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The Synthetic Biology Institute at UC Berkeley (SBI) 
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"Over the past year or so, I have been doing a lot of thinking, reading, and ruminating about several topics: the outdated thinking of Web-2.0 startups, the need for a revolution in the microblogging space , what identity in the Social Web is really all about, and the meaning of a truly user-centric Social Web. As I’ve been furiously writing about these topics, in the back of my mind, I’ve been wondering where all of these advancements may eventually lead...."
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Ensuring benefits of synthetic biology are realized through responsible development. Synthetic biology specific news, events, publications and more.
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"I’m sure you’ve probably heard about the “man without a pulse” artificial heart recipient, who’s been in the news so much lately, but if you haven’t, Popsci has an excellent article on it here. I’m bringing it up today because it’s an illustration of one of the biases that we as transhumans will have to overcome to actually become “Trans” humans...."
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"Much of the so-called ‘nature’ in our lives has taken on an artificial authenticity. Engineered tomatoes are redder, rounder, and larger than the ones from our gardens. We have made fluorescent fish, featherless birds, and botanical gardens that contain species from every corner of the globe. Human design has made nature hypernatural. Hypernature is an exaggerated simulation of a nature that never existed. It’s better than the real thing: a little bit prettier, slicker and safer than the old kind. Hypernature is culture in disguise..."
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"Non-coding RNAs (ncRNAs) are versatile regulators in cellular networks. While most trans-acting ncRNAs possess well-defined mechanisms that can regulate transcription or translation, they generally lack the ability to directly sense cellular signals. In this work, we describe a set of design principles for fusing ncRNAs to RNA aptamers to engineer allosteric RNA fusion molecules that modulate the activity of ncRNAs in a ligand-inducible way in Escherichia coli. We apply these principles to ncRNA regulators that can regulate translation (IS10 ncRNA) and transcription (pT181 ncRNA), and demonstrate that our design strategy exhibits high modularity between the aptamer ligand-sensing motif and the ncRNA target-recognition motif, which allows us to reconfigure these two motifs to engineer orthogonally acting fusion molecules that respond to different ligands and regulate different targets in the same cell. Finally, we show that the same ncRNA fused with different sensing domains results in a sensory-level NOR gate that integrates multiple input signals to perform genetic logic. These ligand-sensing ncRNA regulators provide useful tools to modulate the activity of structurally related families of ncRNAs, and building upon the growing body of RNA synthetic biology, our ability to design aptamer-ncRNA fusion molecules offers new ways to engineer ligand-sensing regulatory circuits."
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"....When I was first asked to write about why I study science, my initial reaction was, “Well, it’s so interesting!” While as a general topic this holds true, anyone who has had to memorize the structures of the roughly 20 amino acids, analyze pages of H1- NMR results for a grade, or time the descent of balls rolling down an incline plane for the 15th time can tell you, devotion to science isn’t always interesting. In fact, it can sometimes be downright mind-numbing. If science is not always interesting, and the nitty gritty tasks involved in doing science can be so monotonous, why study science at all? In my haste to answer the initial question, I’d left out the most important part. Science isn’t just about facts and collections of data; it is a way of looking at the world. It is about constantly asking questions, wondering, observing, and improving our understanding of the world in which we live. We use the data, often collected by those monotonous and uninteresting methods, to challenge ourselves and our perceptions of the world...."
Gerd Moe-Behrens's comment,
March 5, 2012 7:44 AM
My comment to Katy Chalmers Blog: An Artist’s Angle – essay from an Undergraduate – Synthetic Biology published in Nature
http://bit.ly/ACgvPY "This interesting blog touches the question about how art and science interact, and if art is an integrated part of scientific work, or should be banned from science. This discussion leads us back to discussions of the ancient Greek philosophers and their precursors. The fundamental question was: What is reality? Can we understand the world around us with the help of our senses, or is the world around us a product of our mental concepts? The answers to these questions never were straightforward, and have been heavily discussed during the last 2000 years. During the different periods of history, sometimes it was en vogue to believe that reality is defined by our senses (materialism) other times people preferred to believe that reality is mental (idealism). The concept of idealism was profoundly formulated for the first time by Plato (428/7 – 348/7 BC). Later it was enlivened by different Neo-Platonic movements. E.g. Leonardo Da Vinci (1452 –1519), a follower of Neo-Platonism, did not make a clear distinction between art and science. If the reality of the world basically is a mental product, all mental products including art, play an as equally important role. Idealistic scientific thinking fell out of favor by the end of the nineteenth century. The main paradigm was now materialism. Idealistic thinking was highly criticized as unscientific. The external world and its observation by experiments became the main subject of science. Reflection about how our brain is structuring the world, and its meaning for scientific discovery were excluded from scientific methodology. Materialistic, scientific approach survived as a leading paradigm until today. Such materialistic orientated science banned art and artistic thinking from science. Art was viewed as a separate area, which could not give valuable contributions to scientific discovery. However, a number of twentieth century scientists are known to have concerned themselves with Neo-Platonic, artistic thinking, such as earlier described in e.g. Goethes (1749 – 1832) theory of color, a theory focused on the mental reception of color. Among these modern scientists are the logician and mathematician Kurt Goedel (1906 – 1978), the theoretical physicist Werner Heisenberg (1901 – 1976) the mathematical physicist and pioneer of chaos theory Mitchell Feigenbaum (born 1944), to mention a few. Feigenbaum has even said, “Goethe was right about color”! All the above-mentioned use mathematics as their scientific tool. Only mathematics and mathematical logic survived as a respectable science as the paradigm changed to materialism at the turn of the nineteenth century. Mathematics is a product of our brain and thus conceptually idealistic. On first sight a modern eye will often judge idealistic concepts as quite fantastic, naive, strange and far away from all reality. A modern scientist would use exactly these descriptions hearing what Plato claims in his Timaeus; the world is built out of triangles. However, this becomes less suspicious, if one stops to focus on the triangles and starts to reflect over the basic idea behind this concept. In modern theoretical physics we can find such thinking. In quantum theory, as an example, a mathematical model is used to describe the material world of atoms. The Schrödinger equation plays a central role in this theory. The sine function stands central in the solution of this equation. The sine is a function of an angle in the right triangle. So even with his triangles Plato might not have been so wrong and naive as it initially may look. Neo-Platonic thinking in science again became acceptable during the last decades. E.g. Norbert Wiener (1894 – 1964, an American mathematician) reintroduced the concept self-organization in 1965 in the second edition of his “Cybernetics: or Control and Communication in the Animal and the Machine” During the years following this publication, the concept of self-organization became popular among scientist working in the field of complex systems. The work of Wiener was influential for the development and understanding of scientific concepts about complex systems. These holistic, systems theory based concepts play an important role in modern scientific movements such as systems biology and synthetic biology. Conceptual thinking plays an important role in the contemporary design and art movements. A new intersection between science and art is taking place, since scientific thinking is re-opened for such idealistic concepts. In the following years it will be interesting to see how design and art will influence the development of the field of synthetic biology and vice versa. Design in this modern sense is an approach from the general to the detail. Apple is one of the few companies, who are using this design oriented approach very extensively and consequent. Steve Jobs saw himself between (design) art and (computer) science. This means in science to make a holistic design of the project at the beginning and use a huge amount of time for the design process. In this respect science can learn a lot from designers, especially from people like Jonathan Ive. Such holistic design thinking might be an important solution for the problem of big and complex data, which is of special importance for Synthetic Biology, which aims to design a complex nature."
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Google translate: "Researchers at the University of Artificial intelligence has been the inspiration for countless books and films as well as aspiration of many scientists and engineers. Researchers at the California Institute of Technology (Caltech) have taken a major step in the creation of artificial intelligence - not a robot or a silicon chip, but a tube. Researchers are the first to make an artificial neural network DNA, creating a circuit and interacting molecules that have memories based on incomplete patterns, as well as the brain. "The brain is amazing," said Lulu Qian, a bioengineer from Caltech. "It allows the recognition of patterns of events, memory formation, decision making and actions. We ask ourselves, rather than a network of nerve cells connected physically, is a soup of interacting molecules can present a typical behavior of the brain? "The answer, as they showed is yes. Consisting of four artificial neurons made of 112 distinct bands of DNA, the neural network was "trained" to "recognize" four scientists whose identities are represented by a specific set of answers to four questions yes-or-not. After considering a scientist, a human player provides a subset of responses that partially identify the scientist. The player is driving lanes for the network to drip strands of DNA corresponding to those responses within the test tube. The network identifies which was the scientist that the player had thought through communication by fluorescent signals. Or, the network can "say" that there was insufficient information to choose only one of the scientists in their memory or that the clues contradict what has been remembered. The researchers played the game with the network using 27 ways to answer questions (a total of 81 possible combinations) and she answered correctly each time. This neural network demonstrates the ability of DNA from an incomplete pattern, find out what he represents - a characteristic of a brain. "We are good at recognizing things. We can recognize them by looking at a set of cues or characteristics, "said co-author Jehoshua" Shuki "Bruck. The neural network of DNA does it, but in a more rudimentary. Biochemical systems with artificial intelligence - or at least a basic ability to make decisions - could have powerful applications in medicine, chemistry and biology, the researchers said. In the future, these systems could operate in cells, helping to answer fundamental questions of biology or diagnose a disease. Biochemical processes that can respond intelligently to the presence of other molecules could allow engineers to produce chemical compounds increasingly complex or build new types of structures, molecule by molecule. "Although behaviors such as the brain in artificial biochemical systems have been hypothesized for decades," according to Qian, "they are very difficult to understand and decipher." The researchers based their biochemical neural network in a simple neuronal model, called linear threshold function. The neural network model receives input signals, multiplying them by a positive or negative, and if the sum exceeds a certain threshold, the neuron fires, producing an output signal. "This model is a simplification of real neurons," said co-author Erik Winfree. "But it is a good simplification. It has been an extremely productive model to explore how the collective behavior of many simple computational elements can lead to behaviors such as a brain, how to complete the pattern and associative memory. " To build the neural network of DNA, the researchers used a process called strand-displacement cascade. Previously, the team developed this technique to create the largest and most complex network of DNA so far, which computava square roots. Inside the tube, the DNA into the solution contains DNA molecules simple ribbon and partially double-stranded. A single-tape can change its conformation to a partially double-stranded, and if their bases are complementary, the simple-tape joins double-stranded, displacing the other strand of the double helix. A simple tape then acts as Since they can synthesize DNA strands with the sequence they want, researchers can program these interactions to behave as a network of neurons. By adjusting the concentrations of each DNA strand in the network, they can teach her to remember the unique patterns of answers yes-or-not belonging to each of the four scientists. Unlike some artificial neural networks that can learn directly from examples, the researchers used computer simulations to determine the concentration levels needed to implement molecular memory in neural DNA. While this experiment shows the promise of creating networks of DNA that can, in essence, to think, this neural network is limited. The human brain consists of 100 billion neurons, but to create a network with only 40 of these neurons based on DNA - ten times larger than the network shown - would be a challenge, according to researchers. Furthermore, the system is slow, the network in the test tube took 8 hours to identify each mysterious scientist. The molecules are also unable to take off and pair with a different tape of DNA, then the game can be played only once. Perhaps the In addition to technological challenges, engenheirar these systems could also provide an insight into the evolution of intelligence. "Before the brain have evolved, one-celled organisms were also able to process information, make decisions and act in response to the environment "Our paper can be interpreted as a simple demonstration of neuro-computational principles in the intracellular and molecular levels," according to Bruck. "One possible interpretation is that these principles are universal in the processing of biological information. Watch the instructional videos in English, made by the researchers themselves. It was quite dynamic!"
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Are you ready to print your own tissue? "For decades, manufacturers have used 3-D printers to create prototypes. Car designers have used them to create new car models - last year, an entire car was printed. Drug makers print pills with them. One was used recently to replace a patient's jawbone. These kinds of printers are in widespread use in industry. But because of their cost, they've flown under the radar for the general population. Now, Cornell University is stepping in with an open source 3-D printer, that promises to bring this high tech manufacturing tool to your garage. "Mass device" Z Corporation is one of the companies making printers for manufacturers. Their printers cost between $15,000 and $60,000. "I think you have to look at things like Xbox and PS3, I think this thing has to be down around $500 before this thing becomes a mass device," says the company's vice president, Scott Harmon. But researchers are hard at work getting the technology down into that price range. Cornell University's Creative Machine Lab has developed what it calls Fab@Home - a 3-D printer that can be put together from a kit, or by sourcing the parts individually. The end result: a printer that's not much bigger than a microwave, and which looks a bit like a robotic pastry-filler. Here's how it works. First, a design is loaded into the software that directs the printer. The only limit on what material can be used is it has to fit through the tip of a syringe. "We can do everything from Play-Doh to stainless steel and everything in between," says co-creator Jeff Lipton. Once the design file is loaded and the syringe is filled, the user hits "print," and the material is laid down, layer by layer. Making creations come alive The first 3-D printer was created in the '80s. Among its inventors was Michael Cima of MIT. He says the idea was to compete with Japanese car makers by speeding up the design process. "The greatest value is in the design of these products, and we were seeing that going overseas too," says Cima. Cima says the technology is spreading so quickly that it seems like only a matter of time before printers start showing up in homes. Printers already are beginning to show up in classrooms across the country. Don Domes, a teacher at Hillsboro High School in Oregon uses one in his drafting class. "When a student can hold something that they created on the computer, it just makes it come alive," says Domes. He says there are two students applying for each seat in his 3-D printing class, which uses a Z Corp printer that cost $26,000 when the school first bought it. Competing with the big guys Competing with Z Corp's IBM-style model of building machines outside the price range of most consumers is a world of hobbyists, working in their garages and vying to create the 3-D printing industry's version of the Apple II. Bre Pettis is one of those hobbyists. His company, Maker Bot, produces an at-home, easy to use 3-D printer. "We wanted one, but we couldn't afford any of the commercial versions out there that were like $100,000 and so we started hacking and we got it so that we could make one for really cheap," says Pettis. A MakerBot doesn't print with the same detail or colors as a Z Corp printer. But its sticker price is $2,500. And it gets much cheaper if you use the open source designs to build your own. So whether users are coughing up for a Maker Bot, building their own printer in their garage, or sending their ideas off to be printed by another firm, the dream of creating your own spatula or knob, plates or sneakers, is much closer than it used to be."
Gerd Moe-Behrens's comment,
March 2, 2012 9:19 AM
I really love 3-D printers.
You have so much opportunities with this see http://www.thingiverse.com/ and http://store.makerbot.com/3d-printers.html or http://www.thingiverse.com/thing:1483 Tissue printing is also very interesting...... I am also looking forward to a 2 component printer of plastic and an electrical conductor. Moreover, this opens for a total kind of economy.... Think about when you need a thing you just need the software, which in many cases will be free shareware and you can print right away. No more shops, everything right out of your printer...... Awesome possibilities to new business. Furthermore, a step into a world where work will be equal to coding (programming abstraction) and concept design..... 
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"Molecular computing: DNA is sometimes called the software of life. Now it is being used to build computers that can run inside cells EVER since the advent of the integrated circuit in the 1960s, computing has been synonymous with chips of solid silicon. But some researchers have been taking an alternative approach: building liquid computers using DNA and its cousin RNA, the naturally occurring nucleic-acid molecules that encode genetic information inside cells. Rather than encoding ones and zeroes into high and low voltages that switch transistors on and off, the idea is to use high and low concentrations of these molecules to propagate signals through a kind of computational soup...."
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"Over the last two to three years, there has been a noticable increase in the number of institutions of higher education investigating and implementing cloud-based solutions for their IT infrastructure. E-mail, calendaring, collaboration, videoconferencing, and even ERP (enterprise resource planning) and learning management systems are now candidates for cloud-sourcing. Offerings are available to migrate telephone systems, intrusion protection, file storage, and just about every other aspect of IT. None of these options or discussions are unique to higher education. And while cloud-sourcing IT infrastructure can liberate institution resources to focus on educational activities, there have been, to date, very few cloud solutions that speak directly to the core business of higher education, teaching and learning. For sometime there have been solutions like lynda.com to provide training for software applications, and institutional IT help desks are using these tools to help students, faculty, and staff develop new skills that can assist them, indirectly, in the learning experience. Khan Academy took that one step further, providing instruction in basic math and science concepts in small modules designed, at the college level at least, to assist in remediation. As the free offerings at Khan Academy have expanded, there is more content relevant to the higher education experience. Even these tools, though, have dealt with only the most basic — albeit important — aspects of advanced education. Newer entrants into the market have had a deeper focus on higher education. MIT faculty have been offering a subset of their course material via the MIT Open Courseware site. This content is free for anyone but comes with no support or interaction with MIT faculty. Udacity, started by two former Stanford faculty, is offering a limited set of computer science-focused material. The company is relatively new, so it remains to be seen how much instructor interaction hundreds of thousands of students will receive in their model. Both these options, while potentially short on faculty-student interaction, do provide a wealth of valuable educational content for the motivated student or even the industrious faculty member."
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James Collins "Scientists are combining biology and engineering to change the world. With a box of Lego, you can create a whole range of different structures. Snap together pieces of various colours, shapes and sizes to create a multitude of structures — a house, a boat, a tower — with different functions. In the world of biology, a growing group of scientists is thinking about parts of cells in much the same way. Engineers are using genes and proteins as building blocks to create new kinds of cell and new functions for cells. If scientists can build genes from scratch, they can create organisms with new traits. They can create bacteria that can clean up oil spills, rice with genes that keep the plant infection-free, or cells that can churn out new materials. Synthetic biology, the field that revolves around figuring out how to combine genes in new and interesting ways, requires an understanding of biology, creative engineering skills and computing expertise. It is pulling together scientists with different capabilities to solve problems....."
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Experts say at least $20 million to $30 million in government research is needed over the next decade to adequately identify and address the possible ecological risks of synthetic biology, an emerging area of research focused on the design and...
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"This paper describes the development of synthetic biology as a distinct entity from current industrial biotechnology and the implications for a future based on its concepts. The role of the engineering design cycle, in synthetic biology is established and the difficulties in making and exact analogy between the two emphasised. It is suggested that process engineers can offer experience in the application of synthetic biology to the manufacture of products which should influence the approach of the synthetic biologist. The style of teaching for synthetic biology appears to offer a new approach at undergraduate level and the challenges to the education of process engineers in this technology are raised. Possible routes to the development of synthetic biology teaching are suggested...."
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via G+ Jeff Sayre "A new study that shows more flexibility in the brain than previously thought could be a major boost to the development of mind-controlled neuroprosthetic devices that feel natural."
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"The Center for PostNatural History is a distinct crossbreed between a museum and an art gallery. Friday marked the grand opening of its permanent exhibition facility, located at 4913 Penn Ave. Richard Pell, a Carnegie Mellon professor of art and director of the Center for PostNatural History, is the founder of this space. The term “post-natural” refers to genetically altered living organisms. According to the center’s website, its intent is to “acquire, interpret and provide access to a collection of living, preserved and documented organisms of post-natural origin.” The exhibit allows access to a wealth of knowledge about the relationships among culture, nature, and biotechnology. Upon entering, visitors are guided under a dark arch into a dimly lit room with ambient noises quietly adding to the atmosphere. Large, bookcase-like structures tower next to the entrance. Nestled in these dark, wooden barriers are glass windows that provide a glimpse of tiny, intricate dioramas created by Craig Tompkins, an artist based in Santa Fe, New Mexico. These dioramas represent different environments that harbor genetically altered species, such as a military goat farm generating “biosteel goats.” The glass windows also contain a fish tank of Glofish, or zebra fish, a transgenic organism. Edward Wojciechowski III, a first-year linguistics major, said, “I thought it was interesting that they had live organisms. Like, I definitely had those fish as a kid. It was all very familiar.” Other sections of the exhibit display more of these cases, each with a specimen and a phone that viewers can pick up in order to learn the history of the modified organism. These cases include a variety of samples, including sea monkeys and the testicles of a castrated domestic cat. The specimens featured in the exhibit are all donations. A larger portion of the exhibit has a wall dedicated to the Dugway Proving Ground, the largest biological weapons testing site in the United States. The location is illustrated by an eerie landscape photograph of the Utah Granite Peak Installation, accompanied by an aerial view of the land. A pulsating circular projection of the ground inhabits the wall next to the pictures. “For quite a lot of bacterial pathogens, this is their one sort of habitat that exists outside the lab,” Pell explained, when asked why the projection was there. The idea for the exhibit goes back as far as 2005, though the development of the physical space started just a year ago. Pell originally began working with engineers in the field of synthetic biology....."
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The first publicly available iTunes U site. A comprehensive online audio and video collection from Stanford University. Celebrating 5 years of edutechnosharification.
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From
www
"DNA computing, also known as molecular computing, is a new approach to massively parallel computation based on groundbreaking work by Adleman. He used DNA to solve a seven-node Hamiltonian path problem, a special case of an NP-complete problem that attempts to visit every node in a graph exactly once. (This special case is trivial to solve with a conventional computer, or even by hand, but illustrates the potential of DNA computing.)
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"I met Raymond last summer at Singularity University where he is the Co-Chair of Biotechnology & Bioinformatics.
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Genetically Engineered Bacteria Could Help Fight Climate Change - ScienceNOW...
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This week’s issue of Nature includes a special Outlook supplement, Lenses on Biology. The 5 lenses are essays adapted from chapters in a new, interactive undergraduate textbook, Principles of Biology, published by Nature Education. The essays focus on what we know about cancer, stem cells, synthetic biology, ocean health and climate change.
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"Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly.
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"We are poorly prepared to deal with the consequences of an unstable earth.The recent events of March 11 in Japan - earthquake, tsunami causing nuclear radiation leaks remind us just how ill equipped we really are … And the shocking thing is that Japan was as prepared for disaster as it could possible be – it had the latest early advanced warning systems, houses are built to withstand tremors, communications systems are switched to information channels as the disaster unfolds and from an early age children are taught earthquake survival skills .."
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Join the NO. 1 Synthetic Biology competition. The Europe Regional Jamboree for iGEM 2012 will be hosted by VU University Amsterdam, University of Amsterdam, Delft University of Technology, Wageningen University and University of Groningen. For more information check the iGEM websites:
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"Experts say at least $20 million to $30 million in government research is needed over the next decade to adequately identify and address the possible ecological risks of synthetic biology, an emerging area of research focused on the design and construction of new biological parts and systems, or modification of existing ones, to create new applications in areas ranging from energy to chemicals and pharmaceuticals. Without key research into these risks and appropriate federal oversight, certain synthetic organisms might survive and flourish in natural environments, wreaking havoc on local ecosystems, according to a new Commentary piece in the journal Nature ("Four Steps to Stop a Synthetic-Biology Disaster," March 1). The article -- written by Genya V. Dana, Todd Kuiken and David Rejeski of the Synthetic Biology Project at the Woodrow Wilson International Center for Scholars and Allison A. Snow of Ohio State University -- highlights the need to proactively address environmental risks so that the potential benefits of synthetic biology can be realized. "No one yet understands the risks that synthetic organisms pose to the environment, what kinds of information are needed to support rigorous assessments, or who should collect such data," the authors write...."
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