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A Comic Book Guide to Rewiring Life

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.

The Mathematics of "Meh"

 

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

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

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

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

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.

New Media for New Particles

Chasing the Higgs Boson, by Dennis Overbye. New York Times, 2013. Online exclusively.

Reviewed by Sean Carroll.

Back in December, the New York Times published a remarkable online feature: Snow Fall: The Avalanche at Tunnel Creek. In the words of Veronique Greenwood, who reviewed it here at DTU, readers were treated to

a piece not only grippingly reported but physically gorgeous, laced with soaring animations of the mountain, a looping GIF of the wind over the snow, and haunting audio and video captured by the survivors.

The effort paid off. The feature was seen by about three million people, a full third of whom had not previously visited the NYT website.

Now the discovery of the Higgs boson, the biggest physics story of recent years, has been treated to -- well, not exactly the same treatment, but something gesturing a bit in that direction. The March 5 Science Times was given over to a set of articles by Dennis Overbye and accompanying illustrations, all devoted to the Higgs, the Large Hadron Collider, and the future of particle physics. The stories are richly illustrated, with a number of animations, and the package includes a helpful glossary and guide to further reading. (I have it on good authority that entertaining and enjoyable books about this very topic are readily available in stores.)

The Higgs is an interesting challenge for science journalism, since while the excitement among physicists is palpable, it's proven very difficult for anyone (scientists or writers) to effectively convey what is so all-fired important about this particular particle. We sometimes hear that it "gives mass" to other particles -- somewhat true, but somewhat untrue as well. (It gives mass to elementary quarks and leptons, but most of the mass in your body comes from protons and neutrons, which are composite particles that don't get their mass from the Higgs at all.) It is very rarely explained with any effectiveness how this particle ends up giving mass to others. And I have seen almost no attempts at a popular-level explanation of the question that the whole discussion begs: Why do we need a particle to "give mass" to other particles at all? Why can't they just have mass without any help? (The answer comes down to the particular symmetries of the Standard Model of particle physics, which treat versions of particles with different kinds of spin as very different beasts, preventing the appearance of mass unless something breaks the symmetries. Hey, there's a good reason why you don't hear a lot of people trying to explain this stuff.)

Overbye, I think wisely, doesn't spend much time on yet another half-successful whack at Higgs pedagogy. Rather, he spins the human tale of the scientists who searched for the particle, conveying the sense of excitement by letting the physicists speak for themselves. And he is a master at teasing out the telling anecdotes. When physicist Eilam Gross brings his girlfriend down to the cavern of the ATLAS experiment to ask her to marry him, you get a feeling for the kind of emotional significance their work has for these researchers. (“But believe me, I checked a thousand times with her before to make sure she will say yes," Gross assures us.)

There is no single "Aha!" moment when looking for a particle like the Higgs; the boson itself decays before you can see it, leaving behind debris that could easily be produced in completely different ways. It's the precise amount of debris that matters (what kinds of particles, with what energies). The scientific task relies on accumulating enough data to claim a statistically significant result, so the discovery of a particle like the Higgs necessarily creeps up on you. Overbye recounts the gradually mounting excitment from 2011, when the first hints appeared, to June 2012, when teams were losing sleep in a mad rush to get the most reliable results possible in time for the scheduled July 4 talks.

And after that, the champagne.

The NYT Higgs special isn't distinguished only by length and the depth of its reporting, but by the graphical accompaniments to the story. There's a video, a timeline, and a couple of animations. It's here that the difficult pedagogical tasks are tackled, with mixed success. The reality is that it's not the Higgs particle that is important, it's the Higgs field that pervades all of space and affects the properties of the other particles moving through it. The Higgs boson is a vibration in the Higgs field, just like a photon is a vibration in the electromagnetic field. But we're used to thinking of particles much more than fields. So we reach for analogies, none of them completely successful, and the animations here are no different. They go so far as to tell us that the Higgs field is "made up of Higgs bosons." That's one of those statements that, although there are interpretations of the underlying reality according to which it is strictly true, nevertheless move the general reader further away from correct understanding rather than closer to it.

There are other quibbles one could raise, but I don't want to dwell on them too much. It's a shame that Phil Anderson, the condensed matter physicist who first suggested what we now call the Higgs mechanism, is nowhere mentioned in the piece. Indeed, as important as Peter Higgs himself was to the story, it is an accident of history that it's his name that is attached to the mechanism, and good journalism should work to redress the balance rather than contribute to it.

Overall, though, there is some great reporting here on a truly historic discovery in the history of physics. The Higgs deserves this kind of more-than-the-usual-effort take on a major scientific story. In the age of Twitter and blogs, it's harder and harder for traditional news media to be there first; but they can still use their resources to do it right.

 

According to the New York Times, Sean Carroll is "a cosmologist and well-known blogger." His most recent book is The Particle at the End of the Universe: How the Hunt for the Higgs Boson Leads Us to the Edge of a New World.

Word Rising: In Long-Form Journalism, How Long Is Too Long?

Uprising, by Phil McKenna. Published by Matter, $.99. Visit Matter for details about formats, purchasing, and membership.

Review by Virginia Hughes

In his State of the Union address last month, President Obama made several nods to climate change. To reduce America’s dependence on oil — and the carbon emissions that come from burning it — he pushed for a bigger investment in clean sources of energy, like wind, solar and natural gas. “The natural gas boom has led to cleaner power and greater energy independence,” Obama said. “We need to encourage that.”

Thanks to advances in a technique called hydraulic fracturing, or fracking, natural gas production in the U.S. grew by 8 percent in 2011, the sixth consecutive year of growth, leading the International Energy Agency to call this “a golden age of gas.” When burned, natural gas emits half as much carbon dioxide as coal does. The Obama administration and some prominent scientists — including Obama’s pick for new energy secretary — say natural gas could be used as a “bridge fuel,” curbing our coal consumption until greener alternatives are ready for primetime.

But what if natural gas isn’t so clean?

That’s the question artfully raised in Uprising, the fourth installment from Matter, an online platform for long-form science journalism. Uprising, like Matter’s earlier stories, presents an engaging narrative with juicy characters doing surprising science at a length of around 6,000 words. Unlike the other Matter stories, though, I’m not sure this one needed more than the 3,000 words of a typical magazine feature.

In Uprising, journalist Phil McKenna tells the story of two unlikely collaborators — Bob Ackley, a big-car-loving libertarian with decades of experience as a gas company technician, and Nathan Phillips, a liberal tree-hugging professor — and their wacky adventures cruising the streets of Boston to map natural gas leaks.

When methane, the primary ingredient of natural gas, leaks into the atmosphere (rather than being burned) it’s a much more powerful greenhouse gas than carbon dioxide. But nobody knows exactly how much gas is leaking. That’s where Ackley and Phillips come in.

Uprising tells why Ackley and Phillips started to work together, and what they’ve discovered so far: In a paper published last month in Environmental Pollution, they reported finding 3,356 leaks in Boston, including six where gas levels were high enough to cause an explosion. Their study included a city map tracking the leaks, which Matter recreated as a striking black-and-white grid with swashes of red and yellow to indicate the leaks. (And although the study is behind a pay wall, Matter made it somewhat open-access by linking to a Google Doc of the study’s full data set.)

The problem, for me, is that it’s unclear how (or whether) this single study contributes to the greater international debate about natural gas and climate that McKenna did such a great job setting up. The study focused on the number of leaks, rather than their volume, so it can’t say anything definitive about whether natural gas really is worse for the climate than coal.

It’s not that these investigations don’t matter: We learn that Ackley and others are finding similarly frightening numbers of leaks in other cities, such as Manhattan and Washington, D.C., and that some of this data is driving a major lawsuit against a utility company. It’s entirely plausible that these leaks will put a crimp on the natural gas boom. But the story doesn’t say much about how the wider energy community has reacted to this data. It didn’t include any skeptical voices, or any comments from scientists or policy makers who still believe in natural gas as a bridge fuel.

I was expecting the story to answer the initial question posed: What if natural gas isn’t so clean? And when I didn’t get that answer, I was disappointed, in a way that I might not have been had the story been shorter. The view, for me, wasn’t quite worth the climb.

 

Virginia Hughes is a science writer based in Brooklyn. Her work has appeared in Nature, Popular Science, and Slate, and her blog Only Human is part of National Geographic magazine’s Phenomena. Follow her on Twitter.

A Few Pounds of Microbes, Only Ounces of Insight

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.

 

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.