oh. my. god.

August 27, 2009 at 4:31 pm | | literature

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

August 20, 2009 at 9:00 am | | literature, news, science and the public

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.

ozone-no-reg ozone-reg

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)?

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)


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?

Some lab motivation

August 12, 2009 at 10:46 am | | cartoons, grad life

A labmate made this motivational poster. Enjoy!


A battle brewing over Napoleon Dynamite

August 8, 2009 at 11:08 am | | literature, science community

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?

August 3, 2009 at 3:55 pm | | literature

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 a Title!

What funny titles have you guys seen?

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.

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