Abstract clouds

Hey--

So I'm sure you've all seen word clouds ala wordle, where it takes all the text from a word document or webpage and then uses word frequencies to generate a kind of infographic where you can see the most used words, the big ideas if you will. 

Check it--someone made an app that you can input an author, it pulls all their pubmed abstracts, and then you can input that into wordle. It's called pubmed2wordle.

I decided to look up some of the PIs on my floor, in case I'm ever in the elevator with one of them, I can have some talking points. 

For example, 

I will know to talk about microRNAs with this dude, or

microRNAs but specifically let-7 with this woman, and also, oh look she works on C. elegans and development.

I think can be a great resource if there's a visiting faculty giving a seminar, or you're trying to pick a lab to rotate in, or you just want to know a little bit more about someone's research without spending hours poring over papers, this might be the first place I go from now on for all those things.

And just to mix it up a little big, because contrary to popular belief I'm not only interested in microRNAs...

That's my dad. He works on yeast and kinetochores and chromatin and microtubules!

It also makes for an interesting discussion of how much information do we actually need to understand something. And is relying on a tool like this, is that being lazy or being efficient? Obviously, it will never become a substitute for reading papers, but it's a pretty neat tool regardless. 

Do you think you could find yourself using something like this? Could you see yourself directing a student to it?  

Revolution

I predict that within the next 10 years there is going to be a scientific revolution. And it's going to happen online.

Hear me out--(This is sort of like the time that I told my the dean of the med school that I thought that social media and online presence is going to start becoming an issue for faculty seeking tenure and grants. He may or may not now think I am a teenage moron, but I still go out of my way to say hi when I see him on campus.)

But here's the thing. Me, early-20's, bright-eyed and bushy-tailed, and all of my peers are online all the time.

And, as much as anyone would hate to admit, we're the future of science. Logic would follow then, that you would want to reach out to us. Grab our attention. Mold us into images of yourself.

I'm starting to look at grad schools and while that whole subject is deserving of a post of itself, here's what's really frustrating.

A lot of PIs don't update their websites regularly, and that's a problem. Sure I can find someone's most recent publications through PubMed, but what if I can't get to them because of access issues? (I know--this can also be turned into more of an open access discussion too.) One of the nicest lab's I've looked at, the PI had a list of publications and some of them had an asterisk at the beginning of certain citations, indicating that this paper had come from a graduate student in the lab. This is something that I think people need to, if they don't already, take note of. There are probably few better indicators of a productive and plentiful learning environment than if a lab is producing paper. Notice I said a lab. I've started to become wary of PIs that tend towards review papers, or ones where they're part of a larger collaboration and it's only them, and no one else from their lab. (Gosh I want to say something really mean here OHOKAY I'll just say it, those who can't do, review!!) (I'm also acutely aware of the fact that I know absolutely nothing about anything and may all instances of snark and judgment act karmicly against me in later life--there, I said it for you.)

It's all about the internet.

I'm painfully aware that I'm part of this generation-can't-I-just-look-it-up-on-wikipedia, and if I hear one more disgruntled post-doc telling me that when they were in grad school they had to walk to the library and request a journal, I'll write a blog entry about it, but this is the way it is. Let's not fight it, embrace it. It's so hard to grasp for people that didn't grow up with the internet that you can build substantial relationships and communities online. Yeah, the usual arguments of "impersonal" still exist, but more and more those arguments are vastly outweighed by the enormity of good things that come from the internet.

Take my most recent example of photobleaching. I photobleached my cells. I had one meaningful face to face conversation with someone about the fact that I was probably photobleaching my cells, and then I was depressed and went home and went on facebook, and this happened:

Edited for brevity, and in short, I got tons of comments from real live people, all with real live experiences, with their own labs or microscopy facilities. I learned about 'pseudo-live view' and about different types of fluorophores, all on facebook. facebook!. 

And here's the thing. I do know Wendy and Omar from real life, and hey uncle Ray!, and if I saw them at the grocery store I would definitely stop and say hello (if of course we weren't in different states), but my itty-bitty-in-the-grand-scheme-of-things-although-seemed-like-a-very-huge-deal-at-the-time photobleaching problem was not big enough that I would have thought to pick up the phone and call any one of these vastly-overqualified-to-be-answering-my-questions people. But facebook allowed them to do just that, on their own time. 

The internet is this amazingly powerful beast that I honestly predict is going to allow a lot more people's voices to be heard, scientifically and otherwise. Of course, we're going to have to learn to filter, but you know, you have to filter in real life too, it's not like the crazies only exist on the internet. 

But the advantages: an open access revolution, more transparency about authors on publications, PIs interacting with peers and students online and in real time? Scientific discourse over twitter? Tenure-seeking faculty might poo-poo this now, and half the people in my lab think I'm crazy for even having a blog, but these are really powerful things that the people in academia are going to start to realize are really important to my generation of budding scientists. 

We're young, we're excited. We like to think we're cool, but that's only because we think that being nerdy is cool. If academia can start having real online conversations outside of an ivory tower that I can watch, learn, and maybe even be a part of, well, you'll have my endorsement. Even if that endorsement is in the form of a tweet. And then a grad school application. 

Oh, and update your damn lab webpages more often. 

ETA: in retrospect, everyone in my lab thinks I'm crazy for having blog.

Monday problems

Check on cells or make coffee.
Check on cells or make coffee.

Sit paralyzed at desk wondering whether to check cells or make coffee?

Yep, it's Monday.

That awkward line between tech and student

The day has come. You're all set up to do an experiment. You've spent days preparing. All of your pipets have been lined up the night before. Tip boxes are full, waiting. Media is warm, gloves are out...and your PI walks by your bench and demands that you attend a seminar with him (or her.)

(Alternate universe: Your PI emails you the week before alerting you of the talk and you're really thankful because you didn't have that much to do that day anyway.)

EITHER WAY--you attend dutifully.

On the way to the seminar (in which you lead the way because Techs Know Everything including all the shortcuts between buildings), your PI reveals to you that the seminar speaker is a moron, has submitted a moronic paper to a moronic high profile journal, in which your PI is in the middle of reviewing. But of course he doesn't want to affect your view (yeah right) but instead wants your thoughts on the talk afterwards. (No pressure!)

Tech-PI relationships are a funny beast. It's a fine line between employer-employee (which it is at face value) and mentor-mentee (which it may evolve into). Each has it's own unique sets of issues. I'm in the lucky situation where my PI knows that this job is just a step in the direction of a career for me. He knows that I'm probably going to be leaving soon to go off to grad school in...something, or try to move up and out into a new position...sometime. When your PI knows that, and better yet, respects that--that's when you can start pushing the boundaries of employer-employee into mentor-mentee territory.

However, a big thing to keep in mind is: Cave Canem...ma.

source

Or, for those not well versed in Latin/English (Lat-glish?), beware of dogma.

I think a lot of scientific disagreements, the higher up you get on the ladder, tend to be fueled by competition and ego more than anything, while the differences are more or less just differences in dogma. But vastly different ways to look at problems are more or less what fuels scientific discoveries. I mean, someone has to be thinking outside of the box. I guess if you're the tech you just hope it's your PI.

It's a funny thing...and I'm having trouble writing it now because I'm trying to say it as delicately as possible, but keeping an open mind is the most important thing you can do in this situation. (Apart from staying awake during the actual seminar. Obviously that is priority numero uno.) At this very very very early stage in my career, the most important thing I can be doing is looking for places to think critically. Both of my PI and of his competitors. It's not always easy, and it's obviously very important to keep in mind who's grant you're being paid off of, but it's also really important to remember that thinking critically about something is not synonymous with criticizing it. And dogma and broad generalizations and effective public speakers get funded, because sometimes making things seem black and white is the best way to make sure your research gets noticed...but that's not I as a tech or a student, or whatever weird limbo position I'm in now as I'm starting to have my own ideas and taking ownership over my own research...that's not necessarily the position I want to be stuck in.

I wonder how other people in my position deal with this kind of thing. Thoughts?

Adventures in photobleaching

There are a couple of ways to act when you make a Really Big Mistake in lab.

1) Correct it, tell no one, and pretend it didn't happen. This method is preferable when you do something small and stupid. Like one time some sequencing results didn't look very good. And I realized that I had completely diluted my primers to the wrong concentration. Like, mMols off. This would be an okay mistake not to tell anyone else around you in lab, just as long as you fix it and make sure never to make that mistake again. (And also that no one else will be using your primer stocks.) (This also isn't exactly how it went for me because it took someone else pointing out that I had made a blaring error in my primer dilutions, so everyone knew about it in the end.)

2) Admit you made a mistake, ask for help, correct it, and then pretend it didn't happen (but never make that mistake again.) This method is especially useful when something big is going wrong, and you can't figure it out on your own. This is when you just have to suck it up that you'll look like an idiot for about 5 minutes while someone is explaining what you did wrong (or as I prefer to see it, what you weren't doing right!) but in the end it's all for the best because a) hopefully you learned something, and b) you won't make that mistake ever again. And it's a win-win! Because when you come across another poor soul who's made the same mistake as you, after you help them figure out what they weren't doing right, you can choose whether or not to admit to them that you too made the same mistake.

3) Ask for help, figure out that you were a complete idiot about something, and laugh uproariously about it. This might include just yelling PHOTOBLEACHING every 20 minutes or so for the rest of the evening after you figured your problem out. 


So this may or may not have happened to me today.


I will start off by saying that my lab does not do fluorescent microscopy. No one in my lab has fluorescent microscopy experience, and so we're looking at some fluorescence in our cells (just to check transfection levels) and using a scope in a lab downstairs that we've never really been formally trained on. The one caveat is that I come from a family of fluorescent microscopists--so this what follows is sort of unforgivable.

Here is what happened.

We walked downstairs with our little flasks of cells, and we put them under the microscope. We turned on the light, turned on the laser, made sure we were on the right filter, opened the shutter, and looked at our cells.

"Ooh!" My post doc says, "Pretty glowing cells!"

"Awesome," I say, "Let's put it on the screen!"

(I am clearly paraphrasing here.)

So, with the fluorescence still on, we manually switch the scope from eye to camera, we press "Live", and we wait for the picture to come up on the screen.

(If you're keeping tally of time blasting cells with fluorescence, we're now clocking in at 2 minutes.)

It takes another few seconds for the image to come up, then of course we have to refocus slightly for the image to be in focus for the camera.

Then we take a picture.

(Fluorescence still open, in case you were wondering.)

Then we hmmm and hawww and write down the settings we used so we use the same settings for all the other flasks.

Then we go get another flask.

I will skip the rest of the nitty gritty details, because the short of it is, we kept looking from eye to camera and back again, and since apparently neither my post doc nor I were feeling incredibly competent today, we kept forgetting to manually change the scope from eye to camera, all with the fluorescence on. 


And then we wondered aloud to each other, "Why are all of these flasks getting progressively dimmer?" And of course, being scientists, we say, let's get that first flask out that was really bright!

So we get the first flask out and everything is really dim.

In retrospect:

It didn't even occur to me that this was the problem until later I was talking about what I was doing to someone who actually knows how to do microscopy, and they were just like, You focused with the fluorescence ON?? My post doc still isn't quite convinced that this is the problem, but I think she just doesn't want to admit that it's the problem because it makes us look like complete idiots.

And me?

I am perfectly ok with looking like a complete idiot. Because, you know, how else would you learn? (By actually listening carefully to what people tell you to do so you never make mistakes? Where's the fun in that?)

And for the rest of the evening, yes, I have yelled PHOTOBLEACHING aloud at odd intervals. Because, arrrghhh.....PHOTOBLEACHING!

Incomplete

I love doing homework, reading a problem, knowing exactly where and what in your notes you need to look up, (in this case multiple hypothesis testing) and then seeing this:

Dear god what was I thinking! I clearly was there, I remember the lecture, I obviously knew that multiple hypothesis testing was important, I even underlined it. But what! What about multiple hypothesis testing?

With each question, so many more questions. (<--which ironically is sort of what multiple hypothesis testing is. Or so I would imagine.)

Thank goodness my prof posts his lectures online.

Sketchnotes: The Structure and Stability of Genomes