Everyday Scientist

economic stimulus via science

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

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)

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

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!

“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

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

how to respond to referees

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

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

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.

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

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

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

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

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?

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:

Get it?

volcanoes are your solution to everything

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.