The Tangled Tree: A Radical New History of Life

by David Quammen

What were the major events in the history of life, how did complexity arise, how did the eukaryotic cell originate? Three factors converged to reroute his path, one of which was the Margulis book.

Their results were clear and dramatic. They found that chloroplasts within their red alga differed drastically, by this rRNA measure, from ribosomal RNA in the alga’s own cytoplasm.

these chloroplasts were xenotransplants from a completely different kingdom of life. They matched far more closely with the bacteria, those outsiders chosen for comparison, than with the red alga of which they were functional parts.

one cardinal point of the endosymbiosis theory had been confirmed: yes, chloroplasts in plants are descended from captured bacteria.

blue-green algae are not in fact algae but bacteria (hence they became known as cyanobacteria); and that chloroplasts, at least in some complex organisms, had originated not just as bacteria but specifically as this sort, cyanobacteria. The

mitochondria, as well as chloroplasts, are descended from captured bacteria.

The Margulis hypothesis was confirmed. Based on their ribosomal RNA, the mitochondria of wheat do not resemble wheat. They are alien little beings, co-opted into wheatly service. They came from elsewhere. They resemble bacteria.

all human cells, all your cells and my cells and the cells of the doubters, are powered by captured bacteria functioning as organelles.

These captives have, over the course of maybe two billion years, become part of the machinery inside the cells from which your cells are descended. Their DNA is part of your DNA—the part received exclusively from your mother. Why mother only? Because mitochondrial DNA is passed along via eggs and not via sperm.

scientists who scrutinized its chloroplasts, at the University of Düsseldorf in Germany, found teeny little rings of DNA, only one-thirtieth the size of a typical bacterial chromosome.

Their 2002 book was Acquiring Genomes: A Theory of the Origins of Species, proposing at length what she had claimed elsewhere: that neo-Darwinism (the twentieth-century school of thought merging Darwin’s theory with Mendel’s genetics) is wrong about the main source of genetic variation that drives evolutionary innovation. That crucial element, variation—it doesn’t, according to Margulis and Sagan, come mostly from the tiny random mutations that seem sufficient to neo-Darwinists. “Rather,” they wrote, “the important transmitted variation that leads to evolutionary novelty comes from the acquisition of genomes.” It comes from symbiosis, the real origin of species.

monograph on the radiolaria, a group of single-celled planktonic marine creatures that produce elaborate silica skeletons, varying species by species like a gallery of crystal chandeliers.

Ernst Haeckel.

He coined the term ecology. He coined the term phylogeny. He coined the term ontogeny and propounded what he called the biogenetic law, asserting that the embryological development of an individual retraces the course of its evolutionary descent. A human embryo, by this argument, passes through stages at which it looks like the embryo of a fish, then of a salamander, then of a rabbit. Put in three words, as it would later be famously known: ontogeny recapitulates phylogeny.

Protista,

He labeled the trunk Moneres, by which he seems to have meant the simplest of single-celled organisms, resembling bacteria. (For technical reasons, their name, meaning “single,” was later corrected to Monera.) This hypothesis, among his three, was the boldest application of Darwinian theory that could be made at the time. It asserted that all living creatures, including humans, have descended from some common ancestor resembling a bacterium. But in 1866 and for some years after, Haeckel himself was still undecided about which of his three hypotheses was correct.

Ecologists see distinctions that microscopists miss. Among the boldest of those distinctions, Whittaker noted, are three categories of organism: producers, consumers, and decomposers. Animals are consumers, swallowing other creatures for their sustenance. Plants are producers, gaining sustenance from sunlight and water, creating their bodily substance from nonliving materials. Bacteria and fungi are decomposers, taking their sustenance by gently dismantling other creatures, dead or alive, and putting the pieces to new use.

The eukaryotic cell “is now recognized to be a genetic chimera,” a compound creature, resulting from ancient convergence events among several lineages, including the bacteria that became mitochondria and chloroplasts.

“Common ancestral state,” I read. “Not a single ancestor, but an ‘ancestral state.’ Right?” Right, he said. This mound represented a world of precellular life; a world of primeval twitching almost four billion years ago; a world of naked molecules (maybe RNA in particular) that had acquired the capacity to replicate themselves; a world before living things could be sorted into species, let alone into kingdoms.

Darwin knew nothing about the mechanisms of inheritance,

In 1984 he and several colleagues published their analysis of ribosome shapes as seen in representative bacteria, archaea, and eukaryotes.

Whatever did occur during that phase of Earth’s history, its most consequential result was a single lineage, some manner of creature, that became the universal ancestor of all three kingdoms of life. For this certitude, we do have evidence: the universality of the genetic code itself, a system that uses the same coding—these bases specify those amino acids—in bacteria, in archaea, and in eukaryotes. The genetic code is the ultimate shared character, uniting all forms of life within one ancestry. And that ancestry had its origin among progenotes.

these three domains should henceforth be known as the Bacteria, the Eucarya, and . . . the Archaea.

A gene was an abstraction made concrete only by the word itself, that nice little unit of jargon coined in 1909 to stand for an entity of some sort that determines hereditary traits.

Transformation, in the sense of that word as used by Fred Griffith and Oswald Avery, is one of the three cardinal mechanisms of horizontal gene transfer, the most counterintuitive phenomenon discovered by biologists in the past century. Griffith had shown that some mysterious pabulum could transform a nonvirulent type of bacteria into a virulent type. Avery’s group had shown that Griffith’s pabulum is DNA, the physical carrier of genes. And the Avery team had demonstrated that in its naked form—floating loose in the environment after having been liberated from a busted bacterial cell—DNA is capable of getting into another bacterium and causing heritable change.

from one bacterial species to another, from one genus to another, even from one domain of life to another. The transformations that result from such horizontal transfer can be far more consequential than merely changing a pneumonia bug from mild to virulent.

“sex” between bacteria, and was dubbed conjugation. The other involved viruses carrying foreign DNA into the cells they infect, and that was called transduction.

Lederberg was fascinated by Oswald Avery’s discovery: the uptake of naked DNA from a dead bacterium into a live one. Did something like that occur between living bacteria too?

The genes were traded sideways into a more adaptive combination.

“In order that various genes may have the opportunity to recombine,” he wrote in a short paper coauthored with Tatum, “a cell fusion would be required.” Recombine: meaning, rearrange or swap genes. Cell fusion: meaning, a temporary clinch. It might be brief—a quickie—but prolonged enough for genes to be transferred.

in his Salmonella cultures, Zinder found no sign of conjugation. Instead, he detected a different mode of genetic exchange. In this new mode, as far as Zinder could tell, only a small section of DNA was transferred, enough to account for a single genetic trait. And the donor bacterium never came into contact—not

Zinder recognized that the filter-passing agent was a virus—it had to be, since no other biological entity was so small—which evidently picked up some genetic material from one bacterium and carried it into another. This was so different from conjugation that Zinder and Lederberg, when they published the work, gave the process its own name: transduction.

Esther Lederberg found that this curious F factor, bestowing the capacity to initiate mating, could be acquired by a bacterium that didn’t have it. How? Through a different mechanism, which I’ve just mentioned: transduction. That is, carried in by a virus. This was a dizzying compoundment of two kinds of horizontal gene transfer, functioning as a double-stroke process to move DNA between microbes. Take a deep breath and relax with your puzzlement as I say it again: transfer of the F factor—whatever it was—from one bacterium to another, by a virus, gave the second bacterium an ability to mate with still other bacteria.

The net result of conjugation is genetic recombination—mixing—which often proves helpful in the evolutionary struggle. But conjugation itself doesn’t produce babies.

they noted passingly that the ability to conjugate among E. coli was conferred by some other sort of “infective hereditary factor.” Her husband, as sole author of another paper published just a month earlier, had alluded likewise to “infective heredity.”

There were three modes of such sideways inheritance, Zinder explained. The first was conjugation, as discovered by Tatum in collaboration with Zinder’s mentor, Joshua Lederberg. The second mode was transformation, as discovered by Griffith and illuminated by Avery’s team. The third mode was transduction, as discovered (though he didn’t crow) by him and Lederberg. Conjugation

infective heredity.

urgently human implication of the new bacterial discoveries: that resistance to multiple antibiotics among bacteria spreads horizontally. It can happen by conjugation. It can happen by transduction. It can happen in a sudden leap.

‘infective heredity.’ ”

The first sulfa drugs had been introduced in the late 1930s, and immediately there were reports of bacterial strains with resistance. Penicillin was discovered in 1928 and developed for human use beginning in 1942; initially, it was a very potent weapon against Staphylococcus of various sorts; but by 1955, penicillin-resistant strains of staph were turning up, especially in hospitals,

Methicillin became available in 1959, valued highly as an answer to forms of staph—especially Staphylococcus aureus—that had acquired resistance to penicillin.

by 1972 methicillin-resistant Staphylococcus aureus (infamous now a...

And by the early twenty-first century, MRSA was killing more American...

23,000 deaths annually in the United States and seven hundred thousand deaths globally from infection by unstoppable strains of bacteria.

reckless overuse of them for foolish or unnecessary purposes—doctors

feeding low doses of antibiotics routinely to domestic livestock, because that somehow increases their rate of growth.

In the United States during a recent year, more than 32 million pounds of antibiotics were sold for use in livestock, and most of that went for growth promotion and preventive dosing of food-animal populations, regardless of whether the individuals were sick. Globally, total consumption of antimicrobials (that is, drugs against dangerous microbial fungi as well as bacteria) by livestock was roughly 126 million pounds, with China using even more than the United States, and Brazil in third place. Most of that total goes into cattle, chickens, and pigs. A significant fraction of it involves drugs that are also important in human medicine.

the most startling aspects of the trend have been how speedily resistance has spread and how many different kinds of bacteria have acquired multiple resistance—that is, resistance not just to one antibiotic but also to whole arsenals of different kinds.

the appearance of resistance to each drug so quickly, in one strain of bacteria and another, as occurred in the 1940s and 1950s, was a phenomenon that couldn’t be explained by the slow Darwinian process of mutation, natural selection, and ordinary inheritance, occurring independently in each case.

The Japanese work began after World War II in response to an increase in cases of dysentery,