Tag Archives: genes

Taking DNA beyond genetics with living computers and nanobots

You might want to keep a salt shaker with you while reading a June 7, 2016 essay by Matteo Palma (Queen Mary’s University of London) about nanotechnology and DNA on The Conversation website (h/t June 7, 2016 news item on Nanowerk).

This is not a ‘hype’ piece as Palma backs every claim with links to the research while providing a good overview of some very exciting work but the mood is a bit euphoric so you may want to keep the earlier mentioned salt shaker nearby.

Palma offers a very nice beginner introduction especially helpful for someone who only half-remembers their high school biology (from the June 7, 2016 essay)

DNA is one of the most amazing molecules in nature, providing a way to carry the instructions needed to create almost any lifeform on Earth in a microscopic package. Now scientists are finding ways to push DNA even further, using it not just to store information but to create physical components in a range of biological machines.

Deoxyribonucleic acid or “DNA” carries the genetic information that we, and all living organisms, use to function. It typically comes in the form of the famous double-helix shape, made up of two single-stranded DNA molecules folded into a spiral. Each of these is made up of a series of four different types of molecular component: adenine (A), guanine (G), thymine (T), and cytosine (C).

Genes are made up from different sequences of these building block components, and the order in which they appear in a strand of DNA is what encodes genetic information. But by precisely designing different A,G,T and C sequences, scientists have recently been able to develop new ways of folding DNA into different origami shapes, beyond the conventional double helix.

This approach has opened up new possibilities of using DNA beyond its genetic and biological purpose, turning it into a Lego-like material for building objects that are just a few billionths of a metre in diameter (nanoscale). DNA-based materials are now being used for a variety of applications, ranging from templates for electronic nano-devices, to ways of precisely carrying drugs to diseased cells.

He highlights some Canadian work,

Designing electronic devices that are just nanometres in size opens up all sorts of possible applications but makes it harder to spot defects. As a way of dealing with this, researchers at the University of Montreal have used DNA to create ultrasensitive nanoscale thermometers that could help find minuscule hotspots in nanodevices (which would indicate a defect). They could also be used to monitor the temperature inside living cells.

The nanothermometers are made using loops of DNA that act as switches, folding or unfolding in response to temperature changes. This movement can be detected by attaching optical probes to the DNA. The researchers now want to build these nanothermometers into larger DNA devices that can work inside the human body.

He also mentions the nanobots that will heal your body (according to many works of fiction),

Researchers at Harvard Medical School have used DNA to design and build a nanosized robot that acts as a drug delivery vehicle to target specific cells. The nanorobot comes in the form of an open barrel made of DNA, whose two halves are connected by a hinge held shut by special DNA handles. These handles can recognise combinations of specific proteins present on the surface of cells, including ones associated with diseases.

When the robot comes into contact with the right cells, it opens the container and delivers its cargo. When applied to a mixture of healthy and cancerous human blood cells, these robots showed the ability to target and kill half of the cancer cells, while the healthy cells were left unharmed.

Palma is describing a very exciting development and there are many teams worldwide working on ways to make drugs more effective and less side effect-ridden. However there does seem to be a bit of a problem with targeted drug delivery as noted in my April 27, 2016 posting,

According to an April 27, 2016 news item on Nanowerk researchers at the University of Toronto (Canada) along with their collaborators in the US (Harvard Medical School) and Japan (University of Tokyo) have determined that less than 1% of nanoparticle-based drugs reach their intended destination …

Less than 1%? Admittedly, nanoparticles are not the same as nanobots but the problem is in the delivery, from my April 27, 2016 posting,

… the authors argue that, in order to increase nanoparticle delivery efficiency, a systematic and coordinated long-term strategy is necessary. To build a strong foundation for the field of cancer nanomedicine, researchers will need to understand a lot more about the interactions between nanoparticles and the body’s various organs than they do today. …

I imagine nanobots will suffer a similar fate since the actual delivery mechanism to a targeted cell is still a mystery.

I quite enjoyed Palma’s essay and appreciated the links he provided. My only proviso, keep a salt shaker nearby. That rosy future is going take a while to get here.

Genes and jazz: a July 17, 2015 performance in Vancouver (Canada)

A geneticist and a jazz musician first combined forces for Genes and Jazz at a 2008 Guggenheim museum event where it was first conceptualized (and performed?). Vancouver will be lucky enough to enjoy a live performance on July 17, 2015 as part of the 2015 Indian Summer Festival (July 9 – 18, 2015). Here’s more from the festival event page,

What happens when you cross a Nobel prize-winning geneticist with one of New York’s most sought after jazz quintets? Genes & Jazz. Part jazz concert, part scientific talk by one of the world’s finest scientific minds, Genes & Jazz is where the seemingly dichotomous worlds of science and the arts meet.

Dr. Harold Varmus won the Nobel Prize in 1989 for his work on the proto-oncogene, which enhanced our understanding of cancer. [emphasis mine] His son, jazz trumpeter Jacob leads the Jacob Varmus Quintet. [emphasis mine] Together they explore the ways that genes and notes affect complex organisms and compelling music. The father-son duo compares cell biology to the development of musical compositions.

“Mutation is essential to species diversity just as stylistic variation is essential to the arts,” says Dr. Varmus. “Without genetic error, there would be no evolution. Without variety, there would be no development in art, literature or music. Variety is essential to progress.”

Genes & Jazz was sparked in 2008 as part of the ‘Works & Process’ series at the Guggenheim Museum in New York.

Logistics (from the ticket purchase page),

    July 17 – July 17 [2015]
Vancouver Playhouse
600 Hamilton Street at Dunsmuir
Vancouver, BC
Admission: $25 / $40 / $60

For anyone wondering about how the jazz might sound, there’s this from the ticket purchase page,

“…lyrical and self-assured, more Miles Davis than Dr. John.” – The New Yorker

I think the first  person to link jazz with biology was Dr. Mae-Won Ho in a 2006 Institute of Science in Society (ISIS) lecture: Quantum Jazz; the meaning of life, the universe, and everything (free version). The fully referenced and illustrated lecture is available for members only. Here’s an excerpt  from the lecture,

Quantum jazz is the music of the organism dancing life into being, from the top of her head to her toes and fingertips, every single cell, molecule and atom taking part in a remarkable ensemble that spins and sways to rhythms from pico (10-12) seconds to minutes, hours, a day, a month, a year and longer, emitting light and sound waves from atomic dimensions of nanometres up to metres, spanning a musical range of 70 octaves (for that is the range of living activities). And each and every player, the tinniest molecule not withstanding, is improvising spontaneously and freely, yet keeping in tune and in step with the whole.

There is no conductor, no choreographer, the organism is creating and recreating herself afresh with each passing moment.

That’s why ordinary folks like us can walk and chew gum at the same time, why top athletes can run a mile in under four minutes, and kung fu experts can move with lightning speed and perhaps even fly effortlessly through the air, like in the movie Crouching Tiger and Hidden Dragon. This perfect coordination of multiple tasks carried out simultaneously depends on a special state of wholeness or coherence best described as “quantum coherence”, hence quantum jazz.

Quantum coherent action is effortless action, effortless creation, the Taoist ideal of art and poetry, of life itself.

Dr. Ho also gave an interview about her influences and ‘quantum jazz’ which is reproduced in ISIS report 23/06/10 (presumably 23 June 2010),

ATHM [Alternative therapies in health and medicine]: Please tell us a little bit about your background and schooling.

Ho: I was born in Hong Kong; started school in Chinese and then transferred to an English school for girls, run by Italian nuns. I got exposed to serious Western ideas late-ish in life, when I was about 10 or 11 years old. I was quite good in school, and the nuns let me do whatever I liked; didn’t have to listen if I got bored. So I escaped the worst of reductionist Western education because ideas that didn’t fit just rolled off my back. I guess that explains why I’m always at odds with whatever the conventional theory is in every single field that I go into.

I was in the convent school until I entered Hong Kong University to read biology and then biochemistry as a PhD. Again, I learned almost nothing useful during that time. Maybe I exaggerate: I learned, by myself, of things I liked to learn about. After I finished university, I got a postdoctoral fellowship, and began to change fields because I didn’t like the kind of research I was doing. I began to revolt against neo-Darwinism and the reductionist way of looking at things in bits.

I had gone into biochemistry for my Ph.D. because of something I heard from one of the professors who quoted Albert St. Györgyi – the father of biochemistry—that life was interposed between two energy levels of an electron. I thought that was sheer poetry. That made me want to know, “what is life?”

So I went into biochemistry thinking I would find the answer there. But it was very dull because biochemistry then was about cutting up and grinding up everything, separating, purifying. Nothing to tell you about what life is about.

Biology as a whole was studying dead, pinned specimens. There was nothing that answered the question, what is biological organization? What makes organisms tick? What is being alive? I especially detested neo-Darwinism because it was the most mind-numbing theory that purports to explain anything and everything by “selective advantage”, competition and selective advantage.

I spent a lot of time criticizing neo-Darwinism until I got bored. What neo-Darwinism leaves out is the whole of chemistry, physics, and mathematics, all science in fact. You don’t even need any physiology or developmental biology if everything can be explained in terms of selective advantage and a gene for any and every character, real or imaginary.

Finally, I met some remarkable people and learned a lot from them, and completely changed my field of research to try and answer that haunting question, “what is life?” I wrote a book on the ‘physics of organisms’, not ‘biophysics’, which is largely about the structure of dead biological materials and physical methods used in characterizing them. The physics of organisms is about living organization, quantum coherence and other important concepts.

Varmus and Ho may or may not be familiar with each other’s work linking jazz with biology. It wouldn’t be the first time that two or more people came to similar conclusions without reference to each other. At a guess, I’d say Ho’s approach is more about the poetry or the metaphor while Varmus’ approach is more about the music.

Patents as weapons and obstacles

I’m going to start with the phones and finish with the genes. The news article titled Patents emerge as significant tech strategy by Janet I. Tu featured Oct. 27, 2011 on physorg.com provides some insight into problems with  phones and patents,

It seems not a week goes by these days without news of another patent battle or announcement: Microsoft reaching licensing agreements with various device manufacturers. Apple and various handset manufacturers filing suits and countersuits. Oracle suing Google over the use of Java in Android.

After Microsoft and Samsung announced a patent-licensing agreement last month involving Google’s Android operating system, Google issued a statement saying, in part: “This is the same tactic we’ve seen time and again from Microsoft. Failing to succeed in the smartphone market, they are resorting to legal measures to extort profit from others’ achievements and hinder the pace of innovation.”

Microsoft’s PR chief Frank Shaw shot back via Twitter: “Let me boil down the Google statement … from 48 words to 1: Waaaah.”

This was Microsoft’s PR chief??? I do find this to be impressive,but not in a good way. Note: Tu’s article was originally published in The Seattle Times. [Dec.17.11: I’ve edited my original sentence to make the meaning clearer, i. e., I changed it from ‘I don’t find this to be impressive …]

My Sept. 27, 2011 posting focused on the OECD (Organization for Economic Cooperation and Development) and their Science Technology and Industry 2011 Scorecard where they specifically name patenting practices as a worldwide problem for innovation. As both the scorecard and Tu note (from the Tu article),

… technology companies’ patent practices have evolved from using them to defend their own inventions to deploying them as a significant part of competitive strategies …

Tu notes,

Microsoft says it’s trying to protect its investment in research and development – an investment resulting in some 32,000 current and 36,500 pending patents. [emphasis mine] It consistently ranks among the top three computer-software patent holders in the U.S.

One reason these patent issues are being negotiated now is because smartphones are computing devices with features that “are generally in the sweet spot of the innovations investments Microsoft has made in the past 20 years,” said Microsoft Deputy General Counsel Horacio Gutierrez.

There’s no arguing Microsoft is gaining a lot strategically from its patents: financially, legally and competitively.

Royalties from Android phones have become a fairly significant revenue stream.

Investment firm Goldman Sachs has estimated that, based on royalties of $3 to $6 per device, Microsoft will get about $444 million in fiscal year 2012 from Android-based device makers with whom it has negotiated agreements.

Some think that estimate may be low.

Microsoft is not disclosing how much it gets in royalties, but Smith, the company’s attorney, has said $5 per device “seems like a fair price.”

Various tech companies wield patents also to slow down competitors or to frustrate, and sometimes stop, a rival from entering a market. [emphases mine]

It’s not just one industry sector either. Another major player in this ‘patenting innovation to death game’ is the health care industry. Mike Masnick in his Oct. 28, 2011 Techdirt posting (Deadly Monopolies: New Book Explores How Patenting Genes Has Made Us Less Healthy) notes,

A few years ago, David Koepsell, came out with the excellent book, Who Owns You?, with the subtitle, “The corporate gold rush to patent your genes.” It looks like there’s now a new book [Deadly Monopolies] out exploring the same subject, by medical ethicist Harriet Washington.

NPR (National Public Radio) highlights this story in their feature on  Washington’s book,

Restrictive patents on genes prevent competition that can keep the medical cost of treatment down, says Washington. In addition to genes, she also points to tissue samples, which are also being patented — sometimes without patients’ detailed knowledge and consent. Washington details one landmark case in California in which medically valuable tissue samples from a patient’s spleen were patented by a physician overseeing his treatment for hairy-cell leukemia. The physician then established a laboratory to determine whether tissue samples could be used to create various drugs without informing the patient.

“[The patient] was told that he had to come to [the physician’s] lab for tests … in the name of vigilance to treat his cancer and keep him healthy,” says Washington.

The patient, a man named John Moore, was never told that his discarded body parts could be used in other ways. He sued his doctor and the University of California, where the procedure took place, for lying to him about his tissue — and because he did not want to be the subject of a patent. The case went all the way to the California Supreme Court, where Moore lost. In the decision, the court noted that Moore had no right to any share of the profits obtained from anything developed from his discarded body parts.

According to the webpage featuring Deadly Monopolies on the NPR website, this state of affairs is due to a US Supreme Court ruling made in 1980 where the court ruled,

… living, human-made microorganisms could be patented by their developers. The ruling opened the gateway for cells, tissues, genetically modified plants and animals, and genes to be patented.

I gather the US Supreme Court is currently reconsidering their stance on patents and genes. (As for Canada, we didn’t take that route with the consequence that it is not possible to patent a gene or tissue culture here. Of course, things could change.)