Giving Thanks to our Libraries & Bio-Hackers

As I eat a large meal today, I am reminded of so much that we should be thankful for. Most evidently, we should give thanks to the epiglottis, the little valve that flaps with every swallow to keep food and drink out of our windpipe. Unlike other mammals, we can’t drink and breathe at the same time, and we are prone to choking, but hey, our larynx location makes complex speech a lot easier.

Much of our biology is more sublime. With the digitization of myriad genomes, we are learning to decode and reprogram the information systems of biology. Like computer hackers, we can leverage a prior library of evolved code, assemblers and subsystems. Many of the radical applications lie outside of medicine.

For example, a Danish group is testing a genetically-modified plant in the war-torn lands of Bosnia and Africa. Instead of turning red in autumn, this plant changes color in the presence of land mines or unexploded ordinance. Red marks the spot for land mine removal.

At MIT, researchers are using accelerated artificial evolution to rapidly breed M13 viruses to infect bacteria in such a way that they bind and organize semiconductor materials with molecular precision.

At IBEA, Craig Venter and Hamilton Smith are leading the Minimal Genome Project. They take the Mycoplasma genitalium from the human urogenital tract, and strip out 200 unnecessary genes, thereby creating the simplest synthetic organism that can self-replicate (at about 300 genes). They plan to layer new functionality on to this artificial genome, to make a solar cell or to generate hydrogen from water using the sun’s energy for photonic hydrolysis (perhaps by splicing in novel genes discovered in the Sargasso Sea for energy conversion from sunlight).

Venter explains: “Creating a new life form is a means of understanding the genome and understanding the gene sets. We don’t have enough scientists on the planet, enough money, and enough time using traditional methods to understand the millions of genes we are uncovering. So we have to develop new approaches… to understand empirically what the different genes do in developing living systems.”

Thankfully, these researchers can leverage a powerful nanoscale molecular assembly machine. It is 20nm on a side and consists of only 99 thousand atoms. It reads a tape of digital instructions to concatenate molecules into polymer chains.

I am referring to the ribosome. It reads mRNA code to assemble proteins from amino acids, thereby manufacturing most of what you care about in your body. And it serves as a wonderful existence proof for the imagination.

So let’s raise a glass to the lowly ribosome and the library of code it can interpret. Much of our future context will be defined by the accelerating proliferation of information technology, as it innervates society and begins to subsume matter into code.

(These themes relate to the earlier posts on the human genome being smaller than Microsoft Office and on the power of biological metaphors for the future of information technology.)

P.S. Happy Thanksgiving, even to the bears… =)

Nanotech is the Nexus of the Sciences

Disruptive innovation, the driver of growth and renewal, occurs at the edge. In startups, innovation occurs out of the mainstream, away from the warmth of the herd. In biological evolution, innovative mutations take hold at the physical edge of the population, at the edge of survival. In complexity theory, structure and complexity emerge at the edge of chaos – the dividing line between predictable regularity and chaotic indeterminacy. And in science, meaningful disruptive innovation occurs in the inter-disciplinary interstices between formal academic disciplines.

Herein lies much of the excitement about nanotechnology. Quite simply, it is in the richness of human communication about science. Nanotech exposes the core areas of overlap in the fundamental sciences, the place where quantum physics and quantum chemistry can cross-pollinate with ideas from the life sciences.

Over time, each of the academic disciplines develops its own proprietary systems vernacular that isolates it from neighboring disciplines. Nanoscale science requires scientists to cut across scientific languages to unite the isolated islands of innovation.

In academic centers and government labs, nanotech is fostering new conversations. At Stanford, Duke and many other schools, the new nanotech buildings are physically located at the symbolic hub of the schools of engineering, computer science and medicine.

(Keep in mind though, that outside of the science and research itself, the "nanotech" moniker conveys no business synergy whatsoever. The marketing, distribution and sales of a nanotech solar cell, memory chip or drug delivery capsule will be completely different from each other, and will present few opportunities for common learning or synergy.)

Nanotech is the nexus of the sciences. The history of humanity is that we use our tools and our knowledge to build better tools and expand the bounds of our learning. Empowered by the digitization of the information systems of biology, the nanotech nexus is catalyzing an innovation Renaissance, a period of exponential growth in learning, where the power of biotech, infotech and nanotech compounds the advances in each formerly discrete domain. This should be a very exciting epoch, one that historians may look back on with no less portent than the Industrial Revolution.

Clones and Mutants

“Life is the imperfect transmission of code.” At our life sciences conference in Half Moon Bay, Juan Enriquez shared some his adventures around the biosphere, from an Argentinean clone farm to shotgun sequencing the Sargasso Sea with Craig Venter. From the first five ocean samples, they grew the number of known genes on the planet by 10x and the number of genes involved in solar energy conversion by 100x. The ocean microbes have evolved over a longer period of time and have pathways that are more efficient than photosynthesis.

• Clone Farms
Juan showed a series of photos from his October trip to a farm in Argentina. With simple equipment that fits on a desk, the farmer cloned and implanted 60 embryos that morning. All of the cows in his field came from a cell sample from the ear of one cow.

Some of the cows are genetically modified to produce pharmaceutical proteins in their milk (human EPO). These animal bioreactors are very efficient and could replace large buildings of traditional manufacturing capacity.

Whether stem cell research and treatment for ALS, or cloning cows, Argentina is one of the countries boldly going where the U.S. Federal government fears to tread.

• Three Wing Chickens
Juan also showed a genetically engineered three wing chicken. The homeobox gene that has been modified is affectionately called “Sonic Hedgehog” (his son really likes SEGA!)

The homeobox genes are my favorites. They are like powerful subroutine calls that have structural phenotypic effects.

I recommend Juan’s book As the Future Catches You for an exploration of the economic imperative of technology education, especially literacy in the modern languages of digital code and genetic code. And for a populist description of the homeobox genes, I recommend Matt Ridley’s Genome, a very fun primer on genetics. Here is a selection:

“Hedgehog has its equivalents in people and in birds. Three very similar genes do much the same thing in chicks and people… The hedgehog genes define the front and rear of the wing, and it is Hox genes that then divide it up into digits. The transformation of a simple limb bud into a five-fingered hand happens in every one of us, but it also happened, on a different timescale, when the first tetrapods developed hands from fish fins some time after 400 million years ago.”

"So simple is embryonic development that it is tempting to wonder if human engineers should not try to copy it, and invent self-assembling machines.”

One of Juan’s slides was the first hand drawn map of the Internet, circa 1969. Larry Roberts had drawn that map, and happened to be in the audience to brainstorm after the talk.

P.S. The most popular phone at our conference was the Moto Razor, Chinese edition.

P.S.S. The most popular blog photo so far (with over 12,000 visitors) is a simple message…