Saturday, November 26, 2011

Finally legal!

Yup - it's time for Christmas music without remorse! We've been listening to 8-Bit ChristmasMannheim Steamroller and Enya Christmas albums all day while we decorate. The dog is confused about why we put a tree in the living room. He spends a lot of time looking at it.

Sunday, November 20, 2011


I needed to calculate a free energy today. I knew the equation I needed to use. And it involved Faraday's constant. I looked at a table of F values (with various units) and none of them seemed to make sense. I figured out how to get free energy in units of (mv*C*kcal)/mol, which seemed fairly unreasonable. So finally, after thinking through several possible values/units of F, I gave up and e-mailed my PI. Turns out the solution to my problems is knowing that volt=joule/coulomb. Somehow I don't think I EVER knew this.

So of course, I head to Wikipedia, where I find out that not only can joules be defined as kg*m2/s2 i.e. Newton meters,  they can also be defined as the work required to move a charge of one coulomb through one volt potential difference! Obviously my physics teachers failed to prepare me for real life, because I swear I've only ever heard the Newton meter definition.

Wednesday, November 16, 2011

Best Poster Title Ever

The best poster I saw at SfN:

331.06 How does galactic cosmic radiation alter adult hippocampal neurogenesis? J. A. LEBLANC*; M. COLE; P. RIVERA; H. SHIH; B. P. C. CHEN; A. J. EISCH. UT Southwestern Med. Ctr., UT Southwestern Med. Ctr., UT Southwestern Med. Ctr. 

I actually laughed out loud when I walked by it, but they had a big crowd so maybe they're on to something!

Saturday, November 12, 2011

SfN 2011 - Neurobiology and the Law

Went to a GREAT symposium at SfN today: The Fred Kavli Public Symposium, which was titled "The Brain on Trial: Neurobiology and the Law." This symposium had speakers addressing 4 issues
  1. Memory and the courts - C.E. Stark, UC Irvine
  2. The biology of violence and the law - A. Raine, U Penn
  3. The adolescent brain and implications for the juvenile justice system - A Baird, Vassar
  4. Addiction and the control of behavior - S. E. Hyman, Harvard
There were so many great issues and I could recap the whole entire thing from my 7 pages of handwritten notes but I'll spare you. Instead, I'd like to pose a series of questions based on the lectures with some small anecdotes...

Can eyewitnesses pick out suspects?
  • Dr. Hyman points out that we best recognize people we know, and showed that people of similar ages and races can more accurately pick out someone they've seen only briefly in a line-up. 
Is eyewitness testimony reliable?
  • Our memories not only fade, but we fill them in with false memories (unconsciously). 
  • Some people believe that memories created in highly emotional situations are more accurate and less forgettable, such as where you were you when you heard about the World Trade Center on 9/11. But this seems unlikely, and two cases were presented
    • >200 college students were interviewed  immediately after the OJ Simpson verdict and again at 15 and 32 months. At the later timepoints, elements of their stories were classified as accurate, minorly distorted, majorly distorted relative to their original sotry, or they simply said that they didn't know certain detail. At 15 months, 40% of details/stories were accurate and a similar percentage had only minor distortions and a significant percentage of students admitted to not knowing some details. However at 32 months, most details were majorly distorted and NO ONE admitted to not knowing something. Not only were they less accurate, they were more confident!
    • In a simulated POW situation, soldiers were confined and subjected to harsh interrogation. Two days later, each soldier was given a packet of pictures and asked to identify their interrogator. Some packets had a picture of their interrogator, but others had no picture of that soldiers interrogator. Yet ~70% of soldiers chose a picture that they said was their interrogator in either case.
Can we predict violent behavior? Is it ethical to do so? Will it stigmatize individuals into crime? Or is early intervention necessary and responsible to avert violence?
  • Psychopaths have been shown to have a reduced volume in the amygdala (which controls the "4 F's:" fight, flight, feeding and sex). Their main reduction is in areas that control the fear response/conditioning system. In a study of 1800 3-year-olds, their fear responses (a proxy for amygdala function) were measured and the children were followed for 20 years. After 20 years, 137 of them had been convicted of a crime, and (as a group) they had shown reduced fear responses at the age of 3. 
If neurobiology plays such a big role in criminal behavior, how do we define responsibility?

  • A study imaged the brains of psychopaths and controls as they answered a "moral dilemma" question. 80% of people answer the question the same way, including psychopaths. But the areas of the brain used to answer the question are different between psychopaths and controls. In normal subjects, their emotional circuits and amygdala light up. In psychopaths, their cognitive areas light up. This (and other data) implies that while psychopaths know right from wrong, they don't have a feeling of right and wrong. In situations that also show that they have reduced empathy and impulse control, how much control over their behavior do they have relative to a control subject?
  • A more extreme case presented was a case of acquired pedophilia. A man with no criminal or abnormal psychological history began to collect child pornography and made sexual advances to his minor stepdaughter. He was reported and sentenced to rehabilitation or prison and picked rehab. He entered treatment, where he made sexual advances to the staff and was expelled from the program and headed to prison. Right before heading to prison he had intense headaches and suicidal ideation and was hospitalized (where he made sexual advances to medical personnel). Due to his intense headaches, he receive a brain scan where they found a large tumor! After resection of the tumor, he completed rehab successfully and returned home without issue. A few years later, he had intense headaches again and his wife found pornography on his computer. He immediately had a brain scan - and the tumor had grown again! After a second surgery, his life returned to normal. How responsible was he for his actions?
Are teenagers dealt a fair hand in sentencing in the juvenile justice system? Are they judged by juries "of their peers" who can really understand their behavior patterns?

  • Adolescents have immense development in the prefrontal cortex as they learn social behavior. Adult and adolescent brains were imaged as they answered whether a choice was good or bad. Adults had automatic responses (in the amygdala) very quickly. Swimming with sharks - bad. Lighting your hair on fire - bad! Adolescents mostly got the same answers, but much more slowly. And the areas of their brain involved in answering were cognitive areas, as they actually had to consider whether lighting your hair on fire is a good idea or not. As they mature, these responses become faster/more automatic.
  • Additionally, juveniles are hugely influence by peer  pressure. In an imaging study where some adolescents were told that their data would be visible to peers, they make worse decisions more automatically!
  • Social development during adolescence lasts for life. When teenagers are incarcerated, they are socialized as prisoners, which is evident in the correlation between re-incarceration and age.
Do drug courts and rehab programs actually help addicts reform?

  • Substance addiction overloads reward circuits and is classified as "highly valuable" by the brain, making drugs the highest reward. In rat studies, electrical stimulus of reward areas is prioritized even over food and sleep and rats can kill themselves self stimulating these pathways with a lever! Imaging of addicts shows reduced prefrontal cortex action (as in psychopaths). This means that an addict is physiologically incapable of adequately prioritizing at certain stages of drug use. Their ability to prioritize fluctuates with time since last drug dose, and a decision made at one time may not carry over to the next phase of their drug experience.
  • Addiction causes permanent changes in brain structure and reward systems, which makes even recovered addicts subject to relapse in response to cues and stress.
Obviously, there are no easy answers! However, neuroscience data is likely to play a role in dictating sentencing and perhaps should even prompt fundamental changes in the criminal justice system as we gain a more nuanced understanding of human capacity for responsibility and control of behavior.

BONUS EDIT: For further lay reading, check out this article from the Atlantic.

Friday, November 11, 2011

Not science - still dorky

Apparently working on computers all the time has made me pine for manual labor - I actually made a stuffed toy! By hand! during my train commute! I must be crazy. 

Lesson learned: threading a needle while standing on a swaying train = blood letting

Fig 1: Cute little stuffed Minecraft creeper

I'm sure this will be cured when I go back to my lab and start swearing at minute tubing that won't thread onto connectors and tiny glass pipettes that melt into globs when I've barely heated them at all.

Disclaimer: I do not play Minecraft. This was a gift to Mr. Alethea.

Wednesday, November 9, 2011

How did I become a graphic designer?

The public perception seems to be that grad students and other academic types are smart. You know, abstractly brainy, maybe good at math... What no one seems to realize is that in science not only are we supposed to be able to comprehend abstract concepts, to be successful we need to:

  • Write well
  • Be good at public speaking and presentation
  • Fix equipment (in my area, this means I can duct tape stuff, fix plumbing, wire things, solder, super-glue, etc.)
  • Create what you need from scratch out of stuff you find around the lab or buy cheap
  • Negotiate with product vendors to get good quotes on stuff
  • Be proficient with data analysis and graphing software
  • Be a graphic designer
It's this last one that trips me up (ok, that and the fact that I have wretched eye-hand coordination). I used to complain about this in my experimental lab, where all I had to generate was graphs. I love a good graph, it's always great when you graph something and suddenly a pattern is clear. But then you have to get these things ready for publication/presentation. I'd make a (simply dazzling) figure, and my PI would say, "Hmmm, maybe increase the axis line weights, add minor tick marks, change the color of the one line to a darker red and don't have little serifs on the scale bar." I would do all that, he'd look again and say, "What if we used open circles instead of filled circles? Let's show the correlation with a dashed line, not a solid one. Also, how about swapping panel C with panel F?" And so on.

But little did I know - it could be so much worse. Dun dun dun.

I'm getting preparing my first manuscript in the computational lab that I've been working in. I've got some really cool structural simulation data, and now I have to find the perfect way to display each aspect with 2D images. Really, it's all best shown with movies, but you can't publish a movie. So here I am in my program (called VMD - visual molecular dynamics) sitting on a pile of choices.

  • Do I use depth cuing? What perspective? Which frame of the movie? 
  • Then there are all the ways of showing a protein structure. Do I want my helix to look like a cartoon twisty? A cylinder? van der Waals radii of all atoms? Sticks? Ball and stick? Only show the protein surface? Implausible things, like licorice and paper chains? 
  • Then I can choose how to color: by atom name, residue name, secondary structure, subunit, charge, conformation... 
  • I also have a choice of "material" which is what the representation I've chosen is "made of" in the program. These choices have some obvious ones, like opaque, transparent, shiny and also some weirder ones like ghost, glass, brushed metal and chalk
  • Don't like the preset red? You can adjust it with the color manipulator. How opaque is opaque? There's a slider for that too!
Worse still, I'm often superimposing structures, or showing ligand molecules with the structure, so I may have two cartoon helices superimposed in different transparent colors with a ghostly surface representation of the rest of the protein and the drug molecule colored by atom name in licorice representation.

All of these parameters take ages to tweak so that my awesome discoveries are shown looking their best. I will never again criticize structure figures in any paper. And my advice is, if you're looking at a structure paper and they have a supplementary movie, save yourself some squinting and download it already!

An explanation

Last month was rough. As demonstrated by my total lack of posts. My husband had two close family members pass away three weeks apart, and my time and energy has been completely consumed with supporting him and being with family. His family lives about an hour away, so being at hospitals, houses, funerals, etc. kept me on the road most evenings and weekends.

Amazingly, both of us kept up with our respective graduate work all month, but boy did our home life suffer. Our wastebaskets overflowed, we ran out of milk twice because no one went shopping for most of the month, and when we did go shopping it was because we had no milk, all invitations were met with a stock "sorry, we can't make any commitments right now" response, we hadn't had a sit-down meal together at home in a month (I don't think I've alternated between starvation and fast-food that much in my whole life) and I seriously need a haircut before I go to SfN (in two days!).

In the last week we've been slowly returning to normal. And thus I will be returning to my normal (which is still seldom!) posting rate. Coming soon: figure-making - did I sign up to be a graphic designer?