Snowfallization

Posted on October 24, 2013 by Carl Zimmer

Review of "Sea Change," by Steve Ringman and Craig Welch, Seattle Times. Web site.

Review of "The Course of Their Lives," by Mark Johnson and Rick Wood, Milwaukee Journal-Sentinel. Web site.

Last year on Download the Universe, Veronique Greenwood wrote a review of a story about an avalanche. Journalists write about avalanches fairly regularly, but this piece, called "Snowfall" was different. It was a one-man-band of text, video, maps, and unfolding photos. The story attracted millions of readers and earned scads of awards, including a Pulitzer. And it has ushered in an era of big, ambitious online packages of newspaper reporting. Not surprisingly, science offers some of the best stories for the Snowfall approach.

One recent example is "Sea Change," published last month by the Seattle Times. Photographer Steve Ringman and reporter Craig Welch tackled the immense but little-known disaster that is ocean acidification. The carbon dioxide we pump into the atmosphere doesn't just warm the atmosphere. It also lowers the pH of sea water, making the chemistry of the ocean dangerous for some species. Oyster companies are already feeling the effects of the dropping pH, and if we continue to acidify the oceans at our current rate, the ecological effects could be tremendous.

Here's a nine-minute video from the project:

The package Ringman and Welch have created has three main text stories. It starts with an overview of acidification research, which is followed by two close-ups on fisheries that are being affected–namely, oysters and crabs. (Both are economically important to the Seattle Times's local readers.) Welch reports the stories in the classic mode of environmental journalism, mixing together in-person reporting in far-flung locations with explanations of the research that revealed the scale of the problem. The photos are impressive, the videos are well made, and the visualizations–which try to convey how big the phenomenon of ocean acidification is–are fairly successful.

If you've already read "Snowfall," the presentation of "Sea Change" doesn't feel like a bolt out of the blue. But that just shows how much our expectations have shifted. Just look back seven years to a similar series called "Altered Oceans" from the Los Angeles Times, to see what I mean. The authors, Kenneth Weiss and Usha Lee McFarling, won a Pulitzer for their efforts, which were even more ambitious than "Sea Change." Rather than focus on one way we're ravaging the oceans, they set out to create a picture of all of them, from pollution to climate change.

Although it came out in 2006, the "Altered Oceans" package of stories holds up well today. But the packaging is showing its age. The fancy front page takes you to five stories that are nothing but text. There are also animations and photos, but they're squirreled away in slow-loading pages. After looking at one of these pages, I discovered there was no way to find my way back to the front page again. Seven years of programming advances made "Snowfall" possible–and now raise our expectations for such ambitious online pieces. (Welch recently discussed the making of "Sea Change" with the Columbia Journalism Review.)

From the mountaintops of "Avalanche" and the open oceans of "Sea Change," we take a claustrophobic trip indoors with "The Course of Their Lives." It's a four-part series from the Milwaukee Journal-Sentinel about medical students dissecting the cadavers of people who donated their bodies to science. There's no news here, no warning of an impending disaster. Instead, reporter Mark Johnson and photographer Rick Wood faithfully follow students through a remarkable experience–getting to take apart another human being, down to the brain and guts. Wood and Johnson both bring an emotional sensitivity to the project that makes reading it a deeply moving, human experience.

While I would heartily recommend "The Course of Their Lives," I would also point out some shortcomings. I don't want to belittle the piece by talking about them; they're worth talking about as a way to ponder the kinds of decisions that newspapers make when they create Snowfall-esque stories about science.

Some of the bells and whistles attached to "The Course of Their Lives" don't add much. The videos are mostly of talking heads, who sometimes speak stiltedly. Distilling people's words down in compelling written prose remains a superior technology to a video camera that's simply switched on.

I was also underwhelmed by the interactive anatomical diagrams that went along with the stories. They're meant to illustrate the lessons that the students learned about the cadavers, organ by organ. But who actually needs to see lungs light up on a diagram of a body to know what lungs are? The powers of visualization, both online and in apps, are spectacular. (My favorite anatomical example remains this ebook about Leonardo Da Vinci's anatomical sketchbooks.) But there's no point in using those powers simply to check off a box in a to-do list. It's another lesson that we should respect the technology of prose.

Ironically, the prose itself in "The Course of Their Lives" also felt a bit antiquated. American newspaper journalism long ago settled on a certain style. The paragraphs became short, and the sentences shorter. The words needed to be plain and serviceable. There were perfectly good reasons for this approach–but a lot of them had to do with the physical properties of printed newspapers. Stories couldn't be made of densely packed paragraphs, for example, because editors would need the freedom to cut off sections of stories at the last minute to make them fit their available space.

These were good reasons, but they had some odd consequences. Along with their standard fare of short news pieces, newspapers would also prepare a few massive, long-form pieces–Pulitzer-bait, essentially–but these pieces often retained the staccato structure of short news stories. In these sprawling pieces, that style read strangely. And once New Journalism's masters like Tom Wolfe and Gay Talese turned magazine features into a new art form, the adherence to the old style in newspapers became even more peculiar.

Today, as newspapers and magazines shift online, that style has grown even more out of date. If you read stories from publications that got their start online, such as the Atavist, you never find the staccato style of old newspaper stories. There's no need to adhere to it.

Thus "Sea Change" and "The Course of Our Lives" serve as illustrations of journalism in transition–created by people trying to figure out how to bring the best of the old world of newspapers and leave the rest behind.

(Photos: Top-Steve Ringman, Bottom-Rick Wood)

Zimmer author photo square Carl Zimmer writes the "Matter" column for the New York Times and is the author of 13 books, including Evolution: Making Sense of Life.

Rejoicing In Ants With A Citizen Science Ebook

Posted on May 3, 2013 by Carl Zimmer

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.

Continue reading “Rejoicing In Ants With A Citizen Science Ebook” →

A Comic Book Guide to Rewiring Life

Posted on March 28, 2013 by Carl Zimmer

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.

Continue reading “A Comic Book Guide to Rewiring Life” →

In Search Of Our Inner Salamander

Posted on March 8, 2013 by admin

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.

A Few Pounds of Microbes, Only Ounces of Insight

Posted on March 1, 2013 by Carl Zimmer

Honor Thy Symbionts, by Jeff Leach. Kindle

Guest review by Kevin Bonham

In 2003, the Human Genome Project–an effort to sequence every gene in a human being–was completed. The success, announced to great fanfare, was supposed to herald a new era in health care. Unfortunately, the promises of personalized medicine, in which treatments are tied to a person's genetic sequence, have not yet come to fruition. A few of the reasons for this are obvious (at least in hindsight). Knowing the location and sequence of a gene is one thing, knowing what it does is quite another. And understanding the role that a gene or gene variant plays in a disease, especially when many afflictions are influenced by tens or hundreds of genes, is even harder.

Complicating matters further is the re-emerging realization that genes are not destiny, and now many new "-omics" projects are beginning to gain attention. From the transcriptome (what genes are actually expressed), to the proteome (proteins and protein modification), to the epigenome (modifications of the DNA that regulate gene expression), more and more researchers are attempting large-scale analysis of entire biological systems and trying to extract meaningful information from enormous data sets. In his new ebook, Honor Thy Symbionts, Jeff Leach aims to tackle what is, in my opinion, the most fascinating of these new -omics revolutions: The Human Microbiome Project.

I desperately wanted to like Leach's book. Even though I've repeatedly heard the refrains, "There are 10 times more bacteria cells in your body than human cells," and "There are 100 times more bacterial genes in your gut than there are human genes," and "Bacteria account for 5 to 10 percent of your body mass," these facts never cease to amaze me. And I've been to enough microbiome-related research talks to know that the microscopic bugs that live in our guts can have profound impacts on our health–from metabolic disorders and type-II diabetes to multiple sclerosis and inflammatory bowel disease. The microbiome deserves a book-length discussion, but Honor Thy Symbionts falls short.

Problems

Problem 1 (I think this is the underlying reason for all of this book's problems): It's not a book, it's a collection of "essays" that are really just blog posts.

In fact, you can go to Leach's website and read almost all of the "chapters" for free on his blog. As I read his alleged book on my Kindle, it was abundantly clear that Leach simply did a large-scale copy-paste, without much additional effort. Spelling and grammatical errors abound, and phrases like "In a series of blog posts starting with this one[…]" only serve to call attention to the fact that I paid three dollars to download something I could just as easily have read on the Internet for free. In one chapter, the text refers to a graph that apparently didn't make it in the migration to Kindle. And since each chapter is really just a blog post, there's no cohesive narrative to tie the book together. Even the unifying "theme" of the microbiome is misleading, since several of the chapters don't even mention microbes.

Problem 2: A lot of the science is overstated.

Throughout this book, I had the same feeling of professional scientific unease I get when reading Malcolm Gladwell, without the benefit of Gladwell's ability to spin a narrative. For instance:

Though improved hygiene has many benefits, scrubbing soil from our bodies and food has thrown our immune system into an over reactive tailspin and is responsible for the skyrocketing increase in allergies and autoimmune disease.

There are several lines of evidence suggesting that hygiene may increase the risk for many inflammatory disorders, but there are plenty of other factors that may play a role, and a marginal increase in risk is a far cry from an "over reactive tailspin."

In another case, Leach describes compelling research suggesting that fiber intake can alter the levels of certain types of microbes. But then he leaps to a prescription how many grams of fiber we should eat each day (an amount significantly higher than current nutritional guidelines).

And in yet another case, Leach spends several pages discussing research on the protein consumption of spider monkeys. Based on this study, he draws conclusions about everything from human diets to agribusiness, sociology and the economics of poverty and health, finally concluding the chapter by pointing out that

This all assumes, of course, that the protein leverage theory plays any role in all of this. Maybe it doesn’t.

At least he admits the ambiguity this time. But then why all the self-assured conclusions? At times I wanted to pull my hair out.

Further complicating this scientific over-reach is Leach's failure to cite the research he's referring to. There's an extensive collection of references at the back of the book, but no link within the text to the reference itself. This seems to be another symptom of copy-pasting from a blog post. The blog posts have web links, but they were apparently were stripped out when the conversion was made.

Problem 3: Inconsistency of style and complexity.

Leach jumps back and forth from lofty rhetoric:

It is at this interface between the terra firma of our evolutionary past and the enhanced material standard of living[…]

to colloquialisms that border on inanity. Sometimes he makes the jump within a single sentence:

In just a few thousand centuries, our kind has gone from nesting in trees, to making stone tools and digging roots, to kindling fires, to subduing flora and fauna, to erecting massive cities, and finally to downloading Angry Birds over 1 billion times (and counting).

Leach routinely throws in random and unnecessary digs at creationists. At one he point calls health-care workers who recommend baby formula "predatory." I found the constant movement between grandiosity and link-bait trolling to be jarring.

Leach also routinely mixes lay-accessible and jargon-laden writing. I know what 16S ribosomal RNA and shotgun pyrosequencing (misspelled as prosequencing) are, but I doubt the target audience of this book will. In some cases, the jargon is useful and adequately explained, but in others it just seems like Leach is trying to show off.

Redeeming Qualities

Despite these glaring problems, I don't think Leach should be written off entirely. A lot of the science he talks about is interesting and important. Our obsession with cleanliness probably does play some role in the increased prevalence of allergies and autoimmunity, even if it's not the only cause. People probably should be eating more fiber, even if we can't make a specific grams/day recommendation. The cheap cost of corn and expense of protein probably explains at least a portion of the paradoxical association of poverty and obesity, even if we can't draw a straight line between spider monkey diets and our own. And the main thesis of this book, that our dietary decisions need to be increasingly informed by our emerging understanding microbiome, is almost certainly correct.

Strangely, Leach himself makes much the same point in the introduction to this book.

While researchers are cautious and right not to oversell the microbiome (much work is still needed to confirm causation for many ailments), the direct or indirect implication of microbes in a staggering number of ailments and diseases of the modern world, reinforces that we are on the cusp of a paradigm shift from the orthodox notions of health and disease.

It's a shame that the author failed to exercise some of that caution himself.

Final Verdict

There are too many problems for me to recommend this book. Prepare an enormous grain of salt and head over to Leach's blog instead. You'll get most of the same material, including web links to the relevant research so you can fact check any claims that seem overwrought. Meanwhile, I will anxiously await a book that tackles the microbiome and does justice to this amazing new field of research.

10.27.1KevinBonham16 Kevin Bonham is a graduate student studying the immune system at Harvard University. He blogs about microbes and the immune system at We, Beasties on the Scienceblogs network.