you’re doing it wrong

August 9, 2010 at 10:15 am | | everyday science, stupid technology

Fluctuations in a “cold” room I walked past.

That’s not good.

how do you read PDFs?

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

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

[poll id=”3″]

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

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

Other options?

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:

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)

avoid mistakes in lab

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

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

1. Use a checklist.

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

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

4. Repetitive pipetting: be consistant and use bookmarks.

5. Don’t multitask too much.

6. Get set up before you start.

7. Prepare in bulk.

8. Don’t spend so long in the lab.

9. Get enough sleep.

10. Take responsibility.

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

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

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

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

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

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


even the computer gods don’t want me to work on my thesis

November 11, 2009 at 2:14 pm | | everyday science, grad life, great finds

The driver to my video card exploded yesterday, right in the middle of working on my thesis. Easy to fix (thanks to Brian), but it took a major chunk of my thesis-writing time.

Then, on top of that, SNL was hosted by the greatest musical artist since that hairy guy who banged two rocks together. I had to watch that.

OK, back to the thesis…

hey, that was my idea

August 3, 2009 at 8:14 am | | everyday science, literature

Good thing I didn’t pursue an idea I had a month ago, because I would have been scooped very quickly.

The basic idea is to write 3D microfluidic channels in situ by photoconverting a hydrophobic gel to a hydrophilic surface (or vice versa). In the regions that are photoconverted, water should be able to enter and flow.

And that’s what they did in this JACS paper:


Pretty cool. Given that this is on silica particles instead of a gel, it may not be suitable for the applications I had in mind. Still, I like it.


July 2, 2009 at 3:33 pm | | everyday science

I just had a manuscript rejected from Angew. Chem. I think I’m going to rework it into a full article in J. Phys. Chem. B. I’ll look on the bright side: now all the data and methods will be published instead of hidden in the SI.

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.)


April 23, 2009 at 5:17 pm | | everyday science, nerd

I had a nightmare that our controls were failing.

some light reading

April 17, 2009 at 7:31 am | | everyday science, grad life, literature, nerd, science community

What do you read…


…while on the toilet?

Space Storms, 2012, and End of the World?

March 24, 2009 at 4:39 pm | | everyday science, literature, science and the public

A recent article in New Science magazine suggests that a severe solar storm may destroy the electrical infrastructure of the Western World (source).

Apparently from time to time, giant plasma fireballs known as coronal mass ejections escape the sun’s surface on a solar wind.  If one of those ejections should hit the Earth’s magnetic shield, it would cause rapid short-lived changes in the configuration of the Earth’s magnetic field which would induce DC currents in the long wires of modern power grids.  This increased DC current in turn would induce strong magnetic fields that would saturate a transformer’s magnetic core, which would result in a runaway current that would cause the transformer’s wiring to heat up and actually melt.

Read more of this post…

kimwipes claim science

February 26, 2009 at 9:38 am | | everyday science, stupid technology

Apparently, “science” is a term trademarked by Kimberly Clark:


* Trademark of Kimberly Clark

I don’t really think that’s fair.

electronics cleanup

December 19, 2008 at 2:27 pm | | everyday science, grad life, great finds, hardware

We needed to move several pieces of electronic equipment from a table because they were “blocking” some circuit-breaker boxes. So we discarded of all the spare monitors that were stored under laser tables to make room for the no homeless equipment:


In the process, we found some desiccated rats. W.E. found one that had a frikkin’ wasp nest growing inside it.


Weird. And very gross.

clamp that AOM, boy!

November 6, 2008 at 11:14 am | | everyday science, hardware

Sometimes you can’t find that nice new equipment. Like the quick clamps that were sitting on the bench for weeks: now that you need them, they’re nowhere to be found. So you find the old hardware:

My labmate didn’t want to hold that AOM on the mount while the epoxy dried, so it was either tape or these monster C-clamps.

I just liked the juxtaposition of the monster clamp and the fragile little quartz Bragg cell.

late referee reports

October 21, 2008 at 8:13 am | | everyday science, science community

I just recieved two referee reports with my proof. Strange, that seems sorta late for me to be editing the content of my paper. Thank goodness the comments are generally positive.

First, we received only one referee’s report, with very little to change. That’s actually not very helpful, because I don’t know what parts of the paper need changing. And then we received a late referee report, right when we were about to submit our revision. Now we’re getting two more reports at the proof stage.

Of course, I’m happy that the editors sent us these referee comments, so I can fix things. (I wish the editors of another journal had sent my referee notes to the authors!) Nevertheless, maybe the editors should have waited an extra few weeks before telling us to start making revisions (it was a very fast turn-around). But it could be my own fault, for submitting an invited paper a couple weeks later than the editors asked. That’ll teach me.

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