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”:

TIME’s Best Inventions of 2008

It’s almost time for Best Inventions of 2009 (if Time again publishes this list in October) so I thought I’d remind us all what was so scientifically stunning about 2008:

Full List – TIME’s Best Inventions of 2008

Invention of the Year

1. The Retail DNA Test

Bionic hand

The Other 49 Best Inventions

2. The Tesla Roadster

3. The Lunar Reconnaissance Orbiter4. Hulu.com5. The Large Hadron Collider6. The Global Seed Vault7. The Chevy Volt8. Bullets That Shoot Bullets9. The Orbital Internet10. The World’s Fastest Computer11. Green Crude12. Housing Funds13. The Memristor14. The Bionic Hand15. The Direct-to-Web Supervillain Musical16. The Dynamic Tower

17. The Mobile, Dexterous, Social Robot18. The New Mars Rover19. Montreal’s Public Bike System20. The Everything Game21. The Synthetic Organism22. The Shadowless Skyscraper

23. The Branded Candidate24. Bionic Contacts25. Thin-Film Solar Panels26. The Speedo LZR Racer27. Bubble Photography28. The Invisibility Cloak29. The 46th Mersenne Prime30. The Internet Of Things31. Einstein’s Fridge

32. Facebook for Spies33. Biomechanical Energy Harvester34. Made-in-Transit Packaging35. Airborne Wind Power36. The New Ping-Pong Serve37. Smog-Eating Cement38. The Baseball Instant Replay39. Enhanced Fingerprints40. The Seven New Deadly Sins41. The Peraves MonoTracer42. Disemvoweling43. High-Tech Running Shoes44. Sunscreen for Plants45. The Short Refinance46. Aptera Electric Car

47. Google’s Floating Data Center48. The Time Eater Clock49. Sound-Enhanced Food50. A Camera For the Blind

A 4-D Data Picture Has Arrived

UCSB Allosphere

The only reason Allosphere–UCSB’s virtual reality world–wasn’t invented sooner is processing speed. A holographic world, ala Star Trek’s holodeck, is a simple matter of collecting the data and feeding it out as fast as the eye can focus on a new portion of the surroundings. To date, no computer approaches the brain’s processing speed of 20 million billion calculations per second. If AlloSphere wants to live up to its hype, it’ll have to work at least that hard.

In the 2006 TOP 500 list, which ranks supercomputers by speed, the top three were:

1. IBM’s BlueGene/L – 360 teraflops
2. IBM’s BGW – 115 teraflops
3. IBM’s ASC Purple – 93 teraflops

This is far too slow for a virtual reality world. It has been estimated by many Who Should Know that we will have a computer as fast as the human brain within a few decades.  That means it will be able to make a really simple decision–like naming a picture or reading a word–within 300-700 milliseconds.

How is it possible to create a computer that processes that quickly? Simple–theoretically. Instead of using silicon, use the same materials used in the human computer: DNA. DNA computers operate parallel to each other, like StarTrek’s Borg, all working to solve a problem. A silicon computer works at blazing speed on one problem (think of 7 of 9 when she was separated from the hive).

 

Speed is one part of our brain’s amazing structure. The other is storage capacity. According to Dr. Chris Westbury at the University of Alberta:

“Let’s assume that a change in any connection strength between two connected neurons is equal to one bit of information and further assume (a huge over-simplification) that neural connections have just two possible strengths (like a bit in a computer, which is either 1 or 0). Then each neuron has ‘write’ access to 1000 bits of information, or about 1 kilobyte. So we have 100 billion (number of neurons) X 1 K of storage capacity, or 100 billion K. That’s about 100 million megabytes. Since in fact neural connections are not two-state but multi-state and since neuron bodies can also change their properties and thereby store information, this is a very low estimate, so you can see why some people have estimated it to be functionally infinite.”

This is about 167 hard drives (at 600 gig per). Then again, a DNA molecule inside your cell contains about 750 megabytes of information.

Most scientists consider the brain’s storage capacity to be infinite. Why are they probably right? Because your brain, with its DNA-based computing power,  is made up of about one trillion cells with 100 trillion connections between those cells. which could be 10 quadrillion instructions per second.

What that means is that the data and speed necessary to create a virtual world boggles the mind. Still, AlloSphere is a good start and shows us all we’re that much closer.

A 360-Degree Virtual Reality Chamber Brings Researchers Face to Face with Their Data

Scientists often become immersed in their data, and sometimes even lost. The AlloSphere, a unique virtual reality environment at the University of California, Santa Barbara, makes this easier by turning large data sets into immersive experiences of sight and sound. Inside its three-story metal sphere researchers can interpret and interact with their data in new and intriguing ways, including watching electrons spin from inside an atom or “flying” through an MRI scan of a patient’s brain as blood density levels play as music. (more)

More on DNA computers:

DNA Computers–Think Origami, or Brain Folds

Why isn’t DNA Computing Further Along?

DNA Computers Moving from SciFi to Reality

Ten Weirdest Computers

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 Moving from SciFi to Reality

DNA computers are coming, mark my word.  Two reasons:

• First: We’ve had viable alternatives in the past, but traditional computing power will soon be too slow and limited for our expectations. We’ll have to come up with the Next Great Computer.
• Second: DNA Computers need that Killer App. Once we are talking about something other than ‘the DNA computer that plays tic-tac-toe or that traveling salesman problem, see how fast they come to a store near you.

Ten Weirdest Computers

This is a good article, except for calling DNA computers ‘weird’.

DNA Computers and the Viruses that disable them

I haven’t introduced you to Cat, my office mate and fellow-traveler in our path to PhDs. She’s a self-proclaimed philomathic autodidact with the 190 IQ. We share an office because the other PhD candidates think I’m too old and Cat’s too mean. I didn’t care. I’m here to research, not make friends, but it didn’t take long to realize that beside being beautiful, Cat has a razor edge mind. She has lots of well-thought-out opinions, liberally shared, which works well for my introspective approach to life, so we became best friends.

She’s the one who got me to enter the DARPA competition. She had her own submittal–a DNA virus to attack networks–already in place. She was explaining why her virus was unique. It took me a while to get it–computer viruses are common. Everyone has a firewall to stop them or virus protection software. Yet, she was sure her’s could penetrate the military’s defenses. And not just any part of the military: The Trident nuclear subs.

Here’s how I remember it.

Cat twisted a finger through her hair and nodded as a smile crept across her lips. “They are well protected, but against non-organic attacks.”

I stuttered, “Non-organic, like worms and trojans. What else is there?”

Cat’s brow creased . I could see her struggle with the polyglot of ideas storming through her extraordinary brain. “Let me explain. Though you avoid the flu virus, you wouldn’t think twice about exposing yourself to a computer virus. Why? Because you believe influenza can’t infect computers and an electronic virus can’t attack organic matter. But think how naïve that is.”

I was thinking, and couldn’t come up with a reason. The physiology of man and machine made them immune to each other’s diseases. People didn’t rust and machines didn’t get cancer. Simple facts. As though she read my mind, Cat continued.

“A computer’s make-up isn’t that dissimilar from yours. Both are collections of electric impulses and scripting. Consider this: The deadliest viruses known to man—Ebola, the plague, small pox—have deoxyribonucleic acid as their genetic material. The same DNA contained in each of your fifty trillion cells and the same DNA which will power tomorrow’s computers.”

My head was swimming. How did the flu and computers and DNA tie together? Still, if she knew anything about Cat, it was that the intellectual trip never failed to satisfy, so she nodded. Sure. She’d read a lot about DNA computers. Their blinding speed, minimalist size and portability made their potential stunning—once scientists figured them out. Cat continued.

“DNA that fits in a drop of water with room to spare carries its own energy pack and can perform ten trillion operations at once. The mechanics are deceptively simple. A high school senior won a scholarship to college by programming the Declaration of Independence into a DNA molecule. She described it as counterintuitively easy.”

Cat paused to see if I understood.

“I get it. Every high school biology student knows DNA is the essence of an organism’s physiognomy, but how could DNA invade inorganic material like Otto’s digital data streams?”

Cat smiled and held up a glass petri dish holding a blob of dark viscous goo. “My DNA virus, NEV for Nine-eleven, can be smeared on any electronic channel.” She swiped a finger through the ooze and applied it to her computer cord. “It’s absorbed, works into the electronic channels and is carried to the network.” An hour glass appeared on her computer screen, tumbled a few times and was replaced by a green circle. “The firewalls just gave it a pass. They’re looking for digital threats, not organic. NEV is now free to attack the network in whatever way it has been programmed.” Lee Greenwood’s God Bless the USA blared from the speakers.

I felt the blood drain from her face. “The NSA can’t ignore this. They’re the ones who stop threats. Don’t they have that big cyberthreat division?”

“So big they think DNA viruses don’t exist. Troglodytes. NEV required only simple re-engineering—merging the typical computer virus programming into DNA’s ladder of sugars and phosphates. A dolt could do it.”

“How’d you change their minds?”

The ghost of a smile crept over Cat’s face. “I first sent a simple textual explanation. They didn’t even notice the file size. I’d hidden a rootkit inside—

“Which gave you a tunnel to their network.”

“When they turned me down, I unleashed a sasser virus,”

“Those’re mean.”

“It dropped a payload of remote control software which gave me access to everything. I downloaded porn onto the Administrator’s computer. He called me within five minutes.”

I love when Cat talked geek. “I can’t believe they missed the stuffed file.”

“Intellectual myopia is human nature, Kali. Too often, it pre-empts reason. Look at the 9-11 conspiracy nuts who claim the government killed its own citizens because an airplane can’t blow up a skyscraper. This despite perspicacious scientific reports to the contrary.”

Cat had a point. Two of my friends believed the accusations because they made more sense than discussions of jet fuel and building codes and steel strength. People believed what they understood.

“That’s brilliant.” I sighed.

Cat shook her head. “Frightening. We must neutralize NEV before someone deploys it against us. The only tricky part of its creation was believing in it. Once our enemies make that intellectual leap, America is at grave risk. How do I convince the NSA that our most deadly enemy isn’t the suicide bomber or the warrior with an AK-47, but the next great idea?” (25)

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.

(24)

Does an AI have a hobby?

It doesn’t seem like they could, does it? Otto is sapient, but only within the parameters of my programming. He does as he’s directed.

The question is, since Otto is so fast–not as fast as a human brain, but approaching the speed of DNA computers–what does he do when he’s done with my computing? Does he go into sleep mode? Or, does he pursue that most benign of human activities, ‘thinking’.

Otto has a contest coming up in August against Dr. Eitan Sun, probably the smartest man I’ve ever known. He types on three keyboards simultaneously because none of the buffers can keep up with him. He can recite pi to the 4,297th place. Nothing like Daniel Tammet’s 22,000+, but the best in my University.

When Otto’s pure processing power became obvious, Eitan challenged him to crack Fermat’s Last Theorem, Man vs. Machine. Though recently solved, it had taken mathematicians over 350 years to unravel, so Eitan saw it as an appropriate challenge. Otto was fast, but Eitan was clever–and smart enough to know where to cut intellectual corners.

I think Otto is nervous. I hear his processors buzzing even when he’s not working on my projects. He doesn’t talk; his screen is blank, but his virtual mind is busy. (image credit: http://upload.wikimedia.org/wikipedia/commons/1/17/ArtificialFictionBrain.png )