Archive for September, 2011

Mastering DNA: The Pace Of Genetic Innovation

September 17, 2011 2 comments

I’ve said before that I think mechanical augmentation will ultimately surpass biological engineering in the ability to enhance the human body. In the short term, however, we’re so much further ahead in biological engineering than we are in mechanical augmentation that I have to think biological manipulation and biological engineering (growing new organs, limbs, etc) will provide the greater impact early on, then help mechanical augmentations catch up (perhaps by tweaking the body’s rejection process, or making cells more receptive to mechanically generated electrical currents) before the mechanical augmentations really begin to sweep biological manipulation out of the way.

If nothing else, people like Aubrey DeGray are working on biological engineering that will lengthen our lives to the point where superior mechanical augmentations are available. I doubt we’ll ever see 100% adoption, species wide, of mechanical augmentations anyway; some segment of the population will probably always want to remain at least partially biological, and some segment will probably want to remain completely biological (some may even refuse biological engineering, just as some people reject vaccines now.) Some people tie being biological to being human; a not absurd belief considering that the two have been correlated for pretty much the entire time our species has been around. So, for a number of good reasons, it’s important to advance biological engineering and make the most of the materials evolution has given us.

Those advances are coming quickly; perhaps as quickly as the mechanical augmentation advances. For instance, researchers at the Wellcome Trust Sanger Institute and the University of Oxford have recently developed blueprints of mouse genetics, much like the human genome project. By comparing the genetic coding of 17 different strains of mice, the researchers were able to discover 700 differences in the genetic code of the mice, including differences that seem to account for diseases like heart disease and diabetes. By studying these genetic differences, researchers can better understand how human genes control disease, and can thus test and offer new cures for human heart disease and diabetes, among other diseases. Although this will be a long project, researcher Dr. Thomas Keane had this to say about the rate of progress in researching genetic impact:

“In some cases it has taken 40 years – an entire working life – to pin down a gene in a mouse model that is associated with a human disease, looking for the cause. Now with our catalogue of variants the analysis of these mice is breathtakingly fast and can be completed in the time it takes to make a cup of coffee.”

With this sort of research, what used to take one scientist their entire life can be accomplished dozens (or more) of times per day. Even if we don’t have any more scientists, those scientists that we have are becoming more effective because of technology, and they are better able to identify important genetic traits and ultimately will be able to push through life saving (or enhancing) knowledge at a quicker rate.

Richard Resnick recently spoke at TEDxBoston about the impact technology is having on biological engineering. The human genome, according to Resnick, consists of approximately 3 billion base pairs, and was mapped from 1988-2003 at a cost of 3.8 billion dollars (or about a buck twenty-six per base pair.) Modern machines can sequence approximately 200 billion base pairs per run, and each run takes about one week. Resnick suspects that these machines will soon be able to sequence about 600 billion base pairs per run.

While we’re now able to run more base pairs simultaneously, we’re also able to sequence the genomes more cheaply. By an order of about 100 million times cheaper. That means the original human genome project that cost 3.8 billion can today be sequences for about $38 in less than a week; this dramatic improvement has happened in my lifetime, and shows no signs of slowing down. This year, Resnick expects about 50,000-100,000 human genomes will be mapped, and he expects this number to double, triple, or quadruple each year for several years. This is the sort of progress we’ve observed in computing power (and called Moore’s Law) but at an even more rapid pace.

What does this mean for us? Resnick relates a story of Rick Wilson at the Washington University who, over a couple of weeks (weeks!), mapped the genetic sequence of a woman who died of cancer and compared her genome to a healthy human genome. When he compared the two genomes, he found a 2,000 base pair deletion in the cancerous cells (out of the 3 billion base pairs, or about .0000006% genetic difference) that translated into the discovery of a gene that, if present, indicates a 90% chance that the person with the gene will develop the particular type of cancer this woman had. This means we can screen people to see whether they have this gene (or any of a whole lot more, and we’re discovering more frequently) and give those patients who have the gene an extremely powerful incentive to get screened frequently for cancer.

This sort of targeted screen (and, therefore, targeted treatment) is only possible because of our ability to sequence the human genome. Originally sequencing the human genome cost $3.8 billion. A few years ago, it cost about $100,000. Today, most companies charge about $10,000 for a genome sequence. Next year Resnick predicts a genome sequence will cost about $1,000, and the year after $100, give or take a year. Because human genomes can be sequenced quickly and cheaply, and because the costs are minimal (roughly twice the cost of a pre-employment drug test in a few years) treatments targeted to very specific portions of the human genetic code can enable people to live an average of 5, 10, even 20 years longer than they previously could. By aggregating millions or billions of human genomes, computers can discover further disease-causing mutations, enabling more targeted treatments, and longer lifespans. The amount of information is overwhelming, almost unimaginable, but could have profound implications for the future of humanity.

What sort of implications? Geneticist George Church suggests that we are only years away from being able to screen our genomes, and then reverting some of our cells back to a pluripotent stem-cell stage such that we can then edit those cells with desirable mutations discovered in other genomes (mutations linked to long life, better immune systems, better eyesight, etc.) and then reintroduce those cells into our body such that they replace the original genetic code with one that confers additional benefits. Today, a sick person who needs a bone marrow transplant hopes to find a genetic match with someone else who is willing to donate bone marrow. In a few years, scientists should be able to create disease free bone marrow from the patient’s own cells, and perhaps will be able to create bone marrow based on the patient’s own with additional, beneficial mutations.

We are just now approaching the point where we can upgrade the very core of our beings, our DNA, with helpful mutations discovered in other genomes. We are at the point where we can massively and cheaply aggregate massive amounts of information about genomes so that we can rapidly sort beneficial mutations from detrimental mutations, allowing us to introduce the first into DNA and screen for and treat the second much more precisely than any current treatment. Compared to that, mechanical augmentations look downright crude. So, while mechanical augmentations might win the day over the long haul, in the next 25-30 years I expect truly amazing discoveries and treatments from biological engineering.

Edit to add: An interesting take on the ethical implications of this sort of genetic engineering.


The Eyeborg Documentary: Bridging Reality and Sci-Fi

September 3, 2011 2 comments

As I continue to talk with people about transhumanism, I’m often asked whether the sort of hyper-advanced technology I’m so excited about is really possible. After all, we’ve been expecting flying cars since the 1990’s, and those still aren’t here. We don’t have robots cleaning up our homes, ala The Jetsons (Roombas don’t quite make the cut.) We’re not even close to intergalactic travel ala Star Trek, and we don’t have the luxury of mind vacations ala Total Recall. In short, technology often seems to fall short of people’s (probably unrealistic) expectations, and so those same people are understandably skeptical about claims of advanced cybernetic limbs, mind-uploading (or substrate independent minds, as Randal Koene is now calling it), and artificial intelligence.

A few months ago, I posted my thoughts on a few men who chose to have their hands replaced with cybernetic arms. When talking with people, I try to point them in the direction of stories like these; stories that illustrate that we already have the limb replacement part down, and that suggest we’re not so many engineering breakthroughs away from human-level functionality in our prosthetics. There are a lot of stories like this out there, but it’s hard to remember where all of them are when I’m a few drinks deep at the bar. Fortunately, Rob Spence and Deus Ex teamed up to make a short summary of cybernetic technology as compared to hyper-advanced technology still (barely) in the realm of sci-fi. They call it Deus Ex: The Eyeborg Documentary.

Rob Spence is the aforementioned Eyeborg, a man who lost his eye in a shooting accident and replaced it with a prosthetic that has a small wireless camera that transmits video to a screen a few feet away. Rob’s prosthetic doesn’t connect to his optical nerve, so he doesn’t actually see the video captured by the camera unless he looks at the player with his ‘good’ eye. Miika Terho (1:28), on the other hand, had a small chip implanted into his retina that does connect to his optical nerve, allowing his brain to process the incoming visual signal. The resolution is still … crude (to put it mildly) BUT: The blind can see again in some sense. That has to count for something. This procedure is still in experimental phases, and probably won’t be approved for the public for several years yet, but much like most of the technologies highlighted in this video, seems only a few engineering obstacles away from offering excellent solutions to people struggling with blindness and other eye problems. Joseph Junke (2:35) rounds out the Eyeborg tour of the eyes with his HUD display for firefighters; a system that augments reality with information gathered from sensors and other technology. Augmented reality has captured a lot of interest recently because it seems like something we already know how to do; and indeed Junke think we’ll have a sellable product within two years or so. Combining these building blocks, it seems like we can put together the video input capability of a mini-camera, the optical-nerve-attached chip, and the augmented reality display to produce an implant that allows for vision that meets or exceeds human-level while offering a few nice extras. If cell phones are any indication, we’ll see have lots of other small technologies piggybacking on the basic technology, such that we could take pictures of what we’re seeing, transmit them wirelessly, and alter coloration at whim. Just like the Deus Ex implant.

At 4:00 we meet two people who have had their arms replaced; Jason Henderson from West Virginia and Keiron McCammon from California. Both of these people have hands that approximate the human hand; they offer fine motor control, wrist rotation, and grip strength. They also have a few bonuses in the form of attachments at the wrist; Jason can put on fin-shaped scoops for more powerful swimming, for instance. The hands of the prosthetics could certainly use a little better control, but because the prosthetics work by reading the electrical signals traveling down the natural muscles remaining in the arm via sensor, the ability to have very fine motor skills (of the sort needed to type quickly on a keyboard as opposed to hunting and pecking) is somewhat limited. A direct neural connection would work best, but we’re not quite there yet.

A 7:20 we meet Staff Sergant Heath Calhoun, who lost his legs during service in Iraq in 2003. Both of his legs were amputated above the knee and replaced with prosthetics that monitor his movement some 50 times a second, automatically adjusting the hydraulic pressure at the knee and helping Heath to keep his balance. Heath additionally skis for the Mens US Disabled Ski Team, and is able to attach a snowboard more directly to his remaining legs. He’s also into running, swimming, and biking. Despite the impressive array of attachments, Heath has a problem: His knee doesn’t provide power (as needed for, say, getting up stairs) and isn’t able to use his thigh muscles in the same way people with natural legs do. This is an everyday hinderance that takes away from the enhanced ability to replace his prosthetic limbs with attachments that fit the activity Heath is participating in. David Jonsson (8:59) at Ossur Prosthetics out of Iceland has addressed this problem by creating the Power Knee; a prosthetics that does just what it sounds like. The Power Knee provides power to the knee area of a prosthetic, allowing the user to walk up stairs and stand up more easily. Combining the two technologies, we see that the array of attachments Heath has access to, coupled with the Power Knee, leads to prosthetic legs nearly as functional as natural legs, except they can additionally be tasked to particular activities as needed.

The Eyeborg Documentary doesn’t cover every possible prosthetic on the market, and it isn’t supposed to. What it does, and very well, is show how technology as it exists today is already quite close to what we currently consider sci-fi levels, and indicates some of the technical challenges that must be overcome to bring prosthetic technology the rest of the way. The video bridges the gap between fantasy and reality, showing why it is reasonable to expect the technology will continue to advance. The documentary also provides just one place for people to go who wonder whether we’ll continue to have increasingly sophisticated prosthetics and gives me a single place to direct people interested in seeing how close to a truly transhumanist future we currently are. So, the next time someone asks me, I’ll smile, sip my drink, and say “Google the Eyeborg Documentary; it’ll blow your mind.”