Archive for: November, 2010

Scoopage

Nov 19 2010 Published by under Uncategorized

After a few days of peace and quiet, the folks in my lab are starting to trickle back from the Society for Neuroscience annual meeting. Today I had this conversation with my grad student after he returned from the meeting:

"OH MY GOD!!! We need to get my paper published NOW, there was a poster at the meeting describing the exact same experiment as mine, they're breathing down our necks and… they're German!!"

"Whoa now, Hobo Joe, tell me what the poster was about…"

"Well they are working on the same neurological condition we are and they also applied the treatment twice and the results were the same as mine, and they did the same thing, with the double treatment and we're TOTALLY SCREWED!!!"

"Yes, but what was the point of their experiment, what was the question?"

"Um…"

"OK, let's look at the abstract, what lab was this?"

"They were German."

So we finally find the abstract and read it over, calmly.

"Dude, did you actually read the poster, or did you just read the title, the first panel and then freak out?"

"Um…"

"Because this has nothing to do with what you are working on, at least not more than in a very superficial way. Sure, they are working on the same condition like another three-thousand people are, and they did apply the treatment twice, but they're not even close to doing anything that resembles your project."

"Um… but they were… German..."

This led me to think about scooping. Not the kind that I do after I walk my little mutt every morning, but scientific scooping. The question is, how likely is it really that one's project might get scooped by another lab, and more importantly, does it really matter? In certain types of scientific research where there is a single answer to a question, such as a crystal structure to a protein, or a specific receptor to a ligand or a gene sequence, I guess scooping would matter. Particularly if you want to be able to say, "Wooohooo! We were the first to describe the structure of blah, blah, blah…" By this point, the contribution of the lab coming in second place would not be that significant. But most science is not really like this. Usually, one is either describing a complex process, or testing a series of interrelated hypotheses, and there is lots of room for different approaches, methods and even answers. Unless it is a very low-hanging fruit, the chances that two labs are doing the same experiment in the exact same way is extremely low. And in fact this is a good thing, because (assuming both labs are competent and good at what they do) that means that the different labs will validate each other's results, using slightly different approaches, making the discovery more likely to be significant and true. And if one lab does it better than the other, then even if that lab published second, that lab's paper is likely to become the go-to citation for that finding.

I remember when I first joined PhD lab, my advisor showed me a paper with a very interesting finding, published in a very crappy (and I mean crappy) journal, with somewhat crappily-done experiments. He said, "to start, why don't you repeat these experiments?" I said, "but why, they've already done it?" He replied that "yes, but it is a potentially very interesting finding which, if true, could change the way we think about our field, but I don't really believe the results. If you are able to replicate them, and extend them, not only will you kick-ass thesis project, but will be able to get some kick-ass publications." And he was right on both counts. And I was surprised that we were able to publish this in a high profile journal even though we explicitly stated we were not the first ones to discover this phenomenon.

So if you find out a competing lab is working on a similar project, should one be worried about being scooped? In most cases, if you are working on a complex enough problem, I think its worth making sure your science is as strong as possible, rather than rush to publish something that is suboptimal just to beat a competitor. Because in the end the best science will have the most lasting power, and nobody will care if it came out in 2010 or 2011. If you are chasing down a receptor or a really obvious experiment, or your competitors are German, then maybe you should panic.

As far as my student, he should get his paper out anyway. Maybe I should have let him panic a bit more.

Scoopage in action.

9 responses so far

Cry Baby Cry

Nov 15 2010 Published by under Uncategorized

Often times it is easy to get stuck in a rut, and these ruts are mostly due to habits we have picked up along the way. This applies as much to life in general as well as to things like lab work and cooking. My wife and I are fairly good cooks and we make a wide variety of dishes usually without the aid of a recipe. You just sort of learn what goes together well and then basically combine things to make your own dishes. Some are better than others but after while we find we keep repeating the same things over and over until everyone seems particularly sick of them and cooking becomes more of a chore, rather than a creative endeavor. We scan the internet occasionally for new ideas for things to cook, but these are usually uninspired and inferior versions of what we routinely make at home. So how to get out of this rut? This is where cookbooks come in.

Unlike the internet which has a mixed bag of recipes of unknown and untested provenance, a good cookbook is where someone who has devoted their life to cooking and is inspired by cooking can show off their stuff. And while some cookbooks are more like a reference that tell you how long to steam artichokes or how to clean squid, others are works of inspiration, and usually, if I think back at some of our favorite recipes, they originated from a handful of particularly good cookbooks. That is why I find it helpful to occasionally revisit the original recipe of a dish that I've prepared a million times. Recipes have a tendency to evolve over time, such that after a while, the way you cook something is somewhat different and not necessarily better than the way you started cooking it originally. When you revisit an old recipe you have big revelations like "Shit, I forgot I was supposed to marinate the lamb for 24 hours, no wonder it tasted like fucking cardboard!" or "Grapes!? This recipe never called for grapes! How the hell did I end up putting grapes into my meatloaf?" Today I was getting ready to make some delicious lamb and beef kofta for dinner when I decided to double check the original recipe in one of my favorite cookbooks. This is "A Book of Middle Eastern Food" by Claudia Roden. I bought this as a used paperback as a college student and it has been nothing short of amazing. You can find pretty much any Middle Eastern recipe you are looking for – anything ranging from medieval Persian recipes to Syrian sheep's brain salad. Most recipes are actually very accessible and usually have only a handful of ingredients, like the chicken with chick peas, onions, turmeric and lemons. But anyway, back to the kofta. Kofta are little kebabs made with well-spiced ground beef or lamb. The recipe was pretty much as I remembered it, except for one crucial difference. It called for an onion, but grated rather than chopped. I have to say this was a revelation. Grating an onion just causes it to release so much juice and flavor, which then infuses throughout the ground meat, making everything moist and oniony. Yet grating an onion is not for the faint of heart. Occasionally when chopping a fresh onion I get stinging in my eyes and a few tears. When you grate an onion – holy cannoli – it was an unending torrent of stinging tears coming out of my eyes. I cried. I mean I really cried. But it was totally worth it. I'm totally going to do this from now on whenever I  make burgers and such. But in any case, my point is, is that it is always good to go back to basics, because often you miss important details the first time around which make a huge difference.

This is also true in the lab. Whenever one of my lab peeps comes in complaining that they can't get something to work, I always tell them to check the original recipe, be it a methods section in a paper, a protocol book or a lab manual. Lab protocols tend to drift over time such that we teak thing here and there to make things work more optimally. But occasionally these tweaks add up over time, such that what we are doing is very different from the original protocol. It also turns out that many of these tweaks are completely unnecessary and just make the whole procedure way more complicated. I mean if you switch a specific incubation time and things suddenly work, are you really going to go back to the old way even if you are not sure that the incubation time had anything to do with your experiment suddenly working? No fucking way. Many of these experimental tweaks and turns basically border on what I call "lab voodoo", and we just do them because at some point they seemed to help . But by the end, the protocol is so twisted and disfigured that if it stops working it is impossible to troubleshoot. Which is why it helps to go back to the beginning and try again. It also helps to read some old papers. Recently I re-read some not exactly-classic papers, but papers that set the experimental framework in my field and the whole impetus for my research. And there was so much in there that I can't believe I missed the first time. There are so many unexplored leads, and hidden experimental gems, that after re-reading them I came out with a buttload of new ideas I wanted to try.

So keep this in mind next time you find yourself in a rut. Go back to the source and start over, you'll catch all the things you missed the first time around and remember some you had forgotten. This applies for cooking and lab work, your mileage may vary in real-life situations.

6 responses so far

Teach me!

Nov 09 2010 Published by under Uncategorized

This post has been cross-posted at Lab Spaces.

So today at Lab Spaces, we're writing about our different experiences with mentoring styles. I think a good mentor, particularly in grad school, is one who teaches you HOW to do science. Yeah, yeah, career advice, hand-holding and people skills are nice, but really you go to grad school to learn how to do the shit you are supposed to be doing.

When I was a grad student, my advisor spent a large amount of time working in the lab, was always accessible and basically had memorized every paper he had read.  Which was spooky. He could tell you in which figure so-and-so did which experiment in what paper. Even crappy papers he knew. He wasn't what I would call a "hands-on" kind of advisor who would hold your hand while you went through the difficult bits, but he also wasn't an asshole. In fact he was pretty friendly and easy to get along with, he had eclectic interests outside the lab and was very generous with his time. Someone you would like to hang out and be friends with. But mostly, he was an excellent scientist. He was always excited about what he was doing and extremely lucid when explaining anything. However, he did expect people in the lab to show a great deal of independence and initiative. He would of course help you pick a good project, and when you proposed a given experiment he could tell you exactly why it would or wouldn't work. But you had to ask. If you didn't ask for help he would not offer it. Thus, some people in the lab just foundered, because they never sought help. Despite being a great scientist and teacher, he had relatively poor managerial skills. During my time in lab there were a few epic conflicts between lab members, and he was totally oblivious to it. Or maybe he knew but he figured that it was better for us to deal with our own dysfunctions.

For me this was the perfect environment. I could work independently, without someone breathing down my back, yet had all the help I could possibly want form one of the smartest people I have ever met. And as a result I loved grad school.

My postdoc mentor was a bit different. The lab was larger (~12 peeps), and my mentor spent very little time in lab. However, she also let people work independently and was also very accessible to help when you got stuck. And like my PhD advisor she was inspiringly smart. In her lab it was expected that you would learn from the other lab members how to do different techniques and that you would do them for your project. So rather than having the same people do the same assays for all the projects, everyone learned all of the techniques. Sure, some people were better than others at a given thing, but everyone did their own molecular biology, electrophysiology and imaging. So again, a great learning environment. And as a result I loved being a postdoc.

One thing both my mentors have in common is that they have been very good at promoting people from their labs. Both in talks, and by letters and talking to their colleagues at other universities. As a result, most people from their labs have found decent tenure-track jobs. I keep in frequent contact with both of my mentors and they continue to be a great source of advice and friendship, and they really look out for their former trainees.

I try and maintain a similar style in my lab. My door is always open and people are free to barge in almost at any time with questions about data, experiments, problems with their equipment, comments about the latest seminar speaker or crappy paper from our competitors, whatever. That's why I'm here, to ensure they do the best science possible, since this is what we're supposed to be doing here. I know I'm not as freakishly intelligent as my mentors, but hopefully I can inspire them as they inspired me.

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Strange Anatomy

Nov 07 2010 Published by under Uncategorized

I've always been a fan of rouge taxidermy,  cryptozoology, and fake museum exhibits. I like the idea of someone creating an alternate reality which is hidden in plain sight and not always obvious as to what is real and what is fake. Sort of like in the novel "The Crying of Lot 49" by Thomas Pynchon about a secret alternative postal service operating in the shadows. In any case, I recently came across this post aggregating photos of skeletons and anatomical models of cartoon and video game characters. Some of these are amazing, I would totally love to have a Pac-Man skeleton for my office. Also check out the anatomical drawing of the baloon dog, I love the location of the brain, and the roadrunner is awesome. Here's a couple of examples. Go visit the post for more!

Goofus ridicularis.

Gingerbread Man - Internal Anatomy

3 responses so far

Otherworldly Voices

Nov 04 2010 Published by under Uncategorized

Earlier this week I was having problems finding my own voice. No, not my inner voice or my writing voice, but literally, my real voice. On Tuesday, whenever I would try to talk, some raspy, otherworldy whisper would emanate from my mouth. I blame my kids of course, those vectors of disease that live in my house, who a few days earlier were themselves emanating raspy otherworldly whispers while they coughed all over my breakfast. Normally, this is not a big deal, after a few days of this my voice usually comes back gradually. But alas, I was scheduled to give my tenure talk two days later (more on that in a bit), plus I had agreed months earlier to give a guest lecture on a large intro class which happened to be on the same day. So that there was no way I could talk for 2 ½ hours unless my voice improved.

What is a tenure talk? In my department it is part of the tenure process that one gives a seminar, open to the public, about everything you've done during the past 5 or 6 years. This allows faculty members who will be voting on your case to get a chance to hear what you've been up to in a format other than what you put in your CV and research statement. So it better be good.

Needless to say I was panicked. I couldn't really back down from the guest lecture but I guess I could have rescheduled my tenure talk. But I was worried that that would look bad – so I decided to stick it out. I have to say that this process is somewhat stressful and I keep second guessing every move. For example, a colleague suggested that it might be a good time to apply for other outside jobs. The logic being was that even if I get tenure, if I have another offer I am in a good position to negotiate the terms of my reappointment in terms of salary, lab space, etc. Also, I get to see what else is out there and maybe get a good offer. Its not that I am unhappy where I am. I like the university, the students, my department and my colleagues. I also like the city where I live, but there might be other places just as good. And also, if I don't get tenure, then I feel like I was pro-active in finding another position. I don't think my colleague was implying that I was in trouble and should be looking elsewhere, at least I hope that's not what he was implying, but I figured what he said made some sense. Also when one prepares a tenure dossier, one basically is preparing the same type of statements and CV that you would for a job application so its not that much extra work to apply for jobs. I'm curious if any tenured folk reading this applied for jobs as they were coming up for tenure.

Anyway, by Wednesday my voice was improving so I decided not to postpone anything and this morning it was almost back to normal. Until I gave the guest lecture. About a third into this hour-and-a-half lecture I felt my voice getting weaker and weaker, raspier and raspier. The room kept getting hotter and hotter and the four-hundred freshmen staring at me kept wondering what was going on. About halfway through I mumbled something about larynxes and ran out of the auditorium, clutching my throat, to get a drink of water. I think I told them to take a little break, I don't remember. I managed to finish the lecture which involved a lot of talk about sex in voles and bats, so no matter how bad one's delivery is, the students always like it because of the topic. After lecture I had a couple of hours before my tenure talk, so I made some tea, closed my office door to rest my voice and promptly fell asleep. I woke up panicked and in a coughing fit. Fortunately my voice was partially restored and I headed down to the seminar room, where my supercool wife was waiting for me with cough drops. So in the end I sort of pushed through the talk, gently whispering into the podium mike about all the cool research done in my lab. I think it went well, but it is always hard to tell what people are thinking. I only saw one person fall asleep, but then again I usually fall asleep in about 60% of seminars, regardless of how good or bad they are. Let's hope that my colleagues thought my research was groovy too.

As far as job applications, we'll see what happens. I asked my chair if I should apply to other places, based on what my other colleague had mentioned. He shrugged his shoulders and said it wasn't really necessary to do so and to stop worrying, but that's easier said than done.

So that's done. I got home and had a few shots of tequila, and now my voice is feeling great.

4 responses so far

Calaveras

Nov 02 2010 Published by under Uncategorized

Today in Mexico is Day of the Dead, or Día de Muertos. Typically, people set up altars with various offerings to honor their dead, and this can either take place at the cemetery, at home or in public spaces. Growing up we never really celebrated the day of the dead since my family is Jewish, but we did eat the delicious pan de muertos (which my super-cool wife was fortunate enough to find yesterday at a local Mexican bakery in chilly New England!), and at school we set up an altar or ofrenda with little decorated  sugar skulls with our names on them, yellow cempazuchitl flowers, paper cut-outs and all sorts of other colorful decorations. In many small towns surrounding Mexico City you could see amazing ofrendas in the town squares and my favorite ofrenda was one in a place called the Anahuacalli, which was Diego Rivera's house and every year they would display all of the day of the dead decorations this artist made.

One of my favorite day of the dead tradition is writing calaveras. These are typically fake "obituaries", written in verse, which you write for your family and friends, as if they had died. Usually they satirize some aspect of the person and are accompanied by a caricature of the person in skeleton form. Newspapers usually carry calaveras of politicians and other national figures. This custom dates back about 100 years to the time of José Guadalupe Posada, who was a journalist and artist who pioneered the use of calaveras as a form of political satire.

So in honor of Día de Muertos, I decided to write some calaveras for some of my fellow science bloggers, particularly those who's blogs I read and commented on regularly, before deciding to start my own blog. So here it is, the first annual "Take it to the Bridge" calavera-fest!

Drug Monkey, R.I.P.

The ol' Drug Monkey has passed on.

He thought his fight was won.

But NIH said his grants were "Too descriptive."

And things like: "Marihuana's not addictive."

So his grants were all rejected.

And he was all dejected.

La Doctora Isis, murió en una crisis.

¡Pobrecita Doctora Isis!

Murió en una triste crisis.

El tacón de su zapato se rompió.

Su experimento fracasó.

Y en la cocina, la comida se le quemó.

Compañero PhysioProf

El camarada PhysioProf is dead.

Too much 'fucken' cursing it is said.

"But I've really been repentant

since the Yankees lost the pennant!"

Yet it was too late for whining.

With death he was already dining.


Poor Bora (and parrot dinosaur)

Poor poor Bora just as things were going so well.

He accidentally rang death's doorbell.

"Is this Scientific American?" Bora said.

"No it's not", said the reaper, and now he's dead!

16 responses so far