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?

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