Maxwell's Demoness

PhD wins again

noreply@blogger.com (Maxwell's Demoness) — Mon, 01 Sep 2008 20:31:00 +0000

See this?

That last panel? That is me. Right now. It's uncanny.

I have been a busy little demoness lately. Yes.

Phase States of a Career Woman

noreply@blogger.com (Maxwell's Demoness) — Fri, 01 Aug 2008 02:12:00 +0000

Many days, gender really is not an issue. Many days, it is. YMMV, etc. One of the biggest problems many women encounter, as Ms. PhD points out, is walking the fine line between not promoting yourself and being overlooked, versus promoting yourself and being viewed as arrogant or pushy. Hence my humble attempt at illustrating the difficulty as a graph, thus:

Quote of the day: Enjoy your education!

noreply@blogger.com (Maxwell's Demoness) — Thu, 31 Jul 2008 17:55:00 +0000

"It has always seemed strange to me that in our endless discussions about education so little stress is laid on the pleasure of becoming an educated person, the enormous interest it adds to life. To be able to be caught up into the world of thought - that is to be educated." Edith Hamilton

Trying to focus on the positive... this week it's been a little rough. Need Data!

Politics- Best Campaign Ever

noreply@blogger.com (Maxwell's Demoness) — Mon, 28 Jul 2008 19:04:00 +0000

Running for Office: It's Like A Flamewar with a Forum Troll, but with an Eventual Winner

Sean Tevis is running for state representative in Kansas- xkcd style!!!

Support Pro-Science, Pro-Geek candidates!

Friday Fun- Classic Science Music Video Edition

noreply@blogger.com (Maxwell's Demoness) — Fri, 25 Jul 2008 19:16:00 +0000

I've been saving this one for a while, and thought it would be a good video with which to celebrate the completion of my first first-author paper.

This Science Music Video is the keystone of my collection. A classic in the truest sense of the word.

The first time I saw this video, it was actually a film. As in 16mm film old-school projector style. It is a tradition to show this film as a treat after the first exam in the undergraduate biochemistry class I took back in the day.

The second time I saw this video, it was on a battered VHS. It is also a tradition to show this video on the first day of the graduate biochemistry module for my PhD program. This time it was presented by a professor who actually claims to have been at (although not in) the filming of this illustrious masterpiece.

It is interesting to see how times change. Now this rare and treasured video, narrated by the marvelous Paul Berg, is readily accessible on YouTube. It pretty much speaks for itself, so without further ado Maxwell's Demoness' Masterpiece Theater presents:

Protein Synthesis: An Epic on the Cellular Level

Manuscript Submitted

noreply@blogger.com (Maxwell's Demoness) — Thu, 24 Jul 2008 16:35:00 +0000

Ahhhhhh.

My first ever First-Author (well, co-first author) paper has just been submitted. It's just a short little technical thing with the finally-finished data set Chtulhu, a bit about hypothesis Duh and the preliminary framework for hypothesis yet-unnamed. But! It is mine (and a few other peoples') and it is done and it is sent out into the aether. In my field, that's not bad for where I am in my degree.

Wish me luck!

Friday Fun- Dr. Horrible's Sing-Along-Blog

noreply@blogger.com (Maxwell's Demoness) — Thu, 17 Jul 2008 22:06:00 +0000

I am an unashamed fan of the following:

Musicals
Cheesy Scientist Super Villains (in appropriate context)
Joss Whedon
Gratuitous Shots of Lab Glassware (in appropriate context)
Nathan Fillion
Social Commentary
Gratuitous Shots of Nathan Fillion (aka Captain Tightpants)
General Silliness
Musicals

Alas, I have never seen them all combined.

Until now.

Dr. Horrible's Sing-Along Blog is a three-part miniseries defining the "Superhero Musical" genre. Think "Once More with Feeling" with more silly if you are a Buffy fan. I strongly recommend checking this one out.... where else can you find a musical with songs like "My Freeze Ray" and lines like "I have a PhD in Horribleness*". (Actually there are many much, much better lines, but I don't want to spoil anything.) The music is actually pretty good too. (If you like this kind of thing. I looove this kind of thing.)

Available free until this Sunday only!

*Can I have a PhD in Horribleness?
How about Naughty? Dr. Naughty.

Er, I better go before I wind up saying something Silly.

Professors = Ninjas?

noreply@blogger.com (Maxwell's Demoness) — Thu, 10 Jul 2008 18:54:00 +0000

PhD comics has an interesting comparison chart mapping out the similarities between Professors and Ninjas. Interestingly, I know quite a large number of graduate students who really like Pirates. Everybody knows pirates and ninjas do not get along. I feel like there is some kind of deeper truth here, but it is eluding me. I will have to ponder this further...

Pirates	Grad Students
Drink A lot	Drink A lot
Are often disheveled	Are often disheveled
Rarely leave the ship	Rarely leave the lab
Pillage Villages	Pillage the Free Food
Are Rebels	Want to Rebel

Fred/Fnord update.

noreply@blogger.com (Maxwell's Demoness) — Wed, 09 Jul 2008 21:20:00 +0000

The more we stare at the "Fnord" data, the more inconclusive it looks for hypotheses Fred (ie the phenomenon we are looking for would almost certainly be swamped out if it is there). It's really irrelevant for hypothesis Duh, which the first paper is mostly about anyway (1). So we just took out most of the forshadowing about hypothesis Fred from the manuscript we are working on, and meanwhile we are currently slogging through some experiments to address the issue from a different angle. One of the cool things about EPR is that you can be like, "Oh yeah? Well try this pulse sequence, bee-yotch, and see if you can still hide from me!"

(1) Yay for short, technical, "Dear FSM I need to get my name out there and mark my proverbial territory while I work out the kinks in the cool stuff!" papers.

Yay update!

noreply@blogger.com (Maxwell's Demoness) — Mon, 07 Jul 2008 23:18:00 +0000

My annual Seminar presentation and Progress Report and Committee Meeting (of DOOM) occurred recently, so I had to go hide for a while and bust my arse on those. Everything went about as I had expected.

Fun Fact: If you make a word cloud out of my progress report one of the larger words is "promiscuous". Another is "cleavage". SWAM and I get naughty-flagged emails from each other all the time. Yes, I really am in biophysics, why do you ask?

My poor Teaching Portfolio finally made its weary way though all the required committees so I have a shiny certificate that states I will get a Minor in Higher Education (if/when I finish my PhD).

Anybody out there going to the Gibbs conference? It's usually a rollicking good time. I'm trying to make my mind up about it for this year though, because I usually go with BFF Senior Grad Student who is going to be busy writing or something silly like that, and it's quite a trip from where I am.

Friday Fun- Peer Reviewed Lolz?

noreply@blogger.com (Maxwell's Demoness) — Fri, 06 Jun 2008 08:07:00 +0000

Alternate Caption:

Ok guys, I totally could not help it this time. I swear. Sorry. Inspired by my previous post.
Consider it revenge on Dataset Cthulhu.

Breaking news in Cuttlefish Intellligence Research!

noreply@blogger.com (Maxwell's Demoness) — Thu, 05 Jun 2008 23:35:00 +0000

(Above image from the BBC article)

The BBC version

The original article, for those with access.

Citation:

Darmaillacq, A.-S., et al., Embryonic visual learning in the cuttlefish, Sepia officinalis, Anim. Behav. (2008), doi:10.1016/j.anbehav.2008.02.006

Summary:

This is an example of a really elegant preliminary experiment. It is simply designed and clearly tests an interesting question- can vertebrate embryos (specifically cuttlefish) learn via visual stimulation?

The researchers tested this question by exposing embryonic cuttlefish to a normal, but not favorite food source-crab. The embryos could see the crabs, but not interact with them in any other way. This was accomplished by using a special tank setup in which the cuttlefish embryos were kept in a compartment that totally separated them physically from the crabs while allowing them to see the crabs. (paper figure 1). The tanks were designed so that once the cuttlefish hatched, they would fall down to a part of the tank where they could no longer see the crabs.

Paper Figure 1:

After hatching, the cuttlefish were kept away from all food for 7 days. During this time the cuttlefish lived on their remaining embryonic reserves. The researchers then compared the feeding preferences of cuttlefish who had been visually exposed to crabs vs. those that had not. The cuttlefish were offered both crabs and shrimp and the researchers tracked which food the cuttlefish chose first. The differences were quite striking, despite the small sample size used. (paper figure 2). Cuttlefish exposed to crabs had a strong preference for crabs, cuttlefish not exposed to any particular food had a strong preference for shrimp. Neat! This research could lead to a lot of interesting follow-up questions- comparing different food preferences, determining how long they need to see the prey to imprint, is there a particular time where they imprint-i.e. do they imprint right before hatching, or does an earlier exposure influence them as well? I think it is really fascinating that the embryos retained the imprinting for seven days... that is better memory retention then some of my students demonstrate. No wonder cuttlefish write such good poetry. They are smart!

Paper Figure 2:

Dataset Cthulhu: Aka, where I went this last month (the cold room).

noreply@blogger.com (Maxwell's Demoness) — Thu, 05 Jun 2008 03:00:00 +0000

Dataset Cthulhu:

Against all odds, I actually managed to pull off the infamous contingency plan omega. Have I mentioned that my EPR sample-prep protocols are cruel? I do not recommend attempting SDSL of persnickety* proteins unless you have a lot of moxie. And persistence. And the ability to work five 16hr shifts followed by a 38hr shift. Note: my protocol looks almost nothing like the one on the Wiki, although it's about what I started with. But I digress. The point is I finally got the last sample needed for dataset Cthulhu to work beautifully. The data are very pretty, my best ever. Except:
I've been working on a hypothesis. We shall call him Fred. Dataset Cthulhu is the preliminary data to support Fred. Cthulhu involves examining eight various combos. Combos 1-7 all say: Fred. Combo 8 (the result of contingency plan omega) says: Fnord. Well, huh. Now I have to try to design experiments to see if I am really looking at a Fnord, or if Fnord is a Fred in disguise. Fnord doesn't invalidate Fred, but it might complicate and confuse him a bit. Back to the literature! (Someone should make that a movie).
We were totally far along on the draft for Paper 1 (short technical/groundwork mid-level-I-hope paper). Fnords might involve some heavy re-write. This is what we get for working ahead.

*Persnickety: Highly sensitive to temperature, buffer conditions, pH, time of day, astrological phenomena, cosolutes, concentration, and vibrational motion. Is known to crash out if you : vortex the tube (even on gentle-don't do it!) let it get above 4C for even a second, keep it at 4C for "too long"--highly variable, centrifuge it "too hard", sneeze while holding the tube, play music it doesn't like, or look at it funny. Is fond of Brian May for reasons unknown. Cannot be correctly re-folded by any known method. Yes, I need the active form.

Scientific Romance

noreply@blogger.com (Maxwell's Demoness) — Thu, 08 May 2008 20:38:00 +0000

One of the odd habits my lab homies and I engage in is trying to make up names for scientific romance novels. You know, the type of novels you see at the grocery store with titles like "Unbridled Passions" and the picture of a cowboy on it and some chick with her shirt ripped half off. Like those, but with science. Our current favorites are:

"As the Centrifuge Turns." (-may be better as a soap opera)
"Bunsen's Flames." (-Retrospective Fake-Historical)
"Hot Reactions". (-For the PG-13 set)
"Precipitating Evening " (One-night stand)
"Le Volatile" (Artsy soft-core)

Our #1 ranked title is.........................

"Scintillating Encounters."

[crickets] See, because of the Scintillation Count-er. Get it? eh? [/crickets]

Anyone got a title they want to share? I wanna see!

Go compete at the stupid poster session!

noreply@blogger.com (Maxwell's Demoness) — Thu, 08 May 2008 02:53:00 +0000

A rant:

A few times a year, The University decides to show off the fact that it has grad students who do things. The upper administration never quite stoops to interacting with us directly, but they decree events like "Graduate student showcase" or "Science extravaganzapalooza" or some such silly name. There are generally long-winded speeches, fancy food, and, oh yeah, a poster session to show off what the graduate students are up to. So that graduate students actually bother to attend, the poster session usually includes a competition for various cash prizes and shiny certificates printed on stock paper from Office Depot.

Most graduate students in the sciences who have been around long enough to have a bit of data, also have a fairly decent, fairly recent poster. At least at my school they do. We have an annual shindig that we are supposed to have posters for anyway, so most of us have posters that are less than a year old literally sitting there on the wall. So you would expect that tons of grad students would attend these poster competitions, right? It is simply a matter of dressing up slightly (or not) pulling the poster down from the wall, walking a block or two, standing there for two hours, and walking back. It gets you out of the lab, it's good practice for bigger conferences, and there is free food. Yet despite this, hardly anyone goes. I don't get it, personally. I have won close to 1k in book store certificates and travel grants for a total of 8hrs of work. That's like a 8% raise when you are on a grad student salary! It's nice resume padding and helps you improve your poster and communication skills so you can look super-professional at big conferences, where prizes or no, the impressions you give are important.

The thing that really torques me off, is the other students who say things to me like "How do you always win all these prizes? I wish I could do that." I respond appropriately in person, but this is almost always coming from people who never go. You can't win if you don't play, guys.

Grad school interrupticus updaticus.

noreply@blogger.com (Maxwell's Demoness) — Wed, 07 May 2008 03:42:00 +0000

Now with updates in pretty colors!

Big piles of science need to happen because S.W.A.M. is presenting at conference X in June that is so cool I can't even get in to go listen. She has promised to give me mad props if I can finish dataset Cthulhu by then.
~~Final Teaching Portfolio requirement for my Higher Ed minor due~~ ~~early May.~~ TOMORROW, errr looking at the time, actually that would technically be today. YIPE!!! You should see the monster I have going. BFF Postdoc is measuring my progress by how many centimeters it grows every day. Whee! Turned in. Now it has to go through at least two separate committees before I find out what the lowdown is. This is the last requirement for my minor. Will I reach my goal of finishing it by the end of 2008? Looks good so far... but portfolio revisions have occasionally been known to last for multiple semesters...
In other news, Dataset Cthulhu still kickin' my ass. We also had a "fun" cold-room incident that set everyone back about two weeks. Who needs drama when you have science?
Due to the above-mentioned "cold room collapse of '08" which killed plan theta, we are now officially resulting to "contingency plan omega" to try to get sample Cthulhu-NS to our EPR collaborators in time. I don't like contingency plan omega. It's one of those all-or-nothing, if you cut the wrong wire civilization as we know it (or several months of work) shall die a horrible death sort of scenarios. But it's the best plan I have and a girl's gotta do what a girl's gotta do. *salutes bravely* Wish me luck! (For the next few weeks, kthx)
After a two-year track record of getting my PCR reactions to work within three tries (site-directed mutagenesis, fragment amplification, you name it, I could do it) I am suddenly completely stuck on something. I had a nearly-identical reaction totally optimized and did it (literally) several dozen times without incident. WTF? *head-desk* I am suddenly suspicious of all of my reaction components, despite being super-sterile girl.

Macromolecule Monday -RFP alternate caption

noreply@blogger.com (Maxwell's Demoness) — Mon, 05 May 2008 21:15:00 +0000

Sorry, this one doesn't even have PyMol in it. It's been a rough couple weeks. Anyone out there have a favorite macromolecule? I would be curious to see if anyone has requests. My sense of LOLz has taken a beating lately, although I have a couple of non-macromolecule LOLz in mind.

Grad school interrupticus updaticus.

noreply@blogger.com (Maxwell's Demoness) — Mon, 05 May 2008 07:32:00 +0000

Now with updates in pretty colors!

Big piles of science need to happen because S.W.A.M. is presenting at conference X in June that is so cool I can't even get in to go listen. She has promised to give me mad props if I can finish dataset Cthulhu by then.
~~Final Exam/Paper for Scary Biophysics Class is due in a couple weeks. Finished, waiting for grade~~....A+++! So there, Scary Physicists!
Final Teaching Portfolio requirement for my Higher Ed minor due ~~early May.~~ TOMORROW, errr looking at the time, actually that would technically be today. YIPE!!! You should see the monster I have going. BFF Postdoc is measuring my progress by how many centimeters it grows every day. Whee!
In other news, Dataset Cthulhu still kickin' my ass. We also had a "fun" cold-room incident that set everyone back about two weeks. Who needs drama when you have science?

Gradschoolus Intteruptus Updaticus

noreply@blogger.com (Maxwell's Demoness) — Wed, 30 Apr 2008 06:15:00 +0000

Now with updates in pretty colors!

Big piles of science need to happen because S.W.A.M. is presenting at conference X in June that is so cool I can't even get in to go listen. She has promised to give me mad props if I can finish dataset Cthulhu by then.
~~Final Presentation for Scary Biophysics Class next week (I initially forgot this one because of the defense thing.) /~~PWND.
~~Final Exam/Paper for Scary Biophysics Class is due in a couple weeks~~. Finished, waiting for grade....
Final Teaching Portfolio requirement for my Higher Ed minor due early May. YIPE!!!
In other news, Dataset Cthulhu still kickin' my ass.

Faculty of 1000

noreply@blogger.com (Maxwell's Demoness) — Wed, 23 Apr 2008 22:58:00 +0000

I love Faculty of 1000. I really, really do. It's a fabulous resource for a variety of situations. Say, hypothetically you have to write a paper about a journal article for a class, with the only restrictions being that the article you select should be "good", "about biophysics," "maybe have some kind of tech advance", and "not be about anything in your field". (In my case, no "proteins, nucleic acids, crystal structures, or EPR." *sob*) Also, let's say that hypothetically you've been procrastinating on the paper because of benchwork catastrophes [1] A, B, &C and the really cool visiting speaker, and... yeah. So now you have to find a "good" paper meeting certain criteria and you don't have time to sift through all of PubMed. Worry not! Faculty of 1000 will help you find a great paper with a "tech advance" stamp, and it's very easy to sort through various topics. The downside being, every time I go to the website I keep getting sidetracked by -oh, that looks cool, or hmm, is that a technique I could use, or wow, I should really read that! Then I download about 50 PDFs to throw in my "interesting papers to read" folder where they may never be seen again.

[1] S.W.A.M. always says I shouldn't call it a catastrophe unless "Something important is on fire, someone ends up in the hospital, something worth over $5000 is broken, or it sets you back more than 3 months; so don't be so melodramatic!" For the record, all of the above have happened to me at some point during grad school. During such catastrophes, I am incapable of using words as long as catastrophe, so I use it when I can. Fortunately, none of these have happened recently. Unfortunately, that means it's only a matter of time. Once, two of the above were simultaneous. Guess which two for 100 points.

Return of Macromolecule Monday-RFP!

noreply@blogger.com (Maxwell's Demoness) — Tue, 22 Apr 2008 00:23:00 +0000

I know this is like, so three months ago, but I wanted to clear up any misconceptions about "Radioactive cheezeburgers".

Kittehs from various news sources, RFP rendered by moi in Pymol from:

Wall, M.A., Socolich, M., Ranganathan, R. (2000) The structural basis for red fluorescence in the tetrameric GFP homolog DsRed. Nat.Struct.Biol. 7: 1133-1138

PDB id: 1ggx

Return of Macromolecule Monday! RFP edition.

noreply@blogger.com (Maxwell's Demoness) — Mon, 21 Apr 2008 23:34:00 +0000

Iz temporarily delayed because Blogger isn't letting me upload images right now. =-(

*kicks things*

Preaching to the choir and doing my page-rank-part

noreply@blogger.com (Maxwell's Demoness) — Thu, 17 Apr 2008 22:26:00 +0000

Go here.

In other news, still busy like crazy... it's been one of those weeks. Our 4c fridge died a sudden death first thing Monday morning, and things have just gone downhill from there.

Friday Fun- LoL Cats

noreply@blogger.com (Maxwell's Demoness) — Sat, 12 Apr 2008 03:29:00 +0000

Because I like putting crazy captions on funny pictures as much as anyone, I felt like sharing this comic from xkcd, one of my perennial favorites.

Rapid Communication

noreply@blogger.com (Maxwell's Demoness) — Wed, 09 Apr 2008 22:44:00 +0000

From the "I need to get out more" department, the header for this paper has had me laughing all day. Yes, I know better, but I keep getting mental images of wired-up rats operating telegraph machines with their brains.

SOS! Is anyone listening! Help! We are trapped in a lab with a bunch of weird humans! We are out of cheese! Help!

Yes, I know this is a good and serious paper with patch clamps and electro-chemistry and cell-culture and math and physics and all those lovely and serious things. But the circuit diagrams aren't helping.

Repeat: We are trapped in a lab and we are out of cheese!

I think my brain is trying to defend itself because every time I read about interfacing living cells with circuits directly, it kinda creeps me out. Some people are weirded out by needles or snakes, I am squicked by phrases like "Field-effect transistors form spontaneously capacitive junctions with cultured cells from rat brains." That's just how I roll. It is a cool paper, though.

Citation:
Neurons from rat brain coupled to transistors
S. Vassanelli, P. Fromherz
Appl. Phys. A 65, 85–88 (1997)