Reality meets sci-fi

I made a video.

In part, it’s because I was home with a head cold and didn’t want to do real work.  So I listened to a local classical music station and curled up on the couch in the fetal position. Then I heard a piece by Beethoven that reminded me of 2001: A Space Odyssey.  Which is an awesome movie.

It was released in 1968–a whole year before the first moon landing–and yet watching the movie you feel like mankind was (is) ready to travel to Jupiter.  My favorite scenes are those that make space travel appear totally natural.  Eating meals on a shuttle, landing at a moon base as if it’s another trip to the airport, jogging around a spaceship.  And so, in that vein, I used video from NASA space shuttle and International Space Station missions to create my own Kubrick-esque short movie.  It’s a silly thing, but a reminder that in science fiction there are great ideas.  And, sometimes, those ideas can become reality.  And that’s a pretty exciting thought for this scientist…

This work was created using both audio and video from the Internet Archive ( The videos were from NASA images.  Specifically, I used scenes from STS-6 (1984), STS-9 (1984), STS-66 (1994), and Expedition 8 (2003).   There are images of real experiments conducted in space including:  a cylinder filled with silicon oil to model fuel storage, a water droplet forming a perfect sphere, a recording of an eye during a visual-vestibular test where the participant stared at a moving pattern and eye motion was tracked using a special contact lens.  There a pictures of the Earth from space, of lightning storms at night, of the moon setting on the horizon of the planet.  There’s a clip of a Russian resupply module approaching the ISS, shuttle launches and landings.  I would urge you to check out the archives because the full length videos are mesmerizing and the bravery, professionalism, and humor of the astronauts they feature is truly inspiring.

The audio is Beethoven’s Symphony No. 4, in B-flat major, Op. 60 and was recorded by the Cleveland Orchestra with George Szell conducting and was released under a Creative Commons Attribution-Noncommercial ShareAlike license.

Everything in this video is either licensed for remix/reuse or is in the public domain.  This video is released under a Creative Commons Attribution-Noncommercial ShareAlike license.

Did you remember to change your internal clock with Daylight Savings?

I consider myself a morning person, and am always a little sorry the morning of the March daylight savings time change. I feel like somehow, having woken up so many mornings in the dark that I have “earned” those sunrises and to have them abruptly taken away on Sunday feels like a rip-off. Otherwise, I hardly notice the change because I hardly ever know what time it is anyway.

But that’s where I’m wrong. Even though I don’t consciously perceive it, each sunrise is unconsciously sending signals via light-sensitive cells in my eye back to my brain that put my circadian rhythms in sync with the break of daylight and the setting of the sun. Circadian rhythms are changes in gene and protein expression that vary throughout the day that help your body keep time. They control sleepiness, alertness, hunger and hormones. They are responsible for changes in body temperature and surges of glucose. Outside of the TSA and flight delays, they are what make international travel so dang hard. And, it’s why you might have had trouble going to sleep after you changed your (external) clock this week.

This is not my area of expertise, but I find it fascinating. For an approachable discussion of circadian rhythms by people who know what they are talking about, try this podcast or maybe this less formal one.   Or, if you are so inclined and bothered by my lack of citations, here’s nice scientific review article for you.

Probably because I have been reading a lot of science fiction lately, it makes me wonder just how adaptable our circadian rhythms are. They are amazingly flexible—which is why you can travel to the other side of the planet and adjust to that timezone—but also inflexible in that it takes time to make this adjustment (about a day) and in the absence of other signals (like light) people still generally have about a 24 hour circadian rhythm. My limited understanding of this is that the rate at which the genes and proteins involved in these clocks get expressed, made, and destroyed during this timeframe is roughly equivalent to 24 hours.

So…if you moved to a planet with a 32 hour light-dark cycle would you adjust to it? Or would you end up recreating a 24 hour Earth day on another planet?   Some people claim to have longer or shorter “rhythms” anyway and so maybe it wouldn’t be a big deal.  But, I would argue that extensive studies in shift workers and in people whose clocks are artificially set out of whack (by being placed in isolation rooms with odd light cycles) seems to indicate that this ultimately wouldn’t work well. At least in these groups, it looks like body chemistry changes so that systems don’t work as efficiently.  Also, there are strong links between altered circadian rhythms and obesity, diabetes, disorders like depression, and even neurological diseases (including Alzheimer’s—but it is still unclear whether altered rhythms cause the disease or the disease causes the altered rhythms).    Of course how much of this is something we are born with and something we gain with age? After all, babies are notorious for not having set circadian rhythms and the 24 hour sleep-wake cycle only seems to emerge with development. So maybe if you were born on another planet you might be better adapted and protected from some of the effects of change that we experience here?

I don’t know the answer to these questions. But if you’re still thinking about how much you hate the time change, think instead about how cool it is we all share the experience of having our internal circadian rhythms forced out of sync biannually.

And then think about how we can do away with this dumb daylight savings thing.



Very Superstitious.

Knock on wood. Cross your fingers. A black cat crosses your path…

I just finished isolating RNA from cells. For those of you who aren’t science inclined, a quick reminder: bmicrocentrifugetubeefore proteins are made in your body, you have to make RNA from your DNA (which you have probably heard of—if not, you need to watch the educational film ‘Jurassic Park’). Isolating RNA is relatively straightforward, but there are lots of things that can degrade it. So it is EXTRA important to handle everything very, very carefully.   Also, and this is especially true if you are trying to isolate RNA from only a few thousand cells (or maybe even a single cell!), you have to come to terms with the fact that nothing you are going to do will be visible. You must believe that you put the cells in the tube, that the RNA was isolated from the rest of the cellular gunk, and that in the final steps you successfully re-dissolved a tiny bit of invisible RNA in a tiny bit of water. Oh, and in between there are many other invisible processes that could destroy your precious RNA. Often, I find myself dedicating large chunks of my time (days!) going through the steps to do something like RNA isolation only to find out that all the work was for nothing.


Not surprisingly, it is easy to become superstitious when you work with things that can’t be seen. Need to check the Farmer’s Almanac before you start your experiment? Great idea! Moon phase may be indicate conditions are not perfect for experimentation.

Now, this may come as a surprise to you. Superstition AND science? At the SAME time? Yes. In fact, I might argue that this is at the heart of scientific reproducibility—the notion that an experiment performed several times will yield the similar if not the same results. For example, if when you isolate RNA you perform a chicken dance after your last ethanol wash before you elute it from a column (Quiagen RNAeasy kit step 8-9, for those of you following along at home), then you should always do a chicken dance after your last ethanol wash. And, most importantly, when you publish your paper, please make sure to include it in your methods section.


A walk home from lab at night.

I hadn’t planned to leaved the lab so late and I was worried that the light jacket I had brought wouldn’t be warm enough outside.   I stepped through the heavy building doors to walk home.

It was surprisingly pleasant outside though, and walking at a brisk pace felt good after sitting still so long.   I had spent most of my day motionless in a cold room, looking at tiny things through microscopes.  My neck hurt from being bent over and I was tired, thinking about how I would have to repeat the whole experiment again and it would likely take just as long to finish tomorrow.  I rolled my shoulders and stretched my head back feeling the tenseness in my spine dissipate a little as I did so.

The movement brought my gaze up from the pavement–up above the orange glow of the street lamps and up to the cloudless night sky.  It seemed like the sky was blacker than it should be with all the light pollution from the city, and the crisp air was bringing several stars into sharp focus.  Small dots were rapidly changing colors and burning with a light that was all at once more intensely bright-hot and cold-hued than the artificial lamps around me.  It stuck me how these pinpoints of light were, in reality, orders of magnitude larger than anything I had thought about or looked at today.

A light breeze picked up and I shivered for the first time, my gaze returning to the sidewalk.

I still had a ways to go.


So you stumbled upon a time-machine…

First of all, congratulations!  You found a time-machine!  Second–what are you still doing here?

If I ran into a DeLorean just sitting around with a fully charged flux capacitor, I would travel back in time to warn myself about a career in science (er…I mean, ‘to provide some helpful advice’).  Here’s what I would tell my naïve self:

You (I?) will spend a considerable amount of time making things.  And it’s probably not what you are thinking.  I mean, really building things, using power tools, various glues, soldering irons, 3D-printers, you name it.  Sometimes it’s because science is ridiculously expensive and a couple hours of “crafting” can save hundreds of dollars.  Other times it’s because a specific component doesn’t exist.  The following skills will be extremely useful to you:

  1. Computer programming.  Many of my daily problems to be solved if I possessed more than a wisp of knowledge in this area.  For example, I could be a whiz at sorting and analyzing excel spreadsheets with custom-made macros.  I could breeze through data using programs written in Matlab.  I could finally get those two pieces of hardware talking to each other again so I don’t need to scream in panic as precious samples get liberally sprayed around the room by robots.  But I digress…
  2. Soldering.  I first learned to solder as a kid with one of those “build-it yourself” kits where you attach little LEDs onto a Christmas tree shaped circuit board.  I wish I had done more (there are some surprisingly awesome kits available now).  Despite being more expensive than equipment  you would buy for your home, science equipment is often much more “custom” and far less robust.  Sometimes the only thing between finally completing your experiments and catastrophic failure is the gumption to grab a soldering iron and put it all back together.
  3. A knowledge of power tools.  Some scientists work in specialized rooms that were designed and constructed for a very specific purpose.  Some don’t.  I’m not saying that I have drilled holes through walls and tables in our building…but sometimes the environment does need a little modification.  Knowing which tools to use when and where is important.

In other words, I would say to myself “learn to be more handy, past me!”.  And “work out more, your upper body strength is deplorable”.

Your future self will thank you.


Why work on one thing when you can work on 25,000 things?

Oops.  I did it again. (Brittany Spears reference, ha!  Geez, I’m a postdoc, and thus not particularly cool, ok?).

Anyway, I managed to apply the same process to this blog as I am to my research.  Here are my “Ten Steps to Success”:

  1. Start a project.  (Oooo, this will be fun!)
  2. While researching that project discover something else that looks more interesting (because that first project already seems boring and/or ridiculously difficult).
  3. Start that next project.
  4. Realize you are being an idiot and try to simultaneously work on the first one as well.
  5. Start a third project just for the hell of it.
  6. In your stress-induced haze of frantic working, have an ah-ha! moment and realize that if you just work on “this other thing” you can actually have something completed in a day or two.
  7. Work frantically on all four projects.
  8. Realize that four projects is really eight.
  9. Spend a day planning how to work on all eight projects.
  10. Effectively end up not getting anything done.

No.  Please do not EVER follow these steps.  Not if you are a postdoc, undergrad, blogger, stay-at-home mom, rocket scientist, or otherwise.  In fact, if your actual intention is to do nothing, then following these steps will ultimately result in doing WAY too much work.  And the loss of your sanity.

So I guess what I’m saying is…I have been working on several exciting blog posts over the month of December and I may eventually get one of them up in the next month or two.



Items you will need on your scientific quest Part II.

Remember those things I said are universal to the pursuit of science?  I found a couple more items…

#3  A really great travel mug.

Screen Shot 2015-11-29 at 9.00.54 PMBecause face it.  You need coffee.  A LOT of coffee.  But everytime you get a cup of coffee from your favorite terrible coffee place, someone comes and asks you a question about experimental methods before you can drink it and then you have to fix a microscope for someone else.  So a travel mug becomes critical to the pursuit of science.  Look for one that has a) adequate volume for your coffee drinking habits and b) top-of-the-line insulation for maximum drinkability later (because cold coffee and hot coffee are both great, but that middle range is really quite aweful).

#4 An extra pair of pants.

Screen Shot 2015-11-29 at 8.47.20 PMFor when you spill a large volume of really-hot-even-though-you-got-it-hours-ago coffee all over the pair of pants that you were wearing just before you have to meet with the boss.  An extra pair of pants can be extremely useful.