should i join the postdoc union?

October 25, 2010 at 8:07 am | | open thread, postdoc life, science community

Postdocs at Berkeley (in fact the whole UC system) formed a union a few years back. Recently, the union negotiated a better contract with UC, which brings the postdoc pay up to … wait for it … the NIH minimum! That’s actually a big step. (Read more about it in Nature.)

Pro:

  • I can listen to Woody Guthrie without feeling guilty
  • it supports a good cause: I do think that postdocs need someone looking out for their interests
  • it is a relatively small amount of money to ensure that postdocs have representation

Con:

  • it costs 0.28% of my paycheck to join (although that’s only around $100)
  • my money might go towards those terrible political ads on TV
  • the general possibility of making my relationship with my PI more adversarial

I’m conflicted. Thoughts?

2010 nobel predictions

September 2, 2010 at 11:32 am | | news, nobel, open thread, science and the public, science community

In previous years, I’ve awarded Edsel-Nobels, which no one really cared about. Maybe this is the year I’ll make predictions for the actual Nobel. Paul at Chembark already started his predictions, and everyone else will be buzzing about it soon enough.

In no particular order (and without much forethought):

  1. Solar: Grätzel
  2. Super-resolution optical microscopy: Betzig, Hell, Zhuang, Hess
  3. Cloaking: Pendry
  4. Birth control: Djerassi
  5. Laser-induced fluorescence: Zare
  6. Inorganic: Gray, Lippard
  7. Single-molecule spectroscopy: Moerner, Orrit, Rigler, Xie
  8. Chaperonins and protein folding: Horwich, Hartl, Lindquist, Ellis
  9. DNA fingerprinting: Jefferys
  10. Electrochemistry: Bard, Nocera
  11. Polymer synthesis: Matyjaszewski, Wang
  12. NMR and membranes: McConnell
  13. Discovery of kinesin: Sheetz, Vale, Brady
  14. Nano: Whitesides
  15. Peace: Twitter
  16. Cross-coupling: Suzuki, Heck, Sonogashira
  17. Electron Transfer in DNA/Electrochemical DNA Damage Sensors: Barton, Giese, Schuster
  18. Pd-catalyzed Alkyne/Alkene Coupling and Atom-Economy: Trost
  19. Nuclear hormone receptors: Chambon, Evans, Jensen, O’Malley
  20. Two-photon microscopy: Webb, Denk, Strickler
  21. DNA microarrays: Brown
  22. NLO: Harris (as predicted by The Simpsons)

So there. The only one I’m confident about it Twitter.

Please feel free to add more in the comments. I will probably continue to update this…

UPDATE: Paul now has updated odds. Very impressive. He’s put a lot more thought into this than I. I’ve added cross-coupling to the list. Additions are in italics.

UPDATE: Can you name all the Chemistry Nobel winners?

UPDATE: Thompson has released their predictions.

UPDATE: The Simpsons also have some predictions.

how do you read PDFs?

July 28, 2010 at 8:59 am | | everyday science, help me, literature, open thread, software, stupid technology

I now have a longer commute, with at least 30 minutes of quality reading time. I don’t really want to carry my laptop everyday, so I’m seeking a better way to read journal articles. I’m not going to print them out, so don’t suggest reading them on paper. :)

[poll id=”3″]

Of course, cost is a factor, but I don’t want to go for the cheapest option if I end up never using it! My guess is that the Kindle DX is the best for reading PDFs, but loses on other fronts (e.g. large, expensive, limited, only grayscale). The iPad is a versatile color reader and I can sync with programs such as Papers or Mendeley (soon for the latter), but it is very expensive. Also, the screen isn’t as nice for reading print. The iPhone is way too small to read PDFs.

Man, I need to test-drive these devices for a month!

Other options?

what the heck is permanent press?

July 10, 2010 at 9:47 pm | | nerd, open thread, science@home

OK, what the heck is the “permanent press” cycle on my washer? On the dryer, I think it just adds a cool tumble to the end to avoid wrinkles. But what about for the washer?

Wiki says that some machines might spray a little water during the spin, but I’m fairly sure that my cheap washer does not have that feature. From what I can tell, the perm press wash cycle is 2 min shorter than the “normal” setting, and the second rinse is a “cool down” rinse. However, my washer make the second rinse cold anyway, so I don’t think this makes perm press special. I wonder if the agitation is weaker (or stronger) for perm press compared to normal, but I sorta doubt it.

So, in conclusion, I have no idea what the “permanent press” settings on my washer are for. Maybe they just had extra space on the settings knob, so they added some fictional settings?

UPDATE: I called GE to ask them this question about their washer. The woman at the technical service said, “I have no idea.” And sorta laughed. No help there.

avoid mistakes in lab

December 4, 2009 at 11:26 am | | everyday science, how-to, lab safety, open thread

Nick at BiteSizeBio gives of a list of ways to make fewer mistakes in lab.

1. Use a checklist.

2. New protocols and SOPs: write out your own version.

3. Annotate. If you make a mistake in a protocol, annotate your copy so that you won’t make the same mistake again.

4. Repetitive pipetting: be consistant and use bookmarks.

5. Don’t multitask too much.

6. Get set up before you start.

7. Prepare in bulk.

8. Don’t spend so long in the lab.

9. Get enough sleep.

10. Take responsibility.

I’d like to add a few of my own, from my vast experience making mistakes:

Clean up after yourself as you go and maintain a tidy workspace. Obvious, but often forgotten. Tidying up will make your next experiment easier, and shows respect for your fellow labmates.

Label samples with sufficient information. When you come back tomorrow (or in a month), having a dozen ambiguously labeled epi tubes means you’ll probably have to start over (or screw up your experiment by grabbing the wrong one).

Write down a plan (in your lab notebook!). Maybe even a decision tree to plot out the experimental path you will take, what to do if unexpected results occur (i.e. anticipate the unexpected), what data you will collect in the experiment, and what controls are necessary. This will help avoid that terribly frustrating situation where you realized during data analysis that you collected only (n-1) of the necessary data points and have to start all over the next day.

Ask questions! If you don’t know how to use a piece of equipment, don’t know how to properly use or store a chemical, don’t know a protocol, or are simply stumped by a problem, ask a labmate. Most people would rather answer a question or demonstrate a technique than find out you broke a piece of shared equipment. Of course, respect your labmates: plan ahead and ask someone on their schedule, read manuals and protocols before asking for help, and avoid going to the same person every time.

When something isn’t working, take a deep breath and think. No matter what Murphy says, often the problem is minor and obvious. Before you start twisting knobs on a laser that isn’t lasing, confirm that the shutter is open.

Others?

open letter to journals about RSS

November 25, 2009 at 9:14 am | | literature, open thread, science community, wild web

Dear all journal publishers,

If the RSS feed to your journal is missing a TOC image or a full list of the authors, you need to correct that.

rss-no-toc_crop

Reading just titles can be hard, especially when you skim through many journals. TOC images make that much more enjoyable. It’s the way to go, and if your journal does not include TOC images, you’re behind the times.

Also, it’s very simple to include all authors in the RSS feed. First authors only is not helpful: it’s very helpful to be able to check who the corresponding author is on a paper you might be interested in. (I’m talking to you ACS.)

Mitch’s ChemFeeds is great, but I doubt it can add TOC artwork to journals that don’t request it from their authors!

Happy Thanksgiving, everybody!

royce doesn’t like 8-page papers

June 10, 2009 at 10:27 pm | | literature, open thread, science community

Royce Murray—the famous analytical chemist and great educator—has written an interesting editorial in Analytical Chemistry. Since 1995, the page limit for AC has been 7 pages, including figures. But papers are getting longer.

“In 1983, 1989, 1994, 2000, 2006, and 2008, the average length of papers published in our research section was 3.8, 6.4, 6.7, 7.1, 7.0, and 8.0 pages, respectively. I consider an average seven-page length already long, and an average of eight pages is alarming.”

royce1Royce is careful to acknowledge the various justifiable reasons papers might be longer today than before, including that figures have grown bigger. But he remains convinced that a 10-page paper is basically unreadable to most AC subscribers. His solutions are twofold. First, Royce implies that authors should write the same information with fewer words and smaller figures. Secondly, he explicitly suggests that authors take advantage of Supporting Information sections.

I am of two minds on this issue. On the one hand, I agree that an 8-page average means that causually reading AC is going to be difficult. On the other hand, I don’t think that dumping results into the SI is an adequate solution: SIs are less carefully written, refereed, and read, and therefore are not an appropriate medium to report scientific data or analysis. In 50 years, will SIs still be accessible? Will our generation of scientists be proud of them if they are? SIs are great for detailed methods as well as superfluous, tangential, or extra results. However, there needs to be a place to be able to publish significant scientific results, even if it takes 10 pages. AC should probably be one of those journals (as should J. Phys. Chem. ABC and others).

So here is my solution. (1) Allow longer papers when they represent a significant body of work. I think Royce agrees here. (2) For a very long but good paper, have the authors split it into two halves. Each half should tell a distinct story, but together could easily be read as a whole. These two halves would be published alongside each other. (3) If a manuscript is 10 pages of drivel and bullshit figures, reject it or require a significant rewrite.

Other thoughts?

deja boo?

June 2, 2009 at 9:53 am | | everyday science, literature, open thread, science community, scientific integrity, wild web

I’d like to know everyone’s opinion about Deja Vu, the database of “duplicate” scientific articles. Most of the articles in the database are “unverified,” meaning that they could be entirely legitimate (e.g. a reprint). Some are instances of self-plagiarism: an author recycling his or her own abstract or intro for a new paper or review. A few instances are true plagiarism: one group of authors stealing the words (entire paragraphs or papers) of other authors. You can read more in Science.

I can imagine several possible responses (see the poll below):

  1. Great! Now there’s a way for authors, journals, and institutions to better root out plagiarism and unauthorized copying.
  2. Granted, this is information in the public domain, so authors should expect their work to be scrutinized. However, it’s worrisome to have a computer algorithm put red flags on articles that may be legitimate. Deja Vu is probably a good idea, but needs to be reworked.
  3. Careers will be unfairly destroyed by this approach. Labeling a paper as a “duplicate” sounds negative, even when listed as “sanctioned” or “unverified.” This database takes a guilty-until-proven-innocent approach that has the potential to sully the reputation of good scientists.
  4. Um, haven’t these people seen Terminator 2? What is Deja Vu becomes self-aware and starts killing plagiarists.

[poll id=”2″]

Fortunately, an author can check his or her work in the eTBLAST database before submission, to see if a coauthor copied a section, or if the text will unfairly put up red flags. But I found that the results were confusing (e.g. I can’t find the meaning of the “score” or the “z-score”) and unhelpful (of course papers in the same field will have the same keywords). And the results page was really buggy (maybe just in Firefox?).

Personally, I vote #2: Deja Vu is a good idea, but needs to be more careful about the papers it lists as “duplicates,” even “unverified” or “sanctioned.” When a junior faculty member  gets a hit in the database, his or her name will be associated with plagiarism. Some people will not bother to check if it was a legitimate copy, or even who copied whom. I think that the current approach that Deja Vu takes is reckless and unfair. Even lazy.

Moreover, self-plagiarism is not necessarily bad. Copying your own abstract is different than copying your entire paper. Obviously, at some point, self-plagiarism is unacceptable (e.g. submitting the same paper or review to two journals).

I think this topic deserves more nuance than Deja Vu offers.

(Deja Vu has it’s own survey here.)

grad school microloans

March 25, 2009 at 2:19 pm | | grad life, open thread, stipends

Despite the fact that we are very expensive to our PIs, we graduate students receive a stipend that just barely pays for our living expenses. In fact, according to Stanford’s own estimate, our expenditures are a couple hundred dollars more than our annual income.

Coin JarOne result of this is that many of my fellow students live paycheck-to-paycheck, and do not have adequate savings to buffer against large expenses. This means that many students end up carrying a balance on their credit card, taking out a loan, or applying for another card to pay for unexpected peaks in spending (e.g. buying a plane ticket home, paying a rental deposit,  or while waiting to be reimbursed for a conference). Having a small amount of interest-free borrowable money could help some students keep their heads above the water.

So, basically, I want to start a microcredit account for Stanford Chemistry grad students. This could be as simple as a checking account with a couple thousand dollars that could serve as a source of small, interest-free loans to students in need of some cash before their next paycheck or while they are waiting for reimbursement to clear.*

I envision a system in which individuals who contribute even a small amount to the account could withdraw a couple hundred dollars to pay for emergency expenses, then pay back the money in a month or so.

Here are some problems:

  • Will People Contribute to the Fund? If 25 people contribute $25 each, and 50 more contribute a dollar, that’s already approaching a grand. If there a few angel investors—maybe grad students who are married to people with real jobs—contribute a few hundred each, you could reach a few thousand dollars. That doesn’t mean that people will actually be interested in joining the cause, or risking their money. Even if the account were interest-bearing, a few percent of a couple thousand spread among many isn’t a big motivator.
  • Will People Borrow from the Fund? This is probably the biggest problem. Borrowing would probably mean contacting the person who holds the debit card, filling out a form, etc. That might be too much work for just for a few hundred bucks. I suspect this getting people to actually borrow would be the real problem with the idea.
  • Will Borrowers be Forced to Grovel? If one person is the official owner of the account, then borrowers would have to go to that person to get the debit card. That might feel like groveling. Or it might be embarrassing. And that’s assuming that the account owner is nice and responsible.
  • Should the Loans be Public or Secret? Making the loan amounts and borrowers “public”—even if only among the people who have contributed to the fund—might cause borrowers to feel embarrassed. Conversely, if the loans are kept secret, then there’s less encouragement to repay loans quickly and fully. A compromise might be to only announce names and amounts when repayments are late. That would encourage delinquent accounts to be repaid.
  • Will People Repay? I think this wouldn’t be a problem. Because the fund is community-sponsored, and because the funders and borrowers all know each other, and because the loans will be small and we do have incomes, I think that almost all the loans would be paid back in full. Peer pressure can be effective at encouraging repayments.
  • Other Logistics? This can be complicated. Do you have one responsible person open a checking account, or are there group accounts available? Google Spreadsheets and Forms, or even just Excel, could be useful for much of the logistics (contribution and loan amounts, repayment dates, etc.). What about when the owner graduates? They’d have to pass the account on to another student, which could be messy. How do you distribute interest and losses to the contributors?

Any suggestions?

UPDATE: Using PayPal might help a lot of the logistics, and even reduce the face-to-face groveling required to get money.

________________

* I don’t know how it works elsewhere, but grad students at Stanford are required to pay their own way to conferences and flights, then get reimbursed. The poor students are basically giving the rich University an interest-free loan while waiting for reimbursement to clear. For some reason, we can’t be preimbursed for our conference expenses. Usually, you are reimbursed before you have to pay your credit card bill, but it still is a stupid system that puts undue burden on the students. The microcredit account could serve as a low-bureaucracy alternative to the stupid reimbursement system when a student is very short on cash or has already maxed out their credit card.

what to do about supporting information

March 9, 2009 at 3:54 pm | | literature, open thread, science community, wild web

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.

khemistry klassics

December 5, 2008 at 3:49 pm | | great finds, history, open thread, science community

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: TriphenylmethylJ. Am. Chem. Soc. 190022(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 ElementsPhysical 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. 200443, 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.

ACS’ new website

November 13, 2008 at 2:30 pm | | literature, news, open thread, wild web

ACS is upgrading its website. It looks like the Supporting Info link will be a little more visible, which is a very good idea. And an option for PDF with links. It looks like the new ACS site will be even more slick than it already is. Actually, ACS has one of my favorite publisher/journal websites. Better than ScienceDirect. Far better than PNAS, I’d say. ACS is clean and neat and obvious. It doesn’t look like they’ll lose those characteristics with the redesign.

I’m sure some bad will come with the redesign. For instance, it looks like they’re adding a coverpage to each PDF with the TOC figure. I see the reasoning—otherwise the TOC figure is not in the PDF at all—but I’ve never liked coverpages on articles: just an extra page that I rarely need. (Oh well, I’ll just print from pages 2-end.) Also, they include social networking links, like Facebook, but leave out CiteULike. Maybe they’ll fix that. Who posts JACS articles to their Facebook page??

On a side note, one feature that they should fix is in the Advanced Article Search tab: you used to be able to just insert the volume and page, and the engine would output all articles with that combination, regardless of which journal. It was a nice shortcut, because there were rarely more than three or four matches. Now the search forces you to choose a journal, which adds a slow, often unnecessary step to the search.

What do y’all think? Good or bad?

Poll: Laser Breath

May 2, 2008 at 4:23 pm | | hardware, open thread

The above original adornment of our laser head had to be removed, ostensibly due to the possibility of back reflections, fire, and the subsequent destruction of sensitive optics. Although the first thing my boss said when he saw it was, “I really hate that guy;” so maybe that logic is only a smokescreen.

In either case, now that we’ve reconfigured the case, it is possible to redecorate it with something shooting a laser beam. As such, I leave it up to you to suggest possible candidates. Some suggestions were another Nixon, Reagan, Chuck Norris, Bishop Desmond Tutu, or the Hello Kitty. What do you think?

FRETing about forster vs. fluorescence

March 2, 2008 at 7:19 pm | | everyday science, open thread, tutorial

fret-plot.jpgUntil recently, I thought FRET stood for “Förster resonance energy transfer”; I figured that “fluorescence resonance energy transfer” was a bastardization used by biologists. But a friend challenged me on that point, claiming that fluorescence was more specific and meaningful than Förster. I was all confused.

My reasoning was this: Förster’s equation for long-range dipole-dipole nonradiative energy transfer is a specific case of RET; other cases (e.g. Dexter electron exchange) have different mechanisms and follow different scaling laws. Moreover, because fluorescence is not necessary in the FRET mechanism, I thought it was misleading.

But how true is all that? Does Dexter ET count as RET? Is FRET the only way to transfer the potential to fluoresce from one molecule to another? My friend claimed that Dexter should not be called RET, because it is electron exchange instead of Coulombic.

So I refer to the experts.

Bernard Valeur, in Molecular Fluorescence, says:

The term resonance energy transfer (RET) is often used. In some papers, the acronym FRET is used, denoting fluorescence resonance energy transfer, but this express is incorrect because it is not the fluorescence that is transferred but the electronic energy of the donor. Therefore, it is recommended that either EET (excitation energy transfer or electronic energy transfer) or RET (resonance energy transfer) are used.

That doesn’t help solve the Förster vs. fluorescence dilemma, but instead adds another term (EET, gross) to throw into the mix. But I think this sorta supports my using “Förster” because “fluorescence” is misleading and too broad. Anyway, good ol’ Bernard goes on to carefully describe the different RET mechanisms and formulas.

So what does Joseph R. Lakowicz say? First, he calls it “fluorescence resonance energy transfer,” but then echoes Valeur that RET is a preferable term because “the process does not involve the appearance of a photon.” But Lakowicz also differentiates RET and Dexter electron exchange (because the latter is purely quantum-mechanical).

In Turro’s Modern Molecular Photochemistry, the energy-transfer chapter starts right in with a “Golden Rule” for the transitions between states, and demonstrates that the probability includes an exchange term and a Coulombic term. (Valeur’s book also includes a nice mathematical explanation of the two terms; it might even be in Lakowicz somewhere!)

So now I’m mostly reconvinced that FRET should be Förster resonance energy transfer, not fluorescence. That is, RET is the general term for nonradiative excitation-energy transfers, and FRET is a specific mechanism—the specific mechanism applied in practically all biophysical measurements using RET to study distances.

What do you think? Am I way off?

UPDATE: IUPAC says I’m right.

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