Monthly Archives: March 2013

De-extinction: the wooly mammoth is the biophysicist’s cancer

On my first day teaching bioinformatics, I brought Michael Crichton’s book Jurassic Park to class. I showed the students a DNA sequence from the book  – a long string of A, T, C, and G that was supposed to form part of one dinosaur gene. As a class exercise, I asked students to convert that string into a protein sequence (it seems more bioinformatics teachers had the same idea).

The students were instantly intrigued. I attribute that class’ success to Jurassic Park. Both book and movie are embedded in our collective imagination. Who isn’t enthralled by the possibility of engineering dinosaur DNA and bringing the lumbering giants back to life?

Can we bring back the Tasmanian tiger? Photo by the author.

Can we bring back the Tasmanian tiger? Mike Archer at TEDx. Photo by the author.

I was able to attend the TEDx DeExtinction event in DC, thanks to an awesome boss and crew, who came along. There, molecular biologists and conservationists discussed the possibility of resurrecting extinct animals, while fans vouched for their favorite species (hello, dire wolf). The lecturers presented the technology, while ethicists and ecologists watched in horror.

The passenger pigeon is another candidate for de-extinction. Photo by the author.

The passenger pigeon is another candidate for de-extinction. Ben Novak at TEDx. Photo by the author.

There was talk of bringing back the wooly mammoth, passenger pigeon, bucardo, Tasmanian tiger and others. But like speaker and “molecular paleontologist” Beth Shapiro points out, we are still very far from step one. No surprise here. I went to this event not expecting to see a herd of mammoths any time soon. I went there to marvel at technology  and its applications. Or, like my colleague described it, “the moon race for biologists”.

Beth Shapiro is cautiously optimistic. Photo by the author.

Beth Shapiro is cautiously optimistic. Photo by the author.

Conservation efforts can benefit from de-extinction technologies. Lack of genetic diversity among captive breed populations is a serious problem. Breeding programs and SSPs (species survival plan) keep a studbook: a record of the genetic make up of all individuals of that species. Pairings are carefully calculated in order to increase genetic diversity. TEDx host Stewart Brand (check out his Reddit AMA) believes de-extinction can help with that: “de-extinction technology… can be applied immediately to help diagnose and treat genetic issues with endangered populations of living species. Viable cryopreserved DNA … can be used to reintroduce genetic variability in ‘genetic bottleneck’ situations for animals now rare and facing inbreeding problems.” And that’s not all. Cloning or iPCS (induced pluripotent stem cells) are technologies with immense potential, with applications that range from tissue engineering to livestock breeding, and perhaps even to support reproduction.


Stewart Brand at TEDx. Photo by the author.

Funding dictates what research projects will go on and which ones will die.  And that is why I’m ok if a woolly mammoth or Jurassic Park-based creature functions as research ambassadors. Scientists depend heavily on policymakers and public support to guarantee funds for their work. It is increasingly difficult to obtain funds for basic research or anything that doesn’t have the word “cancer” or “heart disease” attached to it. Throughout my PhD I happened to work with both most of the time (design of protein inhibitors for breast cancer, and angiogenesis molecules for cardiovascular disease). I mean most of the time: when an application is not so direct or obvious (e.g., of studying the folding of a protein) we always highlight its future, potential, exciting, indirect and perhaps one day possible outcome (e.g., better understand Alzheimer’s). The woolly mammoth is the biophysicist’s cancer, and the passenger pigeon is his heart disease. I believe de-extinctioners were trying this PR approach.

Biotechnology for de-extinction. Photo by the author.

George Church explains the biotechnology behind de-extinction. Photo by the author.

But did it backfire? I saw many ecologists and ethicists disapproving of the entire thing. Are they spreading the fear? Is fear of science creeping out and reaching our scientific and (scientific-supporting) community? As Brand pointed out in his AMA, “fear has been institutionalized, not only by government but by (…) environmental groups broadcasting irrational fear of GMOs and radiation (to the detriment of genuine green goals like more wild lands and damping of climate change)”.

Very much alive (i.e. non extinct) blue hyacinth Margaret was present at the event. Photo by the author.

Very much alive (i.e. non extinct) blue hyacinth macaw Margaret was present at the event. Photo by the author.

George Mallory was a mountain climber and one of the English pioneers to Mount Everest expeditions on the 20’s. Why take on such endeavor? It was risky, challenging, and with no direct application. So, “why climb the Everest?”, he was asked.

“Because it is there.”

Sometimes it is all the motivation we need.

To infinity and beyond: what I learned in Cape Canaveral during the NASA SpaceX launch


SpaceX launch. Photo by the author.

What surprised me the most was the air shaking. When you watch it from TV, you never really expect the atmosphere changing around you. Not only that, but the crowd gasping, shutters clicking, and the PA announcer’s countdown giving you chills. Those experiences are never possible unless you are standing there, witnessing the rocket launch then disappear into the clouds.

I flew to Cape Canaveral last Wednesday as a guest of NASAsocial and sponsored by Owen Software. The rocket launch (SpaceX commercial rocket Falcon9, carrying a Dragon capsule) would take place on Friday. Until then, I’d join in private tours and press conferences.   I was feeling out of place among all the mechanical and aerospace engineers, until I met this guy:

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Simon Gilmore. Photo by the author.

Sorry, I meant THIS guy:

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Aradbidopsis thaliana. Photo by the author.

The press conference on the research experiments onboard Dragon emphasized biology projects – that’s when they started speaking my language. One of the passengers inside Dragon was Arabidopsis thaliana, engineered to be more sensitive to oxygen conditions. Turns out that gene expression in plants is completely different once exposed to microgravity. Which genes are turned off and on? Gilmore’s lab may find out once the A. thaliana comes back from space.

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Michael Johnson. Photo by the author.

We also talked about protein crystals: a brick-shaped rack with 150 proteins (in 10k different crystallization conditions) was being transported on Dragon. Fingers crossed that the astronauts will be able to crystallize those proteins. Back in my day, some people hat to resort to adding cat hair to get a proteins to crystallize (true story). Will adding microgravity do it? Cats may be cheaper than space crystals, but that still won’t crystallize membrane proteins – which may be onboard future capsules.

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Where’s Waldo at Press conference. Photo by NASA.

Along with the other NASAsocial guests, I was taken on a tour of the Vehicle Assembly Building. Please include gasps of excitement:


In front of the Vehicle Assembly Building


Vehicle Assembly Building – Interior. Photo by the author.

Which is where I met one of my favorites: the crawler. The largest land vehicle on the planet, responsible for transporting the shuttles from the building to the launch pad. (While leaving a path of destruction behind. Kind of. Its weight completely compresses the road every time it passes by.) Please see chair for scale.

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Crawler at Vehicle Assembly Building. Photo by the author.

All of which culminated in Falcon9 launch on March 1st. It was a visceral experience. I never thought I’d be antsy and nervous listening to a countdown. The 40 minutes I stood there flew by. Next thing I know is: TEN-NINE-EIGHT and dozens of eyes focus on their viewfinders, fingers pressed to the camera triggers. SEVEN-SIX-FIVE and the photographing starts: it is a moment you can’t miss. FOUR-THREE-TWO and the puffs of smoke and engine grumbles tell you it will be soon. ONE — and liftoff.  I take a dozen photographs and stop to watch the show. A show that cannot be reproduced on TV or even in writing.