Category Archives: Education

Using Virus to Build Batteries

MIT researchers have shown they can genetically engineer viruses to build both the positively and negatively charged ends of a lithium-ion battery. We have posted about similar things previously, for example: Virus-Assembled Batteries – Using Viruses to Construct Electrodes and Biological Molecular Motors. New virus-built battery could power cars, electronic devices

Gerbrand Ceder of materials science and Associate Professor Michael Strano of chemical engineering, genetically engineered viruses that first coat themselves with iron phosphate, then grab hold of carbon nanotubes to create a network of highly conductive material.

Because the viruses recognize and bind specifically to certain materials (carbon nanotubes in this case), each iron phosphate nanowire can be electrically “wired” to conducting carbon nanotube networks. Electrons can travel along the carbon nanotube networks, percolating throughout the electrodes to the iron phosphate and transferring energy in a very short time. The viruses are a common bacteriophage, which infect bacteria but are harmless to humans.

The team found that incorporating carbon nanotubes increases the cathode’s conductivity without adding too much weight to the battery. In lab tests, batteries with the new cathode material could be charged and discharged at least 100 times without losing any capacitance. That is fewer charge cycles than currently available lithium-ion batteries, but “we expect them to be able to go much longer,” Belcher said.

This is another great example of university research attempting to find potentially valuable solutions to societies needs. See other posts on using virus for productive purposes.

Google Server Hardware Design

Ben Jai, Google Server Platform Architect, discusses the Google server hardware design. Google has designed their own servers since the beginning and shared details this week on that design. As we have written previously Google has focused a great deal on improving power efficiency.

Google uncloaks once-secret server

Google’s big surprise: each server has its own 12-volt battery to supply power if there’s a problem with the main source of electricity. The company also revealed for the first time that since 2005, its data centers have been composed of standard shipping containers–each with 1,160 servers and a power consumption that can reach 250 kilowatts.
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Efficiency is another financial factor. Large UPSs can reach 92 to 95 percent efficiency, meaning that a large amount of power is squandered. The server-mounted batteries do better, Jai said: “We were able to measure our actual usage to greater than 99.9 percent efficiency.”

E.O. Wilson: Lord of the Ants

This is a great webcast on E.O Wilson‘s career studying ants and animal behavior from NOVA.

Not only is the scientific knowledge very interesting it again shows that challenging conventional wisdom, while part of the scientific method, does not mean it is an easy process for those pioneers. From his web site:

In 1971 Wilson published his second major synthesis, The Insect Societies, which formulated the existing knowledge of the behavior of ants, social bees, social wasps, and termites, on a foundation of population biology. In it he introduced the concept of a new discipline of sociobiology, the systematic study of the biological basis of social behavior in all kinds of organisms. In 1975 he published Sociobiology: The New Synthesis, which extended the subject to vertebrates and united it more closely to evolutionary biology. The foundational discoveries of sociobiology are generally recognized to be the analysis of animal communication and division of labor, in which Wilson played a principal role, and the genetic theory of the origin of social behavior, which he helped to promote and apply in his 1971 and 1975 syntheses. Sociobiology: The New Synthesis was later ranked in a poll of the officers and fellows of the international Animal Behaviour Society as the most important book on animal behavior of all time, and is regarded today as the founding text of sociobiology and its offshoot, evolutionary psychology.

Related: Journey to the Ants: A Story of Scientific Exploration
by Bert HÃ¶lldobler and Edward O. Wilson – Huge Ant Nest – Symbiotic relationship between ants and bacteria – Royal Ant Genes – posts on ants – Encyclopedia of Life

Robot with Biological Brain

The Living Robot by Joe Kloc

Life for Warwick’s robot began when his team at the University of Reading spread rat neurons onto an array of electrodes. After about 20 minutes, the neurons began to form connections with one another. “It’s an innate response of the neurons,” says Warwick, “they try to link up and start communicating.”

For the next week the team fed the developing brain a liquid containing nutrients and minerals. And once the neurons established a network sufficiently capable of responding to electrical inputs from the electrode array, they connected the newly formed brain to a simple robot body consisting of two wheels and a sonar sensor.
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At first, the young robot spent a lot of time crashing into things. But after a few weeks of practice, its performance began to improve as the connections between the active neurons in its brain strengthened. “This is a specific type of learning, called Hebbian learning,” says Warwick, “where, by doing something habitually, you get better at doing it.”
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“It’s fun just looking at it as a robot life form, but I think it may also contribute to a better understanding of how our brain works,” he says. Studying the ways in which his robot learns and stores memories in its brain may provide new insights into neurological disorders like Alzheimer’s disease.

Cardiac Cath Lab: Innovation on Site

Photo of John Cooke at the Cardiac Catheterisation Labs at St. Thomas’ hospital in London

I manage several blogs on several topics that are related. Often blog posts stay firmly in the domain of one blog of the other. Occasionally the topic blurs the lines between the various blogs (which I like). This post ties directly to my Curious Cat Management Improvement Blog. The management principles I believe in are very similar to engineering principles (no surprise given this blog). And actual observation in situ is important – to understand fully the situation and what would be helpful. Management relying on reports instead of seeing things in action results in many poor decisions. And engineers doing so also results in poor decisions.

Getting to Gemba – a day in the Cardiac Cath Lab by John Cooke

I firmly believe that it is impossible to innovate effectively without a clear understanding of the context and usage of your final innovation. Ideally, I like to “go to gemba“, otherwise known as the place where the problem exists, so I can dig for tacit knowledge and observe unconscious behaviours.
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I didn’t disgrace myself and I’ve been invited back for another day or so. What did I learn that I didn’t know before? The key things I learnt were:

the guide wire isn’t just a means of steering the catheter into place as I thought. It is a functional tool in it’s own right
Feel is really critical to the cardiologist
There is a huge benefit in speeding up procedures in terms of patient wellbeing and lab efficiency
Current catheter systems lack the level of detection capability and controllability needed for some more complex PCIs (Percutaneous Cardiac Interventions)

The whole experience reminded me that in terms of innovation getting to gemba is critical. When was the last time you saw your products in use up-close and personal?

Personal Robots Being Developed in Japan

Robots Lend a Hand in Japan by Tony McNicol

The most numerous, and certainly the most high-profile, service robots in Japan are for entertainment. Ever since 2000 when Honda amazed the world with its walking humanoid Asimo, other Japanese companies have been fast on their heels. Notable examples include Mitsubishi’s lemon yellow home helper Wakamaru, Toyota’s trumpet-playing humanoid, and Murata Manufacturing’s bicycle-riding robot. Although such impressive PR robots are too expensive to sell, Japan also has popular home entertainment robots. The best known to date is Sony’s robot pooch Aibo, which was produced between 1999 and 2006.
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Another potential role for service robots is dealing with Japan’s imminent demographic crisis. A low birthrate and unrivalled longevity mean the number of elderly Japanese will increase dramatically over the coming decades. In the absence of mass immigration (which Japan has been keen to avoid) a severe shortage of caregivers seems inevitable. Some people believe robots are the answer. Takanori Shibata, a senior research scientist at the National Institute of Advanced Industrial Science and Technology, says that robot caregivers can be divided into physical service and mental service robots. The former are designed to help with tasks such as washing or carrying elderly people, although given the limitations of current technology, not to mention safety concerns, they are still quite a long way from commercialization.

Mental service robots on the other hand are already here. One of the best known is Paro, an interactive robot seal designed by Shibata himself. The sophisticated robot can remember its name and change its behavior depending on how it is treated. It has been extensively tested in homes for elderly people and in hospitals. In 2002 the Guinness Book of Records named Paro as “the world’s most therapeutic robot.” The robot reminds patients of the pets or children they once cared for, says Shibata. “Paro is a kind of trigger to provoke something in the mind of the owner,” he suggests. About 1,000 of the robots, which cost about 3,000 dollars, have been produced since 2004. Overseas sales will begin shortly.

The effective use of personal robots finally seems to be fairly close at hand. Undoubtedly the initial attempts will seem limited. See Clayton Christsen’s ideas on disruptive innovation for an understanding of how I think the adoption will play out. Robots will be poor substitutes for other alternatives but as we experiment with how to make them effective we will figure out niches for which they work well. It is hard to predict what will happen but my feeling is we may finally be a the point where real uses of personal robots stat to take hold and then the growth may surprise us.

Image of the Common Cold Virus

image created by Dr. Jean-Yves Sgro, Institute for Molecular Virology, University of Wisconsin-Madison, from published X-ray data. larger image

Sequences capture the code of the common cold

Conducted by teams at the University of Maryland School of Medicine, UW-Madison and the J. Craig Venter Institute, the work to sequence and analyze the cold virus genomes lays a foundation for understanding the virus, its evolution and three-dimensional structure and, most importantly, for exposing vulnerabilities that could lead to the first effective cold remedies.

“We’ve had bits and pieces of these things for a long time,” says Ann Palmenberg, of UW-Madison’s Institute for Molecular Virology and the lead author of the new study. “Now, we have the full genome sequences and we can put them into evolutionary perspective.”

As its name implies, the common cold is an inescapable, highly contagious pathogen. Humans are constantly exposed to cold viruses, and each year adults may endure two to four infections, while schoolchildren can catch as many as 10 colds.

“We know a lot about the common cold virus,” Palmenberg explains, “but we didn’t know how their genomes encoded all that information. Now we do, and all kinds of new things are falling out.”
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The newly sequenced viruses also show, says Palmenberg, why it is unlikely we will ever have an effective, all-purpose cold vaccine: The existing reservoir of viruses worldwide is huge and, according to the new study, they have a tendency to swap genetic sequences when cells are infected by more than one virus, a phenomenon that can lead to new virus strains and clinical manifestations.
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The ability of different cold virus strains to swap genes and make entirely new strains was thought to be impossible, notes Claire M. Fraser-Liggett, a co-author of the new study and director of the Institute for Genome Sciences and professor of medicine and microbiology at the University of Maryland School of Medicine. “There is the possibility that this could lead to the emergence of a new rhinovirus strain with fairly dramatic properties,” says Fraser-Liggett.

Value of Prostate Cancer Screening Questioned by Two Studies

Ben Goldacre, in his bad science blog, again takes on journalist’s articles of health research in: Venal, misleading, pathetic, dangerous, stupid, and busted

1410 men would need to be screened to prevent one death. For each death prevented, 48 people would need to be treated: and prostate cancer treatment has a high risk of very serious side effects like impotence and incontinence. These figures are not hard to find: they are in the summary of the research paper.

For complex risk decisions like screening, it has been shown in three separate studies that patients, doctors, and NHS purchasing panels make more rational decisions about treatments and screening programmes when they are given the figures as real numbers, as I did above, instead of percentages. I’m not saying that PSA screening is either good or bad: I am saying that people deserve the figures in the clearest form possible so they can make their own mind up.
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So newspapers ignore one half of the evidence, and they fail to explain the other half properly.
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They can also link directly and transparently to scientific papers, which mainstream media still refuses to do. Journalists insist that we need professionals to mediate and explain science. From today’s story, their self belief seems truly laughable.

He also says some journalists got it right including the Washington Post in, Prostate Cancer Screening May Not Reduce Deaths:

The PSA blood test, which millions of men undergo each year, did not lower the death toll from the disease in the first decade of a U.S. government-funded study involving more than 76,000 men, researchers reported yesterday. The second study, released simultaneously, was a European trial involving more than 162,000 men that did find fewer deaths among those tested. But the reduction was relatively modest and the study showed that the tests resulted in a large number of men undergoing needless, often harmful treatment.

I think it is true that most people need help having science mediated to some extent. But he is also right that those doing so need to do better. And also everyone needs to learn about science to understand the choices they personally and politically (for policy issues) need to make decisions on. Being scientifically illiterate is dangerous.

Image of Viral Coat

image of exterior of virus - made up of 5 million atoms

High-energy X-ray diffraction was used to pinpoint some 5 million atoms in the protective protein coat of the PsV-F virus. The coat’s symmetrical features are shared by hundreds of viruses. The red and yellow sections illustrate how building blocks of four proteins come together to form the spherical shell.

The image reveals the structure of a type of protein coat shared by hundreds of known viruses containing double-stranded RNA genomes. The image was painstakingly created from hundreds of high-energy X-ray diffraction images and paints the clearest picture yet of the viruses’ genome-encasing shell called a “capsid.”

Viruses can reproduce themselves only by invading a host cell and highjacking its biochemical machinery. But when they invade, viruses need to seal off their genetic payload to prevent it from being destroyed by the cell’s protective mechanisms. Though there are more than 5,000 known viruses, including whole families that are marked by wide variations in genetic payload and other characteristics, most of them use either a helical or a spherical capsid.

“Spherical viruses like this have symmetry like a soccer ball or geodesic dome,” Pan said. “The whole capsid contains exactly 120 copies of a single protein.” Previous studies had shown that spherical capsids contain dozens of copies of the capsid protein, or CP, in an interlocking arrangement. The new research identified the sphere’s basic building block, a four-piece arrangement of CP molecules called a tetramer, which could also be building blocks for other viruses’ protein coats.

Full press release

MIT Faculty Open Access to Their Scholarly Articles

MIT faculty open access to their scholarly articles

In a move aimed at broadening access to MIT’s research and scholarship, faculty at the Massachusetts Institute of Technology have voted to make their scholarly articles available to the public for free and open access on the Web.

The new policy, which was approved unanimously at an MIT faculty meeting on Wednesday, March 18 and took immediate effect, emphasizes MIT’s commitment to disseminating the fruits of its research and scholarship as widely as possible.
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Under the new policy, faculty authors give MIT nonexclusive permission to disseminate their journal articles for open access through DSpace, an open-source software platform developed by the MIT Libraries and Hewlett Packard and launched in 2002. The policy gives MIT and its faculty the right to use and share the articles for any purpose other than to make a profit. Authors may opt out on a paper-by-paper basis.

MIT’s policy is the first faculty-driven, university-wide initiative of its kind in the United States. While Harvard and Stanford universities have implemented open access mandates at some of their schools, MIT is the first to fully implement the policy university-wide as a result of a faculty vote. MIT’s resolution is built on similar language adopted by the Harvard Faculty of Arts & Sciences in 2008.

It is good to see scientists putting advancing science above outdated journal business models. It is a bit of a shame that we have to be happy for such a small thing but given the state of those fighting against open science it is good to see those in favor of open access to science make progress.