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.


Efficient enantioselective transformation of lemons to lemonade: a reflection

December 24, 2009

What kind of blogger would I be if I didn’t include some nod to the end of the year? The kind that asks rhetorical questions, I suppose…

But I feel I may as well contribute my 2 cents on 2009 – mostly reflecting on myself, and maybe a little on chemistry as a whole.

With respect to myself, I feel like I’ve learned so much over the past year, and in particular, the past semester. Efforts included an attempt at the C8-C12 fragment of callystatin A for my synthesis class, and synthesizing a small library of heterocycles for the research lab! And to think, back at the dawn of 2009, I was only starting orgo II…

As mentioned before, the synthesis class hit a brick wall when the use of a chiral auxiliary simply failed to work. Infact, out of the three people with my project, I think I was the only one to actually isolate 6 (nevertheless, in complete shit yield – a mere 2%). However, as the morale of my compatriots began to sink toward the end of the semester, I remained vigilant; the more problems I encountered, the deeper my desire to “beat” the reaction. Although I didn’t quite make it to the C8-C12 fragment, I went out swinging. During the final lab period, I was left with 9 mg of crude 7, a promising, yet narrowly RF’d TLC, no time, and no prep-TLC plates. [1]

Results from the research lab were much more promising. Through out the semester, I was a little skeptical of the idea of a library synthesis. I had signed up for research well before I was romanced by the idea of total synthesis, and I quickly grew restless doing the same few reactions over, and over, and over, as I began to yearn for target-oriented hot pursuit. Almost the entirety of the semester was spent testing/generalizing reaction conditions, and prepping starting materials for a final parallel combinatorial synthesis, and right when it was high time for parallel synthesizing, I got that nasty flu. What could have taken place during the last week of actual class had been pushed back into the study period/final exam period. The pressure of time running low sparked something, and I started to view the chemistry as something I couldn’t let beat me, and seeing the work of the entire semester come together gave me hope. In a final sprint to the finish, I cranked everything out in time, and submitted samples for biological screening, reaching the established goals for the semester. Then I did a happy little dance, and took a well deserved nap.

Finishing off the year: my fledgling attempts at real scientific writing. For both my synthesis lab, and research/independent study, I had to write up a full research paper detailing the semesters work. Gone are the days of “lab reports” with slightly differing formats from class to class, having to show monotonous calculations (remember back in the day when you to include the actual calculations for percent yield? yeah…), and trying to “discuss” painfully straightforward reactions.  Full papers just feel right, putting the skill sets developed from lab reports to practical and purposeful work.

On the opposite end of things, actually writing the papers was a gruelingly tedious endeavor. I had thought I kept pretty good notebooks, and don’t get me wrong, I had all the necessary information when it came to writing, but I could have organized things a little better. Multiple iterations of the same step got pretty confusing, pretty fast, and I’m going to have to develop/adopt a much better means of databasing intermediates, reaction steps, etc etc. Also, when it came time to input data/crunch numbers, fuckall, especially for the library synth. For the parallel synth, I input the raw data into an excel spreadsheet, and did the calculations that way. However, I need to bone up on my word-excel tips and tricks, because manually transferring all the data into word was a major pain.

Back in the day, our orgo II professor was testing out the use of electronic notebooks in the academic lab. Then, it seemed highly unnecessary – the user interface isn’t intuitive, we don’t need results from single experiments beyond the week that we do them, and the chemical library is limited enough that it’s usually just faster to do everything in a pen/paper notebook anyway. However, for lengthy projects, I’m beginning to see the benefits of it, and am seriously considering what stage of my project I’d like to be inconvenienced.

Ultimately, for even a single semester’s worth of struggle and success, compiling everything into a single polished entity was, and still is, incredibly rewarding. If this is the kind of “runners high” and agony/elation one gets from thesis writing (and eventually finishing the damn thing), count me in! I live for this kind of suck.

With respect to the chemistry community at large (and mostly, as comment/response to excimers latest post on CBC), the year as a whole did suck a bit. The economy is shit, H1N1 will kill us all, and I firmly believe that western civilization is headed for some kind of zombie apocalypse. Oh yeah, and a fair share of scientific skulduggery went down, too.

But, maybe we’re looking at the suck-age in the wrong light… Unfortunately, the amount of lies, falsifications, hoaxes, and half-truths, is highly open to speculation. Maybe the amount is increasing or decreasing over time, staying constant, or dependent upon phases of the moon, tides, and rate/magnitude of recent celebrity deaths. Maybe it’s straight up random….

At the end of the day (year), it’s a shame that any kind of ‘bad science’ happens in the first place, and it’s a damn shame that it does make its way into good/reputable journals from time to time;  because there’s no way gauge the amount of bad science that goes unchallenged compared to bad science that gets what it deserves, it’s an overall triumph that bad science got called out, period. At least, that’s the approach I’m taking…

So happy holidays. Eat, drink, enjoy friends and family, and be merry while your at it, even if its for all the wrong reasons (like chemistry). Hell, maybe even get a gift for your biologist friend acquaintance. To balance out the starry eyed nature of this post, I might have something delightfully cynical coming up soon. But maybe I’ll save that for early January when everyone starts dropping their new years resolutions…

[1] Sorry the .gif looks a little grody. Even the tried and true Tot. Syn method produced weird lookin’ results… Just give it a click, I promise it looks better. At least, a little better.


November 30, 2009

Finally! Back home where I have a wifi connection… Thanksgiving with the ladyfriend was lovely, except her grandparents house did not have wireless. It’s weird how a (broadband) internet connection is a completely integral part of modern day computing. It’s a brave new world we’re living in… Anyway, hope you had a lovely Thanksgiving, too. If you don’t live in the US and don’t do the whole Thanksgiving thing,well, I hope you had a lovely November 26th.

Regardless, Thanksgiving in suburbia, and away from the internet led to a fair amount of TV watching, which in turn, led to this. Because we have reality shows for Evrything, and I have yet to see the idea elsewhere, I call dibs on the idea: Chemistry Reality Show. America’s Next Top Chemist? Iron Chemist? Real Chemists of Boston/Chicago/Berkeley/San Diego/etc? Whatever you call it, I’m sure it will eventually make its way to the airwaves, and when it does, I expect royalty checks to start rolling in.

There’d be the obligatory challenges: the severly time limited challenge, best use of a reagent challenge, the limited equipment challenge, discipline specific challenges, chromatograpy deul. Historical challenges – recreating classic experiments with classic reagents/apparatus. It’d be great! Kyle Finchsigmate and Dylan Stiles would totally be called in to guest judge.

And if that doesn’t wet your whistle, I’m also proposing MTV: Labs. Similar to Cribs, a member of the lab would welcome the camera at the door, give the full tour, include a little bit of product placement and mandatory “inside the fridge” shot (maybe inside the hood?), show off any ghetto-fabulous or fabulously ghetto equipment and instruments, and finally kick the camera crew out when the tour is over. If you and any co-workers are the right kind of geeky, and have a little spare time and a video camera, I invite you to give it a try, and to post your results!

Scientific Accuracy

November 12, 2009

I’m going to hazard a guess that the things I lay awake and think about at night are far different than whatever keeps you up at night.

Take, for example, the new Jameson Whiskey commercial…

I suppose, in a world where a man can dive in after his beloved cargo, fend off a giant octopus, weather a storm, and make it to shore, then anything goes, but what I’m really curious about: would a barrel of whiskey even sink?

Whiskey is marginally lighter than water¹, and most woods seem to be lighter than water², so I suppose it would come down to the amount of cast iron used to bind the barrel together…

Granted, for 99.99%³ of people, you’re drinking whiskey because you enjoy the smooth, mellow taste, or because it gets you drunk. Or both. But, damnit, I’m a proud member of that .01% that also enjoys a stiff glass of fact-checking with their drink, too. I also enjoy drinks that pour shots for you. Seriously, so helpful.

Good to know that if chemistry doesn’t work out, I can apply to be a Mythbusters intern.

[1] I ❤ WolframAlpha

[2] Wood Facts While less definitive than WolframAlpha, and considering I’m no expert on the deciduous trees of Ireland, the wood choice might play a considerable difference. However, I’m going to assume they weren’t using fine hardwoods for barrel construction, either…

[3] Stat’s are approximate. However, if you can give me any other reasons to drink whiskey, please let me know. I’ll write a thesis on it….

Steal this blog post

October 11, 2009

Wait, scratch that. Don’t steal it. But if you do, at least link to it for pete’s sake.

Anyway, while biologists were busy stealing the nobel prize¹, I was busy stealing books and software. Thus, I’ve had piracy on the brain lately. Something something something, Somalia joke.

But on the real, what’s the moral concensus on stealing things in the name of science? (And weird that only the music industry really seems to care about pirated goods. But that’s for another blog post. Perhaps even another blog…)

Aside from tuition, food, and housing, I reckon that books/software make up a significant chunk of student expenses. Frankly, the only reason I buy required textbooks is because nobody has invented a convenient way to access books digitally. Paper > PDFs any day, especially when it comes to several-hundred-page textbooks. But, when it comes to non-required books, references, or “fun” reads, all bets are off.

Take, for example, the plethora (and expense) of reference books offered by John Wiley & Sons. Many of these books are easily available through illegitimate means, simply though a quick google search. Of course, stealing is wrong and I’d never ever condone such actions: downloading these books, redistributing them, referencing them without citation would probably fall into the “stealing is wrong category.” But, what about downloading the book for use as a quick reference? What if that reference is already available on wikipedia? What if I could walk into my bookstore, pick up the book, flip through it, find exactly what I need, then set it down and walk out without buying it? What if my library has a copy of it, and I’m just saving myself a trip there? What if I’m not even denying any money to public transit to facilitate my trip to the library because I would have biked anyway?

For all intents and purposes, each of these scenarios still probably falls within the domain of “stealing is wrong.” However, when the magnitude of the “wrongness” gets smaller and smaller, attempting to classify the stealing as right or wrong kind of becomes trivial. If your library doesn’t have some critical reference you were looking for, then what do you do? Run to the bookstore to have a look at it, shell out the cash to buy it, illegally download it, or keep looking until you (hopefully) find the information elsewhere?

Similarly, let’s have a look at software. In particular, ChemDraw and MestRe Nova. I’ve use both, I enjoy working with both, both are fairly expensive. (Academic pricing: $150 for a perpetual license on standard ChemDraw, and no updates. 305€ for MestRe Nova. Nearly $450 USD, and only includes 1 year of updates/support.)  Luckily, I have a license to both through my university. If I didn’t, I’d be in a real pickle. Of course, there are free options, but realistically, it makes little sense to familiarize yourself with obscure software that’s not widely used out in the real world, and furthermore, they’re frankly not as good. Reason? I don’t care if free software can do everything that the big name software can do if it can’t do it efficiently/with an intuitive user interface. Unfortunately, that comes at a price.

While other forms of piracy (music/movies/gaming software) are generally for entertainment, the piracy reference books and scientific software can greatly impact the work of a chemist. Maybe they won’t make one’s work better, but I’m damn sure that “proper” references and software can make work easier, more efficient, less aggravating, and less time consuming. So if your school does not offer the resources you need, you’re roped into a pretty dismal cost-benefit analysis. Same goes for the workplace, but that’s (hopefully) less of in issue, given that you’d (hopefully) be making big boy money, and not be scraping by on a grad student stipend or even paying for your undergrad education. In either case, you can: pony up for the goods, waste time dealing with subpar resources, or find an illegitimate source. What do you do?

1) For the non scientists out there, or for the scientists out there who have been living in a hole the past week, it’s been blogged about everywhere

Other microwave reactions

October 6, 2009

In pchem today, we briefly mentioned the electromagnetic spectrum. As one of those fun little “snapple facts” that my professor threw in todays lecture: the microwaves a standard microwave oven emits are ~2.45 GHz. I’ve never really thought about what frequency a microwave operates at, and as luck would have it, haven’t had such a problem ever as homework. It seems like such an obvious homework question, too…

But, regardless, my prof mentioned that microwaves operate at 2.45 GHz….

According to wikipedia, the concept of the microwave oven was patented in 1945. Between the 80s and 90s, the microwave oven saturated domestic America.

In the late 80s, the cordless phone came to pass, and by the late 90s, the technology seemed well within reach of average consumers. In 1998, the FCC allocated the frequency of 2.4 GHz for cordless phones. (And up until 2003, when they allocated 5.8 GHz, most new cordless phones were hawked with 2.4 GHz as a ‘feature.’)

Therefore, whenever I’m at home-home and have access to both a microwave and a landline/cordless phone, one conversation is usually comprised of unintelligible fuzz.

It’s rarely an issue for me, but considering that microwaves had been commonplace for longer than the cordless phone frequency range: what ‘tard over at the FCC allowed the overlap/interference to be a problem in the first place?
Just wondering…