* BASF Plant Science takes Amflora case to EU Court
* Potent potato to boost food security
* Annual European Union Report
* Nigeria - Annual
* Vietnam biotechnology report
* China Certifies LibertyLink Soybeans
* New Bt cotton variety developed in Andhra
* GM bananas set for initial trial
* GM ban a poll scare tactic: researcher
* Gene-chips prove transgenes are clean genes
* Study predicts crop-production costs will soar
* Better living through chemurgy
* New computer language enables proteomics
BASF Plant Science takes Amflora case to EU Court
- BASF Plant Science (press release/web posting), July 24, 2008
* BASF filed action against the EU Commission for failure to act
* Approval for Amflora still not granted despite positive safety assessments and a 12-year approval process
* Amflora is a safe and environmentally friendly product that brings a yearly added value of more than Eur100 million to Europe's farmers and potato starch industry
Limburgerhof, Germany - July 24, 2008 - BASF Plant Science today filed an action with the European Court of First Instance in Luxembourg against the EU Commission for failure to act. According to the company, the approval process of the cultivation of Amflora, its genetically improved potato, has been unjustifiably delayed by the EU Commission on several occasions. In particular, this includes the period between July 2007 and May 2008 during which Commissioner Stavros Dimas did not adopt the approval for the cultivation of Amflora following the completion of all other procedural steps.
"EU Commissioners have postponed Amflora's approval despite repeated positive safety assessments by EFSA, the European Food Safety Authority. Although we welcome some positive signs by the Commission and President Barroso, such as their commitment to base decisions regarding genetically modified products purely on science, we are not prepared to accept any further delays," said Dr. Stefan Marcinowski, Member of the Board of Executive Directors of BASF SE.
"We are filing this case in order to ensure that European farmers and starch producers get access to an innovative product that offers them a potential added value of more than Eur100 million annually. In addition, we estimate that failure to approve Amflora is depriving BASF Plant Science of peak license income of Eur20 to 30 million per lost cultivation season," said Dr. Hans Kast, CEO and President of BASF Plant Science GmbH.
The process to date:
* The Amflora approval process was initiated 12 years ago with the request for authorization submitted in August 1996.
* During the moratorium on genetically modified products between 1998 and 2004, no approvals for genetically modified plants where granted in the EU.
* BASF Plant Science resubmitted a dossier for cultivation and a dossier for food and feed use in 2003 and 2005, respectively, due to modified EU regulations.
* In 2006, EFSA concluded for both dossiers that Amflora is as safe for humans, animals and the environment as any conventional potato.
* In November 2006, Commissioner Dimas forwarded his proposal for authorization of cultivation of Amflora to the EU Member States.
* After two inconclusive votes in the Regulatory Committee in December 2006 and the Council of Agricultural Ministers in July 2007, Commissioner Dimas failed to adhere to the defined approval procedure defined by the EU and to adopt the proposal for cultivation.
* BASF addressed the issue through an open letter to Commissioner Dimas on April 17, 2008.
* The dossier for food and feed use was voted upon in the Standing Committee in October 2007 and Council of Agricultural Ministers in February 2008. According to the defined EU approval procedure, the responsible Directorate-General Health and Consumers has been responsible for adopting the proposal since February 2008.
* In its "orientation debate" on genetically modified plants on May 7, 2008, the Commission decided to request EFSA to prepare a new consolidated scientific opinion on the use of antibiotic resistance marker genes in genetically modified plants by September 30, 2008. Such a marker gene is also used in Amflora.
* In a press release following the debate, Commission President Barroso stated that Amflora will be approved "if and when" EFSA confirms the safety of antibiotic resistance marker genes.
* EFSA responded recently that an opinion can be finalized not earlier than by December 15, 2008.
* On May 19, 2008, BASF Plant Science formally requested access to any documents in the possession of the EU Commission in connection with the authorization procedure for Amflora. These documents did not reveal any new scientific evidence regarding the safety of Amflora.
* Today, one year after the vote in the Agricultural Council, the last formal step prior to adoption of a decision, BASF Plant Science filed an action with the European Court of First Instance against the EU Commission for failure to act.
Amflora is a genetically optimized potato that produces pure amylopectin starch and is ideal for technical applications. Conventional potatoes produce a mixture of amylopectin and amylose starch. For many technical applications, such as in the paper, textile and adhesives industries, only amylopectin is needed; separating the two starch components is uneconomical. Amflora produces pure amylopectin starch and thus helps to safe resources, energy and costs. Moreover, paper produced with amylopectin starch has a higher gloss. Concrete and adhesives can be processed for a longer period of time.
Guest ed. note: "Better living through chemurgy", below, helps put this situation in perspective.
Potent potato to boost food security
- Business Report (South Africa), Jul. 24, 2008
Johannesburg - The development of a genetically modified potato by the Agricultural Research Council (ARC) is a major boost for the biotech sector in South Africa, said AfricaBio executive director Jocelyn Webster.
Webster said potato is a major staple crop and a boon to smallhold farmers to help ensure food security and alleviate hunger.
The potato developed by the council is resistant to the potato tuber moth, which causes losses of up to R40 million each year to the South African potato industry.
"No insecticide is registered against the potato tuber moth in South Africa under storage conditions. Now the smallholder has an insurance to help provide food security," said Webster.
"To control the tuber moth, producers have to rely on insecticide spraying at weekly intervals, depending on infestation, from to eight to 12 times a year.
"Estimated cost can be as much as R1 000 per hectare and control is not always satisfactory. Smallholder farmers cannot afford these expenses, often resulting in total crop failure," she said.
"The only strategy that gives consistently good control against the tuber moth is the GM potato. Studies, after six years of testing by the ARC, have shown that GM potatoes are as safe to grow and eat as conventional potatoes," said Webster.
AfricaBio, a non-profit biotechnology association, lists its mission statement as "the safe, ethical and responsible research, development and application of biotechnology and its products".
Annual European Union Report
- US Department of Agriculture, Foreign Agricultural Service, Jul. 17, 2008
This report gives a complete overview of food laws currently in force in the EU-27. The following sections were updated: labeling requirements (allergen labeling, nutrition and health claims), packaging (pack sizes), pesticides, contaminants, specific standards (GMOs, novel foods, wine and spirit drinks, organic foods, beef labeling, egg marking, other), import procedures European Commission proposals which may have an impact on U.S. exports are also included.
View the Acrobat version: http://www.fas.usda.gov/gainfiles/200807/146295146.pdf
View/Download the MS Word version: http://www.fas.usda.gov/gainfiles/200807/146295146.doc
Nigeria - Annual
- US Department of Agriculture, Foreign Agricultural Service, Jul. 17, 2008
The executive summary and section III of this report have been updated. In November of 2006, the Nigerian Biosafety Committee submitted the draft biosafety bill to the then Minister of Environment. Two years after the bill was presented, no progress has been made towards the passage of the bill into law because of a change in government and key personnel. However, there are indications that the new government of President Yar'adua is committed to moving the process forward.
View the Acrobat version: http://www.fas.usda.gov/gainfiles/200807/146295148.pdf
View/Download the MS Word version: http://www.fas.usda.gov/gainfiles/200807/146295148.doc
Vietnam biotechnology report
- US Department of Agriculture, Foreign Agricultural Service, Jul. 11, 2008
Report highlights: Vietnam has completed a new draft Biodiversity Law which is expected to be ratified by the National Assembly in October 2008. Chapter 6 of this law pertains to the management of Genetically Modified (GM) Organisms. The Implementing regulations to allow field trials of biotech crops have still not been approved, but the Ministry of Agriculture and Rural Development remains hopeful that it will be signed before the end 2008 so that field trials may begin this year. Vietnam will likely not achieve its targets to release GM crops for commercial production by 2010. Vietnam also has concerns about the lack of skilled biotech personnel and plans to send more students overseas for advanced degrees in biotech related fields.
Full report: http://www.fas.usda.gov/gainfiles/200807/146295193.pdf
China Certifies LibertyLink Soybeans
- Farm Chemicals International, Jul. 22, 2008
A safety certificate for Bayer CropScience's LibertyLink soybeans, which allows soybean imports into China - the largest importer of US soybeans - has been granted by the Chinese Ministry of Agriculture, bringing it closer to commercialization in that country. LibertyLink soybeans will bring important benefits and choice to growers, says Bayer CropScience, explaining that the LibertyLink trait enables growers to maintain current production practices and rotate herbicide tolerant systems to manage weed resistance and preserve the technologies, as well as delivering benefits such as tillage, labor, fuel and equipment reductions, and the ease and convenience of non-selective, post-emergent weed control with crop safety in competitive, high-yielding varieties.
"We're very pleased the Chinese government has cleared LibertyLink soybeans for import," said Andy Hurst, LibertyLink product manager for Bayer CropScience. "We're well on track to meet our projected commercial launch target of 2009 in the United States."
To date, LibertyLink soybeans are fully approved for food, feed, and cultivation in the US and Canada, as well as for importation and/or cultivation in Argentina, Australia, Japan, Mexico, New Zealand, Russia, South Africa, and Taiwan.
New Bt cotton variety developed in Andhra
- oneindia, July 24, 2008
Hyderabad: In a major effort to compete with private seed companies, three prestigious agriculture institutes across the country have developed 'Bikaneri narma', a new biotech cotton variety which is not only pest-resistant, but also cheaper than the other varieties available in the market.
The New Delhi-based Indian Agriculture Research Institute (IARI), Central Institute of Cotton Research (CICR) in Nagpur and University of Agricultural Sciences (UAS) in Dharwad have jointly developed the cotton variety.
The National Research Centre on Plant Biotechnology (NRCPB) at IARI had worked for over 10 years towards the development of the biotech gene on the popular Bikaneri variety cotton, used by farmers across the country, and transferred it to the CICR and UAS for field trials.
The Genetic Engineering Approval Committee (GEAC) had cleared the 'Bikanari narma' a few weeks back and it would be made available to the farmers through the National Seed Corporation and other public sector seed companies in the current season, Professor KC Bansal of NRCPB told the media.
The new Bt cotton variety was pest-resistant and about 20 to 25 per cent cheaper, but provided yield equivalent to the Bt cotton varieties being sold by the private companies, he added.
The new variety was also suitable for different soil conditions.
Over the next two to three years, CICR and other institutions in the national agriculture research system would be releasing four to five new seed varieties.
At the NRCPB centre, efforts were underway to develop biotech Brinjal, Okra (ladies finger) and transgenic mustard, besides drought-tolerant rice, wheat and tomato. These varieties, including the golden rice, were tested in the 'Green house' at the centre and was likely to be released to farmers over the next four or five years after field trials.
GM bananas set for initial trial
- ABC News (Australia), Jul. 24, 2008
Approval has been granted for Australia's first trial of genetically-modified bananas will go ahead in Innisfail in Far North Queensland.
Scientists from the Queensland University of Technology will conduct two trials to test their nutrient content and to improve disease resistance.
Professor James Dale says the plants are sterile so there is no danger of cross-pollination with other crops.
"They don't form any seed and the pollen is essentially sterile so the chances of there being any cross-pollination from the genetically modified bananas to conventional bananas is, I would say nil," he said.
GM ban a poll scare tactic: researcher
- Kate Tarala, The West Australian, Jul. 23, 2008
The State Government's ban on genetically modified crops is a politically motivated scare campaign designed to win votes and the support of the Greens, WA's peak agricultural and biotechnological research body said yesterday.
"There has been absolutely no authenticated evidence of any effect or risk to the environment from GM crops," Mike Jones, director of the State Agricultural Biotechnology Centre at Murdoch University, said.
"In WA it is mainly a political decision purely based on votes. I think if they can frighten people then they can get more votes and get the Greens onside. It's got nothing to do with the science."
Professor Jones said GM crops had been an astounding success, accounting for about 65 per cent of soya bean crops and a major share of maize, corn, cotton and canola worldwide.
Victoria and NSW have lifted bans on commercial GM crops and Queensland has never had a ban.
Agriculture Minister Kim Chance said there was no plan to lift the moratorium on commercial GM crops but he supported more trials in WA.
Gene-chips prove transgenes are clean genes.
- GMO Pundit a.k.a. David Tribe (blog), Jul. 25, 2008
Recent empirical evidence from gene-chips is confirming the considered judgment of geneticists - that genetic engineering is more precise than conventional breeding- is indeed correct.
These gene activity testing devices are providing solid confirmation that transgenic rice, wheat , soybean and thale cress are substantially equivalent to their non-transgenic counterparts.
Gene chips (known also as microarrays) enable the activity of thousands of genes to be measured. Many new studies with these chips listed below convincingly demonstrate that insertion of transgene DNA causes minor perturbation to transcription activity of other genes.
Use of gene-chips to comprehensively survey tens of thousands of genes is revealing that the unintended, unexpected effects of transgenes are small compared to perturbations caused by conventional cross-breeding, which typically perturb an order of magnitude more unrelated genes away from those at the insert target (Baudo 2006, Batista 2008, Cheng 2008, El Ouakfaoui, Miki 2005)
Radiation treatment used to deliberately create mutations in many existing crops also causes many more gene activity perturbation than does transgene insertion (Batista 2008, Dubouzet 2007, Zhang 2006). Note that apart from the intended trait, transgene insertion is generally silent in terms of change to plant phenotype(appearance) (Bouché N, Bouchez D. 2001) .
Yes indeed, transgene inserts are generally clean events as far as unexpected changes to untargeted gene activities. Transgenes are clean genes.
[citations and excerpts continue at the link above]
Study predicts crop-production costs will jump dramatically in 2009
- University of Illinois at Urbana-Champaign (press release) via EurekAlert, Jul. 23, 2008
CHAMPAIGN, Ill. - Soaring energy prices will yield sharp increases for corn and soybean production next year, cutting into farmers' profits and stretching already high food costs, according to a new University of Illinois study.
Costs to get crops in the ground will jump by about a third in 2009, fueled by fertilizer prices expected to surge 82 percent for corn and 117 percent for soybeans, said Gary Schnitkey, an agricultural economist who conducts the annual survey of input costs.
Fertilizer - the biggest non-land expense for corn and soybean farmers - is tethered to the same cost spiral that has driven steep gasoline and heating price increases over the last few years, said Schnitkey, a professor of agriculture and consumer economics.
"Roughly 80 percent of the cost of producing nitrogen fertilizer is natural gas, so as natural gas costs have gone up so have the costs of those inputs," he said. "Phosphorus and potassium are mined, and as energy costs increase, mining costs increase."
With commodity prices high, the increased production costs should merely trim farm profits rather than sinking balances into the red, said Schnitkey, who predicts farmers will likely post solid earnings again in 2009.
"But it's one of those things," he said. "When are the good times going to end? Could it be next year? And what happens if a drought or some other disaster cuts yields dramatically?"
While farmers will likely absorb some of the added costs, Schnitkey says consumers also should expect to pay more for products ranging from cereals and syrups to grain-fed beef.
"There's not going to be a reduction back to lower food costs as long as we have these higher production costs," he said. "Energy prices are driving a lot of what's going on and ultimately that hits the consumer."
Along with fertilizer, grain farmers also will see hefty cost increases next year for inputs ranging from seed to fuel for tractors and other machinery, according to the study.
The study projects non-land production costs for corn will total $529 an acre next year, up 36 percent from 2008 and nearly 85 percent higher than the average of $286 per acre from 2003 to 2007. At $321 an acre, soybean input costs are projected to rise 34 percent from 2008 and more than 78 percent from the 2003-2007 average of $180 an acre.
Schnitkey says the per-acre costs are based on high-producing farmland in Central Illinois, but corn and soybean farmers across the country will see similar increases.
Assuming cash-rent fees of $200 an acre, the study projects a break-even price of $3.82 a bushel for corn in Central Illinois, based on an average yield of 191 bushels an acre. Soybeans would break even at $9.65 a bushel, based on yields of 54 bushels per acre.
Schnitkey says 2009 prices should be significantly above break-even prices. Based on futures markets, corn should sell for about $6 a bushel next year, with soybeans in the $13 to $14 range.
"Looking further ahead, though, a lot of things could happen to bring that down," he said. "Demand could bring on more land in Argentina and Brazil, or the Ukraine might get its act together and increase production."
Higher production costs will likely force farmers to try to hold down cash-rent payments, monitor commodity markets closely to sell at the best price and consider increasing crop-insurance levels, Schnitkey said.
"Input prices will have doubled in just a few years and that's a major investment for farmers," he said. "If something bad happens that hurts yields, their downside risk is much higher now."
Guest ed. note: See also, "Agriculture Production Costs on the Rise, According to New Rabobank Report", Rabobank (press release), Jul. 24, 2008, http://news.moneycentral.msn.com/category/topicarticle.aspx?feed=PR&Date=20080724&ID=8934535&topic=TOPIC_ECONOMIC_INDICATORS&isub=3 Rising fuel prices will make GM crops even more attractive than before, because they reduce the need for tillage and pesticide spraying.
Better living through chemurgy
Efforts to replace oil-based chemicals with renewable alternatives are taking off
- The Economist (print edition), Jun 26, 2008
NEW YORK - FORTY years ago Dustin Hoffman's character in "The Graduate" was given a famous piece of career advice: "Just one word...plastics." It was appropriate at the time, given that the 1960s were a golden age of petrochemical innovation. Oil was cheap and seemed limitless. Since then, scientists have kept on coming up with wondrous new products made from petroleum that helped to ensure, in the words of one corporate slogan, better living through chemistry. Even so, someone offering advice to today's promising graduates might invoke a different, uglier word: chemurgy.
This term, coined in the 1930s, refers to a branch of applied chemistry that turns agricultural feedstocks into industrial and consumer products. It had several successes early in the 20th century. Cellulose was used to make everything from paint brushes to the film on which motion pictures were captured. George Washington Carver, an American scientist, developed hundreds of ways to convert peanuts, sweet potatoes and other crops into glue, soaps, paints, dyes and other industrial products. In the 1930s Henry Ford started using parts made from agricultural materials, and even built an all-soy car. But the outbreak of the second world war and the shift to wartime production halted his experiment. After the war, low oil prices and breakthroughs in petrochemical technologies ensured the dominance of petroleum-based plastics and chemicals. Click Here
But now chemurgy is back with a vengeance, in the shape of modern industrial biotechnology. Advances in bioengineering, environmental worries, high oil prices and new ways to improve the performance of oil-based products using biotechnology have led to a revival of interest in using agricultural feedstocks to make plastics, paints, textile fibres and other industrial products that now come from oil.
This form of biotechnology has not attracted as much attention as biotech drugs, genetically modified organisms or biofuels, but it has been quietly growing for years. BASF, a German chemical giant, estimates that bio-based products account for some Eur300m ($470m) of sales in such things as "chiral intermediates" (which give the kick to its pesticides). The sale of industrial enzymes by Novozymes, a Danish firm, brings in over Eur950m a year, about a third of it from enzymes for improving laundry detergents. Jens Riese of McKinsey, a consultancy, reckons industrial biotech's global sales will soar to $100 billion by 2011 - by which time sales of biofuels will have reached only $72 billion.
Will this boom really prove to be more sustainable than the first, ill-fated blossoming of chemurgy? One potential problem is that oil-based polymers are very good at what they do. Early bioplastics melted too easily, or proved unable to keep soft drinks fizzy when they were made into bottles. Pat Gruber, a green-chemistry guru who helped start NatureWorks (a pioneering biopolymers firm) says customers are sometimes too risk-averse to retrain staff or modify equipment to accept a new biopolymer - even if it is cheaper or better.
It seems likely that oil-based products will be around for a long time in some applications. But the big advances in oil-based polymers happened decades ago, whereas the number of patents granted for industrial biotechnology now exceeds 20,000 per year. Such is the pace of innovation, says Tjerk de Ruiter, chief executive of Genencor, a industrial-biotech firm that is now a division of Denmark's Danisco, that processes that once took five years now take just one. And Steen Riisgaard, the boss of Novozymes, insists that new technologies can indeed push old ones out of the way, provided they are clearly superior (and not just greener). Brewers raced to adopt Novozymes' novel enzymes, for example, in order to cash in on the Atkins Diet craze with "low carb" beers.
A second potential obstacle is that incumbent companies will quash the fledgling new technologies. But concern about oil's reliability as a feedstock means that even oil-dependent incumbents are interested in alternatives. Oil companies such as Royal Dutch Shell and BP see novel bioproducts not as threats but as useful tools for blending into, and possibly extending, remaining oil reserves. And chemicals giants such as Dow and DuPont are also big fans of novel industrial biotechnologies. Chad Holliday, DuPont's boss, is sure that Sorona, his firm's new biofibre, will be a multi-billion dollar product and "the next nylon". DuPont expects its sales of industrial biotechnology products to grow by 16-18% a year, to reach $1 billion by 2012.
Perhaps the biggest worry is that today's industrial-biotech boom is an artefact of the soaring price of oil. If the oil price plunged and stayed low, the boom would surely turn to bust. Short of outright collapse, however, even a sharp price drop need not burst the biotech bubble. Mr Riese has scrutinised the economics of sugar and oil - the chief rival feedstocks - and concludes that the "bio-route" will be cheaper even at an oil price of $50-60 a barrel. Brent Erickson of BIO, an industry lobby, argues that "this was happening long before the oil-price spike - $100 oil is just gravy." Industry bosses agree, noting that the flurry of projects now approaching commercial use were deemed viable and initiated a few years ago, when the oil price was closer to $40 a barrel.
For proof that industrial biotech is ready for the big time, look to Brazil. The country already has a large and efficient industry producing ethanol fuel from sugar cane. Now rival consortia are rushing to build plants to turn sugar cane into bioethylene. This is striking. Unlike many other industrial biotech efforts which target niche markets, this is an assault on the $114 billion market for ethylene, the most widely produced organic compound of all.
Erin O'Driscoll of Dow, a chemical giant now investing in Brazilian bioethylene, says the firm is confident the technology is ready for commercialisation. The chief reason for such optimism is that industrial biotechnology is better and cheaper than it was back in the heyday of chemurgy. Dow has even come up with a material made from soyabean oil that it plans to sell to carmakers to replace oil-based foam. Ford and his friend Carver would be proud.
Harvard Medical School Biology enters 'The Matrix' through new computer language
- Harvard Medical School (press release) via EurekAlert, Jul. 22, 2008
BOSTON, Mass. - Ever since the human genome was sequenced less than 10 years ago, researchers have been able to access a dizzying plethora of genomic information with a simple click of a mouse. This digitizing of genomic data - and its public access - is something that would have been unthinkable a generation earlier.
But as molecules go, DNA is pretty straight forward. With its simple composition and linear structure, it easily lends itself to mathematical models. Not so with proteins. In fact, proteins are an order of magnitude more complex than DNA. It is proteins, not DNA, that carry out the cell's heavy lifting. However, with their intricately folded three-dimensional shapes determining a seemingly endless range of possible functions and their manifold interactions with other proteins and with DNA, the leg-work required to mathematically capture the protein universe seems absurd.
And it is.
That is why a team of Harvard Medical School researchers have decided to attack this issue from an entirely new angle. Rather than build a mountain range of proteomic data one grain of dirt at a time, they have developed a computer program that can take on the responsibility of assembling such a gargantuan model.
Enter Little b, a computational language that can penetrate the "mind" of a cell.
"Through incorporating principles of engineering, we've developed a language that can describe biology in the same way a biologist would," says Jeremy Gunawardena, director of the Virtual Cell Program in Harvard Medical School's department of systems biology. "The potential here is enormous. This opens the door to actually performing discovery science, to look at things like drug interactions, right on the computer."
These findings will be published in the July 23 issue of Journal of the Royal Society Interface.
Most current computational methods of modeling biological systems are not unlike writing a document with pen and paper. Each new project starts from scratch; there are no facilities for cutting and pasting, for linking to other texts, for including images, etc. - things that come so "naturally" to electronic documents.
Harvard Medical School researcher Jeremy Gunawardena, a mathematician by training, teamed up with Aneil Mallavarapu, a cell biologist and computer scientist, to lead a project that would bypass these limitations.
"We knew that the secret to doing this would be to assimilate fundamental concepts of engineering, concepts like modularity and abstraction, into the biological realm," says Mallavarapu, who was recently awarded the Merrimack prize by the Council for Systems Biology in Boston for developing this program.
Modularity involves breaking a problem down into separate modules and constructing each module so that it can interact with the others. Abstraction refers to extracting generic biological properties and incorporating them into the modules, so that they can use this abstract information in concrete contexts. Put another way, abstraction means that, unlike the old days of pen and paper, each new model does *not* need to be built from scratch. Models can be built upon each other and their individual modules refined and re-used.
To do this, Mallavarapu used the programming language LISP, a language widely used in artificial intelligence research. LISP is famous among computer scientists due to its ability to write code that, in turn, can write code, enabling a programmer to derive new mini-languages.
"LISP isn't like typical programs, it's more like a conversation," says Gunawardena. "When we input data into Little b, Little b responds to it and reasons over the data."
For example, Gunawardena's lab works on kinases, a kind of protein that transfers phosphate chemicals to other proteins in order to regulate their activity. While this property is common to all kinases, there is a great deal of variety in how particular kinases carry this out. Little b, however, understands this basic property of kinases, this abstraction.
Here, the researchers demonstrated how they were able to interact with Little b to build complex models of kinase activity, using Little b as a kind of scientific collaborator, and not simply a passive tool.
On a larger scale, the researchers also used the program to query the development of fruit fly embryos. As a result, they discovered levels of complexity in these embryonic structures that previous research had missed.
"This language is stepping into an unknown universe, when your computer starts building things for you," says Gunawardena. "Your whole relationship with the computer becomes a different one. You've ceded some control to the machine. The machine is drawing inferences on your behalf and constructing things for you."
The researchers sometimes admit, half-joking, that Little b sometimes feels a little bit like "The Matrix" - referring, of course, to the film trilogy in which human beings lived in a computer-generated virtual world.
Mallavarapu and Gunawardena have a pretty clear vision for this project: they want every biologist in the world to use it.
But in order to bring the program out from the early adopter community, where it is currently being used by colleagues in the Harvard community, it needs to be more accessible.
"The next step is to create an interface that's easy to use," says Gunarwardena. "Think of web page development. Lots of people are creating web pages with little or no knowledge of HTML. They use simple interfaces like Dreamweaver. Once we've developed the equivalent, scientists will be able to use our system without having to learn Little b."
And the more people use it, the smarter it gets. As researchers around the world input their discoveries into Little b, the program will assimilate that information into its language.
The ultimate goal is to have an in silico, virtual cell - a dynamic biological system living in software.
"Sure, it's a long way off," says Gunawardena, "but we're getting there."
Journal of the Royal Society Interface, online publication, July 23, 2008
"Programming with models: modularity and abstraction provide powerful capabilities for systems biology"
Aneil Mallavarapu, Matthew Thomson, Benjamin Ullian, and Jeremy Gunawardena
*Andrew Apel, guest editor