Metabolic rate determines mutation rate

ScienceDaily has a story describing a new paper showing that the rate of protein evolution is subject to allometric scaling.  Actually, now that I have written that, I remember that allometric scaling describes a specfic mathematical relationship between metabolism and body mass, but the paper in question doesn't appear to be online yet so I can't say for sure allometric scaling is the appropriate mechanism to cite.

At any rate, ScienceDaily reports that James Gillooly, and colleagues have shown that: "...A 10-degree increase in temperature across species leads to about a 300 percent increase in the evolutionary rate of proteins, while a tenfold decrease in body size leads to about a 200 percent increase in evolutionary rates."

"Generally, there are two schools of thought about what affects evolution," said Andrew P. Allen, Ph.D., a researcher with the National Center for Ecological Analysis and Synthesis in Santa Barbara, Calif. "One says the environment dictates changes that occur in the genome and phenotype of a species, and the other says the DNA mutation rate drives these changes. Our findings suggest physiological processes that drive mutation rates are important."

That is pretty interesting.  Warm, small animals evidently experience a greater rate of protein evolution than to large, cold ones.  This suggests to me that warm-blooded, smaller animals have an evolutionary advantage because they are better able to produce physiological variation in the context of a changing environment, and thus better able to compete at the species level in the face of natural selection.  The ScienceDaily story doesn't make that point, but I would assume the paper in Biology Letters, when it is published, will.

Here is the press release from the University of Florida.

Amyris Raises Additional US$ 70 Million for Micriobial Biofuels Production

Amyris Biotechnologies today announced the first portion of their B round financing for US$ 70 million.  This brings the total company financing for microbial production of biofuels to just under US$ 100 million in the last year.  The press release also notes Amyris already has bugs in the lab producing "bio-jet", "bio-diesel", and "bio-gasoline".  The latter is interesting because previous announcements had suggested butanol as a target product rather than a hydrocarbon.  Immiscible hydrocarbons will be much easier (read "less expensive") to separate from the fermentation broth than water soluble alcohols.

In any event, the company is clearly moving faster than even my earlier optimistic estimates (see "The Need for Fuels Produced Using Synthetic Biology").  While the speed of engineering efforts is still an issue (see "The Intersection of Biofuels and Synthetic Biology"), and will be for some time to come, I have been spending more time lately trying to understand the issue of scale.  The petroleum industry is absolutely enormous, and replacing any significant amount of petro-fuels with bio-fuels will require feedstocks in abundance.  It is by no means clear that the U.S. can meet the demand with domestic biomass production.  More on this as the topic develops.

Sony's Enzyme-Powered, Sugar Fueled Power Supply

Sony has apparently demonstrated a power supply for consumer electronics that uses enzymes to covert sugar to useful electrons (via Gizmodo).  Not many details are available (to non-Japanese speakers, anyway), but it looks like each "module" generates ~50 mW from an unspecified amount of sugar.  It is evidently just an engineering demonstration, but it's pretty cool nonetheless.  No word on how the digested sugar is converted to electrical power.

The Intersection of Biofuels and Synthetic Biology

New players are appearing every day in the rush to production biofuels using synthetic biology.  I just noticed an announcement that Codon Devices has signed an agreement with Agrivida for:

The discovery, development, and commercialization of engineeredproteins for use in so-called 'third generation' biofuel applications. Under the terms of this agreement, Codon Devices will deliver to Agrivida optimized enzymes to be embedded in crops for biofuels production.

...Agrivida, an agricultural biotechnology company, is developing such third generation biofuels by creating corn varieties optimized for producing ethanol. First generation methods for manufacturing ethanol make use of the corn grain only, leaving the remaining plant material, such as the corn leaves, stalks, and husks in the field. Central to Agrivida’s ethanol-optimized corn technology are engineered cellulase enzymes that are incorporated into the corn plants themselves. These enzymes will efficiently degrage the entire mass of plant material into small sugars that can then be readily converted to ethanol.

The step of putting some of the biofuel processing into crops was inevitable, but I can't say I am particularly thrilled about it.  I am not opposed to the principle of open planting of GM crops, but, because many GM plants do not behave as predicted once placed in a complex ecosystem (i.e., nature), I wonder if  we shouldn't be more circumspect about this particular engineering advance.

In other interesting developments at Codon, they also recently announced a deal with Open Biosystems wherein the latter will:

Sell and distribute Codon Devices’ gene synthesis offering to researchers with needs that fall below Codon’s minimum order threshold.  The partnership will enable a wide range of new customers to utilize high-quality, low-cost gene synthesis in their research, and will greatly strengthen Codon Devices’ presence within academic, government and other non-profit institutions.

I also notice Codon is now advertising gene synthesis for $.69 per base for constructs between 50 and 2000 bases in length, with "typical delivery" in 10-15 days.  2001-5000 bases will cost you $.84 per base and 15-20 days.  Last year at SB 2.0, Brian Baynes suggested they would be at about $.50 per base within a year, so costs continue to fall pretty much apace.  But delivery times are staying above two weeks, and this is now becoming a problem for some of Codon's customers.  I am not at liberty to divulge names, but some synthetic biology companies that rely on outside gene synthesis are starting to chafe at having to wait two weeks before trying out new designs.  This is something we predicted would happen in the "Genome Synthesis and Design Futures" report from Bio-era, though I am a bit surprised it is happening so soon.  This may be another indication of how quickly SB is becoming an important technology in the economy.  Engineers trying to turn around products aren't satisfied with the NIH/academic model of trading off time for money -- the market, to first order, only cares about products that are actually for sale, which means those that make it through R&D quickly and generate revenues in what will become an increasingly crowded field.

Concerns about delays in the R&D cycle due to outsourced gene delivery are also becoming confounded by IP issues.  Personally, I am certainly not thrilled about sending my protein designs around via email, and I know of another SB company (which again I am not at liberty to name) that is becoming less and less comfortable with sending sequences for new genetic circuits out the door in electronic form.  This can only be exacerbated by the deal Codon Devices has just signed with Agrivida, an explicit competitor to anybody trying to produce anything in hacked/engineered organisms.  A couple of months ago, I had a conversation with Brian Baynes (which I will post here sometime soon) in which he outlined Codon's plans for participating in markets beyond gene synthesis.  I suspect Codon Devices will have to start paying more and more attention to conflict of interest issues generated by its simultaneous role as a fabrication house and provider of design services.

I'll argue again that the two trends of IP concerns and R&D time scales will drive the emergence of a market in desktop gene synthesis machines, whether you call them "desktop gene printers" or  something else.  This weekend at SciFoo, Drew Endy suggested such instruments are a long ways off.  Drew has been paying more attention to the specific engineering details of this than I have, if for no other reason that his involvement in Codon, but, in addition to my own work, I think that there are enough technological bits and pieces already demonstrated in the literature that we could see a desktop instrument sooner rather than later; that is, if a market truly exists. 

Environmental Effects of Growing Energy Crops

News this week that the dead zone in the Gulf of Mexico, caused by agricultural run-off from the mid-west, is again this year going to be quite large.

There is some disagreement about exactly how large.  A article from Minnesota Public Radio leads off with: "A scientist with the National Oceanic and Atmospheric Administration, NOAA, says this summer's dead zone could be as large as 8500 square miles. That's 77 percent larger than the average size of the dead zone over the last two decades."

The article continues:

The issue of nitrogen is especially important this year because it's the main fertilizer used on the nation's corn crop.

U.S. farmers this spring planted one of their largest corn crops ever, up almost 20 percent from a year ago. Much of the increase will go to meet the demands of the ethanol industry.

Runoff from farm fields carries nitrogen into streams and rivers and eventually the Gulf of Mexico. NOAA's David Whitall says the corn-biofuels-dead zone link is one area researchers will examine as they search for answers.

...One federal study says if ethanol production continues to expand, nitrogen loads to the Gulf could increase another 30 percent.

At CNN, on the other hand, the size of the dead zone is portrayed somewhat differently:

The oxygen-poor "dead zone" off the Louisiana and Texas coasts isn't quite as big as predicted this year, but it is still the third-largest ever mapped, a scientist said Saturday.

...The 7,900-square-mile area with almost no oxygen, a condition called hypoxia, is about the size of Connecticut and Delaware together. The Louisiana-Texas dead zone is the world's second-largest hypoxic area, she said.

This year's is about 7.5 percent smaller than [had been] predicted, judging by nitrogen content in the Mississippi River watershed.

[Previous predictions were] about 8,540 square miles, which would have made it the largest measured in at least 22 years. More storms than normal may have reduced hypoxia by keeping the waters roiled.

No mention at CNN of any role any role in the dead zone of biofuels.  The difference between the numbers cited by the two sources is less than 5%, which probably isn't a big deal, especially give then fact that neither article cites error bars.  But there is a difference in focus.  On the one hand, the dead zone is bigger than ever, on the other, not so bad.  Corn acres are certainly up in the U.S., and the effects of the consequent increase in irrigation and fertilizer use is something to keep an eye on.

LS9 - "The Renewable Petroleum Company" - in the News

LS9, "The Renewable Petroleum" Company, has just hired a former oil executive as its new CEO.  The promise of direct microbial fuel production is so great that this news even made The Huffington Post.  Why all the sudden buzz?  The answer is that this technology is really quite new, but is making great strides.  Moreover, as I wrote about a couple of weeks ago (see "The Need for Fuels Produced Using Synthetic Biology"), the economics of producing fuels from microbes is so radically different from what we are used to that it will upend our notions industrial infrastructure.  That said, it will still take some time before all the impacts are fully appreciated.

Last Thursday, I did a short interview for the series Questions for the Future, produced by CNBC Europe/Asia in association with Shell, during which the host was somewhat perplexed about why there was not yet more widespread discussion of this technology.  At The Huffington Post, David Roberts starts his post with a note of skepticism:

Picture a liquid fuel that is derived from the same feedstocks as cellulosic ethanol (switchgrass, sugar cane, corn stover) but contains 50% more energetic content and is made via a process that uses 65% less energy.

Unlike cellulosic ethanol, this fuel can be distributed via existing oil pipelines rather than gas-hogging trucks and trains, dispensed through existing gas stations rather than specialized pumps, and used in existing engines rather than modified "flex-fuel" engines.

In short, it is a biofuel that can be substituted directly and immediately for gas or diesel, on a gallon-for-gallon basis.

Sounds pretty good, eh? Too good to be true?

Which illustrates one reason why this topic isn't so much in the news.  It does sound too good to be true.  But it is quite real, with Amyris Biotechnologies on track to produce jet fuel from microbes by 2011 at an equivalent cost of US$ 40 per barrel.

Another interesting thread to this discussion is the potential internal conflict generated in "Greens" by the notion of reducing carbon emissions ("Good!") using genetically modified organisms ("Bad!").  I've been working this idea into an essay about laying the foundations for a bio-economy, but Roberts makes it explicit in his post; "I know there are greens who feel creepy about genetic engineering, and they probably won't like the fact that LS9 is trying to patent a life form. But I don't really share those concerns, so I'll just skip them."  No worries.  Just like that.  I am not so certain Greenpeace et al. will follow along so quietly.

In the press release from LS9, new CEO Robert Walsh says:

After years of leadership roles in the traditional petroleum industry and responsibility over all aspects of the hydrocarbon supply chain, I can see clearly how LS9's products will fit into existing infrastructure and deliver significant value to partners and consumers compared with other biofuel alternatives.  LS9 has the opportunity to fundamentally change the transportation fuel equation, which makes me incredibly excited to join this talented team.

While it's true that these engineered synthetic fuels will likely find first use within existing distribution channels, it is the potential for distributed manufacturing that truly changes the game.  It will be interesting to see how long it takes for this part of the story to work its way into the broader conversation.

Finally, here is additional coverage of the LS9 announcement at GreenCarCongress.