I have a book review coming out next month in BioScience (the publication of AIBS, the American Institute of Biological Sciences, which is a good organization that works toward integrating the life sciences). The text of the review is below. The copyright agreement allows me to present the text here, but to see the typeset version you have to go to BioScience; please do that, because AIBS needs the support.
A Nutshell Guide to the Changing Biological Sciences
Biocode: The New Age of Genomics
Dawn Field & Neil Davies
206 pp. 15 B&W Illus. $29.95 (ISBN13:9780199687756).
This slim, but packed volume presents an introduction to genomics, and goes on to show how this young field touches all of the life sciences, and in many ways all of our lives. It will be of interest to a broad audience of technically savvy readers, including scientists, school teachers, undergraduates, and the scientifically-minded lay readership. Genomics is a discipline that moves with lightening speed, and Biocode provides a timely encapsulation of what is emerging as a major discipline. As the cost of nucleotide sequencing plummets it has become possible to answer questions that would have been almost unthinkable only a few years ago. Just as information technology has dramatically altered the pursuit of science and almost every aspect of our daily lives, so genomics is shepherding in a revolution that started in the molecular biology lab, and slowly but surely is altering all of the life sciences and everything they touch.
Field and Davies bring a broad environmental perspective to genomics. Dawn Field is a Senior Research Fellow at the Oxford eResearch Centre in the UK and is an expert on metagenomics, the sub-discipline that examines the ecology and evolution of organisms in situ by sequencing their genomes directly from environmental samples rather than from cultivated strains. Neil Davies is the Executive Director of the University of California Berkeley’s Gump South Pacific Research Station on Moorea, and is the lead principal investigator of the Moorea Biocode Project, an ambitious effort to collect DNA sequence data (barcodes) from all non-microbes on the island. Together they bring the expertise to cover all of life, from large to small, along with a global environmental perspective.
Genomics in its modern form began with the Human Genome Project, a brainchild of the National Institutes of Health, and initially had a distinctly medical focus. That vein still runs deep, but the early acquisition of microbial genomes soon led to an expansion of genomics into microbial ecology, which has exploded as a discipline in large part because of insights that can be gained from DNA sequencing technologies. Field and Davies start by introducing DNA – the stuff of genomes – but rather than descending into a technical discussion of the structure of DNA they emphasize its role as an information molecule, a kind of a biological tape recorder that is everywhere in our world. They then go through the invention of genomics as a discipline, and illustrate the history by which the techniques were developed to acquire and analyze genomic data, which can comprise very large and enormously complex datasets. The remainder of the book explores how genomic methods are being applied to environmental and ecological questions. Although genomics may have started with medical questions, the techniques are so powerful that they give access to the unseen microbial world, and make it feasible to sample communities of larger organisms with remarkable speed and precision. The book ends on a grand scale, contemplating what implications these insights have for our understanding of, and stewardship for, the planetary ecology.
Much of the book is built around vignettes that illustrate the principles being discussed rather than by direct exposition. Thus, the chapter titled “The Zoo in My Sequencer” introduces the utility of high-throughput sequencing for biodiversity studies, but it does so by means of a series of brief stories showing how genomic data can help with challenges ranging from tracing outbreaks of food-borne illness to reconstructing the biology of Denisovans (mysterious relatives of Neanderthals) from a finger-bone and a few teeth. This use of vignettes and anecdotes helps maintain interest and keeps the tone light, which is no small feat given the grand scope of the book and its brevity.
A grand scope in a short space necessarily leads to omissions, but given the challenge of covering such a broad and active field, I was impressed with the accuracy of the book. There were, of course, some minor technical glitches and awkward analogies, but by and large Biocode gets its facts right. The essay on pandas (“2 percent of pandas”) is wonderful, showing how deep sequencing of panda genomes has yielded – in addition to conservation information – both fundamental insights and data that have the potential to be economically important, in the form of novel cellulases. What is particularly nice about this essay is that it brings together in two and a half pages of text a cogent argument for the importance of conservation and fundamental research, because pandas, as charismatic as they may be, are generally not considered to be economically important animals. Who would have thought that their genomes might give insights into the energy economy? I doubt that pandas will provide the path to efficient biofuels and a clean energy future, but the realization that an understanding of their genomes can help is a powerful illustration of the importance of the diversity of life and the value of understanding it in all its complexity.
The compactness of the book also helps bring some important ideas forward in a way that would not occur with a lengthier text. This is true for the book as a whole, which squeezes the science behind the sequencing of the human genome together with efforts to genetically barcode all of life in a compact text. But the benefits of brevity also express themselves in a more fine-grained way throughout the text; the chapter on “Terra-Genoming” weaves together metagenomics, the history of human migration and evidence for pre-Columbian contact between Polynesians and Native Americans, invasive species, horizontal gene transfer, and the exploration of the world’s oceans. Each of these topics could easily justify a book in its own right, but putting them together helps illustrate the ways in which they interact and reinforce each other. Naturally much of the detail had to be omitted, but there are copious endnotes, and an interested reader can easily follow any of these threads into a deeper literature.
I also appreciated the delicacy with which the authors handled some of the pillow-fights within the genomics community. The ENCODE project is an international effort to identify and catalog all of the functional elements within the human genome, integrating information from many datatypes into a single database. This is a difficult undertaking, and there have been critiques of the project, some well justified, others not. Sadly, some of the discussion has descended to the level of ad hominem attack. It must have been tempting to delve into a scientific soap opera, and the fact that the authors of Biocode were disciplined enough to stay focused on the matter at hand and neglect some of the tawdry details was much appreciated by this reader. This reflects the generally hopeful tone of the book, which faces our current global environmental crisis head-on, but does so without hand-wringing. Instead it documents the severity of the situation, and then shows how genomic technology, applied wisely, can facilitate stewardship. DNA was first discovered as a cellular component in the 1860s, and by the 1960s it had been established that it is the primary genetic material of the cell and its structure described. It is truly remarkable that it is now possible to think in terms of sampling genomes on a planetary scale, and Biocode makes a compelling case for the power and promise of such an undertaking. It may be a slim volume, but it points at great things.
Charles Delwiche
Professor, Department of Cell Biology and Molecular Genetics
University of Maryland, College Park
2108 Bioscience Research Building
4066 Campus Drive
College Park MD 20742