DNA Computers and DNA Viruses

Cat’s the one who started me on DNA computers (we share a grad student office). My AI Otto is struggling with my need for speed in his computations and his need for energy to complete the work. When I ask him a question, he sorts through a datasphere the size of the digital Library of Congress (all public sources on the internet. Imagine if you searched ‘Homo erectus’ on the internet and then read and absorbed the one million hits–that’s what Otto does just to get started) to create the simulated reality required for his movies. You can see the importance of speed.

Here’s what I know about DNA computers. They weigh almost nothing, carry their own energy pack, can perform ten trillion operations at once and store an amazing amount of information–all in a drop of water with room to spare. The mechanics are deceptively simple. A high school senior won a scholarship by programming the Declaration of Independence into a DNA molecule. Here’s a link to How Stuff Works if you’d like more information.

The problem, from what Cat’s explained, is the amount of error in DNA computing. In our human genome, we call them mutations and they’re considered part of our uniqueness. The average child has around 6.3 billion base pairs of DNA with around 277 mutational differences from his/her parents. Many are noninvasive because 1) cells have built-in redundancies, 2) parts of our genetic make-up are inactive. Maybe they used to be active, but with H. sapiens sapiens, they aren’t. 3) some have nothing to do with how we get along in the world.

But, for traditional computing needs, we need more accuracy than that. The theorists believe that within highly-structured uses, they can be controlled. Taiwan has already created a chip out of DNA.

How’s a DNA Computer Work

You’ve probably read a lot about DNA computers. The next generation of

computing power. Based on the idea that our cells program our entire genome with DNA and its six bases. All our bodies do is rearrange the position of the bases and the length of the message. Kind of like the bases are letters, strung together into words, or sentences (without the space between the words). A high school senior won a scholarship by programming the Declaration of Independence into a DNA molecule. She described it as counterintuitively easy.

Scientists accept that DNA computers are the future. DNA is the most common molecule on earth. A DNA computer that fits in a drop of water, carries its own energy pack , stores millions of times the data of a personal computer, operates hundreds of thousands of times faster than conventional silicon computers–and performs ten trillion operations at once.

A typical problem that a DNA computer excels at is the so-called “burnt pancake problem”:

DNA Computers–Think Origami, or Brain Folds

Scientists have struggled for over thirty years to market a DNA computer to the masses. It can play tic-tac-toe and solve the Traveling Salesman Problem (best way for a national sales guy to visit twenty-thirty cities–quite relevant to everyday people). Now the experts are considering using DNA computer apps to fight disease. But, for us middle Americans, we are far from benefiting from the power, affordability and tiny size of DNA computers.

Here’s a clever idea I stumbled across on MIT’s blog. We all know that the reason the brain can do so much is it relies on the folds that cover its surface. Technically, they’re not ‘folds’; they’re Gyri or Gyrus (singular) and the ‘valleys’ between the Gyri are called Sulci or Sulcus. Anyway, Mother Nature added these to give that umph to our brains in power, storage capacity and speed that no computer comes close to matching. Why not add them to DNA computers? Here’s a discussion:

DNA Origami for Faster, Smaller Computer Chips

Using DNA structures, researchers may be able to construct tinier, cheaper chips

Artificial, self-assembling DNA structures may help make smaller and cheaper microchips, according to research presented in the latest issue of Nature Nanotechnology. Tinier microchips would allow faster computers and other electronics.

Researchers from IBM and the California Institute of Technology used a technique known as DNA origami, where a long strand of DNA is folded into a shape with many shorter strands dubbed staples, creating a three-dimensional shape. In the paper, the researchers demonstrated using DNA origami-shapes as a scaffold for carbon nanotubes–a trick that could eventually be used to create nanoscale microchips.

The DNA structures are tiny enough to have features measuring six nanometers–the current industry standard for microchips is 45 nanometers. The process could replace the expensive tools manufacturers currently use to make tiny chips, although IBM suggests that it could take up to 10 years to test and refine the process for manufacturing.

Why isn’t DNA Computing Further Along?

Here’s another exciting article–this from BBC–about the potential of DNA computers. What surprises me is they aren’t further along than what is outlined below. The molecule DNA programs our entire genome, including our brain. That’s pretty versatile, not to mention quick and adaptive. We can see it’s power by looking in the mirror.

From the get-go, DNA uses a more powerful language–six-digits compared to binary’s two-digit language (binary being the popular language of today’s silicon computers). I’m guessing the roadblock to unlocking DNA’s computing potential is our problem-solving skills and our ability to understand what it is DNA does.

Nevertheless, here’s an update on our progress:

DNA Computer Answers Questions

A computer with DNA as its information carrier can solve classic logic conundrums, researchers say.

DNA has been used to do simple number crunching before, but a system developed by Israeli scientists can effectively answer yes or no questions. (more)

DNA Computers and DNA Viruses

Cat’s the one who started me on DNA computers (we share a grad student office). My AI Otto is struggling with my need for speed in his computations and his need for energy to complete the work. When I ask him a question, he sorts through a datasphere the size of the digital Library of Congress (all public sources on the internet. Imagine if you searched ‘Homo erectus’ on the internet and then read and absorbed the one million hits–that’s what Otto does just to get started) to create the simulated reality required for his movies. You can see the importance of speed.

Here’s what I know about DNA computers. They weigh almost nothing, carry their own energy pack, can perform ten trillion operations at once and store an amazing amount of information–all in a drop of water with room to spare. The mechanics are deceptively simple. A high school senior won a scholarship by programming the Declaration of Independence into a DNA molecule. Here’s a link to How Stuff Works if you’d like more information.

The problem, from what Cat’s explained, is the amount of error in DNA computing. In our human genome, we call them mutations and they’re considered part of our uniqueness. The average child has around 6.3 billion base pairs of DNA with around 277 mutational differences from his/her parents. Many are noninvasive because 1) cells have built-in redundancies, 2) parts of our genetic make-up are inactive. Maybe they used to be active, but with H. sapiens sapiens, they aren’t. 3) some have nothing to do with how we get along in the world.

But, for traditional computing needs, we need more accuracy than that. The theorists believe that within highly-structured uses, they can be controlled. Taiwan has already created a chip out of DNA.

For my purposes, itmay be the only method of addressing Otto’s massive requirement for speed and power. I might tinker with it this summer. Logically, it makes sense: I have a specific requirement, a single use (which is what DNA computers have been successful in to date), and Zeke has background in DNA manipulation.

Cat jumped right over DNA computers–assuming as only her big brain would that their invention was far enough along to no longer be a challenge to her–to DNA viruses. More on that later.

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