Checklists Help Maintain Sanity

Or so I hear. Thus, I will use this space to keep me on track of things this week and next.

Motivational thinking: It's almost over...and then it's Illinois! w00t w00t!

Now I completely understand why it is called "dead week".

• Finish up synthesis lab reports (due ASAP!!!)
• Make and give analytical presentation (due April 29th)
• Make and give statistical mechanics presentation (due April 30th)
• Write formal report for analytical project (due May 1st)
• Make corrections on senior thesis (due May 1st)
• Complete digital portfolio for communication certification (due May 2nd)
• Write formal report for synthesis project (due May 5th)
• Write formal report for statistical mechanics project (due May 7th)
• Write formal report for special topics in physics (due ???)

Facebook Has a New Chat Feature

Facebook has a new chat feature that allows you to IM your friends who are online.

Like I needed any more distractions this semester?

PhD Comics Sums Up My Life

I don't know how many times my professor has walked in on me dinking around on the internet after I had submitted a job to the supercomputer or did a happy dance for a working algorithm. So, I enjoyed this PhD comic much:

Memory Lane: Circuits

I'm an overachiever a double major in chemistry and physics. One of the classes required of physics majors is an instrumentation course. Basically this course translates into circuit design. The first half of the course was building various circuits using common circuit elements that manipulated the current. There was greater emphasis on the particular designs that gave way to particular outcomes, such as the high pass filter. I remember the professor attempted to teach us circuit analysis using impedance, but he botched the lecture the first day of class and since then no one knew what he was really talking about in the lectures. [1] [2] The first half was ended with designing a circuit that would use a thermal resistor and thus give us an idea of the temperature of the room.

The second half of the course was on microprocessors and designing circuits to utilize the power of the microprocessor. It was two-fold. First, we had to learn the assembly language of the microprocessor used. Then, we had to understand the architecture of the microprocessor. This sequence ended with a project that was to build a circuit with a microprocessor that would determine the current of the thermal resistor and display on an LCD the temperature of the lab.

I have fond memories building rat nests in this class due to the random lengths of wires my partner often had fetched for me. [3] The following pictures I found on my phone are not one of the rat nests, unfortunately. Also unfortunately, I don't recall what this circuit does. Nor am I going to figure it out before I've had my coffee. Feel free to analyze it for me. There will be a bonus quiz after lunch.



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[1] And the seminal book, Horowtiz' and Hill's Art of Electronics, was too intimidating and boring to drudge through just to understand circuit analysis, a concept we were never tested on nor expected to comment on in our lab reports.

[2] When I mean botched, I mean he lectured us for a month one way, and then found out he was incorrect for an entire month. Welcome to my undergraduate career in physics ;-)

[3] My lab partner, who is my best friend and current roommate, was probably the worst lab partner I've had at LSU. This includes the pre-med who stuck a very hot round bottom flask of various organics into an ice bath to "quickly cool down" the reaction so she could make her hair appointment...GRRRR, pre-meds!!!

Roto-Vap Woes and Amazing Colors

The roto-vaps in the undergraduate lab suck. No, wait. They don't suck. That is, their vacuum simply is non existent. That means if you have a lot of solvent to get rid of, expect to take several hours. unless you're ingenious like me and ice the mofo down.

The multi-colored bowls on the side are acting as awesome molding for the ice.

But when push came to shove, I just went to another lab that had a REAL vacuum pump for their roto-vaps and stayed there. I even had a little friend while I did several filtrations to remove the DCU from the oil. [1] S/he ran several laps around the lip of the water bath before disappearing.
So with as much of the DCU filltered out as I am willing to fight for, onward to step two.
Thus, for the past two hours I have been adding the obtained oil from the first reaction into a D-Lysine and sodium bicarbonate solution in a THF:water mixture. Now, we have some pretty colors. Before adding dropwise:

Notice the cloudiness. Now, add some oil in a THF solution (~140 ppm oil):

The cloudiness is gone. Sort of. It's definitely a lot less cloudy. Once all the oil has been added, you get this: [2]

Let this stir for about two hours and then bring the pH down to 2 by adding 0.5 M HCl dropwise to the reaction vessel. That's my next step before synthesis class begins at 7:30am. Woohoo!

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[1] The best technique to remove the greatest quantity was to wait a couple of hours to allow the DCU to crystallize and crash to the bottom of the flask. Apparently DCU makes pretty spindly white crystals when allowed to.
[2] Sorry for the blurry images. My brother was the photography major, so all the steady handedness I could have inherited went to him.

Who Did It?

Who did it? What sophomore or junior put acetone dichloromethane in the plastic cuvette? Seriosuly. Rawr!

*UPDATE*

One of the lurkers on this blog from my school has confessed to being the culprit. I shouldn't have been so hasty with my generalization that it was an undergraduate. It was a grad student! Curse you for melting all the cuvettes. Revenge will be mine!

Moar Expelled lulz!

This time, from Skeptic magazine's Michael Shermer:

It was with some irony for me, then, that I saw Ben Stein’s anti-evolution documentary film, Expelled: No Intelligence Allowed, opens with the actor, game show host and speech writer for Richard Nixon addressing a packed audience of adoring students at Pepperdine University, apparently falling for the same trap I did.

Actually they didn’t. The biology professors at Pepperdine assure me that their mostly Christian students fully accept the theory of evolution. So who were these people embracing Stein’s screed against science? Extras. According to Lee Kats, Associate Provost for Research and Chair of Natural Science at Pepperdine, “the production company paid for the use of the facility just as all other companies do that film on our campus” but that “the company was nervous that they would not have enough people in the audience so they brought in extras. Members of the audience had to sign in and the staff member reports that no more than two to three Pepperdine students were in attendance. Mr. Stein’s lecture on that topic was not an event sponsored by the university.” And this is one of the least dishonest parts of the film.

I wish I had known this before going to the movie. It would have added more enjoyment for the ending scene.

**SPOILER**

The ending shows Stein at the podium which he was at the beginning giving a "heartfelt" speech about freedom. His speech is intertwined with video from Reagan concerning the fall of the Berlin wall. The Reagan references simply explode at this point.

If American commercials were this entertaining

If American commercials were this entertaining, I would watch more TV.

Expelled Lulz, Again

So, a couple of friends of mine and I went and saw Ben Stein's movie Expelled. Imagine Al Gore's documentary merged with Michael Moore's having butt sex with Ronald Reagan. That pretty much sums up the quality of the editing.

There are enough cut scenes to soviet bloc Germany and references to the Berlin wall to make the film very boring. Combine that with Stein's monotone voice and a random segment of him getting lost in Seattle, and the movie ends up being a snore.

Luckily, there are interviews that do instigate "teh lulz" from my friends. The one which made me nearly laugh out loud was the interview with Caroline Crocker, former George Mason instructor of cell biology. She claimed she was "disciplined" for having a couple slides about intelligent design. Much to the discredit of the movie, they never explained that her job was a non-tenure track instructor position. They also do not mention that she had joint positions at GMU and Northern Virginia Community College. they do not mention that it was her students that complained about the instruction material and how it did not relate to the scope of the course. They did not explain that her position as a contingent faculty member is dependent on (1) student reviews from course evaluations and (2) staffing needs.

The entire movie is based on this tactic of not going deeply into the matter of each person who was "expelled". For a movie that begins with the premise of freedom of inquiry, it seems to me that inquiry ended only at the point where they could build their case and not at the deep heart of the matter for each individual.

Another "lulz" moment was when Stein said he sought out top scientists to discuss this topic with, and the first person of a long string of one-liners from various scholars was Daniel Dennet. Now, I like Dennet. I would not call him a scientist: his main profession is philosophy of the mind. And he has written a good book about evolution. But he's still not a scientist by any stretch of the imagination, and he readily admits it at public appearances I've seen of him. So I chuckled to myself in my seat.

The last "lulzy" moment I'm going to bring up is an interview Stein had with a professor of the history of biology. [1] It was part of the movie which showed that atheists in the biological sciences justify their atheism with their knowledge of evolutionary biology. PZ Myers and Richard Dawkins were featured in this segment. The professor of history in biology was as well. The professor gave a spiel about how evolutionary biology removes god, purpose, and free will. I couldn't resist but laugh very hard in the theater that my friend clasped my mouth to shut me up. Daniel Dennet has written extensively on the view that determinism and free will are not incompatible. His presence in the movie and the movie's attempt to drive home that evolutionary biology necessitates the end of free will was too much irony. Too much.

And the last relic is my friend's response to the molecular biology video ripped from Harvard's XVIO. During the video, I was chuckling due to the cheesy 2D-1/2 graphics on the screen. But when the clip was over, my friend yelled at the top of his lungs "EPIC FAIL!" 'Twas funny.

If you haven't seen the movie yet but are going to, please do me a favor. Can you count the Reagan references throughout the movie? Reagan pictures are like an Easter egg throughout the entire film. That's a new game now.

The only thing I got out of the film was that I wanted a pull-out back scratcher like Stein had in one of the clips. That's basically it for this weird conglomeration of soviet bloc Germany, chopped interviews, and Ben Stein getting lost in various cities.

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[1] I unfortunately do not remember his name.

Graduate School

I almost forgot that graduate school decisions had to be made soon (eg. yesterday).

I'm off to the University of Illinois at Urbana-Champaign in the fall. That's only so I can drink excimer's perylene and other experiments.

I'm simulating benzene

I'm in a statistical mechanics class this semester, and we have a final project to do. The final project consists of running at least two different stat. mech. simulation types to study some observable properties of a particular chemical species. My group decided to simulate benzene across different pressures and temperature to study phase-change phenomena, amongst other variables.[1] [2]

We're going to run a Monte-Carlo caluclation in a yet-to-be-determined staistical ensemble and molecular dynamics simulation in a microconanical ensemble. [3] If time permits, I want to do a potential of mean force calculation. Aside from phase change phenomena, I want to also study the heat capacity, chemical potential, free energy, viral coefficiant, pair radial distribution function, time-correlation function, and the diffusion constant. [4]

All simluations will hopefully be ran on the supercomputers at LSU. If not, I'll dedicate my desktop's computing powers to the project. [5]

Now, someone give me more time to do this project, because it's due around the same time as my other projects :\

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[1] This group is different than the group for the analytic project.

[2] Benzene is "big enough" to seem complicated, but "simple enough" in the calculations due to some approximations.

[3] My group can't come to a consensus of Gibbs ensemble versus canonical. I have a previously developed binary for the Gibbs model, so I want to use it (I used it to study orthoterphenyl with benzene impurities in a range of temperatures including the temperature of glass-formation). They want the canonical because it's easier for them to understand it >.<

[4] From previous research, I have or have found code that calculates each from the Gibbs model and/or from the output of PLINY_MD. Another reason I want to use Gibbs ensemble >.<

[5] That would suck because I hate how my Windows compiler compiles FORTRAN code. And I hate DOS commands. Period.

I'm looking for bad things

Concurrent to the senior synthesis project, the senior analytical project I am involved in is pretty interesting. My group are looking for PAHs and heavy metals in local soil samples. Unfortunately, there isn't enough time available to do a significantly large statistical sampling of different location-types as found in most of the environmental literature, such as comparison between residential and urban areas or high-traffic versus low-traffic locales. But there is enough to compare soil from LSU with soil from two spots on the Mississippi River: one near ExxonMobil and the other near the bridge. For each location we gathered three representative samples.

The bulk of the project is sample preparation (as always is in analytical settings). The PAHs are being extracted from our soil samples using dichloromethane as the solvent. The extraction is being expediated (and made safer) by using a microwave oven instead of other traditional methods. Heavy metal extraction is a simple acid digestion in concentrated nitric acid. Instead of using the "old school" hot plate method of acid digestion, again we're using a microwave oven to expediate extraction (and it simultaneously makes the procedure safer). [1]

We're using GC-MS to quantitate the PAHs, and we're using flame-AAS or flame-AES to quantitate the heavy metals. [2]

Let's see how "clean" these soil samples are? I'll post results in ~two weeks (because that's when it's due).

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[1] An interesting note, we want to study lead and copper particularly. However, our group got into a bit of an argument over whether we would have extracted enough of either within our detection limits. I argued we wouldn't based on a few articles I read from the literature which used hydrofluoric acid to extract lead and copper. We'll see, though.[a]

[a] Funny story, a labmate argued that HF wasn't a dangerous acid because it wasn't a "strong" acid. I think the only thing saving him from serious scorn from me would be the fact that he's a pre-med >.<

[2] I'm arguing we run both the absorption and emission experiments. It's not hard to change experiments on the user interface, and I haven't had the time to peruse the literature or any standard procedures to see which would be better for which metal. It's easier to throw away useless data than realizing you're missing useful data.

Previous Outburst

The previous outburst was generated by a frustrating aspect of my senior synthesis project. The full schematic is shown below:
The product (1) seems simple enough of a reaction to me. But, the cursed side product (dicyclohexylurea, DCU, a white solid) is driven strongly by Le Chatelier's principle. So, to slow it down, it's a good idea to stick it in a refrigerator once dicyclohexylcarbodiimide (DCC) had been added (if the reaction vessel wasn't iced, expect everything to crash out VERY quickly) [1].

So I thought I did everything well according to procedure. Prepare a round bottom flask with ~250mL THF, and dissolve the ether-acetic acid and hydroxysuccinimide in the vessel. Dissolve the DCC in ~50mL THF [2]. Ice both for ~30 minutes. Pour. Cap. Stick in refridgerator. Have beer.

So you would expect some DCU. But I didn't expect 13.8g, especially when I used ~14g of the DCC. Granted, I haven't done the calculations to determine how much of my DCC was lost to DCU, but ~13.8g seems like a bit much.

And I haven't even gotten all of it out of my reaction vessel. DCU is stubborn and wants to stay in my reaction vessel and not come out of solution. Plus, I think the pumps to the roto-vap lack sucking power and create a poor vacuum to remove the THF from the r.b.f.

At the end of the day I need a 140ppm solution of the pyrole-ether-acetate product. Hope for the best? If not, expect more inane bitching about synthesis. [3]

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[1] DCC is disgusting to use. It's a very chunky solid that requires chiseling to obtain. Secondly, it's very, very soluble in organic solvents and oils, particularly those found on your skin. So, it's readily absorbed through your skin. And, it's a sensitizer, so I feel bad for anyone who continuously uses DCC, like protein chemists. (Oh, and I know there's worse chemicals, but I'm not working with those at the moment)
[2] Oh, did I mention DCC has a high vapor pressure as a solid? Scared now? Muhahaha!
[3] Why oh why did i not change my concentration to chemical physics? The silly notion of being a well-rounded chemist has given me headaches, lol!

Dicyclohexylurea

gtfo my reaction chamber!

>.<

Expelled Lulz

Remember that intelligent design movie called Expelled that has been circling around the blogosphere causing all sorts of hoots and laughter? Want to know something very funny? FOX News didn't like it. Serious lulz!

(Look for the subtitle "Ben Stein: Win His Career")

Rush Limbaugh: Dishing teh stoopid

I had the unfortunate opportunity to hear Rush Limbaugh's show yesterday. Even worse, I read the transcript. See anything stricking:

By the way, it is this vast particle collider at the CERN research centre that
they say could replace the Internet, with speeds so fast that you'll be able to
download a high definition movie, a two-hour high definition movie in three
seconds. They're going to use a particle accelerator and collider for it.

NO! The Large Hadron Collider (LHC) outputs large datasets that data-transfer is burdened by current technologies. By utilizing essentially parallel computing technologies (interfacing both hardware and software) you can overcome the data-transfer problem. The 'Grid' is not equivalent to the LHC, though it was developed as an answer to the so-called large data problem.

In other words, he's looking for a "God particle." He's looking for a
particle to prove God. Dr. Higgs, please, just look out the window. You see that
tree? You see the grass? Whatever is outside your window, all of it, it's God
particles. Every aspect of it is God particles.

I liked Leon Lederman's book. It was a fun read. Limbaugh has ruined the book for me. Thank you idiotic commentator on current events for ruining science for me.

But in all seriousness, the Higg's boson, which would essentially explain the reason for the massless photon and heavy W and Z bosons, is an important fundamental particle of the Standard Model. I wouldn't have called it the "God particle" as Lederman playfully called in his book, but that's just a diversion from the more important aspect of its discovery: electroweak symmetry breaking.

But Limbaugh and other media sources have sipped from teh stoopid kool-aid. They lacked reading comprehension to see why Lederman called the Higgs boson the God particle. I'm too frustrated at the moment to expand any further. Teh stoopid hurts my brain too much.

These scientists, they fear God because God has the answers, God's smarter
than they are.

God's a civil engineer. Only a civil engineer would put a recreational area in a waste zone.

But seriously, the above quote is one of those "he didn't just say it, right?" *shrug* I don't fear God. His followers scare me enough as it is.

In fact, one of these guys in Ben Stein's movie, guy named Hawkins who's over at
Oxford I think, Oxford or Cambridge, Ben Stein goes over and interviews him in
this movie, Expelled.

Hawking is a theoretical physicist from Cambridge. Dawkins is an ethologist and evolutionary biologist from Oxford. Only Limbaugh would be capable of combining the names together in a horrific screed.

And the movie is the laughing stock of the blogosphere. Especially when PZ Myers was kicked-out of a screening despite him actually being in the film.

Ugh. The internet has exemplified teh stoopid which existed even before the internet was popular outside of physicists. Shame on the internet for promoting teh stoopid to higher levels. And shame on Limbaugh for being a participant in teh stoopid.

Offsetting "teh stoopid"

Human civilization has an impact on the local and global environment. Everytime we cook food or drive to the grocery store, we are creating waste products that are literally dumped into the local ecology to handle.

There are several thingss we can do that lessens or offsets our impact on our environments. The most obvious first step is to do a cost-benefit analysis of our activities and remove those activities which are deemed more wasteful than beneficial, such as showering three times a day or flushing twice after fecal expulsion. The next step is to invest our resources into developing new methods to accomplish the same goals that decrease our impact on the environment, such as researching for alternative fuel sources or cost-efficient, energy-efficient white-light sources.

Obviously there is a need to determine what resources we have for such endeavors. Not everyone has the necessary background to be actively involved in the research. However, we can be passively involved. Such endeavors require money, both for materials and to pay for the labor involved. [1] The best method for the average citizen would be to write your Congressman or Congresswoman and demand more funding for the National Science Foundation, the Department of Energy, and other government institutions that are the prime source of scientific funding.[2] You could also purchase carbon offsets to account for the necessary activities of your daily life that releases carbon emissions by offsetting such release via supporting energy resources that sequester such carbon instead.

Just like the environment, there are necessary evils involved in entertainment. Some of us are drawn to "teh stoopid" because we get some marginal enjoyment from observing "teh stoopid" in action. Our enjoyment has come to where it has become necessary for us sometimes to econimcally support "teh stoopid" on accident just to get our kicks. This is obviously bad for the total intelligence of human society. We need a way to offset our finacnical support of "teh stoopid".

One route is to write our Congress again. However, sometimes "teh stoopid" infects our politicians. It would be better to invest in lobby groups to simultaneously combat "teh stoopid" in politics and in general.

Thus, if you do an activity that somehow gives money to "teh stoopid", then I recommend offsetting your contribution by donating to an organization that opposes "teh stoopid". For example, if you purchase a book on creationism, purchase a book on evolution. If you purchase a conservative's screed (eg. Anne Coulter) purchase a more balanced analysis of the current event topic. If you bought materials from a company that denies global warming, invest more in lobbying groups that are pushing for anti-global warming legislation through Congress. If you watch YouTube or MySpace and click their ads, then listen to NPR or watch PBS and donate money to your local broadcasting station. [3]

"Teh stoopid", however entertaining it is, must not be allowed to gain an economic advantage from those of us who are purely entertained by its existence. Thus, we must donate and offset our contribution to "teh stoopid".

Do it. Nao! I demand it.



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[1] Graduate students need money to buy ramen, too!).
[2] And if you're rich, please donate to a research institute to create an endowed chair. That simultaneously creates a source of funding for research as well as recruits top-notch researchers to that institution. And, your name will be immortalized; so, that's always cool!
[3] YouTube, however funny internet phenomena is, needs to be offset by the introduction of news and current events. Tron man IS NOT a current event.

ACS convention

The national ACS meeting starts Sunday in New Orleans, LA. This means I will be boozing it up in New Orleans this weekend. Send me a facebook or a myspace or email my gmail (recspecz) if you'll be in town and want to booze, talk about chemistry/physics, bitch about being an undergraduate/graduate, or booze some more.

I'll be at the undergraduate poster session Monday from 2-4pm. Check out my poster (#944: "Application of a kink-based path integral formulation to molecular systems"). Unfortunately, it isn't an open bar environment so my science may be weakened by my socially-awkward, sober self.

Did I mention there will be booze in New Orleans?

Give her the Shock(er) Absorber

The burning question of why women wear sports bras has finally been answered for those of us who prefer to learn visually. This website will show you the awesome power athletic activity has on boobs.

Do FF+G on extreme activity level. It really looks like to me that the nipples would cut the girl's elbow in two. Maybe it's just me.

This is me right now

Yeah, my hair is in a very confirmationally irregular poisition as well and tends to stay that way all day.