Tag Archives: Caltech

Robots built from living tissue

Biohybrid robots, as they are known, are built from living tissue but not in a Frankenstein kind of way as Victoria Webster PhD candidate at Case Western Reserve University (US) explains in her Aug. 9, 2016 essay on The Conversation (also on phys.org as an Aug. 10, 2016 news item; Note: Links have been removed),

Researchers are increasingly looking for solutions to make robots softer or more compliant – less like rigid machines, more like animals. With traditional actuators – such as motors – this can mean using air muscles or adding springs in parallel with motors. …

But there’s a growing area of research that’s taking a different approach. By combining robotics with tissue engineering, we’re starting to build robots powered by living muscle tissue or cells. These devices can be stimulated electrically or with light to make the cells contract to bend their skeletons, causing the robot to swim or crawl. The resulting biobots can move around and are soft like animals. They’re safer around people and typically less harmful to the environment they work in than a traditional robot might be. And since, like animals, they need nutrients to power their muscles, not batteries, biohybrid robots tend to be lighter too.

Webster explains how these biobots are built,

Researchers fabricate biobots by growing living cells, usually from heart or skeletal muscle of rats or chickens, on scaffolds that are nontoxic to the cells. If the substrate is a polymer, the device created is a biohybrid robot – a hybrid between natural and human-made materials.

If you just place cells on a molded skeleton without any guidance, they wind up in random orientations. That means when researchers apply electricity to make them move, the cells’ contraction forces will be applied in all directions, making the device inefficient at best.

So to better harness the cells’ power, researchers turn to micropatterning. We stamp or print microscale lines on the skeleton made of substances that the cells prefer to attach to. These lines guide the cells so that as they grow, they align along the printed pattern. With the cells all lined up, researchers can direct how their contraction force is applied to the substrate. So rather than just a mess of firing cells, they can all work in unison to move a leg or fin of the device.

Researchers sometimes mimic animals when creating their biobots (Note: Links have been removed),

Others have taken their cues from nature, creating biologically inspired biohybrids. For example, a group led by researchers at California Institute of Technology developed a biohybrid robot inspired by jellyfish. This device, which they call a medusoid, has arms arranged in a circle. Each arm is micropatterned with protein lines so that cells grow in patterns similar to the muscles in a living jellyfish. When the cells contract, the arms bend inwards, propelling the biohybrid robot forward in nutrient-rich liquid.

More recently, researchers have demonstrated how to steer their biohybrid creations. A group at Harvard used genetically modified heart cells to make a biologically inspired manta ray-shaped robot swim. The heart cells were altered to contract in response to specific frequencies of light – one side of the ray had cells that would respond to one frequency, the other side’s cells responded to another.

Amazing, eh? And, this is quite a recent video; it was published on YouTube on July 7, 2016.

Webster goes on to describe work designed to make these robots hardier and more durable so they can leave the laboratory,

… Here at Case Western Reserve University, we’ve recently begun to investigate … by turning to the hardy marine sea slug Aplysia californica. Since A. californica lives in the intertidal region, it can experience big changes in temperature and environmental salinity over the course of a day. When the tide goes out, the sea slugs can get trapped in tide pools. As the sun beats down, water can evaporate and the temperature will rise. Conversely in the event of rain, the saltiness of the surrounding water can decrease. When the tide eventually comes in, the sea slugs are freed from the tidal pools. Sea slugs have evolved very hardy cells to endure this changeable habitat.

We’ve been able to use Aplysia tissue to actuate a biohybrid robot, suggesting that we can manufacture tougher biobots using these resilient tissues. The devices are large enough to carry a small payload – approximately 1.5 inches long and one inch wide.

Webster has written a fascinating piece and, if you have time, I encourage you to read it in its entirety.

DNA origami as Van Gogh’s Starry Night

This glowing reproduction of "The Starry Night" contains 65,536 pixels and is the width of a dime across. Credit: Ashwin Gopinath/Caltech

This glowing reproduction of “The Starry Night” contains 65,536 pixels and is the width of a dime across.
Credit: Ashwin Gopinath/Caltech

It may take you a few seconds (it did me) but it’s possible to see Van Gogh’s Starry Night in this image. A July 12, 2016 news item on ScienceDaily reveals more,

Using folded DNA [deoxyribonucleic acid] to precisely place glowing molecules within microscopic light resonators, researchers at Caltech have created one of the world’s smallest reproductions of Vincent van Gogh’s The Starry Night.

A July 12, 2016 Caltech news release (also on EurekAlert) by Richard Perkins, which originated the news item, provides more information about the image, DNA origami, and this latest research on coupling light emitters to photonic crystal cavities (Note: Links have been removed),

The monochrome image—just the width of a dime across—was a proof-of-concept project that demonstrated, for the first time, how the precision placement of DNA origami can be used to build chip-based devices like computer circuits at smaller scales than ever before.

DNA origami, developed 10 years ago by Caltech’s Paul Rothemund (BS ’94), is a technique that allows researchers to fold a long strand of DNA into any desired shape. The folded DNA then acts as a scaffold onto which researchers can attach and organize all kinds of nanometer-scale components, from fluorescent molecules to electrically conductive carbon nanotubes to drugs.

“Think of it a bit like the pegboards people use to organize tools in their garages, only in this case, the pegboard assembles itself from DNA strands and the tools likewise find their own positions,” says Rothemund, research professor of bioengineering, computing and mathematical sciences, and computation and neural systems. “It all happens in a test tube without human intervention, which is important because all of the parts are too small to manipulate efficiently, and we want to make billions of devices.”

The process has the potential to influence a variety of applications from drug delivery to the construction of nanoscale computers. But for many applications, organizing nanoscale components to create devices on DNA pegboards is not enough; the devices have to be wired together into larger circuits and need to have a way of communicating with larger-scale devices.

One early approach was to make electrodes first, and then scatter devices randomly on a surface, with the expectation that at least a few would land where desired, a method Rothemund describes as “spray and pray.”

In 2009, Rothemund and colleagues at IBM Research first described a technique through which DNA origami can be positioned at precise locations on surfaces using electron-beam lithography to etch sticky binding sites that have the same shape as the origami. For example, triangular sticky patches bind triangularly folded DNA.

Over the last seven years, Rothemund and Ashwin Gopinath, senior postdoctoral scholar in bioengineering at Caltech, have refined and extended this technique so that DNA shapes can be precisely positioned on almost any surface used in the manufacture of computer chips. In the Nature paper, they report the first application of the technique—using DNA origami to install fluorescent molecules into microscopic light sources.

“It’s like using DNA origami to screw molecular light bulbs into microscopic lamps,” Rothemund says.

In this case, the lamps are microfabricated structures called photonic crystal cavities (PCCs), which are tuned to resonate at a particular wavelength of light, much like a tuning fork vibrates with a particular pitch. Created within a thin glass-like membrane, a PCC takes the form of a bacterium-shaped defect within an otherwise perfect honeycomb of holes.

“Depending on the exact size and spacing of the holes, a particular wavelength of light reflects off the edge of the cavity and gets trapped inside,” says Gopinath, the lead author of the study. He built PCCs that are tuned to resonate at around 660 nanometers, the wavelength corresponding to a deep shade of the color red. Fluorescent molecules tuned to glow at a similar wavelength light up the lamps—provided they stick to exactly the right place within the PCC.

“A fluorescent molecule tuned to the same color as a PCC actually glows more brightly inside the cavity, but the strength of this coupling effect depends strongly on the molecule’s position within the cavity. A few tens of nanometers is the difference between the molecule glowing brightly, or not at all,” Gopinath says.

By moving DNA origami through the PCCs in 20-nanometer steps, the researchers found that they could map out a checkerboard pattern of hot and cold spots, where the molecular light bulbs either glowed weakly or strongly. As a result, they were able to use DNA origami to position fluorescent molecules to make lamps of varying intensity. Similar structures have been proposed to power quantum computers and for use in other optical applications that require many tiny light sources integrated together on a single chip.

“All previous work coupling light emitters to PCCs only successfully created a handful of working lamps, owing to the extraordinary difficulty of reproducibly controlling the number and position of emitters in a cavity,” Gopinath says. To prove their new technology, the researchers decided to scale-up and provide a visually compelling demonstration. By creating PCCs with different numbers of binding sites, Gopinath was able to reliably install any number from zero to seven DNA origami, allowing him to digitally control the brightness of each lamp. He treated each lamp as a pixel with one of eight different intensities, and produced an array of 65,536 of the PCC pixels (a 256 x 256 pixel grid) to create a reproduction of Van Gogh’s “The Starry Night.”

Now that the team can reliably combine molecules with PCCs, they are working to improve the light emitters. Currently, the fluorescent molecules last about 45 seconds before reacting with oxygen and “burning out,” and they emit a few shades of red rather than a single pure color. Solving both these problems will help with applications such as quantum computers.

“Aside from applications, there’s a lot of fundamental science to be done,” Gopinath says.

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

Engineering and mapping nanocavity emission via precision placement of DNA origami by Ashwin Gopinath, Evan Miyazono, Andrei Faraon, & Paul W. K. Rothemund. Nature (2016) doi:10.1038/nature18287 Published online 11 July 2016

This paper is behind a paywall.

Nanodevices and quantum entanglement

A May 30, 2016 news item on phys.org introduces a scientist with an intriguing approach to quantum computing,

Creating quantum computers which some people believe will be the next generation of computers, with the ability to outperform machines based on conventional technology—depends upon harnessing the principles of quantum mechanics, or the physics that governs the behavior of particles at the subatomic scale. Entanglement—a concept that Albert Einstein once called “spooky action at a distance”—is integral to quantum computing, as it allows two physically separated particles to store and exchange information.

Stevan Nadj-Perge, assistant professor of applied physics and materials science, is interested in creating a device that could harness the power of entangled particles within a usable technology. However, one barrier to the development of quantum computing is decoherence, or the tendency of outside noise to destroy the quantum properties of a quantum computing device and ruin its ability to store information.

Nadj-Perge, who is originally from Serbia, received his undergraduate degree from Belgrade University and his PhD from Delft University of Technology in the Netherlands. He received a Marie Curie Fellowship in 2011, and joined the Caltech Division of Engineering and Applied Science in January after completing postdoctoral appointments at Princeton and Delft.

He recently talked with us about how his experimental work aims to resolve the problem of decoherence.

A May 27, 2016 California Institute of Technology (CalTech) news release by Jessica Stoller-Conrad, which originated the news item, proceeds with a question and answer format,

What is the overall goal of your research?

A large part of my research is focused on finding ways to store and process quantum information. Typically, if you have a quantum system, it loses its coherent properties—and therefore, its ability to store quantum information—very quickly. Quantum information is very fragile and even the smallest amount of external noise messes up quantum states. This is true for all quantum systems. There are various schemes that tackle this problem and postpone decoherence, but the one that I’m most interested in involves Majorana fermions. These particles were proposed to exist in nature almost eighty years ago but interestingly were never found.

Relatively recently theorists figured out how to engineer these particles in the lab. It turns out that, under certain conditions, when you combine certain materials and apply high magnetic fields at very cold temperatures, electrons will form a state that looks exactly as you would expect from Majorana fermions. Furthermore, such engineered states allow you to store quantum information in a way that postpones decoherence.

How exactly is quantum information stored using these Majorana fermions?

The fascinating property of these particles is that they always come in pairs. If you can store information in a pair of Majorana fermions it will be protected against all of the usual environmental noise that affects quantum states of individual objects. The information is protected because it is not stored in a single particle but in the pair itself. My lab is developing ways to engineer nanodevices which host Majorana fermions. Hopefully one day our devices will find applications in quantum computing.

Why did you want to come to Caltech to do this work?

The concept of engineered Majorana fermions and topological protection was, to a large degree, conceived here at Caltech by Alexei Kiteav [Ronald and Maxine Linde Professor of Theoretical Physics and Mathematics] who is in the physics department. A couple of physicists here at Caltech, Gil Refeal [professor of theoretical physics and executive officer of physics] and Jason Alicea [professor of theoretical physics], are doing theoretical work that is very relevant for my field.

Do you have any collaborations planned here?

Nothing formal, but I’ve been talking a lot with Gil and Jason. A student of mine also uses resources in the lab of Harry Atwater [Howard Hughes Professor of Applied Physics and Materials Science and director of the Joint Center for Artificial Photosynthesis], who has experience with materials that are potentially useful for our research.

How does that project relate to your lab’s work?

There are two-dimensional, or 2-D, materials that are basically very thin sheets of atoms. Graphene [emphasis mine]—a single layer of carbon atoms—is one example, but you can create single layer sheets of atoms with many materials. Harry Atwater’s group is working on solar cells made of a 2-D material. We are thinking of using the same materials and combining them with superconductors—materials that can conduct electricity without releasing heat, sound, or any other form of energy—in order to produce Majorana fermions.

How do you do that?

There are several proposed ways of using 2-D materials to create Majorana fermions. The majority of these materials have a strong spin-orbit coupling—an interaction of a particle’s spin with its motion—which is one of the key ingredients for creating Majoranas. Also some of the 2-D materials can become superconductors at low temperatures. One of the ideas that we are seriously considering is using a 2-D material as a substrate on which we could build atomic chains that will host Majorana fermions.

What got you interested in science when you were young?

I don’t come from a family of scientists; my father is an engineer and my mother is an administrative worker. But my father first got me interested in science. As an engineer, he was always solving something and he brought home some of the problems he was working. I worked with him and picked it up at an early age.

How are you adjusting to life in California?

Well, I like being outdoors, and here we have the mountains and the beach and it’s really amazing. The weather here is so much better than the other places I’ve lived. If you want to get the impression of what the weather in the Netherlands is like, you just replace the number of sunny days here with the number of rainy days there.

I wish Stevan Nadj-Perge good luck!

Café Scientifique on March 29, 2016 *(cancelled)* and a fully booked talk on April 14, 2016 in Vancouver, Canada

There are two upcoming science events in Vancouver.

Café Scientifique

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*Cancellation notice received via email March 29, 2016 at 1430 hours PDT:

Our sincerest apologies, but we have just received word that The Railway Club is shutting it’s doors for good, effective immediately.  Unfortunately, because of this tonight’s event is cancelled.  We will do our best to re-schedule the talk in the near future once we have found a new venue.

The Tues., March 29, 2016 (tonight) Café Scientifique talk at 7:30 pm,  Café Scientifique, in the back room of The Railway Club (2nd floor of 579 Dunsmuir St. [at Seymour St.]), has one of the more peculiar descriptions for a talk that I’ve seen for this group. From a March 1, 2016 announcement (received via e-mail),

Our speaker for the evening will be Dr. Jerilynn Prior.  Prior is Professor of Endocrinology and Metabolism at the University of British Columbia, founder and scientific director of the Centre for Menstrual Cycle and Ovulation Research (CeMCOR), director of the BC Center of the Canadian Multicenter Osteoporosis Study (CaMOS), and a past president of the Society for Menstrual Cycle Research.  The title of her talk is:

 

Is Perimenopause Estrogen Deficiency?

Sorting engrained misinformation about women’s midlife reproductive transition

43 years old with teenagers a full-time executive director of a not for profit is not sleeping, she wakes soaked a couple of times a night, not every night but especially around the time her period comes. As it does frequently—it is heavy, even flooding. Her sexual interest is virtually gone and she feels dry when she tries.

Her family doctor offered her The Pill. When she took it she got very sore breasts, ankle swelling and high blood pressure. Her brain feels fuzzy, she’s getting migraines, gaining weight and just can’t cope. . . .

What’s going on? Does she need estrogen “replacement”?  If yes, why when she’s still getting flow? Does The Pill work for other women? What do we know about the what, why, how long and how to help symptomatic perimenopausal women?

This description seems more appropriate for a workshop on women’s health for doctors and/or women going through ‘the change’.

Unveiling the Universe Lecture Series

This is a fully booked event but I suppose there’s always the possibility of a ticket at the last minute. From the 100 Years of General Relativity: From the Big Bang to Black Holes, Gravitational Waves and Interstellar on the University of British Columbia (UBC) website,

We invite you to join us for an evening with renowned theoretical physicist Kip Thorne.

100 years ago, Albert Einstein formulated his wildly successful general theory of relativity—a set of physical laws that attribute gravity to the warping of time and space. It has been tested with high precision in the solar system and in binary pulsars and explains the expansion of the universe. It even predicts black holes and gravitational waves. When combined with quantum theory, relativity provides a tentative framework for understanding the universe’s big-bang birth. And the equations that made Einstein famous have become embedded in our popular culture via, for example, the science fiction movie Interstellar.

In a captivating talk accessible to science enthusiasts of all ages, Professor Kip Thorne will use Interstellar to illustrate some of relativity’s deepest ideas, including black holes and the recent discovery of gravitational waves.

Professor Thorne of the California Institute of Technology is one of the world’s foremost experts on the astrophysics implications of Einstein’s General Theory of Relativity, including black holes—an expertise he used to great effect as scientific advisor to the movieInterstellar. Thorne was also one of the three principal scientists (with Rainer Weiss and Ron Drever) behind the LIGO experiment that recently detected gravitational waves, an achievement most expect will earn them a Nobel Prize.

Here are the details from the event page,

Speaker:

Dr. Kip Thorne

Event Date and Time:

Thu, 2016-04-14 19:0020:30

Location:

Science World (1455 Quebec St )

Local Contact:

Theresa Liao

Intended Audience:

Public

Despite the fact that are no tickets, here’s the registration link (in the hope they make a waiting list available) and more logistics,

Free Registration Required

Doors Open at 6:00PM
Lecture begins at 7:00pm

This event is organized by Science World, TRIUMF, and the UBC Department of Physics & Astronomy. It is part of UBC’s Centennial Celebration.

Sadly, I did not receive details and a link for registration in a more timely fashion although I was able to give readers a heads-up in a Jan. 22, 2016 posting. (scroll down about 25% of the way down).

Identifying performance problems in nanoresonators

Use of nanoelectromechanical systems (NEMS) can now be maximised due to a technique developed by researchers at the Commissariat a l’Energie Atomique (CEA) and the University of Grenoble-Alpes (France). From a March 7, 2016 news item on ScienceDaily,

A joint CEA / University of Grenoble-Alpes research team, together with their international partners, have developed a diagnostic technique capable of identifying performance problems in nanoresonators, a type of nanodetector used in research and industry. These nanoelectromechanical systems, or NEMS, have never been used to their maximum capabilities. The detection limits observed in practice have always been well below the theoretical limit and, until now, this difference has remained unexplained. Using a totally new approach, the researchers have now succeeded in evaluating and explaining this phenomenon. Their results, described in the February 29 [2016] issue of Nature Nanotechnology, should now make it possible to find ways of overcoming this performance shortfall.

A Feb. 29, 2016 CEA press release, which originated the news item, provides more detail about NEMS and about the new technique,

NEMS have many applications, including the measurement of mass or force. Like a tiny violin string, a nanoresonator vibrates at a precise resonant frequency. This frequency changes if gas molecules or biological particles settle on the nanoresonator surface. This change in frequency can then be used to detect or identify the substance, enabling a medical diagnosis, for example. The extremely small dimensions of these devices (less than one millionth of a meter) make the detectors highly sensitive.

However, this resolution is constrained by a detection limit. Background noise is present in addition to the wanted measurement signal. Researchers have always considered this background noise to be an intrinsic characteristic of these systems (see Figure 2 [not reproduced here]). Despite the noise levels being significantly greater than predicted by theory, the impossibility of understanding the underlying phenomena has, until now, led the research community to ignore them.

The CEA-Leti research team and their partners reviewed all the frequency stability measurements in the literature, and identified a difference of several orders of magnitude between the accepted theoretical limits and experimental measurements.

In addition to evaluating this shortfall, the researchers also developed a diagnostic technique that could be applied to each individual nanoresonator, using their own high-purity monocrystalline silicon resonators to investigate the problem.

The resonant frequency of a nanoresonator is determined by the geometry of the resonator and the type of material used in its manufacture. It is therefore theoretically fixed. By forcing the resonator to vibrate at defined frequencies close to the resonant frequency, the CEA-Leti researchers have been able to demonstrate a secondary effect that interferes with the resolution of the system and its detection limit in addition to the background noise. This effect causes slight variations in the resonant frequency. These fluctuations in the resonant frequency result from the extreme sensitivity of these systems. While capable of detecting tiny changes in mass and force, they are also very sensitive to minute variations in temperature and the movements of molecules on their surface. At the nano scale, these parameters cannot be ignored as they impose a significant limit on the performance of nanoresonators. For example, a tiny change in temperature can change the parameters of the device material, and hence its frequency. These variations can be rapid and random.

The experimental technique developed by the team makes it possible to evaluate the loss of resolution and to determine whether it is caused by the intrinsic limits of the system or by a secondary fluctuation that can therefore by corrected. A patent has been applied for covering this technique. The research team has also shown that none of the theoretical hypotheses so far advanced to explain these fluctuations in the resonant frequency can currently explain the observed level of variation.

The research team will therefore continue experimental work to explore the physical origin of these fluctuations, with the aim of achieving a significant improvement in the performance of nanoresonators.

The Swiss Federal Institute of Technology in Lausanne, the Indian Institute of Science in Bangalore, and the California Institute of Technology (USA) have also participated in this study. The authors have received funding from the Leti Carnot Institute (NEMS-MS project) and the European Union (ERC Consolidator Grant – Enlightened project).

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

Frequency fluctuations in silicon nanoresonators by Marc Sansa, Eric Sage, Elizabeth C. Bullard, Marc Gély, Thomas Alava, Eric Colinet, Akshay K. Naik, Luis Guillermo Villanueva, Laurent Duraffourg, Michael L. Roukes, Guillaume Jourdan & Sébastien Hentz. Nature Nanotechnology (2016) doi:10.1038/nnano.2016.19 Published online 29 February 2016

This paper is behind a paywall.

Using scientific methods and technology to explore living systems as artistic subjects: bioart

There is a fascinating set of stories about bioart designed to whet your appetite for more (*) in a Nov. 23, 2015 Cell Press news release on EurekAlert (Note: A link has been removed),

Joe Davis is an artist who works not only with paints or pastels, but also with genes and bacteria. In 1986, he collaborated with geneticist Dan Boyd to encode a symbol for life and femininity into an E. coli bacterium. The piece, called Microvenus, was the first artwork to use the tools and techniques of molecular biology. Since then, bioart has become one of several contemporary art forms (including reclamation art and nanoart) that apply scientific methods and technology to explore living systems as artistic subjects. A review of the field, published November 23, can be found in Trends in Biotechnology.

Bioart ranges from bacterial manipulation to glowing rabbits, cellular sculptures, and–in the case of Australian-British artist Nina Sellars–documentation of an ear prosthetic that was implanted onto fellow artist Stelarc’s arm. In the pursuit of creating art, practitioners have generated tools and techniques that have aided researchers, while sometimes crossing into controversy, such as by releasing invasive species into the environment, blurring the lines between art and modern biology, raising philosophical, societal, and environmental issues that challenge scientific thinking.

“Most people don’t know that bioart exists, but it can enable scientists to produce new ideas and give us opportunities to look differently at problems,” says author Ali K. Yetisen, who works at Harvard Medical School and the Wellman Center for Photomedicine, Massachusetts General Hospital. “At the same time there’s been a lot of ethical and safety concerns happening around bioart and artists who wanted to get involved in the past have made mistakes.”

Here’s a sample of Joe Davis’s work,

 Caption This photograph shows polyptich paintings by Joe Davis of his 28-mer Microvenus DNA molecule (2006 Exhibition in Greece at Athens School of Fine Arts). Credit: Courtesy of Joe Davis

This photograph shows polyptich paintings by Joe Davis of his 28-mer Microvenus DNA molecule (2006 Exhibition in Greece at Athens School of Fine Arts). Credit: Courtesy of Joe Davis

The news release goes on to recount a brief history of bioart, which stretches back to 1928 and then further back into the 19th and 18th centuries,

In between experiments, Alexander Fleming would paint stick figures and landscapes on paper and in Petri dishes using bacteria. In 1928, after taking a brief hiatus from the lab, he noticed that portions of his “germ paintings,” had been killed. The culprit was a fungus, penicillin–a discovery that would revolutionize medicine for decades to come.

In 1938, photographer Edward Steichen used a chemical to genetically alter and produce interesting variations in flowering delphiniums. This chemical, colchicine, would later be used by horticulturalists to produce desirable mutations in crops and ornamental plants.

In the late 18th and early 19th centuries, the arts and sciences moved away from traditionally shared interests and formed secular divisions that persisted well into the 20th century. “Appearance of environmental art in the 1970s brought about renewed awareness of special relationships between art and the natural world,” Yetisen says.

To demonstrate how we change landscapes, American sculptor Robert Smithsonian paved a hillside with asphalt, while Bulgarian artist Christo Javacheffa (of Christo and Jeanne-Claude) surrounded resurfaced barrier islands with bright pink plastic.

These pieces could sometimes be destructive, however, such as in Ten Turtles Set Free by German-born Hans Haacke. To draw attention to the excesses of the pet trade, he released what he thought were endangered tortoises back to their natural habitat in France, but he inadvertently released the wrong subspecies, thus compromising the genetic lineages of the endangered tortoises as the two varieties began to mate.

By the late 1900s, technological advances began to draw artists’ attention to biology, and by the 2000s, it began to take shape as an artistic identity. Following Joe Davis’ transgenic Microvenus came a miniaturized leather jacket made of skin cells, part of the Tissue Culture & Art Project (initiated in 1996) by duo Oran Catts and Ionat Zurr. Other examples of bioart include: the use of mutant cacti to simulate appearance of human hair in the place of cactus spines by Laura Cinti of University College London’s C-Lab; modification of butterfly wings for artistic purposes by Marta de Menezes of Portugal; and photographs of amphibian deformation by American Brandon Ballengée.

“Bioart encourages discussions about societal, philosophical, and environmental issues and can help enhance public understanding of advances in biotechnology and genetic engineering,” says co-author Ahmet F. Coskun, who works in the Division of Chemistry and Chemical Engineering at California Institute of Technology.

Life as a Bioartist

Today, Joe Davis is a research affiliate at MIT Biology and “Artist-Scientist” at the George Church Laboratory at Harvard–a place that fosters creativity and technological development around genetic engineering and synthetic biology. “It’s Oz, pure and simple,” Davis says. “The total amount of resources in this environment and the minds that are accessible, it’s like I come to the city of Oz every day.”

But it’s not a one-way street. “My particular lab depends on thinking outside the box and not dismissing things because they sound like science fiction,” says [George M.] Church, who is also part of the Wyss Institute for Biologically Inspired Engineering. “Joe is terrific at keeping us flexible and nimble in that regard.”

For example, Davis is working with several members of the Church lab to perform metagenomics analyses of the dust that accumulates at the bottom of money-counting machines. Another project involves genetically engineering silk worms to spin metallic gold–an homage to the fairy tale of Rumpelstiltskin.

“I collaborate with many colleagues on projects that don’t necessarily have direct scientific results, but they’re excited to pursue these avenues of inquiry that they might not or would not look into ordinarily–they might try to hide it, but a lot of scientists have poetic souls,” Davis says. “Art, like science, has to describe the whole word and you can’t describe something you’re basically clueless about. The most exciting part of these activities is satiating overwhelming curiosity about everything around you.”

The number of bioartists is still small, Davis says, partly because of a lack of federal funding of the arts in general. Accessibility to the types of equipment bioartists want to experiment with can also be an issue. While Davis has partnered with labs over the past few decades, other artists affiliate themselves with community access laboratories that are run by do-it-yourself biologists. One way that universities can help is to create departmental-wide positions for bioartists to collaborate with scientists.

“In the past, there have been artists affiliated with departments in a very utilitarian way to produce figures or illustrations,” Church says. “Having someone like Joe stimulates our lab to come together in new ways and if we had more bioartists, I think thinking out of the box would be a more common thing.”

“In the era of genetic engineering, bioart will gain new meanings and annotations in social and scientific contexts,” says Yetisen. “Bioartists will surely take up new roles in science laboratories, but this will be subject to ethical criticism and controversy as a matter of course.”

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

Bioart by Ali K. Yetisen, Joe Davis, Ahmet F. Coskun, George M. Church, Seok Hyun. Trends in Biotechnology,  DOI: http://dx.doi.org/10.1016/j.tibtech.2015.09.011 Published Online: November 23, 2015

This paper appears to be open access.

*Removed the word ‘featured’ on Dec. 1, 2015 at 1030 hours PDT.

A nanoscale bacteria power grid

It’s not often you see the word ‘spectacular’ when reading a science news item but it can be found in an Oct. 21, 2015 news item on ScienceDaily,

Electrical energy from the socket — this convenient type of power supply is apparently used by some microorganisms. Cells can meet their energy needs in the form of electricity through nano-wire connections. Researchers from the Max Planck Institute for Marine Microbiology in Bremen have discovered these possibly smallest power grids in the world when examining cell aggregates of methane degrading microorganisms. They consist of two completely different cell types, which can only jointly degrade methane. Scientists have discovered wire-like connections between the cells, which are relevant in energy exchanges.

It was a spectacular [emphasis mine] scientific finding when researchers discovered electrical wiring between microorganisms using iron as energy source in 2010. Immediately the question came up if electric power exchange is common in other microbially mediated reactions. One of the processes in question was the anaerobic oxidation of methane (AOM) that is responsible for the degradation of the greenhouse gas methane in the seafloor, and therefore has a great relevance for Earth climate. The microorganisms involved have been described for the first time in 2000 by researchers from Bremen and since then have been extensively studied.

This image accompanies the research,

Caption: Electron micrograph of the nanowires shows connecting archaea and sulphate reducing bacteria. The wires stretch out for several micrometres, longer than a single cell. The white bar represents the length of one micrometre. The arrows indicate the nanowires (A=ANME-Archaeen, H=HotSeep-1 partner bacteria). Credit: MPI f. Biophysical Chemistry

Caption: Electron micrograph of the nanowires shows connecting archaea and sulphate reducing bacteria. The wires stretch out for several micrometres, longer than a single cell. The white bar represents the length of one micrometre. The arrows indicate the nanowires (A=ANME-Archaeen, H=HotSeep-1 partner bacteria).
Credit: MPI f. Biophysical Chemistry

A Oct. 21, 2015 Max Planck press release (also on EurekAlert), which originated the news item, provides more information about methane in the ocean, power wires, and electron transporters,

In the ocean, methane is produced from the decay of dead biomass in subsurface sediments. The methane rises upwards to the seafloor, but before reaching the water column it is degraded by special consortia of archaea and bacteria. The archaea take up methane and oxidise it to carbonate. They pass on energy to their partner bacteria, so that the reaction can proceed. The bacteria respire sulphate instead of oxygen to gain energy (sulphate reducers). This may be an ancient metabolism, already relevant billions of years ago when the Earth’s atmosphere was oxygen-free. Yet today it remains unknown how the anaerobic oxidation of methane works biochemically.

Gunter Wegener, who authors the publication together with PhD student Viola Krukenberg, says: “We focused on thermophilic AOM consortia living at 60 degrees Celsius. For the first time we were able to isolate the partner bacteria to grow them alone. Then we systematically compared the physiology of the isolate with that of the AOM culture. We wanted to know which substances can serve as an energy carrier between the archaea and sulphate reducers.” Most compounds were ruled out quickly. At first, hydrogen was considered as energy source. However, the archaea did not produce sufficient hydrogen to explain the growth of sulphate reducers – hence the researchers had to change their strategy.

Direct power wires and electron transporters

One possible alternative was to look for direct connections channelling electrons between the cells. Using electron microscopy on the thermophilic AOM cultures this idea was confirmed. Dietmar Riedel, head of electron microscopy facilities at the Max Planck Institute in Goettingen says: “It was really challenging to visualize the cable-like structures. We embedded aggregates under high pressure using different embedding media. Ultrathin sections of these aggregates were then examined in near-native state using transmission electron microscopy.”

Viola Krukenberg adds: “We found all genes necessary for biosynthesis of the cellular connections called pili. Only when methane is added as energy source these genes are activated and pili are formed between bacteria and archaea.”

With length of several micrometres the wires can exceed the length of the cells by far, but their diameter is only a few nanometres. These wires provide the contact between the closely spaced cells and explain the spatial structure of the consortium, as was shown by a team of researchers led by Victoria Orphan from Caltech.

“Consortia of archaea and bacteria are abundant in nature. Our next step is to see whether other types also show such nanowire-like connections. It is important to understand how methane-degrading microbial consortia work, as they provide important functions in nature”, explains Antje Boetius, leader of the research group at the Institute in Bremen.

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

Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria by Gunter Wegener, Viola Krukenberg, Dietmar Riedel, Halina E. Tegetmeyer, & Antje Boetius. Nature 526, 587–590 (22 October 2015) doi:10.1038/nature15733 Published online 21 October 2015

This paper is behind a paywall.

Carbyne: 40x stiffer than diamond

A material that’s tougher than diamond is the object of interest for researchers at the US Department of Energy’s Lawrence Livermore National Laboratory (LLNL) according to a Sept. 18, 2015 news item by Beth Ellison on Azonano (Note: A link has been removed),

Researchers at Lawrence Livermore National Laboratory (LLNL) have explored a method that uses laser-melted graphite to develop linear chains of carbon atoms.

This material, referred to as carbyne, could possess numerous unique properties, such as modification of the quantity of electrical current passing through a circuit according to the needs of a user. This research could probably lead to the creation of tiny electronics capable of turning on and off at an atomic scale.

A Sept. 17, 2015 LLNL news release (also on EurekAlert) details the research (Note: A link has been removed),

Carbyne is the subject of intense research because of its presence in astrophysical bodies, as well as its potential use in nanoelectronic devices and superhard materials. Its linear shape gives it unique electrical properties that are sensitive to stretching and bending, and it is 40 times stiffer than diamond. It also was found in the Murchison and Allende meteorites and could be an ingredient of interstellar dust.

Using computer simulations, LLNL scientist Nir Goldman and colleague Christopher Cannella, an undergraduate summer researcher from Caltech, initially intended to study the properties of liquid carbon as it evaporates, after being formed by shining a laser beam on the surface of graphite. The laser can heat the graphite surface to a few thousands of degrees, which then forms a fairly volatile droplet. To their surprise, as the liquid droplet evaporated and cooled in their simulations, it formed bundles of linear chains of carbon atoms.

“There’s been a lot of speculation about how to make carbyne and how stable it is,” Goldman said. “We showed that laser melting of graphite is one viable avenue for its synthesis. If you regulate carbyne synthesis in a controlled way, it could have applications as a new material for a number of different research areas, including as a tunable semiconductor or even for hydrogen storage.

“Our method shows that carbyne can be formed easily in the laboratory or otherwise. The process also could occur in astrophysical bodies or in the interstellar medium, where carbon-containing material can be exposed to relatively high temperatures and carbon can liquefy.”

Goldman’s study and computational models allow for direct comparison with experiments and can help determine parameters for synthesis of carbon-based materials with potentially exotic properties.

“Our simulations indicate a possible mechanism for carbyne fiber synthesis that confirms previous experimental observation of its formation,” Goldman said. “These results help determine one set of thermodynamic conditions for its synthesis and could account for its detection in meteorites resulting from high-pressure conditions due to impact.”

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

Carbyne Fiber Synthesis within Evaporating Metallic Liquid Carbon by Christopher B. Cannella and Nir Goldman. J. Phys. Chem. C, 2015, 119 (37), pp 21605–21611 DOI: 10.1021/acs.jpcc.5b03781 Publication Date (Web): July 9, 2015 (print): Sept. 17, 2015

Copyright © 2015 American Chemical Society

This paper is behind a paywall.

Dexter Johnson in a Sept. 18, 2015 posting about the latest carbyne developments on his Nanoclast blog (on the IEEE [Institute for Electrical and Electronics Engineers] website) provides a little history (Note: Links have been removed),

A couple of years ago, a material dubbed carbyne—which is a chain of carbon atoms held together by either double or alternating single and triple atomic bonds—was awarded the title of the world’s strongest material. Later, scientists also demonstrated that it has the unusual property of being able to change from being a conductor to an insulator when it’s stretched by as little as 3 percent.

Here’s an image illustrating the process,

A carbyne strand forms in laser-melted graphite. Carbyne is found in astrophysical bodies and has the potential to be used in nanoelectronic devices and superhard materials. Image by Liam Krauss/LLNL

A carbyne strand forms in laser-melted graphite. Carbyne is found in astrophysical bodies and has the potential to be used in nanoelectronic devices and superhard materials. Image by Liam Krauss/LLNL

US National Institute of Standards and Technology and molecules made of light (lightsabres anyone?)

As I recall, lightsabres are a Star Wars invention. I gather we’re a long way from running around with lightsabres  but there is hope, if that should be your dream, according to a Sept. 9, 2015 news item on Nanowerk,

… a team including theoretical physicists from JQI [Joint Quantum Institute] and NIST [US National Institute of Stnadards and Technology] has taken another step toward building objects out of photons, and the findings hint that weightless particles of light can be joined into a sort of “molecule” with its own peculiar force.

Here’s an artist’s conception of the light “molecule” provided by the researchers,

Researchers show that two photons, depicted in this artist’s conception as waves (left and right), can be locked together at a short distance. Under certain conditions, the photons can form a state resembling a two-atom molecule, represented as the blue dumbbell shape at center. Credit: E. Edwards/JQI

Researchers show that two photons, depicted in this artist’s conception as waves (left and right), can be locked together at a short distance. Under certain conditions, the photons can form a state resembling a two-atom molecule, represented as the blue dumbbell shape at center. Credit: E. Edwards/JQI

A Sept. 8, 2015 NIST news release (also available on EurekAlert*), which originated the news item, provides more information about the research (Note: Links have been removed),

The findings build on previous research that several team members contributed to before joining NIST. In 2013, collaborators from Harvard, Caltech and MIT found a way to bind two photons together so that one would sit right atop the other, superimposed as they travel. Their experimental demonstration was considered a breakthrough, because no one had ever constructed anything by combining individual photons—inspiring some to imagine that real-life lightsabers were just around the corner.

Now, in a paper forthcoming in Physical Review Letters, the NIST and University of Maryland-based team (with other collaborators) has showed theoretically that by tweaking a few parameters of the binding process, photons could travel side by side, a specific distance from each other. The arrangement is akin to the way that two hydrogen atoms sit next to each other in a hydrogen molecule.

“It’s not a molecule per se, but you can imagine it as having a similar kind of structure,” says NIST’s Alexey Gorshkov. “We’re learning how to build complex states of light that, in turn, can be built into more complex objects. This is the first time anyone has shown how to bind two photons a finite distance apart.”

While the new findings appear to be a step in the right direction—if we can build a molecule of light, why not a sword?—Gorshkov says he is not optimistic that Jedi Knights will be lining up at NIST’s gift shop anytime soon. The main reason is that binding photons requires extreme conditions difficult to produce with a roomful of lab equipment, let alone fit into a sword’s handle. Still, there are plenty of other reasons to make molecular light—humbler than lightsabers, but useful nonetheless.

“Lots of modern technologies are based on light, from communication technology to high-definition imaging,” Gorshkov says. “Many of them would be greatly improved if we could engineer interactions between photons.”

For example, engineers need a way to precisely calibrate light sensors, and Gorshkov says the findings could make it far easier to create a “standard candle” that shines a precise number of photons at a detector. Perhaps more significant to industry, binding and entangling photons could allow computers to use photons as information processors, a job that electronic switches in your computer do today.

Not only would this provide a new basis for creating computer technology, but it also could result in substantial energy savings. Phone messages and other data that currently travel as light beams through fiber optic cables has to be converted into electrons for processing—an inefficient step that wastes a great deal of electricity. If both the transport and the processing of the data could be done with photons directly, it could reduce these energy losses.

Gorshkov says it will be important to test the new theory in practice for these and other potential benefits.

“It’s a cool new way to study photons,” he says. “They’re massless and fly at the speed of light. Slowing them down and binding them may show us other things we didn’t know about them before.”

Here are links and citations for the paper. First, there’s an early version on arXiv.org and, then, there’s the peer-reviewed version, which is not yet available,

Coulomb bound states of strongly interacting photons by M. F. Maghrebi, M. J. Gullans, P. Bienias, S. Choi, I. Martin, O. Firstenberg, M. D. Lukin, H. P. Büchler, A. V. Gorshkov.      arXiv:1505.03859 [quant-ph] (or arXiv:1505.03859v1 [quant-ph] for this version)

Coulomb bound states of strongly interacting photons by M. F. Maghrebi, M. J. Gullans, P. Bienias, S. Choi, I. Martin, O. Firstenberg, M. D. Lukin, H. P. Büchler, and A. V. Gorshkov.
Phys. Rev. Lett. forthcoming in September 2015.

The first version (arXiv) is open access and I’m not sure whether or not the Physical review Letters study will be behind a paywall or be available as an open access paper.

*EurekAlert link added 10:34 am PST on Sept. 11, 2015.

Science snobbery and the problem of accessibility

There’s a look you see in people’s eyes when you say ‘science’ or ‘mathematics’ or ‘engineering’ or ‘technology’. It’s not happiness or excitement.

At some point in our schooling, the sciences, mathematics, technology, and engineering became the exclusive property of those who were deemed to be talented in those areas and the rest of us weren’t necessarily treated well by the teachers or ‘talented’ fellow students.  Some people are so wounded by the experience they lose any interest or curiosity they might once have had and refuse to engage at all.

The odd thing is that most of us have more experience with science, engineering, and mathematics than we commonly believe.

There are very few people today compared to thirty years ago who don’t more or less understand how a computer operates. Car mechanics typically have to repair very sophisticated mechanical and electronic systems featuring computers and wireless technology. Hairdressers need to know a lot about chemicals and how hair and skin might react to them.  And, on it goes.

A sense of superiority seems to be a feature of human nature as if somehow we need to be better than someone else. That sense of superiority is found in many areas, as well as, within the sciences and mathematics and engineering and technology communities. Chemists are superior to engineers who are superior to technologists and all of them are superior to social scientists who return the favour and look down on scientists who they view as having low moral character and having, undeservedly, lots of money (I was in a session at a 2007 conference where that was the gist of the presentation and comments).

In this somewhat balkanized atmosphere it’s good to see people trying to establish a discussion about science, technology, mathematics, and engineering that doesn’t require an advanced degree or discount the comments of an amateur.

There’s a delightful Aug. 5, 2015 posting by John Hinton for the Guardian science blogs that espouses the joy of a ‘scientist pretender’,

I adored science at school. But my coursework assignments bewildered my teachers. Details of experimentations were often accompanied by personal anecdotes and quotes from obscure song lyrics. Irrelevant clip-art was rife. So when I had to pick a path through the labyrinth of life, i.e. select my A-levels, science fell away in favour of subjects where personal anecdoture and obscure lyricalism are paramount.

Despite my enforced rebuttal of science as a professional pursuit, it always retained a very special place in both my brain and bookshelf. Deep down, I wanted to be a scientist. And if you pretend for long enough (it has been suggested by non-scientists), eventually you become the thing you’re pretending to be.

So six or seven years ago, I started pretending to be a scientist. Specifically, I started pretending to be Charles Darwin in my first science-theatre show, THE ORIGIN OF SPECIES … And people were fooled – they came from far and wide to hear me speak, invited me to Australia and Norway and Croatia and Hemel Hempstead. …

Hinton has also pretended to Einstein but I find his latest pretence the most interesting,

Now it’s not easy, we’re told by lots and lots of people, to recruit women into the sciences – and it’s rendered even harder by off-hand remarks made by Nobel laureates. So I started wondering whether I could pull off the ruse of the century and pretend to be a woman scientist, to see if that’d help matters at all.

The scientist I chose was Marie Curie. Like the other two I’d pretended to be, she is the linchpin to a whole branch of science (evolution, relativity and radioactivity respectively). Like the other two, her discoveries have been used both for good (conservation, GPS, radiotherapy) and bad (eugenics, nuclear bombs, radium quackery). And like the other two, I don’t look very much like her.

I’ve already pretended to be Marie Curie in Brighton, where the reception was very positive, and I shall shortly be pretending to be Marie Curie in Edinburgh. And in a few decades’ time, we’ll see whether my efforts have led to a redress of the gender bias (the scientific basis I’ll use to judge my eventual success shall be strictly cum hoc ergo propter hoc, if you know what I mean).

Hinton will be at the 2015 Edinburgh Fringe Festival, so if you should happen to be in the vicinity,

The Element in the Room: a radioactive muscial comedy about the death and life of Marie Curie runs at Edinburgh Fringe’s Pleasance Courtyard, 5-31 August 2015 at 3.30pm, alongside the full trilogy playing in rep.

More information here.

While this next bit concerns women and science, it still pertains to the main theme of this posting which is that anyone can participate in science/mathematics/technology/engineering, including comedians. David Bruggeman in an Aug. 4, 2015 posting on his Pasco Phronesis blog reveals information about a very interesting new video series (Note: Links have been removed),

Last fall [2014] Megan Amram released Science…For Her!, a science textbook written as though by a women’s magazine writer who knows little about science.

If you couldn’t be bothered to read the whole thing, but still want to dive in, Amram has a solution.  She has partnered with Amy Poehler’s Smart Girls on a web series, Experimenting with Megan Amram.  (Poehler’s website has a great deal of science, technology, engineering and mathematics – STEM – content worth exploring, not just this series.)

I find it inspiring that comedy writers want to talk about science. You can find Experimenting with Meg Amram here. I understand from David’s posting that this is comedy with some science and the first episode features an interview with Dr. Beverly McKeon, associate director of the Graduate Aerospace Laboratories at the California Institute of Technology (CalTech).

Meg Amram and her book were featured here in a May 25, 2014 posting about the then upcoming book. For anyone unfamiliar with Meg Amram and Amy Poehler you can check out the Internet Movie DataBase (imdb.com) for their various television and movie credits.