2014: A Storyful Year

Thanks to everyone for sharing a year of science with me over the course of 2014. It was a year of frantic writing, as I tried (and failed) to keep up with all of the new research that expanded my appreciation of the natural world. In addition to blogging here, I wrote my weekly “Matter” columns for the New York Times, published a few longer pieces, and spent time in Second Edition World, revising a couple of my books. (Details to come in a few months.)

Looking over the year, I put together a list of the pieces I was most fond of (plus some radio work). If you’re looking for some reading (or listening) to fill the languorous spaces between gift-opening and holiday-meal-snarfing, check these out…

From the Loom:

What Slipped Disks Tell Us About 700 Million Years of Evolution

Evolution’s Baby Steps

The Old Old Earth

The Zoo in the Mouth

Parasite Cuisine: Eating the Eaters

The Mystery of the Sea Unicorn

The Erotic Endurance of Whale Hips

Your Inner Feather

How A Dog Has Lived For Eleven Thousand Years–In Other Dogs

 

From the New York Times:

White? Black? A Murky Distinction Grows Still Murkier

The Strange Tale of a New Species of Lizard

Scientists Rein In Fears of Ebola, a Virus Whose Mysteries Tend to Invite Speculation

How Caffeine Evolved to Help Plants Survive and Help People Wake Up

Our Microbiome May Be Looking Out for Itself

Putting a Price Tag on Nature’s Defenses

In a First, Test of DNA Finds Root of Illness

Young Blood May Hold Key to Reversing Aging

The Continuing Evolution of Genes (See also this TED-Ed video for which I wrote the script, based on some the research in this article.)

Seeing X Chromosomes in a New Light


From around the longform universe:

Secrets of the Brain (National Geographic, February)

Mindsuckers (National Geographic, November)

Why Do We Have Blood Types? (Mosaic, July 15)

The New Science of Evolutionary Forecasting (Quanta, July 14)

How Lives Became Long (the introduction to Rachel Sussman’s photography book, The Oldest Things in the World)

 

The spoken word:

Worth (Radiolab–I talked about putting a price tag on nature)

The Black Box (Radiolab–I talked about anesthesia and the mysteries of consciousness)

Translation (Radiolab–I talked about how we translate the messages in our genes into our biology)

Safety Carl Versus Gamera (Story Collider)

Darwin in the City (Harvard lecture)

My Guide to the Giant Sandworms of Dune (Studio 360)

Ebola and a Planet of Viruses (Radio Times on WHYY)

Translation: A New Episode of Radiolab

The good folks at Radiolab have a new episode out. It’s on the many different senses of the word translation. The show ranges from vision-sensing tongue vibrators to high-level diplomatic misunderstandings. At the end of the show, I talk to Jad Abumrad about the most fundamental translation of all: the process by which our cells turn information in our DNA into proteins. Here’s the embedded episode. And for more, see my recent story for Nautilus.

Talking With Sam Kean This Evening

From samkean.com
Sam Kean, the author of a couple delightful books about science (The Disappearing Spoon and The Violinist’s Thumb), has a third book out now on one of my favorite topics, the brain. In The Tale of the Dueling Neurosurgeons, Kean finds stories about kings, assassins, and other interesting people that illuminate how scientists have come to understand how the brain works.

This evening at 7 pm ET, I’ll be talking to Sam about the book on Booktalk Nation, an online show. You can register to see the conversation here.

Attack of the Monster Turtles

My family and I were trapped once in our house by a terrorizing turtle. Last week, I told the saga of that day–and of my lifelong obsession with strange animals–at Story Collider, an evening of live story-telling about science. The recording is now online, and so you can listen to it here. May you have many peaceful encounters with turtles in your life.

From Microbiomes to Neanderthals

I’ll be taking the week off from blogging. Let me leave you with an hour-long interview on public radio in Charlotte, NC, which was recorded on Friday when I was in town to give a lecture for the North Carolina State Science Festival. We ranged over a lot of material, from de-extinctions to science literacy to personalized medicine and more. See you next week!

Flying Through Inner Space

It’s hard to truly see the brain. I don’t mean to simply see a three-pound hunk of tissue. I mean to see it in a way that offers a deep feel for how it works. That’s not surprising, given that the human brain is made up of over 80 billion neurons, each branching out to form thousands of connections to other neurons. A drawing of those connections may just look like a tangle of yarn.

As I wrote in the February issue of National Geographic, a number of neuroscientists are charting the brain now in ways that were impossible just a few years ago. And out of these surveys, an interesting new way to look at the brain is emerging. Call it the brain fly-through. The brain fly-through only became feasible once scientists started making large-scale maps of actual neurons in actual brains. Once they had those co-ordinates in three-dimensional space, they could program a computer to glide through it. The results are strangely hypnotic.

Here are three examples, from the small to the big. (Click on the cog-wheel icon if you can to make sure you’re watching them at high resolution.)

First is a video from a project called Eyewire. Volunteers play a game to map the structure of individual neurons. Here are a handful of neurons from the retina of a mouse. (More details about the video can be found here.)

The second video is a flight through the entire brain of a mouse, made possible by a new method called CLARITY. This method involves first adding chemicals to the brain to wash out the lipids and other chemicals that give it color. The brain is rendered transparent, even though its neurons remain intact.

Next, scientists douse the brain with compounds that only latch onto certain types of neurons, lighting them up. The researchers can then take pictures of the brain from different angles and combine them into a three-dimensional representation of the brain in which you can distinguish individual neurons. In this video, from the lab of Karl Deisseroth at Stanford University, a very common type of neuron is colored. Flying through the brain, we can start to get a feel for the large-scale connections that stretch across it.

And finally, we come to the newest method–one that didn’t even exist when I was working on my article. Adam Gazzaley of the University of California at San Francisco and his colleagues have made it possible to fly through a representation of a thinking human brain–as it thinks.

Here’s how they built this fly-through, which they call the Glass Brain. First, they gave volunteers a high-resolution MRI scan to get a very detailed picture of the overall shape of their brain. MRI doesn’t let you see individual neurons, but it does mark out the major structures of the brain in fine detail.

Next, they added in more anatomy with a method called diffusion tensor imaging. To use this method (known as DTI for short), scientists reprogram MRI scanners to measure the jostling of water molecules inside of neurons. Many of the neurons in the brain are located in the outer layers of the brain, and they extend long fibers across the inner regions and link up to the outer layers at a distant spot. Many of these fibers are organized together in pathways. The water molecules in the fibers jostle back and forth along that pathway, and so scientists can use their movement to reconstruct their shape.

The combination of MRI and DTI gave Gazzaley and his colleagues both the structures of the brain and the pathways connecting them, all lined up in the same three-dimensional space.

Now came the third ingredient: recordings of the brain’s activity. Gazzaley used EEG, a method that involves putting a cap of electrodes on someone’s head and measuring the electrical activity that reaches from the brain up through the skull to the scalp.

EEG is very fast, measuring changes in brain activity at a resolution of a tenth of a second or less. The drawback to EEG is that it’s like trying to eavesdrop on people in the next room over. A lot of detail gets blurred away as the signals travel from their source. To reconstruct the brain’s inner conversations, Gazzaley and his colleagues programmed a computer to solve mathematical equations that allow it to use the scalp recordings to infer where in the brain signals are coming from. Their program also measured how synchronized signals in different regions were with each other. Combining this information with their map of the brain’s pathways, the scientists could reconstruct how signals moved across the brain.

And here’s a video of what they ended up with. In this case, the volunteer was simply asked to open and shut her eyes and open and close her hand.

As gorgeous as this is simply as a video, there’s more to it. It didn’t take Gazzaley’s computer weeks to crunch all the data from the experiment, calculate the sources of the EEG signals and map them onto the brain. The system can create this movie in real time.

Imagine, if you will, putting on an EEG cap and looking at a screen showing you what’s happening in your brain at the moment you’re looking at it. That’s what this system promises.

I called Gazzaley to get the details of this new view of the brain. It took him and his team a year to build and to validate it–that is, to make sure that the patterns in the video have the same features that well-studied imaging technologies have found in the brain. Now Gazzaley hopes to start using it to record data during experiments and to test some prominent ideas about how the brain processes information.

And this imaging may be useful outside the lab. Gazzaley and his colleagues recently designed a video game that improved the cognition of older people. It may be possible to incorporate their new brain display into a game, allowing people to try to alter their brain activity through a kind of neuro-feedback.

Just recently, Gazzaley got another idea. He put an EEG cap on a colleague and then pushed the output to a set of Oculus Rift virtual reality goggles. Gazzaley put the goggles on and then used an Xbox joystick to fly through his colleague’s brain, which he could look at all around him in three dimensions.

“I had never seen a brain inside out before,” Gazzaley told me. “After that I couldn’t get back to work. I had to lay on the grass for a while.”

Tomorrow I will be speaking about brain mapping in Rochester, New York, in their Arts & Lectures series. You can get information about tickets here.

Catching Up: Resurrected Viruses, Sex-Driven Smarts, And Some Upcoming Talks

My late winter is revving up into a state of rolling semi-controlled chaos, and so I’ve let a few items slip here at the Loom. Consider this a catch-up post.

1. On Thursday, I wrote my “Matter” column for the New York Times about an intriguing experiment on the evolution of learning. As I’ve written before, animals pay a price to become better learners, and so scientists have been investigating what the benefits are for different species. It turns out that competition for sex can drive the evolution of better learning, at least in flies. Randomly pairing flies into monogamous couples for a hundred generations leads to worse learning.

2. This week my “Matter” column is appearing today, to coincide with the publication of an especially riveting paper: scientists have revived a virus from 30,000-year-old Siberian permafrost. Aside from the dark twist on de-extinction, this story is compelling for another reason: the virus in question is a so-called “giant virus”--the biggest virus ever found, in fact. (I dedicate a chapter of my book A Planet of Viruses to the discovery of giant viruses–one of the most remarkable hiding-in-plain-sight stories around.) And for more on today’s news, check out fellow Phenomena-ster, Ed Yong, reporting for Nature.

3. Talks talks talks! After a quiet few months, I’m on the road. I was in Washington a couple weeks ago to talk about my cover story for National Geographic (video will go online soon, and I will post it here). Then I headed to Auburn last week to talk about genetically modified foods. But I’m just getting started. My future travels include:

–March 20: Rochester NY. Rochester Arts & Lectures. I’ll be talking about the mapping of the brain.

–March 24: Harvard. This talk is entitled, “Darwin in the City: How Modern Civilization Drives Evolution.” 

–March 28: Charlotte NC. North Carolina Science Festival. I’ll be doing two talks in one day. One is a panel discussion about the genome. The other will be a public lecture about the microbiome.

–April 25: New York. American Society of Journalists and Authors. I’ll be talking about the craft of science writing.

–April 26: Washington. USA Science & Engineering Festival. I’ll be leading a panel discussion about personalized medicine. Panelists include Francis Collins, the director of the National Institutes of Health.

I also expect a couple more additions to my spring schedule–details to come.

Scientists On the Loose! My AAAS Talk

On Thursday I participated in an interesting day of talks at the annual meeting of the American Association for the Advancement of Science in Chicago. The theme was “Communicating Science.” I was on a panel in the morning made up of four journalists, who shared our experiences with the changes roiling the field. You can watch it here. I speak from 10:55 to 18:00. After 48:33, the panel and the audience had a long conversation that I thought was pretty interesting.

I thought I’d put my prepared remarks here, with links, in case anyone wanted to chase down the things I was talking about…

–Good morning. We are going to collectively spare you the hassle of Powerpoint. And so, instead of looking at a slide, I’d like to start this morning’s discussion by having you look at a mental picture. The picture is of Stephen Hawking. You can picture the physicist thanks to us–the media—thanks to the magazine covers, newspaper portraits, web site photos, TV documentaries, episodes of the Simpsons, and dust jackets where he has appeared. For over twenty years, Hawking has been at the media’s frontier, helping to define how scientists present themselves to the public and are represented by others. And just three weeks ago, at age 72, Hawking once again did something new. He posted a two-page document online.

This is actually a much bigger deal than it may sound at first. Hawking recently gave a talk about a new idea he has about black holes. This is interesting, since Hawking has been so important in our current understanding of these strange things. Some recent developments in cosmology and quantum physics have caused him to rethink black holes in a serious way. Hawking once thought that when things fell into black holes, there was no way for us to get any information about them ever again. But now he is suggesting that when things get pulled into a black hole, some information can leak out, in a jumbled form. Black holes are not black holes as we knew them, in other words.

Hawking did what scientists usually do: he wrote up this idea in a paper. But he didn’t proceed to keep it secret until it appeared in a peer-reviewed journal. Instead, on January 22, he uploaded the paper, “Information Preservation and Weather Forecasting for Black Holes” to the physics pre-print site known as arXiv. Two days later, Nature had a detailed article about Hawking paper. New Scientist published an explainer piece the same day. These stories swiftly got a lot of attention on sites like Digg and Facebook, driving hordes of readers their way.

Today, three weeks later, the paper is still only available on arXiv, where anyone can download it for free. The arXiv page conveniently links to some of the blog posts that people have written about the paper—including posts by his fellow scientists. I highly recommend this new piece on Slate by Matthew Francis. Reasonably web savvy teenagers can gather all this information in a few minutes, to digest later at their leisure.

To me this episode epitomizes the huge changes in our field. I’m not saying the individual elements of this story are new. Physicists have given talks for centuries. Arxiv has been around for 23 years. By the early 2000s, people were blogging regularly about science. On February 4 this month, we marked the tenth anniversary of the day a Harvard computer science major launched a site called thefacebook.com.

But recently these elements have crossed two thresholds–of scale and connection. And the result is a drastically new way for scientists to reach the public.

If Hawking had this idea ten years ago, things would have worked differently. To get a wide audience for his new idea, Hawking might have submitted his paper to a prominent journal. The journal would then send it to anonymous reviewers. If the reviewers judged it good science, it would go into press. But it would only be available to people with thousands of dollars to spend on a subscription to the journal.

The journal might promote the paper with press releases. They’d let us journalists look at a preprint—but only if we respected an embargo and stayed quiet till then. Or maybe journalists would get wind of the paper through a press release from Cambridge University.

At this point, the outside world would have known nothing about the paper. Only when the major print outlets unveiled their stories would they find out. Only in the comments the reporters offered from other scientists would people get a hint of what the scientific community thought. And ten or twenty years ago, this process made a few scientists into celebrities—like Steven Hawking.

Every step of this process has changed—or, rather, there is now a set of parallel steps. Arxiv has become a required stop on the road to publication for physicists. Biologists are following their lead now, too. Some of the most provocative biology papers I know of—on topics like exactly when Neanderthals and modern humans interbred—were first posted online on preprint servers like bioRxiv. The curtain-raising ritual at high-impact journals is losing a bit of its magic. It becomes not an unveiling, so much as a stage of maturation in the life of a research project.

I have no idea when or where Hawking will ultimately publish his new paper. It’s possible that the journal he chooses will offer the final paper as freely as arXiv did. Open access publishing is steadily growing. Just yesterday afternoon, AAAS, the host of this meeting, announced they were launching their first open-access online journal, called Science Advances.

Peer review is also becoming more open. Scientists are increasingly reviewing papers in public, after they are published or even when they are on a preprint server–as happens on Haldane’s Sieve. If you visited the early post-peer review forums at places like the Public Library of Science, you heard crickets. Now that’s changing. There are more comments on papers, and more forums. Even the prime portal to biomedical research, Pubmed, is now starting to post comments on papers, which appear right below your search results.

It’s common for scientists to debate new research as soon as it’s published, on blogs, Twitter, or Facebook. New companies are launching in order to measure this response, and to create an alternative to the traditional ways of measuring the impact of a paper. Instead of looking at the number of times it shows up in the footnotes of other papers, maybe the number of Tweets matters, too.

What do these changes mean for people like the four of us on the panel–the journalists? A lot. It makes science journalism more fun. You don’t have to sit dutifully by your computer, waiting for some journal to deign to let you know about a new paper. You can go hunting. You can turn up a new paper that’s just sitting quietly in a preprint archive, and share it with the world.

And you can get a more realistic understanding of how scientists toss around ideas. If research simply appears in an august scientific journal, it can be hard to figure out how it actually fits into the current scientific debates. The last thing a journalist wants to do is present research as if it’s the discovery of extraterrestrial life, when, in fact, it’s arsenic life.

The new ways that scientists share their ideas and opinions helps us. We can take the pulse on Twitter. We can follow comment threads. We can throw questions into these debates in real time if we so wish.

But it also presents new risks that we journalists should be mindful of. The scientist who tweets the most may not be the wisest expert on a particular topic. If you come across a preprint, you have to ask, “Does its mere existence constitute news?” Or is that preprint just a flakey idea that will never make it into a serious journal? Should journalists wait for the journals to give these papers their seal of approval? Is that what journals are for now—to designate important science? Or are they simply seizing that role for themselves from the scientific community as a whole?

I honestly don’t have answers to those questions. But Stephen Hawking has made it clear to me that I need to find some.

Stepping off the Spaceship

Recently a producer from the radio show Studio 360 called me up to talk science fiction. They wanted to throw a light on some of the artists who gave us the pictures we have of other worlds–of what we see when we step off the spaceship.

It just so happens that I grew up knowing one of them, named Jack Schoenherr, so I threw his name in the hat. It turns out that Studio 360 also runs a series of pieces called “Aha Moments” about experiences with art that change people’s lives. So we decided to combine the two, and I talked about what it’s like to be a ten-year-old boy walking into a barn studio full of giant sandworms and elephants and astronauts.

The piece is airing this week. You can listen to it on the Studio 360 web site and check out a slide show of a few of Schoenherr’s paintings. I’ve also embedded the piece below [Note–the sound isn’t working in this embedded version on Safari at the moment, but it is in Chrome and on the show site.]:

For more on Schoenherr, see this remembrance I wrote when he died in 2010, or head over to a blog maintained by his son Ian, himself an accomplished children’s book illustrator.

John Schoenherr, "The Flight through the Shield Wall." Courtesy of Ian Schoenherr
John Schoenherr, “The Flight through the Shield Wall.” Courtesy of Ian Schoenherr

Opening the Black Box with Radiolab

It’s always a pleasure to talk with Jad Abumrad and Robert Krulwich and their crew at the show Radiolab. For their latest episode, “Black Box,” we talked about the mystery of consciousness and how I got in an argument with my anesthesiologist before I had my appendix taken out.

I’ve embedded the whole episode here:

Anesthesia is deeply fascinating, even if you’ve never gone under, because it brings us face to face with the mystery of consciousness. I’ve written about it here and here.

The Scientists We Lost in 2013

A couple weeks ago, All Things Considered asked me to talk about the deaths in 2013 of three Nobel-prize winning scientists: Francois Jacob, Frederick Sanger, and David Hubel. I had blogged about Jacob’s death in April, and reflecting on his career in conjunction with those of Sanger and Hubel was a thought-provoking experience. In some ways, these three scientists seemed worlds apart–Jacob poring over bacteria feeding on sugar, Sanger tearing apart insulin molecules, and Hubel using electrodes to eavesdrop on neurons in the brains of cats.

But what unites them all, I think, was their ability to use the very simple scientific tools available to scientists in the 1950s to open up vast realms of biological complexity–from the orchestral activity of the genome to the reality-building network of cells in our brains.

Here’s the story that NPR producer Rebecca Hersher put together for last night’s show. I’ve embedded it below:

Of course, there would have been plenty to say about many other troikas of scientists who passed away this year. On Twitter, ecologist Jacquelyn Gill reminded me of the pioneering ecologist Ruth Patrick, for example. Neuroscientist John Kubie pointed me to his homage to Robert Muller, who did ground-breaking work on memory. The Scientist has a longer list on their blog. While we mourn their loss, science preserves their memory in the research that goes on today, made possible by their earlier work.