readcube and deepdyve update

June 6, 2013 at 7:48 am | | literature, science community, software

I just wanted to reiterate how great the ReadCube recommendations are. I imported all my PDFs and now check the recommendations every day. I often find great papers (and then later find them popping up in my RSS feeds).

Also, I wanted to let folks know that DeepDyve, the article rental site, is now allowing free 5-min rental of journal articles. Try it out!

google reader alternatives

April 3, 2013 at 8:12 am | | everyday science, literature, science community, software

Now that Google Reader is going the way of the dodo Google Gears, how am I going to keep up with the literature?!? I read RSS feeds of many journal table of contents, because it’s one of the best ways to keep up with all the articles out there (and see the awesome TOC art). So what am I to do?

There are many RSS readers out there (one of my favorites was Feeddler for iOS), but the real problem is syncing! Google servers took care of all the syncing when I read RSS feeds on my phone and then want to continue reading at home on my computer. The RSS readers out there are simply pretty faces on top of Google Reader’s guts.

But now those RSS programs are scrambling to build their own syncing databases. Feedly, one of the frontrunners to come out of the Google Reader retirement, claims that their project Normandy will take care of everything seamlessly. Reeder, another very popular reader, also claims that syncing will continue, probably using Feedbin. Feeddler also says they’re not going away, but with no details. After July 1, we’ll see how many of these programs actually work!

So what am I doing? I’ve tried Feedly and really like how pretty it is and easy it is to use. The real problem with Feedly is that its designed for beauty, not necessarily utility. For instance look how pretty it displays on my iPad:

feedly

But note that its hard to distinguish the journal from the authors and the abstract. And it doesn’t show the full TOC image. Feedly might be faster (you can swipe to move to the next articles), but you may not get as much full information in your brain and might miss articles that might actually interest you.

Here’s Reeder, which displays the title, journal, authors, and TOC art all differently, making it easy to quickly scan each  article:

reeder

 

And Feeddler:

feeddler

I love that Feeddler lets me put the navigation arrow on the bottom right or left, and that it displays a lot of information in nice formatting for each entry. That way, I can quickly flip through many articles and get the full information. The major problem is that it doesn’t have a Mac or PC version, so you’ll be stuck on your phone.

I think I’ll drop Feeddler and keep demoing Reedler and Feedly until July 1 rolls around.

slate

October 3, 2012 at 2:39 pm | | news, nobel, science and the public, science community

Paul and I were interviewed for a Slate.com article about Nobel Prize predictions. More details back at my original post on the 2012 Prize.

2012 nobel prize predictions

September 10, 2012 at 1:35 pm | | nobel, science community

It’s time again for my annual blog post Nobel Prize predictions. This year I’m limiting to the chemistry prizes. Of course there are many more individuals and discoveries that should be listed below and even more who deserve a Nobel Prize!

 

Single-Molecule Spectroscopy

Moerner, Orrit

Single-molecule imaging has matured to an important technique in biophysics. Just go to a Biophysical Society meeting and see all the talks and posters with “single molecule” in the title! Single-molecule techniques have begun to answer biological questions that would be obscured in traditional imaging. Moreover, super-resolution techniques such as PALM and STORM rely directly on detecting single molecules and the spectroscopic techniques developed in the late 80s and 90s. W.E. Moerner won the 2008 Wolf Prize in Chemistry.

 

Electrochemistry/Bioinorganic Electron Transfer

Bard, Gray

Al Bard won the 2008 Wolf Prize in Chemistry; Harry Gray won it in 2004.

 

Polymer Synthesis

Matyjaszewski, Frechet

Jean Frechet invented chemically-amplified photoresists and developed dendrimer synthesis. Kris Matyjaszewski won the 2011 Wolf Prize in Chemistry for ATRP polymerization. Of course, others were involved in both discoveries.

 

GPCR Structure

Kobilka, Stevens, and Palczewski

Biomolecule structures have won chemistry Nobels in the past, so I’m including G-protein coupled receptors here. A lot of buzz in the last couple years about GPCRs and Nobel. Good article here.

Update 10/10/12: Kobilka wins.

 

Chaperonins

Horwich, Hartl

Although these are biological molecules, they are still molecules. And many Chemistry Nobels have gone to bio-related discoveries in the last couple decades. Both won the Lasker Award in 2011.

 

Biomolecular Motors

Vale, Spudich, Sheetz

Another bio subject, but you really never know with the Chemistry prize. All three just won the Lasker Award this year.

 

(BTW, check out other predictions at ChemBark and The Curious Wavefunction and Thompson. And my prior predictions.)

(P.S. W.E. Moerner was my PhD advisor. Also, I worked in a collaboration with Kris Matyjaszewski when I was an undergrad.)

Update 9/11/12: I added chaperonins and biomolecular motors because I figure this year’s Chemistry Nobel might be more biological.

Update 10/3/12: Paul and I were interviewed for a Slate.com piece on Nobel Prize predictions. I like Paul’s section, especially about Djerassi. Anyway, here is what I said:

The line between chemistry and other fields (especially biology) is often blurred, and that’s a wonderful thing; but this fact sometimes results in a chemistry Nobel Prize being awarded for a decidedly biological discovery (like the 2009 prize for the structure of the ribosome). This may be exacerbated by the fact that the physiology or medicine prize tends to go to things directly related to health, and the chemistry prize often is used to cover the more basic biological science feats. Personally, I think it is a testament to the central position the field of chemistry holds in the Venn diagram of science.

My top prediction is for single-molecule spectroscopy. In 1989, W.E. Moerner at IBM (now at Stanford) was the first to use light (lasers) to perform measurements on single molecules. Before this, millions or trillions of molecules or more were measured together to detect an average signal. His amazingly difficult feat required ultrasensitive detection techniques, perfect samples, and temperatures just above absolute zero! A year later, Michel Orrit in France observed the fluorescent photons from a single molecule. With those early experiments, Moerner and others laid the experimental groundwork for imaging single molecules.

Single-molecule spectroscopy and imaging has become a subfield unto itself. I performed my Ph.D. research in the Moerner lab, and I know firsthand that the technique reveals events that would otherwise be hidden in averages of “bulk” measurements. Biophysics, the field of understanding how cells and biomolecules operate on a physical level, is particularly aided because rare events can have major effects in biology. (Think of a single cell mutating and then dividing into a tumor.) For example, Sunney Xie at the Pacific Northwest National Laboratory (now at Harvard) performed the early work on how individual enzymes experience multiple states, which otherwise would be averaged away in a bulk experiment. More recently, imaging single molecules has been instrumental in novel “super-resolution” techniques that reveal structures in cells at tenfold higher resolution than ever available before. Several companies (Pacific Biosciences, Helicos, Illumina, Life Technologies) have either released or are developing products that use single-molecule imaging to sequence individual strands of DNA. My prediction is bolstered by others along the same vein. In 2008, Moerner won the Wolf Prize in Chemistry, which is often considered a harbinger for the Nobel. More importantly, The Simpsons were betting on Moerner in 2010. Of course, that was Milhouse’s prediction, and maybe it’s more reasonable to go with Lisa.

My other prediction is for biomolecular motors (aka molecular motors). These are proteins in cells that move important cargo around, and on a more practical level, make muscles contract. Ron Vale (now at University of California, San Francisco) and Michael Sheetz (now at Columbia) discovered kinesin, a protein that walks along tiny tubes and pulls cargo to different parts of the cell. This is supremely important because it would take far too long (months in some cases) for diffusion alone to bring nutrients and signaling molecules to all parts of the cell. (Interestingly, kinesin was discovered from the neurons of squids because they are extraordinarily long cells!) Jim Spudich (at Stanford), Sheetz, Vale, and others have developed many important techniques for studying the actions of these tiny machines. Spudich shared this year’s Lasker Award, which many see portending a Nobel, with Vale and Sheetz.

It’s hard not to allow hope to creep into almost anything we humans do, and I have clearly failed to prevent my own desires from influencing my predictions: I would be thrilled to see either of the above discoveries—or any that I list on my blog—win a prize. But there are many, many deserving scientists who have discovered amazing things and helped millions of people. Unfortunately, only a handful of these amazing individuals will be awarded the ultimate recognition in science. So it goes.

PeerJ

June 8, 2012 at 9:39 am | | literature, science and the public, science community

This is an interesting idea. PeerJ sounds like it’s going to be an open access journal, with a cheap publication fee ($99 for a lifetime membership). I wonder if it will be selective?

I’m more excited about HHMI’s new journal eLife.

self-plagiarism and JACS

April 25, 2012 at 7:52 am | | literature, science community, scientific integrity

Hi all! I’m back! Well, not exactly: I won’t be posting nearly as much as I did a few years ago, but I do hope to start posting more than once a year. Sorry for my absence. There’s no real excuse except my laziness, a new postdoc position, commuting, and a new baby. I suppose those are good excuses, really. Also, I’m sorry to say, that I’ve been cheating on you, posting on another blog. We love each other, and I won’t stop, but I want to keep you Everyday Scientist readers in my live, too. I’m just not going to pay as much attention to you as I used to. You’re cool with that, right?


Anyway, I thought I’d comment on the recent blogstorm regarding Ronald Breslow’s apparently self-plagiarized JACS paper. Read the full stories here (1, 2, 3, etc.).

I feel bad for Breslow, because I like him and I respect his work and I think his paper in JACS is valuable. However, I think he should retract his paper. Sorry, but if some no-name had been caught completely copying and pasting his or her previously published paper(s) and submitting that to JACS as an ostensibly novel manuscript, that paper would be retracted when found out. If he had just copied the intro paragraph, I’d be more forgiving, but the entire document is copied (except, that is, the name of the journal)!

That said, it might be possible to save the JACS paper, but the editors would have to label the article as an Editorial or Perspective or something, and explicitly state that the article is reprinted from previous sources. I know that might not be fair, to give Breslow special treatment, but life isn’t fair. Famous scientists might get away with more than peons. And, honestly, Breslow’s paper remaining in JACS might be good for future humanity, because JACS archive will probably be more accessible than other sources. That way, we’ll be able to look up what to do when space dinosaurs visit us!

wtf?! acs fall meeting deadline is already passed?

March 25, 2011 at 3:41 pm | | conferences, news, science community

Before the Spring meeting has even started? This is not cool.

It’s almost impossible to actually find out, but the deadline for submitting an abstract to the ACS Fall meeting in Denver has already passed. This is how I tried to find out:

First, I went to the ACS website, and clicked on the “Meetings” tab. The Fall 2011 meeting isn’t even listed there (see screenshot on the left). OK, that’s silly.

Next, I searched “deadline” from the ACS homepage and clicked on the top link, “Events & Deadlines.” That brings me to the Events & Deadlines page. Where the Denver meeting doesn’t even have a link. The Anaheim meeting’s link is live, but you can’t click on the Denver meeting. OK, maybe that means the deadline is so far away that you don’t need to worry about it. Wrong. Apparently, the Events & Deadlines page is only for past deadlines. Why have a deadlines page only for past deadlines?!? Wouldn’t future deadlines be a bit more helpful? I guess, the “Events & Deadlines” page is more a shrine to the deadlines you’ve already missed, not intended to help you meet future deadlines.

OK, let’s try going directly to the Denver meeting homepage. Not a lot of info there. But it turns out that, if you click on the symposia link, you’ll find that many of the deadlines have already passed!!! And the Spring meeting hasn’t even started yet! (There’s also this strange PDF I found somewhere on the ACS website; it list different deadlines.)

That really, really sucks. I feel like, with all the stupid emails I get from ACS every day, I’d have seen this deadline coming. I suppose it’s all my own fault: I should have been paying attention. But I figured that the deadline for the next meeting wouldn’t be before the current meeting starts. And I do blame the ACS website: I’ve been looking at the “meetings” tab for info on Denver, but it isn’t even there yet.

My suggestion: Why doesn’t ACS have one deadline for all the divisions, have it after the current meeting is finished, and actually announce that deadline on their webpage?

I am annoyed.

why is author ID taking so long?

March 22, 2011 at 11:13 am | | literature, science community

DOI is magical. Why is it taking so long for the same thing to happen with authors? Arguably, having unique author IDs is more important and helpful than document identifiers. Yet it’s 2011 and there’s no standard way to ID an author.

Thompson has it’s ResearcherID, but it hasn’t really seem to have caught on. And it’s certainly not a open or universal standard, given it’s based off of ISI. ORCID seems to be (slowly) working on a solution to that. NIH claims that it’s working on a Pubmed Author ID project, but what’s the holdup? Hasn’t the problem of multiple authors with the same or similar name been recognized for years?

There must be some technical and economic hurdles that I don’t quite understand. DOI seemed to arrive on the scene pretty early after the internet started becoming mainstream. That was a few years ago.

chemistry should not focus on the origin of life

March 18, 2011 at 10:16 am | | science and the public, science community

Several chemists (e.g. here and here) have recently suggested that the origin of life (OOL) should be the next big question the field of chemistry could tackle.

Here’s why I disagree:

  • OOL research is not (directly) practical. Studying OOL won’t directly result in new technologies, products, or cures that the public can use. I prefer the Deutch and Whitesides approach. There are more pressing challenges that chemists can contribute to solving (cancer, disease, chemistry of biology, global warming, alternative energy sources, etc.). OOL comes across as an intellectual pursuit for armchair chemists.
  • OOL is politically, emotionally, and religiously charged. The last thing we need is idiots trying to cut chemistry funding because their faith says something different than the science. Studying OOL is the perfect way to offend a bunch of folks and make the field of chemistry a target of religious nuts. I don’t think we should guide our research on what religious nuts want, but why kick the beehive?
  • OOL is basically unanswerable. We might be able to test theories of the OOL, but we won’t be able to observe the true origins of life on this planet. Until we invent a time machine. That makes OOL research speculative and uninteresting to me. And even if we could find out, who really cares? Will that change our day-to-day life? OOL seems like more of a religious question than one of science.

Of course, some chemists should work on OOL. Just like some physicists should work on counting the number of alternate universes. But I don’t think chemistry as a whole should devote a major portion of its efforts to the “big questions” like OOL and what the universe was before the Big Bang. Chemistry is a practical science that answers questions about our everyday life. Let’s harness that power instead of trying to be as “cool” and big-question oriented as physics.

There. I hope I offended everyone who works on OOL. :)

P.S. Harry Gray and Jay Labringer have a recent editorial in Science stating that the Big Questions in chemistry are harder to see. They suggest understanding photosynthesis as one of those Questions.

what your laser pointer says about you

March 10, 2011 at 4:50 pm | | conferences, hardware, nerd, science community

Red: You either don’t really care if anyone can see what you’re pointing at or you’re cheap and you use the free pointer you got from a vendor at the expo. Of course, you could be one of those considerate folks who buy very bright red pointers, because you stubbornly like what red looks like even though human eyes are not sensitive to 633 nm. That’s fine.

Green: You want your audience to see what you’re pointing at. Unless you bought a 5+ mW laser (either because you’re showing off or because you didn’t realize how sensitive the human eye is to 532 and bought the brightest laser you could find). In that case, you’re blinding your audience. If you’re going to get a 5 mW laser, get it in red. That’s classy and visible!

Blue: You’re a bad-ass. You don’t care that blue lasers are more expensive and slightly harder to see, you want the audience to know that you’re a real laser jock. (Or maybe you’re worried about leaking 1064 nm from green laser pointers.)

Purple: You’re so bad-ass you’re crazy. You don’t care that the human eye can hardly detect and can’t focus on 405 nm. You want to show that you support Blu-ray.

Yellow: You think blue lasers are soooooo 2009.

Invisible: You have a UV or IR laser pointer? Maybe a tripled or undoubled Nd:YAG? You’re nuts.

Maser pointer: I want one.

interrupting student

March 1, 2011 at 1:11 pm | | science community

A (grad?) student walked into a seminar lecture, went up the the speaker in mid-sentence, and said, “Sorry to interrupt, but can I borrow some chalk?”

Everyone in the seminar room started chuckling at the kid. It was strange and awkward.

What a dumdum.

f1000

February 11, 2011 at 12:10 pm | | literature, science community, stupid technology, wild web

UPDATE2: OK, it turns out that the daily(ish) email isn’t too terrible. I now use it and I’m no longer upset that they don’t have an RSS feed. I correct myself and now fully endorse F1000!

Faculty of 1000 is extremely powerful with a lot of potential, but simultaneously completely worthless.

F1000 is like mini-peer-review post-publishing: it uses its “Faculty,” experts in various fields, to rate publications that those experts think are worth reading. It’s like … nay, it is … getting suggestions on what to read in the recent literature from a large group of experts. That is very cool. Of course, there are various databases like Cite-U-Like and Mendeley that are trying to mine their data to find interesting papers, but there’s something great about getting little mini-reviews from actual people.

OK, so why am I annoyed? F1000 doesn’t have an RSS feed! So I have to remember to go and check the website every week. Even if I happen to remember, there’s no way to mark which reviews I’ve already seen and the new ones. What is this, 2002?

UPDATE: rpg comments below with some good news: F1000 is actively trying to get RSS on the site. The comments also explain why it’s a challenge. I eagerly await RSS.

new chemistry dictionary for Word and OO.o

January 20, 2011 at 9:40 am | | science community, software

Check it out: azmanam has a new version of the chemistry dictionary for Word:

http://www.chemistry-blog.com/2011/01/19/chemistry-dictionary-for-word-processors-version-3-0/

Now you can eliminate all those red squiggly lines under half the words in your document.

Enjoy!

royce makes a funny

January 13, 2011 at 9:16 am | | literature, nerd, science community

Prof. Royce Murray’s recent editorial in AC is fun. I actually do find these type of sarcastic instructions for writing a paper helpful. To an extent. These devices are great reminders of the essentials to making a paper readable. I might find even more helpful a template of a paper that tells you what each paragraph and caption should say. Maybe I’ll make that someday for teaching purposes…

My fav line is: “Diagrams are worth a thousand words, so in the interest of writing a concise paper, omit all words that explain the diagram, including labels. Let the reader use his/her fertile imagination.”

Another anti-suggestion from Royce is: “It should be anathema to use any original phrasing or humor in your language, so as to adhere to the principle that scientific writing must be stiff and formal and without personality.” Which reminds me of this line from an old Chem. Rev. paper: “Evans boldly put 50 atm of ethylene (C2H4, trans-C2H2D2, or C2D4) in a cell with 25 atm of O2. The apparatus subsequently blew up, but luckily not before he had obtained the spectra shown in Figure 8.”

I think Royce should have added another rule: Make sure your TOC art is unreadable, phallic, or filled with math formulas (or even just “Maths“).

P.S. I see that CBC scooped me on Royce’s editorial!

CV of failures

December 10, 2010 at 12:34 pm | | postdoc life, science community, scientific integrity

Nature Jobs has encouraged folks to spread the word of their failures, as well as their successes. So I made a CV of my failures. I’m probably forgetting a lot of failures, but I’m not really motivated to spend a lot of time trying to remember. Anyone else want to air their dirty laundry?

rip paul barbara

November 10, 2010 at 9:25 am | | science community

Doug at Nanoscale Views brought my attention to the news that Paul Barbara died very recently. That is sad and surprising. He was a fun, exciting, and important scientist. RIP.

JOOT: the journal of one try

November 1, 2010 at 9:43 am | | literature, science community

Today my labmate suggested someone start the Journal of One Try. It could have two sections per issue: “worked” and “didn’t work.”

JOOT would be dedicated to publishing scientific experiments tried only once. It would be an excellent resource for young graduate students to see if they should try an experiment (i.e. if it’s been published in the “worked” section) or try a different route (if it’s been published in “didn’t work”).

This is different than the Journal of Irreproducible Results: The results in JOOT would be reproducible … probably … just no one tried. Because it worked (or didn’t) the first time. Also, it wouldn’t be silly or funny science, simply experiments no one had the patience to try again. And this is different from the Journal of Negative Results, because many of the results would be positive. Well, once.

Maybe I’ll start that journal someday…

nature highlight

October 28, 2010 at 7:41 am | | cool results, literature, science community, single molecules

My colleague’s JACS paper was highlighted in Nature. I’m especially excited about that, because I’m a coauthor. ;)

The strange thing is that, despite our suggestions otherwise, the Nature folks chose a not-the-most-interesting figure from the paper. Of course, I’m more than happy that they showed any of our awesome figures! But, instead of showing one of the super-resolution images that Hsiao-lu made, the highlight shows a proof-of-labeling image, which is diffraction-limited. That said, they did select one of the live-cell images. I suppose it could be worse: they could have picked one of the controls. Or not displayed a figure at all.

Thanks Nature. I don’t mean to look a gift horse in the mouth.

Well, I’ll highlight our paper here. And choose my favorite figure (it’s protein localization in a little-bity bacteria):

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?

caveat grumptor

October 13, 2010 at 8:05 am | | blogs, science and the public, science community

Royce Murray doesn’t like blogs.

No that’s an oversimplification of his editorial. Actually, his worry is that science blogs are more fun and easier to read than real science journalism (which, by the way, is hard to find); meanwhile, bloggers have no required credentials, no accountability, and might just be lying to everyone.

Damn straight.

UPDATE: In case it isn’t clear, Royce Murray is one of my favorite chemists and teachers. UNC is my Alma Mater, and I really appreciated his class. While most bloggers are pretty unhappy with Royce’s editorial, I wasn’t offended. I basically agree that neither the public nor scientists should be getting information from blogs without a grain of salt. Especially this blog. I’m sarcastic 83% of the time.

crick’s lost letters

October 1, 2010 at 7:05 am | | history, news, science community

Some revealing letters of Francis Crick have been found—mostly to Maurice Wilkins—and they discuss Rosalind Franklin. Here are some of the excerpts that I found interesting. For instance, this letter from Wilkins to Watson and Crick after they proposed the double-helix model:

My dear Francis,

I gather you have got the coordinates of your model or some worked out. Do you think we could have a copy of what you have?

The crystalline data is clearing up nicely. To think that Rosie had all the 3D data for 9 months & wouldn’t fit a helix to it and there was I taking her word for it that the data was anti-helical. Christ.

We have redone a lot of the 3D more accurately on mouse & will need all the extra accuracy for dealing with some of the finer points.

Regards & to Odile too.

Yours

M

P.S. I think I have a flat.

But “Rosie” had been focusing on the A structure of DNA, which generated clearer crystal diffraction pattern images. Unfortunately for her, crystalline DNA-A wasn’t helical. Crick agreed when he eventually saw her data:

This is the first time I have had an opportunity for a detailed study of the picture of Structure A, and I must say I am glad I didn’t see it earlier, as it would have worried me considerably.

All in all, it sounds like Franklin was generally unfriendly to her colleagues (and competitors). Wilkins wrote to Crick of Franlkin’s leaving King’s College:

I hope the smoke of witchcraft will soon be getting out of our eyes.

It sounds like her colleagues didn’t like her too much. But there was friction from the beginning: Wilkins thought that Franklin was going to work for him … or at least they would work together on DNA … and Franklin had been told that she would work independently. What a mess.

I feel bad for Franklin having to deal with these sexist jerks. Watson and Crick were probably the most annoying, because they didn’t do any experiments; instead, they’d listen to Franklin (and others) present their data, then run off and make a model. Annoying. Intellectual thievery almost. (And Watson and Crick admit as much, referring to it as “burglary” in one of their letters.)

But on the other hand, it seems Franklin made some serious mistakes interpreting her data and was quite abrasive. No angels here. No devils (or witches?) either.

I suspect that if everyone had worked together and been friendly, Watson and Crick would have proposed the correct structure much earlier. Not only that, but I think Franklin would have been given more credit by the boys. But that’s just my speculation. I just know that I’d prefer to collaborate with folks than fight with them.

NRC finally releases updated school rankings

September 28, 2010 at 3:12 pm | | news, science and the public, science community

Phew. That was a long wait. Since 1995.

But the wait wasn’t really worth it. NRC released basically a gimungous table of data, and didn’t actually give departments rankings. I don’t have time to wade through all this data. Someone needs to tell me that my department(s) are better than Harvard.

To make things worse, their spreadsheet doesn’t work on MS Excel 2008 on Mac (only on 2004). Maybe I’ll update sometime if I can wade through the data. In the meantime, see if your school has posted its own analysis. (Berkeley has. It looks like Stanford is still in the process of manipulating the data to make themselves look awesome.)

UPDATE:

Here are the top chemistry programs (ranked on research activity):

And programs containing the word “biophysic”:

So there. You can go make your own tables. I find this very confusing.

UPDATE: Not surprisingly, there are some serious errors being found in the piles and piles of numbers being released by the NRC ranking. And come to think of it, since when does Stanford chemistry have 50 faculty members??? Something is very wrong…

NRC should just list schools according to the US News and World Report rankings and keep their data hidden. jk.

the simpsons have their own nobel predictions

September 27, 2010 at 3:19 pm | | nerd, news, nobel, science and the public, science community

This was on The Simpsons last night:

(the screenshot is from 1 min 22 sec on Hulu)

I may update my predictions to reflect the venerated opinions of cartoon writers.

By the way, seeing my PhD advisor and a member of my dissertation committee listed on The Simpsons feels really strange.

(My/our real predictions are here.)

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.

TOC ROFL

August 23, 2010 at 8:50 am | | crazy figure contest, literature, nerd, science community, wild web

My (very nerdy) friends started a internetted-web-blog to celebrate/mock hilarious/terrible table-of-contents images: TOC ROFL. (In reference to NCBI ROFL.) I might even submit my own once in a while; you can too!

economic stimulus via science

August 16, 2010 at 9:44 am | | news, political science, science and the public, science community

Senators McCain and Coburn (who is a physician!) released a political report complaining about stupid stimulus projects. Now, it’s not surprising that Republicans are calling for cutting science funding and mocking silly-sounding science, so of course there are several science programs funded by stimulus money that this report calls out. Here are a couple:

“A Better Way to Freeze Rat DNA”

[S]cientists at the University of Missouri received stimulus funds ““to develop freezing protocols for epididymal rat sperm which would allow reconstitution of genetics by using standard artificial insemination and in-vitro fertilization methods.”” The scientists note that“ “[o]ver the last few years, our laboratory has generated ample amount of data related with optimal sperm handling.”

“Reducing Menopausal Hot Flashes Through Yoga”

“Weather Predictions for Other Planets”

“In a time when jobs are hard to come by, several high school and college students have gotten federal funding to inspire their scientific curiosity.”

OK OK, I understand that some of these seem silly, but when Senators start mocking scientific programs without acknowledging the broader context, those Senators come across as ignorant and foolish. The rat DNA one is especially annoying: Hehe, it says sperm! What, do they get middle-schoolers to write this stuff?

We could make any scientific project sounds silly if we wanted: Scientists try to send light down a tiny glass tube; federal government spending billions to develop satellites that will see where your phone is; some nut is trying to make a horseless carriage.

The point of gov’t stimulus is to get money flowing and jumpstart the economy. Most economists acknowledge that Federal spending has a significant multiplier effect, so spending money on construction projects, scientific research, and infrastructure isn’t really that silly. I can understand how some would question how studying rat DNA could make any money flow back into the economy, but those people would be forgetting about scientific-supply companies like Nalgene (originally of Rochester NY), ThermoFisher (of Waltham MA), Invitrogen (of Carlsbad CA), Sigma-Aldrich (St. Louis MO), etc. I’m sure those and many other companies that employ Americans are very happy about stimulus money going to scientific research!

Still, I do agree that these spending projects should not be beyond reproach. I’m not convinced that science funding is always the most efficient approach to stimulating a national economy in the short run. We should check up on our stimulus funding and try to measure how well each project is benefitting American taxpayers. But what McCain and Coburn have done is lazy—and ignorant. Instead of mocking science because it involves sperm or yoga (or even both), step up and take a mature approach to critiquing our spending policies!

(via Nature)

academic genealogy

July 13, 2010 at 11:02 am | | history, science community

Jeremy over at Chemistryblog posted a few sites with info on academic lineage of many chemists. That inspired me to finish researching my academic genealogy. Kallie’s page at UT’s site was a nice confirmation of the lineage I had independently found. But I actually found links further back (through Rowland to Helmholtz, and eventually back to Leibniz’s dad); I’m not exactly sure why the UT page stops at Mendenhall.

I also explored my lineages from my undergrad and postdoc advisors. Interestingly, those two lines meet up in the mid-1800s (Liebig).

Anyway, below is the entire tree.

(I know this is a little self-indulgent. But whatever.)

Sam’s Academic Genealogy (via PhD advisor)

Samuel Joseph Lord
Postdoctoral research 2010- (under Jay T. Groves)
PhD Stanford 2010 (under W.E. Moerner)
BS University of North Carolina at Chapel Hill 2004 (under Sergei S. Sheiko)

William Esco Moerner (Stanford)
PhD Cornell 1982 (under A.J. Sievers)
BS Washington University 1975

Albert John Sievers III (Cornell)
PhD Berkeley 1962 (under Michael Tinkham)
BA Berkeley 1958

Michael Tinkham (Berkeley, later Harvard)
PhD MIT 1954 (under M. W. P. Strandberg)
BA Ripon College

Malcom Woodrow Pershing Strandberg (MIT)
PhD MIT 1948 (under A.G. Hill)
BS Harvard 1941

Albert Gordon Hill (MIT)
PhD Rochester 1937 (under Lee Alvin DuBridge)

Lee Alvin DuBridge (Rochester)
PhD University of Wisconsin–Madison 1926 (under Charles Elwood Mendenhall)

Charles Elwood Mendenhall (Wisconsin)
PhD Johns Hopkins 1898 (under Henry Rowland)

Henry Augustus Rowland (Johns Hopkins)
Civil Engineering degree Rensselaer Polytechnic Institute 1870
later studied under Helmholtz in Berlin

Hermann von Helmholtz (Berlin)
PhD Royal Friedrich-Wilhelm Institute (under Johannes Peter Müller)

Johannes Peter Müller
Bonn University (under Philipp Franz von Walther & Karl Rudolphi)

Karl Rudolphi … Friedrich Leibniz (1597-1652) [Gottfried Wilhelm Leibniz’s father]
Philipp Franz von Walther … Gerard van Swieten (1700-1772)

Sam’s Academic Genealogy (via postdoc advisor)

Samuel Joseph Lord
Postdoctoral research Berkeley 2010- (under Jay T. Groves)
PhD Stanford 2010 (under W.E. Moerner)
BS University of North Carolina at Chapel Hill 2004 (under Sergei S. Sheiko)

Jay T. Groves (Berkeley)
PhD Stanford 1998 (under Steve Boxer)
BS Tufts 1992

Steven G. Boxer (Stanford)
PhD Chicago 1976 (under Gerhard L. Closs)
BS Tufts 1969

Gerhard L. Closs
PhD Tübingen 1955 (under Georg Friedrich Karl Wittig)

Georg Friedrich Karl Wittig
PhD Marburg 1923 (under Karl Friedrich von Auwers)

Karl Friedrich von Auwers
Berlin, 1885

August W. von Hofmann
Giessen, 1841

Justus von Liebig
Erlangen, 1822

. . .

Niccolò Leoniceno (1428-1524)

Sam’s Academic Genealogy (via undergraduate advisor)

Samuel Joseph Lord
Postdoctoral research Berkeley 2010- (under Jay T. Groves)
PhD Stanford 2010 (under W.E. Moerner)
BS University of North Carolina at Chapel Hill 2004 (under Sergei S. Sheiko)

Sergei S. Sheiko (UNC)
Habilitation University of Ulm 2000 (under Martin Möller)
PhD Institute of Chemical Physics of the Russian Academy of Sciences 1990
MS Moscow Physico-Technical Institute 1986

Martin Möller (Ulm)
Postdoctoral research University of Massachusetts (under Robert W. Lenz)
PhD University of Freiburg 1981 (under Hans-Joachim Cantow)

Hans-Joachim Cantow (Freiburg)
PhD University of Mainz 1950 (under G.V. Schulz)

Gunter Victor Schulz (Mainz)
PhD Kaiser Wilhelm Institute of Physical Chemistry and Electrochemistry 1932 (under Herbert Freundlich)

Herbert Freundlich (Kaiser Wilhelm Institute)
PhD University Leipzig 1903 (under Wilhelm Ostwald)

Wilhelm Ostwald (Leipzig)
PhD 1878 Dorpat University (under Carl Schmidt)

Carl Schmidt (Dorpat)
PhD University of Giessen 1844 (under Justus von Liebig)

Justus von Liebig
Erlangen, 1822

. . .

Niccolò Leoniceno (1428-1524)

seminal (hehe)

May 17, 2010 at 3:52 pm | | science community

This has got be be a joke, right? The letter to the editor suggests that the term seminal is “sexist” because it refers to semen (figuratively meaning full of potential).

No way this is serious.

P.S. The letter writer describes the word as “distasteful.” Hehe.

naturally depressed

May 14, 2010 at 10:36 am | | everyday science, grad life, science community

The documentary video “Naturally Obsessed” follows some graduate students at Columbia through their trials and tribulations in science. Personally, I found parts quite depressing. However, it is an interesting video and I wish they would film other labs to round out the picture.

Or watch here: http://www.thirteen.org/naturally-obsessed/

Here are some of my thoughts (spoiler alert!):

The nature of their research, protein crystallization, is especially depressing: because the results are all-or-nothing, the students work very hard and may see zero reward. In other bench sciences, this can also be true. However, it is often the case that there are many small discoveries and accomplishments along the way. Protein crystallization work, on the other hand, means that if you find the structure, you publish; if the protein doesn’t crystallize well enough to get a structure, you don’t publish. Ouch.

The person I felt the worst for was the blond kid, Kil. He was so positive at the beginning of the film—almost to a fault. Near the middle, he begins complaining about the strains being a graduate student has on his life and relationship with his fianceé. At the end, we learn that Kil and his fianceé broke up (at least partially because of grad school), and he has no interest in academic science. The viewer is at least relieved to discover that Kil gets a good job after graduation!

The ending of the film reminded me of the end of The Graduate: it was bitter, but maybe only intended it to be sweet? Rob, earns his PhD, has a baby, is happy, and becomes a postdoc. But I feel bad for him trying to raise a child on a postdoc’s salary (his wife is also a graduate student). Not to mention the fact that he is already over 30 years old and has several years of a postdoc ahead of him. I’m just not sure it’s the happy ending the film-makers intended. On the other hand, Rob seems really motivated and wants to become a professor, so maybe he’s on his way!

My overall opinion is that the film is interesting, and fairly accurate. However, I think a couple more episodes could really strengthen the documentary. This episodes follows a graduate student as he “succeeds” by toiling away for years, getting a chance success, and then publishing in Science. Instead, I would like to see the day-to-day, week-to-week, year-to-year successes of graduate work: positive interactions and collaborations with fellow students and postdocs, brainstorming in meetings, little “ah-ha!” moments while sitting over a sample, and publishing in J. Phys. Chem. B. In the end, I think this little documentary does a good job of portraying the ups and downs of grad school. However, I think another few episodes in different types of labs would reveal a more realistic overview. Moreover, I think it would be healthy to show students accomplishing smaller steps along the way to their PhD or best paper, instead of the view that students must toil away for 6 years with no rewards until the end.

(via BiteSizeBio)

go get your own alligator!

January 15, 2010 at 1:16 pm | | literature, science community

“They cannot argue with this data,” she said. “I have three lines of evidence. If they don’t believe it, they need to get an alligator and make their own measurements.”

(via Randy and Eric.)

check out this cool link

December 19, 2009 at 11:29 pm | | nerd, science community, wild web

Check it out here. I promise you won’t be rickroll’d.

how to respond to referees

December 15, 2009 at 10:42 am | | how-to, literature, science community

Now that I’ve listed some pointers on how to write a referee report, I want to discuss how to respond to reviews of your own manuscript. Again, I’m still a novice at this, so I’d love input from the audience!

  1. Try not to be offended. It’s hard not to, but try not to hate the reviewer when they criticize your manuscript. Usually, I get one referee who says the paper is great and another who says it’s crap. It’s hard not to want to hurt that latter type. Bad. But they might be partially right, so correct the issues they find that have merit, and defend your original manuscript against the foolish criticisms.
  2. Organize your response. I like to make tables with one row being the referee’s comment and the other being my response, with each comment on a separate row. Any way you do it, respond to each referee point-by-point. In your cover letter to the editor, summarize the major requests by the referees and the main changes in the revised manuscript.
  3. Stand your ground when you’re right. Don’t make changes that make your manuscript worse. If the referee is wrong about something, say so (gently). Your goal is the editor seeing that you are right. If you’re too rude in your response to an incorrect referee, the editor may think you protest too much and become suspicious.
  4. …but don’t pull an Einstein. Sometimes referees find a problem with your science or reasoning that, no matter how much it pains you, is worth seriously considering. Referees can make your papers much better, so it is important to listen to them.

Number 1 is the one I have the most problems with. I don’t understand why some referees have to be so unreasonable and wrong when writing their reports. I usually draft very snarky responses, only to replace them with polite disagreement before sending my revisions to the editor. And complain to friends a lot. Not sure if that helps me or keeps me angry.

Others?

how to referee a paper

December 11, 2009 at 8:55 am | | how-to, literature, science community

Here are some pointers about how to referee a scientific journal article. I’ve picked these up both from having refereed papers myself (with my PIs) and more importantly from reading referee reports (good and bad) of my own manuscripts.

  1. Be timely. Editors often proceed with the publication process after getting back only two (or sometimes one) review. If yours is the third to come back, it may be too late. I’ve learned the hard way that, if you take too long to submit your review, your hard work might be all for naught. Of course, it is totally inappropriate to sit on a review purposefully to give yourself time to scoop a competitor.
  2. Be positive. Authors will be more willing to make the changes you suggest if you “sandwich” the constructive criticism between positive comments about the manuscript. It’s easy as a reviewer to only see the bad and forget that the science and writing took a lot of effort from the authors.
  3. Organize your criticisms. At minimum, split the changes you’re asking for into essential and minor. For instance, don’t bury a serious problem you found among a bunch of nit-picky points. First list the essential changes that need to be made in order to make the manuscript publishable, then you may list typos and minor points if you wish. This way, the authors (and editors) will immediately understand your assessment of the paper, and not get offended by what feels like an endless list of complaints. Remember: you’re a referee of the science, not an editor. UPDATE: Also, as MRW says in the comments, write your report so it can be responded to point-by-point.
  4. Do unto others… Remember what you appreciate in a review of your own manuscripts (and what drove you mad), and go from there. The authors are not your enemies—even though some of them torture you with their unclear writing and lackluster science—treat them like you would want to be treated.
  5. But be a good filter. Don’t let fatally bad science into the literature.

The best referees are the ones that help the authors make the paper better. Try to be that kind of referee. The worst are the ones that don’t read the manuscript closely enough, then unfairly criticize it. The just plain unhelpful are the ones who just say “publish as is.”

I’m sure I have a lot more to learn, but these are some things I’ve picked up so far. Others?

(Later, I’ll talk about how to respond to referee reports of your own manuscripts.)

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!

alivisatos

November 19, 2009 at 1:26 pm | | news, science community

Not a surprising move, but nice that it’s finalized now. Paul Alivisatos is now the director of the Lawrence Berkeley National Lab. He’s taking Steve Chu’s old job. Good luck, Paul.

that’s one way to get your message approved

November 17, 2009 at 1:22 pm | | science community, wild web

I received this email forward, BCC’d mistakenly (I presume) to ACS’s PHYS email list:

HI Anne,

I agree with all of you that we don’t want to do this direct e-mail stuff!

Cheers, Martin

On Tue, Nov 17, 2009 at 4:17 AM, Anne wrote:
> > Martin, Martin, Sharon and Mark,
> >
> > Please see the message from ACS – my inclination is negative regarding the
> > mailing, but don’t have a problem promoting the conf on the website and even
> > mentioning that conf are posted there in my next mailing.
> >
> > Before I reply, I’d be interested in your thoughts.
> > Thanks
> >
> > ANne
> > —– Original Message —–
> > From: Richard
> > To:
> > Cc: Division
> > Sent: Tuesday, November 17, 2009 7:14 AM
> > Subject: FW: Official RSC Request to Engage PHYS Division
> >
> > Laurie and Ann,
> >
> >
> >
> > I am forwarding you a request from the Royal Society of Chemistry to use the
> > PHYS mailing list to promote a new conference, Challenges in Physical
> > Chemistry and Nanoscience (ISACS2), July 13 – 16, 2010, Budapest, Hungary.
> >
> >
> >
> > Please read through the request below from Valerie with the RSC.
> >
> >
> >
> > If approved, I recommend sending the RSC the list as an Excel file with just
> > the email addresses and PHYS member names, not the entire eRoster list.
> >
> >
> >
> > Let me know if you need any additional information.
> >
> >
> >
> > Thanks,
> >
> >
> >
> > Richard

LOL.

red laser pointers

October 13, 2009 at 3:42 pm | | conferences, nerd, science community

Open letter to presenters at Optical Society of America Meeting:

You are presenting at an optics meeting. It is unacceptable to use a cheap keychain red laser pointer. As a member of OSA, with a tag on your shirt that reads “LaserFest,” red laser pointers are embarrassing. (I suppose very bright red laser pointers are OK.)

Green pointers are best. Human eyes are highly sensitive in the green. At 630 nm, eyes are not nearly as sensitive.

Given that you’re at a lasers/optics conference, it is even cool to use a blue pointer—even though it is inefficient—just to demonstrate that you’re a stud.

-Sam

ribosomes are cool

October 7, 2009 at 1:19 pm | | science and the public, science community

There’s a lot of complaining on the chem blogosphere and in chemistry departments around the world about this year’s Nobel Prize in Chemistry. What? Going to biologist again!?!?

Personally, I don’t find this year’s chemistry prize at all offensive. We chemists love to tout chemistry as the nexus of all fields of science, from physics to biology. So we shouldn’t be too upset when researchers outside our personal subfield wins a chemistry prize.

Moreover, the chemistry Prize has always been awarded a range of experiments. (Think nuclear physics in the early part of the 20th century.) Biology is today a maturing field with amazing breakthroughs daily, so it’s not surprising that biological chemistry wins prizes.

And ribosomes are very cool.

what do CCDs and optical fibers have in common?

October 6, 2009 at 8:57 am | | history, science and the public, science community

Answer: they’re both super important. (And they both won this year’s Nobel Prize in Physics.)

Upon hearing this prize announcement, just about everyone I know thought, Yup, those are important. Some people also thought, Why are they sharing the same prize? And at least one person thought, How did they shoot live video before the CCD?

They used basically a reverse television, the pickup tube:

pickup-tube-wiki

Get it?

volcanoes are your solution to everything

September 30, 2009 at 5:04 pm | | science community, seminars, stupid technology

After John Deutch‘s talk this afternoon, one student asked three (!) questions. His third one was: “Why don’t we just take nuclear waste, seal it in some container, then put it at the bottom of the Mariana trench. That way, it would get sucked up into the center of the Earth and not be a problem.”

I’m serious. That was his question … his third question.

Deutch’s response was: “It’s probably not best if each person comes up with their own technological solutions to the energy problems.”

There needs to be a one-question-per-first-year rule.

AC now has letters

September 22, 2009 at 9:13 am | | literature, science community

Anal. Chem. has begun accepting shorter publications as letters. I think that’s probably a good idea: another option when publishing a short, timely, interesting result.

2009 EDSEL-Nobels

September 16, 2009 at 9:27 am | | EDSELs, science community

edsel_nobelTime for the 2009 EDSEL-Nobels. Just to clarify, these are not predictions for the real Nobel. Instead, they are relatively arbitrary awards given to great scientists.

This year’s criteria include: how many papers/books I’ve read from the scientists, whether I’ve seen them give a talk, and how they’ve contributed to a field I am interested in.

The 2009 EDSEL-Nobel Prizes go to Nicholas J. Turro (Columbia) and Josef Michl (Colorado) for their research and literary contributions to photochemistry.

I have used both their books (here and here) extensively in my own research. I had the pleasure of seeing an interesting talk by Turro last year and look forward to seeing Michl in a couple weeks at Stanford’s Johnson Symposium.

man bites dog

August 14, 2009 at 9:47 am | | grad life, news, science community, scientific integrity

Former Stanford graduate student Christopher Sclimenti is suing his former PI, Prof Michele Calos, for patent infringement and plagiarism. See stories here, here, and here. The complaint can be read here.

The summary is as follows:

  • Student was originally on a patent application.
  • At some point, Stanford and/or prof removed student’s name from application, which becomes this patent. Prof Calos is the only inventor listed on the patent.
  • Prof filed a second patent, which is a continuation of the first. Prof Calos is still the only inventor listed.
  • Prof filed two other applications (here and here), still the sole inventor listed, with significant portions copied from the student’s dissertation. (Stanford Daily found about 20 paragraphs in one application that were essentially identical to paragraphs in his dissertation!)

All parties agreed to an Alternative Dispute Resolution (ADR) with a neutral party. The ADR panel concluded that the student was a co-inventor and should have been included in the patent. As a result, Stanford agreed to add him to the issued patent (but I see no evidence that that has occurred yet).

CalosAccording to Stanford’s OTL page, inventorship is different than what most scientists would consider authorship. For instance, “A person who contributed only labor and/or the supervision of routine techniques, but who did not contribute to the idea—the concept of one of the embodiments of the claimed invention—is not considered an inventor.” For the prof and the University to claim that the student was not an inventor, they implied that he was only a technician and did not contribute to conceiving any of the claims in the patent. That’s possible, but the ADR panel disagreed. It seems pretty straightforward that the student should have been on at least the first patent!

Why would Prof Calos and Stanford University fight so hard against their former student, who clearly contributed enough to the invention to appear on the original patent application? Is splitting the royalties from one patent with one extra person, a student who contributed to the work, so terribly painful? Stanford’s policy is to divide the royalties (after paying for the patenting and lawyer fees) 1/3 to the inventors, 1/3 to the department, and 1/3 to the school. So the prof loses half of her royalties by re-including her former student as an inventor, but the University loses nothing.

Is the recent patent application plagiarized from the student’s dissertation? Only if the dissertation was not first self-plagiarized from an earlier paper. Who knows. Regarding the plagiarism complaint, Stanford had this to say:

“I think we’ve really done our part at this point,” Dunkley said. “The inventorship has been corrected. He has been made whole for any amount that he would have received if he had been an inventor from the beginning. So from the University’s perspective, all necessary action has been taken to rectify any differences on the inventorship issue.” (source: Stanford Daily)

Sclimenti

That’s not really very satisfying. What if the roles were reversed and a student copied significant portions of his PI’s earlier grant proposal into his dissertation without the PI’s permission? Or submitted a paper without the PI’s knowledge? That student would probably be kicked out of Stanford at a minimum. The least the University could do is investigate this case and if Prof Calos has a history of taking credit for other peoples’ work. Maybe Prof Calos is innocent and the student is trying to steal credit, but it would be nice if the University would check into it.

All in all, the entire situation is not clear-cut. I suspect that the whole incident is the result of large egos, hurt feelings, and greed—from all parties! This is why it is very important to not burn bridges and to try to empathize with your PI or your student. I suspect this conflict could have been resolved early on if all parties had been more understanding and willing to listen and compromise.

Bottom line though, I find it unfortunate that the University would fight one of its own students.

P.S. Guess what Sclimenti is doing now?

A battle brewing over Napoleon Dynamite

August 8, 2009 at 11:08 am | | literature, science community

I was scanning NCBI ROFL the other day and I came across this little gem of a comment:

Napoleon Dynamite Has Asperger’s? Gosh, It’s Called Cultural Competence, You Freakin’ Idiots

Acad Psychiatry 31:248, May-June 2007
doi: 10.1176/appi.ap.31.3.248

This guy is angry. But wait, there’s more! Here is another comment on the offending paper:

Ligers Lived
Acad Psychiatry 31:247, May-June 2007
doi: 10.1176/appi.ap.31.3.247

So what’s all the commotion all about? Here’s the offending paper on PubMed, but I haven’t been able to download the original yet.

Sounds like a hoot.

academic grandfather

June 18, 2009 at 2:45 pm | | grad life, science community

I met my academic grandfather recently: A.J. Sievers was my PhD advisor’s—W.E. Moerner’s—PhD advisor at Cornell. He is a really friendly guy. Also, he told me interesting stories of when he worked for the Varian brothers and beat Hewlett (or was it Packard?) in a ping-pong match!

missing link?

June 16, 2009 at 7:20 am | | science and the public, science community, scientific integrity

I read this interesting editorial in Science about the media hyping of a recent archeological find. Just look at Jørn Hurum, the team leader:

hurum

The report of finding the intact skeleton of a monkey-thing was reported in PLOS One, but not before the media hype started. There is a TV documentary of the find and the research on the fossil, and the group is touting the find as the next Rosetta Stone and the “missing link” between apes and humans. For instance, here are a few quotes from the team that reported the find:

“This specimen is like finding the lost ark for archaeologists. It is the scientific equivalent of the Holy Grail.” –Jørn Hurum

“[It is] like the eighth wonder of the world.” –Jens Franzen

What douchebags. This kind of bullshit is seriously likely to undermine the credibility of science in the public eye. Going around claiming that you’ve found the missing link—not to fellow scientist but to the public at large—is very dangerous: when it turns out that your monkey-thing is not a little human, the incident will only add gasoline to the anti-evolution fire. If it really is the missing link, let your fellow paleontologists make those statements.

I find this type of grandstanding by the authors scary, and very reminiscent of the Fleischmann and Pons cold fusion debacle. In fact, I recently watched a 60 Minutes episode about cold fusion, in which Fleischmann stated that his only regrets were naming the effect he saw “fusion” and holding a press conference. In other words, if he and Pons had not overhyped their results directly to the media, then maybe they wouldn’t have been run out of science when their science turned out to have fatal flaws.

Hurum claims that he’s only hyping in this fashion in order to help get children intersted in science. But clearly, his base motivation is to make himself rich and famous. Yes, we should get children excited about real science, but not at the expense of scientific integrity.

Or maybe this little monkey-thing will end up being seen as a great scientific discovery for generations. But I doubt it.

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?

allen j. bard

June 5, 2009 at 8:21 am | | science community

bardI have been hosting the famous electrochemist Al Bard for a colloquium at our department. This is the first time I’ve met him, and it’s been a real pleasure. He is a super nice guy and really down-to-earth. I ran him around campus all day meeting with student groups, and he never complained. And at dinner with students, he was very entertaining and had great perspective on the science world, especially publishing (he was the Editor-in-Chief of JACS for years, afterall). Truly one of the nicest famous chemists I’ve ever met.

His talk was excellent: he explained his system and technique very clearly, and the results were interesting. Perfect combination! If you ever get a chance to meet Bard or go to one of his talks, I highly recommend it.

citeulike and mendeley collaborate

June 4, 2009 at 8:34 am | | literature, science community, wild web

It has begun: Mendeley is integrating CiteULike libraries.

CiteULike is an online program for extracting metadata (e.g. authors, titles, etc.) from webpages of journal articles, then storing and organizing that data. I use it to organize the citations and DOIs of all the articles I find interesting.

Mendeley is an online database for storing and sharing PDFs of papers (plus a desktop application). I still don’t find Mendeley to be very helpful yet: still too buggy, too slow, and missing some vital features (e.g. effective metadata extraction, searching for metadata, finding duplicates). But there’s a lot of potential: they’re still in beta!

I use Papers for organizing and reading PDFs, but it only exists on the Mac, and doesn’t have a simple way to share libraries of PDFs across computers. There are probably some serious copyright issues with PDF sharing, and it will be interesting to see how Mendeley and Papers adapts.

UPDATE: Mendeley is quickly getting better. Their metadata extraction is more accurate, there is a PDF viewer, and linking to CUL means tagging is simple. Duplicate finding and merging is still needed, but the software is much better than when I first wrote this. Although I’m still using Papers somewhat because of inertia, I might suggest a newcomer try Mendeley right-off-the-bat.

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.)

Next Page >

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