Friday, December 9, 2011
I have three weeks to collect some much needed data for a grant, and while I had started some of this type of work before I left, I only did it for a few weeks. Now I'm trying to get set up again and it's HARD! Two nitrogen tanks had run out, someone let my cells (that they were supposed to be care-taking) get to passage 40 without thawing new ones, we didn't have the kind of glass capillaries I needed, the incubator water levels were low and I had to remake solutions. Needless to say, I did not get started on the actual work as fast as I wanted.
I'm trying to be patient about how long it's taking to ramp back up to my normal experimental output level, but given the grant deadline patience is hard to come by!
Saturday, November 26, 2011
Sunday, November 20, 2011
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
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
- Memory and the courts - C.E. Stark, UC Irvine
- The biology of violence and the law - A. Raine, U Penn
- The adolescent brain and implications for the juvenile justice system - A Baird, Vassar
- Addiction and the control of behavior - S. E. Hyman, Harvard
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.
- 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.
- 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.
- 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?
- 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.
- 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.
BONUS EDIT: For further lay reading, check out this article from the Atlantic.
Friday, November 11, 2011
Wednesday, November 9, 2011
- 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
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!
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!
Tuesday, October 4, 2011
This is remarkable, because I've felt like this for years in an experimental lab. In fact, I started interning in an experimental lab at twelve, so apparently, microbiology is so easy a twelve-year-old can do it. And as I've seen more and more techniques I continue to discover that a kid could do it.
- Making solutions - check
- Western blotting - check
- Flow cytometry - check
- Cell culture - check
- Pipetting - check
- Minipreps - check
Wednesday, September 28, 2011
Monday, September 26, 2011
The Nocebo Effect:
Friday, August 26, 2011
Why teach only two sides of the creation story? The world may have hatched out of an egg! So I guess biology class will soon become mythology class.
Personal favorites: California, Indiana, Kentucky, Maryland, Nevada (OK, I kind of <3 New Mexico!), and what is Miss Washington even saying?
Note: Candidates are in alphabetical order by state if you want to hit the highlights.
After you've seen all you can stomach of the first video, watch the parody!
Wednesday, August 24, 2011
Then, as I looked at the Facebook event page, I thought, "I wonder if I'll be the only white person there..." Then I realized that the converse is my husband's situation at least 80% of his life, if not more. And I kept my mouth shut.
Tuesday, August 23, 2011
Our tech/lab manager type person is away this week. Our tech is a 20-something who didn't get into pharmacy school and makes beer in his parents' basement. I didn't like him at first. But he is astonishingly long-suffering and good-natured, and even though I don't think he gives a darn about the science we do, everything always runs smoothly.
But, as previously stated, he is away. So is one of the other grad students and our research assistant is sick. Thus, I am somehow in charge. In charge of ordering. In charge of the frogs. In charge of making my own solutions and electrodes. And stuck with frog surgery.
So, I go up to anesthetize the frog. This rarely works in the time-frame described in our protocol. 45 minutes later the frog is still kicking. At an hour it's not. But then I flip it over, and I can see it's throat pulsing. Back in the anesthetic. Meanwhile, my surgery suite reservation is running out of time. (N.B.: I did not reserve the suite, our blessed lab manager did, I didn't even know we needed to reserve it!). Finally, the frog is out. I realize I have no gauze for dabbing blood. I figure, oh well, I'll just deal. I start the surgery.
As soon as I start extracting eggs, the person who had the surgery room reserved starting 5 minutes before pokes her head in. I say I need 15 more minutes, she says no problem, she'll use a different room. It's all good. Then I go to stitch the frog back up. I swear to goodness, that thing had HIDDEN the other side of the muscle layer (it could have been all the blood that I couldn't mop up sans gauze). I was stressing. My new (very professional hair) was in my face and sticky. This is because I had no hairnet (they're not required in this situation, but are helpful for hair restraint). For some reason, the little supply station on this floor was out of hair nets. Finally, in extreme frustration, I leave the suite in search of a hair retainer. The little supply station is just outside the door. I grab a shoe cover and stick it over my head and return to fishing around for the muscle layer. When I eventually put the frog back together and start hauling all my supplies (and the frog) back to where they belong, I get strange looks in the hall. This is when I realize I still have a bright blue, waterproof shoe-cover on my head.
Thank heavens he's only gone a week. I will remember to be extra-nice to him when he comes back (until I forget).
Thursday, August 18, 2011
PS - There are also programs that try to address the minority pipeline issues by supporting STEM students from a very young age with high-quality mentoring and research opportunities. I recently became aware of the extremely rigorous physician-scientist training program, and there are many others.
Wednesday, August 10, 2011
Tuesday, August 2, 2011
I came back from vacation just in time to revise a paper, draft another paper and resubmit my F31. After all that serious science-writing, I couldn't summon the willpower to do more than whimper about science.
Now, however, various entities are casting their blood-curdling gaze upon my other work, so I have time to write here again. Cool science is on its way!
Monday, July 4, 2011
Mr. Alethea, despite being twenty-something, had high cholesterol. I made him start running. Then I felt like a jerk for making him exercise while I never do. So, I started too, with Zumba and a Jillian Michaels DVD. (Parenthetical remark: I feel like an absolute fool doing Zumba, but it sure is fun, as long as I'm not in front of the mirror!)
While home alone over a long weekend, I thought, "OK, I really need to release some endorphins and I've been on level 1 for like a month. I should try level 2." Yeaaaah. I'm pretty sure I will just ride my rolly chair around the lab tomorrow instead of walking.
Friday, July 1, 2011
Now to get it published before I get scooped!
Thursday, June 30, 2011
Now, this dude, given that he must be in anesthesiology research if he was at my talk, should have known better. And definitely should have known better than to ask it as if he had stumbled across a trick question that would unravel all my research, because that's just jerk-y.
But it actually isn't a dumb question. Unconsciousness is much more complicated than simple suppression of all neuronal activity. During anesthesia, some neurons fire more and some neurons fire less. And the hard truth is - we're not totally sure which neurons do what or how that leads to anesthetic endpoints. In general what changes is firing PATTERN, which causes changes in how neurons talk to each other ("integration" for those wanting a more technically accurate term).
Consciousness and anesthesia are so much more complicated than simple reduction in total brain activity, but that's what makes it fun!
Tuesday, June 28, 2011
Tuesday, June 21, 2011
I have the world’s most adorable little doggie at home, and I’m totally crazy about him. I am on my university’s IACUC (Institutional Animal Care and Use Committee), which I’m sure I’ll rant more about later. I use animals in my research. If I could eliminate the use of animals in research, I would.
In all likelihood, animal research is going to come up pretty frequently here, given my involvement. It’s a complicated issue, and easier not to engage, but it is ethically important for scientists to know what they think and continually evaluate to ensure they’re following best ethical practices.
I know that some extremist animal rights groups think that animal research can and should be stopped short, right this minute. Unfortunately, their arguments are pretty flawed.
One big argument is that animal research hasn’t discovered anything beneficial to humans, or that all these things could have been discovered another way. This is simply untrue. Many important breakthroughs in disease treatment have been made in animal models. Farm animals, pets and endangered animals are also beneficiaries of animal research. Just Google it.
Another major argument is that animals are not good models for humans and consequently research done in animals will have little relevance to human disease. Some such groups advocate for using cell culture or computer models only, instead of animals models. There’s a reason all these things are called models: they only approximate the human situation in key respects.
I’m pretty sure there isn’t a scientist alive who wouldn’t rather use a cell or a computer instead of an animal. Animals are expensive, require constant care, enormous amounts of paperwork, and specialized training. But sometimes they’re just better than a computer or a cell. The problem with creating a cell-culture or computer model is that you can only recapitulate the aspects of your system that you completely understand. But the whole problem is that we don’t completely understand most tissues or disease processes. So if you make a computer model that tells you everything we know about liver cancer, you won’t be able to cure liver cancer. The good thing about an animal model is that it’s a real tissue, that will act like a real tissue does, even in the ways we don’t understand. Unfortunately, it is true that animal systems aren’t exactly like human ones. This can sometimes be optimized by choosing the right animal, or creating a transgenic animal to better mimic key features of the human system, but even so, it isn’t perfect. That’s why it’s a model. The best science utilizes multiple modeling systems to eventually develop hypotheses that can safely be tested in humans.
The hardest argument to answer, though, is the ethical/moral argument. Is it “species-ist” to treat a living thing from another species in ways that would be unacceptable to treat humans? Research makes it clear that vertebrate animals have experiences analogous to human pain, fear, pleasure and other emotional states. Rights advocates claim that these emotional and cognitive faculties make animal eligible for membership in the moral community with equal or near-equal rights to humans. This argument can’t be answered with facts or a utilitarian argument, it is about what an individual believes about the rights of non-human species. Even among anti-species-ist advocates, you can find dissent about which animals deserve what rights from worms to mice to monkeys.
Where I am:
I fall on the utilitarian end of the spectrum. Though I strongly support alternatives to animal use and sticking to the 3Rs when animals are necessary, in the end I conclude that the potential benefits of animal research outweigh the harm to animal research subjects. I think this campaign sums it up for me:
I chose to serve on my university IACUC to learn more about federal regulations concerning animal research. I got much more than I bargained for as I hear from many sides: from researchers, from regulators and from rights activists about balancing animal welfare with human welfare. There are never easy answers.
Scientists often feel pressure to justify animal research in the face of extremists who bomb, poison and mail razorblades to researchers, but most scientists will confess that it’s not a black-and-white issue. Respect for life at all levels, from proteins to cells to organisms, is central to biomedical research, and engaging with animal rights issues is important for animal users as we work to preserve the welfare of animals as best we can.
Monday, June 20, 2011
Crystals are made of atoms arranged in repeating blocks called “unit cells,” where the atoms in each repeating block are arranged the same way. Piezoelectric crystals have asymmetric arrangements of atoms in each unit cell. At rest, these crystals are electrically neutral, because the charges of the atoms are arranged such that each positive charge is balanced by a negative charge (really this has to do with dipole moments, if you’re into that level of detail). But when you squeeze or stretch the crystal, you upset this delicate balance of cancelling charges as you move atoms out of place, causing the crystal to have net charge on its faces. Same deal if you apply charge: you apply electrical force that makes the atoms rearrange in an attempt to cancel the charge, causing the shape of the crystal to change. This effect can be pretty large: applying 500 foot-pounds of force to a cubic centimeter of quartz can produce 12500 volts!
It makes me wonder how many other things I use operate on near-miraculous science!
Thursday, June 16, 2011
In Greek mythology, Mnemosyne was a Titaness, the goddess of memory, who is credited with discovering reason and language. The most well-known fact about her is that she slept with Zeus (after all, who didn’t?) and begot the nine muses. What is often forgotten is that she also presided over a river (or pool/well/spring) in Hades. The river of Mnemosyne was the opposite of the river of Lethe. Upon arriving in Hades, one would supposedly have to choose to drink either from Lethe or Mnemosyne. Choosing Lethe, the river of forgetfulness, would erase your memory of your past life and allow you to reincarnate. Choosing Mnemosyne, however, would make you omniscient.
My name, Alethea, again plays on the Mnemosyne-Lethe dichotomy. The Greek word Lethe means “oblivion” or “forgetfulness”, while Alethea is derived from the Greek word for “truth” or “un-forgetfulness.” I hope it’s obvious which Kool-Aid I drank! J
N.B. I love parenthetical statements. I know it's bad English. And I don't care.
Wednesday, June 15, 2011
I'm a 4th year PhD student at a research university. As such, I am naturally possessed of an abundance of both angst and opinions.
Last night I had a total meltdown about my life, because let me tell you, even if you don't have kids, there is no such thing as work-life balance when you're in grad school (or probably if you're in academia at all)! Then today, as I watch my seal resistance aimlessly climb to 900 megaohms and hover there without getting a gigaseal for about the millionth time this week(I do patch clamp electrophysiology), I realized that I needed a better outlet for my rage than my poor husband.
Hence, I am officially "on the internet." Here, I will tell you what life is like as a female grad student in an all-male biophysics lab, rant about my life in general, and post the cool stuff (research, comics, videos) that helps me remember why being a scientist is worth it.
So, if you like blue-haired snarky biophysicists, you want to hear what science I think is awesome, or you just wonder why grad students are such basket cases, I hope you'll stick around!
Alethea (not my real name)