Saturday, January 23, 2010

You can talk to me! Can I talk to you?

Hi everyone! This is Paul from Colorado. He's a masters student in Course 16 (Aero-Astro), and he's in the Air Force. He's currently taking this really awesome sounding class called System Architecture (ESD.34), and his project is to analyze this really neat-sounding military helicopter. The idea of the class, and of the project, is that you take a sort of half-reversed approach to analyzing complex engineered systems. What is this part for? How does it relate to the other parts around it, and how does it fit into the system as a whole? How did this system evolve? What was the designer thinking at this step? How can I take this big monolithic-looking complicated thing and break it up into meaningful parts? The helicopter he's looking at is an 80s model which was based on an architecture originally built in the 60s for search and rescue, then adapted for some of the surprisingly similar circumstances of special ops (flying at night in horrible weather, for example), but with the greatly expanded capabilities necessary to deal with things like hostile airspace.

Most other people in his class are also analyzing large mechanical devices (one girl is doing the ISS), but one or two are doing more abstract things. Someone is studying air traffic control, and oh there was another neat project topic that I unfortunately forgot.

We thought it would be amusing to analyze the Saferide shuttle system from this perspective. If it hadn't inexplicably held up for ten minutes at the student center, we would never have started talking.

Figure 1: No, really.

Why don't I do this more often? Just strike up a conversation with random people? You do have to exercise care in choosing the right opening question ("What are you doing this glorious IAP?") and refrain from talking too much about yourself... but it really, really isn't hard. There's not even any risk. The worst that happens is that the conversation fizzles and you go back to your book or iPod or whatever. But despite what people tend to think when locked up inside their own heads, everyone else is a thinking human being with interests and passions and opinions and experiences, and these can differ from your own in fascinating ways.

I'm not saying that everyone should be engaged in conversation all the time. I enjoy reading on the bus too, and I certainly enjoy solitary time, being somewhat introverted. But there's no reason to fear or avoid the nontrivial stranger conversation.

Tomorrow I think I'll strike up a conversation with the bus driver.

[The only problem I have with the "Just Shy" shirt is that it automatically puts the onus on the other party to initiate conversation. I think that, in wearing it, one must also resolve to initiate more conversations oneself. If that is done, there can be no harm in advertising that your ears are open for business.]

Thursday, January 21, 2010

Focusing on the high order bits

I was flipping through some bookmarks just now and ran across Scott Aaronson's post on Umeshisms, a particular type of exhortation to think about important things and not about trivia. Now, I usually find it difficult, if not impossible, to keep my focus on the high order bits in life, including both the Important Science Questions bits and the Stop And Smell The Roses type of bits. This puts me into a bit of an existential quandary, as it seems to be particularly important for scientists (and scientific engineers) to think Big Important Thoughts and not get distracted by minutiae.

Partly, perhaps, this is because I'm still an undergrad and lack the context to ask the Big Important Questions. (I'm taking a seminar-type course next semester, which I hope will help. But really, at what academic age are you supposed to learn how to ask Big Questions?) Partly also, perhaps, I have been trained all my life to turn every assignment in on time, get every point, answer every question, take every note, and it's proving difficult for me to evolve into something other than a student. I've certainly come a long way since freshman year, but naturally I begin to recognize how very far I have to go. And, anyway, I've been this way all my life. Call me "conscientious" if you wish to be kind, and "neurotic" if you don't.

Today in lab, I was tired and made a conscious decision to stop working on Science and start working on chores like pouring petri plates and unpacking boxes of pipette tips. I'm unsure how much this was due to my being tired and having a mediocre-to-poor week in general, versus being due to my intrinsic inclination toward the more brainless side of technical work. My brain seems to be at its happiest when I'm doing mildly repetitive, not particularly demanding work that is nonetheless not entirely stupid and requires concentration. Despite how tired I became the other week when I was doing the growth curve, I actually really enjoyed it because by the fifth or sixth hour I had the whole process down to an entirely mechanical, meditative series of pipettings and platings. For a further example, in high school I made a lot of chainmaille (both armor and jewelry) -- and it doesn't get much more repetitive than concatenating hundreds or thousands of little metal rings.

For this reason, I'm thinking hard about where I actually want to end up when I graduate. Reportedly, there exist jobs where one is primarily a lab technician but can also do a small research project on the side, and I'm extremely tempted by such a job. But I feel like if I did that, I'd be wasting my education or something. What to think?

Friday, January 15, 2010

I, for one, welcome my new bacterial overlords

Over the past 24 hours, and yes, I really do mean the past 24 hours, I've been constructing a growth curve in my lab. The idea is this: there's an easy way and a hard way to tell how many bacteria there are in a culture. The hard way is to take a sample of that culture, spread it out on a plate, and count the colonies by hand (assuming each colony arose from a single bacterium of the original culture). The easy way is basically a more sciency version of "just look what color it is".

Figure 1: Shall I compare thee to a summer's day? Thy color is more lovely and more linearly related to the pH of the solution. [Source]

The bug I'm working with ferments sugars for a living, so as it grows it makes its environment more acidic. This is really handy, because we have wonderful molecules like phenol red that change color according to pH. In this particular case, yellow means acidic and red/pink means basic, so as the bacteria grow, the ratio of yellowness to redness should tell us something about how long the cells have been growing and how many there are. Here's a paper by another group that used this method, although they did so much other (amazing!) stuff that you'd have a hard time finding the details (look at figure S4 on page 41). So it really does boil down to "just look at what color it is", except that if you need to be precise, you use a spectrophotometer instead of your eyes.

The trouble is that the yellow/red ratio doesn't actually tell you anything about the number of cells in your culture, unless you take the trouble to do it the hard way and the easy way at the same time and figure out how they correlate. This is called doing a growth curve, and it's something that has to be done for every different bug if you want to measure it by any method that's easier than counting spots in a dish the day after you wanted to know.

So... while I can't say I have been in lab for the past 24 hours (I took a couple hours off last night to go get food and a nap), I have been running this same experiment for the past 24 hours and taking samples more or less every hour. It's tiring in multiple ways. I could barely make myself come back from my dinner-and-nap break because I was in physical pain from being tired. Also, having to go do something for 15 minutes out of every hour is hell on your ability to get anything else done.

When I said I had blocked out the entirety of my IAP for this research position... I guess I really meant the entirety of my IAP. All hail science!

Tuesday, January 12, 2010

Obligatory navel-gazing

...or gazing at whatever counts as a blog's navel. I don't think blogs are placental mammals, after all.

Figure 1: Also not a placental mammal.


When I signed up for the Iron Blogger challenge (blog >=once a week or contribute $5 to a communal beverage pool), I could have started an entirely new blog, as many participants did, even if they had old fossilized never-updated blogs. I was really tempted to do so, because I named this blog The Dendritic Arbor back when I thought I was going to study neuroscience or cognitive science. Dendritic arbors are cool, but they really don't have much to do with synthetic biology.

Figure 2: Santiago Ramón y Cajal's drawing of this blog under a microscope using Golgi's silver nitrate stain.

But then I got lazy and I realized that if I attempted to set up an entirely new blog, I would be trapped in the same yak shaving that was trapping my friends. Yak shaving, while fun, is not very productive. I already shaved yaks to produce this blog. Besides, what would you call a synthetic biology blog? Genetic Memory? On The Scaffold?

Of course, that means I have to come up with a retroactive justification for naming my blog after a Neuroscience Thing. Dendritic arbors are some of the most gorgeous, elaborate cellular structures anyone has ever seen. More abstractly, they allow a single neuron to take thousands of individual inputs from dozens or hundreds of other neurons, and they integrate the total incoming signal to allow the cell to make its perpetual decision: fire, or don't fire?

I like to think that I can source interesting information from all over the place and integrate it all together here for your viewing pleasure.

(ScienceBlogs fans will note that I'm imitating the picture usage style of the fabulous Dr. Isis, which always makes me laugh, but I'm not sure how well it works for other people. It's an experiment; I'm sure I can never live up to the science goddess' hilariosity and fabulosity.)

Monday, January 11, 2010

Lab Resolutions

Last summer I had an undergrad research position (UROP) in the lab of Tom Knight, one of the founders of synthetic biology. It was pretty good, but I really didn't make as much of it as I could have.

Then I went incommunicado for an entire semester. I just dropped off the face of the planet, as far as TK was concerned. Taking a break from research for a semester is not in itself terrible -- if you have a difficult course load, you have a difficult course load. However, just dropping off the face of the planet is highly unprofessional and not recommended.

In about half an hour I'll be in a meeting with TK, beginning my re-entry into the lab. There'll be random technical detail updates to go over... but privately, there are a lot of things I want to improve about the way I approach lab work. Thus, this list of resolutions, which I'll be periodically updating.

Scheduling / Productivity

- I will filter my internet access while at work, both WWW and zephyr. (I already have filtering mechanisms; it's just a matter of applying them strictly.)

- During IAP: I will go in to lab every weekday, and if I miss a lot, try to make up a bit on the weekend. Once term starts: I will schedule blocks of lab time among my classes, going in at least 3x a week... I'm undecided about the weekend. I will adhere to this lab schedule as if it were a class schedule, i.e. no skipping.

- If I didn't pipet something or run a gel or look at my cells or do any other Real Lab Thing, it didn't count as being in lab. (I'm not sure about this one... probably needs some caveats about "what if I'm waiting for my primers to come in the mail" or something.)

Communication & Stuff

- I will continue working on my M. florum project from the summer, and also discuss with TK what's best to do about the fact that I don't actually find it tremendously interesting. The solution may involve picking up a second project.

- If I'm having difficulty extracting some nugget of information from the literature, I will get help by the next day instead of putting it off. I will strive to ensure that said help actually improves my literature-searching skillz instead of being just "Professor Awesome saves the day again".

- In order to keep myself accountable for time management, and to keep a clear view of overall project goals instead of being bogged down in minutiae, I will have some kind of meeting or status update with TK every day I am in lab unless he's out of town. If he's out of town for several days running, frequent email updates.

- I will figure out a way of explaining my research to my relatives that does not include the word "plasmid" (and probably should not include the words "user interface" either -- last summer I got lazy and made up a computer analogy that wasn't very accurate).

Saturday, January 9, 2010

Do I get a Home Improvement merit badge now?

I didn't grow up tinkering or making things or using tools, and this has always sort of bothered me -- especially since coming to MIT, which is full of tinkerers and makers, even in the more theoretical majors. And, the DIYbio movement notwithstanding, mainstream biological research is not exactly hands-on or building-intensive. I've learned to program a little and taken an excellent hands-on circuits class, but that's about it. So you can imagine my trepidation going into Help Week, in which the pledges of my fraternity kick the initiates out and devote lots of time to home-improvement projects.

My pet project was to install a towel bar in the women's bathroom so that people have someplace to put their washcloths that dirty water won't get all over the shelves. At the beginning, I knew absolutely nothing about how this was done. I spent some time deciphering the pictorial instructions that came with the towel bar, then went to the Internet and learned about using plastic anchors to put screws in drywall.

The trouble started when I realized I didn't know what size hole to drill in the wall. The internet said to use a bit "a little smaller than the diameter of the anchor", but it didn't say how much smaller, and the towel bar package didn't specify a bit size appropriate to the anchors that were included. So I just guessed too small to start with. After enlarging the holes once or twice, I attempted to hammer the anchors into the wall. The first one went in fine, but the other three didn't go in straight. It was here that I discovered I was using craptastic cheap anchors -- when I hammered on the last one, it bent and broke rather than going into the wall.

So now I had to figure out how to get them out. I had an idea, but I wasn't sure it would work, so I went back to the internet. It suggested (a) pulling them out with pliers, (b) pushing them all the way into the wall with a screwdriver, or (c) cutting them away with a drill in the process of enlarging the original hole. I was able to pull out three with no trouble, but the fourth wouldn't come out. So I pushed on it -- no progress. So I drilled on it -- also no progress. (Why? Was my drill bit dull or something?) So I went back to the original idea I had before consulting the internet: screw a screw halfway in, then pull it out using a regular hammer. Thankfully, that worked.

However, I was now without anchors. A quick search of the hardware closet found no extra anchors, and I was just about to start getting upset when I realized they must have been taken upstairs by the person who was working on fixing the banister. Sure enough, there they were -- actual quality plastic anchors with actual mechanical strength, able to withstand hammering, plus matching screws. And get this, the package even specified the appropriate drill bit size! I attacked the wall for the third time...

...and luckily, before I hammered the new anchors in, I thought to test the depth of the screws. Turns out they were too long for the wall. What to do now? I went back to the package and looked at all the mysterious numbers written all over it, and eventually decided that "#10" must refer to the size of the screw shaft. Then I looked through our Big Box O' Screws and found some more #10 screws that were shorter.

It was amazing how much better the new anchors worked. They went smoothly into the wall with no trouble, and I had the towel bar on the wall inside five minutes. Hey! I did a thing with tools and screws and stuff! I performed an act of home improvement by myself! Why isn't there a Science Scouts badge for biologists who step outside their academic bubble like this?

Figure 1: Hells yeah. That towel bar ain't going nowhere.

Thursday, January 7, 2010

A women-in-science take on Avatar

A lot of the critical analysis of Avatar that I've seen so far is, unsurprisingly, from a racial standpoint. You can find that discussion by googling; I have nothing to add to it. I'm somewhat surprised, though, that none of the women-in-science bloggers I follow have said anything about Dr. Grace Augustine. Compared to discussing the plot flaws and the ecology and the racial aspects, I suppose it is a little bit peripheral (or maybe they haven't seen it yet). The only comment I've seen from the science blogosphere is from Sheril Kirshenbaum, about how Dr. Augustine and the rest of the movie scientists are a good portrayal of scientists in general:

1) Dr. Grace Augustine. Sigourney Weaver’s portrayal of a research scientist was uncharacteristically good. Instead of the typical caricature we see in Hollywood, she wasn’t socially inept (i.e. typical Rick Moranis roles) or out to destroy everything (i.e. Dr. Evil). Instead, Grace conveyed the natural curiosity about the world that I observe so often in colleagues. Also noteworthy, she was funded by a program with corporate interests, but really using the opportunity to pursue her own research. Sound familiar to anyone?

Since I've never personally encountered serious sexism, I'm a little new to the game of thinking hard about portrayals of female scientists, but my impressions were generally very positive. As Sheril and others have noted, the scientists were realistic curious-about-the-world types, and they were Good Guys too. The lab population seemed pretty diverse, with female technicians in addition to Dr. Augustine. And clearly they've done a lot before the main character even gets there (written books, learned the Na'vi language, taught the Na'vi English, etc.) There's a scene where Dr. Augustine has been mortally injured and is being carried past some biological wonder, and instinctively murmurs, "I should take a sample!" Awwwww.

(Also, points for bio-lab realism: there was a fridge labeled "Only FOOD in this fridge".)

I'm a little curious about why Cameron et al chose to make the head Avatar scientist a woman. Possibly just because Sigourney Weaver is awesome (and I'm sure I'd have more to say about this if I had seen the Alien movies). Possibly because the Good Guys are fairly diverse in general, including women and ethnic minorities, as part of the overall racial-tolerance message. The one possible motive that bothers me is that perhaps it was felt that a male head scientist couldn't possibly spout all this unity-of-nature Gaia interconnectedness stuff, but that seems like a weak motivation compared to the chance to have Sigourney Weaver. When Dr. Augustine explains to The Evil Corporate Weenie how Pandora is all interconnected and networked, he is naturally incredulous, and I picked up a "you women and your earth-mother crap" vibe from him, but he's a Bad Guy so of course he's allowed to think that way. The film overall implies nothing about Dr. Augustine's femininity affecting the validity of her conclusions about Pandora.

Perhaps best of all, Dr. Augustine struck me as having a decent mix of stereotypically masculine and feminine traits. In her first scene, after she's woken up to meet the main character, she acts like just another unfriendly hard-ass who thinks Jake Sully is incapable (by lacking scientific training, not by being disabled). Her "where's my cigarette? What's wrong with this picture?" line reminded me of Noah Vosen the abrasive CIA team leader from the Bourne movies, which I had just been watching. But as we get to know her better, she reveals quite a bit of depth for a minor character. She's not a dumb blond and she's not socially dysfunctional. She's a good mentor to her research assistants, and takes a nurturing role towards Jake Sully when he starts neglecting his human body in favor of his avatar (making sure he eats and at one point covering him with a blanket when he falls asleep in front of the video log). And she doesn't take any crap from the military-industrial folks who are cramping her style -- she doesn't stop doing science until she's physically restrained in one fight scene.

It took me a while to realize this, because I had to get past the fact that she's a field scientist and I'm not, but Dr. Grace Augustine is something like the kind of scientist I'd like to grow up to be. I'm pleased that she exists as a role model.


Grace Augustine is actually the first Sigourney Weaver doll that you can take home to play with. "I didn’t want a Ripley doll. That’s why there’s a Ripley doll with blue eyes. But Grace, I hope she has a few little pieces of plants and things like that. I hope she comes with a little botany kit. It’s good for girls to see a woman scientist who’s so good at what she does." [source]

Awesome! I want a little botany kit!

Wednesday, January 6, 2010

The sovereign importance of mentorship

A few days ago I met up with the professor from the lab at Stanford where I worked in high school. I had a pretty rough fall semester, and I felt totally unmotivated and lost, so I wanted to hear what an Actual Successful Scientist had to say on the subject.

We spent nearly two whole hours talking, and his message boiled down to: "Mentorship is the most important thing."

This Ur-message applies, or has applied, or will apply, to my life in many different ways. I'll do my best to summarize here. (Context: I'm currently aiming for grad school and academic research, but considering alternate careers. In particular I have half-formed intentions of taking a gap year after I finish undergrad, and working in industry to see what it's like.)

If you have good grades, lab experience matters more than improving your grades. I have a very good GPA, mostly because I still have the overachieving high school student complex. I'm a perfectionist and I prioritize classwork above everything else. Last semester, I prioritized classwork above continuing my research from the summer, which was a big mistake. I was trapped by the subconscious impression that I absolutely had to maintain my very good GPA or else... what?

Really good lab experience, including good mentorship, is harder to come by than well-taught or interesting classes, and much harder to come by than an A+. It also yields greater benefits later on. I had to take this part on faith a little, because I haven't been to grad school, but it seems very plausible. "Lab hands" are very hard to teach, but a small gap in knowledge is easily corrected.

This is going to be really difficult for me to implement, because I'm so well trained at Being A Student that it's difficult to even imagine doing anything else as a primary occupation. But it has to happen eventually, and it may as well happen now.

The best mentors are those with proven track records in both scholarship and mentorship. It's often said that there's a tradeoff involved in choosing an older or younger advisor for your Ph.D.: the older profs are better mentors, but the younger ones are doing all the exciting new stuff. From what I remember of our conversation, and also a little bit from my own experience, I understand that well-established advisors beat young flashy advisors hands down.

A lot of this apparently comes down to having observed the most common failure modes in one's students. My prof was able to advise me particularly aptly because he's seen many people go through similar struggles to my own. It wasn't that he had seen my exact set of problems before; it was that he had seen parts of my problems in many other people and was able to synthesize them. He had something cogent to say about gap years, about engineering vs science, about depression, about grades, about anything I cared to ask.

A diverse lab environment is better for everyone. This goes hand in hand with the previous point: the greater variety of problems a mentor has seen before, the bigger the library of memories they can draw on when advising someone with the same problem or a new problem. (Not to mention issues of sexism etc, which are also very important.)

Finally, never hesitate to ask for help. People who can give good advice love to do so, because it makes them feel helpful and all warm and fuzzy inside. People who don't wish to give you advice may ignore you or brush you off, so there's basically no harm in asking very widely. It took me years to accept that my parents might occasionally have something wise to say, but it's true. Now that I've reached the point where my parents' academic/career advice is no longer particularly helpful, I have to cast a wider net -- but it's crucially important that I actually do so, and not rely on assumptions or PhD Comics.

Saturday, January 2, 2010

My brain just isn't interested in itself.

Reading through jhamrick's last couple of posts at Artificial Awareness made me think about how I used to be enamored of all this stuff -- AI, philosophy of mind, cognitive linguistics... That was everything I was into, around the last two years of high school and first semester of college. It was who I was. I was Going To Be A Cognitive Scientist, I Was. I read all the right blogs and tried to drag my way through some of the right books (though most of the time I ended up rereading The Language Instinct, which I must have read upwards of a dozen times in its entirety).

Then I changed fields. Long, mostly unrelated story.

But I got to wondering why I'm no longer particularly interested in cognition, AI, or related subfields ('cogsci' for short). I think it's a combination of several factors.

  • I had lousy teachers for my introductory psychology and neuroscience classes, and a lousy research experience in cognitive linguistics.

This is not cogsci's fault, but it is a plain fact of my experience and a large part of the reason why I chose to change majors.

  • The field is immature; it hasn't had its Watson and Crick.

I consider biology a mature field because so much of it comes down to simply "DNA makes RNA, RNA makes proteins, proteins build the cell's traits and perform its behaviors (and affect DNA)". This was all elucidated in its basic form many years ago. It provides a framework for understanding new experimental results and generating new questions. It is a Coherent Overarching Theory. Cogsci does not appear to have a Coherent Overarching Theory yet, though it seems to have plenty of contenders. I should note that I would expect the Theory Of Cogsci to be significantly more complex than the Theory Of Biology, and take a much longer time to discover.

(I think this point actually applies to basically all of the brain-related fields, although you could argue that basic neuroscience had its Watson-and-Crick moment when people figured out the structure and function of the neuron. I suppose it's also hard to reconcile my assertion that brain science is immature with the current, legitimately amazing progress in brain-machine interfaces -- but I don't know how well we actually understand how they work, or how well we can distinguish them from magic. Anyone who actually follows the news in that area, care to enlighten?)

  • I'm too lazy to have philosophical opinions.

Perhaps in a few years I will have the energy and the intellectual horsepower to grapple with the philosophical side of cogsci. But as it is, I can only stomach it in the kind of small doses Douglas Hofstadter likes to sprinkle into his books about poetry. I have always had a hard time motivating myself to think hard about philosophical arguments, figure out their axioms, pick holes in them, etc. etc. -- or, most of the time, to even figure out whether I actually agree with them or if I'm just reading along. I'm much more comfortable playing with cells, or even models of cells where the error is quantifiable.


There are enough cognitive/AI people amongst my acquaintance that I expect I'll hear some eloquent defenses -- and I'll be glad to hear them, I really will. I'm just happy the field is in such competent hands. If you put me in charge of AI, after all, we'd never discover anything.