Home, and out of my mind, for the holidays

December 31, 2010

Happy holidays, and a happy New Years (Eve, depending on your timezone) to everybody. As you might expect, I’m in the thick of the holiday slow-down. Granted, many of you will probably be back at the grind some time after the first, but I won’t even be back at school, nor spending any time at “the altar,”* until the 13th. I mean, I don’t mind extended time off, and I certainly enjoy catching up with friends I haven’t seen in six months,  but the last intermediates I was working with are just… sitting there. SITTING THERE!

Considering I’m at the point where I’ve definitely had my fill of family time, I’m conducting some “interdisciplinary” holiday research, just to keep busy. Current projects include “late night leftover feeding habits of the North American undergraduate,” and “New Years Eve: A case study.” Feeding habit data suggests an average of two investigatory trips to the fridge per feeding cycle, followed by an additional trip to the fridge, and consumption of the least unappealing leftovers. These cycles continue until hunger is satisfied, although depending upon metabolic rates, wait time between each step, and “appealing-ness” of leftovers, the process can extend well into after-hours.

Data on the New Years project is forthcoming. Currently, I’m seeking to quantify work published by B.E. Peas, et al., indicating why, and to what degree tonight will be a good night. Meta-analysis of 3 previous New Years Eve data sets will be included.

Anyway, I’ll be finishing grad school applications, bothering my PI to finish his rec’s (on time!), and polishing up a bunch of drafts for the next salvo of posts here. Oh, and enjoying time with friends. I suggest you do the same(the friends part), and I’ll see you in 2011.

*no, not my altar, just a particularly clean lookin’ one.


Arse, ‘innit?

December 8, 2010

Big claims require big proof, especially if they’re contrary to all scientific reasoning thus far. If I were to say, “The moon orbits the earth,” that’s pretty well known at this point, and doesn’t require much to back it up. If I were to say, in all seriousness, “The moon is made of cheese,” then that would require some serious proof, excavated bits of moon-cheese goodness for analytical testing, and of course the subsequent publication of moon-cheese to variety of wine optimization.

So, as a scientist, here’s my obligatory post regarding the whole “Arsenic Replacing Phosphorus in DNA Backbone” thing. I’ll keep it brief, and for scientists and non-scientists alike. Longest of long stories short: Researchers think they’ve found a species of cell that can incorporate arsenic (usually quite toxic) into the backbone of their DNA in place of phosphorus – a big deal, indeed, considering A) usual toxicity of arsenic, and B) any swap of this kind has never before been documented.

Whether or not it’s true, it really seems as though Wolfe-Simon et al. haven’t fully supported their case, and that’s a problem. (If you want a full breakdown of why the paper is kind of flawed, check out commentaries by Derek Lowe, and Rosie Redfield. They offer a far more detailed look than I can offer.) Again, long story short, it’s cool that the bacteria can tolerate the arsenic, and it’s definitely hiding around the cell somewhere, but there’s far from definitive evidence that it’s actually incorporated in the DNA.

In response to criticisms, via Nature News: “We are not going to engage in this sort of discussion,” she wrote in an e-mail to Nature. “Any discourse will have to be peer-reviewed in the same manner as our paper was, and go through a vetting process so that all discussion is properly moderated.”

Wh-what!? Now, it’s very possible that bits of the email have been taken out of context, but if not, seriously? Personally, I think this is the biggest problem regarding the whole situation. If you publish a potentially groundbreaking article, in a journal like Science, I don’t think you’re allowed a “Haters Gonna Hate” attitude towards public criticism, especially if such criticism has generally been logical, and scientifically well reasoned. Eventually, the foremost criticisms just might get peer reviewed, at which point, then what will you do? Diplomatically, it might make a little sense to address these criticisms now, rather than copping out in such epic fashion. So, most diplomatically, I’d suggest that the authors nut up, answer some questions, and maybe admit they didn’t do everything within their means to everything to fully support their claim. (Yes, it’s a diplomatic expression. Kennedy totally used it in the “We Choose to go to the Moon” speech.*)

*So maybe I paraphrased just a little bit.


December 6, 2010

This is the future. Perhaps not the flying-car future we were all promised, but at least the internet has pretty much reached the “information superhighway” status we were long ago promised, and shed much of it’s hideous geocities past. Except some chemistry departments. They’re not all “under construction signs, obnoxious gifs, and visit counters,” but some of them make you feel like it’s a tooth and nail fight to get rapid, accurate information about their department. It’s about time some chem departments realized this and made their websites functional. Or at least less non-functional. In case you’re not aware, here are common offenses, and example offenders:

1. No Mini-Bio/Research Synopsis on main faculty page: Lets say that, for whatever reason, you’re browsing a department web-page, and you want to see a list of who does organic chemistry, and there it is. And that’s it. Just a list. In this case, a list of 15 people, and 14 new windows/tabs you’ll have to open, in addition to the current one you have open, just to casually browse the interests of each professor. I use Columbia as an example, but this is a pretty common error. Give us something to go off of. A quick blurb? Keywords? At least give us keywords? A simple “this, that, and the other” next to your name is better than nothing…

2. Mis-information in mini-bios: Ok, so let’s say you find a university website that has some kind of at-a-glance info on the work of each professor. Yippee. So you click on the professor, and are brought to the department’s page/full bio for the professor. In some cases, you will now be tasked with heading to the professor’s actual group-page to cross reference everything listed in the mini/dept bio of the professor

For example, lets look at UC Irvine’s faculty page, compared to Overman’s bio page and his group page. To the untrained eye, the faculty listing page will have you believe that Overman does “chemical biology, inorganic & organometallic,” and “organic” chemistry. To the discerning who dig further, or those in the know, I’d say it’s better to describe Overman’s work as “asymmetric catalysis, and natural product synthesis.” I can see the connections – ligated transition metals –> inorganic & organometallic, synthesis of biologically active natural products –> chemical biology – however these are not exactly interchangeable. It strikes me similar to the “a square is a rectangle, but a rectangle is not necessarily a square” distinction, and I, for one, would prefer if departmental websites organized their squares and rectangles accordingly.

3. No group-page: Seriously!? You’re a professor in the modern era, and some time or another, someone is going to want to check out your work in detail – detail beyond what even a correct mini-bio can offer, and without having to sci-finder all of your previous work. Please consider getting with the times and putting up a group page of what you do? I can almost understand if you’re an older professor and don’t “do” the internet, but I’m sure there’s some tech-savvy person in your lab, or at least, your department, who can spend an afternoon, copy some code, and set up the de-facto standard group web page for you. Double demerits if you’re not an old coot and definitely have the tech savvyness to know you should have a website (let alone the relative simplicity of setting up an “out of the box” type template, as referenced, or even something like the stand-alone version of wordpress could probably suffice).

4. Remnants of old pages still on the web: UCLA’s the culprit here. While researching, I decided to google the phrase ‘UCLA Kwon” to get to Ohyun Kwon’s page faster than going through the department’s pages. First hit on google is this. I checked her research interests, and everything looked fine, until I checked her publications… which mysteriously end at 2005. “Surely, that couldn’t have been the last time she published anything. Something’s amiss…” And so, I went to the actual UCLA department page, and pulled up Kwon’s actual group page. Curiously, I went back to Kwon’s phantom-page, and clicked on “organic chemistry home.” Turns out, there’s an entire phantom-department-page still up and running for UCLA’s organic chemistry program. Also turns out that it, too, is the first google hit when you search “UCLA organic chemistry,” as opposed to the current organic page. I highly doubt that the old-school pages are really needed on the web anymore. I further doubt that the current chemistry web-admin at UCLA is even aware they’re still up, and mis-directing search results…

Anyway, now you know the warning signs. Be vigilant, and suggest that your group/department streamline and update their web pages. Your future grad students, post docs, and even undergrads will thank you. And to think, once upon a time, all of this information gleaning had to be done sans-internet. How primitive.