Is engineering biology the future of energy?

Jay Keasling, the CEO DOE Joint BioEnergy Institute (JBEI) http://www.jbei.org/ and Professor of Chemistry Engineering and Bioengineering at UC Berkeley thinks so. I heard him give a keynote presentation at the DOE Joint Genome Institute's (JGI) annual meeting this week. Keasling gave a captivating talk about how to apply engineering principles to biology. He said that if you want to build a computer, you don't start from scratch. You make a design, buy the components that are manufactured by someone else, and then build your computer. He then made the same analogy to engineering a chemical plant. You decide what you want to manufacture, you design a factory, and then go buy parts for the factory - all of which will have standard fittings, connections, and sizes. He suggest that in theory, we should be able to engineer biology in the same way.

The biggest difference however, is that with computers and chemical factories, there is a knowledge base to build on. Biology does have a knowledge base of sorts, but not exactly. Most scientist conduct experiments in their own labs their own way, and often do not provide the data or knowledge to the public in any useful way in which to build on. Keasling suggested that we work to standardize and share. The day before his talk, I attended a workshop led by DOE and JGI about how to build a "knowledgebase" database for biology and how to standardize our data so that it can be shared. After the intro to Keasling's talk, it all started to make sense. I understood DOE's motivation for the knowledgebase- after all, the mission of the JGI is "to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup."

After sitting in a workshop all day hearing contradictory views on making standardization protocols (standardizations can stifle creativity), different ideas about work flows, varying estimates of data sizes, and differential needs of the community, I was a bit skeptical that we would see a functioning "knowledgebase" for the genoimics community any time soon. Its not that JGI or the scientists involved aren't doing a good job - I have put my ideas in the hat - but this is a really hard problem, made even harder by the system of funding and tenure in academia, which publishes most of the genomic data. Academic science is about competition for grant money, which doesn't always promote sharing and most labs find their own ways to do analyze data. In computer engineering, parts are standardized because that is the most efficient way to do it and everyone makes more money. For biology to be standardized to encourage efficient engineering, ideally there would be more money for research and the results would be open sourced. JGI and JBEI are part of the government and thus are trying to generate this type of open source data for the community.

Going on the really interesting things Kealing had to say about his group's success in engineering lipid biosynthesis pathway into E. coli, along with complementary gene pathways for breaking down cellulose into sugar to feed itself and exporters to export the newly synthesized lipids out of the cell for easy harvesting, I'd imagine that we will start to see some real progress in this area soon.

If you are interested in JGI's energy genomics program, see this new promotional video they made with ex'pression college for visual arts:
http://www.youtube.com/watch?v=qchN5FX_QN0

Algae Biofuels and Genomics - Where do we stand?

This week, I'm in California for the Joint Genome Institute's (JGI) Annual User's Meeting. The theme of this year is "Genomics of Energy & Environment", and there are a lot of talks in the next few days aimed at how people are using genome sequencing and bioinformatics for biofuels research.

In the algae world, we know some groups such as Saphire Energy are working to genetically engineer algal strains. People have also been working for years to try to engineer more hydrogen production from green algae, and we just learned of a group successfully genetically engineer algae to make proteins for the pharmaceutical industry.

In order to understand how to genetically engineer an organism, we need to have model genetic and genomic systems to learn from and experiment with. For a long time, very few things considered algae had a genome sequence. You hear a lot about the green algae Chlamydomonas reinhardii, because it was the first to have it's genome sequenced. In the past 10 years, only a handful of microbes that fall into the category algae have had a whole genome sequenced, including two diatoms and one of their relatives, a red alga, a coccolithophore, and two other marine green alage. Compare that to at least twice as many plant genomes and over one thousand bacterial genomes.

In my academic work, I use genomes and comparative genomics to study the evolution of algal groups and their physiological capabilities. I also use a new tool, called metagenomics, to look at the combined genome of these organisms in the environment - specifically the ocean. To do this, we go collect community samples of microbes in the ocean, extract total DNA (or RNA) from those samples and then sequence as much as we can from it. Then we identify who was there by comparing to the genomes we have already sequenced. As you might guess, this is a really hard problem when you have only a handful of genomes to compare to.

This limited genomic data also poses challenges for the algae biofuels industry. Many of the scientist doing this work would love to have genome sequence of the potential fuel producing strains. Two weeks ago, a group in Texas announced the genome project of a biofuel favorite, Botryococcus braunii.

http://www.sciencedaily.com/releases/2010/03/100312164659.htm

This will be a contribution to the industry but also to academia, where scientist looking to understand the evolution and physiology of these organism will also be able to make use of the data. B. braunii is just the beginning of sequencing for energy related organisms, that will also help to fill out our understanding of the tree of life.

(I should say that the genomes I mentioned above are the ones that are publicly available. Many labs are in the process of sequencing genomes that are not publicly available yet, and genome sequencing done through industry probably will not be shared... but we can hope.)