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molecular phylogenetics.
Griffith, for instance, in the mid-1920s, while researching pneumonia for the Ministry of Health, noticed an unexpected transformation among bacteria: one strain changing suddenly into another strain, presto, from harmless to deadly virulent.
every human, every animal, every plant, every fungus—are chimerical things, assembled with captured bacteria inside nonbacterial receptacles. Those particular bacteria, over vast stretches of time, have become transmogrified into cellular organs.
science itself, however precise and objective, is a human activity. It’s a way of wondering as well as a way of knowing. It’s a process, not a body of facts or laws. Like music, like poetry, like baseball, like grandmaster chess, it’s something gloriously imperfect that people do.
At the turn of the millennium, Doolittle published an essay titled “Uprooting the Tree of Life,”
Comparing slightly different versions of essentially the same protein (such as hemoglobin, which transports oxygen through the blood of vertebrates), as found in one creature and another, could allow you to draw inferences about degrees of relatedness between them.
enterprise—
“chemical paleogenetics”—and
Scrutiny of such molecules, wrote Zuckerkandl and Pauling, can tell us three things: how much time has passed since the lineages split, what the ancestral molecules must have looked like, and what were the lines of descent. The first of those three kinds of information became known as the molecular clock, although Zuckerkandl and Pauling hadn’t yet named it. The third kind implied trees.
RNA. This was back in the days before
Every living cell, including bacteria, including the cells of our own bodies, including those of plants and of fungi and of every other cellular organism, contains many ribosomes. They function as assembly mechanisms, taking in genetic information, plus raw material in the form of amino acids, and producing those larger physical products: proteins.
the ribosome is a 3-D printer.
A single mammalian cell might contain as many as ten million ribosomes;
Each ribosome might crank out protein at the rate of two hundred amino acids per minute,
RNA can serve as a building block as well as a message. Ribosomes, for instance, are composed of structural RNA molecules and proteins,
The fundamental goal was to sequence variants of a molecule from the deepest core of all cellular life, compare those variants, and deduce the history of evolutionary relationships since the beginning.
This 16S molecule and its 18S variant, therefore, could serve as the reference standard, the great clue, for deducing divergence and relatedness among all cellular organisms. It was, arguably, the single most reliable piece of evidence, molecular or otherwise, for drawing a tree of life. And that recognition, though it never made the front page of the New York Times, was Carl Woese’s single greatest contribution to biology in the twentieth and twenty-first centuries.
The chief distinguishing features of a prokaryote, according to Stanier and van Niel, were: (1) no cell nucleus, (2) cell division by simple fission, rather than the elaborate process of chromosome pairing known as mitosis, and (3) a cell wall strengthened by a certain sort of latticework molecule with a fancy name, peptidoglycan.
We are, at the most basic level of classification, eukaryotes. So are amoebae. So are yeasts.
think of the living world—as divided into proks and euks.
eukaryotes (which carried that slightly different molecule in their ribosomes, 18S rRNA instead of 16S),
A species called Bacillus infernus has been cultured from core samples of Triassic siltstone, buried strata at least 140 million years old, drilled up from almost two miles beneath eastern Virginia. Under the Pacific Ocean, 35,755 feet deep in the Mariana Trench, lie sediments that have also yielded living bacteria. In Antarctica, a body of water known as Subglacial Lake Whillans, lidded by half a mile’s thickness of ice and supercooled to just below zero, harbors a robust community of bacteria. They thrive there in the darkness and cold, eating sulphur and iron compounds
Yellowstone’s Norris Geyser Basin, at a temperature of about 156 degrees Fahrenheit.
Functioning in such heat, Thermus aquaticus contains a specialized enzyme for copying its DNA, one that performs well at high temperatures, which became a key element in the polymerase chain reaction technique for amplifying DNA.
Other heat-loving bacteria can be found around hydrothermal vents on the sea bottom, where they help anchor the food chains, producing their own organic material from dissolved sulfur compounds vented out with the hot water, and being fed upon by little crustaceans and other animals. A giant tube worm, one of those gaudy red creatures that waggle around such vents, with no mouth, no digestive tract, gets its nutrition from bacteria growing within its tissues.
the total mass of bacteria exceeds the total mass of all plants and animals on Earth. They have been around, in one form or another, for at least three and a half billion years, strongly affecting the biochemical conditions in which most other living creatures have evolved.
Prochlorococcus marinus, which drifts free in the world’s tropical oceans and photosynthesizes like a plant, may be the most abundant creature on Earth.
A bacterial cell, on average, is about one-tenth as big as an animal cell.
Although many bacteria live as solitary cells, taking their chances and meeting their needs independently, others aggregate into pairs, clusters, little scrums, chains, and colonies.
Bacteria can also form stubborn, complex films on certain surfaces—the rocks of a sea floor, the glass wall of an aquarium, the metal ball of your new artificial hip—where they may cooperate together in exuding a slimy extracellular substance that helps nurture them collectively, maintain the stability of their little environment, serve as a sort of communications matrix among them, and even protect them from antibiotics.
biofilms,
The little rods of Acinetobacter baumannii are infamous for their ability to lay down persistent biofilms on dry, seemingly clean surfaces in hospitals.
Cyanobacteria, including that monumentally abundant Prochlorococcus, convert light to energy and deliver, as byproduct, a large share of Earth’s free atmospheric oxygen. Purple bacteria photosynthesize too, but do it by drawing upon sulfur or hydrogen instead of water as fuel for the process, and they don’t produce oxygen. Lithotrophic bacteria, the rock eaters, deriving their energy from iron, sulfur, and other inorganic compounds, exist in more ingenious variants than you care to know. Japanese researchers have recently discovered a new bacterium, Ideonella sakaiensis, that digests plastic.
From the premise that 16S rRNA represented a very slow-ticking molecular clock, with a minimum of selected variation, he deduced that his newly found kingdom must represent a very old division.
Scientists studying the evolution of primitive organisms reported today the existence of a separate form of life that is hard to find in nature. They described it as a “third kingdom” of living material, composed of ancestral cells that abhor oxygen, digest carbon dioxide and produce methane.
the cell walls of at least one methanogen were starkly anomalous. They contained no peptidoglycan. Remember that stuff, peptidoglycan—the latticework molecule, a strengthener of cell walls, that Stanier and van Niel had cited as one of the defining characters of all prokaryotes? It didn’t exist, zero, in the cell walls of a certain methanogen
two other kinds of extremity-loving bugs, known by their genus names as Thermoplasma and Sulfolobus, also had weird lipids of the same sort. Those two groups preferred environments that were very hot and very acidic, such as hot springs in areas of volcanic activity. In the technical lingo, they were thermophilic and acidophilic.
How did they arise? How did they diverge from one another? How were each of the three related to the two others? Which came first? Why did just one of the three lineages lead onward to all visible, multicellular organisms—all animals, all plants, all fungi, ourselves—while the other two remained unicellular and microscopic, though still vastly abundant, diverse, and consequential? And what kind of creature, or process, or circumstance preceded them all? Where was the tree of life rooted?
Meiosis in an animal yields four new cells, not two, after two divisions, not one, each resulting cell reduced to a half share of chromosomes. Later,
Chloroplasts are little particles—green, brown, or red—found in plant cells and some algae, that absorb solar energy and package it as sugars. They photosynthesize, like cyanobacteria. Centrioles are crucial too,
chloroplasts, the tiny cell organelles found in plant cells and some algae, enabling them to harvest solar energy by photosynthesis. What are these chloroplast things, Ris and Plaut wondered, and what’s their origin? The two men looked closely at the chloroplasts of a certain green alga. With biochemical staining, they found evidence of DNA. They could see it with their electron microscope.
Cytoplasmic inheritance (also called maternal inheritance) was a very different proposition. If it existed, it wouldn’t be so neatly Mendelian. It wouldn’t be so binary. If genes were afloat in cytoplasm, that would tilt inherited genetic identity toward the female parent, in any sexual reproduction, because eggs carry a lot of cytoplasm, and sperm or pollen carry little.
They survived and proliferated (by Darwinian selection) because they served a function: allowing the algae to derive energy from sunlight.
chloroplasts were simply innate “organs” of each cell, which had “gradually differentiated” out of the otherwise colorless cytoplasm. That was the endogenous theory: chloroplasts had taken shape on the inside of plant cells, formed from internal materials. Not so, he argued. Rather than being homegrown organs, they are “foreign bodies, foreign organisms” that invaded the cytoplasm of animal cells sometime in the distant past and entered into a symbiotic coexistence. According to this theory, a plant cell is nothing but an animal cell with photosynthetic bacteria added.
Wallin offered a version of endosymbiosis that differed from, but complemented, Merezhkowsky’s. He argued that mitochondria in all complex organisms, not just chloroplasts in plants and algae, are descended from captured bacteria.
Symbionticism, Wallin declared, was “the fundamental principle controlling the origin of species.” Darwin’s 1859 idea, natural selection, was secondary, determining only the retention or destruction of species once they have arisen. And there was a third force, an “unknown principle,” accounting for evolutionary progress toward better and more complex forms.
The idea of mitochondria as captured bacteria traced to Wallin, and she knew it. Chloroplasts as captured bacteria traced to Merezhkowsky, and she knew it. In this 1967 paper, she added something more: another aspect of eukaryotic cells, possibly also originating from endosymbiosis. Her addition comprised three features she saw as related: the flagella of tiny swimming eukaryotes such as Euglena gracilis (on which she had done her dissertation); the cilia, little hairs that project from virtually every eukaryotic cell, including the cells of your body; and the centrioles,
Margulis’s innovative idea was that these three other crucial mechanisms in eukaryotic cells—the flagella, the cilia, and the centrioles—are also descended from captured bacteria. Maybe something wiggly and mobile, she suggested, like a spirochete.
She hypothesized that an ancient amoeboid creature, an early eukaryote, had acquired the wiggly thing by eating it. Or perhaps the wiggly thing had attached itself to the outside of the eukaryotic cell. Instead of being digested (if it was inside) or causing harm as an internal parasite, or being sloughed off (if it was externally attached), in at least one fateful case, it had become domesticated. It stuck, it stayed, it assimilated. Some of its genes, including those that coded for a particular structural feature Margulis noticed, were incorporated somehow into the coding genome of the host.
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flagella, cilia, and centrioles all shared that arrangement of nine tiny tubules, distinct in cross section and ordered radially like numbers on a clock. She deduced that eukaryotic cells had inherited that feature, commonly, after acquiring some ancestral spirochete as a symbiont, which then became cilia, flagella, and centrioles.
