Archive for the 'Nanotech' Category


is synthetic life approaching?

By Richard Wheeler (Zephyris) 2007. Lambda rep...
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There has always been a metaphysical aura about life. In addition to the material in a cell or other living thing, most people seem to think that when we say “life” we’re talking about a spark or energy that transcends the material constituents of that living thing.

But suppose that organisms that show all the properties of life can be created by off-the-shelf raw materials of our world and made to function as living through human-designed processes? At no point would some spark or energy be added to jump-start life processes although complex chemical reactions are central to synthesizing the constituent parts. (Is the term Frankenmolecules already taken?)

Researchers are working on just such approaches in an effort to understand the details of how living things get organized, and just recently another step was  taken. Princeton chemist Howard Hecht and his team built proteins from scratch, put them in bacteria, and the bacteria used them to grow and carry on just like the proteins they naturally generate. They demonstrated that there’s nothing mystical or magical about molecules generated in vivo. Actually, there were two artificial steps: they designed artificial DNA that then generated the synthetic proteins.

“What we have here are molecular machines that function quite well within a living organism even though they were designed from scratch and expressed from artificial genes,” said Michael Hecht, a professor of chemistry at Princeton, who led the research. “This tells us that the molecular parts kit for life need not be limited to parts — genes and proteins — that already exist in nature.”

“What I believe is most intriguing about our work is that the information encoded in these artificial genes is completely novel — it does not come from, nor is it significantly related to, information encoded by natural genes, and yet the end result is a living, functional microbe,” said Michael Fisher, a co-author of the paper who earned his Ph.D. at Princeton in 2010 and is now a postdoctoral fellow at the University of California-Berkeley. “It is perhaps analogous to taking a sentence, coming up with brand new words, testing if any of our new words can take the place of any of the original words in the sentence, and finding that in some cases, the sentence retains virtually the same meaning while incorporating brand new words.”

Although millions of proteins from evolved DNA already exist, the ones Nature has produced is only a small fraction of the proteins that could be produced by heretofore unseen DNA and protein combinations. The potential design space is vast. Some people think living things were produced by intelligent design from the beginning, but I think these experiments are getting us closer to the truth. Evolution of the world’s material into living things over a hell of a long time gave us what has gone before, but we’re getting closer and closer to true design of life forms from a huge set of possibilities that will become part of our world in the not-too-distant future.


Single molecule computer chip

Mr. McGuire: I want to say one word to you. Just one word.
Benjamin: Yes, sir.
Mr. McGuire: Are you listening?
Benjamin: Yes, I am.
Mr. McGuire: Plastics.
Benjamin: Just how do you mean that, sir?

In the 1967 movie, The Graduate, a family friend, Mr. McGuire, offers Benjamin (Dustin Hoffman) just one word of advice to set him on a path to future success: “plastics.” That was more than 40 years ago. If I were to adopt a one-word recommendation for the emerging generation it would be: “nanotech.” I’ve mentioned this before.

I was reminded again last week about how dramatic the development in the science and technology of billionth-of-a-meter devices is. Singapore’s Agency for Science, Technology and Research (A*STAR) Institute of Materials Research and Engineering announced a partnership with 10 European Union organizations for the ATMOL project–an effort to build a single molecule computer processor.

A*STAR’s IMRE and 10 EU research organisations are working together to build what is essentially a single molecule processor chip. As a comparison, a thousand of such molecular chips could fit into one of today’s microchips, the core device that determines computational speed. The ambitious project, termed Atomic Scale and Single Molecule Logic Gate Technologies (ATMOL), will establish a new process for making a complete molecular chip. This means that computing power can be increased significantly but take up only a small fraction of the space that is required by today’s standards.

The R&D will work on some cutting-edge techniques for creating molecular components: “The fabrication process involves the use of three unique ultra high vacuum (UHV) atomic scale interconnection machines which build the chip atom-by-atom. These machines physically move atoms into place one at a time at cryogenic temperatures.”

But here’s the thing about this path to success: How do you sustain a career in a field where your current knowledge is as evanescent as the morning dew? Riches will be made in nanotechnology, but knowledge obsolescence has been a problem for mid-career technicians in IT for decades. I don’t see how it’ll get any better.


Paging Dr Nano…

I’m kind of obsessed with the nanoscale world because it’s the scale at which basic living systems start. The macromolecules of cells — the building blocks of organisms — are really doing meaningful processes down at the nanoscale.

Nanotechnology — the technology of things designed and engineered down to the molecular and atomic level — is beginning to show signs for remarkable devices not far from going on the market. And one of the first, robust markets for nanotech is going to be medical nanotechnology, especially for cancer. I’ve been watching this for a few years years now.

I recently stumbled across a nanotechnology newsletter I hadn’t seen before: Nanowerk. It’s a European site focused on technology developments in European countries. Every country with healthy science and technology resources is steaming ahead with nanotech R&D in anticipation of huge future development. The newsletter circulates 10 to 20 briefs per day.

An article from May 4 really got my attention. It’s titled: “Informatics moves into nanomedicine,” and reports on research recently published in Pediatric Research. There are what I think are some interesting assertions about the near future of the field.

…some nanoparticles and nanodevices have already been approved or are about to be approved by the United States Food and Drug Administration, including, for example, superparamagnetic nanoparticles to detect metastases in some types of cancer or new devices that combine microfluids or nanosensors to detect tumours.

These applications of nanomaterials open up new prospects for personalized medicine, the authors add, indicating that classical clinical studies need to be redesigned to adapt to the advances taking place in genomics, proteomics and pharmacogenetics. “The introduction of nanoparticles that can target different molecules or groups of atoms with high precision can significantly advance the personalization of clinical procedures”, the article says.

But the statement that blew my mind is:

The possibility of biomolecular devices acting not only in vitro but also in vivo within diseased human organisms is also opening up new prospects, where biomolecular automata could even intervene to intelligently deliver drugs to the diseased regions of the human body just where they are needed.

In this respect, the authors note that research on a “Doctor in a Cell” is already in progress. This is a genetically modified cell that can operate in a human body. It contains a biological computer that can process and analyse external biological signals, emit a diagnosis and deliver the desired molecular therapeutic signal to treat the patient.

The doc-in-a-cell is “already in progress“?! Not exactly the Fantastic Voyage, but close enough to get me excited!


Turning the corner in nanotechnology

One of the things I like to write about is nanotechnology because — to put it directly — I think it’s going to be the technology that revolutionizes the 21st Century. To suggest it will be the next “industrial revolution” hardly covers it.

Back in 2000 when everybody was prognosticating about the next century I attended a conference put on by The Foresight Institute, an organization that has been pushing nanotechnology since the ’80s. They had a group of venture capitalists who were perhaps the first to invest anything in nanotech talking with an audience of geek enthusiasts and engineers from the Silicon Valley. The VCs were actually very reserved in their forecasts. Perhaps they were just trying to keep the audience from deluging them with proposals for the first billion-dollar nanotech start-up. They cautioned that VCs wanted things that were likely to start returning their investment in five or, at most, ten years. Investment capital is seldom very patient.

One of the really enormous ideas in the field is that nanotechnology will be able to make never-before-seen structures built with atoms placed precisely where they’re wanted. In other words, nano-manufacturing needs some sort of assembler that works in a robotical fashion diligently turning out one nano-widget after another. Imagine something like an auto assembly line where arms reach out to place parts and welds through the endless repetition of robot programs — except on a scale of billions of a meter. To make things that have significance in our macro-world billions and trillions of nano-devices will be needed.

In a recent post to h+— an e-zine that loves far-out, futuristic stuff — there’s a post about recent developments for assemblers.

In a 2009 article in Nature Nanotechnology, Dr. [Nadrian] Seeman shared the results of experiments performed by his lab, along with collaborators at Nanjing University in China, in which scientists built a two-armed nanorobotic device with the ability to place specific atoms and molecules where scientists want them. The device was approximately 150 x 50 x 8 nanometers in size — over a million could fit in a single red blood cell. Using robust error-correction mechanisms, the device can place DNA molecules with 100% accuracy. Earlier trials had yielded only 60-80% accuracy.

What Dr. Seeman is using is DNA origami and structural features of DNA that are used in genetic recombination. Once again — as I described in an earlier post about nano-manufacturing — we are taking lessons from nature’s own original nano-assembler: DNA.


job of the future: nanoengineer

A lot of people in the US are wondering where the next jobs are coming from. If you’re really bright and not intimidated by math you (or more likely, your kid) might want to look into nanoengineering.

A release from UC San Diego says Professor Jen Cha is making breakthroughs in one of the real hurdles in nanotech: manufacturing the little gadgets en masse and cheaply. Her technique: DNA origami.

People have created a huge variety of unique and functional nanostructures, but for some intended applications they are worthless unless you can place individual structures, billions or trillions of them at the same time, at precise locations… We hope that our research brings us a step closer to solving this very difficult problem. […]

“Using DNA to assemble materials is an area that many people are excited about,” Cha said. “You can fold DNA into anything you want – for example, you can build a large scaffold and within that you could assemble very small objects such as nano particles, nano wires or proteins. […]

“My job as a nanoengineer is to figure out what you need to do to put all the different parts together, whether it’s a drug delivery vehicle, photovoltaic applications, sensors or transistors. We need to think about ways to take all the nano materials and engineer them it into something people can use and hold.”

A bright future, I’d wager, if you’ve got the right stuff.


Follow-up: gene sequencing and nanotubes

In the previous post I commented on complaints that genetic sequencing studies haven’t met expectations and shouldn’t get so much funding. That’s a debate that will be ongoing, but one indisputable result of the expectations for gene sequencing is that the technology for doing it has improved in precision while falling in price at a rate even surpassing Moore’s Law in computer chips.

The Human Genome Project was a labor-intensive, high-ticket item: ~$3 billion. But since then the cost of getting full genome sequences has fallen off a cliff. The holy grail of sequencing is ” The $1000 Genome”. That price point is expected within a year or two. At that point it is expected full genome sequencing will begin to become a routine medical procedure. Our genomes can become baseline data at birth for building a picture of how our health will play out in our lifetime. (Critics may warn that it may sell a lot of expensive machines but not contribute as much to fixing what ails us.)

Two reports have been made in just the past couple of weeks about two new nanotechnology techniques that will continue driving the trend. Just today Arizona State U put out a news release saying Stuart Lindsay of their Center for Single Molecule Biophysics at the Biodesign Institute will be reporting in Science his technique for sequencing DNA by getting it to pass through a carbon nanotube. When the DNA passes through it causes electrical fluctuations that can be distinguished and interpreted by carefully measuring changing electrical properties of the nanotube.

This follows a similar report a couple of weeks ago that Boston University Biomedical Engineering Associate Professor Amit Meller has demonstrated a technique for identifying DNA bases by convincing the strand to pass through a silicon nanopore where electrical signatures can be read.

So take your pick: carbon nanotubes or silicon nanopores. As ASU puts it:

Faster sequencing of DNA holds enormous potential for biology and medicine, particularly for personalized diagnosis and customized treatment based on each individual’s genomic makeup. At present however, sequencing technology remains cumbersome and cost prohibitive for most clinical applications, though this may be changing, thanks to a range of innovative new techniques.

…Lindsay emphasizes, DNA sequencing could be carried out thousands of times faster than through existing methods, at a fraction of the cost. Realizing the one-patient-one-genome goal of personalized medicine would provide essential diagnostic information and help pioneer individualized treatments for a wide range of diseases.

Hmm. Let’s wait and see.


Cancer biomarker chip

One of the things I like to talk about a lot on this blog is the amazing new things that are being done with teeny, tiny sensors and detectors. That’s not just because they’re cool and geeky, but because the growing power to look deep into living things and snoop around among the molecules there is how we’re going to understand complex living systems and do something useful with the information.

A report in today’s Nature Nanotechnology is a case in point. A team from Yale University has developed a microfluidic device (aka, lab-on-a-chip) that is able to identify antigens for prostate and breast cancer from small samples of whole blood. Pulling very specific proteins out of blood — a complex solution of things  — is a good trick. The new chip does it with much less preparation and with greater sensitivity than past techniques.

A microfluidic purification chip simultaneously captures multiple biomarkers from blood samples and releases them, after washing, into purified buffer for sensing by a silicon nanoribbon detector. This two-stage approach isolates the detector from the complex environment of whole blood, and reduces its minimum required sensitivity by effectively pre-concentrating the biomarkers.

The payoff is that a device for use clinically by doctors might be available pretty soon.

“Doctors could have these small, portable devices in their offices and get nearly instant readings,” [Tarek] Fahmy said. “They could also carry them into the field and test patients on site.”

The new device could also be used to test for a wide range of biomarkers at the same time, from ovarian cancer to cardiovascular disease, [Mark] Reed said. “The advantage of this technology is that it takes the same effort to make a million devices as it does to make just one. We’ve brought the power of modern microelectronics to cancer detection.”

(Quoted from

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