Tag Archives: DNA origami

Rail system and choreography metaphors in a couple of science articles

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If you are going to use a metaphor/analogy when you’re writing about a science topic  because you want to reach beyond an audience that’s expert on the topic you’re covering or you want to grab attention from an audience that’s inundated with material, or you want to play (for writers, this can be a form of play [for this writer, anyway]), I think you need to remain true to your metaphor. I realize that’s a lot tougher than it sounds.

I’ve got examples of the use of metaphors/analogies in two recent pieces of science writing.

First, here’s the title for a Jan. 23, 2012 article by Samantha Chan for The Asian Scientist,

Scientists Build DNA Rail System For Nanomotors, Complete With Tracks & Switches

Then, there’s the text where the analogy/metaphor of a railway system with tracks and switchers is developed further and abandoned for origami tiles,

Expanding on previous work with engines traveling on straight tracks, a team of researchers at Kyoto University and the University of Oxford have used DNA building blocks to construct a motor capable of navigating a programmable network of tracks with multiple switches.

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In this latest effort, the scientists built a network of tracks and switches atop DNA origami tiles, which made it possible for motor molecules to travel along these rail systems.

Sometimes, the material at hand is the issue. ‘DNA origami tiles’ is a term in this field so Chan can’t change it to ‘DNA origami ties’ which would fit with the railway analogy. By the way, the analogy itself comes from (or was influenced by) the title the scientists chose for their published paper in Nature Nanotechnology (it’s behind a paywall),

A DNA-based molecular motor that can navigate a network of tracks

All in all, this was a skillful attempt to get the most out of a metaphor/analogy.

For my second example, I’m using a Jan. 12, 2012 news release by John Sullivan for Princeton University which was published in Jan. 12, 2012 news item on Nanowerk. Here’s the headline from Princeton,

Ten-second dance of electrons is step toward exotic new computers

This sets up the text for the first few paragraphs (found in both the Princeton news release and the Nanowerk news item),

In the basement of Hoyt Laboratory at Princeton University, Alexei Tyryshkin clicked a computer mouse and sent a burst of microwaves washing across a silicon crystal suspended in a frozen cylinder of stainless steel.

The waves pulsed like distant music across the crystal and deep within its heart, billions of electrons started spinning to their beat.

Reaching into the silicon crystal and choreographing the dance of 100 billion infinitesimal particles is an impressive achievement on its own, but it is also a stride toward developing the technology for powerful machines known as quantum computers.

Sullivan has written some very appealing text for an audience who may or may not know about quantum computers.

Somebody on Nanowerk changed the headline to this,

Choreographing dance of electrons offers promise in pursuit of quantum computers

Here, the title has been skilfully reworded for an audience that knows more quantum computers while retaining the metaphor. Nicely done.

Sullivan’s text goes on to provide a fine explanation of an issue in quantum computing, maintaining coherence, for an audience not expert in quantum computing. The one niggle I do have is a shift in the metaphor,

To understand why it is so hard, imagine circus performers spinning plates on the top of sticks. Now imagine a strong wind blasting across the performance space, upending the plates and sending them crashing to the ground. In the subatomic realm, that wind is magnetism, and much of the effort in the experiment goes to minimizing its effect. By using a magnetically calm material like silicon-28, the researchers are able to keep the electrons spinning together for much longer.

Wasn’t there a way to stay with dance? You could have had dancers spinning props or perhaps the dancers themselves being blown off course and avoided the circus performers. Yes, the circus is more colourful and appealing but, in this instance, I would have worked to maintain the metaphor first introduced, assuming I’d noticed that I’d switched metaphors.

So, I think I can safely say that using metaphors is tougher than it looks.

Coatings that shake off bacteria and biological photocopying

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The American Vacuum Society (AVS) is holding its 58th International Symposium and Exhibition from Oct. 30 – Nov. 4, 2011 in Nashville, Tennessee. Presentations are not focused on vacuuming (hoovering) floors but rather on something called vacuum science and they span from a presentation on bacteria and coatings to another on photocopying DNA to more.

From the Oct. 31, 2011 news item on Nanowerk,

“Sea water is a very aggressive biological system,” says Gabriel Lopez, whose lab at Duke University studies the interface of marine bacterial films with submerged surfaces. While the teeming abundance of ocean life makes coral reefs and tide pools attractive tourist destinations, for ships whose hulls become covered with slime, all this life can, quite literally, be a big drag. On just one class of U.S. Navy destroyer, biological build-up is estimated to cost more than $50 million a year, mostly in extra fuel, according to a 2010 study performed by researchers from the U.S. Naval Academy and Naval Surface Warfare Center in Maryland. Marine biofouling can also disrupt the operation of ocean sensors, heat-exchangers that suck in water to cool mechanical systems, and other underwater equipment.

I think rather than describing sea water as ‘aggressive’  which suggests intent, I’d use ‘active’ as Lopez does later in another context (excerpted from the news item),

Lopez and his group focus on a class of materials called stimuli-responsive surfaces. As the name implies, the materials will alter their physical or chemical properties in response to a stimulus, such as a temperature change. The coatings being tested in Lopez’s lab wrinkle on the micro- or nano-scale, shaking off slimy colonies of marine bacteria in a manner similar to how a horse might twitch its skin to shoo away flies. The researchers also consider how a stimulus might alter the chemical properties of a surface in a way that could decrease a marine organism’s ability to stick.

At the AVS Symposium, held Oct. 30 – Nov. 4 in Nashville, Tenn., Lopez will present results from experiments on two different types of stimuli-responsive surfaces: one that changes its texture in response to temperature and the other in response to an applied voltage. The voltage-responsive surfaces are being developed in collaboration with the laboratory of Xuanhe Zhao, also a Duke researcher, who found that insulating cables can fail if they deform under voltages. “Surprisingly, the same failure mechanism can be made useful in deforming surfaces of coatings and detaching biofouling,” Zhao said.

“The idea of an active surface is inspired by nature,” adds Lopez, who remembers being intrigued by the question of how a sea anemone’s waving tentacles are able to clean themselves. [emphasis mine] Other biological surfaces, such as shark skin, have already been copied by engineers seeking to learn from nature’s own successful anti-fouling systems.

(I did profile some biomimicry work being done with shark skin in my comments on part 4 of the Making Stuff programmes broadcast as part of the Nova series on PBS (US Public Broadcasting Stations) in my Feb. 10, 2011 posting.)

This next presentation is in the area of synthetic biology. From the Oct. 31, 2011 news item (DNA origami from inkjet synthesis produced strands) on Nanowerk,

In the emerging field of synthetic biology, engineers use biological building blocks, such as snippets of DNA, to construct novel technologies. One of the key challenges in the field is finding a way to quickly and economically synthesize the desired DNA strands. Now scientists from Duke University have fabricated a reusable DNA chip that may help address this problem by acting as a template from which multiple batches of DNA building blocks can be photocopied. The researchers have used the device to create strands of DNA which they then folded into unique nanoscale structures.

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“We found that we had an “immortal” DNA chip in our hands,” says Ishtiaq Saaem, a biomedical engineering researcher at Duke and member of the team. [emphasis mine] “Essentially, we were able to do the biological copying process to release material off the chip tens of times. [emphasis mine] The process seems to work even using a chip that we made, used, stored in -20C for a while, and brought out and used again.”

After releasing the DNA from the chip, the team “cooked” it together with a piece of long viral DNA. “In the cooking process, the viral DNA is stapled into a desired shape by the smaller chip-derived DNA,” explains Saaem. One of the team’s first examples of DNA origami was a rectangle shape with a triangle attached on one side, which the researchers dubbed a “nano-house.” The structure could be used to spatially orient organic and inorganic materials, serve as a scaffold for drug delivery, or act as a nanoscale ruler, Saaem says.

I’m not very comfortable with the notion of an “immortal DNA chip” but then I have many reservations about synthetic biology. Still, I think it’s important to pay attention and consider the possibility that my fears about synthetic biology might make as much sense as the fears many had about electricity in the 19th century.