary basic solutions might contain net negative charge.

So far everything has been “quirky”, it isn’t until the end when you perceive something really odd.

Water appears able to adopt two structural networks that have mirror symmetry to one another. The fact that these networks are macro phenomena deserves further study.

A second and related issue is the potential for disturbance of these structural networks. It is now established that when water is left standing for long periods, it develops thixotropic properties, implying macrostructure.7 Such macrostructure is expected to be fragile. The fact that removing and inserting electrodes did not apparently ruin the charge-containing structure implies that, once formed, the structural network can re-form rather readily. This is an additional subject requiring further study.

7:Vybiral, B. Water and the Cell; Pollack, G. H., Cameron, I., Wheatley, D., Eds.; Springer: New York, 2006; pp 299-314.

It is with that last statement you say to yourself, “Oh, I get it. This is a homeopathy paper.” Water being able to adopt structures of the solutes that were dissolved in it is a hallmark of the quackery that is homeopathy. O&P’s claim isn’t that bold, but it has hints of the same idea. Claiming macrostructures (~mm) of water that extend past the picosecond domain is absurd.

Although I haven’t discussed the results of their paper, would you really trust it anyways?

Horacio Corti and Agustin Colussi have done an excellent job dissecting the technical irregularities of the paper and I encourage you to read their comments on the article (link below). If you come to a different conclusion or find me in error, please leave a comment and join the discussion.

Links

• Can Water Store Charge? (Ovchinnikova and Pollack)
• Do Concentration Cells Store Charge in Water? Comment on Can Water Store Charge? (Corti and Colussi)
• Reply to Comment on Can Water Store Charge? (Ovchinnikova and Pollack)
• Response to Reply to Comment on Can Water Store Charge (Corti and Colussi)

Mitch

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Like Natalie Imbruglia’s One Hit Wonder, I’m Torn

So it’s been a while since my last entry, but grad school has eaten me up. But over the past several months, I have been getting seduced by the Dark Side of the Force. No, I’m not talking about industry, I’m talking about another entity entirely.. the world of intellectual property law.

OMGWTFBBQ? That’s probably your response right now, but as someone who has been rather myopic in my career path due to academe being the only thing I know, (and me not really feeling like a perfect fit in industry), the seductive path of law school is in the way.

One of the things I have learned through informational interviews with my local alumni is that law schools LOVE technical backgrounds and patent law is one of the hottest and fastest growing fields at the moment. Of course, things are cyclical which means it might not be great later, but the past 5 years has seen tremendous growth.

There are lots of other scientists going to the other side, but here’s my dilemma…

There are firms that offer patent agent programs to seduce scientists to law. What is this patent agent program? You work at a firm (with zero to little experience in law) and get trained as you work. You get paid a great salary (think average 2.5 to 4 times the highest grad student stipend depending on where you go), with amazing benefits (401k plan, full medical/dental/vision benefits, etc), get to work in a fancy office, feel like a real world adult, get to dress up in fancy clothes and get trained. After a year, you’re probably ready for the patent agent exam, and if you pass, said firm will offer tuition reimbursement if you attend law school.

Yes, they’ll pay for expensive law school. Then you go back to the firm as a full J.D/(M.S. or PhD) as well, get promoted and commit for a few years, then you can go around to other firms as well!

So what’s a chemist to do? I do love research and academe, but my pragmatic side is telling me to join the dark side.

I know I’m not the first to be seduced, and I definitely won’t be the last! Intellectual property law, when it concerns chemistry, is actually quite fascinating. It’s like being a grad student with all the reading, researching and writing you have to do, but you get paid way more and you’re not inhaling chemical fumes. It’s another career path available out there for grad students in chemistry, and I know I hadnt considered it before and just recently learned about it, so I’m throwing it out there, so like me, perhaps your blinders can be taken off and you might consider more options post PhD!

That’s all! I’ll let y’all know what I do in the coming months! For now I have lots of thinking to do.

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Condensed Print Format

My boss has pointed out this piece of news covered by C&EN. Apparently, starting from July, all ACS journals will be printed in a “rotated and condensed” format, that is two pages on one printed page in landscape format. This is an effort to reduce printing and distribution costs.

In my opinion, this change is just one further step towards purely electronic journals that are not printed at all. I think this will deeply affect the way we present our data and how we look at formatting. Preparing a manuscript in a way meant for printing is different from one which will never appear in print. Some may welcome this change because it saves paper, others will probably miss the possibility of flicking through a new issue of JACS. Although I rarely go to the library to pick up a printed journal, I admit to reading printouts very often (see this post).

Update: Apparently, in 2010 the print versions will stop completely, with the exception of JACS, Acc. Chem. Res. and Chem. Rev. See also Nature News.

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Shifting Constants

“]One of the first things that pops up in chemical education at the high school level is stoichiometric equations where a student is supposed to determine such things as yields, coefficients, and amounts of substance on a purely theoretical basis. This quickly becomes old hat for many students. In high school, my stoichiometric technique (if you could call it that) left a lot to be desired. I tended to “divine” my answers on tests and quizzes by playing with numbers until an answer made sense- then using it. It worked surprisingly well- and I got through classes learning very little but with decent grades. At the time, I wasn’t terribly interested in chemistry, and the class really was boring up until the end, where we got to learn about electrochemistry. I didn’t realize at the time that the subject matter wasn’t being done any justice. To me a mole was a mole was a mole. I just knew there were these numbers that I used to divine answers.

Read more »

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Printing

Most of the printing of our group (~30 people) is done on just one laser printer. I often find myself walking from the lab to the group library, where the printer is located, and back because of paper jams or printing orders that have misteriously vanished into the digital nirvana. This is making me crazy! Somehow I am unable to proofread a manuscript on my computer screen, so I always need a printout. Maybe I should try and get my own printer.

This leads me to my question: Do you often print papers for reading, or do you always read the PDFs directly? I try to read most things directly, but the papers I cite the most, I also keep in printed form.

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Chemistry Journalism

Recently, Chemical and Engineering News had to cut 16% of their staff due to decreasing ad revenue.^[CS] Advertisers have been trending towards less spending, but this is often attributed to a lower subscription base. The number of C&EN’s subscribers do not fluctuate enough to account for this type of lost revenue, so what is causing the decrease?

After the layoffs there are now 48 C&EN’s staffers. If I assume the average salary is ~$5,000 per month, I have no clue if this is valid but it seems like a lower limit dollar value, then C&EN needs to make $240,000 per month to just cover payroll. Our dues pay for their paper, printing, and distribution costs. So let’s compare C&EN’s revenue model to Chemistry Blog. First we need to define some terms.

• Uniques, defined as the number of unique people that read a website/magazine in a given week.
• Revenue per unique per month. Average amount of revenue generated per unique reader in a month

With a weekly subscription volume of ~140,000, C&EN has a monthly unique volume of 560,000. Which means C&EN needs to make a minimum revenue per unique of $0.43 per month to cover my lower estimate of their payroll costs. On the other end of the spectrum, Chemistry Blog generated $15.00 in April from 20,000 uniques, this translates to ~$0.0008 of revenue per unique per month. The gist of this story is uniques are cheap online.

We at Chemistry Blog fully admit that C&EN is a better news source, better journalism, and a better target audience for advertisers. But from a purely marketing angle, Chemistry Blog is cheap at a cost of one fifth of one percent for what C&EN sells their uniques. I would guesstimate $0.10-$0.20 of revenue per unique per month is a more sustainable model that a huge niche journalism outlet like C&EN will be force to aim for in 10-20 years. Unfortunately, this means many more painful cuts in C&EN’s future.

Below are my suggestions to shore up C&EN balance sheets.

• Expand to non-ACS web advertising: C&EN already has a relationship with advertisers, if they initiated an affiliate program where independent chemical websites get a share of what advertisers are willing to pay for adspace. This expands the audience they can tell advertisers will see their ads.
• Many journalism outlets are scuttling their science sections. C&EN could sell their stories to these papers at a marked discount for what it costs to staff science journalists.
• Participate more strongly in ACS membership drives, more members equals more subscriptions which will hopefully be proportional to more ad revenue.
• Get a larger chunk of the budget subsidized from ACS.

None of these ideas are going to be the savior of chemical journalism, but it might ease the coming pain.

Mitch

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