Category Archives: synthetic biology

Funding trends for US synthetic biology efforts

Less than 1% of total US federal funding for synthetic biology is dedicated to risk research according to a Sept. 16, 2015 Woodrow Wilson International Center for Scholars news release on EurekAlert,

A new analysis by the Synthetic Biology Project at the Wilson Center finds the Defense Department and its Defense Advanced Research Projects Agency (DARPA) fund much of the U.S. government’s research in synthetic biology, with less than 1 percent of total federal funding going to risk research.

The report, U.S. Trends in Synthetic Biology Research, finds that between 2008 and 2014, the United States invested approximately $820 million dollars in synthetic biology research. In that time period, the Defense Department became a key funder of synthetic biology research. DARPA’s investments, for example, increased from near zero in 2010 to more than $100 million in 2014 – more than three times the amount spent by the National Science Foundation (NSF).

The Wilson Center news release can also be found here on the Center’s report publication page where it goes on to provide more detail and where you can download the report,

The report, U.S. Trends in Synthetic Biology Research, finds that between 2008 and 2014, the United States invested approximately $820 million dollars in synthetic biology research. In that time period, the Defense Department became a key funder of synthetic biology research. DARPA’s investments, for example, increased from near zero in 2010 to more than $100 million in 2014 – more than three times the amount spent by the National Science Foundation (NSF).

“The increase in DARPA research spending comes as NSF is winding down its initial investment in the Synthetic Biology Engineering Research Center, or SynBERC,” says Dr. Todd Kuiken, senior program associate with the project. “After the SynBERC funding ends next year, it is unclear if there will be a dedicated synthetic biology research program outside of the Pentagon. There is also little investment addressing potential risks and ethical issues, which can affect public acceptance and market growth as the field advances.”

The new study found that less than one percent of the total U.S. funding is focused on synthetic biology risk research and approximately one percent addresses ethical, legal, and social issues.

Internationally, research funding is increasing. Last year, research investments by the European Commission and research agencies in the United Kingdom exceeded non-defense spending in the United States, the report finds.

The research spending comes at a time of growing interest in synthetic biology, particularly surrounding the potential presented by new gene-editing techniques. Recent research by the industry group SynBioBeta indicated that, so far in 2015, synthetic biology companies raised half a billion dollars – more than the total investments in 2013 and 2014 combined.

In a separate Woodrow Wilson International Center for Scholars Sept. 16, 2015 announcement about the report, an upcoming event notice was included,

Save the date: On Oct. 7, 2015, the Synthetic Biology Project will be releasing a new report on synthetic biology and federal regulations. More details will be forthcoming, but the report release will include a noon event [EST] at the Wilson Center in Washington, DC.

I haven’t been able to find any more information about this proposed report launch but you may want to check the Synthetic Biology Project website for details as they become available. ETA Oct. 1, 2015: The new report titled: Leveraging Synthetic Biology’s Promise and Managing Potential Risk: Are We Getting It Right? will be launched on Oct. 15, 2015 according to an Oct. 1, 2015 notice,

As more applications based on synthetic biology come to market, are the existing federal regulations adequate to address the risks posed by this emerging technology?

Please join us for the release of our new report, Leveraging Synthetic Biology’s Promise and Managing Potential Risk: Are We Getting It Right? Panelists will discuss how synthetic biology applications would be regulated by the U.S. Coordinated Framework for Regulation of Biotechnology, how this would affect the market pathway of these applications and whether the existing framework will protect human health and the environment.

A light lunch will be served.


Lynn Bergeson, report author; Managing Partner, Bergeson & Campbell

David Rejeski, Director, Science and Technology Innovation Program

Thursday,October 15th, 2015
12:00pm – 2:00pm

6th Floor Board Room


Wilson Center
Ronald Reagan Building and
International Trade Center
One Woodrow Wilson Plaza
1300 Pennsylvania, Ave., NW
Washington, D.C. 20004

Phone: 202.691.4000


Safety mechanisms needed before synthetic biology moves from the labs into the real world

A Sept. 17, 2015 news item on Nanotechnology Now makes note of an article where experts review the state of the synthetic biology field and discuss the need for safety as synthetic biology is poised to move from the laboratory into the real world,

Targeted cancer treatments, toxicity sensors and living factories: synthetic biology has the potential to revolutionize science and medicine. But before the technology is ready for real-world applications, more attention needs to be paid to its safety and stability, say experts in a review article published in Current Opinion in Chemical Biology.

Synthetic biology involves engineering microbes like bacteria to program them to behave in certain ways. For example, bacteria can be engineered to glow when they detect certain molecules, and can be turned into tiny factories to produce chemicals.

Synthetic biology has now reached a stage where it’s ready to move out of the lab and into the real world, to be used in patients and in the field. According to Professor Pamela Silver, one of the authors of the article from Harvard Medical School in the US, this move means researchers should increase focus on the safety of engineered microbes in biological systems like the human body.

A Sept. 16, 2015 Elsevier press release, which originated the news item, expands on the theme,

“Historically, molecular biologists engineered microbes as industrial organisms to produce different molecules,” said Professor Silver. “The more we discovered about microbes, the easier it was to program them. We’ve now reached a very exciting phase in synthetic biology where we’re ready to apply what we’ve developed in the real world, and this is where safety is vital.”

Microbes have an impact on health; the way they interact with animals is being ever more revealed by microbiome research – studies on all the microbes that live in the body – and this is making them easier and faster to engineer. Scientists are now able to synthesize whole genomes, making it technically possible to build a microbe from scratch.

“Ultimately, this is the future – this will be the way we program microbes and other cell types,” said Dr. Silver. “Microbes have small genomes, so they’re not too complex to build from scratch. That gives us huge opportunities to design them to do specific jobs, and we can also program in safety mechanisms.”

One of the big safety issues associated with engineering microbial genomes is the transfer of their genes to wild microbes. Microbes are able to transfer segments of their DNA during reproduction, which leads to genetic evolution. One key challenge associated with synthetic biology is preventing this transfer between the engineered genome and wild microbial genomes.

There are already several levels of safety infrastructure in place to ensure no unethical research is done, and the kinds of organisms that are allowed in laboratories. The focus now, according to Dr. Silver, is on technology to ensure safety. When scientists build synthetic microbes, they can program in mechanisms called kill switches that cause the microbes to self-destruct if their environment changes in certain ways.

Microbial sensors and drug delivery systems can be shown to work in the lab, but researchers are not yet sure how they will function in a human body or a large-scale bioreactor. Engineered organisms have huge potential, but they will only be useful if proven to be reliable, predictable, and cost effective. Today, engineered bacteria are already in clinical trials for cancer, and this is just the beginning, says Dr. Silver.

“The rate at which this field is moving forward is incredible. I don’t know what happened – maybe it’s the media coverage, maybe the charisma – but we’re on the verge of something very exciting. Once we’ve figured out how to make genomes more quickly and easily, synthetic biology will change the way we work as researchers, and even the way we treat diseases.”

Lucy Goodchild van Hilten has written a Sept. 16, 2015 article for Elsevier abut this paper,

In January, the UK government announced a funding injection of £40 million to boost synthetic biology research, adding three new Synthetic Biology Research Centres (SBRCs) in Manchester, Edinburgh and Warwick. The additional funding takes the UK’s total public spending on synthetic biology to £200 million – an investment that hints at the commercial potential of synthetic biology.

In fact, according to the authors of a new review published in Current Opinion in Chemical Biology, synthetic biology has the potential to revolutionize science and medicine. …

Here’s a link to and a citation for the paper,

Synthetic biology expands chemical control of microorganisms by Tyler J Ford, Pamela A Silver. Current Opinion in Chemical Biology Volume 28, October 2015, Pages 20–28  doi:10.1016/j.cbpa.2015.05.012

I believe this paper is open access until January 16, 2016.

As the paper has a nice introductory description of synthetic biology, I thought I’d include it here, as well as, the conclusion which is not as safety-oriented as I expected,

Synthetic biology allows scientists to re-program interactions between genes, proteins, and small molecules. One of the goals of synthetic biology is to produce organisms that predictably carry out desired functions and thereby perform as well-controlled so-called biological devices. Together, synthetic and chemical biology can provide increased control over biological systems by changing the ways these systems respond to and produce chemical stimuli. Sensors, which detect small molecules and direct later cellular function, provide the basis for chemical control over biological systems. The techniques of synthetic biology and metabolic engineering can link sensors to metabolic processes and proteins with many different activities. In this review we stratify the activities affected by sensors to three different levels: sensor-reporters that provide a simple read-out of small molecule levels, sensor-effectors that alter the behavior of single organisms in response to small molecules, and sensor effectors that coordinate the activities of multiple organisms in response to small molecules …


We have come to the point in synthetic biology where there are many lab-scale or proof-of-concept examples of chemically controlled systems useful to sense small molecules, treat disease, and produce commercially useful compounds. These systems have great potential, but more attention needs to be paid to their stability, efficacy, and safety. Being that the sensor-effectors discussed above function in living, evolving organisms, it is unclear how well they will retain function when distributed in a patient or in a large-scale bioreactor. Future efforts should focus on developing these sensor-effectors for real-world application. Engineered organisms will only be useful if we can prove that their functions are reliable, predictable, and cost effective.

Customizing bacteria (E. coli) into squares, circles, triangles, etc.

The academic paper for this latest research from Delft University of Technology (TU Delft, Netherlands), uses the term ‘bacterial sculptures,’ an intriguing idea that seems to have influenced the artistic illustration accompanying the research announcement.

Artistic rendering live E.coli bacteria that have been shaped into a rectangle, triangle, circle, and square (from front to back). Colors indicate the density of the Min proteins that represent a snapshot in time (based on actual data), as these proteins oscillate back and forth within the bacterium, to determine the mid plane of the cell for cellular division. Image credit:  ‘Image Cees Dekker lab TU Delft / Tremani’

Artistic rendering live E.coli bacteria that have been shaped into a rectangle, triangle, circle, and square (from front to back). Colors indicate the density of the Min proteins that represent a snapshot in time (based on actual data), as these proteins oscillate back and forth within the bacterium, to determine the mid plane of the cell for cellular division.
Image credit: ‘Image Cees Dekker lab TU Delft / Tremani’

A June 22, 2015 news item on Nanowerk provides more insight into the research (Note: A link has been removed),

The E.coli bacterium, a very common resident of people’s intestines, is shaped as a tiny rod about 3 micrometers long. For the first time, scientists from the Kavli Institute of Nanoscience at Delft University have found a way to use nanotechnology to grow living E.coli bacteria into very different shapes: squares, triangles, circles, and even as letters spelling out ‘TU Delft’. They also managed to grow supersized E.coli with a volume thirty times larger than normal. These living oddly-shaped bacteria allow studies of the internal distribution of proteins and DNA in entirely new ways.

In this week’s Nature Nanotechnology (“Symmetry and scale orient Min protein patterns in shaped bacterial sculptures”), the scientists describe how these custom-designed bacteria still manage to perfectly locate ‘the middle of themselves’ for their cell division. They are found to do so using proteins that sense the cell shape, based on a mathematical principle proposed by computer pioneer Alan Turing in 1953.

A June 22, 2015 TU Delft press release, which originated the news item, expands on the theme,

Cell division

“If cells can’t divide properly, biological life wouldn’t be possible. Cells need to distribute their cell volume and genetic materials equally into their daughter cells to proliferate.”, says prof. Cees Dekker, “It is fascinating that even a unicellular organism knows how to divide very precisely. The distribution of certain proteins in the cell is key to regulating this, but how exactly do those proteins get that done?”


As the work of the Delft scientist exemplifies, the key here is a process discovered by the famous Alan Turing in 1953. Although Turing is mostly known for his role in deciphering the Enigma coding machine and the Turing Test, the impact of his ‘reaction-diffusion theory’ on biology might be even more spectacular. He predicted how patterns in space and time emerge as the result of only two molecular interactions – explaining for instance how a zebra gets its stripes, or how an embryo hand develops five fingers.

MinD and MinE

Such a Turing process also acts with proteins within a single cell, to regulate cell division. An E.coli cell uses two types of proteins, known as MinD and MinE, that bind and unbind again and again at the inner surface of the bacterium, thus oscillating back and forth from pole to pole within the bacterium every minute. “This results in a low average concentration of the protein in the middle and high concentrations at the ends, which drives the division machinery to the cell center”, says PhD-student Fabai Wu, who ran the experiments. “As our experiments show, the Turing patterns allow the bacterium to determine its symmetry axes and its center. This applies to many bacterial cell shapes that we custom-designed, such as squares, triangles and rectangles of many sizes. For fun, we even made ‘TUDelft’ and ‘TURING’ letters. Using computer simulations, we uncovered that the shape-sensing abilities are caused by simple Turing-type interactions between the proteins.”

Actual data for live E.coli bacteria that have been shaped into the letters TUDELFT.
The red color shows the cytosol contents of the cell, while the green color shows the density of the Min proteins, representing a snapshot in time, as these proteins oscillate back and forth within the bacterium to determine the mid plane of the cell for cellular division. The letters are about 5 micron high.
Image credit:  ‘Fabai Wu, Cees Dekker lab at TU Delft’

Spatial control for building synthetic cells

“Discovering this process is not only vital for our understanding of bacterial cell division – which is important in developing new strategies for antibiotics. But the approach will likely also be fruitful to figuring out how cells distribute other vital systems within a cell, such as chromosomes”, says Cees Dekker. “The ultimate goal in our research is to be able to completely build a living cell from artificial components, as that is the only way to really understand how life works. Understanding cell division – both the process that actually pinches off the cell into two daughters and the part that spatially regulates that machinery – is a major part of that.”

Here’s a link to and a citation for the paper,

Symmetry and scale orient Min protein patterns in shaped bacterial sculptures by Fabai Wu, Bas G. C. van Schie, Juan E. Keymer, & Cees Dekker. Nature Nanotechnology (2015) doi:10.1038/nnano.2015.126 Published online 22 June 2015

This paper is behind a paywall but there does seem to be another link (in the excerpt below) which gives you a free preview via ReadCube Access (according to the TU Delft press release),

The DOI for this paper will be 10.1038/nnano.2015.126. Once the paper is published electronically, the DOI can be used to retrieve the abstract and full text by adding it to the following url:


DNA (deoxyribonucleic acid), music, and data storage

David Bruggeman (Pasco Phronesis blog) has written up, as he so often does, a fascinating art/science piece in his May 28, 2015 post (Note: A link has been removed),

Opening next month [June 2015] at the Dilston Grove Gallery at GDP London is Music of the Spheres, an exhibition that uses bioinformatics to record music.  Dr. Nick Goldman of the European Bioinformatics Institute has been working on new technologies for encoding large amounts of information into DNA.  Collaborating with Charlotte Jarvis, the two have worked on installations of bubbles that would contain DNA encoded with music (the DNA is suspended in soap solution).

There’s more information about the exhibit on the Music of the Spheres webpage on the CGP London website,

Music of the Spheres utilises new bioinformatics technology developed by Dr. Nick Goldman to encode a new musical recording by the Kreutzer Quartet into DNA.

The DNA has been suspended in soap solution and will be used by visual artist Charlotte Jarvis to create performances and installations filled with bubbles. The recording will fill the air, pop on visitors skin and literally bathe the audience in music.

Dr. Nick Goldman and Charlotte Jarvis have been working together for the past year to create a series of moving visual and musical experiences that explore the scope and future ubiquity of DNA technologies.

The Kreutzer Quartet’s new composition for string quartet loosely follows the traditional form of a concerto, in comprising of three musical movements. The second movement only exists in the form of a recording encoded into DNA.

For the exhibition the DNA will be suspended in soap solution and used to create silent installations filled with bubbles. The bubbles will be accompanied by a video projection showing the musicians playing in the server room of the European Bioinformatics Institute, Cambridge.

In response to the growing challenge of storing vast quantities of biological data generated by biomedical research Dr. Nick Goldman and the European Bioinformatics Institute have developed a method to encode huge amounts of information in DNA itself. Every day the huge quantities and speed of data pouring into servers gets larger. When research groups sequence DNA the file sizes are too large to be kept on local computers. It is this problem that was the motivation for Nick Goldman to develop his new technology. Their goal is a system that will safely store the equivalent of one million CDs in a gram of DNA for 10,000 years. Nick’s work was has been featured in The New York Times, The Guardian and on BBC News amongst other media outlets.

The Kreutzer Quartet will play the full-length composition live during the preview on 12 June [2015] timed with the setting of the sun through the large westerly windows. [emphasis mine] During the passage of the second movement the stage will fall silent, the music will be released into the auditorium in the form of bubbles. The performance will be accompanied by film projection and a discussion about the project.

The exhibit runs from June 12 – July 5, 2015. Hours and location can be found on the CGP website.

The Music of the Spheres DNA/music project was first mentioned here in a May 5, 2014 post about the launch of the book ‘Synthetic Aesthetics: Investigating Synthetic Biology’s Designs on Nature’. The launch featured a number of performances and events, scroll down abut 80% of the way for the then description of Music of the Spheres.

Synthetic Aesthetics update and an informal Canadian synthetic biology roundup

Amanda Ruggeri has written a very good introduction to synthetic biology for nonexperts in her May 20, 2015 Globe and Mail article about ‘Designing for the Sixth Extinction’, an exhibit showcasing designs and thought experiments focused on synthetic biology ,

In a corner of Istanbul’s Design Biennial late last year [2014], photographs of bizarre creatures sat alongside more conventional displays of product design and typefaces. Diaphanous globes, like transparent balloons, clung to the mossy trunk of an oak tree. Rust-coloured patterns ran across green leaves, as if the foliage had been decorated with henna. On the forest floor, a slug-like creature slithered, its back dotted with gold markings; in another photograph, what looked like a porcupine without a head crawled over the dirt, its quills tipped blood-red.

But as strange as the creatures looked, what they actually are is even stranger. Not quite living things, not quite machines, these imagined prototypes inhabit a dystopic, future world – a world in which they had been created to solve the problems of the living. The porcupine, for example, is an Autonomous Seed Disperser, described as a device that would collect and disperse seeds to increase biodiversity. The slug would be programmed to seek out acidic soils and neutralize them by dispersing an alkali hygroscopic fluid.

They are the designs – and thought experiments – of London-based Alexandra Daisy Ginsberg, designer, artist and lead author of the book Synthetic Aesthetics: Investigating Synthetic Biology’s Designs on Nature. In her project Designing for the Sixth Extinction, which after Istanbul is now on display at the Design Museum in London, Ginsberg imagines what a synthetic biology-designed world would look like – and whether it’s desirable. “

I have a couple of comments. First, the ‘Synthetic Aesthetics: Investigating Synthetic Biology’s Designs on Nature’ book launch last year was covered here in a May 5, 2014 post. where you’ll notice a number of the academics included in Ruggeri’s article are contributors to the book (but not mentioned as such). Second, I cannot find ‘Design for the Sixth Extinction’ listed as an exhibition on London’s Design Museum website.

Getting back to the matter at hand, not all of the projects mentioned in Ruggeri’s article are ‘art’ projects, there is also this rather practical and controversial initiative,

Designing even more complex organisms is the inevitable, and controversial, next step. And those designs have already begun. The British company Oxitec has designed a sterile male mosquito. When the bugs are released into nature and mate, no offspring result, reducing the population or eliminating it altogether. This could be a solution to dengue fever, a mosquito-carried disease that infects more than 50 million people each year: In field trials in Cayman, Panama and Brazil, the wild population of the dengue-carrying mosquito species was reduced by 90 per cent. Yet, as a genetically engineered solution, it also makes some skittish. The consequences of such manipulations remain unforeseen, they say. Proponents counter that the solution is more elegant, and safer, than the current practice of spraying chemicals.

Even so, the engineered mosquito leads to overarching questions: What are the dangers of tinkering with life? Could this cause a slide toward eugenics? Currently, the field doesn’t have an established ethics oversight process, something some critics are pushing to change.

It’s a surprising piece for the Globe and Mail newspaper to run since it doesn’t have a Canadian angle to it and the Globe and Mail doesn’t specialize in science (not withstanding Ivan Semeniuk’s science articles) or art/science or synthetic biology writing, for that matter. Perhaps it bodes an interest and more pieces on emerging science and technology and on art/science projects?

In any event, it seems like a good time to review some of the synthetic biology work or the centres of activity in Canada.  I believe the last time I tackled this particular topic was in a May 24, 2010 post titled, Canada and synthetic biology in the wake of the first ‘synthetic’ bacteria.

After a brief search, I found three centres for research:

Concordia [University] Centre for Applied Synthetic Biology (CASB)

[University of Toronto] The Synthetic Biology and Cellular Control Lab

[University of British Columbia] Centre for High-Throughput Biology (CHiBi)

Following an Oct. 27 – 28, 2014 UK-Canada Synthetic Biology Workshop held at Concordia University, Rémi Quirion, Vincent Martin, Pierre Meulien and Marc LePage co-wrote a Nov. 4, 2014 Concordia University post titled, How Canada is poised to revolutionize synthetic biology,

Rémi Quirion is the Chief Scientist of Québec, Fonds de recherche du Québec. Vincent Martin is Canada Research Chair in Microbial Genomics and Engineering and a professor in the Department of Biology at Concordia University in Montreal. Pierre Meulien is President and CEO of Genome Canada. Marc LePage is the President and CEO of Génome Québec.

Canada’s research and business communities have an opportunity to become world leaders in a burgeoning field that is fast shaping how we deal with everything from climate change to global food security and the production of lifesaving medications. The science of synthetic biology has the transformative capacity to equip us with novel technology tools and products to build a more sustainable society, while creating new business and employment opportunities for the economy of tomorrow.

We can now decipher the code of life for any organism faster and less expensively than ever before. Canadian scientists are producing anti-malarial drugs from organic materials that increase the availability and decrease the cost of lifesaving medicines. They are also developing energy efficient biofuels to dramatically reduce environmental and manufacturing costs, helping Canadian industry to thrive in the global marketplace.

The groundwork has also been laid for a Canadian revolution in the field. Canada’s scientific community is internationally recognized for its leadership in genomics research and strong partnerships with key industries. Since 2000, Genome Canada and partners have invested more than $2.3 billion in deciphering the genomes of economically important plants, animals and microbes in order to understand how they function. A significant proportion of these funds has been invested in building the technological toolkits that can be applied to synthetic biology.

But science cannot do it alone. Innovation on this scale requires multiple forms of expertise in order to be successful. Research in law, business, social sciences and humanities is vital to addressing questions of ethics, supply chain management, social innovation and cultural adaptation to new technologies. Industry knowledge and investments, as well as the capacity to incentivize entrepreneurship, are key to devising business models that will enable new products to thrive. Governments and funding agencies also need to do their part by supporting multidisciplinary research, training and infrastructure.

It’s a bit ‘hype happy’ for my taste but it does provide some fascinating insight in what seems to be a male activity in Canada.

Counterbalancing that impression is an Oct. 6, 2013 article by Ivan Semeniuk for the Globe and Mail about a University of Lethbridge team winning the top prize in a synthetic biology contest,

If you want to succeed in the scientific revolution of the future, it helps to think about life as a computer program.

That strategy helped University of Lethbridge students walk away with the top prize in a synthetic biology competition Sunday. Often touted as the genetic equivalent of the personal computer revolution, synthetic biology involves thinking about cells as programmable machines that can be designed and built to suit a particular need – whether it’s mass producing a vaccine or breaking down a hazardous chemical in the environment.

The five member Lethbridge team came up with a way to modify how cells translate genetic information into proteins. Rather than one bit of DNA carrying the information to make one protein – the usual way cells go about their business – the method involves inserting a genetic command that jiggles a cell’s translational machinery while it’s in mid-operation, coaxing it to produce two proteins out of the same DNA input.

“We started off with a computer analogy – kind of like zipping your files together – so you’d zip two protein sequences together and therefore save space,” said Jenna Friedt, a graduate student in biochemistry at Lethbridge. [emphasis mine]

There are concerns other than gender issues, chief amongst them, ethics. The Canadian Biotechnology Action Network maintains an information page on Synthetic Biology which boasts this as its latest update,

October 2014: In a unanimous decision of 194 countries, the United Nation’s Convention on Biological Diversity formally urged countries to regulate synthetic biology, a new extreme form of genetic engineering. The landmark decision follows ten days of hard-fought negotiations between developing countries and a small group of wealthy biotech-friendly economies. Until now, synthetic organisms have been developed and commercialized without international regulations. …

Finally, there’s a June 2014 synthetic biology timeline from the University of Ottawa’s Institute for Science, Society, and Policy (ISSP) which contextualizes Canadian research, policy and regulation with Australia, the European Union, the UK, and the US.

(On a closely related note, there’s my May 14, 2015 post about genetic engineering and newly raised concerns.)

I sing the body cyber: two projects funded by the US National Science Foundation

Points to anyone who recognized the reference to Walt Whitman’s poem, “I sing the body electric,” from his classic collection, Leaves of Grass (1867 edition; h/t Wikipedia entry). I wonder if the cyber physical systems (CPS) work being funded by the US National Science Foundation (NSF) in the US will occasion poetry too.

More practically, a May 15, 2015 news item on Nanowerk, describes two cyber physical systems (CPS) research projects newly funded by the NSF,

Today [May 12, 2015] the National Science Foundation (NSF) announced two, five-year, center-scale awards totaling $8.75 million to advance the state-of-the-art in medical and cyber-physical systems (CPS).

One project will develop “Cyberheart”–a platform for virtual, patient-specific human heart models and associated device therapies that can be used to improve and accelerate medical-device development and testing. The other project will combine teams of microrobots with synthetic cells to perform functions that may one day lead to tissue and organ re-generation.

CPS are engineered systems that are built from, and depend upon, the seamless integration of computation and physical components. Often called the “Internet of Things,” CPS enable capabilities that go beyond the embedded systems of today.

“NSF has been a leader in supporting research in cyber-physical systems, which has provided a foundation for putting the ‘smart’ in health, transportation, energy and infrastructure systems,” said Jim Kurose, head of Computer & Information Science & Engineering at NSF. “We look forward to the results of these two new awards, which paint a new and compelling vision for what’s possible for smart health.”

Cyber-physical systems have the potential to benefit many sectors of our society, including healthcare. While advances in sensors and wearable devices have the capacity to improve aspects of medical care, from disease prevention to emergency response, and synthetic biology and robotics hold the promise of regenerating and maintaining the body in radical new ways, little is known about how advances in CPS can integrate these technologies to improve health outcomes.

These new NSF-funded projects will investigate two very different ways that CPS can be used in the biological and medical realms.

A May 12, 2015 NSF news release (also on EurekAlert), which originated the news item, describes the two CPS projects,

Bio-CPS for engineering living cells

A team of leading computer scientists, roboticists and biologists from Boston University, the University of Pennsylvania and MIT have come together to develop a system that combines the capabilities of nano-scale robots with specially designed synthetic organisms. Together, they believe this hybrid “bio-CPS” will be capable of performing heretofore impossible functions, from microscopic assembly to cell sensing within the body.

“We bring together synthetic biology and micron-scale robotics to engineer the emergence of desired behaviors in populations of bacterial and mammalian cells,” said Calin Belta, a professor of mechanical engineering, systems engineering and bioinformatics at Boston University and principal investigator on the project. “This project will impact several application areas ranging from tissue engineering to drug development.”

The project builds on previous research by each team member in diverse disciplines and early proof-of-concept designs of bio-CPS. According to the team, the research is also driven by recent advances in the emerging field of synthetic biology, in particular the ability to rapidly incorporate new capabilities into simple cells. Researchers so far have not been able to control and coordinate the behavior of synthetic cells in isolation, but the introduction of microrobots that can be externally controlled may be transformative.

In this new project, the team will focus on bio-CPS with the ability to sense, transport and work together. As a demonstration of their idea, they will develop teams of synthetic cell/microrobot hybrids capable of constructing a complex, fabric-like surface.

Vijay Kumar (University of Pennsylvania), Ron Weiss (MIT), and Douglas Densmore (BU) are co-investigators of the project.

Medical-CPS and the ‘Cyberheart’

CPS such as wearable sensors and implantable devices are already being used to assess health, improve quality of life, provide cost-effective care and potentially speed up disease diagnosis and prevention. [emphasis mine]

Extending these efforts, researchers from seven leading universities and centers are working together to develop far more realistic cardiac and device models than currently exist. This so-called “Cyberheart” platform can be used to test and validate medical devices faster and at a far lower cost than existing methods. CyberHeart also can be used to design safe, patient-specific device therapies, thereby lowering the risk to the patient.

“Innovative ‘virtual’ design methodologies for implantable cardiac medical devices will speed device development and yield safer, more effective devices and device-based therapies, than is currently possible,” said Scott Smolka, a professor of computer science at Stony Brook University and one of the principal investigators on the award.

The group’s approach combines patient-specific computational models of heart dynamics with advanced mathematical techniques for analyzing how these models interact with medical devices. The analytical techniques can be used to detect potential flaws in device behavior early on during the device-design phase, before animal and human trials begin. They also can be used in a clinical setting to optimize device settings on a patient-by-patient basis before devices are implanted.

“We believe that our coordinated, multi-disciplinary approach, which balances theoretical, experimental and practical concerns, will yield transformational results in medical-device design and foundations of cyber-physical system verification,” Smolka said.

The team will develop virtual device models which can be coupled together with virtual heart models to realize a full virtual development platform that can be subjected to computational analysis and simulation techniques. Moreover, they are working with experimentalists who will study the behavior of virtual and actual devices on animals’ hearts.

Co-investigators on the project include Edmund Clarke (Carnegie Mellon University), Elizabeth Cherry (Rochester Institute of Technology), W. Rance Cleaveland (University of Maryland), Flavio Fenton (Georgia Tech), Rahul Mangharam (University of Pennsylvania), Arnab Ray (Fraunhofer Center for Experimental Software Engineering [Germany]) and James Glimm and Radu Grosu (Stony Brook University). Richard A. Gray of the U.S. Food and Drug Administration is another key contributor.

It is fascinating to observe how terminology is shifting from pacemakers and deep brain stimulators as implants to “CPS such as wearable sensors and implantable devices … .” A new category has been created, CPS, which conjoins medical devices with other sensing devices such as wearable fitness monitors found in the consumer market. I imagine it’s an attempt to quell fears about injecting strange things into or adding strange things to your body—microrobots and nanorobots partially derived from synthetic biology research which are “… capable of performing heretofore impossible functions, from microscopic assembly to cell sensing within the body.” They’ve also sneaked in a reference to synthetic biology, an area of research where some concerns have been expressed, from my March 19, 2013 post about a poll and synthetic biology concerns,

In our latest survey, conducted in January 2013, three-fourths of respondents say they have heard little or nothing about synthetic biology, a level consistent with that measured in 2010. While initial impressions about the science are largely undefined, these feelings do not necessarily become more positive as respondents learn more. The public has mixed reactions to specific synthetic biology applications, and almost one-third of respondents favor a ban “on synthetic biology research until we better understand its implications and risks,” while 61 percent think the science should move forward.

I imagine that for scientists, 61% in favour of more research is not particularly comforting given how easily and quickly public opinion can shift.

Life-on-a-chip; protein synthesis could be possible with artificial cells

An Aug. 18, 2014 Weizmann Institute of Science (Israel) news release (also on EurekAlert but dated Aug. 19, 2014) describes an artificial cell system and its ability to synthesize protein,

Imitation, they say, is the sincerest form of flattery, but mimicking the intricate networks and dynamic interactions that are inherent to living cells is difficult to achieve outside the cell. Now, as published in Science, Weizmann Institute scientists have created an artificial, network-like cell system that is capable of reproducing the dynamic behavior of protein synthesis. This achievement is not only likely to help gain a deeper understanding of basic biological processes, but it may, in the future, pave the way toward controlling the synthesis of both naturally-occurring and synthetic proteins for a host of uses.

The system, designed by PhD students Eyal Karzbrun and Alexandra Tayar in the lab of Prof. Roy Bar-Ziv of the Weizmann Institute’s Materials and Interfaces Department, in collaboration with Prof. Vincent Noireaux of the University of Minnesota, comprises multiple compartments “etched” onto a biochip. These compartments – artificial cells, each a mere millionth of a meter in depth – are connected via thin capillary tubes, creating a network that allows the diffusion of biological substances throughout the system. Within each compartment, the researchers insert a cell genome – strands of DNA designed and controlled by the scientists themselves. In order to translate the genes into proteins, the scientists relinquished control to the bacterium E. coli: Filling the compartments with E. coli cell extract – a solution containing the entire bacterial protein-translating machinery, minus its DNA code – the scientists were able to sit back and observe the protein synthesis dynamics that emerged.

By coding two regulatory genes into the sequence, the scientists created a protein synthesis rate that was periodic, spontaneously switching from periods of being “on” to “off.” The amount of time each period lasted was determined by the geometry of the compartments. Such periodic behavior – a primitive version of cell cycle events – emerged in the system because the synthesized proteins could diffuse out of the compartment through the capillaries, mimicking natural protein turnover behavior in living cells. At the same time fresh nutrients were continuously replenished, diffusing into the compartment and enabling the protein synthesis reaction to continue indefinitely. “The artificial cell system, in which we can control the genetic content and protein dilution times, allows us to study the relation between gene network design and the emerging protein dynamics. This is quite difficult to do in a living system,” says Karzbrun. “The two-gene pattern we designed is a simple example of a cell network, but after proving the concept, we can now move forward to more complicated gene networks. One goal is to eventually design DNA content similar to a real genome that can be placed in the compartments. ”

The scientists then asked whether the artificial cells actually communicate and interact with one another like real cells. Indeed, they found that the synthesized proteins that diffused through the array of interconnected compartments were able to regulate genes and produce new proteins in compartments farther along the network. In fact, this system resembles the initial stages of morphogenesis – the biological process that governs the emergence of the body plan in embryonic development. “We observed that when we place a gene in a compartment at the edge of the array, it creates a diminishing protein concentration gradient; other compartments within the array can sense and respond to this gradient – similar to how morphogen concentration gradients diffuse through the cells and tissues of an embryo during early development. We are now working to expand the system and to introduce gene networks that will mimic pattern formation, such as the striped patterns that appear during fly embryogenesis,” explains Tayar.

With the artificial cell system, according to Bar-Ziv, one can, in principle, encode anything: “Genes are like Lego in which you can mix and match various components to produce different outcomes; you can take a regulatory element from E. coli that naturally controls gene X, and produce a known protein; or you can take the same regulatory element but connect it to gene Y instead to get different functions that do not naturally occur in nature. ” This research may, in the future, help advance the synthesis of such things as fuel, pharmaceuticals, chemicals and the production of enzymes for industrial use, to name a few.

Here’s a link to and a citation for the paper,

Programmable on-chip DNA compartments as artificial cells by Eyal Karzbrun, Alexandra M. Tayar, Vincent Noireaux,and Roy H. Bar-Ziv. Science 15 August 2014: Vol. 345 no. 6198 pp. 829-832 DOI: 10.1126/science.1255550

This paper is behind a paywall.

While trying to find more information about the work on artificial cells and the Weizmann Institute, I discovered a Canadian chapter of what is, in addition to being a scientific research institute in Israel, a worldwide organization. Here’s more from the Weizmann Institute Canada About us webpage,

Weizmann Canada is part of a worldwide network of supporting organizations for the Weizmann Institute of Science, in Rehovot, Israel.

The Weizmann Institute is one of the world’s leading multidisciplinary research institutions. Hundreds of scientists, laboratory technicians and research students embark on fascinating journeys into the unknown. Every day, these researchers attempt to push the limits of scientific knowledge, exploring the Earth’s mysteries and making the world a better place.

Since 1964, Canadian supporters have helped fund some of the world’s most talented scientists who are conducting cutting-edge research, which has a major impact on the world we live in.

Behind every scientist, there is a donor who has made it possible for them to carry out their groundbreaking research.

With over 1200 research projects, there are over 1200 ways in which you can support the Weizmann Institute.

As I noted earlier today in an Aug. 19, 2014 posting about 14nm computer chips and limits to computation, the question about limits can be applied to other areas of endeavour including the creation of artificial cell systems.

Newcastle University (UK) has a PhD Studentship in Synthetic Biology and Nanotechnology available

Open to UK, European Union, and international students, the studentship deadline for applying is Aug. 18, 2014. Here’s more from the Newcastle University notice on the website (Note: Links have been removed),

PhD Studentship in Synthetic Biology and Nanotechnology – Towards Algorithmic Living Manufacturing (TALIsMAN)

Value, Duration and Start Date of the Award
The Doctoral Training Award is for £20,000 per annum. This award covers fees and a contribution to an annual stipend (living expenses).

Three year PhD

Start date: 14 September 2014

Science Agriculture and Engineering Faculty Doctoral Training Awards

Project Description
The discipline of Synthetic Biology (SB), considers the cell to be a machine that can be built -from parts- in a manner similar to, e.g., electronic circuits, airplanes, etc. SB has sought to co-opt cells for nano-computation and nano-manufacturing purposes. During this scholarship programme of doctoral studies the student will pursue investigations at the interface of computing science (biodesign & biomodeling), chemical sciences (nanoparticle delivery systems), microbiology (bacterial genetic engineering) and nanoscience (DNA origami).

Name of the Supervisors
Professor Natalio Krasnogor (Lead Supervisor), School of Computing Science

Dr David Fulton, School of Chemistry

Dr Chien-Yi Chang, Centre for Bacterial Cell Biology

Person Specification and Eligibility Criteria
You must have an MSc in synthetic biology, microbiology, organic chemistry or computing science. You also should have demonstrable independent research skills, e.g. having completed a successful MSc dissertation or having a publication in a recognised peer reviewed conference or, ideally, journal. The candidate must have substantial laboratory experience and excellent programming and numeracy skills.

This award is available to UK/EU and International candidates. If English is not your first language, you must have IELTS 6.5.

Closing Date for Applications
Applications will be considered until Monday 18 August 2014. However, awards may be made to successful applicants before this date and early application is recommended.

So according to the line above, it’s better to apply sooner rather than later. Good luck!

Sand and nanotechnology

There’s some good news coming out of the University of California, Riverside regarding sand and lithium-ion (li-ion) batteries, which I will temper with some additional information later in this posting.

First, the good news is that researchers have a new non-toxic, low cost way to produce a component in lithium-ion (li-ion) batteries according to a July 8, 2014 news item on ScienceDaily,

Researchers at the University of California, Riverside’s Bourns College of Engineering have created a lithium ion battery that outperforms the current industry standard by three times. The key material: sand. Yes, sand.

“This is the holy grail — a low cost, non-toxic, environmentally friendly way to produce high performance lithium ion battery anodes,” said Zachary Favors, a graduate student working with Cengiz and Mihri Ozkan, both engineering professors at UC Riverside.

The idea came to Favors six months ago. He was relaxing on the beach after surfing in San Clemente, Calif. when he picked up some sand, took a close look at it and saw it was made up primarily of quartz, or silicon dioxide.

His research is centered on building better lithium ion batteries, primarily for personal electronics and electric vehicles. He is focused on the anode, or negative side of the battery. Graphite is the current standard material for the anode, but as electronics have become more powerful graphite’s ability to be improved has been virtually tapped out.

A July 8, 2014 University of California at Riverside news release by Sean Nealon, which originated the news item, describes some of the problems with silicon as a replacement for graphite and how the researchers approached those problems,

Researchers are now focused on using silicon at the nanoscale, or billionths of a meter, level as a replacement for graphite. The problem with nanoscale silicon is that it degrades quickly and is hard to produce in large quantities.

Favors set out to solve both these problems. He researched sand to find a spot in the United States where it is found with a high percentage of quartz. That took him to the Cedar Creek Reservoir, east of Dallas, where he grew up.

Sand in hand, he came back to the lab at UC Riverside and milled it down to the nanometer scale, followed by a series of purification steps changing its color from brown to bright white, similar in color and texture to powdered sugar.

After that, he ground salt and magnesium, both very common elements found dissolved in sea water into the purified quartz. The resulting powder was then heated. With the salt acting as a heat absorber, the magnesium worked to remove the oxygen from the quartz, resulting in pure silicon.

The Ozkan team was pleased with how the process went. And they also encountered an added positive surprise. The pure nano-silicon formed in a very porous 3-D silicon sponge like consistency. That porosity has proved to be the key to improving the performance of the batteries built with the nano-silicon.

Now, the Ozkan team is trying to produce larger quantities of the nano-silicon beach sand and is planning to move from coin-size batteries to pouch-size batteries that are used in cell phones.

The research is supported by Temiz Energy Technologies. The UCR Office of Technology Commercialization has filed patents for inventions reported in the research paper.

Here’s a link to and a citation for the research paper,

Scalable Synthesis of Nano-Silicon from Beach Sand for Long Cycle Life Li-ion Batteries by Zachary Favors, Wei Wang, Hamed Hosseini Bay, Zafer Mutlu, Kazi Ahmed, Chueh Liu, Mihrimah Ozkan, & Cengiz S. Ozkan. Scientific Reports 4, Article number: 5623 doi:10.1038/srep05623 Published 08 July 2014

While this is good news, it does pose a conundrum of sorts. It seems that supplies of sand are currently under siege. A documentary, Sand Wars (2013) lays out the issues (from the Sand Wars website’s Synopsis page),

Most of us think of it as a complimentary ingredient of any beach vacation. Yet those seemingly insignificant grains of silica surround our daily lives. Every house, skyscraper and glass building, every bridge, airport and sidewalk in our modern society depends on sand. We use it to manufacture optical fiber, cell phone components and computer chips. We find it in our toothpaste, powdered foods and even in our glass of wine (both the glass and the wine, as a fining agent)!

Is sand an infinite resource? Can the existing supply satisfy a gigantic demand fueled by construction booms?  What are the consequences of intensive beach sand mining for the environment and the neighboring populations?

Based on encounters with sand smugglers, barefoot millionaires, corrupt politicians, unscrupulous real estate developers and environmentalists, this investigation takes us around the globe to unveil a new gold rush and a disturbing fact: the “SAND WARS” have begun.

Dr. Muditha D Senarath Yapa of John Keells Research at John Keells Holdings comments on the situation in Sri Lanka in his June 22, 2014 article (Nanotechnology – Depleting the most precious minerals for a few dollars) for The Nation,

Many have written for many years about the mineral sands of Pulmoddai. It is a national tragedy that for more than 50 years, we have been depleting the most precious minerals of our land for a few dollars. There are articles that appeared in various newspapers on how the mineral sands industry has boomed over the years. I hope the readers understand that it only means that we are depleting our resources faster than ever. According to the Lanka Mineral Sands Limited website, 90,000 tonnes of ilmenite, 9,000 tonnes of rutile, 5,500 tonnes of zircon, 100 tonnes of monazite and 4,000 tonnes of high titanium ilmenite are produced annually and shipped away to other countries.

… It is time for Sri Lanka to look at our own resources with this new light and capture the future nano materials market to create value added materials.

It’s interesting that he starts with the depletion of the sands as a national tragedy and ends with a plea to shift from a resource-based economy to a manufacturing-based economy. (This plea resonates strongly here in Canada where we too are a resource-based economy.)

Sidebar: John Keells Holdings is a most unusual company, from the About Us page,

In terms of market capitalisation, John Keells Holdings PLC is one of the largest listed conglomerate on the Colombo Stock Exchange. Other measures tell a similar tale; our group companies manage the largest number of hotel rooms in Sri Lanka, own the country’s largest privately-owned transportation business and hold leading positions in Sri Lanka’s key industries: tea, food and beverage manufacture and distribution, logistics, real estate, banking and information technology. Our investment in Sri Lanka is so deep and widely diversified that our stock price is sometimes used by international financial analysts as a benchmark of the country’s economy.

Yapa heads the companies research effort, which recently celebrated a synthetic biology agreement (from a May 2014 John Keells news release by Nuwan),

John Keells Research Signs an Historic Agreement with the Human Genetics Unit, Faculty of Medicine, University of Colombo to establish Sri Lanka’s first Synthetic Biology Research Programme.

Getting back to sand, these three pieces, ‘sand is good for li-ion batteries’, ‘sand is a diminishing resource’, and ‘let’s stop being a source of sand for other countries’ lay bare some difficult questions about our collective future on this planet.