Better cover letters — so what is your paper about?

(by namnezia) Mar 16 2016

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

(by namnezia) Mar 15 2016

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

(by namnezia) Mar 11 2016

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

(by namnezia) Mar 10 2016

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


(by namnezia) Mar 10 2016

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

(by namnezia) Mar 10 2016

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!

(by namnezia) Mar 10 2016

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!

2 responses so far

Calaveras 5.0

(by namnezia) Nov 02 2014

In México, November 2 is Día de Muertos or Day of the Dead. One venerable tradition is to write little obituaries for living people you know with a little skeleton of themselves, or a sugar skull with their name to accompany it. Newspapers will write funny obituaries, usually in verse of politicians and other public figures. These fake obits are known as "Calaveras". For the last couple of years, I've written some calaveras of a few fellow science bloggers and then of a few more, and even some more. To continue the tradition I'm happy to present a new set of calavers of some fellow bloggers I've had the pleasure to interact with in the previous year. Enjoy!


We knew her as Bam two-ninety four
Her woodchipper she instilled fear as she walked through the door.
But the fame went to her noggin,
As soon as she started guest bloggin'
She fell in the chipper, after she tripped on a slipper
And now she'll be woodchipin' no more.



On an iceberg Neuro Polar Bear sat
Eating penguins and sea lions and getting all fat
Until the earth started warming
And the ice started melting
And to the ocean bottom he sank, just like that



Katie scientific was an itinerant blogger
She spread her great wisdom throughout the land,
As she covered big meetings with the back of her hand.
From pharmacology to neural prosthetics
Until she got trampled at a poster about optogenetics.

2 responses so far

Make it Funky

(by namnezia) Feb 13 2014

Back when I was starting in my faculty position and failing to get grants funded and papers accepted, I had a tendency to blame the system. "How could they not SEE how brilliant my ideas are and how IMPORTANT my findings are? The system must be broken!" And I don't blame myself for doing so, because up to that point everything I'd done had validated those claims. I had great publications, nice grants as a trainee, I got a job at a fancy school, so how could I not be brilliant? That's right. I considered myself that special snowflake. However, one of the most important pieces of advice I got from one of my senior colleagues who was acting as an informal mentor was this: Maybe the system isn't perfect, or fair. Maybe there's bias in the review process. But complaining about it and blaming the system is NOT going to get you papers accepted, your grants funded or you tenure. What you need to do is go back, and try harder. Make the next grant proposal better, the next paper revision more interesting. But only by trying harder are you going to make it through this. And she was right.

And the hard part is, that after every grant you send or paper you submit, you feel like you DID try hard, and that it couldn't be better. But in truth, it can always be better. No proposal or paper is perfect. No scientist is super special. And I agree, it does suck, because this results in a lot of wasted effort. But the important lesson is, it's OK to vent by complaining and feeling indignant, you may have good reason to do so, but unless you keep trying, and trying harder, no amount of self-righteousness is going to get you anywhere.

So, to paraphrase James Brown, "what you gonna play now? I don't know but what's it ever I play, it's got to be Funky!"

So…make it funky!


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Musings about tenure

(by namnezia) Dec 31 2013

I was just thinking about an interesting post by Hope Jahren about what it means to have tenure. I agree with her in that I think that the point of tenure is not really to enable academic freedom in the classical sense (I mean really, how many of us have academic ideas SO controversial that we risk being shut down by the university?), but rather to enable us academics to do things that we normally wouldn't and to function as agents for real change. That is, since having tenure I've definitely felt encouraged to get involved in all sorts of different new directions and participate in aspects of the university which I wouldn't have before. But here I think is my key divergence with her, in that I never felt I couldn't participate in these new endeavors because I felt they wouldn't be valued by my peers, or that I'd be negatively judged for this, but rather I simply didn't have the time. When I started my faculty job I was given very clear expectations of what I needed to accomplish by a given time frame in order to get tenure. Add to this having two kids and a major illness, there really wasn't time for much else if I were to meet these milestones. So I passed up these opportunities. But I never felt silenced, like I couldn't speak my mind or call bullshit when I saw it. And I often did and still do. Maybe once I kept silent when I should have said something, even if me saying it would've been pointless anyway. But maybe I happen to have a fairly congenial department and very supportive chair, I don't know, this probably makes a big difference.

In any case, tenure doesn't really take away the pressure to perform. I still need to publish and get grants if I want to keep my lab running and my peeps employed. But on the other hand, we have gone in riskier new directions with our research and I've been encouraging my peeps to really stretch into new directions with higher payoff. There's still the risk these things won't pay off, but somehow not having tenure hanging over your head makes these risks a little more palatable. As I've said, having a little breathing room has also allowed me to experiment more with my teaching and to become involved with parts of the university that I had never had contact with for causes that are important to me. Maybe I'll write more about these efforts some day. So am I working less hard? No way! I'm working more. Am I less stressed? Definitely, and I'm having a lot more fun.

Finally, I diverge with Hope Jahren in one more important thing. Getting tenure IS a big deal, and is a result of a lot of hard work and if you get it, you should be damn proud. WHen I found out I got tenure, damn right I told everyone, if they wanted to diminish this or weren't impressed, that's their problem, not mine. Had I not been so sick at the time, I'd have thrown a huge party, because, why the fuck not.

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