Archive for 'In teh lab'

Loopy TLC plate


Well, I don’t think I have ever seen that on my TLC.  Goddamn spots ran as loops. Also, I have no starting material left.  And I have blue glowie fluorescence!  WOOT!  Easiest macrocycle I’ve ever made.

(My normal lab camera, a Nikon D80, is resting at home.  If you’re going to get a camera for lab and blog use, you should invest in a decent digital SLR.  As you can see, that picture is bullshit.

Up next… Sigma Aldrich, I fucking hate you.

I purchased a MacBook Pro.  It’s sexy, yes, but that’s not why I bought it.  Let me convince you why you should consider the same purchase.

First of all, you have probably noticed a recent proliferation of polycarbonate and aluminum notebooks floating around the undergraduate masses.  If you’re a parent of a reasonably articulate child, they have undoubtedly asked of some type of brand name Apple accessory, if not the full Monte.  This sudden emergence of omnipresence is more than just a trick on your eyes or a sudden perception – it’s a monumental ground swell occurring under the feet of the Millennial Generation (which would be my generation, I suppose) as the personal computer is increasingly an item of both utility and luxury and those that can afford luxury, buy a more personalized and stylish device.

To the left, you see an increasing percent of Apple computers owned by undergraduates at the University of Virginia as it pushes 40% while a concomitant decrease in the number of PCs owned occurs.  It’s not reading tea leaves – the data is clear – as the hardware market moves, so too does the software market.  Apple already has a hand up academia’s skirt and with the influx of undergraduate consumers, that hand has gone full on into shocker mode.

While the popularity of the computers is promising, the transition to Intel architecture also means that writing code (creating programs) and porting existing software for the mac will be easier and, as the popularity increases, I would anticipate software developers to be less shy about porting their software to OSX since it’s a port between two x86 systems and not from x86 to a RISC system.  It also means that software packages that emulate Windows, like Parallels, can run PC software seamlessly over the OSX environment:

OSX running parallels

From the above image you can see I’m running ACD’s 1D NMR software over OSX with Keynote running in the background.  You can even pop up the Windows Start Menu to launch other Windows applications, all of which run nearly seamlessly (you can’t copy Mac Chemdraw structures into PC Chem3D, for instance, though you can copy text and images to your heart’s delight.)

Compatibility and fear of being on a lonely island being excluded, the final two points are cost and power and, not surprisingly, they are related.  The laptop I own is top-of-the line (no shit) running a 15″ LED display at 3.06 GHz with 6MB of L2 Cache.  That setup isn’t even possible through Toshiba direct, let alone there are no other vendors of laptops that contain dual graphics cards, one with 512 MB of RAM.  The only company that could produce such a beast would be Lenovo – a company that also produced great laptops.  If you build a comparable system (you can’t get an LED display and a 500 GB  hard drive) you end up spending $100 more than I did with my Developer discount (if you use an educational discount, you’ll spend $100 more for the Apple product.)

In short, you pay a very high price for a very high end system and, because the lowest end laptop Apple sells is still spec’d out well above the average Toshiba you find sitting in Best Buy, you get the feeling Apple is ripping you off…  but that’s not really the case.  And speaking of case, the whole laptop weighs about 3-8 pounds less than what you would get from Lenovo (depending on the specific brand.)

I’ll admit it:  I got an Apple because I wanted something different, too.  Something to change the scenery and something new to play around with.  I’ve been faithfully using a PC since I was given one in the 4th grade by my super-smart-kids elementary school and I’ve never had any beef with them.  Windows XP is a great OS (Vista can suck my nuts) and seems to be as stable as Mac OSX, if not more so, assuming you’re not retarded and download random shit with Internet Explorer (which, like Safari, is inferior when compared to Firefox.)

Since starting my postdoc no less than 45 days or so ago I haven’t really commented on the subject, though I think I can now comment on, at the very least, the first 3 days (what with having all this time to reflect upon them and all).

The position of a post doc is a confusing one, to say the least.  You’re really not that much better than a 4th or 5th year graduate student, despite having additional initials after your name and, if you didn’t fuck up, you’re probably at a bit more of a competitive lab or a more impressive school (or it was, at the least. a lateral promotion to something equivalent.)  Either way, the people around you are fucking smart and ready to take you and everyone else on intellectually.  Now is not the time, of course, to retreat into your shell… this would be a mistake.  Instead, you have to toss yourself out there as simultaneously self assured and humble.  It is the postdoc, after all, that crashed into the delicate ecosystem of the lab and as the guest I find myself silently listening to world around me.

What is this madness that I have begun?  A group 3 fold larger than the one I left, I find each of us (that is, all the members) attempt to be unique snowflakes with varying degrees of success.  The office layout is horrible – the separation of the lab into multiple offices in different hallways has lead to apparent cliques and associations.  While, granted, my former lab was separated by floors, we were always close.  If I were to, say, go out to lunch with some of my group members, trash talking was more along the lines of “if so and so doesn’t get their shit together they’re going to fucking piss me off” and not so much the “I’m going to fuck so and so in the eye socket in front of her children.”  The cordial flavor of a provincial department has given way to the cutting edge of brutality.  I’m ensconced in brilliance, laziness and madness all at once and am supposed to be a leader of this ragtag crew and, while there is a clear thirst for knowledge and a love for science, there is also a dynamic that eludes me.  Make no mistake:  it’s a super group of the highest order and it’s sink or swim; I’m happy to be here and love everything going on around me but it’s overwhelming – daunting even, fuck… I can’t even remember everyone’s names.

So I sit quietly waiting for the first years to filter through, hopefully I can catch some of them and convince them to follow me on my own wild scientific quest for the latest in high science and high praise.  For now, I’m focusing on doing something major – a novel innovation.  It’s unbelievably difficult to come up with something novel, I appreciate that now, particularly when you have to keep it in the context of what the scope of the lab is doing.  I have some ideas, but they’re not ripe enough to pick from the tree…

So I sit, reading the literature for 10 hours a day… waiting for inspiration to strike me.

I hope it strikes soon…

UPDATE:  It struck.  And I’m off to the races…

As a function of my new post-doc, I found myself in the need of a refillable fountain pen, which could contain organic solvents. It also needed to be refillable by a plunger or cantilever and, once I was done with the science, I wouldn’t mind converting it to a nice pen for my own use.  (You may be wondering, wtf kind of chemistry are you doing where you’d be using a fucking FOUNTAIN PEN?  To wit:  I am doing awesome chemistry.)

In any regard, I have (as most scientist do) an inexplicable compulsion (it has nothing to do with masturbation, just FYI… I know that’s a common one.)  My compulsion happens to be the exclusive use gel pens. I thus figured, if I’m going to get a refillable fountain pen, I might as well inquire into the availability of that gel ink they use in gel pens. (It’s not really available…)


Of course, at the time, I didn’t know what made them so gel-like and why I loved them so… but regardless, now I appreciate that I can feel much safer knowing that the federal government can’t track my ink. (DOI:10.1111/j.1556-4029.2006.00144.x)

As every Republican can tell you The Federal Government has been evil for at least the last 3 months – ever since Glenn Beck started warning you that “they” are coming for your guns and your personal rights and your Fieros and whatever redneck accoutrement that you find so appealing yet have parked out on your lawn.  What you may not know is that the feds have been keeping a meticulous database of inks since the 1920′s and at ANY TIME they could take your ink and compare it to their stock samples of ink by… wait for it… TLC! (oh noes! blow up teh fedural buldins!)

Srsly.  Co-spotted and everything.  The fucking FBI will compare ink composition by how far the little constituent dyes run up a TLC plate:

TLC is one of the most widely used and generally accepted scientific methodologies used to compare and help characterize ink formulations. TLC has been discussed extensively by Witte (21), Brunelle and Pro (22), Brunelle and Reed (23), Brunelle and Crawford (24), Kelly and Cantu (25), and Aginsky (26). TLC analysis begins by removing an ink sample from a document, and subsequently extracting the ink in an appropriate solvent. The extract is then applied to a specially coated TLC plate (e.g., glass or plastic surface coated with silica), and placed in a solvent-equilibrated glass chamber containing a solvent or mixture of solvents. The sample components then migrate up the plate via capillary action. Typically, the colorants (e.g., dye components) that are present in the ink sample will separate into colored bands or spots. As described in the aforementioned study conducted by Roux et al. (20), ‘‘thin layer chromatography had the highest discriminating power for the individual techniques at 0.98 for blue and 0.99 for black.’’

I know, I know… we sent fucking human beings to the moon 40 years ago and we still don’t have one of those fantastic neon lit LC/GC/MS/Magic box from CSI that spits out the type of ink and where it was purchased.  But fear not, they can (and will) track your shit down with the almighty TLC plate…  unless… you use gel pens.  Turns out gel inks are poorly soluble in the highly polar solvents they use for TLC (EtOAc:EtOH:water in a ratio of 70:35:30… not a typo… [these people fucking solve crimes]). While most pens contain inks that are water soluble or organic soluble – gel inks contain both, plus some insoluble pigment shit.

The Gelly Roll, a name which could only be dreamed up by the psychotic lotus eating scientists of Japan at Sakura Color Products Corporation was the first gel pen invented in the mid 80′s and contains water and oil based inks dissolved in an aqueous mixture thickened by xanthan gum and pigments suspended therein.  Fountain pens and rollerball pens use water based inks while ballpoint pens use organic derived dyes.  Thus, the inherent insoluble nature, as well as the broad range of polarities in the gel pen resulted in EPIC FAILS:

The colorants in 15 of the writing inks did not extract into solvents and/or migrate on the TLC, which indicates that they are pigment based. These inks were not feasible for comparison with the library of standards based on their lack of a colorant profile on a TLC plate; however, this would not preclude additional comparative testing using alternate methods such as Fourier transform-infrared spectrometry (FT-IR), gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and/or scanning electron microscopy (SEM) coupled with energy-dispersive X-ray analysis (EDXA). It is noted that 14 of the 15 inks that were not extractable were gel inks [...]

I am pleased to know that the feds will be unable to know where I purchased my ink.  That’s one more “freedom” I can keep. (I purchased them at Sam’s Club. Great fucking deal. I got, like, 50 of them for $40.)

Here is a trick you can play if you want to get an Apple system for, all intents and purposes, the price of a comparably spec’ed PC:  Become a student Apple developer (you actually have to be a student.)  Here’s how -

Buy a student membership to Apple’s “Cult of iTurds” developer connection by going here.  After a few hours they will send you an activation code, which you will input when you create yourself an account here.  Once you’ve done that, then you need to send them a copy of your student ID as well as your current course schedule to prove you’re a student.  I photoshopped mine, since I joined after I graduated.  (I know… bad me.  But fuck Apple – srsly.)  Once you’ve done all that, purchase your computer at the developer store for about $500-600 less than retail from here.

I have done all but the last step as I’m still unsure of what I want to get.  My new post-doc is festooned with granola munching Macintards and I’ve been told that my ultra famous post doc advisor cries when he sees PC’s (on the inside, of course).  I have thus committed to getting a (goddamm dirty) Mac.

It really has put me into a fucking bind.  I have been a PC user my whole life, ever since my elementary gave us one to take home and learn on waaaay back in 1989.  For whatever reason, scientists have flocked disproportionately to Apple products which leaves us, quite collectively, between selecting computers that no one uses (PCs) or computers no one makes software for (Macs).   And don’t tell me iNMR is awesome, because I’ve used it.  It isn’t awesome.  It’s fucking a piece of trash.  I mean that.  It actually has sex with trash.  It’s a very expensive piece of trash that has intercourse with other trash.

On the other hand, Macs are pretty sexy.  I think I shall get one of their 17″ laptops with the anti-glare screen.  The specs cause much motion in my trousers.