Everyday Scientist

Rube Goldberg Science

Most people have probably heard of or seen pictures of so called Rube Goldberg Machines. These are extremely complicated apparatuses which do extremely simple tasks. Here is an example from the Rube Goldberg website.

This one could actually be useful for those grad students who have bosses that keep track of time in lab.

There are even Rube Goldberg Machine contests, in which teams try to design a machine that can use the greatest number of steps to complete a simple task.

Now, science is often complicated and it doesn’t need any extra help from us grad students to make it more complicated but I fell into the trap myself and let this be a warning to all those who think they have a really good idea… think again.

The required task is: Do a pump-probe anisotropy measurement using infrared light. Simple enough at face value, but all you visible spectroscopists out there must keep in mind that IR polarizers are ~1000 times worse than visible polarizers and there is no such thing as a broadband IR half wave plate. Tack onto that the fact that IR detectors are much less efficient that visible detectors and you’ve got a passel of stumbling blocks in front of you when you’re trying to do this experiment. I’ve tried a number of different techniques and because the IR polarizers and half wave plates are a little sketchy, transmission always seems to screw things up. So I thought to myself, what if we did everything using reflections! Then it would be achromatic and everything would be hunky dory. Here’s a schematic diagram of what the pump beam is subjected to in this scheme. The actual layout is much more complicated but I didn’t have a digital camera with me.

The periscope serves to change the polarization of the pump beam so that it will be parallel or perpendicular to the probe. The bottom mirror in this periscope is on a computer controlled rotation stage so that it can rotate to spit the beam out in two different directions depending on the polarization you want. In addition to that, since there are now two beam paths we added a computer controlled mirror that could flip in and out of the beam depending on which beam path you were using (which polarization). It was a thing of wonder to watch these things rotate and flip on the click of a mouse button, almost mesmerizing and utterly satisfying as well. Needless to say, it didn’t actually work for the purpose it was designed for. I wasn’t able to align the two beam paths well enough and/or the mechanical devices weren’t repeatable enough to consistently steer the beams in the same direction. Bummer. Like so many things that seem perfect on paper, real life imperfections rear their ugly head when you try to make it work in practice.

Now, this experiment isn’t a simple task by any stretch of the imagination, but making it more complicated is certainly not going to make it work better. It was only after I was humbled by the lack of repeatability of my fancy new system that I remembered Rube Goldberg and kicked myself for falling into his trap.

Fun with lines

Found this figure on the JACS online front-end graphic in this month’s edition.

They drew a line through 2 points, and missed one of the points in the process. Having never actually collected data to publish, I’m a little mystified by these graphics, since they aren’t from the paper. I’m sure in some context it would make sense, but I’m going to go ahead and just assume they haven’t pulled out the ol’ bore sighter for their fitting software in a while.

While we’re on the subject, do you submit these graphics in addition to your manuscript? I recall one graphic that looked like it was drawn on a piece of notebook paper a while ago.

great line from Gaussian manual

I’m not a huge fan of the Gaussian online manual. Maybe I’m spoiled by Matlab, but G03MANTOP is soooooo confusing and not user-friendly. Even William thinks it’s tough to understand. Here’s my favorite line I’ve found:

CIS Output. There are no special features or pitfalls with CI-Singles input.

Maybe this isn’t funny to everyone, but I just like the idea that they didn’t add any special pitfalls to the CIS input format.

(BTW, that claim is bull. I haven’t been able to get my CIS calcs to work too good so far.)

what independence day means to grad students

This is a little email conversation I had with William:

I asked Kevin. He told me.

sam wrote:
> seriously?

> william wrote:
>> sure, but what’s this week?

>> sam wrote:
>>> [no journal club this wednesday,] obviously. can you go next week?

I’m glad that TJ wasn’t a chemist.

Aerogel Jewelry

Source

Aerogel Jewelery: +10 nerd, +4 chemistry cred, and -10 charisma*. Personally, I’m holding out for a pendant full of radium, Curie style.

*These statements have not been evaluated by the FDA. This product is not intended to diagnose, treat, cure, or prevent any disease.

what’s the point of peer review, anyway?

I’m pissed off.

My PI recently asked me to help him referee a manuscript (obviously the authors and journal will remain unnamed). I read the paper carefully and wrote a detailed report, requesting several changes before being appropriate for publication.

This manuscript had many major issues (including reproduced but uncited figures, inconsistent structures, poor statistics, and claims of data in the abstract that were nowhere in the paper). My referee report was friendly but asked for corrections. I was even kind enough to split the comments into major and minor.

We never heard anything back from the editors of the journal after we submitted our referee report.

So I was shocked to see the paper published recently … without any of the changes we requested! The reproduced figure—identical to an earlier publication—remains parading as original data, the structures remain inconsistent, the extraneous claims remain in the abstract, the statistics remain unjustifiable. WTF? Maybe two other referees said to publish without changes, but my comments should have been helpful to the authors and editors! I was trying to make the article better and help the authors emphasize their results. What was the point of all my work?

[Update] I think that the editors must not have sent on or looked at my referee report, because the authors didn’t even correct a wrong page number on one of their references. What jerks!