Too Short for a Blog Post, Too Long for a Tweet 183

Here are a few excerpts from a book I recently read, "The Tangled Tree: A Radical New History of Life," by David Quammen.




Darwin and Darwin’s followers owned the tree image now. It would remain the best graphic representation of life’s history, evolution through time, the origins of diversity and adaptation, until the late twentieth century. And then rather suddenly a small group of scientists would discover: oops, no, it’s wrong.

Sometime in 1957 Crick gathered his thoughts and his informed guesses on this problem—about how DNA gets translated into proteins—and in September he addressed the annual symposium of the Society for Experimental Biology, convened that year at University College London. His talk “commanded the meeting,” according to one historian, and “permanently altered the logic of biology.” The published version appeared a year later, in the society’s journal, under the simple title “On Protein Synthesis.” Another historian, Matt Ridley, in his short biography of Crick, called it “probably his most remarkable paper,” comparable to Isaac Newton’s Principia and Ludwig Wittgenstein’s Tractatus. It was a commanding presentation of insights and speculations about how proteins are built from DNA instructions. It noted the important but still-fuzzy hypothesis that RNA (ribonucleic acid), the other nucleic acid, which seemed to exist in DNA’s shadow, is somehow involved. Might RNA play a role in manufacturing proteins, possibly by helping express the order (coded by DNA) in which amino acids are linked one to another? Amid such ruminations, Crick threw off another idea, almost parenthetically: ah, by the way, these long molecules could also provide evidence for evolutionary trees. 

As published in the paper: “Biologists should realize that before long we shall have a subject which might be called ‘protein taxonomy’—the study of the amino acid sequences of the proteins of an organism and the comparison of them between species.” 

He didn’t use the words “molecular phylogenetics,” but that’s what he was getting at: deducing evolutionary histories from the evidence of long molecules. 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. Those inferences would be based on assuming that the variant hemoglobins had evolved from a common ancestral molecule and that, over time, in divergent lineages, small differences in the amino sequences would have crept in, by accident if not by selective advantage. The degree of such differences between one hemoglobin and another should correlate with the amount of time elapsed since those lineages diverged. From such data, Crick suggested, you might draw phylogenetic trees. Humans have one variant of hemoglobin, horses have another. How different? How long since we shared an ancestor with horses? It could be argued, Crick added, that protein sequences also represent the most precise observable register of the physical identity of an organism, and that “vast amounts of evolutionary information may be hidden away within them.” 

Having tossed off this fertile suggestion, Crick returned in the rest of the paper to his real subject: how proteins are manufactured in cells. That was his way. A passing thought, with the heft of a beer truck. Essentially he had said: Look, I’m not pursuing this protein taxonomy business, but somebody should.

The central theme of the Richards biography is that Anna’s death was the defining moment in Haeckel’s life, killing whatever remained of his religious faith, his sense that there existed a spiritual dimension apart from the material dimension, and turning him to Darwinian theory as a kind of substitute theology. Going beyond even Darwin (who underwent his own loss of faith, catalyzed partly by the death of his favorite daughter), Haeckel replaced God with natural selection, as the central force in what he called his “religion of monism.” What he meant by monism was a bit paradoxical and woozy: God is nature, nature is God, mind and matter are two manifestations of some single underlying reality, neither can exist without the other, and therefore (by implication) immortal souls and eternal rewards don’t exist. Haeckel called this “the purest kind of monotheism,” but Judeo-Christian theologians wouldn’t agree. For orthodox believers of Haeckel’s day, Richards writes, monistic metaphysics “could only be viewed as transparently shrouded atheism.” Whatever Haeckel’s monism was, ineffable or just dreamy, it guided his version of Darwinian theory—as he promulgated that theory (or anyway, that version) in his writings and lectures over the next fifty-five years.



Molecular biologists now understand, Jan Sapp wrote in his draft introduction to the book that never happened, that “bacteria evolve by leaps and bounds through the inheritance of acquired genes.” It sounded more Lamarckian than Darwinian, he well knew. HGT was what he had in mind. 

And this wasn’t true just of bacteria, evolving by leaps and bounds. Animals do it too, sometimes. And not just insects and bdelloid rotifers. Mammals do it too, sometimes. “The cells that make up our bodies have also not arisen gradually in the typical Darwinian manner of gene mutation and natural selection.” Some of the changes occurred by quantum leaps. Our mitochondria came aboard suddenly, deep in the past of our eukaryote or pre-eukaryote lineage, as captured bacteria. Plants acquired their chloroplasts the same way. Our genomes are mosaics. We are all symbiotic complexes, even us humans. 

“Consider too,” Sapp wrote, “that a great percentage of our own DNA is of viral origin.” The figure most commonly cited is 8 percent: roughly 8 percent of the human genome consists of the remnants of retroviruses that have invaded our lineage—invaded the DNA, not just the bodies, of our ancestors—and stayed. We are at least one-twelfth viral, at the deepest core of our identities.