Charles Darwin - the Evolutionary Tree of Life: three major approaches to the Tree of Life concept in his theory In On the origin of species, Charles Darwin ( –) evoked an Darwin's tree, in effect, was a family tree of all life, in which the buds were individuals and WRIGHT, G. H. von, The tree of knowledge and other essays. Leiden.
Although bacteria are still around, still vastly successful, dominating many parts of the planet, they were thought in to be the closest living approximations of early life-forms. Oh, just a billion years farther back? Woese was always an ambitious thinker. And from such deductions, such ancestral forms, Woese hoped to glean some understanding of how creatures evolved in the very deep past. He was talking about molecular phylogenetics, without yet using that phrase, and he hoped by this technique to look back at least three billion years.
But which molecules would be the most telling? Woese had in mind a tiny molecular mechanism, common to all forms of cellular life, called the ribosome. Nearly every cell contains ribosomes in abundance, like flakes of pepper in a stew, and they stay busy with the task of translating genetic information into proteins. Hemoglobin, for instance. That crucial protein transports oxygen through the blood of vertebrate animals. Architectural instructions for building hemoglobin molecules are encoded in the DNA of the animal, but where is hemoglobin actually produced?
In the ribosomes. They are the core elements of what Woese called the translation apparatus. In plain words: Ribosomes turn genes into living bodies. These particles had only recently been discovered, and at first no one knew what they did. Then they became recognized as the sites where proteins are built, but a big question remained: How? Some researchers suspected that ribosomes might actually contain the recipes for proteins, extruding them as an almost autonomous process. Matt Ridley has described the moment in his biography of Crick:.
Crick began talking back just as fast. Everybody else in the room watched in amazement. Brenner had seen the answer, and Crick had seen him see it. The ribosome did not contain the recipe for the protein; it was a tape reader. This was back in the days before digital recording, remember, when sound was recorded on magnetic tape. Ribosomes are among the smallest of structures within a cell, but what they lack in size they make up for in abundance and consequence.
A single mammalian cell might contain as many as 10 million ribosomes; a single cell of the bacterium Escherichia coli, or E.
Each ribosome might crank out protein at the rate of about 20 amino acids the constituent units of all proteins per second, altogether producing a sizzle of constructive activity within the cell. Few people, in , saw the implications of that ancient, universal role of ribosomes more keenly than Carl Woese. What he saw was that these little flecks — or some molecule within them — might contain evidence about how life worked, and how it diversified, at the very beginning.
Scientific elegance lay in generating the minimum of data needed to answer a question. His approach would be more of a slog. He would need a large laboratory, set up for reading at least portions of the ribosomal RNA. That itself was a stretch, at the time. The sequencing of very long molecules — DNA, RNA or proteins — is so easily done nowadays, so elegantly automated, that we can scarcely appreciate the challenge Woese faced. He could expect only glimpses, short excerpts, read from fragments of ribosomal RNA molecules, and even that much could be achieved only laboriously, at great cost in time and effort.
He planned to sequence what he could, from one creature and another, and then make comparisons, working backward to an inferred view of life in its earliest forms and dynamics. Ribosomal RNA would be his rabbit hole to the beginning of evolution.
The mechanics were intricate, laborious and a little spooky. They involved explosive liquids, high voltages, radioactive phosphorus, at least one form of pathogenic bacteria and a loosely improvised set of safety procedures. Courageous young grad students, postdocs and technical assistants, under a driven leader, were pushing their science toward points where no one had gone before. OSHA, though recently founded, was none the wiser. Woese had already settled on that one universal element of cellular anatomy, the ribosome, as the locus of his internal fossil record.
But there remained a crucial decision: Which ribosomal molecule should he study?
He settled on a longish molecule that serves as a structural component in one of the two ribosomal subunits. Its shorthand label is 16S rRNA.
Woese noticed something about Sogin during their early interactions: The kid was not just smart but also handy around equipment. Some combination of talents — dexterity, mechanical aptitude, precision, patience, a bit of the plumber, a bit of the electrician — made him good not just at experimental work but at creating the tools for such work. Another professor had ordered and paid for a collection of apparatus to be used for RNA sequencing, then accepted a position at Columbia University, leaving behind the hardware.
No one who knew how to use the equipment, that is, until Sogin joined his lab. Woese himself was not an experimentalist. He was a theorist, a thinker, like Francis Crick. None of it — unless you count the light boxes for reading film images of RNA fragments, the shorter pieces of the molecule once Sogin had used enzymes to cut them into workable bits. Sogin himself built these fluorescent light boxes, on which the images of the fragments, cast by radioactive phosphorus onto large X-ray films, could be examined.
He converted an entire wall of bookshelves, using translucent plastic sheeting and fluorescent tubes, into a single big vertical light box, like a bulletin board. They called that one the light board. Viewed over a box or taped up on the light board, every new film would show a pattern of dark ovals, like a herd of giant amoebas racing across a bright plain. This was the fingerprint of an RNA molecule. Recollections from his lab members at the time, as well as a few old photographs, portray Woese gazing intently at those fingerprints, hour upon hour.
The shortest useful fragments were at least four letters long, and no more than about Each film, each fingerprint, represented ribosomal RNA from a different creature. The work was deceptively perilous. Sogin described to me the deliveries of radioactive phosphorus an isotope designated as P 32 , with a half-life of 14 days , which amounted to a sizable quantity arriving every other Monday.
What a stunning example of a biology that operates from an engineering perspective, a biology that has no genuine guiding vision! All the dinosaurs disappeared, except for one branch whose scales had become modified into feathers. It was their way of thinking about and investigating the structure of a complex molecule that is found in the genes of all animals, DNA. By Eileen Markey. Animals more suited to their environment survive longer and have more young.
Sogin would draw out a measured amount of the liquid and add it to whatever bacterial culture he intended to process next. By , the Woese lab had become one of the foremost users of such RNA-sequencing technology in the world.
While the grad students and technicians produced fingerprints, Woese spent his time staring at the spots. Was this effort tedious in practice as well as profound in its potential results? Failing initially to persuade Woese of his aptitude for that, Fox was banished back to the lab, set to the tasks of growing radioactive cells and extracting their ribosomal RNA. But he continued, in flashes, to show his value to Woese as a thinker.
That offended some scientists. Another factor was that Woese lacked facility as an explainer.
He had never developed the skills to give a good lecture. Rockets took off, and they wrote the most unscientific nonsense you can imagine. Wolfe himself heard from colleagues immediately. Among his phone calls on the morning of Nov. He never called back. But the broader damage was done.
The scientific community just totally rejected the thing.
As a result, this whole concept was set back by at least a decade or 15 years. In Woese received a MacArthur Fellowship for his efforts in phylogenetic analysis and his discovery of the archaea, and in he was elected to the National Academy of Sciences. Despite the MacArthur honor, and because the Academy had elected him relatively late at 59 , he still thought of himself as a neglected outsider. That gave him some latitude to continue being ambitious, bold and ornery.
Jean-Baptiste Lamarck — produced the first branching tree of animals in his Philosophie Zoologique However, Lamarck did not believe in common descent of all life. Instead, he believed that life consists of separate parallel lines advancing from simple to complex. The American geologist Edward Hitchcock — published in the first tree of life based on paleontology in his Elementary Geology.