No Longer Science Fiction: Data Encoded In DNA

Game-changing research just published in Science.. Geneticists at Harvard have encoded an entire book into DNA:

Biology’s databank, DNA has long tantalized researchers with its potential as a storage medium: fantastically dense, stable, energy efficient and proven to work over a timespan of some 3.5 billion years…Church’s team married next-generation sequencing technology with a novel strategy to encode 1,000 times the largest amount of data previously stored in DNA. (via Science Daily)

The result? 5.5 petabits, or 1 million gigabits, per cubic millimeter! Further, ~4 grams of DNA could theoretically store all of the digital data humankind creates in one year. The prospect? As geneticist George Church explains in WSJ:

“A device the size of your thumb could store as much information as the whole Internet.”

Emerging technologies in science are exciting. When the research is conducted by a friend, they’re even more so… Congratulations to Sri Kosuri and his team at the Wyss Institute.

Using next-generation sequencing technology and a novel strategy to encode 1,000 times the largest data size previously achieved in DNA, a Harvard geneticist encodes his book in life’s language. (Credit: Image courtesy of Harvard Medical School)

After Fukushima, Generations of Abnormal Butterflies In Japan

A sad, but fascinating scientific report in the journal Nature describes the physiological and genetic damage observed in generations of butterflies following the collapse of the Fukushima Dai-ichi Nuclear Power Plant. While it’s been difficult to study the biological impacts of the accident on animals, scientists have concluded that the pale grass blue Zizeeria maha (a common lycaenid butterfly in Japan) suffered increasingly severe abnormalities over time due to radioactive materials released into the environment.

Representative abnormalities of individuals that ingested contaminated leaves. From the top left to the right bottom, the panels show right antenna malformation (Iitate montane region), right palpus abnormality (Fukushima), dented left compound eye (Iitate flatland), eclosion failure (Fukushima), bent wings (Fukushima), additional bent wings (Hirono), aberrant wing colour patterns (Fukushima), and an ectopic black spot beside the discal spot (Iitate flatland; enlargement in the inset). Arrowheads indicate abnormal parts, and arrows indicate deformed wing spots. Scale bars for the top four panels indicate 1.0 mm, and those for the bottom four panels indicate 5.0 mm.

Although epigenetic effects cannot be entirely excluded, it is most likely that the abnormal phenotypes observed are produced by random mutations caused by the exposure to radiation. This outbreak of abnormal phenotypes in the Fukushima area is very different from the outbreak of wing colour-pattern changes previously observed at the northern range margins of this species, i.e., the Fukaura area, which is located approximately 400 km northwest of the Fukushima Dai-ichi NPP. The Fukaura populations at the time of the outbreak were composed of temperature-shock types that exhibit distinct wing colour-pattern modifications but no other wing modifications or aberrations. Moreover, to the best of our knowledge, no malformations of appendages and other parts have been detected. In contrast, the outbreak in the Fukushima area includes various unexpected abnormal phenotypes. These abnormalities cannot be expressed within the range of phenotypic plasticity exhibited by normal populations. This information and the experimental data obtained in this study allow us to conclude that the present outbreak of abnormal individuals in the Fukushima area was caused by random genetic mutations in addition to physiological effects due to the artificial radionuclides from the Fukushima Dai-ich NPP.

For those interested in heritable genetic damage due to low-dose radioaction exposure, this article is a must-read.

What Water Crisis?

I often write about what I consider to be the most significant challenge of the 21st century: the looming water crisis. As I explained earlier this year at NPR:

As temperatures rise due to climate change, evaporation and precipitation have increased. This means that the atmosphere holds more water. Unfortunately, the condition is anticipated to lead to storms and floods of increased severity in some parts of the world, with prolonged and more intense droughts elsewhere.

“Extreme extremes,” says [Jay Famiglietti, director of the University of California’s Center for Hydrologic Modeling], which could lead to greater conflict over the scarce resource.

In other words, prepare for water wars. This is a big deal. But based on this new data from the UT Energy Poll, it appears that most of us here in the United States still do not understand what’s taking place on our watch:

What will it take?

Culture of Science

Some curious stipulations lead me to say goodbye to Wired. Three other communities have graciously offered invitations, but after touring so many networks, I’m excited to announce I’m finally going solo with complete control over content, comments, and site design again.

I’ve been thinking a lot about this possibility since sitting next to the lovely and talented Maria Popova of brainpickings.org on the flight back from TED. Maria has developed her site from the start and I admire the way she runs it independently.

This blog began in 2006 as conversation to share ideas with readers and build a constructive dialogue. I’ve been frustrated by having to request maintenance from someone with authority over my content.

So even though the trend since 2010 has been to join a network, I’m choosing the red pill and breaking out of the Wired matrix. I don’t post for traffic and it’s time to return to how this blog began. (Of course, networks are excellent for some contributors and I particularly love the way the SciAm community is highlighting a new “generation” of science bloggers, as well as seasoned contributors).

For the first time ever, all of the archives from various incarnations of my blog are finally together here. Make yourself at home and contribute whenever you’d like. This is your space too. Let me know what you think of the new site and make any general suggestions in comments. I’m learning CSS so expect continued design updates over the coming weeks. A great big thanks to the brilliant Razib Khan of Gene Expression for kindly helping me with this transition.

Finally, those familiar with my work may recognize that Culture of Science is a nod to C.P. Snow:

“We require a common culture in which science is an essential component. Otherwise we shall never see the possibilities, either for evil or good.”

Under The Microscope: Feminism, Scientists and Sexiness

Earlier this year Nicholas Kristof wondered aloud (via twitter), “Why are most pundits men?” In another context, we might ask why men compose 97% of OpEds in the Wall Street Journal. Both involve the hesitancy of women to express opinions. Yet prominent female voices in our culture matter tremendously because they help to define our place in society. But if men get cast into the spotlight, you might say that women are examined under the microscope. As an author, blogger, researcher, and former Hill staffer, I regularly observe problems with the status quo across arenas. Rather then help women find their voices, we tend to send those testing the waters of public punditry dashing back out of focus.

Having spent my formative years as a run-of-the-mill tomboy, I never considered using the “feminist” label and naively assumed that since I was as good at science and math as the boys, my sex wouldn’t matter. But a funny thing happened when I entered academia; I learned that when a woman expresses herself visibly in any traditionally male-dominated field, the platform comes with the expectation that she will address gender issues. And over time it becomes a necessity. Last week Luke Muehlhauser caused a stir when he included me on a list of “sexy scientists.” Early on that thread, “Hansen” noted:

Oh dear, you may be in serious trouble now for placing Sheril Kirshenbaum on that list.

The link leads to “Singled Out“: My response from March 2009 to the remarks about my appearance heard ’round the science blogosphere when Chris and I joined the Discover network. Luke followed up with a second post asking whether he’s sexist, a third summarizing the hundreds of comments piling in, and a fourth on objectification. He also emailed me personally and seems genuinely interested to hear my perspective. So I’ve decided to weigh in and explore the topic with readers.

Long before I set out to write a book dealing with human sexual behavior, I knew that evolution primed us to notice the alluring qualities of other members of our species. These are often indicative of health and fertility and women are held to different standards of judgment than men. But even if biology has an influence on how we behave, it’s not an adequate scapegoat. After all, we also have a large cerebral cortex that allows us to choose the way we interact in our communities.

In my profession today I work closely with many talented men. We write on related topics and speak to similar audiences. Yet, I’m regularly reminded that I face many challenges they don’t have to deal with. No one jokingly whispers about their receptivity to sex during conferences just loud enough to overhear. No one questions whether they were hired so the boss could to get some “tail.” These kinds of experiences are common for women in and out of the ivory towers. We rarely complain for fear of being considered troublemakers or worse. We work hard and don’t want special treatment or penalization, so we turn a deaf ear, aware that some will never see past what’s on the surface. We stop speaking up and a negative feedback loop continues to reinforce gender roles over time.

Just consider the political arena: While candidates should never be chosen based on a number of X chromosomes, it would benefit everyone if women became more involved in the decision-making process given we represent about 50% of the population. But watching the way Sarah Palin and Hillary Clinton were each cast as stereotypes, ogled, and photo-shopped by the media during their 2008 campaigns, I often wondered to myself why any little girl would dream of being in that position someday?

So Mr. Kristof, that’s likely why there aren’t more female pundits and commentators. Increasing our numbers will involve changing cultural expectations by highlighting the accomplishments of a wider spectrum of women to demonstrate what we are capable of.

Returning to the hullabaloo over last week’s “sexy scientists” list, I honestly don’t think any real harm has been done to me personally. And it’s worth pointing out that in 2005 when Chris was named one of Wired Magazine’s “Sexiest Geeks,” no one complained. So while this may not be the way I’d most like to be featured, far worse items pop up across the Internet about me on a regular basis. To survive in the blogosphere, you grow a thick skin and keep in mind that there’s more to life than what happens online.

That said, I would like to see Luke, and others, think more carefully about the ripple effects of such posts. He can moderate his own site, but also doesn’t have to deal with the related extended commentary now percolating about the web because of his actions. For example, I’m currently receiving comments such as “I’d hit that,” which are promptly deleted, but do make me uncomfortable regardless. And since I can only filter content here, who knows what else is being added to message boards and websites elsewhere. In other words, it’s important to remember that words travel well beyond one’s own blog and can quickly get out of hand. That’s the nature of new media communication–you can’t control or keep up with what’s out there. So it’s important to acknowledge that there are often unintended consequences down the line for those unknowingly involved.

Additionally, in response to Luke’s commentors, I’ll clarify that I’m not offended by being called a “woman in science.” It’s an accurate description. (In fact, in a few months I’ll be moderating a L’Oreal/Discover panel on Capitol Hill about that very topic). When I wrote that “I’d rather not be labeled a woman in science,” I meant that I would prefer that others recognize there are more dimensions to who I am and what I do than those assigned by base pairs.

What I know for sure is that we need to find more ways to acknowledge women who speak up, take a nontraditional path, defy expectations, and contribute to society in and out of science. And there are better ways to do so than commentary on our physical assets. But I also want to emphasize that I appreciate the way Luke is taking the time to explore a topic that doesn’t get nearly enough attention. When someone is willing to engage others and turn over ideas on sexism and gender–especially when they are attempting to understand the other side–it can be quite a constructive dialog. Further, this conversation isn’t really about photos on a blog post. It’s vastly more complex and deals with social and cultural mores and the objectification of females in our society.

In conclusion, given women will remain under the microscope indefinitely, I hope increasing numbers aim for high magnification for reasons beyond appearances. To achieve more equal representation in all realms, it will be necessary to identify and celebrate a diverse set of talented and motivated individuals so that they may become the role models our children deserve. Superficial beauty is ephemeral after all, so we we ought to spend more time focusing on the qualities that matter more and last indefinitely. And if we succeed, today’s visible voices will motivate the career aspirations of tomorrow’s leaders across the gender divide from Mars to Venus.