Thursday, June 24, 2010

Life lessons for synthetic biologists

1. A serious lesson

"Biology may or may not care about the physicist's insatiable desire for elegance." -- Jeff Hasty

Figure 1: In other words, sometimes this happens. From Hasty et al, Physical Review Letters 2002 | doi:10.1103/PhysRevLett.88.148101

2. Another lesson that is just as serious

Humor in lab is essential, of course. However, if you just heard the great story about the giant biohazard bag full of innocuous things in your PI's car... finish laughing before you load your gel.

The idea, of course, is to prevent this from happening. [Original photo source]

Sunday, June 13, 2010


I'm back from a 2.5-week family jaunt to Oregon and Washington. We bummed around a lot of national parks and did a wide variety of Wilderness Things. Here are some of the highlights:

Moss! We did go whale-watching, but for some reason I just don't get that excited about the large wildlife. I like to look at little things. And it turns out, the temperate rain forest is basically an ideal environment for dozens of moss species to thrive, reaching epic heights of lushness that I never dreamed of, growing up with miles of chaparral on all sides. There's lichens and liverworts too, but for some reason the mosses appeal to me the most. I discovered the macro setting on my camera (!) and took loads of pictures, trying to document as many different species as I could... but then I sat down too quickly on a rock and destroyed the screen. Argh! So I had to stop taking pictures. I don't even have the memory card with me, because my dad took it out when we got home and forgot to give it back to me before I flew back to Boston. So rest assured, I'll post my photos eventually. For now, here's a teaser photo taken by Derrick Ditchburn, who is a far better photographer than I. (More lovely moss photos at Dereila Images (do click on "More Moss" at the bottom).)

Stair-step moss, the most elaborate moss I've ever seen. The main fronds get up to 3-4cm long, and grow in long dangling chains. Picture this carpeting an area of several meters square.

Human-powered transport! I fell in love with biking and kayaking. I think the common thread is that they are both human-powered modes of transport that require a lot more thought than walking/running. I find them spectacularly engaging because I can pay attention to either the scenery or the vehicle, as I like. Plus, there's something satisfying about going twice or three times as fast as I could go unaided, but still without using a motor. I intend to continue both biking and kayaking in Boston -- I've borrowed a bike from a friend who's summering out of town, and apparently you can rent kayaks and go out on the Charles River.

Signing ghost! Yes, that said signing, not singing. We stopped in Ashland and caught a performance of Hamlet by the Oregon Shakespeare Festival, which was of course excellent. But one thing in particular struck me -- the ghost of Hamlet's father spoke in sign language! I looked through a couple of brochures and found out the ghost was played by Howie Seago, "the first deaf actor to play on OSF stages". I don't know any sign, so I couldn't tell whether he was using ASL or SEE or something else, but I thought it was a neat artistic choice to have him play the ghost, as opposed to a living character. (Hamlet spoke the ghost's lines, as if he only half-understood sign and was trying to keep up.) I bet translating Shakespeare into ASL is an interesting problem, too.

Monday, June 7, 2010


Christina Agapakis of Oscillator recently wrote a thought-provoking post about biosafety and synthetic biology. I was particularly struck by this passage:

Why is biology scary to so many people? We've done a very good job of sterilizing our lives, separating ourselves from biology to the extant that when we think of the word bacteria we immediately think of infection that needs to be wiped out, not something that is part of our bodies, part of our everyday ecosystem that keeps us alive.

I've often wondered myself why biology is so scary to so many people, and I think this is a particularly insightful way of putting it. If only more people would play around with sourdough starter or homemade yogurt, or manipulate soil pH to change the color of their hydrangeas, or hell just think harder about the fact that bacterial cells vastly outnumber human cells in a typical human body...

But of course, it's not that simple. Biology is hugely amazing or terrifying to a lot of people -- is there perhaps a good reason this is so? I feel like bio lab work has a really jading, mundanifying tendency: "I have the godlike power to manipulate the very genomes of bacteria!... and the result is that some of these spots are blue where none were blue before." The vast majority of the experiments I've personally done have ended either with a resounding "meh" or with a facepalm and a starting-over. Has this blinded me to the fact that, given sufficient equipment and time, I can engineer freaking life? How wondrous might genetic engineering seem to someone like Leeuwenhoek or Mendel?

What do y'all think? Especially you nonbiologists in the crowd? How weird does it seem to you that biologists collectively have these abilities? (And who's planning on seeing Splice?)