Paleolithic Park

March 6, 2012 § Leave a comment

Perhaps not quite as exciting as revivified dinosaurs, but still amazing: plants from the late Paleolithic era are claimed to have been regenerated from fossil material (Yashina et al. 2012. Regeneration of whole fertile plants from 30,000-y-old fruit tissue buried in Siberian permafrost.  PNAS doi:10.10.73/pnas.1118386109).  This has very little to do with systems biology, but I was interested and thought you would be too.  Perhaps I could trace some kind of connection (did you know that our Artist-no-longer-in-Residence, Brian Knep, shared two Academy Awards for his work on the movie Jurassic Park?) but it would be forced and hardly worth it.  Better to admit to mild frivolity.

The plant material in question came, not from an insect trapped in amber, but from fruits buried in burrows of an Arctic-dwelling squirrel.  Some of these burrows contain hundreds of thousands of fruits and seeds.  I guess when you’re a squirrel living in the Arctic, you grab what’s going while the grabbing is good.  Shortly after the squirrels stored their hoards, about 30,000 years ago, the area froze, was buried deep in icy sludge, and has never since melted.  Constant subzero temperatures, with all available water immobilized as ice, are the best conditions you’re likely to find for cryopreservation.  Although the oldest plant seed previously germinated was only 2,000 years old, the authors were bold enough to make an attempt to grow plants from ancient frozen seeds of the plant Silene stenophylla, the arctic campion.

The placental tissue in a campion fruit. From Yashina et al.

In the end, what Yashina et al. say that they were able to grow was not the seeds themselves but an outgrowth of the placental tissue some of the immature seeds were embedded in.  The authors speculate that part of the reason they were successful with this tissue is because it has especially high levels of organic substances such as sucrose and phenolic compounds that would be expected to offer some protection against frost damage.  The plants derived from these placental tissues grew to maturity and were even capable of breeding.  They look somewhat different from modern Silene stenophylla, and they handle their flowering arrangements differently; flowers of the modern plants are always bisexual, whereas the ancient plants produced female flowers first, followed by bisexual flowers.

Micropropagation of plants from ancient placental tissue. From Yashina et al. 2012.

Though previous claims that plants have been grown from very old seeds have been debunked, the authors say that because the burrows were buried ~20-40 meters down and were apparently undisturbed they are confident that their samples were not contaminated with modern seeds.  They also performed direct radiocarbon dating on their samples.  And the plants that resulted were visibly different from their modern counterparts.  It’ll be fascinating to see the DNA sequence; I’m sure it’s on its way.

Sadly, the last author of the paper, Dr. David Gilichinsky, died just 2 days before the paper was published.

Yashina, S., Gubin, S., Maksimovich, S., Yashina, A., Gakhova, E., & Gilichinsky, D. (2012). Regeneration of whole fertile plants from 30,000-y-old fruit tissue buried in Siberian permafrost Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.1118386109

Repost: What are graduate school interviews like?

January 13, 2012 § Leave a comment

Lots of people found this post from Jue Wang useful last year, so here it is again.  Comments welcome!

Jue Wang writes:

To help 2011 graduate school interviewees, I collected some advice from current Systems Biology graduate students.  Here are their thoughts:

“Relax, have fun, don’t try too hard to impress people, and don’t get drunk at Marc’s house!” [Marc is our Chair of Department]

“Feel free to interrupt a professor’s monologue with questions. Dress warmly. Don’t be scared if your first interviewer makes you perform calculations on the fly :p”

“Have a good ‘elevator pitch’ for any research you’ve done, so you can explain it clearly and quickly when asked. You won’t be asked to recall your entire thesis, coursework, etc.”

“Don’t get thrown off if it seems like the interviewer is quizzing you. They just want to see you talk through some science with them, and don’t expect you to know all the answers. Just be honest about what you don’t know, and they’ll probably help you along.”

Update: another tidbit someone sent me today: “You should interpret the interview invitation as ‘We love you on paper, we’d like to know whether we like you in person. Hey, we hope you like us, too!'”

To give the recruits a little context to these remarks, I’ll just add a basic description of the interview weekend as my murky, pre-grad-school memory has it: a sweet hotel room, a few hours of what seemed like shooting the breeze with faculty members, meeting lots of people who inexplicably seem really excited to talk to you, and free food and drink everywhere. Did I mention the free food and drink everywhere??

I realize some might feel a little nervous about the process, especially if you take the “interview” part to mean something akin to the med school or Wall-Street job interview process. In reality it’s much more laid back. I was fortunate/foolish enough not to have given this much thought, but my first interview was with a faculty who was much taller than I realized, and somehow I found this very intimidating. It didn’t help my nerves that someone told me he was in the middle of writing a grant proposal and hadn’t slept for 3 days, and he was slightly late so I had a good 10 minutes to just sit there and hope that if I said something stupid he’d be too tired to notice. As it turns out, neither my nervousness nor any evidence of his sleep deprivation lasted more than 2 minutes into the conversation, and we had a fascinating, sprawling discussion of his research and the things we were both interested in (with a slight bias toward the former). This is basically how most interviews go.

Some of my classmates had interviews in which they were asked specific scientific questions. This can be nerve-wracking, as at least a few of the G1’s can attest, but like my classmates mention above, it’s best to just take it in stride and talk through your answers. I’ve been told to avoid trying to seem like I know something I don’t, which is confusing advice because I can’t imagine many recruits who’d be consciously trying to mislead people in their interviews. My guess is that it can seem this way if you are not engaged in a conversation and just nod like a zombie, or if you gratuitously mention ideas and jargon out of fear. Another reason to sleep well the night before and have some kind of ‘elevator pitch’ for your past and future interests, so that you can speak plainly and concisely—and therefore seem genuinely interested—about science.

One other thing I remember is being impressed and therefore slightly intimidated by the other recruits. Maybe it’s a function of how diverse — and accomplished — Harvard SysBio’s recruitment base is, but it seemed like everyone was a star at something. Also, some recruits probably went to school in the area or even worked in the department during undergrad, so they sound like they’re already in grad school. These things are a net win though, because you end up having lots of great conversations (and some insider knowledge on the best places to get pizza and whatnot).

Finally I’ll reiterate the most important advice, at least for Boston, which is to dress warmly — the East coast is very cold in late January, and the weather is more unforgiving than any of your interviewers will be. Fortunately there will be plenty of chances to warm up with beer, food, and new friends during the whole experience, so enjoy it!

What I read on my winter vacation

January 10, 2012 § 2 Comments

It’s been a while since I posted anything serious — I can’t help but feel that I should apologize, although I’m sure that very few of you sit by your computers waiting breathlessly for the next update. Anyway, my excuse, if I need one, is that much of my spare time has been taken up with graduate program applications. And I thought some of you, especially potential future graduate school applicants, might be interested in a few thoughts I have about what goes into an application, and how it’s read (or at least, how I read it).

There are  four main pieces of information in an application for an American graduate program in biological sciences: GREs, college grades (supplemented by an academic transcript), the personal statement and the letters of recommendation. From my perspective the GREs and grades essentially act as thresholds. If your GREs and grades are above a certain level, I don’t much care how good they are. Academic achievement has some correlation with likely success as an independent scientist, but the correlation is not a straightforward or linear one. So, if your GREs are below a certain level (and you’re a native English speaker), it may raise a suspicion in me that your brain is not especially agile, and I may start looking for other evidence to support this hypothesis in the rest of the package; if your grades are poor, especially in subjects that are very relevant to your proposed area of study (or, especially at a school with rampant grade inflation), I may worry about your ability to assimilate facts and reasoning strategies; but I’m probably not going to draw much of a distinction between very good grades and perfect grades. And if one of your letter-writers explains that your very-good-but-less-than-perfect grades are due to spending too much time in the lab, I may even like you better than I would have if you had a 4.0 GPA.

After the GRE/GPA threshold is passed, I have two pieces of information left: your statement and the letters written on your behalf by people who know something about your abilities. I don’t have much to say about the statement — it should be personal, after all — except this: don’t feel that you have to treat it as an exercise in creative writing. I suspect that there’s a book out there, or more likely a website, that encourages applicants to begin their statements with an eloquently written personal anecdote that conveys their love of and excitement about science. I suspect this because so many of the statements I read start with something along these lines: “Staring into the dusky red depths of the Grand Canyon, I had a vision of someday creating cybernetic wings that would allow human-powered flight. My passionate dedication to a life in science dates from that day.”

If you really did have some kind of emotional revelation when you were 10 years old, fine. I don’t mind if you tell me about it, though please try not to be too dramatic. (I’m English, after all.) But from the perspective of a specialized interdisciplinary program, I’m much more interested in your mature thoughts about why you want to focus on systems biology in particular. It’s not an easy path, and I want to know you’ve thought about it. It’s fine to try and paint a picture of who you are as a person, but the more you can explain why you’re interested in working in this field in particular, with concrete reasons from lab or theory work you have done or courses you have taken, the better.  What you say will give me some sense of how much you know about what you’re getting into, as well as whether you can write a clear English sentence and put two ideas together in a logical order.

What about the letters? IMHO these are the most important part of the package, and what’s hard about that is that the quality of the letter is almost completely out of the applicant’s control. What I look for in letters is the following: evidence that the applicant has taken the initiative to seek out interesting research experiences, and an opinion from the person writing the letter about whether the applicant has the qualities needed to make a go of independent research. Unfortunately, what I often get is a letter that says that the applicant got very good grades in class, which I already know from the transcript. Letters of this kind aren’t helpful; nor are the letters from your swimming coach or saxophone teacher, or the personal friend who’s known you since childhood. These people may all have theoretically useful things to say about your strength of character or your work ethic, but they’re not scientists and I don’t know what “hard-working” means to them. The ideal application package has at least two letters from people who know what it takes to be a good scientist, who can talk about a substantial project that you did in their group. These letters ideally go into significant detail about how well you performed in the context of a real research environment — for most of the faculty on the committee, nothing speaks louder than a statement from an advisor about the research you personally did while working with him or her.

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Communication as a network problem

November 11, 2011 § 7 Comments

I recently gave a short talk to a group of post-docs who had organized their own mini-symposium and workshop as a way of bringing the Harvard post-doc community in systems biology together.  Those of you who haven’t worked in the Boston area may be surprised that we need special events to bring together a community that is separated by only  ~4 miles, but in fact the trip from Harvard’s main campus in Cambridge to Harvard Medical School in Boston is a frustrating and lengthy one.  Much of the apparent distance is added by the need to cross the Charles River on one of its few narrow, highly trafficked bridges.  I have often wished for a personal helicopter as I sit in the traffic jam at the BU Bridge.  Hence the title of the occasion: “Across the River”.

Since this was an event focused on communicating and bridge-building (or at least, bridge-crossing) I talked about communication.  Here’s my thesis: communication plays a much larger role in the progress of science than most people (and most scientists) are conscious of.  So, one way to become a better scientist is to think more about how you communicate and try to do it better.

This is the point at which it becomes difficult to be talking to an audience you can’t see: some of you will be saying “sure, of course”, while others will be looking puzzled — science is about doing experiments, not about communication!  If I could see you, I could adapt to your reactions.  Since I can’t, I’ll say this to the “sure, of course” group: I think many of us have been persuaded to think about scientists as natural non-communicators, who live in an ivory tower and think deep thoughts and publish inscrutable, dense, leather-bound tomes that are then read by a tiny group of other eggheads.  Actually the most prevalent image in the popular consciousness may be that of the gentleman scientist from the 18th or 19th century, dressed in tweed knickerbockers and stout shoes, scouring the rocks of a cliff face for fossils in proud isolation while smoking a pipe.

A gentleman scientist relaxing at home. As you can see, a pipe is essential.

If scientists ever lived like this, we don’t now.  Even the lonely fossil collector went home to write long letters to like-minded pipe-smokers across the world about the fascinating fossils he — or she, but that’s another, possibly pipe-free, story — had found.  But this is not the way the world thinks about scientists, and so it is often not the way we think about ourselves.  On top of that, we confuse communicating with the public — which, as a group, we are indeed very bad at — with communicating with ourselves, which we do constantly. The need for communication creeps up on you throughout your career: perhaps you don’t need to be talking and reading constantly as a graduate student, but by the time you make it to your first real job the need to be a good communicator pervades your daily life.

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What the judge ate for elevenses

May 20, 2011 § 3 Comments

Andy Hilfinger pointed me to an interesting recent paper that looks at the effect of a judge’s daily routine on the decisions that he or she makes.  The judges in question are 8 Jewish-Israeli judges who preside over the parole board hearings for 4 major prisons in Israel.  Each judge hears, on average, 20 cases per day; most of the cases are requests for parole to be granted, while others request changes in the terms of their sentence.  Roughly 2/3 of the cases were rejected.  The authors wanted to know whether extraneous factors entered into the decision to allow or deny the request, and particularly whether there was any truth in the old saying that “justice is what the judge had for breakfast”.

They don’t actually look at the composition of the judges’ breakfasts, however.  What they look at instead is the rate of positive decision-making relative to the breaks the judges take to eat.  The regular routine in these courts, apparently, is that the judge takes both a mid-morning snack break and a lunch break.  The judge chooses when the break happens and how long it lasts.  The judge cannot decide when to take the break given the order of the upcoming cases: s/he doesn’t know the order of the cases in advance. « Read the rest of this entry »

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