Amyris Renewable Diesel Receives EPA Registration

see here

As Synthetic Biology Becomes Affordable, Amateur Labs Thrive

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Harvard Researchers Create Computer 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 Gunawardena. “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.”

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Everything you needed to know about human-created life forms but were afraid to ask

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Mad Science Contest: Build a Lifeform and We’ll Send You to Hong Kong or Give You $1000

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Synthetic Biology Concept note by the International Risk Governance Council

more hereTechnorati Tags: synthetic biology

Synthetic Biology: social and ethical challenges

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Technorati Tags: synthetic biology

Synthetic biology gives ecosystem clues

Bioengineers have used genetically altered bacteria to provide new insights into how the complex relationship of predator and prey.
more hereTechnorati Tags: synthetic biology, bacteria, ecosystem, ecology, environment,

international electronic conference on the societal aspects of synthetic biology

international electronic
conference on the societal aspects of synthetic biology, which will take
place from Monday 5 May to Tuesday 3 June 2008 at
http://www.synbiosafe.eu/forum

This e-conference on ethical, safety, security and other societal issues of
synthetic biology is hosted by “SYNBIOSAFE: Safety and Ethical Aspects of
Synthetic Biology”, a two years FP6 project funded by the European
Commission. The aim is to stimulate an international and inclusive debate on
these issues at an early stage.

After a first fact finding mission we would now like to share our points of
view and discuss selected societal issues and open questions with a wider
group of experts and interested stakeholders. The issues we would like to
discuss fall under the following three areas:

€ Forum I: Ethical Aspects
€ Forum II: Biosafety Challenges
€ Forum III: Biosecurity Awareness

In addition there is also a section on other societal issues, including

€ Forum IV: Intellectual Property Rights
€ Forum V: Regulation and governance, and
€ Forum VI: Public perception, communication and the media

For more information on these thematic areas, specific questions to be
discussed, and how to post a contribution, please have a look at our
background document:
http://www.synbiosafe.eu/uploads///pdf/SYNBIOSAFE-background_paper.pdf

In case of any technical difficulty with the registration, please contact
Gregor Giersch on gregor.giersch@idialog.eu

We would greatly appreciate your help in forwarding this announcement to
your colleagues and networks.

Kind regards,

Markus Schmidt, IDC
SYNBIOSAFE Project Coordinator

IGEM 2008

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Contrasts: Craig Venter and NSABB on synthetic biology

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University of Groningen Forms Synthetic Biology Center

The key research areas of the CSB are as follows:

- cell factories for producing pharmaceuticals (including antibiotics) and important biological proteins
- systems for controlled drug delivery and new diagnostics
- materials (e.g. biosensors and biochips) based on biological components.

more here

SynBio 4.0

The Fourth International Meeting on Synthetic Biology (SB4.0) will be held from 10-12 October 2008 at the Hong Kong University of Science and Technology in Clear Water Bay, Kowloon, Hong Kong.

The organization of the event is being led by the BioBricks Foundation in partnership with the Hong Kong University of Science and Technology (HKUST), the University of Hong Kong (HKU), and the Chinese University of Hong Kong (CUHK).

SB4.0 will be a significant meeting, building on the past successes of SB1.0 (MIT), 2.0 (UC Berkeley), and 3.0 (ETH Zurich).

UPDATE: Given all the early progress in synthetic biology, plus how much there is still to do, SB4.0 is going to be an amazing meeting. The organizers of the meeting can’t pretend that we understand everything that should be presented or discussed at the conference. Thus, we are asking for your help. If you would like to suggest a topic for discussion, or organize a breakout session, or can suggest whatever would work best for a particular idea, please join the discussion list and let us know.
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The Open Biohacking Project / Kit

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Pursuing Synthetic Life, Dazzled by Reality NY Times

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What can synthetic biology do for you?

iGEM 2007 participants talk about the potential of synthetic biology at the 2007 Jamboree.
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OneWorld Health, Amyris Biotechnologies and sanofi-aventis Announce Development Agreement for Semisynthetic Artemisinin

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Biologist Venter will be visiting scholar at Origins of Life Initiative Harvard University

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Researchers Develop Method for Enzymatic Production of Hydrogen from Biomass at High Yields

The synthetic metabolic pathway for conversion of polysaccharides and water to hydrogen and carbon dioxide. Click to enlarge.

Researchers at Virginia Tech, Oak Ridge National Laboratory ORNL, The synthetic metabolic pathway for conversion of polysaccharides and water to hydrogen and carbon dioxide. Click to enlarge.

more here

here

microorganisms and plants in the synthesis of nanoparticles

Abstract Nanotechnology involves the production,
manipulation and use of materials ranging in size
from less than a micron to that of individual atoms.
Although nanomaterials may be synthesized using
chemical approaches, it is now possible to include the
use of biological materials. In this review, we
critically assess the role of microorganisms and
plants in the synthesis of nanoparticles.
J Nanopart Res (2008) 10:507–517

The dummy’s guide to engineering genes

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New Bionanoscience dept launched at TU Delft Netherlands

Over the next decade, TU Delft will invest €10m derived from its assets in the new department, which will form part of the university’s Kavli Institute of Nanoscience. The Kavli Foundation will also donate $5m (€3.4m).
The new department will explore the full spectrum from nanoscience to cell biology to synthetic biology to create gene regulation systems, artificial biomolecules and nanoparticles that can be deployed within the cell.

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Pursuing Synthetic Life, Dazzled by Reality NY Times

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Solazyme is a synthetic biology company that unleashes the power of marine microbes to create clean and scalable solutions for the renewable energy, industrial chemical, and specialty ingredient markets.

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U.K.’s Parliamentary Office of Science and Technology (POST) note on synthetic biology

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[Synthetic Biology] Bottom-up genome assembly using the Bacillus subtilis genome vector

Japanese group assembles a 134.5 kb rice chloroplast genome from 4-6kb
pieces…

Abstract:
We established a protocol to construct complete recombinant genomes
from their small contiguous DNA pieces and obtained the genomes of
mouse mitochondrion and rice chloroplast using a B. subtilis genome
(BGM) vector. This method allows the design of any recombinant
genomes, valuable not only for fundamental research in systems biology
and synthetic biology but also for various applications in the life
sciences.

http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=18066072&itool=pubmed_DocSum

Extreme Monopoly: Venter’s Team Makes Vast Patent Grab on Synthetic Genomes

here

IGEM International Genetically Engineered Machine Competition 2007

The Winner of this year IGEM (more on IGEM International Genetically Engineered Machine Competition here

Winner Peking University
Towards Self-differentiated Bacterial Assembly Line
Our projects concern with the ability for bacterial cells to differentiate out of homogeneous conditions into populations with the division of labor. We aim at devices conferring host cells with the ability to form cooperating groups spontaneously and to take consecutive steps sequentially even when the genetic background and environmental inputs are identical. To break the mirror in such homogeneous condition, we need two devices respectively responsible for temporal and spatial differentiation. The implementation and application of such devices will lead to bioengineering where complex programs consisted of sequential steps (structure oriented programs) and cooperating agencies (forked instances of a single class, object and event oriented) can be embedded in a single genome. Although this “differentiation” process resemble the development of multicellular organism, we tend to use a more bioengineering style analogy: assembly line. Or maybe after some years from now, this will not be just an analogy.

morehere

second place see some pressrelease here

A biological sensor that catches infections on hospital catheters at an early stage has been developed by Biochemistry and Bioengineering students and researchers at Imperial College London. moresee here

The other projects here

Synthetic biology governance; the newest

1) Synthetic Genomics: Options for Governance see here
The authors are mostly from the synbio field Michele S. Garfinkel, The J. Craig Venter Institute, Rockville, Maryland, Drew Endy, Massachusetts Institute of Technology, Cambridge, Massachusetts, Gerald L. Epstein, Center for Strategic and International Studies, Washington, District of Columbia and Robert M. Friedman, The J. Craig Venter Institute, Rockville, Maryland

2) The NGO response Syns of Omission: Civil Society Organizations Respond to Report on Synthetic Biology Governance from the J. Craig Venter Institute and Alfred P. Sloan Foundation see here

Scientists Synthesize Memory in Yeast Cells

FINDINGS:
Researchers in the Harvard Medical School Department of Systems Biology have constructed a memory loop out of bits of DNA. After being placed in a yeast cell, the loop continued throughout many cell divisions.
morehere

Scientists a step nearer to creating artificial life

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New institute fuses science and engineering with medical research

more here
includes a synbio group

Microbial Fuel Cells

more here

European Conference on Synthetic Biology (ECSB):

Design, Programming and Optimisation of Biological Systems
more here

Newest column of mine NBICS, Cultural Identity and Diversity, and the CBD

NBICS, Cultural Identity and Diversity, and the CBD
this is the second part on the convention on biological diversity CBD
first one is
here

and all my columns are listed here

New recipe for sustainability: stem-cell burgers

more here

Making Gasoline from Bacteria

from here and more here
The biofuel of the future could well be gasoline. That’s the hope of one biotech startup that on Monday described for the first time how it is coaxing bacteria into producing hydrocarbons that could be processed into fuels like those made from petroleum.

LS9, a company based in San Carlos, CA, and founded by geneticist George Church, of Harvard Medical School, and plant biologist Chris Somerville, of Stanford University, had previously said that it was working on what it calls “renewable petroleum.” But at a Society for Industrial Microbiology conference on Monday, the company began speaking more openly about what it has accomplished: it has genetically engineered various bacteria, including E. coli, to custom-produce hydrocarbon chains.

New molecular switch for genes

Researchers have created a molecular switch that can reversibly turn any mammalian gene on or off and control its level of expression. The results, published this week in Cell, provide a new level of precision in studying genes involved in biological processes and diseases, the authors say.
more here

Copyright © 2007 Cell Press. All rights reserved.
Cell, Vol 130, 363-372, 27 July 2007
Resource
A Tunable Genetic Switch Based on RNAi and Repressor Proteins for Regulating Gene Expression in Mammalian Cells

Tara L. Deans,1 Charles R. Cantor,1 and James J. Collins1,
more here

synthetic biology 3.0

my new column is out
see here
older columns here

Countdown to a synthetic lifeform

According to George Church at Harvard Medical School in Boston, who has devised a complete blueprint for a synthetic cell, an investment of around $10 million would be enough to turn the “bottom-up” dream into reality. “Our approach doesn’t require any super new technology,” he says.
more here

Scientists Build Bacteria-Killing Organisms From Scratch

here
here
and here
and here

synthetic biology and nanotechnology nanosynbio

here
and here

Synthetic Biology three pieces in wired news

here

here

and here

Oil giant BP invests in microbe specialist

Petroleum giant BP has invested in Synthetic Genomics–a company founded by geneticist J. Craig Venter–in an effort to better understand, and ultimately exploit, microbes that live underground.
more at source

my new column out: NBICS and the Convention on Biological diversity (CBD)

see here
a list of all columns can be found here

Royal Society Call for views: Synthetic biology

Call for views: Synthetic biology
The Royal Society seeks your views on the emerging area of
synthetic biology. This is your opportunity to shape the focus of
the Royal Society’s future policy work in this important area.
We welcome views from individuals or organisations by 27
August 2007.
see here and here

Researchers Develop Method for Enzymatic Production of Hydrogen from Biomass at High Yields

more at source

three blogs which cover the conference synthetic biology 3.0 going on in the moment

1)The journal Nature
2) ETC
3) The Molecular Systems Biology Blog on Systems & Synthetic Biology

also related Synthetic Biology, Global Push To Advance Research

Videos from BioSysBio2007

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Craig Venter: The Bill Gates of Artificial Life?

see more at source

Genome Synthesis and Design Futures: Implications for the US Economy Report

see at source

Programmable Artificial Cell Evolution project PACE

The European Commission is supporting the Integrated Project PACE in its Future Emerging Technologies program that will create the foundation for a new generation of embedded IT using programmable, self-assembling artificial cells.
more at source

Patenting Pandora’s Bug: Goodbye, Dolly…Hello, Synthia! J. Craig Venter Institute Seeks Monopoly Patents on the World’s First-Ever Human-Made Life Form

ETC Group Will Challenge Patents on “Synthia” – Original Syn Organism Created in Laboratory

Ten years after Dolly the cloned sheep made her stunning debut, the J. Craig Venter Institute is applying for a patent on a new biological bombshell – the world’s first-ever human-made species. The novel bacterium is made entirely with synthetic DNA in the laboratory.

The Venter Institute – named for its founder and CEO, J. Craig Venter, the scientist who led the private sector race to map the Human Genome – is applying for worldwide patents on what they refer to as “Mycoplasma laboratorium.” In the tradition of ‘Dolly,’ ETC has nicknamed this synthetic organism (or ’syn’) ‘Synthia.’….
In Vivo, In Vitro, In-Venter? Published on May 31, 2007, the Venter Institute’s US Patent application (number 20070122826) claims exclusive ownership of a set of essential genes and a synthetic “free-living organism that can grow and replicate” that is made using those genes. The Venter Institute has also filed an international patent application at the World Intellectual Property Organization (WIPO number WO2007047148, published April 27, 2007) which names more than 100 countries where it may seek monopoly patents…..

The patent application is also a wake-up call to synthetic biologists who are advocating for “open source” biology – the idea that the fundamental tools and components of synthetic biology should be freely accessible to researchers……

Syn of Omission? Synthetic biologists may also be dismayed to learn that Synthia is being patented for what it is not. The patent application explains that the inventors arrived at their minimal genome by determining which genes are essential and which are not. Remarkably, their patent application claims any synthetically-constructed organism that lacks at least 55 of 101 genes that they’ve determined are non-essential. “All synthetic biologists developing functionalized microbes are going to have to pay close attention to the claim on a ‘non-essential’ set of genes……

more at source

Synthetic Biology Conference 3.0

The conference will take place at the Swiss Federal Institute of Technology (ETH) in Zurich, Switzerland, from 24th-26th June 2007
more at source.

Safety and Ethical Aspects of Synthetic Biology

SYNBIOSAFE is a scientific project supported fully by the European Commission´s 6th framework programme. It is the first European project to research the safety and ethical aspects of synthetic biology, and aims to proactively stimulate a debate on these issues.
see more at source

Report on synthetic biology by the Rathenau Institute

see here
and download here
WED97
Constructing Life 2006.pdf

Constructing life – Vriend, H. de
titel Constructing life
auteur Vriend, H. de
corporatieve auteur
plaats van uitgave Den Haag
jaar van uitgave 2006
uitgever Rathenau Instituut
ISBN
aantal pagina’s 88
reekstitel Working Document ; 97
korte beschrijving Early social reflections on the emerging field of synthetic biology.
signatuur RP-WED-97
taal engels
project naam Synthetische Biologie
PDF samenvatting

Who we are

The Rathenau Institute carries out research into the development of science and technology.

The institute has two key tasks:

1. Stimulating both public debate and the formation of political judgements. Technological and scientific developments sometimes give rise to more questions than answers. The Rathenau Institute highlights the significance of these developments for individuals and society. What are the possibilities, yet also the risks? In professional jargon this is called Technology Assessment (TA).
2. Describing the Dutch science system. The Rathenau Institute is investigating the dynamics of the scientific and technological process: how is the science system organised, how does it respond to scientific, societal and economic developments, and to what specific scientific developments does this lead? This task is called Science System Assessment (SciSA).

The Rathenau Institute is an independent body and was founded in 1986 by the Ministry of Education, Culture and Science, which also funds it. Administratively the institute falls under the Royal Netherlands Academy of Arts and Sciences (KNAW).

The Rathenau Institute addresses a broad field of interest, varying from biotechnology to spatial planning. The institute can devote resources to any technological or scientific development which could have consequence to Dutch society. These are not exclusively new technologies – such as nanotechnology, genomics or artificial intelligence – but also existing technological systems such as nuclear energy, organ donation or water management (see list of all projects).

Every two years the Rathenau Institute lays down the proposed project’s in a so-called work programme. To select the subjects the institute looks at the political agenda and questions put forward by society (for more information see working methods). The work programme is offered for review to the Minister of Education who sends it with a reaction to the Dutch Lower House. The work programme is published widely, including notification in the Government Gazette. The institute renders an account of work it undertakes in its annual reports.
see here

Synthetic Biology on Display

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LS9 Launches to Deliver Next-Generation Biofuels Through Synthetic Biology

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Extreme Genetic Engineering: An Introduction to Synthetic Biology

ETC Group just published a new report, Extreme Genetic Engineering: An Introduction to Synthetic Biology.

Microsoft Builds Relationships in Synthetic Biology

By Kevin Davies

December 07, 2006 | Microsoft Research (MSR) has launched a new funding initiative in the promising but controversial field of computational challenges in synthetic biology.

Unlike the BioIT Alliance, through which Microsoft encourages links with industrial partners to create solutions in the life sciences, the principal aim of MSR is to forge partnerships with academic researchers. The new request for proposals (RFP) allocates $500,000 for two principle areas of synthetic biology research:

1. The re-engineering of natural biological pathways to produce interoperable, composable, standard biological parts. Examples include the role of computers in the “specification, simulation, construction and dissemination of biological components or systems of interacting components.”
2. Tools and information repositories relating to the use of DNA in the fabrication of nanostructures and nanodevices.
Read More at Source

Scientist, Police Thyself

By Yudhijit Bhattacharjee
ScienceNOW Daily News
5 December 2006
WASHINGTON, D.C.–Thanks to advances in synthetic genomics, an aspiring bioterrorist could turn a harmless virus into a deadly strain—or make a killer bug from scratch—by ordering some strands of DNA. Yesterday, an independent group of biologists and security experts confronted this threat by issuing a draft report that lays out options for regulating commercial gene synthesis and academic research in the field.
Read More at Source

2 N.C.high school students third, win $40,000, in science contest with synthetic biology projct

…
Two students at the North Carolina School of Science and Mathematics in Durham, Sagar Indurkhya and Nicholas Tang, placed third in the Siemens Competition in Math, Science and Technology with their bioengineering research in the area of synthetic biology. It is an emerging interdisciplinary field related to systems biology that uses concepts based on living systems to design biological networks much like electronic networks.

Their project explored methods, models and design patterns for the construction of complex artificial gene circuits at the theoretical level. They will share a $40,000 prize….
Read more at Source

Gene Machine: Cells Engineered To Prevent Sepsis Win Synthetic Biology Competition

A team of eight undergraduates from the University of Ljubljana in Slovenia — cheering and leaping onto MIT’s Kresge Auditorium stage in green team T-shirts — won the grand prize earlier this Month at the international Genetically Engineered Machine (iGEM) competition at MIT.

The group — which received an engraved award in the shape of a large aluminum Lego piece — explored a way to use engineered cells to intercept the body’s excessive response to infection, which can lead to a fatal condition called sepsis.

The goal of the 380 students on 35 university teams from around the world was to build biological systems the way a contractor would build a house–with a toolkit of standard parts.

iGEM participants spent the summer immersed in the growing field of synthetic biology, creating simple systems from interchangeable parts that operate in living cells. Biology, once thought too complicated to be engineered like a clock, computer or microwave oven, has proven to be open to manipulation at the genetic level. The new creations are engineered from snippets of DNA, the molecules that run living cells.

Cells may one day be programmed to manufacture and deliver drugs or key molecules within the body, churn out fuel, detect pollutants and carry out a slew of as-yet-unimagined functions. The MIT team, dubbed “eau d’ecoli,” genetically engineered E. coli bacteria to smell like mint while they were growing and to smell like banana when they were done. The technique could potentially be used to improve the scent of other foul-smelling substances.

“It’s kind of a cool thing to tell your bacteria how to smell,” said team member Veena Venkatachalam, an MIT sophomore majoring in chemistry and physics.

The Slovenian team was one of the few to work with mammalian cells. Ljubljana microbiology student Monika Ciglic said that the team chose the more challenging and complicated mammalian cells over bacteria or viruses because of the potential rewards of coming up with a system that could work in the human body. Sepsis has been cited as the 10th leading cause of death in the United States. But while the other teams had an available toolkit of 500 “BioBricks”–snippets of DNA that have been proven to accomplish certain tasks–the Slovenian team had to build all its BioBricks from scratch.

Information about BioBricks, and a toolkit to make and manipulate them, was provided by the Registry of Standard Biological Parts created by MIT.

The first runner-up was a team from the Imperial College in London for its creation of an oscillator that was stable, had a high signal-to-noise ratio and could be easily integrated into other systems. Such a device has potential biomedical applications.

The second runner-up was the Princeton team for its work on programming mouse embryonic stem cells to differentiate on command. The technique could one day be used to create organs and tissues from stem cells, which have the ability to turn into any part of the body. Other projects with potential applications included the University of Edinburgh’s device to detect arsenic in well water, a problem that affects 100 million people around the world, especially in poorer nations.

The director of iGEM, Randy Rettberg, principal research engineer in biological engineering, said he is convinced synthetic biology will spawn a worldwide industry. The possibilities for start-ups include companies that make and catalog individual parts, as well as companies that exploit the technology to solve myriad problems.

Drew Endy, assistant professor of biological engineering, said that it is “completely remarkable that 40 months ago, none of this was happening anywhere.” A small pilot program held during Independent Activities Period has grown into an international competition, and Endy said that as DNA synthesis becomes more common, the field will expand even more rapidly.

As with any technology, there is the danger of misuse. Perceptions of synthetic biology range from excitement to fear and mistrust. Endy said that the work is so new, it’s bound to scare some people. “A lot of people who were scaring folks in 1975 now have Nobel prizes,” he said.

iGEM is an initiative of the MIT iCampus program, which is funded by Microsoft Corp. Competition winners were selected by a panel of judges from industry and academia.
// www.sciencedaily.com/releases/2006/11/061114193826.htm”>Link to Source

Bedfellows at the Biosecurity Board

2006-11-17 | How US science’s nouveau riche bioweapons constituency is flexing its muscle to carve up safety and security rules.

Karl Rove would probably be impressed by the brand of government “oversight” being developed by the National Science Advisory Board on Biosecurity (NSABB). http://www.biosecurityboard.gov Like a Bush administration investigation of itself, on last Wednesday (October 25th) an NSABB working group moved to creatively thwart its charge. Although it was formed to recommend biosecurity rules to govern the new field of synthetic biology, the working group will instead assault regulation of a wide range of biodefense and biotech risks.

The working group’s outlook is more political than technical. Its science is a veneer that disguises the maturing political muscle of a constituency of bioscientists that has become accustomed, perhaps addicted, to lavish federal biodefense funding. This constituency is challenging the regulations that apply to it and has allied itself with those seeking to block effective regulation of the emerging field of synthetic biology. As such, it will pose a major long-term obstacle bringing under control the wild proliferation of dangerous biodefense research in the US.

The working group’s politics deftly unite two distinct scientific camps under the same banner. One camp is synthetic biology, a burgeoning, dangerous science that currently is an unregulated Wild West free-for-all, a condition that many practitioners believe is desirable. The working group also tapped a deep vein of discontent among its other camp, infectious disease researchers. Specifically, the researchers that receive biodefense handouts; but who resent being required to comply with the Select Agent Rule, a law designed to protect the public from bioterrorism.

In biodefense, the synthetic biologists (who use DNA like building blocks) and the infectious disease bug jockeys (who work with full-blown dangerous microbes) usually don’t get along very well. The synthetic crowd scoffs at the bug jockey’s focus on vaccines and pills for specific microbes, dubbing the narrow approach a “Maginot Line” after the inflexible border defenses that failed to protect France from German invasion in 1940. Genetic tweaks and new bugs, the synthetic biologists say, can outflank these countermeasures. A subtext, of course, is that synthetic biologists think they should get a bigger piece of the biodefense pork pie from the federal budget.

The bug jockeys, on the other hand, argue that the synthetic guys are a bunch of nerdy engineers whose science of using genes like tinker toys is young and unproven. The bug jockeys claim that they can deliver here and now, whereas the synthetic folks are still in scientific diapers, working out basic principles of their discipline. Perhaps interesting down the road, the bug jockeys say, but what counts is the present. (Neither group questions the wisdom of the government bankrolling tens of billions of dollars in biodefense research at hundreds of places across the country.)

What unites these two quarrelling factions? Apart from the fact that their science is potentially dangerous, the two share an appetite for tax dollars and a disdain for federal security rules. The latter point has led to an NSABB marriage of convenience: The synthetic biologists want to shake pressure for new regulation while the bug jockeys want to assassinate the existing Select Agent Rule, enabling both to do as they please with less “interference” from Uncle Sam.

Thus was born a politico-scientific Coalition of the Willing that aims to invade federal rulemaking to take down what they perceive as a threat: biosecurity legislation designed to protect the public. By hijacking the NSABB, they are on well on their way to Mission Accomplished. And because the current political leadership of the US holds itself to its own unique (nonbinding) standards and sees little reason to reign in dual-use research for safety, security, or treaty compliance reasons, the NSABB working group probably won’t have to waterboard anybody in the US government – unless there are radical changes in officialdom.

The specifics of the working group recommendations? They include unusual and dubious arguments about taxonomy, gene sequences, and law. These have far broader implications than the working group apparently paused to contemplate. More on that later.
From an unsurprising “finding” that microbial taxonomy systems are imperfect, the working group leaps to the illogical conclusion that this is justification to eviscerate government regulation of (but not cash handouts for) research with biological weapons agents. That’s quite a jump. Considering the recommendations carefully, however, it is clear that the working group’s intellectual shortcomings – its recommendations don’t logically follow from its findings – stem from an attempt to paper over the distinctions between the need for synthetic biology regulation and the need for the select agent rule.

Synthetic biology may be new; but challenges to taxonomic conventional wisdom are not. Evolution happens. Genes turn up in new places, by the hand of man and through the many ways that biodiversity moves itself. The novel possibilities of synthetic biology are thus not without precedent in nature, in the sense that taxonomy is always encountering the difficult-to-classify and is currently incapable of fully describing naturally occurring diversity.

No matter what is cooked up in a synthetic biology lab, that doesn’t change the fact that there are diseases out there that can kill you. Scientists know what most of them are, and can reasonably define them. Hence the need for the Select Agent Rule is unaltered by the powers to manipulate, even create, dangerous forms of life (and nucleic acids) that is possibly offered by synthetic biology.

But don’t tell the NSABB working group, because that would get in the way of its political agenda. That the working group’s logic doesn’t parse is unsurprising in view of the fact its science is merely a pretext to table a pre-emptive attack on regulation of synthetic biology and the extant Select Agent Rule. For good measure, the working group adds a pork barrel recommendation to loosen controls on smallpox virus and DNA that suffers from the same logical flaws as the other recommendations.

And, in an easy to overlook item, the working group suggests that biosafety of synthetic DNA can be handled by the failed genetic engineering oversight system known as the NIH Guidelines, designed three decades ago and declining ever since. It’s another failure of the logic to parse. The synthetic biologists literally argue that their science antiquates biodefense before it like the Nazi blitzkrieg through Belgium outmoded the Maginot Line. But then they go on to reason that, for biosafety, the scientific equivalent of the Treaty of Versailles (NIH Guidelines) is sufficient to keep the peace!

In the long run, this quagmire of faulty scientific-legal verbiage won’t stop the real risks of biodefense proliferation. It would take an intelligence failure of a very different type than Iraq in order for NSABB to be allowed to thwart its charge and debilitate proper federal oversight of dual-use research. But that may be exactly what NSABB does. Certainly that’s the way that its working group on synthetic biology is heading. And if it is an indicator of how biodefense researchers, a sort of bioscience nouveau riche, intend to flex their political muscle, then we may be in for many more dangerous years before the wild excesses of the biodefense boom are brought under control.

The Sunshine Project http://www.sunshine-project.org and in our Links section

From the UN observer

Bizarre Bacterial Creations

Anyone who has ever smelled E. coli bacteria knows that they smell bad. Putridly bad. So, a group of student bioengineers at MIT set out to sweeten the scent of this commonly used lab bacteria. The team constructed its creation from a collection of biological “parts”–bits of DNA that, when inserted into living organisms, can make the organisms glow, detect light, and perform a number of other unusual functions. The team will showcase its sweet-smelling bug this weekend at the International Genetically Engineered Machine competition (iGEM) at MIT, along with 37 other student groups from around the world.
Read more

NSF funds $16 million synthetic biology center

BERKELEY – A new research center being launched this summer at the University of California, Berkeley, will seek to make it as quick and easy to engineer biology as it now is to assemble microprocessors, hard drives and memory chips into a computer.
Link to source

U.S. Pledges $34.5 Million for Renewable Energy Technologies

13 October 2006
U.S. Pledges $34.5 Million for Renewable Energy Technologies

Biofuels, solar energy and biomass genomics research to benefit from investment

By Cheryl Pellerin
Washington File Staff Writer

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Energy Northwest’s White Bluffs Solar Station near Richland, Washington, is located near the abandoned Washington Nuclear Project One, in the background. The demonstration project, composed of more than 200 photovoltaic panels, is one of the public power agency’s explorations into renewable energy production. (© AP Images)
Enlarge Photo
Energy Northwest’s White Bluffs Solar Station near Richland, Washington. (© AP Images)

Washington — U.S. energy and agriculture officials announced $34.5 million is available to fund new research in biofuels, solar energy and biomass genomics research to accelerate development of alternative fuels.

U.S. Department of Energy (DOE) Secretary Samuel Bodman and U.S. Department of Agriculture (USDA) Secretary Mike Johanns announced the funding October 11 at “Advancing Renewable Energy: An American Rural Renaissance,” a conference hosted by both agencies in St. Louis to further President Bush’s Advanced Energy Initiative.

The initiative seeks to accelerate the commercialization of clean, affordable alternative and renewable sources of energy by changing the way Americans power cars, homes and businesses.

Bodman and Johanns announced nearly $17.5 million for 17 biomass research, development and demonstration projects, and more than $13 million to fund new research in solar technologies.

Raymond Orbach, DOE under secretary for science, announced $4 million for bio-based fuels research, and both departments solicited research proposals for new plant genomics research projects, which would involve the genetic modification of plants for the improved production of fuels such as ethanol or renewable chemical feedstocks.

ENERGY FROM PLANTS

Biomass is an energy resource that includes organic matter, such as wood, agricultural waste, algae, sewage and other living-cell material that can be burned or chemically processed to produce heat energy (See related article.)

Biomass, which supplies about 3 percent of total U.S. energy consumption in the form of electricity, process heat and transportation fuels, helps diversify the energy supply and support rural economies.

“Americans are discovering the road to energy independence is paved with natural resources grown right here at home,” Johanns said. “This is a new era for America’s farmers, ranchers and rural communities as they seize this moment where opportunity meets need, and where American ingenuity breaks a century long addiction to oil.”

The grants are intended to develop technologies needed to help make biobased fuels cost-competitive with fossil fuels in the commercial market. The chosen projects will include research, development and demonstrations of biobased products, bioenergy, biofuels and biopower.

Of the nearly $17.5 million announced October 11, $12.8 million is funded by USDA and $4.7 million by DOE. DOE funds will go to three projects developing cellulosic (from cellulose, the main part of the cell wall in most plants) biomass. USDA will provide funding to address such topics as feedstock production and product diversification.

Under the Biomass Research and Development Initiative, a joint USDA-DOE effort established in 2000 and reauthorized in the comprehensive Energy Policy Act of 2005, projects receiving awards must demonstrate collaboration among biomass experts. (See related article.)

The initiative aims to enhance creative approaches to developing next-generation advanced technologies and promote research partnerships among colleges, universities, national laboratories, federal and state research agencies and the private sector.

BIOMASS GENOMICS

Biotechnology offers the promise of dramatically increasing ethanol production using cellulose, the most abundant biological material on earth, and similar organic materials. Materials such as post-harvest corn plants (stover) and timber residues could be used, along with specialized high-biomass “energy” crops like domesticated poplar trees and switchgrass, a hardy, fast-growing grass native to North America that is considered a good candidate for biofuel production.

“We are seeking to accelerate research breakthroughs that contribute towards making biofuels a cost-effective alternative to fossil fuels, with a goal of replacing 30 percent of transportation fuels with biofuels by 2030,” Orbach said.

“This joint research initiative shows a commitment to acquiring new alternative energy resources and improving the efficiency with which biomass and plant feedstocks are used to produce renewable fuels such as ethanol,” Under Secretary of Agriculture Tom Dorr said.

The new funding continues a 2006 commitment to conduct a fundamental research program in biomass genomics that will build the scientific foundation to facilitate the use of woody plant tissue for bioenergy and biofuels. Developing such crops for energy fuels could use less-intensive production techniques and poorer-quality land, avoiding competition with food production on the most fertile land.

The program will take advantage of advances in breeding, molecular genetics and genomic technologies and build on the existing knowledge of plant biology to help researchers confidently predict and manipulate plants’ biological function for bioenergy resources.

POWER FROM THE SUN

Photovoltaic devices use solar cells or arrays to turn sunlight into electricity and they have little impact on the environment. Photovoltaics can be used in a wide range of products, from small consumer items to large commercial solar electric systems. (See related article.)

The $13 million announced for solar technologies at the St. Louis conference is part of President Bush’s $148 million Solar America Initiative. The funding will support the development of more efficient photovoltaic devices.

“This investment is a major step in our mission to bring clean, renewable solar power to the nation,” Bodman said. “If we are able to harness more of the sun’s power and use it to provide energy to homes and businesses, we can increase our energy diversity and strengthen our nation’s energy security.”

The Solar America Initiative aims to make solar power cost competitive with conventional electricity sources by 2015, by developing materials that convert sunlight directly to electricity.

The $13 million in funding, including about $4.5 million to be awarded for fiscal year 2007, will support several projects, including:

• Solar codes and standards working group leadership, a five-year, $4.2-million project designed to create and operate a national working group to manage solar regulatory codes and standards. Sample work includes recommending or developing model codes and standards and helping in their implementation, developing codes and standards studies, and monitoring emerging codes and standards issues;

• State strategic partnerships, a three-year, $1.35-million project in which DOE will enlist the help of state membership organizations as strategic partners on solar issues, and allow recipients to foster strong relationships with targeted state partners to promote solar energy technology adoption; and

• Utility strategic partnerships, a three-year, $1.35 million cost-shared project to enlist the help of utility membership organizations as strategic partners to deliver key assistance to utilities to enable the success of the Solar America Initiative.

For additional information, see Clean Energy Solutions.

More information on the solicitation and facts about the Solar America Initiative can be found on the DOE Web site, along with information about biomass and the biomass genomics joint research program.

(The Washington File is a product of the Bureau of International Information Programs, U.S. Department of State. Web site: http://usinfo.state.gov)
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Biology via design, and print via 3-D

Biology via design, and print via 3-D
By Conrad de Aenlle International Herald Tribune

Published: October 20, 2006
The marvels of the information age exist mainly in two dimensions on a computer disk or monitor. In the post-information age, they are expected to be more tangible and substantial, occupying the same three-dimensional space we do.

One of the most intriguing developments anticipated by Marina Gorbis, executive director of the Institute of the Future, is “intentional biology,” or genetic, pharmaceutical or mechanical biological alteration. “We’re going to be able to design and manipulate our bodies more and more and hack into them in various ways,” she predicted.

Three pioneers in this field – Synthetic Genomics, founded by Craig Venter, a leading figure in mapping the human genome; Codon Devices; and Amyris Biotechnologies – are hacking into lower forms of life, for now, including organisms invented in their labs.

Two companies Gorbis mentioned that work on the human nervous system were Cyberkinetics, which makes neural stimulation devices, and the drug maker Memory Pharmaceuticals.

Another nascent development expected to flourish in coming decades is a three-dimensional printer that would use nanotechnology to make physical objects by dispersing molecules according to programmed patterns, much as a conventional printer sprays ink to form words and images on a page.

“You put in a formula and design for something, and the printer will etch, layer by layer, the actual three-dimensional object,” Gorbis said. She emphasized that the results would not be holographic images or other facsimiles, but actual objects, including functional electronic equipment.

She expects 3-D printers to be a fact of commercial life “definitely in the next 20 to 30 years,” but some companies, notably Z Corp. and Stratasys, are getting a head start. They make prototypical printers used in industrial design.

The big promise of 3-D printers is that they will usher in a new era of home-based manufacturing and unprecedented choice, Gorbis said. She foresees an intermediate stage in which makers of, say, cellphones invite customers to a store to create the handset of their choice on the spot. After that, she said, they may become fairly ordinary pieces of household equipment.

“This changes the way we think about materials,” she said. “You just get the chemical package and assemble it. This allows us to create light products that are highly flexible and personal.”

The marvels of the information age exist mainly in two dimensions on a computer disk or monitor. In the post-information age, they are expected to be more tangible and substantial, occupying the same three-dimensional space we do.

One of the most intriguing developments anticipated by Marina Gorbis, executive director of the Institute of the Future, is “intentional biology,” or genetic, pharmaceutical or mechanical biological alteration. “We’re going to be able to design and manipulate our bodies more and more and hack into them in various ways,” she predicted.

Three pioneers in this field – Synthetic Genomics, founded by Craig Venter, a leading figure in mapping the human genome; Codon Devices; and Amyris Biotechnologies – are hacking into lower forms of life, for now, including organisms invented in their labs.

Two companies Gorbis mentioned that work on the human nervous system were Cyberkinetics, which makes neural stimulation devices, and the drug maker Memory Pharmaceuticals.

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Nano-forestry

I published a column on Nanoforestry recently
and since than other news appeared e.g. Nanocoating woodfibers results in smart paper. In the column I also dealt with the link between nano-forestry and biofuel and with the link between synthetic biology and biofuel and right after I published my nanoforestry column I saw the news item Amyris Biotechnologies Synthetic Biology Pioneer Expands Into Bioenergy Field which I mentioned in the blog here a few days ago. To be on top of things it seems one has to have ones sensors in the advances of many different sciences and technologies and be aware of the numerous applications all of these sciences and technologies go for. ..

Amyris Biotechnologies Synthetic Biology Pioneer Expands Into Bioenergy Field

Some excerpts from press release
EMERYVILLE, Calif., October 12, 2006 /PRNewswire/ — Amyris Biotechnologies, Inc., a privately-held company applying advances in synthetic biology to produce high-value pharmaceuticals, fine chemicals and biofuels, today announced that the company has raised $20 million in a first round of venture funding.

Mr. Melo stated, “I am excited about this opportunity to join a company that is using cutting-edge tools in chemistry and biology to develop solutions for major world problems, and look forward to guiding Amyris’ expansion into new areas, including polymers, specialty chemicals and nutraceuticals, in addition to biofuels.”

“The completion of this financing validates the strength of Amyris’ core technology and signals an important step in the company’s growth. These new resources will enable the company to expand its capabilities to address major global health and energy challenges, thereby helping to fulfill the promise of synthetic biology,” stated Jay D. Keasling, Ph.D., an Amyris founder, head of the company’s Scientific Advisory Board, and University of California, Berkeley, professor of chemical engineering and bioengineering. “In addition to its ongoing focus on creating a low-cost malaria drug, Amyris will add a new program aimed at renewably producing second-generation, high-performance biofuels with increased cost-effectiveness.”

Amyris Biotechnologies uses synthetic biology techniques to create new metabolic pathways in industrial microbes, turning them into living chemical factories for the efficient production of novel or rare chemicals. Amyris’ primary project to date has focused on the use of synthetic biology to address supply and cost constraints limiting the use of the life-saving anti-malarial drug, artemisinin.
Read the complete one

see also here
Amyris webpage

Synthetic biology Life 2.0

Aug 31st 2006 | From The Economist print edition The new science of synthetic biology is poised between hype and hope. But its time will soon come
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