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Monday, September 1, 2008

PhD wins again

See this?

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

I have been a busy little demoness lately. Yes.

Thursday, July 31, 2008

Phase States of a Career Woman

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!

"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!

Monday, July 28, 2008

Politics- Best Campaign Ever

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, July 25, 2008

Friday Fun- Classic Science Music Video Edition

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

Thursday, July 24, 2008

Manuscript Submitted


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!

Thursday, July 17, 2008

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

I am an unashamed fan of the following:

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

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.

Thursday, July 10, 2008

Professors = Ninjas?

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...


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

Wednesday, July 9, 2008

Fred/Fnord update.

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.

Monday, July 7, 2008

Yay update!

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, June 6, 2008

Friday Fun- Peer Reviewed Lolz?

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.

Thursday, June 5, 2008

Breaking news in Cuttlefish Intellligence Research!

(Above image from the BBC article)

The BBC version

The original article, for those with access.


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


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:

Wednesday, June 4, 2008

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

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.