Seaweed Biofuel, #ArsenicLife, and Synthetic Bioweapons

There have been a few interesting developments in synthetic biology/science generally recently, and I can't help but cram them together in a single post.

1. E. coli Produce Ethanol from Seaweed

The world is facing a global energy crisis that demands both extensive scientific effort and sound policy making. Biofuels will undoubtedly be key in addressing the problem. Today we have an impressively large agricultural biofuel industry; corn ethanol comes to mind. Whether using corn for ethanol is a good move or not is an extremely complex issue that I'd rather not go into here. However, it's clear that corn ethanol cannot address global energy demand, from a practical standpoint if nothing else (the land area required would be outrageous).

An international team of collaborators recently reported success in fermenting ethanol from seaweed^1,2, a plant with the benefit of lacking a pesky molecule called lignin that complicates the fermentation process but with the added challenge that many of the plant's sugars are tied up in a complex polymer called alginate. The fermenters used by the biofuel industry aren't able to digest it. The researchers transferred an alginate-digesting gene from a different bacterium to E. coli. The E. coli secrete the protein (Aly), leaving small fragments of alginate floating outside the cells. After searching through databases, they found a series of genes to transport the fragments into the cell. With the sugars now inside the E. coli, the cells could ferment them into ethanol, yielding 80% of the theoretical maximum.

Seaweed biofuel might someday be an efficient alternative to land crop derived ethanol in coastal regions.

2. #ArsenicLife Comes to Close

If you haven't been following Rosie Redfield's work on the highly criticized discovery of DNA containing arsenic³, as much an experiment in open science⁴ as in biology, then sadly you're a bit too late. After months of control experiments and troubleshooting growth conditions of the strain GFAJ-1, Redfield and her collaborators have provided strong evidence that what Wolfe-Simon et al. found was not arsenic life. In her technical comment⁵, Redfield criticized the author's purification of the DNA, claiming that the observation was contaminating arsenic, not arsenic replacing phosphorus in the DNA.

Her evidence against the claim made by Wolfe-Simon et al. can be summed up in this single graph. DNA extracted from GFAJ-1 cells grown with arsenic (red) and without arsenic (blue) was purified using a CsCl gradient, which separates molecules by density. The two peaks on the lines with solid markers indicate the presence of DNA. If the cells grown in arsenic incorporated it into their DNA, there would be another red peak with the open markers. Based on the 4% As-P replacement reported by Wolfe-Simon et al., we would expect to see a peak with the height of the dotted orange line. What we actually see is no detectable arsenic, so the most likely explanation is that the analysis performed by Wolfe-Simon et al. detected contaminating arsenic, not arsenic covalently incorporated into DNA.

3. Synthetic Biologists Must Define Their Relationship with the Military

Rob Carlson and Daniel Grushkin, two promoters of DIY synthetic biology, wrote a piece in Slate outlining military funding of synthetic biology for weapons research⁷. This issue isn't entirely new⁸, but it's one that demands timely consideration. First, I must emphasize that biological weapons are nowhere to be found in this (non-classified) discussion. The question at hand is whether synthetic biology should be used to produce explosives precursors, given that synthetic biology can produce these compounds in a more environmentally friendly way than can conventional synthesis. It's one of those dilemmas that demands extremely careful thought.

On the one hand, the industrialized world produces an astonishing quantity of explosives. As a commenter on one of the articles pointed out, most of these materials are used for peaceful purposes, in the mining industry in particular. Yet, the research would be funded by defense agencies with their own agendas and not-so-peaceful applications. In the face of that fact, I think the only justification can be that the alternative is an equal number of polluting weapons. I think that overall the benefit will outweigh the harm, in part because the discoveries will spur broader research in biosynthesis of other compounds with peaceful applications.

However I still have lingering reservations about the work. The military doesn't have to worry about anyone stealing an explosives factory today. The building and machinery inside are far too extensive to be stolen. But the game changes when an entire factory can be grown from a single cell. After all, how easy would it be to pocket a cryotube containing billions of self-replicating explosives factories?

Image Credits: Graph: R. Redfield (here); Cryotube: www.dropsahl.com

References:

1. Wargacki, A. J. et al. An Engineered Microbial Platform for Direct Biofuel Production from Brown Macroalgae. Science 335, 308-313 (2012).

2. Stokstad, E. Engineered Superbugs Boost Hopes of Turning Seaweed Into Fuel. Science 335, 273 (2012). [News Article]

3. Wolfe-Simon, F. et al. A Bacterium that Can Grow by Using Arsenic Instead of Phosphorus. Science 332, 1163-1166 (2011).

4. Redfield, R. RRResearch. [Blog]

5. Hayden, E. C. Study Challenges Existence of Arsenic-Based Life. Nature News. January 20, 2012.

6. Redfield, R. Comment on "A Bacterium that Can Grow by Using Arsenic Instead of Phosphorus." Science 332, 1149 (2011).

7. Carlson, R. & Grushkin, D. "The Military's Push to Green Our Explosives." Slate. January 19, 2012.

8. Hayden, E. C. Bioengineers Debate Use of Military Money. Nature 479, 458 (2011). [News Article]