How a locked-in woman took control of a robot arm

Posted on May 16, 2012 by admin

The Electric Mind written by Jessica Benko. The Atavist, 2012. Kindle Singles, The Atavist app , iBooks, and other outlets via The Atavist website.

Reviewed by Ed Yong

Throughout the history of neuroscience, we have gained an inordinate amount of knowledge by studying people with severe brain damage, and watching how they manage to live. HM’s surgically altered brain revealed secrets about how memories are formed – after his death, he was revealed to be an American man called Henry Molaison. KC, a Canadian man whose real name is still unknown, also taught us much about how memory works, following brain damage sustained during a motorcycle accident. SM, a woman with an inherited brain disease, reportedly feels no fear.

These patients are known by abbreviations that preserve their anonymity, but also shroud their contributions. Their hopes, struggles and lives are condensed into patterns of injury and aberrant behaviours, and distilled into pairs of letters. But sometimes, very rarely, we get a privileged opportunity – a chance to unpack the people behind the letters, and to learn not just how they became a part of science, but how science became a part of them.

Jessica Benko’s new story, The Electric Mind, provides just such an insight. It is the latest in an increasingly strong portfolio of stories from The Atavist, a digital publisher that produces stories “longer than typical magazine articles but shorter than books”.

The Electric Mind is the story of Cathy Hutchinson, a woman known in the scientific literature as S3. She’s a mother-of-two who was “always goofing around and singing and dancing”, until a stroke disconnected her brain from her spinal column and left her with an active mind imprisoned in a frozen frame.

For several years, Cathy has been taking part in a groundbreaking experiment called BrainGate – not a sordid cerebral scandal, but a bold project that aims to give paralysed people control over mechanical limbs. The scientists behind the project fitted Cathy with microscopic electrodes that read the neural buzz within her motor cortex – the area of her brain that controls movements. The implant acts like an electronic spine that links Cathy’s brain to a computer or robot, bypassing her own immobilised flesh.

At first, she used the electrodes to control the movements of an on-screen cursor. More recently, she commandeered a robotic arm. As she thought about grabbing a bottle, the electrodes deciphered her mental commands and the arm carried them out. “For the first time in 14 years—indeed, for the first time for any quadriplegic—Cathy was able to reach out into the world.”

The project’s crowning results are published today in the journal Nature, concurrently with the launch of Benko’s story. The paper itself preserves Cathy’s anonymity, and describes her in the starkest of terms. She’s “a 58-year-old woman with tetraplegia caused by brainstem stroke… She is unable to speak (anarthria) and has no functional use of her limbs. She has occasional bilateral or asymmetric flexor spasm movements of the arms that are intermittently initiated by any imagined or actual attempt to move. S3’s sensory pathways remain intact.”

The reality behind these cold, precise words comes through in Benko’s skilful narration. Right from the start, she plunges us into Cathy’s world, as she wakes from a coma to hear the sound of the ventilator beside her bed.

We get to know Cathy through Benko’s eyes, as she tracks down the woman via her son, and meets her for the first time. First-person accounts can break the fourth wall to a distracting extent, and many journalists would balk at inserting themselves so prominently into a story. But Benko earns her place as a protagonist in her own tale, in a way that reminds me of Rebecca Skloot’s The Immortal Life of Henrietta Lacks. The author’s quest becomes an inextricable part of the story itself. Through Benko’s expectations of meeting Cathy, her descriptions of their first meetings, and her difficulties in interviewing a woman who can only communicate via eye-flickers, we learn the extent of Cathy’s disability, and the frustrating complexity of seemingly simple tasks.

Writing about extreme disability (and attempts to overcome it) is not easy. You’re always an adjective away from being mawkish, and an adverb away from being ghoulish. Benko deftly negotiates the tightrope. She cleverly uses essays from other locked-in patients to describe hardships that would sound overwritten from her own hand. And she’s a master of keenly observed but simply delivered prose. When Cathy laughs, for example, it’s “a short burst of air that vibrated across vocal cords she can’t voluntarily control.” No embellishments required. These scenes throw their own punches. Benko just puts you in the ring.

Benko’s eye for detail also elevates her descriptions of experiments that have been reported again and again in the press. We see what Cathy’s nursing home room is like. We learn that the electrodes were fired onto her brain with “a pneumatic device like a tiny air hammer”. We discover that the bottle that Cathy lifted via robot was a thermos full of coffee (she loves coffee), “emblazoned with the initials and insignias of the research team and sponsors”. She finds drama in minutiae. While other reporters rush straight for a snare-drum crash of incredible implications, Benko takes her time with scenes that build to a steady crescendo.

Using Cathy’s story as an anchor, The Electric Mind stretches back in time to look at the historical events that preceded BrainGate (including a horse accident and suspected psychic powers). The story also pulls outwards at other means of reaching the same ends, such as functional electrical stimulation, where electrodes stimulate a patient’s own muscles instead of a robotic limb.

These sections, where we leave Cathy and focus on the field at large, are arguably the weakest elements of the story. Around the two-thirds mark, the tale threatens to veer off course. From rich details about a woman steering a robot arm with difficulty, we’re suddenly plunged into hand-waving speculation about infrared vision, Avatar-like… well…. avatars, and telepathic soldiers (and the irony of reading a journalist’s words about electronic telepathy on a handheld device was not lost on me).

But then, in a rather daring move, it becomes clear that this was exactly the point (keep an eye out for the start of Chapter Seven). All the other characters not involved in BrainGate, from Nicolelis to a ridiculously breathless DARPA spokesperson, serve as foils for Cathy. Their visions are too far removed from the reality of her condition. They remind us about what The Electric Mind could easily have been – a story of technological triumph and glorious futurism. Instead, Benko has treated us to something far better – a story of extreme limitations and what happens when people (and science) run up against them.

*****

Ed Yong is a British science writer who writes the award-winning blog Not Exactly Rocket Science. His work has appeared in Nature, New Scientist, the BBC, the Guardian, the Times, Wired UK, Discover, CNN, Slate, the Daily Telegraph, the Economist and more. He lives in London with his wife. He has never been impregnated by a botfly but he does rather like ants.

Leonardo: The First Great Science Ebook

Posted on May 4, 2012 by Carl Zimmer

Leonardo da Vinci: Anatomy Touch Press Ipad. $13.99 Publisher site

Reviewed by Carl Zimmer

There's no point in beating around the bush. Leonardo da Vinci: Anatomy is simply the best ebook about science that I have ever encountered. To me, it is the exemplar of what ebooks can be.

Leonardo da Vinci: Anatomy comes from Touch Press, whose lavish apps we've reviewed before at Download the Universe (Gems, The Solar System, The Elements). I've personally toyed around with all three of those apps, and while they each offered a number of pleasures, each one felt limited in one way or the other. Gems, for example, lets you twirl diamonds and rubies, but, as Virginia Hughes noted in her review, it doesn't tell you much about them or about their place in human history. The Solar System, reviewed by Jennifer Ouellette, has some very impressive features for navigating among the planets, but Jennifer noted that it lacks a clear story.

Given this track record, I launched Leonardo da Vinci: Anatomy expecting a good-looking but flawed production. No shortcomings came to light, so I tried looking for them. I looked hard. And I couldn't find any. Leonardo da Vinci: Anatomy has everything I could ask for in an ebook about one of the greatest stories in the history of science: a pioneering work on anatomy that was lost for over four hundred years.

Living during the Renaissance, Leonardo's initial understanding of the human body came from ancient scholars like Galen and Aristotle. He was taught that animal spirits traveled through giant holes in the head and then flowed into the nerves. He was taught that blood was produced in the liver and then flowed outward to the ends of the body. One reason that these obviously wrong ideas persisted for over a thousand years was that medieval scholars did not conduct their own autopsies or experiments. Galen and and company had figured out everything there was to know about anatomy, so the best thing they could do was read, not conduct research.

With the Renaissance, that obedience began to crumble. Leonardo was the quintessential do-it-yourself-er. He conceived of new kinds vehicles and weapons; he investigated optics and geology. Wikipedia has set aside a separate page for a startling long list of his accomplishments.

Leonardo also became obsessed with human anatomy, and did not hestitate to make up his own mind about it. He dissected human cadavers. To figure out how the heart worked, he created a glass model of it. To probe the brain, he injected hot wax into the head of a freshly slaughtered ox.

As I wrote in my book Soul Made Flesh, Leonardo had a hard time breaking free from the old notions of how the body worked. When he discovered that the head did not contain three linked chambers, he couldn't break free from the old theory of animal spirits. He could not accept that perhaps the brain itself was responsible for thought. Likewise, although Leonardo discovered a valve in the aorta, he did recognize that blood circulates around the body, pumped by the heart. Nevertheless, his drawings were the greatest anatomical works that existed in his time. Not only were they anatomically correct, but they displayed his artistic mastery.

Leonardo actually came close to publishing a textbook of anatomy while he was living in Milan, but battles in 1511 drove him from the city and he never quite managed to finish it before his death in 1519. Instead, his drawings remained hidden away until the twentieth century.

Today, the Royal Collection is unveiling the largest ever exhibition of Leonardo’s anatomical drawings at The Queen’s Gallery in Buckingham Palace. They also teamed up with Touch Press to create an app based on the show. All the members of the team brought their A game to this undertaking. Leonardo da Vinci: Anatomy contains a richly informative narrative about the artist's hidden career as an anatomist, written by Martin Clayton, Senior Curator of Prints and Drawings at the Royal Collection. It is illustrated elegantly with Leonardo's drawings, as well as interactive images of human anatomy as we know it now. You can see for yourself just how good his drawings of the heart or uterus were. You can turn arms to see how well Leonardo appreciated the body's biomechanics.

These components are copious but never intruding. And they always answer the question raised in the reader's mind by the text. Videos from historians and scientists end each chapter–usually I hate these features, but in Leonardo, the talking heads actually have something to say.

The app also contains Leonardo's notebooks themselves. The interface for this part is nothing short of brilliant. You can search through the pages by organ or system. Each page is presented in its original state, scanned to exquisite resolution. Tap the screen, and the app instantly translates the inscrutable notes Leonardo scribbled by his drawings. Each page is also annotated with useful explanations of what Leonardo was contemplating with each image.

Three decades after Leonardo's death, Andreas Vesalius published Fabrica, which has long been considered the first modern work of anatomy. Leonardo da Vinci: Anatomy demonstrates that Fabrica was not the only masterpiece of the body to come out of the Renaissance. Not many ebooks can claim such achievements.

Zimmer author photo square Carl Zimmer writes frequently about science for the New York Times and is the author of 13 books, including A Planet of Viruses

A Disorganized Celebration of Skulls

Posted on April 13, 2012 by admin

SKULLS. 2011 by Simon Winchester. Touch Press. iPad. App webpage.

Reviewed by Brian Switek

No set of bones better exemplifies the natural history of an animal than its skull. Postcranial skeletons are all well and good – the vertebrae, limbs, and associated parts all testify to how an animal moved and behaved – but skulls are the most iconic aspects of a creature’s ossified frame. The skull is the seat of the brain, and, therefore, the senses, and the critical details of how an organism perceived its world can be detected from this complex arrangement of bones. As much as any group of bones can, a skull summarizes the essence of an organism – to draw from my beloved non-avian dinosaurs, a Tyrannosaurus or Triceratops skeleton would just not seem as magnificent without their fantastic, iconic skulls attached.

Not everyone shares my affection for skulls. I learned this the hard way. A few years ago, I spotted a bleached raccoon skull along the side of a trail in the New Jersey woods. I put the skull in my camera bag, carried it home, and put the cranium in my desk drawer. Fortunately for me, my wife has been very kind about my fascination with bones and thought nothing of it. But when my wife’s best friend was petsitting at our apartment a few months later, and said friend opened my desk in search of a pen, she was horrified to see raccoon remains staring back up at her. To me, the skull was a representation of the raccoon’s life and evolution, but she saw the skull as a symbol of death and decay.

Simon Winchester’s Skulls – an ebook-iPad app hybrid – explores the various meanings of the haunting bones. Skulls are objects of natural history, have been misappropriated to support discrimination, and can act as warnings of impending doom. What a skull means rests in the eye of the beholder (and those eyes, of course, are set into skulls themselves.)

Skulls was not what I was expecting. I thought the app was going to be a virtual museum of various specimens that users would be able to manipulate to get a better look at the various components of the craniums. And while there is that aspect to the program, Skulls tries to be more.

Each of the app's interactive skull images is organized within twelve different sections which focus on cranial components, how the bones are collected, and the cultural meaning of skulls. In the introduction, which outlines what a skull is, a series of representative specimens stream past on the right side of the screen as Winchester explains on the left, with certain keywords linked to particular skulls. (Users can read at their own pace, or choose to have Winchester read to them in his halting cadence.) On that first page, the word “majesty” is linked to one of the fabricated crystal skulls which led Steven Spielberg to run the Indiana Jones franchise into the ground, and the simple mention of “skulls” at the bottom corresponds to the strange cranial architecture of a long-spine porcupinefish. The piscine skull looks like good inspiration for one of H.R. Geiger’s techno-biological horrors.

There’s more than one way to explore the selected skulls. Readers can proceed linearly through each of the twelve short sections, they can hit the “gallery” button at the top of the screen to explore the highlighted skulls in each section, or can simply tap “The Collection” on the main page to bring up a constantly-rotating collection of alphabetized skulls. The best part of the latter option is the ability to view multiple skulls side-by-side via the “compare” button. The saber-fanged weapons of a Smilodon look all the more fearsome when viewed directly next to the much shorter, stouter canines of its distant, living relative, the lion.

But this is also the most frustrating feature of Skulls – the app only allows users to zoom in and rotate along the horizontal axis. You can’t flip the skulls to have a look underneath, or explode skulls to play with their various parts. With a little more effort, Skulls could have acted as a rich, virtual reference for anatomy students or anyone interested in learning more about osteology, natural history, and evolution. Instead, Skulls is more of a virtual museum – you can look, but your ability to learn directly from the bones is severely constrained. (Ironically, the publisher of Skulls, Touch Press, lets you to flip planets and moons in another of their apps, The Solar System, which we reviewed last month.)

Though limited, the app’s gallery of spinning skulls is fun to fiddle around with. The ebook portion only left me puzzled. While I greatly enjoyed the format of having parts of the text correspond directly to the stream of skulls on the right side of the virtual page, there was no central narrative or story. Winchester jumps from a general overview of skulls to a profile of skull collector Adam Dudley before moving on to bizarre cranial modifications and the meaning of osteological iconography. There is no flow between sections – they all stand on their own and vary in style. “A Skull’s Component Parts” – in which Winchester avoids actually describing the various bones which make up a skull – is presented in an encyclopedia format, while Winchester’s visit to the skull of 17^th century Ottoman military leader Kara Mustafa Pasha was composed as part history and part travelogue. And section 6 – “The Skull of the Dodo” – feels entirely out of place. Winchester says almost nothing about dodo skulls, and instead recapitulates the extinction and artistic representations of the extinction icon.

Strangest of all, Winchester goes on a brief tear about paleoanthropology in the “Science and Pseudoscience” portion of the book. After addressing how some misguided researchers used craniometry to buoy their own racist notions, as well as recapitulating the Piltdown Man scandal, Winchester settles into a wandering discussion of human evolution. “It can fairly be said,” Winchester writes, “that in the history of biological science never has so much been imagined by so many on the evidence of so little than those who have studied the skull and wondered about human evolution.” Granted, specimens of fossil humans are rare and often quite fragmentary, but Winchester does nothing to support his claim that much of what we think we know about our ancestors is “imagined.” Indeed, rather than support his claim, Winchester quickly moves on to say that the human skull has changed only little in the past three million years and that human evolution has ultimately halted. The first statement feels contradictory to the rest of the section – in which Winchester mentions how brain size, brow ridges, teeth, and facial construction have changed among our prehistoric kin – and the second assertion is only armchair philosophizing. While changes to our physical form might not be apparent, there is a growing body of scientific evidence that human evolution continues to this very moment and can be tracked in our genes.

Ultimately, Skulls feels like a disorganized tour of a virtual curiosity cabinet. There are lots of fascinating tidbits along the way, and Winchester shows a clear enthusiasm for his subject, but I reached the bottom of the last page without understanding what the point of the entire exercise was. Skulls is a disorganized celebration of cranial bones and is of little utility as a reference. I couldn’t help but laugh in disagreement when, in the last section, the app dubbed itself “a near-perfect survey” of skulls. The mashup of biography, history, editorial, and encyclopedic catalog made Skulls feel like a concept stretched too thin and spread too wide. Unlike an actual skull, the app’s various components never come together to create a functioning whole.

Brian Switek is a freelance science writer and author of the book Written in Stone: Evolution, the Fossil Record, and Our Place in Nature. He regularly blogs about paleontology at the WIRED Science blog Laelaps and the Smithsonian blog Dinosaur Tracking. His next book – A Date With a Dinosaur: On the Road With Old Bones, New Science, and My Beloved Brontosaurus – will be published next year by Scientific American/FSG.

Slog of the Dinosaurs

Posted on April 4, 2012 by admin

March of the Dinosaurs. 2011 by Touch Press. iPad. App webpage.

Reviewed by Brian Switek

Dinosaurs have changed a hell of a lot since I was a kid. My beloved “Brontosaurus” was beheaded and recast as Apatosaurus, Torosaurus might just be the spectacular mature form of Triceratops, and we now know that many dinosaurs were covered in lavish, colorful plumage. I like it. There are plenty of complaints about how paleontologists are ruining cherished childhood memories by altering our understanding of dinosaur lives, but all the immature whining misses the grander point. We know more about dinosaurs lives than ever before, and the more we learn, the stranger and more wonderful the creatures become.

Dinosaurs trodding through the snow is one of my favorite new images. For as long as I can remember, Stegosaurus and company were presented as inhabitants of steaming jungles choked with ferns, cycads, and horsetails. Rudolph Zallinger’s gorgeous mural The Age of Reptiles at Yale and the short, dinosaur-filled segment of Disney’s Fantasia left no doubt in my young mind that dinosaurs lived in a seemingly endless global summer. But this was a holdover from the idea that dinosaurs were sluggish ectotherms that required considerable heat to start up every morning. Not only have such swamp-bound monsters been given a makeover, but a better understanding of the habitats dinosaurs occupied has altered our previous understanding of the world tyrannosaurs, ceratopsians, and their ilk lived in.

Continuing research in Alaska, for example, has even turned up dinosaurs which lived within the Arctic circle. These dinosaurs were not outcasts or vacationers, but part of complex communities which permanently made their homes up north, including everything from the svelte tyrannosaur Gorgosaurus to the feathered, switchblade-clawed raptor Troodon and plenty of Pachyrhinosaurus – a magnificent horned dinosaur with bony hooks jutting from its frill and a big, lumpy boss on its nose. And while prehistoric Alaska was a titch watmer than today, there was still snow and many months of darkness. Here, dinosaurs once slogged through Cretaceous snowstorms.

A paleo drama about these chilled archosaurs – titled March of the Dinosaurs – was released by Impossible Pictures last year. It was another Walking With Dinosaurs wannabe – all computer-generated violence, very little science. I love a feather-covered, acrobatic Albertosaurus sailing through the air with claws extended as much as anyone else, but, without any explanation of how we have come to know of this animal’s existence, the dinosaur is just another special effect. But when fellow Download the Universe contributor Deborah Blum told me there was a March of the Dinosaurs app for the iPad, I felt a stirring of hope. Maybe, with the interactivity an iPad allows, some of the glossy effects might be combined with some scientific explanation.

Continue reading “Slog of the Dinosaurs” →

Look Up In The Sky! It’s A Book! It’s An App! It’s a Bat!

Posted on April 2, 2012 by Carl Zimmer

Bats! Furry Fliers of the Night. 2012. by Mary Kay Carson. Published by Bookerella. iPad. Publisher's page

Reviewed by Carl Zimmer

Yesterday my daughters–Charlotte, 10, and Veronica, 8–were playing some inscrutable game involving two beach balls and running in and out of the house. As they roared through my office, I called out.

"Veronica," I said. "Do you want to read something?"

She stopped. "What?" she asked. There was no eagerness in her voice.

Veronica is always a bit suspicious when I ask her this question, which I often do. She doesn't like to have good-for-you things foisted on her. But she also knows that from time to time, I may have something for her that's actually worth reading. Something involving Egyptian mummies, usually, or the sinking of the Titanic.

"I want to find out what you think about this. It's a book you read on an iPad."

Veronica looked at my iPad as I flipped open the cover and switch on the power.

"Is it a book or an app?" she asked.

Good Lord, I thought. When did this kid become a new media maven?

Just a couple days earlier, I had been reading an interesting article by Adam Penenberg in Fast Company that raised this question. Honestly–the first line of the article is, "When is a book an app and an app a book?"

Continue reading “Look Up In The Sky! It’s A Book! It’s An App! It’s a Bat!” →