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Rejoicing In Ants With A Citizen Science Ebook

2013-05-03T07:54:16-07:00

Dr. Eleanor's Book of Common Ants. Text by Eleanor Spicer Rice. Photographs by Alex Wild. Available at The School of Ants. iPad or pdf. Free.

Reviewed by Carl Zimmer

Many plants grow a thick coat around their seeds. The coat, called an elaiosome, doesn't do the seed any good, at least directly. Its immediate job is to attract an insect known as the winnow ant. (The photo here shows winnow ants discovering blood root seeds.) The eliaosome releases fragrant odors that lure the ants, which carry the seed into their nest. There they gnaw away at the coating but spare the seed. The ants then carry the shucked seedback out to the forest floor, where it germinates.

The winnow ants thus act like gardeners, protecting the seeds from predators that would destroy the seeds, while also spreading them far from their parent plant. Remove winnow ants from a forest, and its populations of wildflowers will shrink.

As a resident of the northeastern United States, I always assume that all the magnificent examples of coevolution must be going on somewhere else. The jungles of Ecuador, the Mountains of the Moon--these are the places where nature-film producers go to find species exquisitely adapted to each other. This, of course, just belies my far-less-than-complete education in natural history. While reading Dr. Eleanor's Book of Common Ants, I discovered that winnow ants are abundant in New England, along with the rest of the eastern United States. The next time I am out on a walk in the local woods, I'm going to keep an eye out for these elegant little insects.

Dr. Eleanor's Book of Common Ants is itself an elegant little book--and an instructive example of how ebooks can become a tool in the growing citizen science movement. "Citizen science" typically refers to research that relies not just on a handful of Ph.D. researchers, but also on a large-scale network of members of the public. Birders have been doing citizen science for over a century, and now the Internet enables people to collaborate on many other projects, from mapping neurons in the eye to folding proteins to recognizing galaxies. Many of these projects yield solid scientific results (see this paper in Nature, with over 57,000 co-authors as an example). They also provide a new way for research to draw non-scientists into their world.

At North Carolina State University, biologist Rob Dunn and his colleagues have built a little empire of citizen science projects. I myself eagerly participated in his survey of the microbial life dwelling in the human belly button. (I've got 58 species, which turns out to be below average.) More recently, they've created a project they've dubbed The School of Ants. Here's how they describe it:

The School of Ants project is a citizen-scientist driven study of the ants that live in urban areas, particularly around homes and schools. Teachers, students, parents, kids, junior-scientists, senior citizens and enthusiasts of all stripes are involved in collecting ants in schoolyards and backyards using a standardized protocol so that we can make detailed maps of the wildlife that lives just outside our doorsteps. The maps that we create with these data are telling us quite a lot about native and introduced ants in cities, not just here in North Carolina, but across the United States.

The School of Ants web site has plenty of information to help amateur ant hunters recognize the species trundling across a nearby sidewalk and then share their findings. But, like most web sites, it one works best as a sprawling reference. Its architecture doesn't lend itself well to the sustained education required to become a backyard myrmecologist. For that experience, it's hard to beat a book.

Hence, Dr. Eleanor's Book of Common Ants. Eleanor Spicer Rice has written a 142-page introduction to these insects. She describes 13 common American species, such as the winnow ants, and also provides a general introduction to their biology. Rice writes for a young audience, but fortunately she doesn't see that as an opportunity to write badly. Her style is clear, fluid, and engaging. (I'm fond of the way she described winnow ants as "rusty ballerinas.")

The design and artwork in the book are also excellent. Neil McCoy created the book using iBook Author, Apple's free software for making ebooks for the iPad. The design is clean, despite the fact it combines text, maps, photo galleries, and videos. I still use a first-generation iPad, waiting (or hoping?) for it to die, but it never struggled as it displayed the elements of Dr. Eleanor's Book of Common Ants. What makes it especially lovely is the abundance of photographs by Alex Wild, the Ansel Adams of arthropods. The tiny size of the photo I included with this review doesn't do justice to his work, but the large-scale format of his images on the iPad does.

I can quibble, but not for very long. This ebook is only available for iPad, for which I blame Apple, not McCoy. (You can get a pdf version, which lacks the galleries and video.) The ebook includes Google maps for each species, but they're not interactive. Readers are instructed to go to the School of Ants web site for interactive versions, with no link on the page to take you there. But I can't follow this line of grousing very long before I remember that this ebook is free (thanks to the support that the project gets from sources such as the Burroughs Wellcome Fund). I would have gladly paid for it. I heartily recommended it not just to people who want to join the School of Ants project, but anyone who wants to appreciate the miniature beauty and complexity of ants. And I hope that Dr. Eleanor's Book of Common Ants inspires other citizen science projects to produce informative ebooks of their own.

Carl Zimmer writes frequently about science for the New York Times and is the author of 13 books, including Evolution: Making Sense of Life.

The Library: April 29 Additions

2013-04-29T07:27:00-07:00

Each week, we add some new titles of science ebooks to the Library. We will review a selection of them. Here are our newest additions:

City 2.0: The Habitat of the Future and How to Get There

The Dilbit Disaster: Inside the Biggest Oil Spill You've Never Heard Of, by Lisa Song and Elizabeth McGowan

The Origin of Darwinism (Essays from The Guardian.)

The Wrong Way to Write about Epigenetics and Violence

2013-04-09T14:44:59-07:00

"The Ghost in the Cell," by Scott C. Johnson. Published by Matter. Available via Web, ePub, Kindle. $.99.

Reviewed by Annalee Newitz

It's a prize that scientists have sought since the early nineteenth century: a biological marker that predicts violent behavior in humans. In the 1830s, phrenologists believed head bumps could reveal a criminal personality -- often, prostitutes and the poor were said to have bumps that marked them as deviants from birth. But today, it seems this pursuit may have moved beyond the realm of pseudoscience.

Thanks to recent discoveries, we have evidence that the genes of abused children are marked by the experience. Over time, these effects leave them prone to depression and make it harder for them to control their violent impulses. Could we be on the cusp of discovering a scientific approach to a social problem? In an essay for Matter magazine, former war correspondent Scott C. Johnson suggests that we are. Unfortunately, Johnson fails spectacularly to explain the complexity of this problem, and winds up telling a story that distorts both the science and the reality of abuse in many people's lives.

Epigenetics is the study of how environment and non-genetic molecular activity affect development. Johnson shows us how seemingly-unrelated studies in the field converge to offer a picture of the violence-haunted brain. One study that Johnson describes suggests there may be an epigenetic pathway to suicide, whereby an abusive childhood leaves the brain starved for the neurotransmitters that normally keep our moods on an even keel. Johnson also delves into public health studies which show that violent behavior has its roots in childhood.

Johnson argues that we need to look at these studies in light of another epigenetic study that shows an abusive childhood can leave its genetic imprint even on the grandchildren of the abused person. The suggestion is that violence isn't just a social cycle, but a hereditary one. These studies and others like them have renewed many researchers' interest in childhood interventions to prevent violent adults. They're especially significant if it turns out to be true that the epigenome, as Johnson puts it, is "more malleable" in early life.

Johnson's science reporting here leads to a few interesting conclusions, but he glosses over many of the questions and controversies in epigenetics. He doesn't mention that other epigenetic studies have shown that humans retain neural plasticity throughout most of their lives. Nor does he admit that "criminality" and "propensity to violence" are traits that are difficult to define, especially at the level of neuroscience and genetics.

But most of The Ghost in the Cell doesn't deal with science. Instead, it deals with the violent life of one woman.

Throughout the essay, Johnson foregrounds the story of Yokia Mason, who lives in a high-crime, African-American neighborhood in Oakland, CA. We assume she's there to provide a human face for his descriptions of how epigenetics researchers and others are tackling at the influence of childhood experiences on gene expression. But we never learn how Johnson met Mason, nor why she's telling her story to a journalist. Has she been working with some of the scientists in the article? No. Is she the subject of a scientific investigation into genetics and violence? No.

So why is Mason in this essay at all? As we learn more about her background, one begins to get the extremely creepy feeling that Mason went to the most impoverished neighborhood in Oakland, the city where he lives, and asked people there to tell him about their violent backgrounds. Though Johnson and the scientists he interviews are careful to explain that they are not trying to bring race into this story of genes and violence, the entire shape of this article belies that assertion. It seems as if Johnson chose to profile Mason entirely because she's a black woman who lives in a low-income area with a lot of gang violence.

Mason feels "haunted" by violence, she tells Johnson, and he takes this to mean that she may be one of these people whose brains are primed for violence by a history of abuse. By extension, he hints, her entire neighborhood may be a hotbed of people whose brains are hardwired for crime. And this is where Johnson's essay moves from merely problematic to simply bad science writing.

As any of the scientists he interviewed could have told him -- if he'd bothered to ask -- Mason is a classic example of somebody whose situation is too overdetermined for us to make any solid claims about her propensity for violence. Is she influenced by a genetic predisposition she inherited, by her own childhood experiences affecting her epigenetically, or by social issues we can't quantify in the lab like economic difficulties, stress from having children when she was a teenager, or living in a neighborhood with gangs? We can't possibly know without studying her brain intensively, and even then the answers would be extremely murky.

Holding Mason up as the human face of these epigenetic studies is worse than misleading. She's a narrative non sequitur whose presence brings up the nineteenth-century notion that black people are somehow biologically destined for poverty and violence. One wonders why Johnson didn't choose to tell the story of somebody who is actually the subject of studies on violence. Instead he simply says that Mason is "the sort of person" who has been studied before, mostly by policy makers and social scientists:

Thanks to the work of Meaney and others, many researchers now believe that the neglect and fear that pervaded the Mason household will have left a powerful chemical imprint in the cells of Yokia and her siblings. If the scientists are right, we may have to change the way we think about tackling violence and crime.

You know, like maybe we'll tackle it by going to the poor areas of Oakland and giving everybody there forced gene therapy?

Given that child abuse is a social problem that's also common in middle-class households of all phenotypes across the United States, one would have hoped that Johnson might have explored this side of the story. What do these epigenetic studies tell us about rage-addicted CEOs whose brains were shaped by abusive parenting and sadistic prep schools?

Instead, Johnson devotes an incredible amount of time to a voyeuristic look inside Mason's life, which he reduces to a series of bullet holes, homicidal men, and children who are already in trouble with the police. This story does not humanize Mason; it objectifies her, and reifies the notion that there are some communities where crime is being bred into the next generation because of child abuse.

Epigenetics is a fantastically promising new field of study, which may ultimately shed light on how childhood shapes our neuroanatomy as well as our neuroses. But Johnson does the field a disservice by situating its story in a narrative like this one. By the end of this essay, you'll feel like you've just read a tale of phrenology rather than epigenetics, where science is being twisted to justify the idea that the people in some communities are just born broken.

Annalee Newitz is a science journalist who is the editor of io9.com and the author of the forthcoming book Scatter, Adapt and Remember: How Humans Will Survive a Mass Extinction (Doubleday).

UPDATE: Scott Johnson, the author of "The Ghost in the Cell," has responded to this review over at Medium.

Autism, Inside and Out

2013-04-02T12:45:50-07:00

Asperger Love: Searching for Romance When You're Not Wired to Connect by Amy Harmon. A New York Times/Byliner Original. Available for Kindle, iPad, Kobo, and Nook, $2.99.

And Straight On Till Morning: Essays on Autism Acceptance, edited by Julia Bascom. Published by the Autistic Self-Advocacy Network. Available for Kindle, $2.99.

Reviewed by Steve Silberman

In the early 1990s, a mother told a conference of autism professionals that the upside of having a teenager on the spectrum at home is that they will never want to do the things that often get kids in trouble. There will be no need for awkward conversations about sex, because people with autism are either uninterested in or incapable of intimacy. Parents won't have to worry about a late-night knock on the door from the local sheriff, because autistic teens have no desire to party. If these generalizations now seem naïve, offensive, or some combination of the two, this mother had a lot of company in her assumptions. The notion that people on the spectrum are disinclined to seek connection with others is embedded in the very word autism, which is derived from the Greek word for self, autos.

One of the world's leading authorities on the subject, psychologist Tony Attwood, devotes only a handful of pages in his Complete Guide to Asperger's Syndrome to sexuality and relationships. Specifically, there are two references to "lack of desire," four to pornography, two to exploitation by predators, and two to celibacy. Casting a further chilling effect on the notion of romance, Atwood cautions potential suitors that people on the spectrum may find a friendly touch on the arm "unpleasant and even difficult to tolerate, let alone enjoy" because of sensory sensitivity, and compares embracing an autistic partner to "hugging a piece of wood." This is the historical backdrop that looms -- albeit invisibly to most readers -- behind the publication of a new ebook by Pulitzer prize-winning New York Times reporter Amy Harmon, Asperger Love: Searching for Romance When You're Not Wired to Connect.

Harmon is one of the most sensitive and savvy reporters on the subject in mainstream media. In 2011, she published "Autistic and Seeking a Place in an Adult World," an account of the search for employment by a young artist named Jason Canha. While dozens of news stories a week speculate about candidate genes, environmental factors, and other possible causes for the condition, Harmon zeroed in on the practical issue that all families face when their kid "ages out" of services: How are they supposed to support themselves and learn to live independently? At more than 7000 words, it was one of the longest features on any subject in the history of the Times, and reader response was overwhelmingly positive. Encouraged, Harmon's editors gave her several months to follow up on an insight she had while reporting on Canha: despite the fact that parents and teachers are often occupied by more pragmatic concerns, young people on the spectrum are as intensely curious about intimacy as their neurotypical peers, as even a brief tour of the discussion forums at WrongPlanet.net can attest.

Harmon's second bout of reporting produced "Navigating Love and Autism," the story of a burgeoning love affair between two young people with Asperger syndrome named Jack Robison and Kirsten Lindsmith. (Jack's father, John Elder Robison, is the author of the bestselling memoir Look Me in the Eye; his new book, Raising Cubby, is about his experiences as the autistic father of an autistic son.) That article provided the foundation for Asperger Love, which is twice as long as the original piece, and includes fuller and more nuanced portrayals of Jack, Kirsten, John Elder and his wife Maripat, and Jack and Kirsten's friend Alex Plank, the founder of WrongPlanet.net.

Asperger Love follows the familiar arc of nearly every classic tale of bright young outsiders who discover a safe haven in each other (see Romeo and Juliet and Wes Anderson's Moonrise Kingdom.) The difference is that in this case, the lovers face not only obstacles posed by the uncomprehending world, but their own difficulties in reading one another's social signals, a profound challenge for people on the spectrum.

Early in the book, we see Lindsmith in high school, before her own Asperger's diagnosis, when she's still trying to make a relationship work with a charismatic extrovert who insists on acting as her life-coach. He urges her to stop speaking in a monotone and fidgeting with her hands; he elbows her when she goes on at length about her interest in animal physiology; he prompts her to be more affectionate and expressive by barking at her, "Don't filter!"

In one of Harmon's characteristically well-turned sentences, she says that Kirsten eventually "chafed at his frequent instructions, which required constant, invisible exertion to obey." The author gets across a lot of information in few words here: the soon-to-be-ex-boyfriend's arrogant presumption that his way of behaving would come naturally to Kirsten if she would just stop filtering herself; the annoyance that those kinds of assumptions produce; and the hard (but "invisible") work demanded of autistics who are asked to just act normal for a change.

In a similarly spare and brilliant passage, Harmon describes the little details of behavior that rise into Jack and Kirsten's mutual awareness as they fall in love:

Jack, Kirsten noticed, bit his lips, a habit he told her came from not knowing how he was supposed to arrange his face to show his emotions. Kirsten, Jack noted, cracked her knuckles, which she later told him was her public version of the hand flapping she now reserved for when she was alone.

In two sentences, Harmon expresses truths that are both universally human and distinctly autistic. Everyone experiences pressure to conform to social norms, but Harmon's description of how Jack must "arrange his face" casts light on the rigorous self-monitoring -- the "constant, invisible exertion" -- required of autistic people to get through a typical day in neurotypical society. Likewise, the detail of the knuckle-cracking deftly paints a picture of two parallel worlds: Kirsten's public life, where she too must "arrange" her spontaneous behavior to avoid calling attention to herself, and her private autistic reality, where she can flap to her heart's content.

With the same reportorial eye for the essential, Harmon skates over aspects of autism history that are so deep and hotly contested that they can best be described as yawning abysses. It's a relief to read an account of the domestic lives of autistic people that never devolves into a discussion of cortical deficits, de novo mutations, and the other impedimenta of autism narratives that make it seem as if people on the spectrum hardly exist outside of clinics, genetic databases, and MRI scanners. In that sense, Asperger Love is like the wedding announcements by same-sex couples that now run routinely in the Times: extraordinary precisely because they're so ordinary.

Only in a couple of places does Harmon's urge to simplify lead her astray. She begins her second chapter with the statement, "Only for about a decade have a group of socially impaired young people with normal intelligence and language development been recognized as the neurological cousins of individuals with classic autism." While I love the phrase "neurological cousins" so much that I will undoubtedly steal it for my own writing, this assertion is either ten years off, or 70 years off, depending on how you look at it.

The broadening of the diagnostic criteria for autism in the fourth edition of the Diagnostic and Statistical Manual of Mental Disorders (commonly known as the DSM-IV) to reflect the full breadth of what we now call the spectrum -- including the addition of "Asperger's disorder" -- took place in 1994, not 2004. It was precisely that change that made the autism of people like Jack and John Elder Robison, Kirsten Lindsmith, and Alex Plank visible to the medical establishment. Before that, all of these characters in Harmon's book would have been excluded from a diagnosis and support services, and written off as "schizotypal," neurotic, or odd.

The first person to notice that people like them are the neurological cousins of kids who are much more obviously disabled, however, was the pediatrician Hans Asperger in his clinic in Vienna way back in the 1940s; that's why the diagnosis given to people like Jack and Kirsten bears his name -- until May, anyway, when the long-awaited DSM-5 will be published, and the subcategory of Asperger's disorder will be dispensed with in favor of the umbrella term "Autism Spectrum Disorder."

The second slight misstep in Harmon's elegant dance is her use of the word "mindblindness" as the title of her second chapter. For reasons that should be self-evident, many autistic people loathe the term, which was coined by British cognitive psychologists Simon Baron-Cohen and Uta Frith in the 1980s. In its original context, the all-too-catchy neologism was their attempt to give a name to the core deficit in a clinical population so various that it encompasses both children unable to speak and brilliant coders who can't seem to shut up about the various incarnations of the Time Lord in Doctor Who. (Thus the truism in the autistic community, "If you've met one autistic person, you've met one autistic person.") The controversy over the term mindblindness -- and its relationship to compassion and empathy -- is one of the most yawning abysses in autism discourse, and too deep to do justice to here. Suffice it to say that Baron-Cohen made things worse by muddying the distinction between an inability to parse social cues in real time -- which seems to be the cognitive issue unifying all points on the spectrum -- and empathy, which is more like a capacity to care about how another person is feeling.

Anyone who has spent time with autistic people can tell you that they're intensely concerned with how other people are feeling, to the point of being overwhelmed. But they often can't piece those feelings together from the usual clues of facial expression, tone of voice, and body language. At the same time, however, autistics are often adept at reading each other's emotional states from signs that would be opaque to their typical peers. There are moments in Harmon's book when Jack and Kirsten seem to be doing that for one another. (This experience is so common that autistics refer to a second sense called "autdar" -- inspired by gaydar -- that enables them to spot a fellow Aspie in a room full of chatty neurotypicals.) Calling autistics mindblind may turn out to be as apt as calling those who don't speak English deaf.

I recently asked Uta Frith about the term and she replied: "I now avoid using it, as it seems to have led to a lot of regrettable misunderstandings. Clearly we have not done a good enough job explaining what we mean. Even the original proponents of the term are not of one mind, and there are interestingly different interpretations. For example, my interpretation is different from Simon's as regards 'empathy.' As you know, a number of my more recent papers conclude that empathy is present in autism." In other words, the term is contested even by the two clinicians who popularized it. Harmon would have been better off shunning it altogether.

That said, Asperger Love is a valuable and humane contribution to the popular literature of autism, and a touching, funny, and engaging love story that should appeal even to readers with no direct connection to the subject. One of my favorite parts of the book is the postscript, when Harmon steps forth from behind the narrative curtain to talk about what she learned by reporting the story. "The more I observed autistic behavior," she reflects, "the more my own was revealed to me in a light not available elsewhere… As I sought to portray the oddness of my autistic subjects, I found that they were altering my view of what passes for normal. Time and again they exposed my own pretensions and highlighted the absurdity of the social mores to which so many of us subscribe."

I asked Harmon to elaborate on this further in email, and she replied:

What changed for me as a result of my reporting is not so much my perception of people with autism, as my perception of the social conventions practiced by the rest of the world. Even in our most intimate relationships, we want our partners to read our minds, we value not having to ask for what we need, we fault the other for not anticipating it. Why? It seemed so refreshing, watching Jack and Kirsten, to be more forthright.

I went from thinking that people with autism needed me to help explain their oddness to the world so they could better fit in, to thinking that the world is a pretty odd place and that maybe we would all be better off rethinking some of the social conventions that seem so alien to people with autism.

Rethinking social conventions in light of autism is precisely the goal of another just-published ebook called And Straight On Till Morning: Essays on Autism Acceptance. The third title published by a non-profit group called the Autistic Self-Advocacy Network, it is an anthology of essays about autism written from the inside. Each of the contributors to the book is on the spectrum themselves, the parent of an autistic child, or an ally in the disability rights movement.

Though both Asperger Love and the third ASAN anthology are text with no bells and whistles, they take advantage of new possibilities opened up by ebooks in different ways. Asperger Love enabled the author of a much-lauded Times feature to add depth and personal perspective. And Straight On Till Morning reminds me of the copies of Co-Evolution Quarterly that I read avidly as a teenager, filled with lively writing that keyed off of current events but wasn't as perishable as most magazine writing. I will be rereading the opening essay many times as one of the most eloquent descriptions of an inner life that I have ever come across, autistic or neurotypical. Written by a disability activist named Amanda Baggs, who electrified YouTube in 2007 with a video called "In My Language," "Plants Outside the Shade" begins humbly like a grade-school report, "This is a personal description of some of what autism means to me." But then it takes flight into dazzlingly original prose-poetry that takes you to the heart of autistic perception.

Autism means that my earliest memories are of floating in among the feel of things. Not how they looked or sounded, but how they felt. Words don't exist for the hundreds if not thousands of variants on this. A way of perceiving the world that has remained dominant for me even after sensory input became stronger and, later, words and ideas. It's the foundation that I always start from when I climb up the cliffs, day after day, that allow me to use words and ideas and move and understand what is around me. And no matter how high I climb, that underlying way of experiencing the world is still there.

A lot of people see this way of relating to the world as that old cliché of compensation. Where people think blind people's hearing must grow more acute. I see it differently. It's a way of experiencing things that could only have developed if more typical ways were absent. There are a lot of plants that cannot grow in the shade of a forest. But if there are no big shade-producing trees, they flourish. It's like that. Many of my experiences and abilities stem from what happens when plants can flourish outside the shade of a forest.

I can spend all day with one marble. Looking at it, feeling it on my face. One problem with trying to describe this is that there are far more possible sensations than there are words for sensations. So an entire day's worth of experiences can come out to only one sentence. And it's harder still to describe the patterns formed between those sensations. Not abstract, logical patterns but concrete, sensory patterns. And those are how I understand and interact with the world.

How might a clinician describe this experience from the outside?

"Patient Amanda B., a 32-year-old female with a pervasive developmental disorder and significant verbal impairment, perseverated with a marble for more than six hours under observation today. (The patient's mother reports that marbles and other small spherical objects are one of her daughter's 'special interests.') Amanda fixated on the marble for an extended period of time and pressed it against her cheeks for the purposes of self-stimulation. This behavior (not significantly self-injurious) was accompanied by nonsense vocalizations."

For nearly five decades, drily clinical, outside views of autism were all we had. The advent of first-person accounts by people like Temple Grandin, Jim Sinclair, Amy Sequenzia, and Julia Bascom is providing an invaluable perspective on what life on the spectrum is really like.

The autistic self has often been invisible to clinicians. Bruno Bettelheim, the psychoanalyst who proposed in the 1960s that autism is caused by "refrigerator mothers" who secretly wish their children dead, called his bestseller on the autistic psyche The Empty Fortress. I once heard a scientist receiving a lifetime achievement award at a major autism conference refer to her early days in the field as "like veterinary medicine."

The cost of that invisibility, and the brutal treatment that came with it, plays out in "The Judge Rotenberg Center on Trial," a deeply reported essay by Shain Neumeier in And Straight On Till Morning that details the case against a "treatment" center in Massachusetts that employs painful skin shocks to punish self-injurious behavior. This isn't something that happened in the dark days of behaviorism run wild in the 1960s -- it's happening now in Massachusetts, and a special rapporteur at the United Nations has deemed it torture. ASAN is currently assisting the legal effort to shut the JRC down.

In an enlightening essay called "From One Ally to the Education Community: A New View of Students with Autism," Cheryl M. Jorgensen proposes rethinking special education to focus on strengthening the natural gifts of autistic students, rather than on correcting their deficits.

"He’s a biter." "She’s a runner." "He is non-verbal." "She’s off in her own world." "There’s nothing really there, there." "He is difficult to be friends with because all he talks about is train schedules." These statements are often used to describe children and adults who have autism and they represent a belief that autism is a disease or a disorder that needs to be cured, and ultimately, eradicated; that people with autism are "abnormal" and the rest of us are "normal." When people with autism are viewed this way, the difficulties or challenges they experience are placed within them and thus, they are required to change in order to be eligible to participate in the full range of inclusive school and community activities and environments. How often have you heard it said that "She could never be included in a general education class because of her sensory issues" Or "He can’t hold a real job because of his challenging behavior issues?"

What if we changed the fundamental way that we viewed students with autism and instead of viewing autism as the problem, we viewed it as a natural part of human diversity? What if, instead of trying to make people with autism "normal," we intentionally looked for their strengths and viewed their challenges as problems with their environment? What if we appreciated the unique talents of students with autism and recognized the contributions that they might make to our schools and communities?

Ideas like this are gaining traction in the special-education community (see Thomas Armstrong's excellent new book Neurodiversity in the Classroom) because they bring out the best in every student, including those with dyslexia, ADHD, and others who think and learn differently from their peers -- while 70 years of trying to force autistic kids to "act normal for a change," and punishing them for harmless behavior like hand-flapping, has only added to their challenges in daily life.

These two new ebooks, with two very different perspectives, arrive at the same conclusion: By understanding autism from the inside, we become more fully human -- no matter where we are on the grand spectrum.

Steve Silberman is the author of the upcoming book NeuroTribes: Thinking Smarter About People Who Think Differently, to be published in 2014 by Avery Books/Penguin. He is also the author of the NeuroTribes blog on the Public Library of Science and a correspondent for Wired magazine.

A Comic Book Guide to Rewiring Life

2013-03-28T16:44:56-07:00

Adventures in Synthetic Biology. Story by Drew Endy and Isadora Deese and the MIT Synthetic Biology Working Group. Art by Chuck Wadey. Originally published in 2005. Available for free, PDF

Reviewed by Carl Zimmer

In the early 1970s, three scientists ran a simple experiment. They cut genes out of the DNA of a frog and inserted them into E. coli. The frog genes functioned in their new home. The microbe was able to make RNA from them, the first step in translating the information in genes into proteins. And when the microbe divided in two, it made new copies of the frog genes along with its own. It was, to some extent, a microbe-frog hybrid.

The experiment was simple only in its concept, though. It had taken the scientists--Herbert Boyer, Stanley Cohen, and John Morrow--years of research to find the tools to do the job, such as enzymes that bacteria use slice up the DNA of invading viruses. And because it had been the first time that anyone had achieved such a feat, it shook the world.

On the one hand, many scientists and pharmaceutical companies saw a huge potential future for gene pasting. Imagine E. coli carrying the gene for human insulin, for example. Instead of harvesting insulin from cow pancreases, it would be possible to brew insulin the same way people brew beer. One company that sprang up in the wake of the frog-microbe experiment, Cetus, promised that by 2000, virtually all diseases would be cured with proteins made through the genetic engineering that Boyer and his colleagues had invented.

On the other hand, critics saw the apocalypse. Some feared that insulin-pumping E. coli would run amok and spread an epidemic of diabetic comas. If the world embraced genetic engineering, the eminent biologist Erwin Chargaff warned, "the future will curse us."

Forty years after Boyer and his colleagues created their frog-microbe hybrid, the extreme predictions at either end of the prophecy spectrum have failed to come true. No diabetic coma epidemic. (E. coli burdened with human insulin genes can't compete with their lean, wild relatives.) Instead, millions of diabetics get a reliable supply of insulin from the microbes. On the other hand, just having a microbial factory doesn't automatically mean you can cure all diseases. Or even many of them. (I write more about how E. coli launched the biotech industry in my book Microcosm.)

Now, however, genetic engineering is morphing into something new. In the late 1990s, a group of engineers and biologists came together to try to manipulate cells the way they might manipulate the circuits in computer. The analogy between computers and cells is far from perfect, because our bodies are the product of evolution rather than a computer factory. Nevertheless, we have genes that switch other genes on and off, and some genes require inputs from several other genes before they make their own proteins. Cells use this genetic circuitry to detect signals, to process information, and to make decisions. The engineers and biologists set out to rewire that circuitry, inserting many different genes in combinations that would produce new behaviors. They called their project synthetic biology.

As Paul Voosen wrote recently in the Chronicle of Higher Education, synthetic biology is having some growing pains, as scientists balance the promise of the science with the struggles they still face to rewire cells. But along the way, they've made some important fundamental advances. Today, for example, Drew Endy from Stanford and his colleagues reported that they had devised logic gates for E. coli--a transistor-like set of genes that can perform the simple operations that can be combined to carry out computation.

This is a big deal, but it's tricky to explain why. Drew Endy has made a notable effort to introduce synthetic biology both to his fellow scientists and to the public, and so he did something unusual when he and his colleagues published their new paper today: he published a video in the supplementary material in which Endy describes what they've done and what it means.

And rather than keep the video hidden behind a subscription paywall, Endy posted it on YouTube. And here it is:

If you're not familiar with both transcription factors and Boolean logic, this video may fail to enlighten. Endy seems to be aware of this, because midway through the video, he refers viewers to a comic book that he and his colleagues put together, called Introducing Synthetic Biology.

The comic book first appeared in 2005 in a special issue of Nature in which Endy and a number of other researchers offered overviews of synthetic biology and discussed the ethical issues raised by rewiring life. At the time, Nature posted the comic book online in a Flash version. You can still see it in that form, but I wouldn't recommended it. Eight years later, it feels cramped and tiny. But Endy has posted it online as a free PDF, where it still feels fresh and informative.

Introducing Synthetic Biology embeds lessons about the fundamentals of the field in a comic book story. Its heroes are a grown-up scientist and a boy whose experiments with bacteria she oversees. Artist Chuck Wadey gives the narrative a stylish, quasi-psychedelic feel. The boy eagerly tries to rejigger the bacteria to fill with gas and become floating balloons, and along the way he realizes how hard it is--but also how vast the possibilities are for synthetic biology.

This is a smart, savvy piece of science writing. Endy has long focused much of his outreach at young people. In 2003, he helped found the International Genetically Engineered Machine Competition, which brought together college kids (and eventually high schoolers) to carry out experiments in synthetic biology and compete for prizes. Rather than just trying to get some old folks in charge of government and private funding to rethink how they support biotechnology research, Endy has for the past decade helped to produce hundreds of new synthetic biologists. They live the story that Introducing Synthetic Biology tells. If you (or your kids, if you've got any) want to learn about the nuts and bolts of synthetic biology, this is an excellent place to start.

It shouldn't be where you finish, though. Introducing Synthetic Biology has an almost nostalgic 1950s feeling of uncritical gee-whiz enthusiasm about synthetic biology. I couldn't help but think about A is For Atom, a 1952 cartoon from General Electric. It's actually a pretty good introduction to subatomic physics and its applications. But it's unquestionably spooky, with weirdly humanized atoms as cartoon characters and a blithe confidence that the power of the atom was firmly in mankind's control. General Electric was hardly an objective judge of the risks and benefits of the atomic age. It made big profits from building nuclear weapons and nuclear power plants (including, it just so happens, the reactors at Fukishima).

Synthetic biology is fraught with ethical questions, too. Who owns the rewired organisms it produces? What happens if they escape into the wild? Will synthetic biology just end up concentrating wealth into large corporations? Will synthetic-biology-driven energy projects end up harming the environment as more land is dedicated to feeding their enormous hunger for sugar?

Drew Endy has not shied away from these issues. He was one of the people who testified before the President's Council on Bioethics when it looked into synthetic biology in 2010. He has argued for open access to an inventory of genetic parts, rather than hiding synthetic biology behind a wall of patents. And he's taken on critics of synthetic biology in public debates, such as this one in 2008.

I will grant that it may be harder to make an engaging comic book about bioethics. But tomorrow's synthetic biologists need both enthusiasm and wisdom.

Drew Endy and Jim Thomas Debate Synthetic Biology from The Long Now Foundation on FORA.tv

Carl Zimmer writes frequently about science for the New York Times and is the author of 13 books, including Evolution: Making Sense of Life.

The Mathematics of "Meh"

2013-03-19T06:02:00-07:00

Minds of Modern Mathematics. IBM/Eames Office. For iPad. Free download.

Reviewed by Jennifer Ouellette

Visitors to the New York Hall of Science in Queens can browse through an impressive installation called "Mathematica: A World of Numbers... and Beyond." Now that exhibit has a digital equivalent in Minds of Modern Mathematics, a new interactive iPad app from IBM/Eames Office released last year.

The original installation dates back to 1961, when the California Museum of Science and Industry opened in Los Angeles, and asked IBM to contribute an exhibit. IBM tapped designer Charles Eames and his wife Ray Eames -- inventors of the classic "Eames chair" among other items -- and the result was "Mathematica."

A duplicate exhibit was made for the Museum of Science and Industry later in 1961, which has since been sold to Boston's Museum of Science as a permanent display (a QuickTime VR can be found here). And in 1964, another copy of the exhibit debuted at the New York World's Fair.

This new iPad app is based on a timeline poster produced in 1966 that grew out of the original "Mathematica" exhibit, featuring the men of modern mathematics from 1000 AD through 1960. So it's got quite an esteemed pedigree. Unfortunately, the end result is disappointing. The original was hugely popular, inspiring the public to embrace math and science; the strongest emotion elicited by the iPad version is a muted "Meh" -- at least in this reader.

It is not without its merits. There are over 500 very short biographies and milestones included in the timeline, complete with colorful images. But it would have been nice to extend and update the original timeline beyond 1960, and maybe include a few more women so that poor Emmy Noether has some company. Yes, men have dominated the field, but it need not be such an unrelenting sausage fest. Where is Sophie Germain? Maria Gaetana Agnesi? Sophia Kovaleskaya (a.ka. Sonia Kovalevsky)?

The best feature of the iPad app is the inclusion of the IBM Math Peep Shows, a series of short films created by the Eames for the original exhibit on such topics as symmetry, topology, exponents, the story of how Eratosthenes measured the Earth, and mathematical functions:

I embedded that video from YouTube. And therein lies the biggest shortcoming of Minds of Modern Mathematics: everything on it is pretty much publically available in this digital age -- the biographies are little more than brief paragraphs with links to Wikipedia entries, which is the epitome of laziness.

Seriously: would it have killed IBM to at least commission some original copy to really bring the stories and personalities alive? How about designing a few interactive functions to enable users to get their hands dirty, virtually speaking, and explore some of the cooler aspects of the world of math that way? The Eames videos are charming, but they're still passive. Math, like physics, is more of a contact sport.

This is a real shame, because Minds of Modern Mathematics is touted as a tribute to the creative and intellectual legacy of Charles and Ray Eames, who embodied the spirit of innovation. They deserve something more than a slick repackaging of old material.

Then again, the app is free. I guess you get what you pay for.

Image: IBM's Mathematica exhibit at the 1964 World's Fair. Credit: IBM.

Jennifer Ouellette is the author of several popular science books, most recently The Calculus Diaries: How Math Can Help You Lose Weight, Win in Vegas, and Survive a Zombie Apocalypse and the forthcoming Me, Myself and Why: Searching for the Science of Self. She also blogs at Cocktail Party Physics. Follow her on Twitter.

The Library: March 18 Additions

2013-03-18T10:06:00-07:00

Each week, we add some new titles of science ebooks to the Library. We will review a selection of them. Here are our newest additions:

Battle at the End of Eden, Amanda R. Martinez

The Science of Optimism: Why We're Hard-Wired for Hope, by Tali Sharot

Shooting Star: The Brief and Brilliant Life of Frank Ramsey, by Karl Sabbagh

A Portable Science Museum

2013-03-18T07:00:00-07:00

Sound Uncovered by The Exploratorium. iPad (iOS6 required), Free.

When I go to science museums, I like to press the buttons. I'm convinced this is a special joy that you just do not grow out of. Hit the button. See something cool happen. Feel the little reward centers of your brain dance the watusi.

But, as a curmudgeonly grown-up, I also often feel like there is something missing from this experience. There have definitely been times when I've had my button-pushing fun and gotten a few yards away from the exhibit before I've had to stop and think, "Wait, did I just learn anything?"

Science museums are chaotic. They're loud. They're usually full of small children. Your brain is pulled in multiple directions by sights, sounds, and the knowledge that there are about 15 people behind you, all waiting for their turn to press the button, too. In fact, research has shown that adults often avoid science museums (and assume those places aren't "for them") precisely because of those factors.

Sound Uncovered is an interactive ebook published by The Exploratorium, the granddaddy of modern science museums. Really more of an app, it's a series of 12 modules that allow you to play with auditory illusions and unfamiliar sounds as you learn about how the human brain interprets what it hears, and how those ear-brain interactions are used for everything from selling cars to making music. It's part of a series that also includes Color Uncovered.

The app is basically a portable Exploratorium. It would be very simple to convert everything in here (from games to text) into a meatspace exhibit. And that's a good thing. There are some big benefits to having access to your own, private museum. A) You get to press the buttons as many times as you want. B) You actually have the time and the headspace necessary to explore the text and learn the things the button-pressing is supposed to teach you.

For instance, one module features a psuedo vintage tape deck that allows you to record yourself speaking, and then play the recording both normally, and in reverse. You're particularly encouraged to try recording palindromes—words and phrases that are spelled the same backwards and forwards. You might think that palindromes would also sound the same backwards and forwards, but you'd be wrong. The phrase "too bad I hid a boot", for instance, sounds more like garbled Japanese when it's played backwards.

Having this all to yourself on an iPad means that you can spend a lot of time being silly (examples of recordings made by this reviewer include palindromes in different accents, "Hail Satan", and multiple swear words) while easily jumping back and forth between the interactive diversion and the explanations of how it works and how it fits into modern society. I can even imagine kids playing with the toy part of this for a while before finally stumbling upon the embedded text and having their games suddenly illuminated with meaning. That's pretty cool. In a museum setting, I've watched plenty of kids muck around with the button pressing and then run off before they ever have a chance to learn that phonemes are distinct units of sound or that backward speech doesn't just reverse the order of the phonemes, but reverses the phonemes themselves. Sound doesn't have palindromes.

The other benefit here is that Sound Uncovered eliminates the need for the role of Boring Adult — the person charged with the futile task of reading the explanatory text out loud to a gaggle of button-pressing children who really do not care about that right now. In doing so, it frees adults to actually have fun and learn something, too. If you don't have to be the education enforcer, and can trust that your kids will discover the explanations as they play with the app over time, then you're able to actually engage in play yourself —both with your kids and without them. The portable museum is a place for kids, and it's a place for adults, too.

That said, I think an adult on their own would probably burn through this pretty quickly. I got most of what I'm going to get out of it on a three-hour plane flight. But it's also free, so it's not like you're out a lot of money for a small amount of information. In general, I'd say Sound Uncovered is a good example of how the digital format can be used to improve science communication in ways that aren't easily possible in the real world.

Maggie Koerth-Baker is the science editor at BoingBoing.net, the science columnist at The New York Times Magazine, and the author of Before the Lights Go Out.

The Library: A New Feature of Download the Universe

2013-03-11T06:29:00-07:00

At Download the Universe, we've got a hefty inventory of ebooks yet to review. Since we have to fit our volunteer reviewing into our regular lives as writers and scientists, we can only give our full attention to a fraction of those titles. With that in mind, we're launching a new feature here called, simply, The Library.

The Library is a growing list of ebooks for your perusal, including all the ebooks we've reviewed, plus other titles we haven't. We'll include links to places where you can get the ebooks, as well as all of our reviews. You can always enter the Library from the eponymous tab at the top of every post.

Each Monday, we will post a short list of the ebooks we've recently become aware of, and will add those to the Library as well. (Writers and publishers are welcome to contact us about new titles.)

Here's our inaugural batch:

Addicted to Food: Understanding the Obesity Crisis, by James Ehrlichman

Half-Life: Reflections from Jerusalum on a Broken Neck, by Joshua Prager

Half-Safe: A Story of Love, Obsession, and History's Most Insane Around-the-World Adventure , by James Nestor.

Save Our Science: How to Inspire a New Generation of Scientists, by Ainissa Ramirez

Happy browsing!

--The Editors

In Search Of Our Inner Salamander

2013-03-08T10:15:03-08:00

Electric Shock: How Electricity Could Be The Key To Human Regeneration. by Cynthia Graber. Matter, Kindle, $0.99

The dystopic science fiction author Richard K. Morgan writes stories of regeneration taken to the limit. In his Takeshi Kovacs series, the wealthy or otherwise privileged among humankind (or post-humans) continuously download consciousness –memories, knowledge, personality, everything that makes a self – into hardened storage that can be transplanted from body to newly produced body. Among much else, these books are meditations on immortality and its discontents, for in Kovacs’ universe, there is death – when one’s body or “sleeve” ceases to function – and the “real death” that occurs when that encapsulated solid-state self gets annihilated. It’s a complicated dream, this vision in which minds persist in infinitely renewable (and/or interchangeable) bodies.

In 21^st century science, the ambition is a little more grounded; scientists studying the regeneration of organs, tissues and body parts can be said to suffer amphibian-envy. As Cynthia Graber writes at the start of Electric Shock, “the axolotl, or Mexican salamander, has the ability to regenerate everything from its limbs and tail to its spinal chord and skin…”* Humans? Not so much: livers and skin can (partly) replace themselves, and children below the age of twelve, Graber writes, can rebuild fingertips they might be unlucky enough to lose.

Thus the premise for Graber’s story: what if it were possible to discover how to rebuild much more of the human body at any point in its lifecycle? Or rather – what if someone out there right now thinks he can make that happen, and soon?

What follows is an elegant bending of a very familiar genre, the common magazine trope of the scientist – profile. Graber traces the career of biologist Michael Levin from his émigré childhood to his current pursuit of an off-center approach to the problem of mammalian (target: human) regeneration. Where almost all the attention in the engineering of human tissue has focused on questions of genetics and – at the cellular level – on the manipulation of stem cells. Such approaches have had their successes, but if the goal is to tell some tissue to “become an arm” then, Levin's story argues, something else is required.

That something else is the stuff of Dr. Frankenstein’s dreams: manipulation of the electrical signaling that takes place in every cell in the body. Graber follows the conventions of profile-writing by taking her readers through a quick tour of Levin’s early life. We learn he was born in Moscow, brought by his parents to Lynn, Massachusetts at the age of nine, and early showed talent for computers and fascination with the living world. The catalyst for a life’s work came for Levin at 17, when he chanced upon a book called The Body Electric, written by Robert Becker, a surgeon with an unorthodox streak (to put it kindly).

The book had its excesses, but Levin responded immediately to its reports of lost experiments that had played with electric currents to spark regeneration in marine animals. During his Ph.D work, he seemed to outward appearance to have returned to more conventional biological interests, performing significant experiments on the genetics and biochemistry of development. But once ensconsed in his own lab, Graber writes, Levin returned to the question of bioelectric signals and the possibility, ultimately, that he could persuade a human arm or eye grow back.

The balance of Graber’s text – roughly the last half – tells what Levin has been able to achieve so far, from growing a four headed flatworm (its own bridge game!) to experiments – still in progress – through which Levin and his collaborators now hope to persuade a mouse finger to grow, replacing an amputated digit. The most riveting moment in Graber’s account isn’t that one, though. That falls to Levin’s colleague Dany Adams, who discovered (and partly stumbled upon) a technique for mapping the sequence of electrical signals in cells that map the structure to be developed before that structure begins to form.

Graber’s science writing chops show up here as she manages to convey both the vivid sense of the moment and the explanation of what her readers glimpse in their minds’ eyes. At the same time she gently – perhaps too much so – points to the big question that (this account, at least) of Levin’s work leaves unanswered: what is the mechanistic role bioelectric signaling plays in a sequence of events that ends at “eye” or “digit.”

That hints at the one gap I found in Electric Shock. Levin’s work, Graber told me, is viewed as solid, excellent science by the small community that works on bioelectric questions But Graber’s account does not return to the question she raises at the beginning, on the interplay between Levin’s view of the body electric and the genetic and cellular processes involved in building new tissues, organs, parts. I grasped Levin’s drive, his pursuit, and his impressive record of successful experiments from this text. I didn’t get that last step, at least not explicitly: how Levin’s off-the-beaten-path approach to regeneration fits into the larger corpus of work on the ways organisms build bodies.

That’s a lot to ask of a relatively brief text, of course, and to be clear, I don’t think either that Graber should have written a tome on developmental biology, nor that Electric Shock fails to deliver on its core promise of a gripping story about science told through the life of one passionate scientist.

But what lifts Electric Shock out of the common run of profiles, is the use Graber makes of the license given her by the fact of e-publication as opposed to a dead-tree assignment. As Virginia Hughes wrote in this space recently, not all feature stories benefit from the elbow room e-published non-fiction novellas offer. Graber's text does, going long to reach through the biographic narrative into the sophisticated ideas behind Levin’s work, and thus welcoming its readers to enter into the arguments his experiments seek to test. But the insight thus gained evokes more questions, the desire to got yet another step into the inquiry. That’s a good result – recall the show business adage to always leave the punters wanting more – but there’s a tricky side to this intermediate length: it’s not always easy to see whether you’ve finished the job.

With that caveat – hell, I’ll even cop to a quibble -- the bottom line remains. It's a long leap from evoking a mouse digit to the dreams (or nightmares) of science fiction. But the fascination with the possibility of mastering life's processes -- maybe even the whiff of making mortalitiy malleable -- is common to both. Electric Shock tells the real story of where that curiousity may lead, the one that's happening now, in a finely wrought account of an intriguing figure. And all for a price that leaves you change out of a buck!

*Full disclosure: the piece was edited by my MIT and Download the Universe colleague Seth Mnookin.

Images: Leonardo da Vinci, Vitruvian Man, 1492, and Studies of Embryos, 1510-1513.

Tom Levenson writes books (most recently Newton and the Counterfeiter) and makes films, about science, its history, and whatever else catches his magpie's love of shiny bits. His work has been honored by a Peabody, a National Academies Science Communication and an AAAS Science Journalism Award, among others. By day he professes science writing at MIT.