Category Archives: Cool Science

Back from NASW Trip

Traveling home from the National Association of Science Writers meeting today felt strange.  The airports were half-empty from all the cancelled flights into and out of New England.  I’m fortunate that I didn’t have to go anywhere near Hurricane Sandy to get to Minneapolis, but still.  Eugh.

As I’m sitting here fighting off sleep so I can get back onto Central time, I thought I’d share with you some pictures from the trip.

The first thing you see when you get out of the terminal at Raleigh-Durham Airport is a full-wall mosaic of various cereal crops.  The Triangle Park region, where the meeting was held, is home to a cluster of important ag-biotech companies.

Sir Walter Scott in a labcoat.  He’s standing outside the convention center where we held our meeting.

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Neat word: Anastomosis

The other day I came across this word when I was searching for something completely unrelated on the Web of Science.

Anastomosis

  1. a natural connection between two tubular structures, such as blood vessels
  2. the surgical union of two hollow organs or parts that are normally separate
  3. the separation and rejoining in a reticulate pattern of the veins of a leaf or of branches

– From the World English Dictionary

So this is a leaf with lots of anastomoses:

Courtesy Wikipedia

My latest pet

Ladies and gentlemen, meet Euphorbia obesa:

She’s a fat little beauty, ain’t she?

One of my labmates just gave this to me as a gift (somebody else has the same obsessions!).  Euphorbia obesa is native to the great Karoo region of South Africa, where it is endangered.  They do so well in cultivation, though, that there are now more of them in pots than there are out in the wild.

Grep – a life skill for everyone

If you know me, you know that I’m not a computational biology kind of gal.  I’m perfectly content to think of my laptop as the magic box that lets me look at cats with captions and write WordPress posts.  I say hats off to you, real computational biologists, you people who can truly understand how a principle component analysis works.*

But last year I did a stint in a computational lab, so somewhat reluctantly I learned Shell scripting.  (Shell scripting is like Sesame-Street-level computer programming.)  The other day I found myself needing to search a large mass of protein sequence for a motif.  How to do it?  The Shell command grep.

Here’s the thing.  If you have a Macintosh, then grep is a super-pimped out search feature that is inside your computer right now.  For searching inside large text files, it’s way more powerful than Spotlight or whatever they’re calling that magnifying glass in the corner these days.  You’ll need to know some kindergarten-level computer programming to be able to use it, but it’s totally worthwhile.

Start by taking the stuff you want to search and pasting it into a text file.  It’s important that it’s plain text and that there aren’t any spaces in the file name.  Save and quit.

Click me to enlarge!

Open the computer program Terminal.  It’s in Applications > Utilities.

Type ls and hit return.  That gives you a top-level list of all the folders on your computer.  Type cd and the name of a folder to open it.  Keep going until you’ve opened the folder that has your file in it.  (Your folders had better not have spaces in their names!)

Type grep whatyou'relookingfor nameoftextfile.

There he is!

But can’t ⌘F do the same thing just as well?  Ah, here is where grep is a pimped-out search feature.  It can use regular expressions.  Here’s a longer explanation of regular expressions, but in short, they let you specify any sort of search criteria you could possibly imagine.  Here’s a real simple example where I remember that the word I’m searching for starts with w, but I don’t know what comes next:

And that’s the magic of grep!

* “Principal component analysis (PCA) is a mathematical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components,” says Wikipedia.

This is Neat: Caulerpa

Source: www.reefcorner.com

How many cells do you think this thing has?

a.  100,000

b.  1 million

c.  10 million

d.  1 billion

One.  This is all one cell.  What you’re looking at is a frond from a genus of seaweed called Caulerpa.  Caulerpa grows in tropical waters and is considered an invasive species in the Mediterranean Ocean.  Each individual of Caulerpa is one huge, enormous cell.  The inside of the plant is a syncytium, which means that millions of cell nuclei are floating around with no cell membranes to separate them.

This is neat: Chip Art

If you take a pair of pliers to your laptop and crack open the plastic casing, you’ll find a greenish motherboard with all the guts of the computer attached to it.  One of these guts is the computer’s CPU, a little square computer chip that probably has the word “Intel” printed on it.  If you strip the epoxy coating off of the CPU and put it under a microscope, what you’ll see will look a lot like the downtown of a city from a helicopter.  Rectangles and rectangles and rectangles of transistors printed on a silicon wafer.

And this.

Source: Chipworks

When there’s extra space on a computer chip, sometimes the chip designers like to have fun with it.

The practice of putting little pictures on computer chips is called chip art.  Though the practice is discouraged, it’s hard to get caught doing it – you’d have to void the warranty on your computer and put it under a microscope to see that it’s even there.  There were even reports of “bill sux” inscribed on a Pentium chip, but it turned out to be a hoax.

Chipworks, a company that specializes in analyzing computer chip circuitry for copyright infringement, keeps a gallery of all the chip art they’ve bumped into over the years.

There he is!
Source: Chipworks

Two Books on Science Writing

You might know that I’ve been taking a class on science writing for popular audiences this semester.  There are two required readings for the course, The Best American Science and Nature Writing 2011, ed. Mary Roach, and A Field Guide for Science Writers, ed. Deborah Blum, Mary Knudson, and Robin Marantz Henig, and I’ve been enjoying them so much that they’ve become oatmeal reading.  Wait, didn’t you know that?  I do all my reading for fun over oatmeal in the morning.

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Source: Amazon

The Best American Science and Nature Writing 2011  The book is pretty much what it sounds like: a collection of the best stuff published in popular science magazines in 2011.  The articles range in subject from how you collect semen samples from chimpanzees* to shock reporting on the Gulf oil spill to a meditation on the limits of what physics might be able to discover.  The book feels like reading many issues of Discover magazine and The New Yorker, because that’s where many of these articles come from.  Except that this book is a highlights reel.

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Source: Goodreads

A Field Guide for Science Writers  This is pretty exciting stuff, because it gets into the nuts and bolts of how one goes about writing about science.  The book is divided into sections, one of which is about actually writing well, one about the peculiarities of certain fields such as medicine, and one about working in all the various print markets.  Print markets.  The biggest problem with this book is that it was published in 2006, and the written word has been through an upheaval since then.  I’d recommend this book for the section on craft alone, but the ten pages on writing for the Web left me wanting more.

I’m leaving this class with more conviction than ever that science writing is very cool stuff.  What could be better than science and writing put together?

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*  A section of PVC pipe lined with K-Y Jelly, in case you were wondering.

Face Blind

It feels like this sometimes

I remember the first day of high school vividly.  I was going to a school far away from my home district, so my family had arranged a carpool with three other girls from the area.  Their names were Sarah, Amber, and Stacey.  Early in the morning that September, I got dropped off at Sarah’s mom’s house, and the three of us hung around in the shade of the live oaks, bubbling with excitement.

Sarah’s mom drove us the 30 minutes to school, then we piled out of the car and went our separate ways to our lockers.

At homeroom, the teacher had us get into groups of 6 and introduce ourselves around in a circle. I noticed that a Latina girl was being awfully quiet – she hadn’t said her name.  I asked her what it was.

She gave me a very strange look.  “Sarah.”

I don’t usually make blunders as bad as that one, but for a long time I’ve suspected that I’m pretty stupid at recognizing people.  I couldn’t tell Merry apart from Pippin to save my life.  And I hate, hate romantic comedies.  Most of the characters are wearing street clothes and they all tend to be the same ethnicity.  What am I supposed to work with?

There’s a name for this problem.  Prosopagnosia, or face blindness.  It sound like a terrifying terminal condition, but it’s actually more common than you might think.  For a class on science writing I’m taking this semester, we read an article by Oliver Sachs, who cites statistics that as much as 2.5% of the population have severe prosopagnosia – they have trouble recognizing even their friends and loved ones.  For the rest of us, the ability to recognize faces is distributed on a bell curve, like IQ is.  Which puts me somewhere in the range of Forrest Gump.

If you’re curious, the Prosopagnosia Research Center at Harvard University has an online test you can use to gauge your own ability to recognize famous faces.  It’s real quick and dirty, but the results are interesting.*

*I thought Princess Diana was Tina Fey.  Just sayin’.

10 Reasons Why Being a Grad Student is Awesome

10.  The schedule is flexible.  The graduate school cares more about whether you do a good job than what time of the day you do it.  That is, unless you’re doing a time-course experiment – then you’re at the experiment’s mercy.

9.  It’s a meritocracy.  To do a good job, you need to do good science.

8.  My boss is a scientist.

7.  You’re surrounded by nerds.  I can rhapsodize about how cool carbonic anhydrase is to my fellow grads, and they’ll know what the heck I’m talking about.*  They probably feel the same way about carbonic anhydrase.

6.  You can spend all day surrounded by your Eppendorf tubes if you want to.

The machine I work with doesn't look like this

5.  You get to work on a Machine.  Or at least I do.  The Machine I work with weighs at least 50 pounds and is controlled by a computer that runs DOS.

4.  Ph.D. Comics.

3.  You get to learn new things every day – you’re supposed to learn new things every day.  The other day I went to a seminar given by a guy who is comparing the geographic patterns of phylogenetic diversity in senita cactus and senita moths.  The best part was that I was required to go to this seminar.  Learning about the latest research on senita cactus is part of my job.

2.  Your research might help people someday.  Check out Norman Borlaug, one of the University of Minnesota’s most famous graduates.  His research on dwarf varieties of wheat started off the Green Revolution.

1.  If you work hard, and you do what you’re supposed to do, eventually you get to be called “Dr. Such-and-such.”

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*  Carbonic anhydrase is cool because it’s ridiculously fast.  It’s an enzyme that turns carbon dioxide into bicarbonate and back again in your body, and it can do this about a million times per second.

Tongue Rolling: Lies, I Tell You!

Yes, that's me, acting like a goofball.

I learned something neat the other day.

Think back to your high school biology class.  When you were studying genetics, your teacher probably told you that being able to roll your tongue is a dominant trait and not being able to roll it is recessive.  That’s not actually true.

There are pairs of identical twins out there where one twin can roll their tongue and the other can’t.

That by itself doesn’t mean that tongue-rolling isn’t genetic.  There are traits out there that are controlled partly by genes and partly by factors we don’t fully understand.  Schizophrenia, for example, is partly genetic.  Yet there are pairs of identical twins out there where one twin gets the disease and the other doesn’t.  Something about the environment triggers the disease in only one of the twins.

You’d expect, though, that if genetics has something to do with tongue rolling, then identical twins should be more likely to both be able (or unable) to roll their tongue than any other two people.  Scientists from the University of Adelaide in South Australia actually tested this way back in 1975.*  They surveyed 47 pairs of twins, some of whom were identical, about their ability to roll their tongue.  The result: the identical twins weren’t any more likely to both be able to roll their tongue than the fraternal twins.  The study didn’t find that genetics had anything to do with tongue rolling.

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*  If you want to read the study, look here: Martin, N.G.  No evidence for a genetic basis of tongue rolling or hand clasping.  J Hered (1975) 66(3): 179-180.