Category Archives: synthetic biology

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 jobs.ac.uk 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

Sponsor
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.

Synthetic Aesthetics: a book and an event (UK’s Victoria & Albert Museum) about synthetic biology and design

Sadly, I found out about the event after it took place (April 25, 2014) but I’m including it here as I think it serves a primer on putting together an imaginative art/science (art/sci) event, as well, synthetic biology is a topic I’ve covered here many times.

First, the book. Happily, it’s not too late to publicize it and, after all, that was at least one of the goals for the event. Here’s more about the book, from the UK’s Engineering and Physical Sciences Research Council April 25, 2014 news release (also on EurekAlert),

The emerging field of synthetic biology crosses the boundary between science and design, in order to design and manufacture biologically based parts, devices and systems that do not exist in the natural world, as well as the redesign of existing, natural biological systems.

This new technology has the potential to create new organisms for a variety of applications from materials to machines. What role can artists and designers play in our biological future?

This Friday [April 25, 2014], the Victoria & Albert Museum’s Friday Late turns the V&A into a living laboratory, bringing science and design together for one night of events, workshops and installations.

It will also feature the official launch of a new EPSRC-funded book ‘Synthetic Aesthetics: Investigating Synthetic Biology’s Designs on Nature’.

The book, by Alexandra Daisy Ginsberg, Jane Calvert, Pablo Schyfter, Alistair Elfick and Drew Endy, emerged from a research project ‘Sandpit: Synthetic aesthetics: connecting synthetic biology and creative design’ which was funded by the UK’s Engineering and Physical Sciences Research Council (EPSRC) and the National Science Foundation in the US.

Kedar Pandya, EPSRC’s Head of Engineering, said: “This event and the Synthetic Aesthetics book will act as a catalyst to spark informed debates and future research into how we develop and apply synthetic biology. Engineers and scientists are not divorced from the rest of society; ethical, moral and artistic questions need to be considered as we explore new science and technologies.”

The EPSRC project aimed to:

  • bring together scientists and engineers working in synthetic biology with artists and designers working in the creative industries, to develop long-lasting relationships which could help to improve their work
  • ensure aesthetic concerns and questions are reflected in the lifecycle of research projects and implementation of products, and enable inclusive and responsive technology development
  • produce new social scientific research that analyses and reflects on these interactions
  • initiate a new and expanded curriculum across both engineering and design disciplines to lead to new forms of engineering and new schools of art
  • improve synthetic biological projects, products and thus the world
  • engage and enable the full diversity of civilization’s creative resources to work with the synthetic biology community as full partners in creating and stewarding a beautifully integrated natural and engineered living world

Weirdly, the news release offered no link to the book.  Here’s the Synthetic Aesthetics: Investigating Synthetic Biology’s Designs on Nature page on the MIT Press website,

In this book, synthetic biologists, artists, designers, and social scientists investigate synthetic biology and design. After chapters that introduce the science and set the terms of the discussion, the book follows six boundary-crossing collaborations between artists and designers and synthetic biologists from around the world, helping us understand what it might mean to ‘design nature.’ These collaborations have resulted in biological computers that calculate form; speculative packaging that builds its own contents; algae that feeds on circuit boards; and a sampling of human cheeses. They raise intriguing questions about the scientific process, the delegation of creativity, our relationship to designed matter, and, the importance of critical engagement. Should these projects be considered art, design, synthetic biology, or something else altogether?

Synthetic biology is driven by its potential; some of these projects are fictions, beyond the current capabilities of the technology. Yet even as fictions, they help illuminate, question, and even shape the future of the field.

About the Authors

Alexandra Daisy Ginsberg is a London-based artist, designer, and writer.

Jane Calvert is a social scientist based in Science, Technology and Innovation Studies at the University of Edinburgh.

Pablo Schyfter is a social scientist based in Science, Technology and Innovation Studies at the University of Edinburgh.

Alistair Elfick is Codirector of the SynthSys Centre at the University of Edinburgh.

Drew Endy is a bioengineer at Stanford University and President of the BioBrick

Now for the event description from the Victoria and Albert Museum’s Friday Late series, the April 25,2014  event Synthetic Aesthetics webpage,

Synthetic Aesthetics

Friday 25 April, 18.30-22.00

Can we design life itself? The emerging field of synthetic biology crosses the boundary between science and design to manipulate the stuff of life. These new designers use life as a programmable material, creating new organisms with radical applications from materials to machines. Friday Late turns the V&A into a living laboratory, bringing science and design together for one night of events, workshops and installations, each exploring our biological future.

The evening will feature the book launch of Synthetic Aesthetics: Investigating Synthetic Biology’s Designs on Nature (MIT Press). The book marks an important point in the development of the emerging discipline of synthetic biology, sitting at the intersection between design and science. The book is a result of research funded by the UK’s Engineering and Physical Sciences Research Council and the National Science Foundation in the US.

All events are free and places are designated on a first come, first served basis, unless stated otherwise. Filming and photography will be taking place at this event.

Please note, if the Museum reaches capacity we will allow access on a one-in-one-out basis.

#FridayLate

ALL EVENING (18.30 – 21.30)

Live Lab

Spotlight Space, Grand Entrance
A functioning synthetic biology lab in the grand entrance places this experimental field front and centre within the historic home of the V&A. Conducting experiments and answering questions from visitors, the lab will be run by synthetic biologists from Imperial College London’s EPSRC National Centre for Synthetic Biology & Innovation and SynbiCITE UK Innovation and Knowledge Centre for Synthetic Biology.

No Straight Line, No True Circle

Medieval & Renaissance, Room 50a
Young artists from the Royal College of Art’s Visual Communication course explore synthetic biology through projections on the walls of the galleries. Each one takes its inspiration from the sculptures around it in a series of site-specific installations.

Xylinum Cones

Lunchroom (access via staircase L, follow signs)
What would it mean for our daily lives if we could grow our objects? Xylinum Cones presents an experimental production line that uses bacteria to grow geometric forms. Meet designers Jannis Huelsen and Stefan Schwabe and learn how they are developing a renewable cellulose composite for future industrial uses.

Selfmade

Poynter Room, Café
This film tells the story of how biologist Christina Agapakis and smell provocateur Sissel Tolaas produce human cheese. Using swabs from hands, feet, noses and armpits as starter cultures, they produce unique smelling fresh cheeses as unusual portraits of our biological lives.

Grow Your Own Ink

Lunchroom (access via staircase L, follow signs)
A workshop led by scientist Thomas Landrain and designer Marie-Sarah Adenis showing how to ‘grow your own ink’. Try out some of the steps, from the culturing of bacteria to the extraction and purification of biological pigments. Discover the marvellous properties of this one-of-a-kind ink.

Bio Logic

Architecture Landing, Room 127 (access via staircase P, follow signs)
Take a trip into the Petri dish, where microchips meet microbes, cells become computers and all is not quite as it seems. Bio Computation, a short film by David Benjamin and Hy-Fi by The Living demonstrate revolutionary design using new composite building materials at the intersection of synthetic biology, architecture, and computation.

Zero Park

Bottom of NAL staircase (staircase L) Where is the line between the natural and the artificial? Somewhere in the midst of Zero Park. Sascha Pohflepp’s installation leads you through a synthetic landscape, which poses questions about human agency in natural ecosystems.

Faber Futures: The Rhizosphere Pigment Lab

Tapestries, Room 94 (access via staircase L)
Bacteria are no longer the bane, but the birth of tapestries! Natsai Audrey Chieza creates a gallery of futurist scarves for which bacteria are the sole agent of colour transformation. In collaboration with John Ward, professor of Structural Molecular Biology, University College London.

Living Things

Fashion, Room 40
Breathing, living, ‘second skins’ change their shape and appearance as you approach. Silicon-like smart-fabrics show movement and moving patterns. The Cyborg project – led by Carlos Olguin, with Autodesk Research – explores possibilities of new software to create materials with their own ‘life’.

The Opera of Prehistoric Creatures

Raphael Gallery, Room 48a
‘Lucy’, the extinct hominid Autralopithecus Afarensis, performs an opera just for you. Marguerite Humeau recreates her vocal tract and cords to bring you the lost voice of this prehistoric creature.

Electro Magnetic Signals from Bacterial DNA

Cast Courts, Room 46a
Can we imagine what it sounds like inside the molecular structure of a DNA helix? This composition is inspired by theoretical speculation on bacteria’s ability to transmit EMF signals, played amongst the V&A’s cast collection.

Living Among Living Things

The Edwin and Susan Davies Galleries, Room 87 (access via staircase L, follow signs)
Will Carey explores how living things will replace the products and foods we use today: from packaging that produces its own drink to skincare products secreted from bespoke microbial cultures. This series of images show exotic commodities that could be normal to future generations.

Neo-Nature

Lunchroom (access via staircase L, follow signs)
Join this workshop to create your own synthetic corals and contribute to the V&A’s very own coral reef. Michail Vanis invites you to bring seemingly impossible scenarios to life and discuss their scientific and ethical implications.

Synthetic Aesthetics on Film

The Lydia and Manfred Gorvey Lecture Theatre (access via staircase L, follow signs)
18.30 – 19.00 & 20.00 – 21.45
DNA replication, Bjork, swallowable perfume… these eight films demonstrate a myriad of cultural crossovers; synthetic biology at its aesthetic finest.
Dunne & Raby – Future Foragers (2009)
Tobias Revell – New Mumbai (2012)
Lucy McRae – Swallowable Parfum (2013)
UCSD – Biopixels (2011)
Zeitguised – Comme des Organismes (2014)
Drew Berry for Bjork – Hollow (2011)
Alexandra Daisy Ginsberg and James King – E. chromi (2009)
Neri Oxman – Silk Pavilion (2013)

FROM 19.00

Synthetic Aesthetics Authors’ Panel Discussion and Book Signing

The Lydia and Manfred Gorvey Lecture Theatre (access via staircase L, follow signs)
19.00 – 20.00 (followed by book signing)
The authors of Synthetic Aesthetics pry open the circuitry of a new biology, exposing the motherboard of nature. A presentation by designer Alexandra Daisy Ginsberg will be followed by a panel discussion with members of the team behind Synthetic Aesthetics Drew Endy, Jane Calvert, Pablo Schyfter and Alistair Elfick. Chaired by The Economist’s Oliver Morton.

Blueprints for the Unknown

Learning Centre: Seminar Room 3(access via staircase L, follow signs)
19.00. 19.30, 20.00 & 20.30
What happens when science leaves the lab? Recent advances in synthetic biology mean scientists will be the architects of life, creating blueprints for living systems and organisms. Blueprints for the Unknown investigates what might happen as engineering biology meets the complex world we live in. Speakers include Koby Barhad, David Benqué, Raphael Kim and Superflux.
Blueprints for the Unknown is a project by Design Interactions Research at the Royal College of Art as part of the Studiolab research project.

DNA Extraction

Learning Centre: Art Studio(access via staircase L, follow signs)
19.00, 20.00 & 21.00
Extract your own DNA in the V&A’s popup Wetlab and chat with synthetic biologists from Imperial College London. Synthetic biology designs life at the scale of DNA, and tonight you can take the raw materials of life home with you. With thanks to Imperial College London’s EPSRC National Centre for Synthetic Biology & Innovation and SynbiCITE UK Innovation and Knowledge Centre for Synthetic Biology.

Music of the Spheres

John Madejski Garden
19.30 & 20.30 (20 minutes)
Your computer’s hard drive is nothing compared to nature’s awesome capacity to record information. Artist Charlotte Jarvis explores how DNA can be used to record things apart from genetics – such as music – in the centuries to come. With scientist Nick Goldman and composer Mira Calix, Music of the Spheres encodes music into the structure of DNA suspended in soap solution. An immersive, surprising performance introduced by Jarvis, Calix and Goldman as they release musical bubbles in the garden. This is a work in progress.

FROM 20.00

Synbio Tarot Cards

Medieval & Renaissance, Room 50b
20.00 – 20.45
Synbio tarot card readings reveal possible outcomes, both desirable and disastrous, to which science might lead us. Exploring the social, economic and political implications of synthetic biology in the cards, from dream world to dystopia.

Synthetic Aesthetics Book Contributors Talks

National Art Library (access via staircase L)
20.30 – 21.30
The new book Synthetic Aesthetics: Investigating Synthetic Biology’s Designs on Nature marks a development in the emerging discipline of synthetic biology. For the book launch, designers, artists and scientists explain how their work bridges the gap between design and science. Drop in and hear Christina Agapakis, Sascha Pohflepp, David Benjamin and Will Carey over the course of the evening with social scientists Jane Calvert and Pablo Schyfter.
(Please note coats and bags are not permitted in the Library. Please leave these items in the cloakroom on the ground floor).

This event had a specially designed programme cover,

Souvenir programme wrap designed by London-based graphic design consultancy Kellenberger–White. kellenberger-white.com

Souvenir programme wrap designed by London-based graphic design consultancy Kellenberger–White.
kellenberger-white.com

 


Having observed how very deeply concerned scientists still are over the GMO (genetically modified organisms, sometimes also called ‘Frankenfoods’) panic that occurred in the early 2000s (I think), I suspect that efforts like this are meant (at least in part) to allay fears. In any event, the powers-that-be have taken a very engaging approach to their synthetic biology efforts. As for whether or not the event lived up to expectations, I have not been able to find any reviews or commentaries about it.

UK’s National Physical Laboratory reaches out to ‘BioTouch’ MIT and UCL

This March 27, 2014 news item on Azonano is an announcement for a new project featuring haptics and self-assembly,

NPL (UK’s National Physical Laboratory) has started a new strategic research partnership with UCL (University College of London) and MIT (Massachusetts Institute of Technology) focused on haptic-enabled sensing and micromanipulation of biological self-assembly – BioTouch.

The NPL March 27, 2014 news release, which originated the news item, is accompanied by a rather interesting image,

A computer operated dexterous robotic hand holding a microscope slide with a fluorescent human cell (not to scale) embedded into a synthetic extracellular matrix. Courtesy: NPL

A computer operated dexterous
robotic hand holding a microscope
slide with a fluorescent human cell
(not to scale) embedded into a
synthetic extracellular matrix. Courtesy: NPL

The news release goes on to describe the BioTouch project in more detail (Note: A link has been removed),

The project will probe sensing and application of force and related vectors specific to biological self-assembly as a means of synthetic biology and nanoscale construction. The overarching objective is to enable the re-programming of self-assembled patterns and objects by directed micro-to-nano manipulation with compliant robotic haptic control.

This joint venture, funded by the European Research Council, EPSRC and NPL’s Strategic Research Programme, is a rare blend of interdisciplinary research bringing together expertise in robotics, haptics and machine vision with synthetic and cell biology, protein design, and super- and high-resolution microscopy. The research builds on the NPL’s pioneering developments in bioengineering and imaging and world-leading haptics technologies from UCL and MIT.

Haptics is an emerging enabling tool for sensing and manipulation through touch, which holds particular promise for the development of autonomous robots that need to perform human-like functions in unstructured environments. However, the path to all such applications is hampered by the lack of a compliant interface between a predictably assembled biological system and a human user. This research will enable human directed micro-manipulation of experimental biological systems using cutting-edge robotic systems and haptic feedback.

Recently the UK government has announced ‘eight great technologies’ in which Britain is to become a world leader. Robotics, synthetic biology, regenerative medicine and advanced materials are four of these technologies for which this project serves as a merging point providing thus an excellent example of how multidisciplinary collaborative research can shape our future.

If it read this rightly, it means they’re trying to design systems where robots will work directly with materials in the labs while humans direct the robots’ actions from a remote location. My best example of this (it’s not a laboratory example) would be of a surgery where a robot actually performs the work while a human directs the robot’s actions based on haptic (touch) information the human receives from the robot. Surgeons don’t necessarily see what they’re dealing with, they may be feeling it with their fingers (haptic information). In effect, the robot’s hands become an extension of the surgeon’s hands. I imagine using a robot’s ‘hands’ would allow for less invasive procedures to be performed.

Learn to love slime; it may help you to compute in the future

Eeeewww! Slime or slime mold is not well loved and yet scientists seem to retain a certain affection for it, if their efforts at researching ways to make it useful could be termed affection. A March 27, 2014 news item on Nanowerk highlights a project where scientists have used slime and nanoparticles to create logic units (precursors to computers; Note: A link has been removed),

A future computer might be a lot slimier than the solid silicon devices we have today. In a study published in the journal Materials Today (“Slime mold microfluidic logical gates”), European researchers reveal details of logic units built using living slime molds, which might act as the building blocks for computing devices and sensors.

The March 27, 2014 Elsevier press release, which originated the news item, describes the researchers and their work in more detail,

Andrew Adamatzky (University of the West of England, Bristol, UK) and Theresa Schubert (Bauhaus-University Weimar, Germany) have constructed logical circuits that exploit networks of interconnected slime mold tubes to process information.

One is more likely to find the slime mold Physarum polycephalum living somewhere dark and damp rather than in a computer science lab. In its “plasmodium” or vegetative state, the organism spans its environment with a network of tubes that absorb nutrients. The tubes also allow the organism to respond to light and changing environmental conditions that trigger the release of reproductive spores.

In earlier work, the team demonstrated that such a tube network could absorb and transport different colored dyes. They then fed it edible nutrients – oat flakes – to attract tube growth and common salt to repel them, so that they could grow a network with a particular structure. They then demonstrated how this system could mix two dyes to make a third color as an “output”.

Using the dyes with magnetic nanoparticles and tiny fluorescent beads, allowed them to use the slime mold network as a biological “lab-on-a-chip” device. This represents a new way to build microfluidic devices for processing environmental or medical samples on the very small scale for testing and diagnostics, the work suggests. The extension to a much larger network of slime mold tubes could process nanoparticles and carry out sophisticated Boolean logic operations of the kind used by computer circuitry. The team has so far demonstrated that a slime mold network can carry out XOR or NOR Boolean operations. Chaining together arrays of such logic gates might allow a slime mold computer to carry out binary operations for computation.

“The slime mold based gates are non-electronic, simple and inexpensive, and several gates can be realized simultaneously at the sites where protoplasmic tubes merge,” conclude Adamatzky and Schubert.

Are we entering the age of the biological computer? Stewart Bland, Editor of Materials Today, believes that “although more traditional electronic materials are here to stay, research such as this is helping to push and blur the boundaries of materials science, computer science and biology, and represents an exciting prospect for the future.

I did look at the researchers’ paper and it is fascinating even to someone (me) who doesn’t understand the science very well. Here’s a link to and a citation for the paper,

Slime mold microfluidic logical gates by Andrew Adamatzky and Theresa Schubert. Materials Today, Volume 17, Issue 2, March 2014, Pages 86–91 (2014) published by Elsevier. http://dx.doi.org/10.1016/j.mattod.2014.01.018 The article is available for free at www.materialstoday.com

Yes, it’s an open access paper published by Elsevier, good on them!

An entire chemistry lab (nanofactory) in a droplet

I love the blue in this image, which illustrates the thousand-droplets test, research suggesting the possibility of a nanofactory or laboratory within a droplet ,

Droplets with a diameter of only a few micrometers act as the reaction vessels for a complex oscillating reaction - Photo: Maximilian Weitz / TUM

Droplets with a diameter of only a few micrometers act as the reaction vessels for a complex oscillating reaction – Photo: Maximilian Weitz / TUM

A Feb. 19, 2014 news item on Azonano reveals more,

An almost infinite number of complex and interlinked reactions take place in a biological cell. In order to be able to better investigate these networks, scientists led by Professor Friedrich Simmel, Chair of Systems Biophysics and Nano Biophysics at the Technische Universitaet Muenchen (TUM) try to replicate them with the necessary components in a kind of artificial cell.

This is also motivated by the thought of one day using such single-cell systems for example as “nanofactories” for the production of complex organic substances or biomaterials.

All such experiments have so far predominantly worked with very simple reactions, however. NIM Professor Friedrich Simmel and his team have now for the first time managed to let a more complex biochemical reaction take place in tiny droplets of only a few micrometers in size. Together with co-authors from the University of California Riverside and the California Institute of Technology in Pasadena, USA, the scientists are presenting their findings in the current edition of Nature Chemistry.

The Feb. 18, 2014 TUM press release, which originated the news item, details the experiements,

Shaking once – investigating thousands of times

The experiment is conducted by putting an aqueous reaction solution into oil and shaking the mixture vigorously. The result is an emulsion consisting of thousands of droplets. Employing only a tiny amount of material, the scientists have thus found a cost-efficient and quick way of setting up an extremely large number of experiments simultaneously.

As a test system, the researchers chose a so-called biochemical oscillator. This involves several reactions with DNA and RNA, which take place repetitively one after the other. Their rhythm becomes visible because in one step two DNA strands bind to each other in such a way that a fluorescent dye shines. This regular blinking is then recorded with special cameras.

Small droplets – huge differences

In the first instance, Friedrich Simmel and his colleagues intended to investigate the principal behavior of a complex reaction system if scaled down to the size of a cell. In addition, they specifically wondered if all droplet systems displayed an identical behavior and what factors would cause possible differences.

Their experiments showed that the oscillations in the individual droplets differed strongly, that is to say, much stronger than might have been expected from a simple statistical model. It was above all evident that small drops display stronger variations than large ones. “It is indeed surprising that we could witness a similar variability and individuality in a comparatively simple chemical system as is known from biological cells”, explains Friedrich Simmel the results.

Thus, it is currently not possible to realize systems which are absolutely identical. This de facto means that researchers have to either search for ways to correct these variations or factor them in from the start. On the other hand, the numerous slightly differing systems could also be used specifically to pick out the one desired, optimally running set-up from thousands of systems.

Investigating complex biosynthetic systems in artificial cells opens up many other questions, as well. In a next step, Friedrich Simmel plans to address the underlying theoretical models: “The highly parallel recording of the emulsion droplets enabled us to acquire plenty of interesting data. Our goal is to use these data to review and improve the theoretical models of biochemical reaction networks at small molecule numbers.”

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

Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator by Maximilian Weitz, Jongmin Kim, Korbinian Kapsner, Erik Winfree, Elisa Franco, & Friedrich C. Simmel. Nature Chemistry (2014) doi:10.1038/nchem.1869 Published online 16 February 2014

This paper is behind a paywall.

*2700th posting: new generation of hybird memristive nanodevices and an update of HP labs and its memristive products

Hard to believe this is the *2700th posting but yay! To commemorate this special occasion I’m featuring two items about memristors, work on protein-based memristors and an update of my Feb. 7, 2013 posting on the HP Labs and its promises of memristor-based products.

Michael Berger’s Dec. 16, 2013 issue of Nanowerk Spotlight focused on memristor research from bioengineers at Singapore’s Nanyang Technological University (Note: Links have been removed),

 Based on the rapid development of synthetic chemistry and bioengineering, researchers have begun to build hybrid nanostructures with various biomolecules to fulfill the functional requirements of advanced nanocircuits. Proteins already perform functions such as signalling, charge transport or storage, in all biochemical processes.

“Although the diversity of these natural molecules is vast – for instance, more than a million variants of an individual protein may be created via genetic engineering – tailoring their structures to fit the variable and complex requirements of both the biological and non-biological world is achievable by leveraging on the rapidly developing bioengineering field,” Xiaodong Chen, an Associate Professor in the School of Materials Science & Engineering at Nanyang Technological University, tells Nanowerk. “On a parallel note, bioengineering may provide an alternative approach to tune the structural and electronic properties of functional molecules leading to further development in the field of molecular electronics.”

Berger provides more context on this work by way of a 2011 Spotlight about the research (featured in my Sept. 19, 2011 posting) and then describes Chen’s latest work,

In new work, reported in a recent edition of Small (“Bioengineered Tunable Memristor Based on Protein Nanocage”) Chen and his team demonstrate a strategy for the fabrication of memristive nanodevices with stable and tunable performance by assembling ferritin monolayer inside a on-wire lithography-generated ∼12 nm gap.

Whereas the protein-based memristor devices in the previous work were fabricated from the commercial horse spleen ferritin, the new work uses the unique high iron loading capacity of Archaeoglobus fulgidus ferritin (AfFtn).

“We hypothesized that if the composition of this iron complex core can be modulated, the switching performance of the protein-based device can be controlled accordingly,” says Chen.

They found that the (tunable) iron loading in the AfFtn nanocages drastically impacts the performance of the memristive devices. The higher iron loading amount contributes to better memristive performance due to higher electrochemical activity of the ferric complex core.

This work is not going to be found in any applications for molecular devices at any time soon but it seems promising at this stage. For those who’d like more information, there’s Berger’s article or this link and a citation to the researchers’ paper,

Bioengineered Tunable Memristor Based on Protein Nanocage by Fanben Meng, Barindra Sana, Yuangang Li, Yuanjun Liu, Sierin Lim, & Xiaodong Chen. Article first published online: 19 AUG 2013 DOI: 10.1002/smll.201300810
© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

This paper is behind a paywall but Wiley does offer a number of viewing options at different price points.

HP Labs and its memristor-based products

Following on last year’s Feb. 7, 2013 update (scroll down about 1/2 way), it seems like another annual update is in order unfortunately, the news seems like a retread. Memristor’-based devices from HP Labs will not be launched (in the marketplace or even to show at technology shows) this year either. In fact, any sort of launch is much further in the future according to Chris Mellor’s Nov. 1, 2013 article for The Register; Note: Links have been removed),

HP has warned El Reg not to get its hopes up too high after the tech titan’s CTO Martin Fink suggested StoreServ arrays could be packed with 100TB Memristor drives come 2018.

In five years, according to Fink, DRAM and NAND scaling will hit a wall, limiting the maximum capacity of the technologies: process shrinks will come to a shuddering halt when the memories’ reliability drops off a cliff as a side effect of reducing the size of electronics on the silicon dies.

The HP answer to this scaling wall is Memristor, its flavour of resistive RAM technology that is supposed to have DRAM-like speed and better-than-NAND storage density. Fink claimed at an HP Discover event in Las Vegas that Memristor devices will be ready by the time flash NAND hits its limit in five years. He also showed off a Memristor wafer, adding that it could have a 1.5PB capacity by the end of the decade.

Fink spoke about the tech in June, but this week a HP spokesperson clarified to The Reg:

As with many other ground-breaking technologies being developed at HP Labs, HP has not yet committed to a specific product roadmap for Memristor-based products. HP does have internal milestones that are subject to change, depending on shifting market, technology and business conditions.

Every time I read about it HP Labs’ memristor-based products  they keep receding further into the future. Compare this latest announcement with what was being said at the time of my Feb.7, 2013 posting,

… Stanley Williams’ presence in the video reminded me of the memristor and an announcement (mentioned in my April 19, 2012 posting) that HP Labs would be rolling out some memristor-enabled products in 2013. Sadly, later in the year I missed this announcement, from a July 9, 2012 posting by Chris Mellor for TheRegister.co.uk,

Previously he (Stanley Williams) has said that HP and fab partner Hynix would launch a memristor product in the summer of 2013. At the Kavli do [Kavli Foundation Roundtable, June 2012], Williams said: “In terms of commercialisation, we’ll have something technologically viable by the end of next year [2014].”

To be fair, it seems HP Labs had abandoned plans for a commercial launch of memristor-based products even in 2013 but now it seems there is no roadmap of any kind.

* Corrected from ‘3000’ to ‘2700’.

Nov. 19, 2013: Myths & Realities of the DIYbio Movement event at Woodrow Wilson Center (Washington, DC)

The Synthetic Biology Project at the Woodrow Wilson International Center for Scholars is releasing a report tomorrow (Tuesday, Nov. 19, 2013) titled: Myths & Realities of the DIYbio Movement. If you’re lucky enough to be in Washington, DC, you can attend the live event,

As the Do-It-Yourself Biology (DIYbio) community has grown, so have concerns among media and policymakers about these science enthusiasts’ ability to wield DNA and manipulate life. In the words of one Wall Street Journal headline, “In Attics and Closets, ‘Biohackers’ Discover their Inner Frankenstein.”

The realities of DIYbio, however, contradict the media myths. In its first-ever survey of DIYbio practitioners, the Synthetic Biology Project at the Woodrow Wilson International Center for Scholars finds the community to be far different from these fearful and often sensationalist representations.

The report challenges seven widely held beliefs about DIYbio practitioners, particularly about their labs, capabilities and goals. The survey finds that the science they practice is far more benign than described in the popular press. In fact, the report suggests that the DIYbio community offers national education and entrepreneurship opportunities, rather than over-inflated risks. The report concludes with six policy recommendations based on the survey results.

What: Join us at the Wilson Center on Nov. 19 for the release of the survey results and analysis, followed by a panel discussion.

Copies of the report will be available at the event and online on Nov. 19 here: http://www.synbioproject.org/events/archive/6673/

You must register to attend the event. Please RSVP here: http://bit.ly/1gGZZLd [there will possibly be a webcast posted at a later date]

More information can be found here: http://www.wilsoncenter.org/event/myths-realities-the-diybio-movement

When: Nov. 19, 2013 from noon – 2:00 p.m. EST (Light lunch available at 11:30 am.)

Who: Daniel Grushkin, co-founder of Genspace and Wilson Center Fellow
Jason Bobe, co-founder of DIYbio.org
Todd Kuiken, Synthetic Biology Project

Where: Woodrow Wilson International Center for Scholars
5th Floor Conference Room
Ronald Reagan Building
1300 Pennsylvania Ave NW
Washington, D.C.

For directions, visit: http://www.wilsoncenter.org/directions

To learn more about the Synthetic Biology Project, visit: http://www.synbioproject.org/about/

According to the Center’s event webpage, there may be a webcast of the event available but it seems they won’t be livestreaming so you will have to wait until it’s posted.

I have mentioned Genspace here in a Sept. 21, 2012 posting titled: A tooth and art installation in Vancouver (Canada) and bodyhacking and DIY (do-it-yourself) culture in the US. Scroll down about 1/2 way to find the mention of Genspace (New York’s Community Biolab) and its activities. (At the time, I was focused on the bodyhacking aspect of DIYbio.)

Jason Bobe’s DIYbio.org is new to me. Here’s a little more about the organization from the homepage (Note: Links have been removed),

DIYbio.org was founded in 2008 with the mission of establishing a vibrant, productive and safe community of DIY biologists.  Central to our mission is the belief that biotechnology and greater public understanding about it has the potential to benefit everyone.

Join the global discussion
Find local groups, people and events near you
Read the diybio blog
Ask a biosafety expert your safety question
Subscribe to the quarterly postcard update
Browse the library of DIY lab hardware
Get the diybio logo and contact info

I checked out the organization’s Local Groups webpage and found three groups in Canada,,

DIYbio Toronto (this is the only city that has any current activity listed on its site)

Welcome to DIYbio Vancouver!

Biospace (Victoria, BC)

Mixing and matching your nanoparticles

An Oct. 20, 2013 Brookhaven National Laboratory (BNL; US Dept. of Energy) news release (also on EurekAlert) describes a technique for combining different kinds of nanoparticles into a single nanocomposite,

Scientists at the U.S. Department of Energy’s Brookhaven National Laboratory have developed a general approach for combining different types of nanoparticles to produce large-scale composite materials. The technique, described in a paper published online by Nature Nanotechnology on October 20, 2013, opens many opportunities for mixing and matching particles with different magnetic, optical, or chemical properties to form new, multifunctional materials or materials with enhanced performance for a wide range of potential applications.

The approach takes advantage of the attractive pairing of complementary strands of synthetic DNA—based on the molecule that carries the genetic code in its sequence of matched bases known by the letters A, T, G, and C. After coating the nanoparticles with a chemically standardized “construction platform” and adding extender molecules to which DNA can easily bind, the scientists attach complementary lab-designed DNA strands to the two different kinds of nanoparticles they want to link up. The natural pairing of the matching strands then “self-assembles” the particles into a three-dimensional array consisting of billions of particles. Varying the length of the DNA linkers, their surface density on particles, and other factors gives scientists the ability to control and optimize different types of newly formed materials and their properties.

The news release details some of the challenges the researchers faced,

… the scientists explored the effect of particle shape. “In principle, differently shaped particles don’t want to coexist in one lattice,” said Gang [Brookhaven physicist Oleg Gang]. “They either tend to separate into different phases like oil and water refusing to mix or form disordered structures.” The scientists discovered that DNA not only helps the particles mix, but it can also improve order for such systems when a thicker DNA shell around the particles is used.

They also investigated how the DNA-pairing mechanism and other intrinsic physical forces, such as magnetic attraction among particles, might compete during the assembly process. For example, magnetic particles tend to clump to form aggregates that can hinder the binding of DNA from another type of particle. “We show that shorter DNA strands are more effective at competing against magnetic attraction,” Gang said.

For the particular composite of gold and magnetic nanoparticles they created, the scientists discovered that applying an external magnetic field could “switch” the material’s phase and affect the ordering of the particles. “This was just a demonstration that it can be done, but it could have an application—perhaps magnetic switches, or materials that might be able to change shape on demand,” said Zhang [[Yugang Zhang, first author of the paper].

The third fundamental factor the scientists explored was how the particles were ordered in the superlattice arrays: Does one type of particle always occupy the same position relative to the other type—like boys and girls sitting in alternating seats in a movie theater—or are they interspersed more randomly? “This is what we call a compositional order, which is important for example for quantum dots because their optical properties—e.g., their ability to glow—depend on how many gold nanoparticles are in the surrounding environment,” said Gang. “If you have compositional disorder, the optical properties would be different.” In the experiments, increasing the thickness of the soft DNA shells around the particles increased compositional disorder.

These fundamental principles give scientists a framework for designing new materials. The specific conditions required for a particular application will be dependent on the particles being used, Zhang emphasized, but the general assembly approach would be the same.

Said Gang, “We can vary the lengths of the DNA strands to change the distance between particles from about 10 nanometers to under 100 nanometers—which is important for applications because many optical, magnetic, and other properties of nanoparticles depend on the positioning at this scale. We are excited by the avenues this research opens up in terms of future directions for engineering novel classes of materials that exploit collective effects and multifunctionality.”

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

A general strategy for the DNA-mediated self-assembly of functional nanoparticles into heterogeneous systems by Yugang Zhang, Fang Lu, Kevin G. Yager, Daniel van der Lelie, & Oleg Gang. Nature Nanotechnology (2013) doi:10.1038/nnano.2013.209 Published online 20 October 2013.

This article can be viewed/previewed on ReadCube or purchased.