DNA: It’s Not Just for the Living Anymore
The smiley-faced DNA above is the work of Paul Rothemund of CalTech. In March 2006, Rothemund achieved what became known in the science world as "DNA origami."
To people who say that true nanomachines — those that assemble themselves from the bottom up — are impossible, the best answer true believers can give is simply to present their own existence as proof of concept. We are self-assembled out of simple building blocks.
For many, this settles the argument quickly. I do not believe it does, but I’ll get into that further down if you’ll stay with me. For now, for the sake of argument, let’s say that all that is left is for us to figure out how nature manages this bottom-up self-assembly. But you do not necessarily need to figure out how this feat was accomplished. You can take a shortcut and use DNA, the gift handed down to us via nature’s laboratory and a few billion years of evolution.
DNA exists to self-assemble and its strands are a scaffolding upon which we can build more and more complex structures. DNA can give us not only the physical frame but also the template by which we can learn how to program synthetic versions to obey our commands. This is outlined in a recent paper co-authored by CalTech’s Paul Rothemund, a DNA nanotech pioneer, in Nature Chemistry.
British scientist Richard Jones, author of “Soft Machines,” noted just this week on his blog that DNA nanotechnology is fast becoming the place to watch for truly amazing developments. Jones writes:
For many years DNA nanotechnology could have been viewed as a marvelous technical tour-de-force with little potential for real applications, but the continuing exponential falls in the cost of synthetic DNA and the increasing sophistication of the devices being created in the growing number of laboratories working in this field makes this conclusion less certain.
Jones was referring specifically to the work of NYU’s Nadrian Seeman, who for a decade or so was pretty much the only person working on the amazing possibilities of DNA nanotechnology. More background on his “DNA Walker” and other cool stuff from Seeman’s lab can be found here.
I’m from Michigan where, once upon a time, we were pretty good at engineering and assembling machines that went places and changed the world. Part of the process of creating these machines was to map them out first on CAD/CAM software. So, a few years ago, I met the creator of a Motor City company that was way ahead of its time. Nanorex, based in suburban Detroit, was a company that set out to create CAD software to help engineers design these new DNA nanostructures.
I first met its founder, Mark Sims, in 2004 just after I had won that year’s prize in communication from the Foresight Institute, a nanotechnology think tank. Mark and I found ourselves sitting next to each other on the plane ride back to Michigan from Washington, D.C., and we got to talking about both of our obsessions — nanotechnology. The difference between us was that I just wrote about it and he was actually doing something useful.
I wrote about his company for a Detroit-area tech magazine called X-OLOGY a little while ago:
When Sims founded the company in 2004, it was focused purely on creating software for the “design, simulation and analysis of atomically precise molecular machine systems.” In other words, taking atoms and using their naturally occurring covalent bonds to stick them together and create just about anything. The problem, Sims says, is that nobody really knows how to actually build these molecular machine systems yet. Maybe they’ll figure it out in 20 years, he predicts, and then commercialize it a few years later.
In the meantime, his shorter-term plan is to create design software for researchers working on another promising branch of nanotechnology.
Rather than create entirely new materials out of nothing but atoms, many leading-edge nanotech researchers have found something better – the beneficiary of 3.6 billion years of evolutionary research: DNA.
“The thing that’s exciting about DNA is that they’re doing it now,” Sims says. “Here you have a material and a system with it that is programmable and capable of bottom-up self-assembly from nanoscale to literally microscale.” More here (PDF 158 KB)
I wrote to Mark a few weeks ago to ask how things were going at Nanorex. He told me that, unfortunately, his company closed shop in 2008 for a number of reasons, but it was primarily that it was entirely self-funded and the economic downturn made it increasingly expensive to keep afloat. But the company was never meant to go anywhere, since so few people were actually doing any DNA nanotechnology. It was purely a labor of love by Sims.
Howard,
The debate is not that self-assembled nanomachines are impossible. Our very existence is fact that they exist. The debate is whether such nanomachines can be made based on “dry” vacuum-phase chemistry rather than the solution-phase chemistry that our bodies are based on. I’m one of those who believe that “dry” nanotechnology is impossible but that it is irrelevant. I think solution-phase nanotechnology (biology being one version of it) will be capable of all of feats described in Drexler’s first book “Engines of Creation”.
The argument that we are assembled out of simple building blocks is erroneous at best and completely misses the point. The complexity of life or any complex machine is in the information that was used to create it – the programming. And that is where I believe our waves of progress will crash fruitlessly for the foreseeable future. We are not even at the point of beginning to understand information. The evidence is that we look at complexity and reduce it to the physical parts without an ability to quantify or articulate the amount of information needed to attain the complexity. We are missing the point.
I agree with you, Don. It’s the point I tried to make in a clumsy way when I wrote reality is analog and not digital. Unfortunately, many early proponents of advanced nanotechnology were computer geeks who believed that you simply had to re-create the world on their screen with a high enough resolution and hit the “print” button. The real world is much more interesting than that.
Cool post, thanks!
Don Matthews’ comment is spot on: “The argument that we are assembled out of simple building blocks is erroneous at best and completely misses the point. The complexity of life or any complex machine is in the information that was used to create it – the programming.”
My comment is intended to challenge you with a contrary view to some assumptions in your post. You say that DNA is “the gift handed down to us via nature’s laboratory and a few billion years of evolution.” How convenient that something as complex and mysterious as DNA can be explained so simply. Obviously, for the true believers it is never necessary to question the origin of the massive amounts of information stored in one DNA strand or the embedded programming that makes such information useful. For them, all of life can be explained by the TAUTOLOGICAL (we obviously evolved because…well, we’re here aren’t we?) so they feel justified turning a blind eye to the THEOLOGICAL.
Forgive me if I don’t blindly believe that just the right mix of chemicals, combined with just the right sequence of external forces, acting over millions of years, was able to produce anything as amazing and wondrous as DNA. This isn’t about science vs. religion! Look at the proof in an objective way. There is no empirical science that reasonably demonstrates the popular view of natural evolution. (Even mutations affect the information that is already present in the organism and are insufficient to explain how such information got there in the first place.) There is much we don’t understand about DNA. Doesn’t it make more sense, when we find a system in a simple flower like a lily whose DNA contains an intelligent program capable of managing sixty times more information than that found in an entire set of Encyclopedia Brittanica, to think that there might be an intelligent being who designed it? Truly, professing to be wise we have become fools.
If this be the case, then “nanotechnology” is a misleading neologism. We’ve had nanotechnology for millennia; we’ve called it “agriculture”.
Thanks Mthorn 10 for stating the obvious. Darwin thought that cells were not much more complex than say a water balloon, now we know they are highly complex structures and that each chromosome is actually the equivalent of millions of lines of code. Attempts at reverse engineering are a tempting start, but not knowing the operating system or the inherent syntax (structure) of the code means a huge process of trial and error. How about us making better use of what we have and ‘modifying’ existing biological systems (say algae or bacteria) to perform chemical change (such as converting sunlight, waste and water to produce bio fuels) or genetic engineering to cure disease would that not make more sense. At what point in all this effort (expense) will the scientist finally throw up their hands and finally admit that some things are beyond all our comprehension and for a biological system to contain this much information and order leads to one inescapable observation – intelligent design?
Really appreciate you sharing this post.Much thanks again. Fantastic.