Everyday Scientist

the matrix begins

“Implanted Biofuel Cell Operating in a Living Snail.”

Implantable biofuel cells have been suggested [BY MACHINES] as sustainable micropower sources operating in living organisms, but such bioelectronic systems are still exotic and very challenging to design.

One thing I never understood about the Matrix was how the machines were getting more power in electricity out of the human farms than they had to put in as food. Don’t the machines know the three laws of thermodynamics? Or just the three laws of robotics?

PeerJ

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.

walking with coffee

I love this paper: H. C. Mayer and R. Krechetnikov. Walking with coffee: Why does it spill? Phys. Rev. E 2012, 85, 046117.

In our busy lives, almost all of us have to walk with a cup of coffee. While often we spill the drink, this familiar phenomenon has never been explored systematically. Here we report on the results of an experimental study of the conditions under which coffee spills for various walking speeds and initial liquid levels in the cup. These observations are analyzed from the dynamical systems and fluid mechanics viewpoints as well as with the help of a model developed here. Particularities of the common cup sizes, the coffee properties, and the biomechanics of walking proved to be responsible for the spilling phenomenon. The studied problem represents an example of the interplay between the complex motion of a cup, due to the biomechanics of a walking individual, and the low-viscosity-liquid dynamics in it.

Genius. Here’s a great figure from the paper:

Fun stuff. It would be especially cool if they designed a new cup shape to minimize coffee oscillations.

heineken solvent

(hat tip to efdm and brsmblog.com.)

3d FtsZ

My friend Julie just published these beautiful 3D images of the FtsZ ring closing off two tiny dividing Caulobacter cells:

The scale bar is only 400 nm. Love it! (Video link here.)

self-plagiarism and JACS

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!

SPRAIPAINT

Great paper from my previous lab. And with a ridiculously hilarious acronym (a play on Hochstrasser’s PAINT): superresolution by power-dependent active intermittency and points accumulation for imaging in nanoscale topography (SPRAIPAINT). This acronym fails almost all my “GINAP” rules for initialisms, but I still love it because it joins the plethora of acronyms in the super-resolution microscopy field: PALM, FPALM, STORM, dSTORM, STED, GSDIM, PAINT, RESOLFT, SMACM, FIONA, SHREC, SHRIMP, SIM, SOFI, NALMS, … and I’m sure I’m forgetting some. This acronym shitstorm certainly deserves more. In all honesty, I think we should drop all the acronyms and just call it “pointillist super-resolution microscopy.”

The images in this paper are just beautiful! The bacteria they image are very small, basically at the diffraction limit of a conventional microscope. But they are able to image three-dimensional helices of protein filaments inside these tiny guys!

The movies are awesome:

(Click here for Movie 2)

Cool. Keep up the good work, Moerner lab.

extraordinarily repeatable data

UPDATE: My friend on Facebook pointed out that Figure S5c in the supporting info is even more fishy (click on the image below to see a zoomed-in version). Clearly, some portions of the image were pasted on top of other parts. On the right, it is obvious that the top part of the image is from a different frame as the bottom part. On the left, it looks like there’s another image hidden behind (see the strip showing through on the left top part of the image). I’ve added red arrows to aid the eye.

This could possibly be mistakes by someone who doesn’t know how to use Photoshop layers, but I’m thinking there might have been some intentional manipulation of the data. Either way, this type of slicing and stitching and Photoshopping of scientific data is totally unacceptable. I think Nature editors and referees should be more than ashamed to have let this slide.

Nature editors announced that they are investigating.

(Original post below.)

This paper in Nature contains some serious errors: some of the images that are purportedly from different samples (different mice, even) appear to be identical! Note the triangle of spots in the two images below:

Many commenters have noticed the weirdnesses in the figures. This is my favorite comment so far:

2011-04-22 09:31 AM aston panda said:
This is an excellent article shows extraordinary .. skills and amazingly repeatable data. for example
Fig.1a, 2 middle vs 3 bottom left
Fig.1c, 2 right side vs 3 left side
Fig.S4, 1 left side vs 2 right side
Fig.S5, c4 middle right vs e4 middle left
GOOD JOB

I suspect that some sloppy organizing by the authors led to them mixing up some files on their computer. That’s my optimistic view. If they were trying to fabricate data, they wouldn’t use the same region of the same image of the same sample! It must have been sloppy bookkeeping. I hope their results stand up after they correct these errors.

It just goes to show that real science can’t get accepted into Nature and Science. ;)

UPDATE 2: RetractionWatch is surprised that this paper eventually was published with only a correction!

great escape

Fun paper:

Harvey, A.; Zukoff, S. Wind-Powered Wheel Locomotion, Initiated by Leaping Somersaults, in Larvae of the Southeastern Beach Tiger Beetle (Cicindela dorsalis media). PLoS ONE 2011, 6(3), e17746. http://dx.doi.org/10.1371/journal.pone.0017746

Escape mechanisms in the animal kingdom can be pretty cool. Or just downright entertaining. This little guy does a somersault, grabs his tail, and rolls away in the wind (see Video 1). Check out Video 4 for a slo-mo version.

why is author ID taking so long?

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.

papers2 review

Scientists have many options for organizing, reading, and syncing PDFs of articles: Papers, Mendeley, iPapers, Endnote, BibDesk, Zotero, and more.

My favorite is still Papers. It’s clean and simple and beautiful. It works awesome on my iPad: reading PDFs is more enjoyable on the Papers iPad app than on my laptop. Syncing to the iPad over wifi is simple and practically bug-free. Syncing libraries between my home and work computers is also possible by putting the Papers folder in Dropbox. (Although Dropbox syncing isn’t technically supported by Papers, many folks use it to sync across computers. I’ve been doing that for half a year without a problem.)

The major downside with Papers is that it works only on Mac OS. Papers2 is now on Windows, too. On my PC, I use Mendeley. Mendeley is nice because it is free and has native syncing to the web and between computers. The reason I’m not completely sold on Mendeley is that it’s just not as clean as Papers yet. Mendeley is not as buggy as it was a year ago, but it still doesn’t seem to find metadata as well as Papers. But, if you’re starting from scratch, Mendeley is a great option. (Edit: And I like the syncing to iPad/iPhone that Papers offers.)

And now Papers2 was just released! Honestly, Papers2 is a little disappointing, so far. But I suppose I was expecting a lot. But I still have high hopes for it. The support staff is working very hard to fix bugs and add functionality that users are screaming about on the discussion boards.

Some of the cool features of Papers2 include:

• A quick way to add citations to Word (or any other application on your Mac) directly from Papers
• Easier keyword tagging
• Automatic metadata importing (although I haven’t seen this work, yet)
• Linking supplemental info to the paper it corresponds to
• Searching multiple databases (e.g. Pubmed and arXiv) simultaneously

The automatic metadata grabbing might be nice, if it ever works. Mendeley tries to do that, too, but I’ve never been impressed. I really liked that Papers1 made manual matching easy (by highlighting the DOI, for instance). The new interface and searching mechanism seems much clunkier in Papers2, and the support staff has already acknowledged as much.

There are several other issues, that make Papers2 feel very beta. Given that it’s brand-new, that’s not exactly surprising. But Papers1 was so refined, that Papers2 seems very clunky in comparison. But I think Papers2 does have a lot of potential.

For those worried about trying Papers2, have no fear: the new version doesn’t overwrite your Papers1 data and PDFs, so you can use both versions side-by-side until you’ve made up your mind. During the 30-day free trial, for instance.

For the Mac, Papers1 has been the cleanest, coolest, and bestest PDF organizer. Hopefully Papers2 cleans up nicely and becomes my new favorite. But right now, Papers2 is not clean enough for me to recommend anyone using Papers1 switch over to the new version.

UPDATE: In the last two weeks, Mekentosj has provided two updates to Papers2 that have made it significantly better. Papers2.0.2 has fixed a lot of the bugs and annoyances in the version I reviewed above. For instance matching is much much better. Like I expected, the folks behind the program are working really hard to make it the best program, evar!

UPDATE2: I use Papers2 daily and I love it. It still has some things on the wishlist that I look forward to, but I think it’s a great program. I guess it just had some bumps at the beginning.

UPDATE3: Papers2.1 is now out at better than ever. Definitely better than Papers1. I can recommend without hesitation that you get this software!

UPDATE4: A bookmarklet for JSTOR.

f1000

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.

royce makes a funny

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!

c&e news archive

Well, Paul inspired me to go check out the C&E News Archives. I looked for some p-chemists at my (PhD) alma mater. I was happy to find an article about my PhD advisor, W.E. Moerner:

The best one I found was on Steve Boxer, mostly because of the photo and caption:

And several articles on Zare, like this one.

History is fun.

UPDATE: A quaint story about a growing department at Stanford.

Also, a cool pic of my old building, from 1961! That building still has those same windows.

JOOT: the journal of one try

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…