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OpenPCR: DNA amplification for anyone

OpenPCR is a cool new project dedicated to building plans for an open source PCR machine. There’s not much inherently complicated about a PCR machine and it’s about time — a PCR machine built with $300 in parts using a modern software controller will likely be as powerful as any non-realtime PCR out there. Of course, the reagent pricing is what gets you.

Josh and Tito are raising money for this project using Kickstarter. $1024 gets them to build you a PCR machine, which is a reasonably good deal in the scheme of scientific equipment. I gave them $8, because I like stickers and already have a PCR machine that doesn’t exactly get a lot of use.

Singularity Summit 2010 in San Francisco to Explore Intelligence Augmentation

Kevin: I’ve been volunteering for the Singularity Institute these last few months. Each year, the Singularity Institute hosts the Singularity Summit, a two-day conference in San Francisco this August that may be of interest to many of the readers of this blog.

Will it ever become possible to boost human intelligence using brain implants, or create an artificial intelligence smarter than Einstein? In a 1993 paper presented to NASA, science fiction author and mathematician Vernor Vinge called such a hypothetical event a “Singularity“, saying “From the human point of view this change will be a throwing away of all the previous rules, perhaps in the blink of an eye”. Vinge pointed out that intelligence enhancement could lead to “closing the loop” between intelligence and technology, creating a positive feedback effect.

This August 14-15, hundreds of AI researchers, robotics experts, philosophers, entrepreneurs, scientists, and interested laypeople will converge in San Francisco to address the Singularity and related issues at the only conference on the topic, the Singularity Summit. Experts in fields including animal intelligence, artificial intelligence, brain-computer interfacing, tissue regeneration, medical ethics, computational neurobiology, augmented reality, and more will share their latest research and explore its implications for the future of humanity.

“This year, the conference shifts to a focus on neuroscience, bioscience, cognitive enhancement, and other explorations of what Vernor Vinge called ‘intelligence amplification’ (IA) — the other route to the Singularity,” said Michael Vassar, president of the Singularity Institute, which is hosting the event.

Irene Pepperberg, author of “Alex & Me,” who has pushed the frontier of animal intelligence with her research on African Gray Parrots, will explore the ethical and practical implications of non-human intelligence enhancement and of the creation of new intelligent life less powerful than ourselves. Futurist-inventor Ray Kurzweil will discuss reverse-engineering the brain and his forthcoming book, How the Mind Works and How to Build One. Allan Synder, Director, Centre for the Mind at the University of Sydney, will explore the use of transcranial magnetic stimulation for the enhancement of narrow cognitive abilities. Joe Tsien will talk about the smarter rats and mice that he created by tuning the molecular substrate of the brain’s learning mechanism. Steve Mann, “the world’s first cyborg,” will demonstrate his latest geek-chic inventions: wearable computers now used by almost 100,000 people.

Other speakers will include magician-skeptic and MacArthur Genius Award winner James Randi; Gregory Stock (Redesigning Humans), former Director of the Program on Medicine, Technology, and Society at UCLA’s School of Public Health; Terry Sejnowski, Professor and Laboratory Head, Salk Institute Computational Neurobiology Laboratory, who believes we are just ten years away from being able to upload ourselves; Ellen Heber-Katz, Professor, Molecular and Cellular Oncogenesis Program at The Wistar Institute, who is investigating the molecular basis of wound regeneration in mutant mice, which can regenerate limbs, hearts, and spinal cords; Anita Goel, MD, physicist, and CEO of nanotechnology company Nanobiosym; and David Hanson, Founder & CEO, Hanson Robotics, who is creating the world’s most realistic humanoid robots.

You can watch videos from past summits and register at www.singularitysummit.com.

Images reconstructed from human brain using fMRI

Very interesting news today, as Japanese scientists published a paper in Neuron discussing the reconstruction of images directly from the human brain using fMRI.  It does seem like neurology is making true progress, despite the popular notion that “we can never understand the human brain.” The future consequences of research like this may be controversial, but it’s the inevitable price of progress. Pink Tentacle covered this story along with a more technical overview by Brain Windows.

Visual Image Reconstruction from Human Brain Activity using a Combination of Multiscale Local Image Decoders.
Yoichi Miyawaki, Hajime Uchida, Okito Yamashita, Masa-aki Sato, Yusuke Morito, Hiroki C. Tanabe, Norihiro Sadato, Yukiyasu Kamitani.
Neuron – 10 December 2008 (Vol. 60, Issue 5, pp. 915-929)

Novelty DTC genetic testing company torpedoes their way into NY Times

Today’s New York Times had a story about a new DTC novelty genetic testing company. It’s a rather obvious example of a torpedo. This article was seeded by a PR company — it’s only news because ATLAS Sports Genetics has investors that know their best shot at success is buying their way into the New York Times.

ATLAS Sports Genetics is offering a test for ACTN3, otherwise known as the speed gene. They charge $149. For $249, you get the “ATLAS Plus” kit. It tells you how high your kid jumps. The $1000 package comes with a timer. I kid you not; they charge an extra 750 dollars for a timer. I have a better idea for finding out if your kid is good at sports: sign him or her up for the soccer team. Or baseball, or football, or gymnastics, or whatever he or she wants to do.

The ACTN3 test is the preeminent example of a novelty genetic test. It tells you nothing useful. It’s for fun — entertainment purposes only. I mean, if they had a genetic test that indicated something useful about athletic ability, that would be one thing. The ACTN3 test gives something of an indication about whether your muscles are more suited for sprinting or endurance. No matter what version of ACTN3 you or your child have, you can still play sports! 23andMe tests for the ACTN3 mutation in their $399 product and ATLAS will not be able to compete with 23andMe. If you’re looking to be entertained by a genetic test, get a 23andMe, not an ATLAS.

Biomarker-driven mental health 2.0 also posted their reaction to this story.

Caltech engineers build first-ever multi-input ‘plug-and-play’ synthetic RNA device

Kevin: Very cool. It’s going to be a while before this is ready for any sort of practical application, but it is another great tool for the cyborg scientists of the future to use.

Engineers from the California Institute of Technology  have created a “plug-and-play” synthetic RNA device–a sort of eminently customizable biological computer–that is capable of taking in and responding to more than one biological or environmental signal at a time.

In the future, such devices could have a multitude of potential medical applications, including being used as sensors to sniff out tumor cells or determine when to turn modified genes on or off during cancer therapy.

A synthetic RNA device is a biological device that uses engineered modular components made of RNA nucleotides to perform a specific function–for instance, to detect and respond to biochemical signals inside a cell or in its immediate environment.

Created by Caltech’s Christina Smolke, assistant professor of chemical engineering, and Maung Nyan Win, postdoctoral scholar in chemical engineering, the device is made up of modules comprising the RNA-based biological equivalents of engineering’s sensors, actuators, and information transmitters. These individual components can be combined in a variety of different ways to create a device that can both detect and respond to what could conceivably be an almost infinite number of environmental and cellular signals.

This modular device processes these inputs in a manner almost identical to the logic gates used in computing; it can perform AND, NOR, NAND, and OR computations, and can perform signal filtering and signal gain operations. Smolke and Win’s creation is the first RNA device that can handle more than one incoming piece of biological information. “There’s been a lot of work done in single-input devices,” notes Smolke. “But this is the first demonstration that a multi-input RNA device is possible.”

Their work was published in the October 17 issue of the journal Science.

The modular–or plug-and-play–nature of the device’s design also means that it can be easily modified to suit almost any need. “Scientists won’t have to redesign their system every time they want the RNA device to take on a new function,” Smolke explains. “This modular framework allows you to quickly put a device together, then just as easily swap out the components for other ones and get a completely different kind of computation. We could generate huge libraries of well-defined sensors and assemble many different tailored devices from such component libraries.”

Although the work in the Science paper was done in yeast cells, Smolke says they have already shown that they can translate to mammalian cells as well. This makes it possible to consider using these devices in a wide variety of medical applications.

For instance, ongoing work in Smolke’s laboratory is looking at the packaging of these RNA devices–configured with the appropriate sensor modules–in human T cells. The synthetic device would literally be placed within the cell to detect certain signals–say, one or more particular biochemical markers that are given off by tumor cells. If those biomarkers were present, the RNA device would signal the T cell to spring into action against the putative tumor cell.

Similarly, an RNA device could be bundled alongside a modified gene as part of a targeted gene therapy package. One of the problems gene therapy faces today is its lack of specificity–it’s hard to make sure a modified gene meant to fix a problem in the liver reaches or is inserted in only liver cells. But an RNA device, Smolke says, could be customized to detect the unique biomarkers of a liver cell–or, better yet, of a diseased liver cell–and only then give the modified gene the go-ahead to do its stuff.

Source: California Institute of Technology

Maung Nyan Win and Christina D. Smolke
Science 17 October 2008:
Vol. 322. no. 5900, pp. 456 – 460
DOI: 10.1126/science.1160311

The PCR Song

Pitt research indicates new virus is culprit, not bystander, in deadly skin cancer

Kevin: Our growing understanding that some cancers are viral in origin starts to make cancer seem a lot less mysterious. I’m optimistic about continued progress in this important area.

University of Pittsburgh scientists are uncovering more evidence that a virus they recently discovered is the cause of Merkel cell carcinoma, an aggressive and deadly form of skin cancer.

The findings, published in this week’s early online edition of the Proceedings of the National Academy of Sciences, put to rest the possibility that MCV infects tumors that already have formed. If that were the case, the virus would be a passenger rather than the driver of the disease.

Experiments in human tumors reveal that the cancer develops in two steps: during infection, the Merkel cell polyomavirus, or MCV, integrates into host cell DNA and produces viral proteins that promote cancer formation. Tumors occur when a mutation removes part of a viral protein needed for the virus to reproduce and infect other healthy cells, explained senior investigator, Patrick Moore, M.D., M.P.H, professor of microbiology and molecular genetics at the School of Medicine and director of the Molecular Virology Program at the University of Pittsburgh Cancer Institute. The virus then can spread only as the cancer cells themselves multiply.

Clearly, “MCV infects normal cells before they turn into cancer cells,” Dr. Moore noted. “The virus could not have infected a tumor afterwards because it can no longer replicate. It looks very much like MCV is the culprit that causes the disease.”

The researchers propose two possible reasons why these mutations develop: If viral replication continues, the immune system could recognize the intruder to eliminate diseased cells, or the viral replication itself will lead to the death of the cancer cells. Both of these possibilities provide promising leads to find better ways to kill Merkel cell cancer cells without harming healthy tissues.

Also, “this research shows evolution within tumors on a molecular level,” Dr. Moore pointed out. “You can see the specific molecular steps.” The team’s current work could account for known risk factors for Merkel cell carcinoma such as UV exposure and ionizing radiation, which damage DNA and can lead to the viral mutations.

Merkel cell cancers are rare, occurring in about 1,500 Americans annually. Half of patients who have advanced disease die within nine months of diagnosis, and two-thirds die within two years. The elderly and people with compromised immune systems are at greater risk of developing the cancer, which arises in skin nerve cells that respond to touch or pressure.

In a paper published in Science in January, Dr. Moore and his wife, Dr. Yuan Chang, who co-directs their lab, reported their identification of the virus and that it could be found in 80 percent of Merkel cell tumors. They cautioned that although up to 16 percent of the population carries MCV, very few will develop cancer.

There is no treatment for MCV infection right now, but identifying the agent and understanding how it triggers disease could lead to targeted interventions, Dr. Moore said.

Source: University of Pittsburgh Schools of the Health Sciences

The original paper: Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma. Huichen Feng, Masahiro Shuda, Yuan Chang, Patrick S. Moore. Science 22 February 2008:Vol. 319. no. 5866, pp. 1096 – 1100

The followup discussed here will be appearing in the upcoming early edition of the PNAS.

I don’t want a 23andMe — I want the real genetic tests

Our friendly government lists some available genetic tests: these are the real deal, high penetrance tests for things you already have or conditions you will get.

Unlike Sergey Brin, I don’t particularly care about a mutation that gives me a slightly increased risk for a disease. That’s not significant, though if the placebo effect of a 23andMe test gets you to exercise more, congratulations.

However, if I knew I was bound to get Huntington’s Disease, I would really live my life differently with the moral superiority provided by knowing that my time on this earth was sadly limited by my genetics. I would just take things so much more seriously than all those suckers blissfully unaware of the cold, cruel nature of reality.

For now, it’s prohibitively expensive to get every single genetic test. With how much I would have to spend today to get 50 patented tests I would be better off waiting a year and getting my genome sequenced, then analyzing the data myself to (illegally?) check for every high penetrance mutation.