DIY Synthetic Biology

Synthetic biology has only been around since about 2004 when the first conference was held at MIT. As the name implies, it is the creation of biological material from scratch. For example, DNA can be created using just the four nucleotides called adenine, guanine, cytosine, and thymine or, as usually abbreviated, A, G, C, and T. In practice, it is cheaper simply to buy DNA strings (oligonucleotides) from labs like GenScript or DNA 2.0 that will create them to your custom design for as little as $0.39 per base pair, where a base pair is either C+G or A+T. Newer techniques are predicted soon to bring that cost down to 20,000 base pairs for one dollar.

Synthetic biology includes several different engineering strategies, including genome design and construction, protein design, natural product synthesis, and the construction of functional genetic circuits in cells and microorganisms. The "products" include, among others, biofuels, drugs, and genetically modified plants.  Much has been written about the potential benefits and dangers of those products, most recently in The New Yorker. But this posting is about Do-It-Yourself synthetic biology.

The computer revolution brought with it patents on software and some virtual software monopolies.  Likewise, patents on genetically modified materials could threaten the rapid development of synthetic biology.  One solution in the computing industry was a trend toward "free and open source" software. In synthetic biology, one solution is BioBricks, standard, unpatented, biological parts like DNA sequences of defined structure and function. A complete parts registry is maintained by Randy Rettberg at MIT. They are the Lego bricks of synthetic biology.

Which brings us to DIYbio.org, an organization that aims to help make biology a worthwhile pursuit for citizen scientists, amateur biologists, and DIY biological engineers who value openness and safety. SEED Magazine has a good review of them. They are basically a focal point for what's going on in the community.

It probably won't produce any Steve Jobs or lead to the biological version of Apple or Microsoft, but bringing people of very diverse backgrounds to look at biological systems is likely to produce some surprises.

Lingua Franca Online

Lingua Franca, a magazine web site I mentioned in my previous post, is a delightfully academic place to browse. For example, the article titled "Mistaken Identity Theory" looks at eponymy, the practice of naming things after people (real or mythical) who are associated with them. The author points out that, in practice, they are usually named after the wrong people. In fact, Stigler's Law of Eponymy, which, in its simplest form, states that "no scientific discovery is named after its original discoverer," was actually formulated by a sociologist of science named Robert K. Merton, according to Stigler himself! The number of other examples given is surprising.


Humorous book reviews, too. Seinfeld and Philosophy: A Book About Everything and Nothing explores the philosophical underpinnings of the Seinfeld show.


Being a philosophical place, there is no section for science, but they do cover the history of science. Lingua Franca is a keeper. I'll bookmark it.

Surfing and Drilling Down

The most rewarding, and time-consuming aspects of surfing the web is "drilling down" through a subject to get more and more detail.  One thing leads to another and often leads to facts or thought processes that one would never encounter outside of a university environment.


Two things came up this weekend, so I confess to getting little else done.

1. TED Talks posted six talks from their conference "Charter for Compassion."  The 15-minute talks included comments by a Christian, a Rabbi, a Tensin, an Imam, a Swami, and an atheist. While I haven't watched them all, I found the one by the atheist Robert Wright best for drilling down. He basically talks about the evolutionary basis for compassion, that is, for the Golden Rule, using simplified game theory. The comments on the talk obviously mentioned Charles Darwin and Richard Dawkins, they were no surprise, but one mentioned George R. Price, an unfamiliar name - so I surfed.  Aside from the Wikipedia article, I found a fascinating biography and review of his work in the archives of Lingua Franca which also explains some of the work of William D. Hamilton. Well worth the time to read because he was such an unusual person.

Robert Wright's web site, http://meaningoflife.tv/, is also worth surfing.


2. The other topic that came up somehow led to an article in American Spectator online magazine titled Unscientific American that pillories the article on the November, 2009 cover of Scientific American magazine. One of my favorite activities is blasting that magazine. So the article was garbage, as usual, but one of the comments led me to a Scientific American article in 2005 titled Smarter Use of Nuclear Waste. It reviews the Integral Fast Reactor (IFR), a fast breeder reactor developed at Argonne National Laboratory in the 1980s which GE later converted to a commercial design called the Advanced Liquid Metal Reactor (ALMR), and started to build a plant on the Clinch River in Tennessee. It was 80% complete when Jimmy Carter cancelled it in 1979. Later, the Clinton administration cancelled the last couple of years of the Argonne program because "Nobody is clamoring for nuclear power." Ronald Regan briefly revived the Clinch River project in1981, but Congress cancelled it in 1983 because cost overruns would make the plant uncompetitive with oil or coal.


The bottom line is that these reactors not only consume the nuclear waste that existing thermal reactors produce, they also consume the Plutonium and other Actinides in the waste.  "A 1,000-megawatt-electric thermal-reactor plant, for example, generates more than 100 tons of spent fuel a year. The annual waste output from a fast reactor with the same electrical capacity, in contrast, is a little more than a single ton of fission products, plus trace amounts of transuranics."  So, instead of producing products with half-lives of 10,000+ years, ... its radiation would decay to the level of the ore from which it came in several hundred years..."  Beyond that, since conventional reactors consume a very small part of the Uranium in their fuel rods, we could face shortages of Uranium within 100 years, about the same time we completely run out of very expensive oil. Fast breeders are 100 times more efficient because they consume 99% of the fuel. And if that's not enough, these reactors are inherently safe. Unlike thermal reactors, they need no mechanical or human intercession if something goes wrong. They shut down on their own.  The worst that can happen is a fire after the release of some liquid sodium. No nuclear debris.


As if that's not enough, these plants are designed to purify their own spent fuel rods in house. No transportation off site is required, nor does the re-processed fuel need to be transported back. Only the original fuel need be brought in, the same fuel that we are now planning to store in Yucca Mountain for 10,000+ years!


I'm surprised I had not known about this technology. If we had been working on it for the last 30 years, it would be perfected by now.  Instead, the Russians, French, Japanese, Chinese, and South Koreans are way ahead of us.