The problem of how to model a biological system has been staring me in the face every day in recent months, and I need a place to indulge in baseless speculation. So if you stick around here at Adaptive Complexity for the next few weeks, you are going to get treated to a dose of half-baked, semi-coherent (at best), partially thought-out musings on what it takes to model a biological system.

One more book to pile on my to-read list. Via Carl Zimmer (go follow the link for a bloggingheads video interview), a fascinating book on bioengineering, Learning to Fly, by Rob Carlson, is coming out this fall.

He has some insightful thoughts:

Today, if you like playing with electricity, you can hop over to Amazon and buy the Extreme Snap Circuits set and put together transistors, switches, lamps, motors, resistors, and capacitors to build all sorts of fun projects, from an auto-off night light to the perpetually entertaining space war timer. More ambitious engineers can buy off-the-shelf parts to build appliances, computers, and control systems for Boeing's 787 Dreamliner.

What if you could engineer biology this way? What would you build? Physicist and scientific prophet Freeman Dyson would love to build genetically engineered pets and ornamental plants. Standford biologist Drew Endy envisions a collection of standardized biological parts called BioBricks, off-the-shelf modules that biological engineers can assemble like snap circuits into amazing biological machines. An annual undergraduate competition, the International Genetically Engineered Machine competition draws teams of biogeeks who design glowing microbes that spell "Hello World" on an agar plate and  gut bacteria that smell like mint or bananas.

This all sounds exciting, but what's the reality? Do biological engineers, or synthetic biologists (as they are most commonly called) have anything close to the know-how of today's electrical or aerospace engineers? The answer, obviously, is no.

Some regions of our genomes are under permanent lockdown because they are hazardous to our health - or at least the health of our future offspring. These secured regions include large swaths of parasite-infested DNA - DNA that contains transposable elements, virus-like genetic parasites that have the ability to hop around the genome and cause harmful mutations.

Because out of control transposable elements are a major danger, cells (ours and those of most other organisms) have an elaborate maximum-security system for shutting these bad boys down. Just how this lockdown system works is an active area of research, and a recent paper revealed how plant cells enforce security and prevent prison breaks by these DNA parasites.