A few pounds of microbes, only ounces of insight

[This is my latest review for Download the Universe]

Honor Thy Symbionts, by Jeff Leach. Kindle

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.