Neil Gaiman’s Commencement Speech

An inspirational speech Neil Gaiman gave about starting a career in a creative field:

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.

What do I do with all these radishes?

I scored a bunch of radishes at the Asian food store the other day, brought them home, then realized: this is a ton of radishes.

This is only about 1/3 of the total radishes

What was I going to do with all of these?  Why did I buy so many?  You only need about one radish to slice up and put on your salad, so this pile represents about 30 salads’ worth of radishes.

Fortunately, the Internet is a wonderful place, so I went searching around for radish recipes.  Turns out you can roast them like any other root vegetable.

First, I sliced the radishes up thinly.

Added some golden potatoes, tossed them with olive oil, salt, and Italian seasoning.

After about 45 minutes in the oven at 350°, they look like this.

The flavor is still spicy like a raw radish, but much more mellow and a little bit earthy.  I think roasted radishes would make a great winter dish.

Consequences of the Printing Press

Something to keep in mind when people complain about all the YouTube poop out there:

“One of the great diseases of this age is the multitude of books that doth so overcharge the world that it is not able to digest the abundance of idle matter that is every day hatched and brought into the world.”

Barnaby Rich, ~1850

Abarat: Absolute Midnight

Ever since the second book of the Abarat series was published in 2004, I’d been eagerly awaiting the arrival of its sequel.  For those who aren’t familiar with the books, let me tell you that the Abarat series is a strange beast: kids’ stuff by Clive Barker.  Yup.

Barker held back a bit with the weird and creepy stuff for the first two books as he told the story of Candy Quackenbush, a girl from Minnesota who finds a portal to a magical dimension.  But in the third one, Abarat: Absolute Midnight, all Hell breaks loose.  I can’t really describe the plot to you.  In third books of five-book series, plots are hard to describe.  But in a nutshell an apocalypse has come to Candy’s Abarat.

We haven’t just got Mater Motley now.  We’ve got eldritch abominations fighting other eldritch abominations.

Highlights include the gorgeous, Barkeresque language, the full-color illustrations every few pages, and Rojo Pixler, who’s like every creepy rumor you’ve heard about Walt Disney.

Romantic spoiler alert: Who the heck is Gazza?  He shows up halfway through the book and instantly he and Candy fall in love with each other.  I was rather rooting for Candy/Malingo.  Although it would have been disturbing, Candy/Carrion or Candy/Finnegan Hob would have made for an interesting story, too.

Oracle, by C. W. Trisef

Check it out!  An old high school friend of mine just published a book!

http://www.trisefbook.com/