Everyday Scientist

how not to choose a title 101

It’s easy for one to find amusement in a poorly conceived figure or in a t-shirt attempting to show the structure of PCP but failing quite miserably or in the egregious cover of an Oxford University Press promotional booklet for ACS publications. But let us not overlook the gems of humor that we encounter everyday in the form of journal-article titles. Throughout the process of writing my dissertation, I have accumulated countless EndNote libraries, the entries of which are fertile grounds for laughter. I challenge you to improve upon these categories (or add new ones):

Greatest disregard for the importance of being concise:

Bennett, M. A.; Yoshida, T. J. Am. Chem. Soc. 1978, 100, 1750-1759.

Most dizzying:

Arroyo, M.; Bernès, S.; Brianso, J. L.; Mayoral, E.; Richards, R. L.; Rius, J.; Torrens, H. J. Organomet. Chem. 2000, 599, 170–177.

Most [{(=flamboyant=)}]:

López, O.; Crespo, M.; Font-Bardía, M.; Solans, X. Organometallics 1997, 16, 1233-1240.

Most clichéd:
Gaydos, C. A. Neurology 2001, 56, 1126-1127.

Longest running series (most pretentious?):
ten Brink, G.-J.; Arends, I. W. C. E.; Hoogenraad, M.; Verspui, G.; Sheldon, R. A. Adv. Synth. Catal. 2003, 345, 1341-1352.

Most in need of an editor (and a vacuum pump to remove those 0.88 +/- 0.04 molecules of methylene chloride):
Usón, R.; Forniés, J.; Espinet, P.; Garcia, A.; Tomas, M.; Foces-Foces, M.; Cano, F. H. J. Organomet. Chem. 1985, 282, C35-C38.

I still have four chapters of my dissertation to write and only four days before a draft is due to my committee.  I can’t help but to ask myself, Is this the best use of my time?

oh. my. god.

“The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy”

Holy cow.

This is the second coolest thing ever done with pentacene!

(Thanks for the tip, Jian.)

ozone hole and global weirding

Nature has a nice News Feature on how humans first caused an ozone hole in the atmosphere, then banded together to fix it. Really pretty inspiring what we can do when we need to. (The scientific story is also interesting.) And a lesson to how we can work together to solve the specter of global climate change and global weirding.

The images on the left show a computer model of what the ozone hole (blue) would have looked like if we had done nothing; the ones on the right are what we’ve (probably) done by eliminating CFCs from the atmosphere. The large ozone hole would have been seriously catastrophic: Living in NYC or Tokyo would mean getting dangerous sunburns in 5 minutes of sun exposure. Ouch.

I think the ozone hole offers two lessons. (1) That climate science is not BS. And (2) that humans can cause and solve global atmospheric problems. The first probably won’t convince any global-warming skeptic, because they could claim that it was the same faulty science then as now, and that there never was a ozone hole.

But the second lesson should inspire all but the most adamant doubters. Humans are powerful enough to dramatically alter Earth’s environment, sometimes in catastrophic ways. Moreover, we can collaborate internationally to solve global problems. Why are we not inspired to slow global weirding (and solve other international problems such as abject poverty)?

quake’s genome

Steve Quake sequenced his own genome. Cute.

A battle brewing over Napoleon Dynamite

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.

Say whaaaaa?

I was clicking through the TOCs for Molecular Cell, when I noticed a not-too-subtle pattern in the titles of the short “Preview Articles.” Most of the articles were trying really really hard to be f(p)unny. Check this one out:

What funny titles have you guys seen?

hey, that was my idea

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.

Pew Pew Pew Pew

What the hell is happening here?  It looks like some sort of epic space battle against ghosts.

fluidFM

FluidFM. I would have called it “Squirty AFM.” They put a little hole through the tip of an AFM cantilever, so they can squirt fluid through the tip.

Or add dye to just one cell.

Rad.

An Electromagnetic Sex Change, Metamaterial Voyeurism, and the Cup that is a Spoon

I haven’t had this much fun with a paper in a while.  Hot off the RSS press from PRL is the absolute gem:  Illusion Optics: The Optical Transformation of an Object into Another Object.  A number of things caught my attention in this one.  Their first application of their metamaterial image transformation is a feat of gender illusion.

Anyone who has spent one night in Bangkok (Choose your own adventure!  The semi NSFW Youtube here, or some boring lyrics here) knows this can be accomplished with far lesser means than metamaterials, but kudos.  Personally, I’ll stick with beer goggles.  Their next trick involves what I can imagine will be the next great party prank, turning a spoon (in this case what appears to be a 1um spoon) into the illusion of a cup.

Next is rendering a “virtual” hole in a wall.  You simply slap their mystical illusion device on the wall (you’ll love this Sam, all the details of what exactly such a device entails, aka the entire basis of the paper, are piled in the supporting materials), and you can look through the virtual hole like it was an actual hole.  I call the device of my own invention that can accomplish this a window(TM), but let’s not argue over semantics of fenestration.  Porky’s would be proud.

Even more ridiculous, they argue that one can even see into a closed container by simply turning on their device and projecting the illusion of free space where the container should be.  Which would totally work, except for this little thing called absorption.  So if you decide to hide 8-balls of Coke in a Mylar balloon, you’re totally screwed.  And an idiot.

royce doesn’t like 8-page papers

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.”

Royce 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?

citeulike and mendeley collaborate

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?

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.)

great TOC

I love clever table-of-contents artwork. I’ve never seen any rules about TOC artwork: it could be just about anything that advertises the paper well.

I love this one. Pretty classy, and it gets the point across. The view also has a hint of 1984-esque industrialistic dystopia. I guess that’s Madison for you.

1966

I guess I was the first one to check out this book since 1966.

It wasn’t worth checking out, by the way.