June 2013 Wired UK

Hacking computers is commonplace today and is at the forefront of national security concerns.  But looking into the the future, hacking DNA is an emerging threat.  Cells are living computers.  DNA is software.  Our bodies are networks.  And they can all be hacked.  Imagine a crime scene where your involvement has been spoofed.  (See a video on counter-spoofing here.)  Or what about genetic spam?  In this article, appearing in the June issue of WIRED UK, cyber security expert Marc Goodman and I look at what some of the future genetic hacks and attacks might look like.  Beautifully photographed in the SF Dogpatch area by famed photographer Art Streiber.

In this study, published in Nature, Yale researchers discovered copy number variation (CNV) in skin cells, indicative that we are “mosaics” of cells with slightly different genomes.  Next generation sequencing technology was used.

You might think about it this way.  If we had a million computers that were brand new, their hard drives would all be identical.  But after booting them up and running them for a year, they would all be different yet similar.  This is because no two computers would be reading/writing information to disk in quite the same way.  We already know our genomes are relatively plastic, that our cells are exposed to mobile genetic elements and viruses, and that cancers represent shifts away from the “normal” genome.  Why would anyone think any two cells’ genomes are identical?

Predictably, as the resolution of DNA sequencing continues to increase, so will the reports pertaining to the number and types of single person genomic variation.

Almost a year ago, I collaborated with Future Crimes visionary Marc Goodman and bestselling author and writer Steven Kotler to speculate how the advances in personalized medicine could be co-opted for less than altruistic purposes.  We submitted the article to the Atlantic Magazine. The article appears in November 2012 issue, on your newsstand now. (Here’s the online version.)

The piece was founded on super-exponential advance in genetic technologies (DNA sequencing is outpacing Moore’s law by up to 500%) and the fact that legions of scientists are working on new technologies to better target and kill cancer cells.  My thesis is that if we have the technologies to selectively target cancer cells in an individual, where there is a small genetic difference, we can target a particular individual in society (a relatively large genetic difference).  We drafted a future scenario whereby this could be done using technologies that are already here although not widely disseminated and then backstopped the scenario with a review of genetic advances and exponential technologies, something we were all comfortable with given our relationships with Singularity University.

It’s been a long haul getting this article published.  The Atlantic staff was incredibly thorough.  It sent out the submission for external review and fact checked every statement.  We had to address over 170 comments in the manuscript.  I am very thankful to the editors, fact checkers, and reviewers for their diligence.  I hope that you enjoy reading the article as much as Marc and Steven and I enjoyed writing it and that it gets you thinking and talking about our genomic future.

This future is coming fast.  Just a couple of weeks ago, the President’s commission on Bioethics published their latest report on genomic progress and privacy.  Heady stuff.  Last April, another White House report announced a blueprint for the emerging bioeconomy.  Clearly, these technologies are important to national and international interests.  They’re also becoming available to just about anyone that’s interested.

This is easiest seen in the direct-to-consumer DNA sequencing and analysis market, recently profiled in Time magazine.  But it’s also just around the corner on the genetic engineering front, too, with online DNA synthesis companies, community biotech labs and, soon, home kits.  This is reminiscent of thirty years ago, when digital computers became more accessible, eventually revolutionizing the way we do routine tasks, communicate, share, and buy.  Now biotech is going mainstream, too.  Where will this take us is in detail is unknowable but the broad sweeps seem apparent enough.  These technologies are going to cheaper and easier, and more and more people will begin to use them.  Overall, biotech is shaping up nicely to be the next IT industry.

There will be hiccups along the way.  We’re talking paradigms shifts here and these are never easy.  They also tend to take a lot longer than expected to develop roots, often a generation, and they can be scary.  I’ve maintained, however, that the scariest outcome of all is that our fears hold us back from being world leaders with these tools, and that our experience with computing (and all the dynamics therein) will help illuminate the way.

The iGEM genetic engineering competition regional events are over and now teams are heading to the World Championship, to be held at MIT in Cambridge November 2-5.  The regional results can be found here.  Overall, 190 teams from over 30 countries are participating and the competition is fierce!  See you there!

Recent News Articles

iGEM Bioengineering Competition Chooses Pittsburgh; Student Teams Compete

UNR students making rice healthier

Synthetic biology ‘MAGEs’ compete

FreiGEM Team Qualifies for Synthetic Biology Science Competition

A paper published October 10, 2012 in the Proceedings of the Royal Society Biological Sciences attempts to measure the half life of DNA.  (Full text not available for free but a good overview can be found here in Nature news.)  By measuring the decay of mitochondrial DNA in bone samples of the extinct New Zealand moa, the authors find that DNA degrades by half every 521 years.  Nuclear DNA appeared to degrade even faster?  Does this mean that the idea of recovering dinosaur DNA and cloning a dinosaur is debunked?  Not so fast, friends.  The Nature article notes, “The team predicts that even in a bone at an ideal preservation temperature of −5 ºC, effectively every bond would be destroyed after a maximum of 6.8 million years.”  This might be true, but if enough sample exists, the complete genomic sequence could be reassembled even if only very short fragments still exist.  Indeed, this is how whole genomes are assembled from the short reads that come off of modern DNA sequencers, which are then assembled by special computer programs.  Really, the limiting step in cloning a dinosaur is whether the DNA synthesizers of the future are up to the task of printing and assembling dinosaur-sized genomes, and of course the challenge of how to boot them if they can be synthesized.  Will elephants be the surrogate mothers?  Who knows.  So keep dreaming, folks.  Dinosaurs may be resurrected (or de-extincted) yet!

Just over a week ago, researchers released the first in silico model of a living organism, the bacterium Mycoplasma genitalium.  This is the first time an entire organism’s metabolic processes have been integrated and modeled and it offers an unprecedented opportunity to do in silico experiments on the organism.  Remarkably, the production of this model required 17 years since the organism was sequenced (1995) and two years beyond it’s synthesis (2010).

For access to the Stanford knowledgebase, click here.

Abundance co-author Steven Kotler recently wrote in the Forbes Blog about a significant upshift in DNA synthesis technology.  It’s called DNA Laser Printing.  Created by a Bay Area startup called Cambrian Genomics, the technique solves a thorny problem with chemistry-based DNA synthesis: make a long enough oligonucleotide and it will contain errors.  This happens because the chemistries are on average 99% efficient.  Cambrian solves this problem by leveraging the incredible accuracy of modern DNA sequencers.  DNA is attached to small beads, the beads attached to a slide, and then sequencing by synthesis is performed.  The result is not just the exact sequence of the DNA on the bead, but the exact location of the bead on the slide.  The slide is removed from the sequencer and a laser beam is used to specifically remove just the beads of interest.  The result?  A 1000x or more reduction in the cost of getting accurate DNA, and no limitations of the size of DNA chain. Cambrian is still developing the technology and people are watching.  The Carlson Curve marches on…

See Steven’s full post here.

In December 2010, the Obama administration published New Directions: The Ethics of Synthetic Biology and Emerging Technologies, a report from the Presidential Commission for the Study of Bioethical Issues. Within the document were recommendations aimed to minimize risks from the technology while ensuring that social and economic benefits are realized.  It suggested revisiting the topic in 18 months.

The Woodrow Wilson International Center for Scholars has created an easy to read scorecard to track the recommendations.  The result?   Some progress is being made in most areas.  Meanwhile, the field continues to evolve.

You can check out the progress for yourself here.

Scientists have successfully turned DNA rewritable memory.  Stanford researcher Drew Endy and his team have, using elements from a bacteriophage, built and demonstrated a rewritable recombinase addressable data (RAD) module.  The system consists of a stretch of DNA flanked by sites that signal to enzymes made by the bacteriophage, instructing them to cut out the DNA and paste it back into the chromosome in the reverse orientation. The DNA can be set and reset repeatedly — up to 16 times. The device is digital, with forward and reverse orientations of the DNA acting like a ’0′ or a ’1′ in binary.  Endy sees the device tracking cellular events, for example, counting the number of cell divisions it takes for a stem cell to become a differentiated adult cell, like a cell in the liver.  Building the system wasn’t easy, though.  It took over 750 different designs to get the device working.  Hopefully, future designs will take less debugging.

Now, in 2012, there’s a need for a new grand challenge, and I can think of none better than to have scientists organize to write a human genome.  If you think this is hard, remember, it’s what every cell has to do each time it divides.

My thoughts on the next human genome project were published in the Huffington Post.