Category Archives: science

Nucleic acid-based memory storage

We’re running out of memory. To be more specific, there are two problems: the supply of silicon and a limit to how much silicon-based memory can store. An April 27, 2016 news item on Nanowerk announces a nucleic acid-based approach to solving the memory problem,

A group of Boise State [Boise State University in Idaho, US] researchers, led by associate professor of materials science and engineering and associate dean of the College of Innovation and Design Will Hughes, is working toward a better way to store digital information using nucleic acid memory (NAM).

An April 25, 2016 Boise State University news release, which originated the news item, expands on the theme of computer memory and provides more details about the approach,

It’s no secret that as a society we generate vast amounts of data each year. So much so that the 30 billion watts of electricity used annually by server farms today is roughly equivalent to the output of 30 nuclear power plants.

And the demand keeps growing. The global flash memory market is predicted to reach $30.2 billion this year, potentially growing to $80.3 billion by 2025. Experts estimate that by 2040, the demand for global memory will exceed the projected supply of silicon (the raw material used to store flash memory). Furthermore, electronic memory is rapidly approaching its fundamental size limits because of the difficulty in storing electrons in small dimensions.

Hughes, with post-doctoral researcher Reza Zadegan and colleagues Victor Zhirnov (Semiconductor Research Corporation), Gurtej Sandhun (Micron Technology Inc.) and George Church (Harvard University), is looking to DNA molecules to solve the problem. Nucleic acid — the “NA” in “DNA” — far surpasses electronic memory in retention time, according to the researchers, while also providing greater information density and energy of operation.

Their conclusions are outlined in an invited commentary in the prestigious journal Nature Materials published earlier this month.

“DNA is the data storage material of life in general,” said Hughes. “Because of its physical and chemical properties, it also may become the data storage material of our lives.” It may sound like science fiction, but Hughes will participate in an invitation-only workshop this month at the Intelligence Advanced Research Projects Activity (IARPA) Agency to envision a portable DNA hard drive that would have 500 Terabytes of searchable data – that’s about the the size of the Library of Congress Web Archive.

“When information bits are encoded into polymer strings, researchers and manufacturers can manage and manipulate physical, chemical and biological information with standard molecular biology techniques,” the paper [in Nature Materials?] states.

Cost-competitive technologies to read and write DNA could lead to real-world applications ranging from artificial chromosomes, digital hard drives and information-management systems, to a platform for watermarking and tracking genetic content or next-generation encryption tools that necessitate physical rather than electronic embodiment.

Here’s how it works. Current binary code uses 0’s and 1’s to represent bits of information. A computer program then accesses a specific decoder to turn the numbers back into usable data. With nucleic acid memory, 0’s and 1’s are replaced with the nucleotides A, T, C and G. Known as monomers, they are covalently bonded to form longer polymer chains, also known as information strings.

Because of DNA’s superior ability to store data, DNA can contain all the information in the world in a small box measuring 10 x 10 x 10 centimeters cubed. NAM could thus be used as a sustainable time capsule for massive, scientific, financial, governmental, historical, genealogical, personal and genetic records.

Better yet, DNA can store digital information for a very long time – thousands to millions of years. Currently, usable information has been extracted from DNA in bones that are 700,000 years old, making nucleic acid memory a promising archival material. And nucleic acid memory uses 100 million times less energy than storing data electronically in flash, and the data can live on for generations.

At Boise State, Hughes and Zadegan are examining DNA’s stability under extreme conditions. DNA strands are subjected to temperatures varying from negative 20 degrees Celsius to 100 degrees Celsius, and to a variety of UV exposures to see if they can still retain their information. What they’re finding is that much less information is lost with NAM than with the current state of the industry.

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

Nucleic acid memory by Victor Zhirnov, Reza M. Zadegan, Gurtej S. Sandhu, George M. Church, & William L. Hughes. Nature Materials 15, 366–370 (2016)  doi:10.1038/nmat4594 Published online 23 March 2016

This paper is behind a paywall.

Exploring the science of Iron Man (prior to the opening of Captain America: Civil War, aka, Captain America vs. Iron Man)

Not unexpectedly, there’s a news item about science and Iron Man (it’s getting quite common for the science in movies to be promoted and discussed) just a few weeks before the movie Captain America: Civil War or, as it’s also known, Captain America vs. Iron Man opens in the US. From an April 26, 2016 news item on phys.org,

… how much of our favourite superheros’ power lies in science and how much is complete fiction?

As Iron Man’s name suggests, he wears a suit of “iron” which gives him his abilities—superhuman strength, flight and an arsenal of weapons—and protects him from harm.

In scientific parlance, the Iron man suit is an exoskeleton which is worn outside the body to enhance it.

An April 26, 2016 posting by Chris Marr on the ScienceNetwork Western Australia blog, which originated the news item, provides an interesting overview of exoskeletons and some of the scientific obstacles still to be overcome before they become commonplace,

In the 1960s, the first real powered exoskeleton appeared—a machine integrated with the human frame and movements which provided the wearer with 25 times his natural lifting capacity.

The major drawback then was that the unit itself weighed in at 680kg.

UWA [University of Western Australia] Professor Adrian Keating suggests that some of the technology seen in the latest Marvel blockbuster, such as controlling the exoskeleton with simple thoughts, will be available in the near future by leveraging ongoing advances of multi-disciplinary research teams.

“Dust grain-sized micromachines could be programmed to cooperate to form reconfigurable materials such as the retractable face mask, for example,” Prof Keating says.

However, all of these devices are in need of a power unit small enough to be carried yet providing enough capacity for more than a few minutes of superhuman use, he says.

Does anyone have a spare Arc Reactor?

Currently, most exoskeleton development has been for medical applications, with devices designed to give mobility to amputees and paraplegics, and there are a number in commercial production and use.

Dr Lei Cui, who lectures in Mechatronics at Curtin University, has recently developed both a hand and leg exoskeleton, designed for use by patients who have undergone surgery or have nerve dysfunction, spinal injuries or muscular dysfunction.

“Currently we use an internal battery that lasts about two hours in the glove, which can be programmed for only four different movement patterns,” Dr Cui says.

Dr Cui’s exoskeletons are made from plastic, making them light but offering little protection compared to the titanium exterior of Stark’s favourite suit.

It’s clear that we are a long way from being able to produce a working Iron Man suit at all, let alone one that flies, protects the wearer and has the capacity to fight back.

This is not the first time I’ve featured a science and pop culture story here. You can check out my April 28, 2014 posting for a story about how Captain America’s shield could be a supercapacitor (it also has a link to a North Carolina State University blog featuring science and other comic book heroes) and there is my May 6, 2013 post about Iron Man 3 and a real life injectable nano-network.

As for ScienceNetwork Western Australia, here’s more from their About SWNA page,

ScienceNetwork Western Australia (SNWA) is an online science news service devoted to sharing WA’s achievements in science and technology.

SNWA is produced by Scitech, the state’s science and technology centre and supported by the WA Government’s Office of Science via the Department of the Premier and Cabinet.

Our team of freelance writers work with in-house editors based at Scitech to bring you news from all fields of science, and from the research, government and private industry sectors working throughout the state. Our writers also produce profile stories on scientists. We collaborate with leading WA institutions to bring you Perspectives from prominent WA scientists and opinion leaders.

We also share news of science-related events and information about the greater WA science community including WA’s Chief Scientist, the Premier’s Science Awards, Innovator of the Year Awards and information on regional community science engagement.

Since our commencement in 2003 we have grown to share WA’s stories with local, national and global audiences. Our articles are regularly republished in print and online media in the metropolitan and regional areas.

Bravo to the Western Australia government! I wish there  initiatives of this type in Canada, the closest we have is the French language Agence Science-Presse supported by the Province of Québec.

A new state for water molecules

ORNL researchers discovered that water in beryl displays some unique and unexpected characteristics. (Photo by Jeff Scovil)

ORNL researchers discovered that water in beryl displays some unique and unexpected characteristics. (Photo by Jeff Scovil)

That striking image from the Oak Ridge National Laboratory (ORNL; US) depicting a new state for water molecules looks like mixed media: photography and drawing/illustration. Thankfully, an April 22, 2016 news item on ScienceDaily provides a text description,

Neutron scattering and computational modeling have revealed unique and unexpected behavior of water molecules under extreme confinement that is unmatched by any known gas, liquid or solid states.

In a paper published in Physical Review Letters, researchers at the Department of Energy’s Oak Ridge National Laboratory [ORNL] describe a new tunneling state of water molecules confined in hexagonal ultra-small channels — 5 angstrom across — of the mineral beryl. An angstrom is 1/10-billionth of a meter, and individual atoms are typically about 1 angstrom in diameter.

The discovery, made possible with experiments at ORNL’s Spallation Neutron Source and the Rutherford Appleton Laboratory in the United Kingdom, demonstrates features of water under ultra confinement in rocks, soil and cell walls, which scientists predict will be of interest across many disciplines.

An April 22, 2016 ORNL news release (also on EurekAlert), which originated the news item, offers more detail,

“At low temperatures, this tunneling water exhibits quantum motion through the separating potential walls, which is forbidden in the classical world,” said lead author Alexander Kolesnikov of ORNL’s Chemical and Engineering Materials Division. “This means that the oxygen and hydrogen atoms of the water molecule are ‘delocalized’ and therefore simultaneously present in all six symmetrically equivalent positions in the channel at the same time. It’s one of those phenomena that only occur in quantum mechanics and has no parallel in our everyday experience.”

The existence of the tunneling state of water shown in ORNL’s study should help scientists better describe the thermodynamic properties and behavior of water in highly confined environments such as water diffusion and transport in the channels of cell membranes, in carbon nanotubes and along grain boundaries and at mineral interfaces in a host of geological environments.

ORNL co-author Lawrence Anovitz noted that the discovery is apt to spark discussions among materials, biological, geological and computational scientists as they attempt to explain the mechanism behind this phenomenon and understand how it applies to their materials.

“This discovery represents a new fundamental understanding of the behavior of water and the way water utilizes energy,” Anovitz said. “It’s also interesting to think that those water molecules in your aquamarine or emerald ring – blue and green varieties of beryl – are undergoing the same quantum tunneling we’ve seen in our experiments.”

While previous studies have observed tunneling of atomic hydrogen in other systems, the ORNL discovery that water exhibits such tunneling behavior is unprecedented. The neutron scattering and computational chemistry experiments showed that, in the tunneling state, the water molecules are delocalized around a ring so the water molecule assumes an unusual double top-like shape.

“The average kinetic energy of the water protons directly obtained from the neutron experiment is a measure of their motion at almost absolute zero temperature and is about 30 percent less than it is in bulk liquid or solid water,” Kolesnikov said. “This is in complete disagreement with accepted models based on the energies of its vibrational modes.”

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

Quantum Tunneling of Water in Beryl: A New State of the Water Molecule by Alexander I. Kolesnikov, George F. Reiter, Narayani Choudhury, Timothy R. Prisk, Eugene Mamontov, Andrey Podlesnyak, George Ehlers, Andrew G. Seel, David J. Wesolowski, and Lawrence M. Anovitz.
Phys. Rev. Lett. 116, 167802 – Published 22 April 2016

This paper is behind a paywall.

An atom without properties?

There’s rather intriguing Swiss research into atoms and so-called Bell Correlations according to an April 21, 2016 news item on ScienceDaily,

The microscopic world is governed by the rules of quantum mechanics, where the properties of a particle can be completely undetermined and yet strongly correlated with those of other particles. Physicists from the University of Basel have observed these so-called Bell correlations for the first time between hundreds of atoms. Their findings are published in the scientific journal Science.

Everyday objects possess properties independently of each other and regardless of whether we observe them or not. Einstein famously asked whether the moon still exists if no one is there to look at it; we answer with a resounding yes. This apparent certainty does not exist in the realm of small particles. The location, speed or magnetic moment of an atom can be entirely indeterminate and yet still depend greatly on the measurements of other distant atoms.

An April 21, 2016 University of Basel (Switzerland) press release (also on EurekAlert), which originated the news item, provides further explanation,

With the (false) assumption that atoms possess their properties independently of measurements and independently of each other, a so-called Bell inequality can be derived. If it is violated by the results of an experiment, it follows that the properties of the atoms must be interdependent. This is described as Bell correlations between atoms, which also imply that each atom takes on its properties only at the moment of the measurement. Before the measurement, these properties are not only unknown – they do not even exist.

A team of researchers led by professors Nicolas Sangouard and Philipp Treutlein from the University of Basel, along with colleagues from Singapore, have now observed these Bell correlations for the first time in a relatively large system, specifically among 480 atoms in a Bose-Einstein condensate. Earlier experiments showed Bell correlations with a maximum of four light particles or 14 atoms. The results mean that these peculiar quantum effects may also play a role in larger systems.

Large number of interacting particles

In order to observe Bell correlations in systems consisting of many particles, the researchers first had to develop a new method that does not require measuring each particle individually – which would require a level of control beyond what is currently possible. The team succeeded in this task with the help of a Bell inequality that was only recently discovered. The Basel researchers tested their method in the lab with small clouds of ultracold atoms cooled with laser light down to a few billionths of a degree above absolute zero. The atoms in the cloud constantly collide, causing their magnetic moments to become slowly entangled. When this entanglement reaches a certain magnitude, Bell correlations can be detected. Author Roman Schmied explains: “One would expect that random collisions simply cause disorder. Instead, the quantum-mechanical properties become entangled so strongly that they violate classical statistics.”

More specifically, each atom is first brought into a quantum superposition of two states. After the atoms have become entangled through collisions, researchers count how many of the atoms are actually in each of the two states. This division varies randomly between trials. If these variations fall below a certain threshold, it appears as if the atoms have ‘agreed’ on their measurement results; this agreement describes precisely the Bell correlations.

New scientific territory

The work presented, which was funded by the National Centre of Competence in Research Quantum Science and Technology (NCCR QSIT), may open up new possibilities in quantum technology; for example, for generating random numbers or for quantum-secure data transmission. New prospects in basic research open up as well: “Bell correlations in many-particle systems are a largely unexplored field with many open questions – we are entering uncharted territory with our experiments,” says Philipp Treutlein.

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

Bell correlations in a Bose-Einstein condensate by Roman Schmied, Jean-Daniel Bancal, Baptiste Allard, Matteo Fadel, Valerio Scarani, Philipp Treutlein, Nicolas Sangouard. Science  22 Apr 2016: Vol. 352, Issue 6284, pp. 441-444 DOI: 10.1126/science.aad8665

This paper is behind a paywall.

Artificial intelligence used for wildlife protection

PAWS (Protection Assistant for Wildlife Security), an artificial intelligence (AI) program, has been tested in Uganda and Malaysia. according to an April 22, 2016 US National Science Foundation (NSF) news release (also on EurekAlert but dated April 21, 2016), Note: Links have been removed,

A century ago, more than 60,000 tigers roamed the wild. Today, the worldwide estimate has dwindled to around 3,200. Poaching is one of the main drivers of this precipitous drop. Whether killed for skins, medicine or trophy hunting, humans have pushed tigers to near-extinction. The same applies to other large animal species like elephants and rhinoceros that play unique and crucial roles in the ecosystems where they live.

Human patrols serve as the most direct form of protection of endangered animals, especially in large national parks. However, protection agencies have limited resources for patrols.

With support from the National Science Foundation (NSF) and the Army Research Office, researchers are using artificial intelligence (AI) and game theory to solve poaching, illegal logging and other problems worldwide, in collaboration with researchers and conservationists in the U.S., Singapore, Netherlands and Malaysia.

“In most parks, ranger patrols are poorly planned, reactive rather than pro-active, and habitual,” according to Fei Fang, a Ph.D. candidate in the computer science department at the University of Southern California (USC).

Fang is part of an NSF-funded team at USC led by Milind Tambe, professor of computer science and industrial and systems engineering and director of the Teamcore Research Group on Agents and Multiagent Systems.

Their research builds on the idea of “green security games” — the application of game theory to wildlife protection. Game theory uses mathematical and computer models of conflict and cooperation between rational decision-makers to predict the behavior of adversaries and plan optimal approaches for containment. The Coast Guard and Transportation Security Administration have used similar methods developed by Tambe and others to protect airports and waterways.

“This research is a step in demonstrating that AI can have a really significant positive impact on society and allow us to assist humanity in solving some of the major challenges we face,” Tambe said.

PAWS puts the claws in anti-poaching

The team presented papers describing how they use their methods to improve the success of human patrols around the world at the AAAI Conference on Artificial Intelligence in February [2016].

The researchers first created an AI-driven application called PAWS (Protection Assistant for Wildlife Security) in 2013 and tested the application in Uganda and Malaysia in 2014. Pilot implementations of PAWS revealed some limitations, but also led to significant improvements.

Here’s a video describing the issues and PAWS,

For those who prefer to read about details rather listen, there’s more from the news release,

PAWS uses data on past patrols and evidence of poaching. As it receives more data, the system “learns” and improves its patrol planning. Already, the system has led to more observations of poacher activities per kilometer.

Its key technical advance lies in its ability to incorporate complex terrain information, including the topography of protected areas. That results in practical patrol routes that minimize elevation changes, saving time and energy. Moreover, the system can also take into account the natural transit paths that have the most animal traffic – and thus the most poaching – creating a “street map” for patrols.

“We need to provide actual patrol routes that can be practically followed,” Fang said. “These routes need to go back to a base camp and the patrols can’t be too long. We list all possible patrol routes and then determine which is most effective.”

The application also randomizes patrols to avoid falling into predictable patterns.

“If the poachers observe that patrols go to some areas more often than others, then the poachers place their snares elsewhere,” Fang said.

Since 2015, two non-governmental organizations, Panthera and Rimbat, have used PAWS to protect forests in Malaysia. The research won the Innovative Applications of Artificial Intelligence award for deployed application, as one of the best AI applications with measurable benefits.

The team recently combined PAWS with a new tool called CAPTURE (Comprehensive Anti-Poaching Tool with Temporal and Observation Uncertainty Reasoning) that predicts attacking probability even more accurately.

In addition to helping patrols find poachers, the tools may assist them with intercepting trafficked wildlife products and other high-risk cargo, adding another layer to wildlife protection. The researchers are in conversations with wildlife authorities in Uganda to deploy the system later this year. They will present their findings at the 15th International Conference on Autonomous Agents and Multiagent Systems (AAMAS 2016) in May.

“There is an urgent need to protect the natural resources and wildlife on our beautiful planet, and we computer scientists can help in various ways,” Fang said. “Our work on PAWS addresses one facet of the problem, improving the efficiency of patrols to combat poaching.”

There is yet another potential use for PAWS, the prevention of illegal logging,

While Fang and her colleagues work to develop effective anti-poaching patrol planning systems, other members of the USC team are developing complementary methods to prevent illegal logging, a major economic and environmental problem for many developing countries.

The World Wildlife Fund estimates trade in illegally harvested timber to be worth between $30 billion and $100 billion annually. The practice also threatens ancient forests and critical habitats for wildlife.

Researchers at USC, the University of Texas at El Paso and Michigan State University recently partnered with the non-profit organization Alliance Vohoary Gasy to limit the illegal logging of rosewood and ebony trees in Madagascar, which has caused a loss of forest cover on the island nation.

Forest protection agencies also face limited budgets and must cover large areas, making sound investments in security resources critical.

The research team worked to determine the balance of security resources in which Madagascar should invest to maximize protection, and to figure out how to best deploy those resources.

Past work in game theory-based security typically involved specified teams — the security workers assigned to airport checkpoints, for example, or the air marshals deployed on flight tours. Finding optimal security solutions for those scenarios is difficult; a solution involving an open-ended team had not previously been feasible.

To solve this problem, the researchers developed a new method called SORT (Simultaneous Optimization of Resource Teams) that they have been experimentally validating using real data from Madagascar.

The research team created maps of the national parks, modeled the costs of all possible security resources using local salaries and budgets, and computed the best combination of resources given these conditions.

“We compared the value of using an optimal team determined by our algorithm versus a randomly chosen team and the algorithm did significantly better,” said Sara Mc Carthy, a Ph.D. student in computer science at USC.

The algorithm is simple and fast, and can be generalized to other national parks with different characteristics. The team is working to deploy it in Madagascar in association with the Alliance Vohoary Gasy.

“I am very proud of what my PhD students Fei Fang and Sara Mc Carthy have accomplished in this research on AI for wildlife security and forest protection,” said Tambe, the team lead. “Interdisciplinary collaboration with practitioners in the field was key in this research and allowed us to improve our research in artificial intelligence.”

Moreover, the project shows other computer science researchers the potential impact of applying their research to the world’s problems.

“This work is not only important because of the direct beneficial impact that it has on the environment, protecting wildlife and forests, but on the way that it can inspire other to dedicate their efforts into making the world a better place,” Mc Carthy said.

The curious can find out more about Panthera here and about Alliance Vohoary Gasy here (be prepared to use your French language skills). Unfortunately, I could not find more information about Rimbat.

Macchiarini controversy and synthetic trachea transplants (part 2 of 2)

For some bizarre frosting on this disturbing cake (see part 1 of the Macchiarini controversy and synthetic trachea transplants for the medical science aspects), a January 5, 2016 Vanity Fair article by Adam Ciralsky documents Macchiarini’s courtship of an NBC ([US] National Broadcasting Corporation) news producer who was preparing a documentary about him and his work,

Macchiarini, 57, is a magnet for superlatives. He is commonly referred to as “world-renowned” and a “super-surgeon.” He is credited with medical miracles, including the world’s first synthetic organ transplant, which involved fashioning a trachea, or windpipe, out of plastic and then coating it with a patient’s own stem cells. That feat, in 2011, appeared to solve two of medicine’s more intractable problems—organ rejection and the lack of donor organs—and brought with it major media exposure for Macchiarini and his employer, Stockholm’s Karolinska Institute, home of the Nobel Prize in Physiology or Medicine. Macchiarini was now planning another first: a synthetic-trachea transplant on a child, a two-year-old Korean-Canadian girl named Hannah Warren, who had spent her entire life in a Seoul hospital. …

Macchiarini had come to Vieira’s [Meredith Vieira, American journalist] attention in September 2012, when she read a front-page New York Times story about the doctor. She turned to [Benita] Alexander, one of her most seasoned and levelheaded producers, to look into a regenerative-medicine story for television.

When Alexander and Macchiarini found themselves together in Illinois for a period of weeks in the spring of 2013—brought there by the NBC special—they met frequently for quiet dinners. The trachea transplant on Hannah Warren, the Korean-Canadian girl, was being performed at Children’s Hospital of Illinois, in Peoria, and the procedure was fraught with risks, not least because Macchiarini’s technique was still a work in progress even for adults. (Christopher Lyles, an American who became the second person to receive an artificial trachea, died less than four months after his surgery at Karolinska.) “He’s a brilliant scientist and a great technical surgeon,” said Dr. Richard Pearl, who operated alongside Macchiarini in Illinois. Like others, Pearl described his Italian colleague as a Renaissance man, fluent in half a dozen languages. Another person, who would get to know him through Alexander, compared Macchiarini to “the Most Interesting Man in the World,” the character made famous in Dos Equis beer commercials.

In Peoria, Macchiarini’s medical magic appeared to have its limitations. Hannah Warren died from post-surgical complications less than three months after the transplant. Her anatomy “was much more challenging than we realized,” Pearl recounted. “Scientifically, the operation itself worked. It was just a shame what happened. When you’re doing something for the first time, you don’t have a textbook. It was the hardest operation I’ve ever scrubbed on.”

Then, there was the romance (from the Ciralsky article),

The personal relationship between Alexander and Macchiarini continued to blossom. In June 2013, they flew to Venice for what Alexander called “an incredibly romantic weekend.” Macchiarini bought her red roses and Venetian-glass earrings and took her on a gondola ride under the Bridge of Sighs. Like a pair of teenagers, they attached love locks to the Ponte dell’Accademia bridge, one of them bearing the inscription “B—P 23/6/13, 4 Ever.” Alexander told me that, “when he took me to Venice, we were still shooting the story … He always paid for everything … gifts, expensive dinners, flowers—the works. When it came to money, he was incredibly generous.”

It is a bedrock principle at NBC and every other news organization that journalists must avoid conflicts of interest, real or apparent. Alexander was not oblivious to this. “I knew that I was crossing the line in the sense that it’s a basic and well-understood rule of journalism that you don’t become involved with one of the subjects of your story, because your objectivity could clearly become compromised,” she told me. “I never once thought about him paying for the trip as him ‘buying’ me in some fashion, or potentially using money to influence me, because, from my perspective anyway … that just wasn’t the case. We were just crazy about each other, and I was falling in love.”

Alexander made her way to Stockholm at a later date (from the Ciralsky article),

Macchiarini was in Stockholm to attend to Yesim Cetir, a 25-year-old Turkish woman whose artificial trachea had failed. As Swedish television later reported, “It has taken nearly 100 surgeries to support the cell tissue around the airpipes. Her breathing is bad, and to avoid suffocation, her respiratory tract must be cleansed from mucus every fourth hour. She has now been lying in the hospital for nearly 1,000 days.” NBC’s special would come to include skeptical commentary from Dr. Joseph Vacanti, who questioned the sufficiency of Macchiarini’s research, but Cetir’s post-operative complications were not mentioned.

Prior to the NBC documentary’s (A Leap of Faith) airing, the romance became an engagement (from the Ciralsky article),

Macchiarini proposed to Benita Alexander on Christmas Day 2013, Alexander said. In the months leading up to the airing of A Leap of Faith, in June 2014, Macchiarini and Alexander went on trips to the Bahamas, Turkey, Mexico, Greece, and Italy. They went on shopping sprees and ate their way through Michelin-starred restaurants. Macchiarini even took Alexander and her daughter to meet his mother at her home, in Lucca. “She cooked homemade gnocchi,” Alexander recalled. Macchiarini’s mother shared pictures from the family photo album while her son translated. Emanuela Pecchia, the woman whom Macchiarini had married years earlier, lived only a short distance away. When Macchiarini informed Alexander, during a dinner cruise later that summer, that his divorce had finally come through, she recounted, he gave her an engagement ring.

In the months that followed, the doctor and his fiancée began planning their wedding in earnest. They set a date for July 11, 2015, in Rome. But their desire to marry in the Catholic Church was complicated by the fact that she is Episcopalian and divorced. Divorce would have been an issue for Macchiarini as well. However, Alexander said, Macchiarini insisted that he would fix things by visiting his friend and patient in the Vatican.

In October 2014, Alexander recalled, Macchiarini told her that he had met with Pope Francis for four hours and that the Pontiff consented to the couple’s marriage and, in yet another sign of his progressive tenure, vowed to officiate. Alexander said Macchiarini referred to himself as Pope Francis’s “personal doctor” and maintained that in subsequent meetings his patient offered to host the wedding at his summer residence, the Apostolic Palace of Castel Gandolfo.

Shortly after quitting her job in anticipation of her July 2015 wedding to Macchiarini, Alexander learned that Pope Francis who was supposed to officiate was in fact scheduled to be in South America during that time.  From the Ciralsky article,

As Alexander would discover with the help of a private investigator named Frank Murphy, virtually every detail Macchiarini provided about the wedding was false. A review of public records in Italy would also seem to indicate that Macchiarini remains married to Emanuela Pecchia, his wife of nearly 30 years. Murphy, who spent 15 years as a Pennsylvania State Police detective, told me, “I’ve never in my experience witnessed a fraud like this, with this level of international flair…. The fact that he could keep all the details straight and compartmentalize these different lives and lies is really amazing.

Ciralsky broaches the question of why someone with Macchiarini’s accomplishments would jeopardize his position in such a way,

To understand why someone of considerable stature could construct such elaborate tales and how he could seemingly make others believe them, I turned to Dr. Ronald Schouten, a Harvard professor who directs the Law and Psychiatry Service at Massachusetts General Hospital. “We’re taught from an early age that when something is too good to be true, it’s not true,” he said. “And yet we ignore the signals. People’s critical judgment gets suspended. In this case, that happened at both the personal and institutional level.” Though he will not diagnose from a distance, Schouten, who is one of the nation’s foremost authorities on psychopathy, observed, “Macchiarini is the extreme form of a con man. He’s clearly bright and has accomplishments, but he can’t contain himself. There’s a void in his personality that he seems to want to fill by conning more and more people.” When I asked how Macchiarini stacks up to, say, Bernie Madoff, he laughed and said, “Madoff was an ordinary con man with a Ponzi scheme. He never claimed to be the chairman of the Federal Reserve. He didn’t suggest he was part of a secret international society of bankers. This guy is really good.”

In addition to the romance, Ciralsky and Vanity Fair checked out Macchiarini’s résumé,

Vanity Fair contacted many of the schools at which Macchiarini claimed to have either earned a degree or held an academic post. While the University of Pisa confirmed that he indeed received an M.D. and had specialized in surgery, the University of Alabama at Birmingham denied that Macchiarini earned a master’s in biostatistics or that he participated in a two-year fellowship in thoracic surgery. In fact, according to U.A.B. spokesman Bob Shepard, the only record the school has for Macchiarini indicates that he did a six-month non-surgical fellowship in hematology/oncology—which according to the current Accreditation Council for Graduate Medical Education guidelines is 30 months shy of what is required for a clinical fellowship in that field. The University of Paris—Sud never responded to repeated requests for comment, but Hannover Medical School wrote to say that Macchiarini had been neither a full nor an associate professor there, merely an adjunct.

Comments

As I noted in part 1, there are medical science and ethical issues to be considered. As well, Macchiarini’s romantic behaviour certainly seems fraudulent as do parts of his curriculum vitae (CV) and there’s more about Macchiarini’s professional accomplishments (read Ciralsky’s entire January 5, 2016 Vanity Fair article for details).

The romantic and CV chicanery may or may not suggest serious problems with Macchiarini’s revolutionary procedure and ethics. History is littered with stories of people who achieved extraordinary advances and were not the most exemplary human beings. Paracelsus, founder of the field of toxicology and an important contributor in the fields of medicine and science, was reputedly a sketchy character. Caravaggio now remembered for his art, killed someone (accidentally or not) and was known for his violent behaviour even in a time when there was higher tolerance for it.

What I’m saying is that Macchiarini may be pioneering something important regardless of how you view his romantic chicanery and falsified CV. Medical research can be high risk and there is no way to avoid that sad fact. However, criticisms of the work from Macchiarini’s colleagues need to be addressed and the charge that a Russian patient who was not in imminent danger and not properly advised of the extremely high risk must also be addressed.

It should also be remembered that Macchiarini did not pull this off by himself. Institutions such as the Karolinska Institute failed to respond appropriately in the initial stages. As well, the venerable medical journal, The Lancet seems reluctant to address the situation even now.

Before dissecting the Alexander situation, it should be said that she showed courage in admitting her professional transgression and discussing a painful and humiliating romantic failure. All of us are capable of misjudgments and wishful thinking, unfortunately for her, this became an international affair.

More critically, Alexander, a journalist, set aside her ethics for a romance and what seems to be surprisingly poor research by Alexander’s team.  (Even I had a little something about this in 2013.) How did a crack NBC research team miss the problems? (For the curious, this Bryan Burrough April 30, 2015 article for Vanity Fair highlighting scandals plaguing NBC News may help to answer the question about NBC research.)

Finally, there’s an enormous amount of pressure on stem cell scientists due to the amounts of money and the degree of prestige involved. Ciralsky’s story notes the pressure when he describes how Macchiarini got one of this positions at an Italian facility in Florence through political machinations. (The situation is a little more complicated than I’ve described here but an accommodation in Macchiarini’s favour was made.) Laura Margottini’s Oct. 7, 2014 article for Science magazine provides a synopsis of another stem cell controversy in Italy.

Stem cell controversies have not been confined to Italy or Europe for that matter. There was the South Korean scandal in 2006 (see a Sept. 19, 2011 BBC [British Broadcasting Corporation] news online post for an update and synopsis) when a respected scientist was found to have falsified research results. Up to that  point, South Korea was considered the world leader in the field.

Finally,  if there are two survivors, is there a possibility that this procedure could be made successful for more patients or that some patients are better candidates than others?

Additional notes

Macchiarini is mounting a defence for himself according to a March 30, 2016 news item on phys.org and a Swedish survey indicates that the average Swede’s trust in researchers still remains high despite the Macchiarini imbroglio according to an April 15, 2016 news item on phys.org.

For anyone interested in the timeline and updates for this scandal, Retraction Watch offers this: http://retractionwatch.com/2016/02/12/reading-about-embattled-trachea-surgeon-paolo-macchiarini-heres-what-you-need-to-know/

Macchiarini controversy and synthetic trachea transplants (part 1 of 2)

Having featured Paolo Macchiarini and his work on transplanting synthetic tracheas into humans when it was lauded (in an Aug. 2, 2011 post titled: Body parts nanostyle), it seems obligatory to provide an update now that he and his work are under a very large cloud. Some of this is not new, there were indications as early as this Dec. 27, 2013 post titled: Trachea transplants: an update which featured an article by Gretchen Vogel in Science magazine hinting at problems.

Now, a Feb. 4, 2016 article by Gretchen Vogel for Science magazine provides a more current update and opens with this (Note: Links have been removed),

The Karolinska Institute (KI) in Stockholm “has lost its confidence” in surgeon Paolo Macchiarini, a senior researcher at the institute, and will end its ties with him. In a statement issued today, KI said that it won’t renew Macchiarini’s contract after it expires on 30 November 2016.

The move comes in the wake of a chilling three-part TV documentary about Macchiarini, a former media darling who was cleared of scientific misconduct charges by KI vice-chancellor Anders Hamsten last summer. Among other things, The Experiments, broadcast in January by Swedish public television channel SVT, suggests that Macchiarini didn’t fully inform his patients about the risks of his pioneering trachea implants. Most of the patients died, including at least one—a woman treated in Krasnodar, Russia—who was not seriously ill before the surgery.

For a profession that has “do no harm” as one of its universal tenets, the hint that a patient not in dire need agreed to a very risky procedure without being properly apprised of the risks is chilling.

Macchiarini’s behavriour is not the only concern, the Karolinska Institute is also being held to account (from the Vogel article),

The film has also raised questions about the way Hamsten and other administrators at KI, Sweden’s most prestigious university and home of the selection committee for the Nobel Prize in Physiology or Medicine, have handled the scandal. Today [Feb. 4, 2016], the Institute’s Board decided to launch an independent review, to be led by an experienced lawyer, into KI’s 5-year relationship with Macchiarini. Among the things the inquiry should address is whether any errors were made or laws were broken when Macchiarini was hired; whether misconduct charges against him were handled properly; and why, given the controversy, he was given a new 1-year contract  as a senior researcher after his appointment as a visiting professor at KI ended in October 2015.

Getting back to Macchiarini (from the Vogel article),

In 2014, colleagues at KI alleged that Macchiarini’s papers made his transplants seem more successful than they were, omitting serious complications. Two patients treated at Karolinska died, and a third has been in intensive care since receiving a trachea in 2012. The Illinois patient also died, as did three patients in Russia. Bengt Gerdin, a professor emeritus of surgery at Uppsala University in Sweden who investigated the charges at KI’s request, concluded in May 2015 that differences between published papers and lab records constituted scientific misconduct. But Hamsten rejected that conclusion in August, based on additional material Macchiarini submitted later.

The documentary shows footage of a patient who says Macchiarini reassured him before the surgery that experiments had been done on pigs, when in fact none had taken place. It also follows the wrenching story of the first patient in Krasnodar. A 33-year-old woman, she was living with a tracheostomy that she said caused her pain, but her condition was not life-threatening. The film suggests that she wasn’t fully aware of the risks of the operation, and that Macchiarini and his colleagues knew about problems with the implant before the surgery. The patient’s first implant failed, and she received a second one in 2013. She died in 2014.

So in May 2015, an investigator concluded there had been scientific misconduct and, yet, Macchiarini’s contract is renewed in the fall of 2015.

Kerry Grens in a March 7, 2016 article for The Scientist provides information about the consequences of the latest investigation into Macchiarini’s work (Note: Links have been removed),

Karl-Henrik Grinnemo, a surgeon at the Karolinska Institute and one of a number of colleagues who voiced concerns about the conduct of fellow surgeon Paolo Macchiarini, is no longer a coauthor on a 2011 The Lancet study led by Macchiarini that described an artificial windpipe. Grinnemo asked to be removed from the paper, and the journal complied last week (March 3).

Grinnemo’s removal from the study is the latest in a string of repercussions related to an investigation of Macchiarini’s work. Last month, the head of the Karolinska Institute, Anders Hamsten, resigned because the institution’s initial investigation concluded no wrongdoing. Hamsten said he and his colleagues were probably wrong about Macchiarini; the institute has launched another investigation into the surgeon’s work.

A March 23, 2016 news item on phys.org announces Macchiarini’s firing from the Karolinska Institute and provides a brief description of his work with synthetic tracheas (Note: A link has been removed),

Sweden’s Karolinska Institute (KI), which awards the Nobel Prize for Medicine, on Wednesday [March 23, 2016] dismissed a Italian transplant surgeon suspected of research fraud and ethical breaches, in an affair that has plunged the renowned institution into crisis.

“It is impossible for KI to continue to have any cooperation with Paolo Macchiarini. He has acted in a way that has had very tragic consequences for the people affected and their families. His conduct has seriously damaged confidence in KI,” human resource director Mats Engelbrektson said in a statement.

Macchiarini, a 57-year-old visiting professor at Karolinska since 2010, rose to fame for carrying out the first synthetic trachea, or windpipe, transplant in 2011.

It was a plastic structure seeded with the patient’s own stem cells—immature cells that grow into specialised cells of the body’s organs.

The surgeon performed three such operations in Stockholm and five others around the world, and the exploit was initially hailed as a game-changer for transplant medicine.

But six of the eight patients reportedly died, and allegations ensued that the risky procedure had been carried out on at least one individual who had not been life-threateningly ill.

Macchiarini is also suspected of lying about his scientific research and his past experience with prestigious medical research centres.

“Paolo Macchiarini supplied false or misleading information in the CV he submitted to KI” and “demonstrated scientific negligence” in his research, said the institute.

H/t to Don Bright, a reader who informed me about this April 2, 2016 posting by Pierre Delaere (a long time Macchiarini critic), published in Leonid Schneider’s blog, For Better Science,

I have written this overview as a trachea surgeon working at KU Leuven and privileged witness of the “Tracheal regeneration scandal” from the very start.

Because of its immense scale, the scandal is difficult to grasp and explain. Fortunately, we have recently been provided with an excellent overview in the 3 x 1-hour documentary by Bosse Lindquist on Swedish national TV. Due to Paolo Macchiarini’s appetite for the spotlights and thanks to the professional standards of the Swedish top producer this is probably the very first case of a medical crime played out in the media. Anyone who has seen this brilliant investigative documentary cannot help but wonder why there are still people who doubt that this is a case of gross medical misconduct.

The story began in Barcelona in 2008 with the publication in The Lancet of a report on a regenerated windpipe, featuring Paolo Macchiarini (PM) as its first author (Macchiarini et al. Lancet 2008). This ground-breaking achievement consisted of bringing to life a dead windpipe from a donor, by putting it in a plastic box, a so-called ‘bioreactor’ together with bone marrow fluid (stem cells). A few weeks later, I wrote a letter to The Lancet, pointing out:

    “The main drawback of the proposed reconstruction is the lack of an intrinsic blood supply to the trachea. We know that a good blood supply is the first requirement in all other tissue and organ transplantations. Therefore, the reported success of this technique is questionable” (correspondence by Delaere and Hermans, Lancet 2009).

Delaere goes on to recount and critique the story of the first synthetic trachea,

…  PM had mounted bone marrow extract (‘stem cells’) on a plastic tube (‘bioartificial trachea’) in a plastic box (‘bioreactor’). After a day or two this creation was ‘successfully’ transplanted in a patient with a trachea defect. This occurred in the Karolinska hospital in July 2011 and was reported on in The Lancet shortly afterwards . Biologically speaking, the procedure is absolutely implausible.

In reality an important part of the windpipe had been replaced by a synthetic tube, and the presence of stem cells made no difference to this whatsoever.

For those not in the field, this procedure may still seem acceptable. A blood vessel can also be replaced by synthetic material because the material can grow into the sterile environment of the blood stream. However, this is completely impossible if the synthetic material is exposed to an environment of inhaled air full of bacteria. The laws of biology allow us to predict accurately what will happen after part of the windpipe has been replaced by a synthetic tube. After some time, the suturing between the synthetic tube and the surrounding tissue will come loose, leading to a number of serious complications. These complications inevitably lead to death in the short (months) or in the mid-long term (a few years). How long the patient will survive also depends on the options still left to treat complications. In most cases so far, a metal stent had to be implanted to keep the airway open in the sutured area.It is entirely predictable that additional complications after placement of the metal stent will ultimately lead to the patient’s death, usually by asphyxiation or by bleeding out after complete rupture of the sutures. This gruesome fate awaiting patients was clearly shown in the documentary. Replacing a part of the trachea by a synthetic tube can therefore be compared to death by medical torture. The amount of suffering it induces is directly proportional to the duration between implantation and the patient’s death.

Delaere describes his own and others’ efforts to bring these issues to light,

Since 2011, I have contacted both the President of KI and the Editors of The Lancet with well-documented information to clarify that what had happened was completely unacceptable. These alerts were repeated in 2013 and 2014. Since 2014, four doctors from KI, who had seen it all happen, have been collecting evidence to show the extent of misconduct [Matthias Corbascio, Thomas Fux, Karl-Henrik Grinnemo and Oscar Simonsson, their letter to Vice-Chancellor Hamsten from June 22, 2015, and its attachments available here; -LS]. Not only did KI not react to the doctors’ complaint, these doctors were in fact intimidated and threatened with dismissal. KI’s Ethical Commission came to a verdict of ‘no misconduct’ in April 2015 following an inquiry based on a series of complaints filed by myself [verdict available from SVT here, -LS]. The Lancet Editor did not even bother to reply to my complaints.

In the reports, eight patients were given synthetic tracheas with six now dead and, allegedly, two still living. Delaere comments,

… To prove that this transplantation technique is effective, reports about the long-term success of this technique in the first 2 patients in Barcelona and London is still being spread. What the real situation of the two patients is at the moment is very difficult to establish. For some time now, reports about these two cases seem to have disappeared from the face of the earth. After the air has been cleared in Sweden, the same will probably happen in London and Barcelona.

Comments

Sometimes medical research can be very dangerous. While, a 25% chance of success (two of Macchiarini’s eight patients undergoing the synthetic trachea transplant have allegedly survived) is not encouraging, it’s understandable that people in dire circumstances and with no other options might want to take a chance.

It’s troubling that the woman in Russia was not in dire straights and that she may not have known how dangerous the procedure is. It would have been unethical of Macchiarini to knowingly perform the procedure under those circumstances.

I am wrestling with some questions about the composite used to create the synthetic trachea and the surviving patients. My understanding is that the composite was designed for eventual deterioration as the patient’s own harvested stem cells fully formed the trachea. Whether the trachea is the one I imagined or he plastic one described by Delaere, how did two patients survive and what is their condition now? The first patient Andemariam Teklesenbet Beyene in 2011 had apparently completed his PhD studies by 2013 (my Dec. 27, 2013 posting). Assuming Beyene is one of the two survivors, what has happened to him and the other one?

As for Delaere’s comments, he certainly raises some red flags not only regarding the procedure but the behaviour of the Lancet editorial team and the Karolinska Institute (they seem to be addressing the issues by firing Macchiarini and with the  resignations of the staff and board).

There are two more twists to this story, which carries on in part 2.

Are they just computer games or are we in a race with technology?

This story poses some interesting questions that touch on the uneasiness being felt as computers get ‘smarter’. From an April 13, 2016 news item on ScienceDaily,

The saying of philosopher René Descartes of what makes humans unique is beginning to sound hollow. ‘I think — therefore soon I am obsolete’ seems more appropriate. When a computer routinely beats us at chess and we can barely navigate without the help of a GPS, have we outlived our place in the world? Not quite. Welcome to the front line of research in cognitive skills, quantum computers and gaming.

Today there is an on-going battle between man and machine. While genuine machine consciousness is still years into the future, we are beginning to see computers make choices that previously demanded a human’s input. Recently, the world held its breath as Google’s algorithm AlphaGo beat a professional player in the game Go–an achievement demonstrating the explosive speed of development in machine capabilities.

An April 13, 2016 Aarhus University press release (also on EurekAlert) by Rasmus Rørbæk, which originated the news item, further develops the point,

But we are not beaten yet — human skills are still superior in some areas. This is one of the conclusions of a recent study by Danish physicist Jacob Sherson, published in the journal Nature.

“It may sound dramatic, but we are currently in a race with technology — and steadily being overtaken in many areas. Features that used to be uniquely human are fully captured by contemporary algorithms. Our results are here to demonstrate that there is still a difference between the abilities of a man and a machine,” explains Jacob Sherson.

At the interface between quantum physics and computer games, Sherson and his research group at Aarhus University have identified one of the abilities that still makes us unique compared to a computer’s enormous processing power: our skill in approaching problems heuristically and solving them intuitively. The discovery was made at the AU Ideas Centre CODER, where an interdisciplinary team of researchers work to transfer some human traits to the way computer algorithms work. ?

Quantum physics holds the promise of immense technological advances in areas ranging from computing to high-precision measurements. However, the problems that need to be solved to get there are so complex that even the most powerful supercomputers struggle with them. This is where the core idea behind CODER–combining the processing power of computers with human ingenuity — becomes clear. ?

Our common intuition

Like Columbus in QuantumLand, the CODER research group mapped out how the human brain is able to make decisions based on intuition and accumulated experience. This is done using the online game “Quantum Moves.” Over 10,000 people have played the game that allows everyone contribute to basic research in quantum physics.

“The map we created gives us insight into the strategies formed by the human brain. We behave intuitively when we need to solve an unknown problem, whereas for a computer this is incomprehensible. A computer churns through enormous amounts of information, but we can choose not to do this by basing our decision on experience or intuition. It is these intuitive insights that we discovered by analysing the Quantum Moves player solutions,” explains Jacob Sherson. ? [sic]

The laws of quantum physics dictate an upper speed limit for data manipulation, which in turn sets the ultimate limit to the processing power of quantum computers — the Quantum Speed ??Limit. Until now a computer algorithm has been used to identify this limit. It turns out that with human input researchers can find much better solutions than the algorithm.

“The players solve a very complex problem by creating simple strategies. Where a computer goes through all available options, players automatically search for a solution that intuitively feels right. Through our analysis we found that there are common features in the players’ solutions, providing a glimpse into the shared intuition of humanity. If we can teach computers to recognise these good solutions, calculations will be much faster. In a sense we are downloading our common intuition to the computer” says Jacob Sherson.

And it works. The group has shown that we can break the Quantum Speed Limit by combining the cerebral cortex and computer chips. This is the new powerful tool in the development of quantum computers and other quantum technologies.

After the buildup, the press release focuses on citizen science and computer games,

Science is often perceived as something distant and exclusive, conducted behind closed doors. To enter you have to go through years of education, and preferably have a doctorate or two. Now a completely different reality is materialising.? [sic]

In recent years, a new phenomenon has appeared–citizen science breaks down the walls of the laboratory and invites in everyone who wants to contribute. The team at Aarhus University uses games to engage people in voluntary science research. Every week people around the world spend 3 billion hours playing games. Games are entering almost all areas of our daily life and have the potential to become an invaluable resource for science.

“Who needs a supercomputer if we can access even a small fraction of this computing power? By turning science into games, anyone can do research in quantum physics. We have shown that games break down the barriers between quantum physicists and people of all backgrounds, providing phenomenal insights into state-of-the-art research. Our project combines the best of both worlds and helps challenge established paradigms in computational research,” explains Jacob Sherson.

The difference between the machine and us, figuratively speaking, is that we intuitively reach for the needle in a haystack without knowing exactly where it is. We ‘guess’ based on experience and thereby skip a whole series of bad options. For Quantum Moves, intuitive human actions have been shown to be compatible with the best computer solutions. In the future it will be exciting to explore many other problems with the aid of human intuition.

“We are at the borderline of what we as humans can understand when faced with the problems of quantum physics. With the problem underlying Quantum Moves we give the computer every chance to beat us. Yet, over and over again we see that players are more efficient than machines at solving the problem. While Hollywood blockbusters on artificial intelligence are starting to seem increasingly realistic, our results demonstrate that the comparison between man and machine still sometimes favours us. We are very far from computers with human-type cognition,” says Jacob Sherson and continues:

“Our work is first and foremost a big step towards the understanding of quantum physical challenges. We do not know if this can be transferred to other challenging problems, but it is definitely something that we will work hard to resolve in the coming years.”

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

Exploring the quantum speed limit with computer games by Jens Jakob W. H. Sørensen, Mads Kock Pedersen, Michael Munch, Pinja Haikka, Jesper Halkjær Jensen, Tilo Planke, Morten Ginnerup Andreasen, Miroslav Gajdacz, Klaus Mølmer, Andreas Lieberoth, & Jacob F. Sherson. Nature 532, 210–213  (14 April 2016) doi:10.1038/nature17620 Published online 13 April 2016

This paper is behind a paywall.

YBC 7289: a 3,800-year-old mathematical text and 3D printing at Yale University

1,300 years before Pythagoras came up with the theorem associated with his name, a school kid in Babylon formed a disc out of clay and scratched out the theorem when the surface was drying.  According to an April 12, 2016 news item on phys.org the Bablyonians got to the theorem first, (Note: A link has been removed),

Thirty-eight hundred years ago, on the hot river plains of what is now southern Iraq, a Babylonian student did a bit of schoolwork that changed our understanding of ancient mathematics. The student scooped up a palm-sized clump of wet clay, formed a disc about the size and shape of a hamburger, and let it dry down a bit in the sun. On the surface of the moist clay the student drew a diagram that showed the people of the Old Babylonian Period (1,900–1,700 B.C.E.) fully understood the principles of the “Pythagorean Theorem” 1300 years before Greek geometer Pythagoras was born, and were also capable of calculating the square root of two to six decimal places.

Today, thanks to the Internet and new digital scanning methods being employed at Yale, this ancient geometry lesson continues to be used in modern classrooms around the world.

Just when you think it’s all about the theorem, the story which originated in an April 11, 2016 Yale University news release by Patrick Lynch takes a turn,

“This geometry tablet is one of the most-reproduced cultural objects that Yale owns — it’s published in mathematics textbooks the world over,” says Professor Benjamin Foster, curator of the Babylonian Collection, which includes the tablet. It’s also a popular teaching tool in Yale classes. “At the Babylonian Collection we have a very active teaching and learning function, and we regard education as one of the core parts of our mission,” says Foster. “We have graduate and undergraduate groups in our collection classroom every week.”

The tablet, formally known as YBC 7289, “Old Babylonian Period Mathematical Text,” came to Yale in 1909 as part of a much larger collection of cuneiform tablets assembled by J. Pierpont Morgan and donated to Yale. In the ancient Mideast cuneiform writing was created by using a sharp stylus pressed into the surface of a soft clay tablet to produce wedge-like impressions representing pictographic words and numbers. Morgan’s donation of tablets and other artifacts formed the nucleus of the Yale Babylonian Collection, which now incorporates 45,000 items from the ancient Mesopotamian kingdoms.

Discoverying [sic] the tablet’s mathematical significance

The importance of the geometry tablet was first recognized by science historians Otto Neugebauer and Abraham Sachs in their 1945 book “Mathematical Cuneiform Texts.”

“Ironically, mathematicians today are much more fascinated with the Babylonians’ ability to accurately calculate irrational numbers like the square root of two than they are with the geometry demonstrations,” notes associate Babylonian Collection curator Agnete Lassen.

“The Old Babylonian Period produced many tablets that show complex mathematics, but it also produced things you might not expect from a culture this old, such as grammars, dictionaries, and word lists,” says Lassen “One of the two main languages spoken in early Babylonia  was dying out, and people were careful to document and save what they could on cuneiform tablets. It’s ironic that almost 4,000 years ago people were thinking about cultural preservation, [emphasis mine] and actively preserving their learning for future generations.”.

This business about ancient peoples trying to preserve culture and learning for future generations suggests that the efforts in Palmyra, Syria (my April 6, 2016 post about 3D printing parts of Palmyra) are born of an age-old impulse. And then the story takes another turn and becomes a 3D printing story (from the Yale University news release),

Today, however, the tablet is a fragile lump of clay that would not survive routine handling in a classroom. In looking for alternatives that might bring the highlights of the Babylonian Collection to a wider audience, the collection’s curators partnered with Yale’s Institute for the Preservation of Cultural Heritage (IPCH) to bring the objects into the digital world.

Scanning at the IPCH

The IPCH Digitization Lab’s first step was to do reflectance transformation imaging (RTI) on each of fourteen Babylonian Collection objects. RTI is a photographic technique that enables a student or researcher to look at a subject with many different lighting angles. That’s particularly important for something like a cuneiform tablet, where there are complex 3D marks incised into the surface. With RTI you can freely manipulate the lighting, and see subtle surface variations that no ordinary photograph would reveal.

Chelsea Graham of the IPCH Digitization Lab and her colleague Yang Ying Yang of the Yale Computer Graphics Group then did laser scanning of the tablet to create a three-dimensional geometric model that can be freely rotated onscreen. The resulting 3D models can be combined with many other types of digital imaging to give researchers and students a virtual tablet onscreen, and the same data can be use to create a 3D printed facsimile that can be freely used in the classroom without risk to the delicate original.
3D printing digital materials

While virtual models on the computer screen have proved to be a valuable teaching and research resource, even the most accurate 3D model on a computer screen doesn’t convey the tactile  impact, and physicality of the real object. Yale’s Center for Engineering Innovation and Design has collaborated with the IPCH on a number of cultural heritage projects, and the center’s assistant director, Joseph Zinter, has used its 3D printing expertise on a wide range of engineering, basic science, and cultural heritage projects.

“Whether it’s a sculpture, a rare skull, or a microscopic neuron or molecule highly magnified, you can pick up a 3D printed model and hold it, and it’s a very different and important way to understand the data. Holding something in your hand is a distinctive learning experience,” notes Zinter.

Sharing cultural heritage projects in the digital world

Once a cultural artifact has entered the digital world there are practical problems with how to share the information with students and scholars. IPCH postdoctoral fellows Goze Akoglu and Eleni Kotoula are working with Yale computer science faculty member Holly Rushmeier to create an integrated collaborative software platform to support the research and sharing of cultural heritage artifacts like the Babylonian tablet.

“Right now cultural heritage professionals must juggle many kinds of software, running several types of specialized 2D and 3D media viewers as well as conventional word processing and graphics programs. Our vision is to create a single virtual environment that accommodates many kinds of media, as well as supporting communication and annotation within the project,” says Kotoula.

The wide sharing and disseminating of cultural artifacts is one advantage of digitizing objects, notes professor Rushmeier, “but the key thing about digital is the power to study large virtual collections. It’s not about scanning and modeling the individual object. When the scanned object becomes part of a large collection of digital data, then machine learning and search analysis tools can be run over the collection, allowing scholars to ask questions and make comparisons that aren’t possible by other means,” says Rushmeier.

Reflecting on the process that brings state-of-the-art digital tools to one of humanity’s oldest forms of writing, Graham said “It strikes me that this tablet has made a very long journey from classroom to classroom. People sometimes think the digital or 3D-printed models are just a novelty, or just for exhibitions, but you can engage and interact much more with the 3D printed object, or 3D model on the screen. I think the creators of this tablet would have appreciated the efforts to bring this fragile object back to the classroom.”

There is also a video highlighting the work,

Skin as a touchscreen (“smart” hands)

An April 11, 2016 news item on phys.org highlights some research presented at the IEEE (Institute of Electrical and Electronics Engineers) Haptics (touch) Symposium 2016,

Using your skin as a touchscreen has been brought a step closer after UK scientists successfully created tactile sensations on the palm using ultrasound sent through the hand.

The University of Sussex-led study – funded by the Nokia Research Centre and the European Research Council – is the first to find a way for users to feel what they are doing when interacting with displays projected on their hand.

This solves one of the biggest challenges for technology companies who see the human body, particularly the hand, as the ideal display extension for the next generation of smartwatches and other smart devices.

Current ideas rely on vibrations or pins, which both need contact with the palm to work, interrupting the display.

However, this new innovation, called SkinHaptics, sends sensations to the palm from the other side of the hand, leaving the palm free to display the screen.

An April 11, 2016 University of Sussex press release (also on EurekAlert) by James Hakmer, which originated the news item, provides more detail,

The device uses ‘time-reversal’ processing to send ultrasound waves through the hand. This technique is effectively like ripples in water but in reverse – the waves become more targeted as they travel through the hand, ending at a precise point on the palm.

It draws on a rapidly growing field of technology called haptics, which is the science of applying touch sensation and control to interaction with computers and technology.

Professor Sriram Subramanian, who leads the research team at the University of Sussex, says that technologies will inevitably need to engage other senses, such as touch, as we enter what designers are calling an ‘eye-free’ age of technology.

He says: “Wearables are already big business and will only get bigger. But as we wear technology more, it gets smaller and we look at it less, and therefore multisensory capabilities become much more important.

“If you imagine you are on your bike and want to change the volume control on your smartwatch, the interaction space on the watch is very small. So companies are looking at how to extend this space to the hand of the user.

“What we offer people is the ability to feel their actions when they are interacting with the hand.”

The findings were presented at the IEEE Haptics Symposium [April 8 – 11] 2016 in Philadelphia, USA, by the study’s co-author Dr Daniel Spelmezan, a research assistant in the Interact Lab.

There is a video of the work (I was not able to activate sound, if there is any accompanying this video),

The consequence of watching this silent video was that I found the whole thing somewhat mysterious.