Archive for: March, 2016

Do you have 100 hours?

Mar 30 2016 Published by under Uncategorized

Allegedly, in Japanese there is a term, Tsundoku, that refers to the growing piles of new, unread books that accumulate around your house. You know, that book you bought in that cool little bookstore last time your were in NY. Or those books your read a review for and ordered on Amazon. If you are like me, you probably already have a pretty large Tsundoku. In addition to my big Tsundoku, I also have a rapidly accumulating list of TV shows and movies I want to watch. I almsot never have time to watch anything on TV or Netflix, HBO, etc. I do make a point of watching some select shows that I like and follow but I have an increasingly growing list of things-I-want-to-watch-but-will-likely-never-find-the-time-to-do-so. To make matters worse, a friend of the blog and twitter user @BanditoKat recently sent me a list of “50 documentaries you need to see”. Personally I don’t feel like I “need to see” anything, but that is a pretty damn impressive list. And I’ve only seen a handful of them. It has a healthy mix of classic documentaries and new ones and some that really changed the way I think about certain topics (I highly recommend Shoah, the most powerful documentary on the Holocaust and a great reminder of why hateful politics are dangerous). Others like Hoop Dreams and The Thin Blue Line are genre defining. And some bring me happy memories of going to see them with my sweetie during grad school, like the Buenavista Social Club. Many are also international and the ones I’ve seen are excellent. The list has some links to ones that are available for free, but you might have to search most of them out on your own. Anyway, here’s the link, hope you have an extra free 100 hours, otherwise expect your video Tsundoku to get a little larger.

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Better cover letters — so what is your paper about?

Mar 16 2016 Published by under Uncategorized

We recently submitted a paper to a fancy journal, and one thing that impressed me was how the journal made sure you carefully structure the cover letter to help the editorial team make the best possible decisions. When I first got started in this business, when submitting a paper I would basically just slap the cover letter on as an afterthought before hitting submit on a journal’s website. Something along the lines of:

“Dear Editor, Check out our new paper. Hope you like it, let us know if ya’ wanna publish it. K’thx."

And while that does convey the basics, over the years my letter has become more refined. Because really you want the letter not just to convey the title of your paper, but you want the editor to know what question you are addressing, why your findings are cool, and who would care to know about it. In this way they can quickly grasp the merits of your brilliant paper, begin to think about appropriate reviewers to send it off too, and more important to get excited about it. In some of the fancier journals this letter can mean whether your paper goes off for review or gets a desk reject.

So what should a cover letter contain? I think the best guidance you can get on this matter is from our friends over on eLife:

• How will your work make others in the field think differently and move the field forward?
• How does your work relate to the current literature on the topic?
• Who do you consider to be the most relevant audience for this work?
• Have you made clear in the letter what the work has and has not achieved?

And the key here is not expound for pages upon pages on this. Just a couple of concise sentences about each point will more than do. Don’t go nuts, don’t be pompous and overpraise yourself, don't write fucking War and Peace, just be helpful and guide the editor to the key points. In fact, it is always good to keep those points in mind while writing your manuscript and developing its narrative arc. It’s no guarantee your paper will be accepted or even reviewed, but at least it’ll improve your chances.

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Digital Tools for Teaching

Mar 15 2016 Published by under Uncategorized

In the past I've written about some of the analog tools I enjoy using in my work. However I also keep a toolkit of digital tools I use in various ways both for my research and teaching work. I want to talk about some of the tools I use to aid in my teaching, mainly in terms of preparing digital materials that can be used online or during presentations. All the tools listed here run on iOS and I use them on my iPad, and sometimes pass on the files to Illustrator, iMovie or Keynote.

Are there any tools you use regularly that would recommend?

1. Options for iPad diagramming, sketching and drawing apps. My top two are these:


Concepts – This is really good. It’s basically a vector drawing app, with lots of tools, easy interface, layers, etc. It can export directly to Adobe CC or to whatever as an SVG file which can be used in Illustrator


SketchBook - From Autodesk, really powerful for drawing and tracing, with lots of brush effects. Export, as far as I can figure out is only as PNG, but working with layers you can copy and move objects around in the app. So good for creating backgrounds, freestanding illustrations for slides, etc. A bit of a learning curve, but not really.


For creating other cool drawings to enhance sides etc I use either Paper by 53 and Procreate, which are the apps that feel the most like using actual drawing tools, especially with a decent stylus. I really like the watercolor effects on Paper.


Aside from those two, I’ve tried:


InkPad - Vector-based simple shapes, etc. Very straightforward and can export as SVG, but not as streamlined and polished as concepts.


Brushes - Very paired down but effective drawing/painting app. Has layers, is easy to use and the interface is totally non-obtrusive. Fun to use. Export only as PNG (or JPG?).


2. I also found good apps for creating animations (but for hand-drawn, stop motion animation, not necessarily moving objects):


Animation HD – really easy to make animated doodles. Basically a layered drawing program that allows you to create animations. E.g. create a face, copy it across frames, then alter the expression, etc. I really like the user interface and the smoothness and simplicity of the app.


Animate it! — Stop motion animation on the cheap. Very rudimentary editing capabilities, could probably be exported onto something else.


I'm still looking for something that let's you draw simple objects and move them around the screen, like to animate a pathway or a mechanism. I use Powerpoint or Keynote for this, but it is really bulky and cumbersome.


3. Digital whiteboards allow you to record video while draw on your screen with different colors and narrate, so you can create little mini lessons you can upload for your class if you want to clarify a concept, or provide some pre-class material:


Educreations – Great digital whiteboard with audio recording. Limitation is that animations reside in their website, so can’t easily be exported.


Doodlecast Pro – Not as good UI as the other one, but allows you to export as a movie file to use as you wish. This is the one I use the most.


Another tool I found that has a lot of potential is called Explain Everything. I'll be trying it out and report back once I've used it. You can incorporate pictures, etc. to your whiteboard presentation


A final note of caution. Don't use Prezi. Ever. It makes everyone nauseous and pisses everyone off.


Hope these are useful!


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Messin' around time

Mar 11 2016 Published by under Uncategorized

I was recently compiling a list of projects a new person coming to my lab could embark on to get their feet wet. These are typically short projects that have a high likelihood of yielding some useful data that could either stand on its own, or be used to test a specific aspect of a larger project. Typically the payoff for these projects is as they say "incremental" but always solid and something to fall back on. Occasionally it leads to something bigger. Usually when a new person joins the lab I'll assign the one of these starter projects and then encourage what we call "Messin' Around Time" (MAT). We actually call it something else, but it's in the same spirit. The idea of MAT, is that said person, once they have a handle on basic  techniques used in lab is encouraged to try all sorts of crazy (but well reasoned) experiments. And the idea is that MAT experiments are basically sketches, which will then give you  a sense whether the project is worth following up. The more improvisational they are, even if imperfectly designed, the better. You might be testing one thing, notice blip in the data, crank up the dial to eleven and amplify this blip which then turns out to be something really interesting. Thus MAT requires the experimenter to keep a heightened level of vigilance, because you never know what will be interesting. It involves looking at your data in real time as much as possible and adjusting the experiment on the fly in order to optimize conditions. I think this improvisational experimentation is a critical exploratory skill that will help trainees formulate hypotheses, and then design proper experiments to see if the interesting effect they just sketched out persists. Since MAT often occurs in parallel with the bread-and-butter safe projects, in the worst case scenario where MAT fails, you still have something to say for your time. I once had a postdoc who would do Freaky Friday experiments. Test all sorts of crazy ideas on Friday afternoons. Most of the time nothing would come of it, but in other case they would end up resulting in a paper. I encourage everyone to do this, whenever possible.

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G-protein coupled receptors and other boring stuff

Mar 10 2016 Published by under Uncategorized

I really hate giving that lecture. I just find the topic so dry and I struggle with finding ways to make it interesting. It's not that the topic isn's important, but at least for me it's hard to get excited over the basics. As opposed to most of the other lectures in the class it just ends up being a straightforward, sit down and listen affair, with not much opportunity to add elements of active learning, or group work or other things that help break up the lectures up a bit. Topics like these are not good candidates for a flipped class session either, since there are no real problems to solve or clear group work that could be done around that topic, especially with a large class of 100+ students. I do have some cool animations, and go over some experiments and data, but much less than I do in the rest of the course. Today I decided to mix it up a bit by simulating a second messenger cascade, and the signal amplification that comes with it, by having students play the part of different transduction molecules and activate each other by giving each other fist bumps. Just with two GPCRs in each corner of the class, we were able to activate the entire lecture hall. Admittedly it was a bit hokey, but at least the students seem to be having fun while doing  it and will definitely remember the concept.

How about y'all? How do you liven up lectures on boring-ish topics? Or do you just skip them altogether and let the students learn about the material outside of class (e.g. via flipping) and do something altogether different during class time? Are you such an inspiring lecturer that you can even make GPCRs shine?

3 responses so far


Mar 10 2016 Published by under Uncategorized

Wow back to blogging and now an old fashioned blog challenge! Our friend Drug Monkey has asked us to list five characters from recent-ish fiction that we would like to be rescued by from a bad situation. Here are my choices:

  1. Agent Scully - because she can sequence a genome in 20 minutes and is a badass.
  2. The dude from the Martian - because he'll science the shit out of everything
  3. Violet Crawley, Dowager Countess of Grantham - she seems to get whatever she sets her mind to
  4. Daenerys Targaryen - because Dragons!
  5. Han Solo and Chewbacca - for obvious reasons

2 responses so far

How not to sound like a douche in your CV

Mar 10 2016 Published by under Uncategorized

Recently I met with someone who came to give a seminar and was sent their CV in advance and I was shocked to find that it was 107 pages, complete with table of contents and appendix. My first thought was "holy shit, I am so intimidated by this person, what am I even going to talk about". But then I read the CV. It really took me about a full 5 minutes before I could find this person's publications. It was a respectable publication record, but really not orders of magnitude better than my measly few, and for the most part large studies with lots of authors with this person's name somewhere in between, maybe a few case studies, MD sorts of stuff. There were hundreds of abstracts, including abstracts of all of this person's trainees, a shitload of talks, including stuff that I wouldn't have included, like small in-house talks or presentations within my working group (ie. lab meetings). Then it started listing every trainee, including high-school students and every single accomplishment of said trainees. Science fairs judged. List of journals for which they reviewed papers for, organized by year. And the more I read, the less and less impressed I was. It really was oozing with insecurity, and unnecessarily so because had the CV been paired down to its essentials, it would have been perfectly fine.

I find that this is a difficult lesson for many trainees to learn. There is a tendency to add as much as possible to one's academic CV, to try and sound as impressive as possible. By all means, I think it is super important to highlight one's accomplishments, but there is a fine line between tooting one's horn and sounding like a total douche.

Recently I came across this tweet:


And while I was a tad annoyed by its smugness, I do see the point. You don't want to present yourself in your CV in a way that makes it seem like your are something that you are not. So for example if the rest of the CV is filled with overinflated fluffernuttiness then listing your current position as "NSF predoctoral fellow" might come across as a tad douchey and put off a future employer. However, if you have a normal CV, then listing your title as say "NSF Graduate Research Fellow" might be fine, and highlight the fact that you received a prestigious fellowship.

So where does one draw the line? It's hard to tell. It's like what some Supreme Court dude once said when asked to define pornography, he said "I know it when I see it" (or something like that). It's the same thing with a CV. You have to look at it as a whole and see if the gestalt of it comes off as off-putting. Better yet ask a colleague, ask your PI (if you have one), ask your lab mates. And tell them to be brutally honest.

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Oh, hello again!

Mar 10 2016 Published by under Uncategorized

I stopped blogging regularly about 2 years ago, mainly because I felt I had run out of things to say, or because others were were saying similar things much more eloquently. Also Twitter happened, providing us scientist bloggers an alternative channel for communication that was more immediate and extended beyond the comments sections of the science blogs. I know it's not the same, and one can have more substantial discussions in a format such as a blog, but for me Twitter scratched my itch. That said, lots has gone on in the intervening time and I feel I have a few new things to contribute, so I'll try and blog a bit more regularly and see how it goes. Hopefully, there'll be someone listening!

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