MIT Advances in Bio-Synthetic Fuels and Chemicals

MIT researchers are tweaking the synthesis pathways of the E. Coli bacteria to facilitate high efficiency production of a wide range of biofuels and high value chemicals.

Images via GCC

Researchers at MIT have adapted the butanol pathway for the synthesis of odd-chain molecules and have also developed a complementary modular toolkit to facilitate pathway construction, characterization, and optimization in engineered Escherichia coli bacteria.

The modular nature of the pathway enables multi-entry and multi-exit biosynthesis of various odd-chain compounds at high efficiency. By varying combinations of the pathway and toolkit enzymes, they demonstrated controlled production of propionate, trans-2-pentenoate, valerate, and pentanol—compounds with applications that include biofuels, antibiotics, biopolymers, and aroma chemicals.

In a paper published in the Proceedings of the National Academy of Sciences (PNAS), Hsien-Chung Tseng and Kristala L. J. Prather note that their bypass strategy was effective even without the presence of freely membrane-diffusible substrates. The approach could prove useful for optimizing other pathways that use CoA-derivatized intermediates, they suggested, including fatty acid β-oxidation and the mevalonate pathway for isoprenoid synthesis. _GCC

Applications of various fermentation products synthesized from recombinant Escherichia coli strains carrying different combinations of pentanol pathway and CoA-activation/removing toolkit enzymes. Tseng and Prather Supplementary Information.

This type of advance in the genetic design of microbial synthesis promises a certain degree of versatility for the future enterprise of moving away from petro-feedstocks in fuels, polymers, and chemicals production.

As noted here many times, the current abundance of natural gas makes the economical production of biofuels more problematic. But as technologies continue to improve at all levels of supply and production, advanced biosynthesis and advanced bioenergy will gradually increase market share -- beginning as soon as natural gas prices increase.

Shortcuts to Custom Bio Production of Fuels and Chemicals

A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression.

Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism. _NatureCommunications

Nature Communications 3, Article number: 929 doi:10.1038/ncomms1928

UCSD researchers have taken an important step toward the ability to custom design the genome of organisms in order to produce synthetic fuels, chemicals, pharmaceuticals, and more, on a commercial scale.

"What you could hypothetically do with our model is simulate the total cost of producing a value-added product, such as a biofuel. That includes all the operating and maintenance costs," said Daniel Hyduke, a project scientist in Palsson's lab. Hyduke said the method has the potential to help streamline industrial metabolic engineering efforts by providing a near complete accounting of the minimal material and energy costs associated with novel strain designs for biofuel, commodity chemicals, and recombinant protein production.

Hyduke and Lerman prototyped the method on the minimal, yet metabolically versatile, hyperthermophile Thermotoga maritima. Because T. maritima is not currently ready for use in industrial applications, Hyduke and Lerman are working as part of a larger team to produce similar models for industrially relevant microorganisms, such as E. coli.

"We've built a virtual reality simulator of metabolism and gene expression for Thermotoga maritima, and shown that it much better approximates phenotypes of cells than modeling metabolism in isolation," said Lerman.

...Their method accounts, in molecular detail, for the material and energy required to keep a cell growing, the research team reported in the journal Nature Communications.

"This is a major advance in genome-scale analysis that accounts for the fundamental biological process of gene expression and notably expands the number of cellular phenotypes that we can compute," said Bernhard Palsson, Galetti Professor of Bioengineering, at the UC San Diego Jacobs School of Engineering.

"With this new method, it is now possible to perform computer simulations of systems-level molecular biology to formulate questions about fundamental life processes, the cellular impacts of genetic manipulation or to quantitatively analyze gene expression data," said Joshua Lerman, a Ph.D. candidate in Palsson's Systems Biology Research Group. _SD

This approach provides more useful information in advance, to researchers considering various approaches to the design of custom chemicals-producing organisms -- particularly microbes, but eventually plants and animals as well.

In summary, the development of this tool should streamline the design and development of organisms capable of producing commercially valuable chemicals and fuels in an economical manner. It should also prevent much wasted energy on the part of researchers, by pointing out dead-end research approaches in advance.

JBEI Berkeley Develops Master Controls for Synthetic Biology

Synthetic biology is an emerging scientific field in which novel biological devices, such as molecules, genetic circuits or cells, are designed and constructed, or existing biological systems, such as microbes, are re-designed and engineered. A major goal is to produce valuable chemical products from simple, inexpensive and renewable starting materials in a sustainable manner. As with other engineering disciplines, CAD tools for simulating and designing global functions based upon local component behaviors are essential for constructing complex biological devices and systems. However, until this work, CAD-type models and simulation tools for biology have been very limited...

...“Because biological systems exhibit functional complexity at multiple scales, a big question has been whether effective design tools can be created to increase the sizes and complexities of the microbial systems we engineer to meet specific needs,” says Jay Keasling, director of JBEI and a world authority on synthetic biology and metabolic engineering. “Our work establishes a foundation for developing CAD platforms to engineer complex RNA-based control systems that can process cellular information and program the expression of very large numbers of genes. Perhaps even more importantly, we have provided a framework for studying RNA functions and demonstrated the potential of using biochemical and biophysical modeling to develop rigorous design-driven engineering strategies for biology.”

Keasling, who also holds appointments with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkley, is the corresponding author of a paper in the journal Science that describes this work. The paper is titled “Model-driven engineering of RNA devices to quantitatively-program gene expression.” Other co-authors are James Carothers, Jonathan Goler and Darmawi Juminaga. _LawrenceBerkeleyLab_via_GCC

The art of dealing with complexity will separate those societies which succeed from those which fail. Some levels of complexity cannot be totally mastered, yet they can be "accomodated" or dealt with.

Learning to fine-program biological organisms to produce substances of use to humans in useful form and quantity, would allow a passage through a threshold separating one type of society from earlier types. This has always been the promise of synthetic biology, but the specific tools to be used have been either lacking, or far too crude. This is changing.

“We needed to formulate models that would be sophisticated enough to capture the details required for simulating system functions, but simple enough to be framed in terms of measurable and tunable component characteristics or design variables,” Carothers says. “We think of design variables as the parts of the system that can be predictably modified, in the same way that a chemical engineer might tune the operation of a chemical plant by turning knobs that control fluid flow through valves. In our case, knob-turns are represented by specific kinetic terms for RNA folding and ribozyme catalysis, and our models are needed to tell us how a combination of these knob-turns will affect overall system function.”

JBEI researchers are now using their RNA CAD-type models and simulations as well as the ribozyme and aptazyme devices they constructed to help them engineer metabolic pathways that will increase microbial fuel production. JBEI is one of three DOE Bioenergy Research Centers established by DOE’s Office of Science to advance the technology for the commercial production of clean, green and renewable biofuels. A key to JBEI’s success will be the engineering of microbes that can digest lignocellulosic biomass and synthesize from the sugars transportation fuels that can replace gasoline, diesel and jet fuels in today’s engines.

“In addition to advanced biofuels, we’re also looking into engineering microbes to produce chemicals from renewable feedstocks that are difficult to produce cheaply and in high yield using traditional organic chemistry technology,” Carothers says. _LBL

Brian Wang provides additional information and materials

Green Car Congress coverage of this story

Re-inventing Oil: The Unstoppable Coming World of Synthetic Biology

If petroleum didn’t exist, we’d have to invent it. Nothing else comes close to oil when it comes to energy density, ease of handling, flexibility, convenience, cost, or scale...

...“There is one thing all energy transitions have in common: they are prolonged affairs that take decades to accomplish,” wrote Vaclav Smil in 2008....Smil, a polymath, prolific author on energy issues, and distinguished professor at the University of Manitoba, believes that while a “world without fossil fuel combustion is highly desirable … getting there will demand not only high cost but also considerable patience: coming energy transitions will unfold across decades, not years.” _The Persistence of Oil

Al Fin energy analysts agree with Vaclav Smil on both counts: Re-inventing oil is a good idea, and the transition from oil to a re-invented oil will take decades.

Synthetic biology is in the process of changing all the rules for making things. We already make life-saving medicines with some of the same tools that synthetic biologists are using. We are even making vehicular tyres using these tools. But we have just gotten started.

Khosla Ventures has started a new $1 billion fund that is specialising in synthetic biology ventures, and related technologies. The US Department of Energy is also funding synthetic biology projects with the aim of re-inventing oil creation. Craig Venter's Synthetic Genomics is being funded by Exxon Mobil to the tune of roughly $500 million to accomplish the same feat.

Oil is going to be around for a long time, because it is so very good at doing the things that humans need it to do. It takes nature between 100,000 and 1,000,000 years to make oil from once-living matter. Synthetic organisms should be able to produce oil in split seconds, using cheap raw materials plus sunshine or other readily available energy supply.

Why bother with all that high tech science when we can grow abundant algal biomass, and turn it into fuel using pyrolysis and IH2 treatment? Simple economics. Pyrolysis + IH2 requires a lot of energy and hydrogen. If you design your synthetic organisms properly, they can function at low temperatures and obtain their hydrogen from water.

The only way for advanced thermochemical biofuels conversion to compete with synthetic biology, is for the thermochemical process heat and hydrogen to be supplied by nuclear reactors. That approach is indeed likely to coexist with advanced synthetic biology fuels in the future.

Is There Anything Synthetic Biology Can't Do?

Synthetic biology involves the creation of new forms of life that have never existed before. These new lifeforms will be designed to produce valuable products such as fuels, medicines, high value chemicals, food products for animals and humans, and more.

Biologists have built two artificial chromosome arms and put them to work in a living yeast. They plan to replace the entire yeast genome over the next five years and then evolve new strains to order.

"Nothing like this has ever been done before," says Jef Boeke of the Johns Hopkins University School of Medicine in Baltimore, Maryland, who is leading the research. As well as designing and building the new genome from scratch, his team has come up with a way to systematically scramble it to produce new strains.

The artificial yeast are similar to Craig Venter's synthetic cells, announced last year. Venter replaced the entire genome of a bacterium with a synthetic genome – but the task is far harder in yeast, because it is a more complex organism and has a bigger genome. _NewScientist

Science is very early into the project of synthetic biological organisms, but no matter how slowly the progress, the information learned will be invaluable.

Yeast has 16 chromosomes, all of which have been sequenced. Boeke started small, replacing the right arm of chromosome 9 and part of the left arm of chromosome 6. He began by designing the new sequences on a computer, using the known sequence as his starting point. He stripped from this virtual DNA all the meaningless "junk" DNA, which does not code for proteins. Then he added markers called loxPsym at the ends of all non-essential genes – those that could be changed or deleted without killing the yeast. In the real world, these markers can be attacked by an enzyme called Cre, which swaps genes between the marker sites. Finally, he created these new sequences in the lab using the chemical building blocks of DNA, and inserted them into a living yeast in place of its natural chromosome arms.
Shuffling genes

"This is another remarkable example of how synthetic biology can be used to rewrite chromosome sequences at a sizeable scale," says Daniel Gibson of the J. Craig Venter Institute in Rockville, Maryland. He says it could help us understand the rules governing genome structure.

For instance, the reshuffling technique can test how different arrangements of genes affect the yeast. Boeke has already done this by shuffling the genes on the artificial chromosomes using the Cre enzyme.

"You can take a yeast gene and insert it somewhere else in the genome, and you tend to get a healthy yeast," Boeke says. That suggests a reshuffle wouldn't matter, but different yeasts consistently use the same order. "Maybe there are hidden rules of genome structure that we can distil," Boeke says.
Make your own yeast

Boeke now intends to repeat this re-engineering process with the other chromosomes in yeast. Once the entire genome is laced with loxPsym sites, Boeke plans to use Cre to make wholesale changes. Because the method targets only non-essential genes, and does not interfere with their internal structure, it should mostly produce healthy yeast. _NS

Very ambitious indeed. And it is just the beginning.

Proterro is a biotech company that aims to produce high volumes of low-cost sugars from water, CO2, sunlight, and basic nutrients -- using their own custom designed micro-organism.

Proterro’s patent-pending biosynthetic process combines an engineered photosynthetic microorganism with an advanced high-density, modular solid-phase bioreactor to provide a fermentation-ready feedstock, called Protose. Produced by combining only water, carbon dioxide, sunlight and nutrients in the biosynthetic process, Protose is projected to cost less than such feedstocks as sugar cane and cellulosics, and can be used to produce a variety of commercial scale fuels and chemicals through standard industrial fermentation methods. _BiofuelsDigest_via_BrianWestenhaus

Proterro's plan is ingenious, but time is a critical factor. If the company cannot produce high volumes of its sugar reliably and economically within the next 5 years, it will probably be crowded out of the market by the other companies highlighted in the article linked above.

Biomass can be grown over 80% of the Earth's surface -- land or ocean -- and does not require the care that special microbial bioreactors require. Dozens of companies are devising better ways to produce cheap sugars from biomass, and at least a few of them are likely to come up with profitable approaches within the next 5 years. Once cheap biomass sugars are available, the cost of making biofuels and other renewable chemicals will suddenly become less of an obstacle.

Small Energy News

Oxford Catalysts is working on its third commercial order for its microchannel F-T GTL reactors.

The order comprises two full scale FT reactors (with a nominal capacity of more than 50 bpd) that form the first installment of reactors towards a commercial synthetic fuels plant expected to start operations in 2012. The customer intends to roll out additional plants following successful completion and operation of this first US commercial facility. The two reactors ordered will be delivered by the fourth quarter of 2011.

This is the Group’s third sale of FT reactors and catalyst, following separate orders for FT units by SGC Energia, SGPS, SA in December 2010 and April 2011. (Earlier post.)

Oxford Catalysts is focused on the emerging market for distributed smaller scale production of synthetic oil via FT synthesis—a market that has the potential of producing as much as 25 million barrels of fuel a day, the company says. _GCC

25 million barrels of synthetic crude per day??? That might put a dent in the dieoff.orgiast's hopes for energy starvation and mass dieoff. Not to mention dashing the desires for doom of all the peak oil doomers singing the echo choir of circular jerkular canons and rounds.

Global Bioenergies and Synthos are partnering to produce bio-butadiene.

Synthos SA, a European leader in the manufacturing of rubber, and Global Bioenergies SA, an industrial biology company developing sustainable routes to light olefins, signed a partnership agreement to develop a new process for the conversion of renewable resources into butadiene, involving research funding, multi-million euro development fees, royalty payments, repartition of exploitation rights, and a €1.4-million (US$2-million) equity investment in Global Bioenergies, representing a 3.6% stake.

Butadiene is one of the major building blocks of the petrochemical industry and is presently exclusively produced from oil. About 10 million tonnes are produced each year, of which two thirds are used to manufacture synthetic rubber. The last third is used to produce nylon, latices, ABS plastics and other polymers. The spot price of butadiene has recently rose to over $3/kg, and as such the global butadiene market is estimated at $30 billion. _GCC

Synthetic biology company LS9 is working with HCL Cleantech to develop a process of biomass to sugars to fuels. They are working under a $9 million DOE grant which covers the entire process from biomass to fuels, using genetically modified organisms.

Speaking of genetically modified organisms and synthetic biology, three names are coming up more often than others: Craig Venter, Jay Keasling, and George Church. George Church has made news with a paper in Science describing a dramatic new synthetic biology tool able to replace specific codons in a multiplex fashion wherever they are found in the micro-organism. This is only big news if you understand what it means. Although this particular incarnation of the tool is aimed at "stop codons," it is still theoretically capable of creating organisms that can synthesise unique proteins as therapeutic products.

The synthetic biologists are mainly concerned with the micro-organisms they can create, and the commercial products these microbes will be able to produce.

Eventually, the idea is to be able to simultaneously modify the genetic coding of a eukaryotic organism (such as a human) across the entire genome, with its complex multi-chromosome arrangement. That will not be so easy.

Biofuels Production of Over US$ 11 Trillion by 2050: IEA

In Washington, the International Energy Agency (IEA) said that it expects biofuels to generate $11-$13 trillion in production between 2010 and 2050, and the global share of biofuel in total transport fuel to grow from 2% today to 27% in 2050. _BiofuelsDigest

PDF IEA Report PDF

UC Berkeley is "all in" on the project. Not only is UCB an integral part of the Joint BioEnergy Institute, the school has also just launched the Synthetic Biology Institute for new research & development in biological engineering, and scale the advances up to industrial levels.

In the meantime, dozens of well-financed biotech companies, such as Joule Unlimited, are rushing ahead to develop custom microbes specifically tailored to produce specific fuels and high value chemical products. Joule is based in Cambridge, Massachusetts, on the opposite side of the US from UC Berkeley, in the middle of a competing high technology startup zone. Similar zones are located near Stanford U., around Austin, Texas, near La Jolla, California, and around dozens of other high tech startup zones across North America.

Clearly, if biofuels are to provide roughly 1/3 of global transportation fuels by the year 2050, a tremendous amount of feedstock will be required. Cellulosic biomass (both marine and terrestrial) will be one type of feedstock, as will waste streams of various types. All types of waste plastics, waste rubbers, waste papers and cardboards, waste foam packing etc etc will be routinely grabbed up by this growing industry, as valuable feedstock. Anything considered "garbage" or "waste" today is likely to be seen as a feedstock to be turned into high value product, by the time period of 2025 to 2050.

This will be simple economics, not an effort to "save Gaia."

Virginia Tech has recently licensed an open software tool tailored for synthetic biology safety. It is meant to monitor chemical reagent and biological agent acquisitions, to minimise the dangers of misuse of synthetic biology technologies, eg for terrorism.

Synthetic Biology and the Future

Synthetic biology is one of the six world-changing basic sciences chosen by an expert panel at the US Department of Defense. Other than advanced cognitive science, it is difficult to conceive of any other science or technology which could have greater impact on the human future than synthetic biology.

Jay Keasling wants to use synth-bio to create jet fuel and diesel.

Here is a brief primer on synthetic biology, and a look at the quest for a "genetic transistor."

Here is a look at another ultra-rich investor (besides Khosla) who is investing big in synthetic biology.

A quick look at one of the powerful new tools of synthetic biology.

The sophisticated genetic modification of microbes, plants, and animals is likely to lead to a number of dramatic disruptive products and technologies -- going far beyond alleviating any conceivable fuel shortage.

While the bulk of energy journalists, pundits, and economists seem to be whining and obsessing over a temporary political peak oil accompanying political unrest in third world MENA countries, smarter people are looking past the insignificant speed bumpts toward longer term goals and technologies.

Many Roads Lead to Biofuels and Bioenergy

More: Waste & garbage super-giant Waste Management has partnered with Genomatica to develop methods of creating high-value and basic chemicals from municipal waste -- via syngas. The "waste to energy and other valuable products" is a common theme in biofuels and bioenergy.

The simplest path to bioenergy from "biofuels" is the combustion of woody biomass to generate electricity. An Alabama sawmill intends to use waste sawdust and bark to generate 7 MW of power. The mill will sell excess production to the local utility.

The gasification of biomass to syngas allows for multiple uses -- including direct syngas combustion, the fermentation of the syngas to alcohols, or the catalytic production of advanced Fischer Tropsch fuels. A research team at the Key Laboratory of Renewable Energy and Gas Hydrate, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, has devised an improved method of catalytic steam gasification of biomass for production of synthetic fuels. The ever-present potential for altering the economic balance of biomass gasification to advanced catalytic fuels, keeps a lot of energy analysts vigilant and wary.

The anaerobic digestion of municipal waste and waste biomass is another fairly simple approach to the production of fuels -- often methane, or in the case of a new Vero, Florida plant, ethanol. The new Florida plant will use naturally occurring bacteria to ferment biomass-derived syngas anaerobically to ethanol.

New research suggests that a US farmer could fuel his equipment with biodiesel grown on between 5% and 7% of his acreage using canola or camelina. Here is an example of a farmer in Washington State who grows his own fuel.

Dry desert areas like US states Arizona or New Mexico could provide a perfect growing climate for algal fuels farming operations. Since such land is not desirable for ordinary food crops, most food-for-fuels agitators should be relatively unperturbed.

Advanced synthetic biology microbial fuels company LS9 has entered into its second business agreement with business giant Procter & Gamble, to provide the large company with renewable high value chemicals for its routine products and operations. This approach is a smart one for microbial fuels companies who wish to build profitable product lines, before trying to go head to head with petroleum fuels in the open market.

Seaweed -- or macro-algae -- is a prolific biomass crop, with 6 harvests a year and rapid growth. Since seaweed can be grown in salty or brackish water, it can greatly expand the growing area for biomass worldwide. A University of Illinois Urbana-Champaigne has further altered the genome of the yeast Saccharomyces Cerevisiae to allow even faster and more efficient fermentation of galactose in seaweed to ethanol. Quite a number of clever means of growing seaweed using saltwater are being devised, which will make wide-scale growing of this biomass crop for fuels more practical.

The planet Earth is a biological world -- the only biological world we know. Plants and microbes have evolved many ways to take advantage of primary solar energy and secondary chemical energies. Smart humans should eventually learn how to work with such evolutionary traits -- tweaking them to help biology to provide humans with most of the liquid fuels and many of the materials and chemicals they need.

The zero sum, doomer mindset, which is so common among academics and activists, is more an impediment to an abundant future than almost anything else on Earth.

LS9 Synthetic Biology Receives Another Round of Funding

LS9 EColi
LS9 has held onto its previous group of investors and added BlackRock, for a $30 million venture funding round.

LS9 uses a one-step fermentation process to convert renewable plant-based materials into a diverse portfolio of fuel and chemical products. The company has successfully operated its pilot plant in South San Francisco, California for more than two years and announced the acquisition of a larger-scale production facility in Okeechobee, Florida in January 2010. In June 2010, LS9 won the Presidential Green Chemistry Challenge Award. _GCC

More on the underlying LS9 approach:

Pushing the frontiers of synthetic biology and industrial biotechnology, LS9 has perfected an elegant 1-step fermentation process that uses patent-pending DesignerMicrobes™ to efficiently convert renewable feedstocks to a portfolio of "drop in compatible" UltraClean™ fuels and sustainable chemicals. LS9's unique technology provides a means to genetically control the structure and function of its fuels and chemicals, enabling a product portfolio that meets the diverse demands of the petroleum economy.

LS9 has developed a new means of efficiently converting fatty acid intermediates into petroleum replacement products via fermentation of renewable sugars. LS9 has also discovered and engineered a new class of enzymes and their associated genes to efficiently convert fatty acids into hydrocarbons. LS9 believes this pathway is the most cost, resource, and energy-efficient way to produce petroleum-replacement products and industrial chemicals. This translates into efficient land and feedstock use and directly addresses tensions between food versus fuel and chemical production. _LS9

As long as one does not expect immediate profits from companies such as LS9, investing in such technology is a rational part of an overall energy portfolio. It is a long-term prospect, like its many well-financed cousins in the advanced biofuels research field.

The underlying science is sound, although problems of conversion to profitable commercial scale may take a decade to solve, and another decade to achieve scaleup. In the meantime, supply and demand questions are likely to drive energy & fuel prices like a whipsaw. But once advanced synthetic fuels achieve profitable scale-up (~20 years... AFE), they are likely to put a price ceiling on crude oil of around $60 a barrel in 2010 USD, according to Al Fin energy analysts.

The Wild, Wild World of Bacteria Unleashed

Bacteria were here long before we were. They can occupy a wider range of environmental niches than humans -- from deep sea hydrothermal vents to the thin cold upper atmosphere. Bacterial spores can even survive an extended transit through the cold vacuum of outer space. They live throughout the inside and the outside of our bodies. We are learning to program some bacteria to produce fuels, medicines, chemicals, foods.... They can make life easier for us -- or they can make it harder. It is our choice.

Lovley’s microbial electrosynthesis converts solar power directly into chemicals, which are then readily stored with existing infrastructure and distributed on demand, and are 90 percent efficient at turning electrons into fuel without further processing.

Lovley and colleagues published their experimental results and discuss implications in the current, May issue of mBIO, an online journal of the American Society of Microbiology, and are presenting this week at the American Society for Microbiology’s annual meeting in San Diego, which runs from May 23–27.

The bench-scale technology, funded by a $1 million DOE grant, is based on the discovery that some bacteria can feed on electrons delivered by electrodes. These microbes live on the electrodes and use electrons released from them as their food source. “This is basically a new form of photosynthesis, in which carbon dioxide and water are combined to produce organic compounds, and oxygen is released as a byproduct,” Lovley explains. Solar energy powers the microbes to “breathe in” carbon dioxide and “exhale” fuels and chemicals. The main product is acetate or acetyl-Co A, from which many fuels and other chemicals can be easily produced, notably butanol, _BiofuelsDigest_more_here

Researchers at the US Department of Energy’s Oak Ridge National Laboratory have identified a key gene in the bacterium Zymomomas mobilis—an anaerobic ethanologen—that, when overexpressed in a new Z. mobilis strain, delivers increased tolerance to acetic acid, a common inhibitor produced in biomass pretreatment. Increased tolerance can yield more cost-competitive cellulosic ethanol. An open access paper on their work was published online 19 May in the Proceedings of the National Academy of Sciences.

...Currently, biomass materials like corn stover and switchgrass must undergo a series of pretreatments to loosen the cellular structure enough to extract the sugar from cellulose. Steven Brown, staff microbiologist in the Biosciences Division and one of the inventors of the improved Z. mobilis strain, said these treatments add new challenges because, although they are necessary, they create a range of inhibitors that stall or stop microorganisms like Z. mobilis from performing the fermentation.

There are two ways to combat recalcitrance, or the difficulty created by the inhibitors. One way is to remove the inhibitors, but this method is very expensive and would not help biofuels become cost-competitive with gasoline. The second way is what we do, which is to develop microorganisms that are more tolerant of the inhibitors.

—Steven Brown _GCC

Now we are learning that some bacteria may even help us learn and think better:

Studies have shown time spent in nature does us all good. Specifically a recent study done with 1,200 people, published in the journal Environmental Health and Technology found that even just five minutes in a leafy park can significantly boost our mood. Well it might be because we inhaled some bacteria among the leaves and grass.

It’s called mycobacterium vaccae and research presented today at the 110th General Meeting of the American Society for Microbiology found that it might also increase an ability to learn. _SciAm

More here.

Bacteria can be tweaked to better help clean up the environment.

Some bacteria may help to affect the weather.

Bacteria love to munch on oil -- which is why oil spills do not leave permanent traces.

Normal bacteria in our foods can help us digest food better, and provide us with vitamins and nutrients that our body cannot produce for themselves.

Now that we are tweaking so many different kinds of bacteria to do our work for us, we had better know how to control strains of bacteria that may try to run out of control.

It is not desirable to try to eliminate all bacteria from our environment. We have co-evolved with bacteria for millions of years. We need them. And as we are learning to control them to make more of the products we need and desire, we should always keep in mind that they were here first. They have had a lot of time to develop nasty surprises for high-flying monkeys wearing suits.

The Future of Biofuels

HeatingOil
Actually, synthetic biology represents the future of a lot of things that make human life interesting, enjoyable, and productive. But we will focus on fuels.

In addition to its potential applications to manufacturing vaccines, cell synthesis technology can and will be used by Dr. Venter’s company, Synthetic Genomics, to improve biofuel production from algae. From the Times:

Synthetic Genomics has a contract from Exxon to generate biofuels from algae. Exxon is prepared to spend up to $600 million if all its milestones are met. Dr. Venter said he would try to build “an entire algae genome so we can vary the 50 to 60 different parameters for algae growth to make superproductive organisms.”

...Synthetic Genomics’ partnership with Exxon began just a few months ago, and was characterized as “an aggressive program” by an Exxon executive. With the huge economic resources of Exxon behind it, the biofuel applications of the synthetic cell technology will likely receive all the support needed to produce commercially viable algae-based biocrude in just a few years. _HeatingOil

Algae-based biocrude in just a few years? If it is indeed commercially viable, that will be an impressive achievement. Venter tends to deliver what he promises, so we will want to keep an eye on progress.

The more conservative timeline projects early competitive commercial-scale fuels from algae within 10 years, with a very significant impact on markets in 20 years. But if microbial fuels can provide marketable fuels in half that time, bring it on.

If the Obama Pelosi regime's energy starvation policy allows it, of course.

Synthetic Biology LS9: Chevron Joins Khosla et al

Big oil companies are heavily investing in biofuels. Chevron has joined an investment group that includes Khosla Ventures and Lightspeed Ventures, investing in synthetic microbe biofuels maker LS9.

LS9's goal is to be able to show that it could produce synthetic diesel for $45 to $50 a barrel by mid-2011. That's capable of being produced. The fuel won't come out commercially, barring unforeseen difficulties or a lack of financing, until 2013. The company now has a fermenter with a 1,000 liter capacity and will open a much larger demo plant next year.

LS9 combines traditional microbiology with synthetic biology, says Haywood. The company's scientists have engineered a strain of e coli with a genome that can convert sugars into a fatty acid methyl ester which is chemically equivalent to California Clean diesel. The traditional part of the equation is to convert sugar into other materials via fermentation; the synthetic part is having a designer strain of E. coli that commits unnatural acts. Added bonus: LS9 does not have to kill its microbes to get the oil. They secrete it naturally and then can live to feed, digest and excrete more dollops of oil. It's not out of guilt: re-using a microbe instead of cultivating a new generation cuts time and costs.

The basic science, says Haywood, is done. "We are now working on the yield and scaling factors," he said.

The company also has a similar microbe that can make fatty alcohols. In May, the company announced an alliance with Proctor and Gamble to try to turn these byproducts into green versions of the surfactants P&G consumes now. _BiofuelsDigest

Other oil companies invested in biofuels include Exxon, Shell, BP, Total, and more.

Everything you have been told about the limits of biofuels is false. Most of the surface of Earth is suitable for the growth of biomass of one type or another. Even the oceans are capable of growing large quantities of algae biomass, and other micro and macro plant life. Arid deserts can be irrigated with salty and brackish water to grow algae and other salt-tolerant plants. Marginal lands can grow prolific grasses and fast growing trees. In temperate areas, winter crops can alternate with spring and summer crops to increase yields.

As we develop better ways of replenishing soils, and taking advantage of plant and microbe species that thrive in harsh conditions, "the limits of biomass" begins to sound like an oxymoron.

Now that we know that even the surface of the moon is covered with a thin layer of water, and we know that we can boost large quantities of water into space (and to the moon) reasonably cheaply using electromagnetic launch, the limits to biology and biomass are disappearing before our eyes.

Biological Approaches to Liquid Fuels Make Gains

Synthetic biology is making great progress in programming microbial cells for energy production. Harvard's George Church, cofounder of LS9, has developed the MAGE platform for rapid cell programming.

Joule Biotechnologies has developed its Helioculture technology for using sunlight for conversion of CO2 to fuels.

Bioscience firm Target Growth has devised a way to cause algae to produce 400% more oil.

Origin Oil has improved its method of extracting oil from algae without destroying the organism.

According to US oil giant ExxonMobil, which recently launched a $600 million research and development project on the issue, algae could yield more than 2,000 gallons of fuel per acre per year of production (7,580 litres). Approximate yields for other fuel sources are far lower, it pointed out:

* Palm — 650 gallons per acre per year (2,463 litres).
* Sugar cane — 450 gallons per acre per year (1,705 litres).
* Corn — 250 gallons per acre per year (947 litres).
* Soy — 50 gallons per acre per year (190 litres).

As a consequence, algae need much less land to grow than conventional biofuels, ending the potential for conflict with food production which comes with increased energy crop cultivation. _Bioenergy

Overview of algae's near term future

Gene Stacks, Cassettes, and Artificial Chromosomes: Giving Plants New Abilities

Chromatin is in the business of transforming plants with "gene stacks", to make crops hardier and more productive. Sugar cane is the latest plant to experience transformative change from Chromatin's gene stacking technology.

Chromatin has developed a novel approach to gene stacking, using the plant’s own DNA to deliver several genes. Under this agreement, Syngenta has obtained exclusive rights to use Chromatin’s stacking technology for trait genes in all plants from the genus Saccharum which includes commercial sugar cane varieties as well as energy cane, and crosses between Saccharum and other plant species. Syngenta obtained non-exclusive rights for use of this stacking technology in corn and soybean in 2007.

“Sugar cane growers and processors will benefit economically and environmentally from access to a combination of advanced traits that this technology could make,” said Ian Jepson, Global R&D sugar cane crop lead. “This new stacking technology, combined with the advanced plant varieties, crop protection choices, and our revolutionary new Plene technology will ensure our customers will have the best solutions in sugar cane and will give us a leading position especially in the large Brazilian market.”

Sugar cane is among the top crops grown today for use in sugar production and biofuels. Syngenta offers a broad range of crop protection products for sugar cane growers and is developing a novel planting technology planned for launch in 2010 under the brand name Plene that will help reduce production costs. New trait combinations in sugar cane could offer growers additional improvements in production efficiency and yield increases. _BiofuelsDigest

The technology to transform a plant by introducing new "gene sets" is in its infancy. It will be a few years yet before new strains of sugar cane will have the ability to grow in cold, dry high deserts, or on subarctic tundra.

But researchers are already introducing new genes into maize plants which will facilitate the conversion of cellulose in stover to simple sugars, for fermentation into fuels and high value chemicals.

As Al Fin always says, it's not nice to bet against Mother Nature. She knows where you live.

Microbial Communities Can Form "Super - Organisms" to Produce Fuels and Other Products Beyond the Ability of Single Microbe Species to Create

Synthetic biologists are working to find ways to manipulate entire microbe communities to get them to do things they ordinarily wouldn’t — like tracking down cancer cells to deliver drugs, fighting antibiotic-resistant infections or manufacturing fuel. _ScienceNews

Most of the microbial approaches to bio-fuels and synthetic fuels involves the attempt to find or create the perfect microbe. This perfect microbe would be able to turn feedstock into a valuable fuel, virtually on its own. But it is possible that a community of multiple microbe species working together might be able to out-perform even the "perfect microbe." Using Adam Smith's famous specialisation of labour, microbe production workers may show the same improved productivity that human factory workers demonstrate on the job.

Ideally, a synthetic bioengineer would be able to choose from a number of organisms to design a community capable of getting the job done. At the moment, most labs are focusing on ways to engineer communities of bacteria made up of a single species because these systems are better characterized and easier to manipulate than multispecies groups. And bacteria’s well-studied system for communicating provides a way for scientists to steer the conversations among congregating microbes by changing the way they talk to each other....

Bacteria sense their neighbors and respond to the presence of others in the colony by exchanging small molecules and bits of proteins called peptides — a process known as quorum sensing. Through this exchange, bacteria send and receive chemical cues that turn genes off or on. This process enables many types of bacteria not only to communicate with their neighbors, but also to collaborate in intricate ways to divide labor and perform tasks requiring multiple steps. At first, quorum sensing, discovered in marine bacteria, seemed a special ability, but in the time since its discovery, scientists have racked up quite a list of chatty microbe species. In fact, some scientists believe that nearly all bacteria communicate in one form or another. _ScienceNews

Synthetic Biology and Biofuels: You Ain't Seen Nothin' Yet

The best time to work on alternatives to fossil fuels is while fuel prices are temporarily low. Better prepare now, because when those prices start rising again it may be too late to block another energy-recession.

Synthetic biology is in its early bloom. Soon, it will begin offering a greater abundance of products such as fuels, plastics, chemicals, pharmaceuticals, and other things unimaginable now. Unless the ever-lurking Luddites burn the bridges before they are built. That is a danger under the current political current. But the need for alternative fuels is so apparent, that it is possible the Luddites in political control will overlook this one shining promise.

Synthetic biology refers to both the design and fabrication of biological components and systems that do not already exist in the natural world, and the redesign and fabrication of existing biological systems. As tools are developed to hone and refine this technology, researchers across multiple disciplines are finding novel applications for it.

...One company that provides the raw material for the creation of biofuels is Agrivida, an agricultural biotech firm that creates renewable, biomass-based alternative fuels and raw materials. “We are working upstream, making plants that are more easily degradable, primarily switchgrass, sugar cane, and corn,” states R. Michael Raab, founder and president. “We are focused on nonfood crops and crop residues that are degradable into fuel.”

...Gevo develops advanced biofuels technology based on butanol and its derivatives. “The magic isn’t in the biology alone,” according to Pat Gruber, Ph.D., CEO. “It’s in the chemistry, fermentation, processing, and genetic engineering all together; knowing what tools you need, and having the tools to make it happen.”

Dr. Gruber points out that three critical pieces of technology have helped Gevo produce these on a commercial scale. “We have a group that’s been working on this for 20 years or longer. Metabolic engineering of suitable host organisms make it possible to use carbon and energy efficiently for fuel production. Process engineering makes it possible to lower product separation costs and chemistry to produce valuable hydrocarbons.”

...Two other companies working in the metabolic engineering space are Mascoma and LS9. Mascoma recently received $26 million in DOE funding, which will be applied toward the development of a cellulosic fuel production facility that uses nonfood biomass to convert woodchips into fuel. Mascoma’s production facility is expected to produce 40 million gallons of ethanol and other valuable fuel products per year.

LS9 developed new metabolic pathways that efficiently convert fatty acids to a broad portfolio of petroleum replacements. It also discovered and engineered a new class of enzymes and their associated genes that catalyze the efficient conversion of fatty acids to hydrocarbons. They recombinantly produce hydrocarbons (oxygen-deficient biocrudes), fatty acid alkyl esters (biodiesel), and a variety of industrial chemicals from sugars via fatty acid biosynthesis.

...Codexis’ technology enables solutions for cost-effective, efficient, and environmentally sound production of pharmaceuticals, transportation fuels, and industrial chemicals, reports David Anton, Ph.D., vp, bioindustrials R&D. The company focuses on biocatalysts—enzymes or microbes that initiate or accelerate chemical reactions. At Codexis, biocatalysis is used to design faster, less costly, and greener chemistry-based manufacturing processes in the life science and energy industries.

According to Dr. Anton, Codexis’ technology makes it possible to customize enzymes capable of selectively and efficiently performing a desired chemical process that doesn’t exist in nature.

...SunEthanol was recently awarded a $750,000 Phase II Small Business Technology Transfer Program contract. This award, made as a follow-up for successfully completing a year-long Phase I grant, will allow SunEthanol to continue pioneering a process that converts plant waste into clean ethanol fuel in one simple step, saving time and money over the traditional two-step cellulosic conversion process, the company claims.

... _GenEngNews

Several more companies are mentioned and linked in the above Genengnews article. It is impossible to keep track of all the research efforts in synthetic biology that will influence biosynthetic fuels development. Every university biology or agriculture department with a significant research program will be working on this problem, in all likelihood. Whether or not the world economy improves, fuel prices will rise. If the Luddites in control suppress energy technologies, energy prices will rise out of scarcity. If the Luddites are given a well-deserved boot in the arse, energy prices will rise as economies improve. Those who are prepared will prosper. Those who are not prepared, will dieoff.org. It is the harsh way of the universe.

Previously published at Al Fin

Next Level Biofuels: Beyond Ethanol and Methanol

Four next level biofuels companies are featured in the current issue of Biomass Mag:

1. LS9
2. Gevo
3. Amyris Biotech
4. Synthetic Genomics

Fatty acids are molecularly similar to hydrocarbons, which are the building blocks of gasoline, diesel and jet fuel, Pal says. By re-engineering the genetic coding of e.coli and yeast, LS9 creates a miniature assembly line (metabolic pathway) to synthesize the biofuel.

Genes missing from the microbes and required to produce intermediate substances and enzymes (which produce biochemical reactions) are inserted into the organisms. Genes producing unwanted substances or diverting energy from the biofuel production process are silenced....LS9’s goal is to create fuel that is cost competitive with oil at $40 to $50 per barrel, Pal says. A small-scale pilot facility, planned for this year, will generate the performance and economic data to support investment in a large-scale commercial facility. Pal expects to have a product to market in three to four years.

Gevo, founded in 2005, initially focused on redesigning the metabolic processes of microbes to convert waste methane gas into methanol....[But] Butanol contains more energy than methanol or ethanol, it can be blended with gasoline without retrofitting engines and it can be distributed in existing pipelines. It is also used as a chemical intermediate, creating numerous market opportunities, Gruber says.

Most efforts to ferment sugars into butanol rely upon bacteria, Clostridium acetobutylicum. But even with genetic modification, the bacterium doesn’t produce enough butanol to be economically viable...Gevo’s approach is to concentrate on organisms, such as e.coli and yeasts, that serve as outstanding platforms for biofuel production, explains Matthew Peters, Gevo vice president and chief scientific officer.

The company recently licensed technology from James Liao, a chemical engineer at the University of California, Los Angeles, which re-engineers e.coli to make butanol. Liao rewired e.coli’s genetic circuitry by adding genes to convert keto acids, produced during metabolism, into butanol...Liao removed genes producing nonessential substances and enhanced the productivity of others. These modifications increased keto acid production, boosting butanol production.

Gevo’s goal is to produce fuel at an unsubsidized price that is less than gasoline, says Tom Dries, vice president of business development. To keep costs down, the company will retrofit existing ethanol plants to run its processes, at a cost of about $20 million per facility. Dries expects to produce its first product sometime in 2009.

The Amyris team is using computation tools to identify the suites of genes to assemble within an organism to produce its biofuels, along with tools to optimize the genes for use in the system. “Dozens of genes are affected, inserted and changed in the process,” Reiling says.

The company is initially focusing its efforts on commercializing its diesel product. “Diesel is growing at two to three times the rate of gasoline,” Melo says. “There is not a scaleable renewable fuel today servicing the diesel market.”...the company is working on increasing the productivity of its process to reach parity with oil at $55 to $60 per barrel.

...Amyris is forming partnerships...In April, Amyris announced a joint venture with Crystalsev, one of Brazil’s largest ethanol producers, to commercialize its diesel technology in Brazil. Crystalsev will provide 2 million tons of sugarcane crushing capacity and will convert two of its ethanol plants to produce Amyris’ renewable diesel from cane juice, Melo explains. Production is slated to begin by 2010.

At Synthetic Genomics, research efforts are also focused on creating all the genetic material for an organism (its genome) from scratch (de novo), tailored to biofuel production. “Most of these organisms have other priorities in life producing substances for their own particular needs,” explains Ari Patrinos, the company’s president. “There is a limit to how much you can tweak them to do what you want.”

“If you can design the genome de novo, you only include those processes and activities of interest to you,” Patrinos says. As a result, the biological processes will be more efficient and productive and include built in tolerances.

....“Once you have demonstrated that you can do the genome, you can add the appropriate promoters that turn on and off genes,” Patrinos says. He envisions inserting sets of genes into the genome, observing the outcomes and then optimizing the final combination of genes that produces the best product at the highest efficiencies.

Patrinos believes Synthetic Genomes will begin producing biofuels in the next few years. “I think we have a leg up on scaling up because the organisms can be tailored for the scaling process.”
_Biomass

Pay attention to the time targets these companies are shooting for. Within 5 years or less. If any of them succeed with large scale production of oil-equivalent under $60 a barrel, the economics of liquid fuels will be overturned overnight. Even well funded biomass to ethanol companies will be pressed to achieve significant scale production with competitive priced product in that time frame. Biomass to liquid fuels will be a huge industry, once it scales up and shakes out. And it will have a lot of two bit oil dictators to thank--for keeping oil prices artificially high long enough for the new bio-fuels to become cost-competitive.

Of course, if massive social and economic unrest occurs in the US due to artificially high oil prices, US taxpayers and Oynklent Green [OTC:OYNK] will know exactly who to thank closer to home. Nancy and Barbara would likely be the first to receive callers, unless Barry becomes an even greater symbol for energy luddism by that time.

30 per cent of All Liquid Fuels from Biomass

Biomass to liquid fuels (BTL) is a potentially lucrative industry, being pursued by numerous companies from different directions. One popular approach with biotechnologists, is the development of micro-organisms and enzyme systems capable of turning biomass into diesel, jet fuel, and gasoline.

Amyris first studied the highest performing compounds of diesel, gasoline and jet fuel, then tinkered with the genetic structures of E. coli and yeast to produce bioequivalents, Renninger says, leveraging the same cutting-edge technology previously employed to produce pharmaceutical-quality medicines at commodity-level prices. ...It projects commercial production of some 30 million gallons of diesel as early as 2010, with production of gasoline and jet fuel roughly one and two years behind, respectively.

LS9 plans to open a pilot facility this summer and a 50- to 100-million-gallon plant three years later, producing a drop-in replacement for diesel, as well as a biocrude to be processed in traditional refineries. Rogue scientist J. Craig Venter, who helped lead an international consortium of scientists to map the human genome, has announced plans to engineer bacteria able to create hydrocarbons not just from sugars, but from CO2 pulled straight from the atmosphere.

"If you look at where sugar cane is in Brazil, or at where biomass will be here in the near future, we're pretty confident that we can compete with oil around the $50-a-barrel range," Pal says. "The key driver of the cost really is the cost of raw materials."

... Until technologies exist to easily derive sugars from tough cellulosic material, such as corn's remaining stalks, leaves and cobs, companies like LS9 and Amyris are likely to feed their fuels with sugar cane—a relatively green source of easy-to-use sucrose, albeit one with limited domestic potential.

As the world continues to consume some 150 million gallons of oil every hour, any potentially game-changing solutions will need not only to work, but to work cheaply and at truly massive scales.

"We could be harvesting on a sustainable basis over a billion tons of dry biomass in the United States if we got serious about it, and that would get us somewhere close to 30 percent of our liquid transportation fuels," NREL's McMillan says. "So while sucrose is undoubtedly part of the solution, to really get that huge volume impact, you have to go to those cellulosic feedstocks."
__PopMech

Once mature, these approaches could compete with petroleum fuels as long as oil is at least $50 a barrel. Once optimised, they will be viable with oil as low as $30 a barrel. But by then, who would want to buy oil at all? Environmental mandates and regulations will probably put oil and coal off-limits, once bioenergy, clean nuclear, enhanced geothermal and other advanced renewables combined with utility scale storage and improved transmission capacity come on-line.

With various unconventional approaches to nuclear fusion on the horizon, along with other even more unconventional approaches to unlimited energy--it is important for all viable approaches to clean energy production to be pursued, to bridge the gap.

Long-term, bioenergy makes sense primarily for small, local economies--particularly in the third world. But until the potential of clean, big energy is achieved through nuclear and other physical means, humans will need to fall back on their oldest energy source. Bioenergy: solar energy with its own built-in storage.

Synthetic Biology Approaches to BioEnergy

Agrivida is one of a number of companies using designer proteins to help produce biofuel. Companies such as Amyris Biotechnologies, Codexis, Gevo, LS9, Mascoma and SunEthanol are trying to develop custom enzymes using synthetic biology to convert non-food biomass into fuel. But unlike Agrivida, most are focusing on growing microbes that will digest the crop in a refinery. __Bioenergycheckbiotech

Working mostly behind-the-scene, biotech companies are trying to cash in on the ravenous appetite of the global economy for fuel. Petroleum prices are currently in control of global economies, and at current levels high oil prices are beginning to put on the economic brakes. To prevent inflation, many central banks have raised interest rates or are threatening to do so.

Bio-energy holds the promise of a virtually limitless, sustainable fuel supply. Call it "solar energy with its own built-in storage." Synthetic biology takes conventional bioenergy approaches, adds steroids and methamphetamine, and threatens to add nitrous oxide and rocket fuel.

...tweaking enzymes and bacteria to our own ends - a process called "synthetic biology" - is potentially big business. For instance, scientists are working on a new generation of corn that will rot from the inside out once harvested and heated, to produce higher-yielding biofuels.

...Now the US-based company Agrivida aims to insert a gene that will make an enzyme that does nothing until the corn is heated in a reactor to around 60C. Triggered by the heat, the enzyme will change shape and function, attacking the tough materials that form the cell wall.

Artificial enzymes are already used in medicine and biological washing powder. But most are the result of accelerated "directed" evolution from enzymes found in the wild. For its protein switch, Agrivida needed an enzyme designed almost from scratch, as nothing in nature came close to doing the job.
__Source

Some companies want to use engineered micro-organisms as living enzyme system reactors. Other companies want to use the enzymes outside of the organism in a reactor. The common element is the flexibility of protein catalysts--enzymes--in design and biosynthesis. Protein engineering is a form of bio-nanotechnology--a growing field. Understanding that molecular nanotechnology is the long range goal, but knowing that biology has already mastered one form of molecular nanotechnology, gives nanotechnologists an excellent starting point.