We live on a microbial planet. Microbes have inhabited Earth for an estimated 3.5 billion years, with animals appearing less than a billion years ago and modern humans evolving within only the last few hundred thousand years. Microbes are essential for the cycling of chemicals on our planet and thus play a critical role in global climate change. There are more microorganisms in a human intestine than there have ever been people alive on Earth.
Despite the importance of microbes, our views of biology and particularly evolutionary theory have been largely driven by insights from macroscopic organisms such as plants and animals. This is not surprising, given that humans rely primarily on sight as we interpret the world around us. But developing evolutionary theory on the basis of macroscopic organisms has the potential to mislead. For example, early descriptions of the tree of life that divided organisms into two main branches—plants and animals—are clearly wrong, given the tremendous variety of microorganisms.
In The New Foundations of Evolution: On the Tree of Life, Jan Sapp documents the history of how our biased view of biodiversity has led us astray. The book achieves two main goals: (1) chronicling the history of the placement of microorganisms on the tree of life prior to the use of molecular (DNA) data, and (2) describing the contributions of Carl Woese and colleagues in transforming the tree of life with the naming of a third major lineage, the Archaea. Sapp is uniquely positioned to weave together these two themes as he is a professor of both evolutionary biology and of the history and philosophy of science at York University, in Toronto.
The first portion of the book is instructive and delightful, starting with the ancient plant-versus-animal dichotomy and working through the development of physiological assays and high-powered microscopes as tools to study biodiversity. Sapp documents the parallel rise in post-Darwinian depictions of the tree of life and discoveries of microbial diversity. Although some biologists, such as Richard Owen and Ernst Haeckel, struggled to place microbial organisms on the tree of life, many in the broader field of evolutionary biology dismissed microbes as unimportant.
Among the gems in this part of the book is a brief discussion of the history of bacterial culturing. Apparently, the use of agar for culturing plates came from Fanny Angelina Hess, the wife and assistant of a coworker of Robert Koch's, who learned about agar from a Dutch neighbor who had previously lived in Java. Another of Koch's coworkers, Richard Petri, developed a method of pouring agar into covered glass plates (thus creating the predecessor of the Petri dish) for easy viewing.
The latter portion of the book focuses on the impact of the work of Carl Woese on our understanding of biodiversity. Woese recognized that molecular data could be used to compare diverse organisms even in cases where morphology was not particularly helpful. (It is difficult to use your eyes to compare an elephant with an Escherichia coli.) In one seminal paper in 1977, Woese and Fox characterized a portion of the machinery that all living organisms use to make proteins—a ribosomal RNA—and recognized that there was a third major type of living organism on our planet.
This third lineage was originally named Archaebacteria, as these organisms were initially isolated from extreme environments—high methane, high salt, high heat—and were believed to represent the descendents of the earliest life forms on Earth. These organisms are now known to live in a diversity of extreme and common habitats, and are no longer viewed as representatives of early life. As Sapp explains, these organisms are now referred to as the domain Archaea to distinguish them from the two other domains of life, Bacteria and Eukaryota. It is evident from the rich detail in this part of the book that Sapp spent considerable time with Woese's writings—his published manuscripts and correspondences.
I suspect that writing about the history of more recent events is challenging because we do not yet know where particular chapters end. Sapp does mention some of the concerns and controversies surrounding the three-domain tree of life. These include the growing evidence of the role of lateral gene transfer in shaping the tree of life. Sequencing genes beyond the ribosomal RNAs has revealed ample evidence of the transfer of genes, and sometimes entire genomes, among diverse lineages. Similarly, analyses of multiple genes and now whole genomes have engendered several hypotheses in which eukaryotes arose through some kind of fusion or symbiotic event between an archaeon and bacterium, contradicting Woese's view that the three domains descended independently from a common ancestral “progenote.” It remains to be seen what impacts these data will have on future depictions of the tree of life.