life only enduringly survived once, and then continuously. We are confident of this because these other forms simply do not exist. At least they have not been discovered: there is a branch of speculation that proposes the rather futuristic-named shadow biosphere. This is the idea that there is a second (or more) undetected tree of life on Earth, with hallmarks different from the ones on the only tree of life we know of. But as it is, every life-form so far examined is based on cells, DNA, and Darwin. Discovery of a second tree of life here on Earth would give much-needed credence to the search for life on other planets, as it would double the number of known successful origin of life events. It would show that we are not a fluke. However, science is based on observable evidence. Therefore, the shadow biosphere, while sounding quite thrilling, is resolutely science fiction.
Pruning the Tree of Life
The next questions seem glaringly obvious. What was Luca, and where did it come from? We can reasonably assume that it had DNA as its genetic code, as all creatures after Luca do, and they are unlikely to have evolved that mechanism independently.
These ideas are largely based on what we share with other lives, whether it is the orientation of molecules, big physical characteristics such as five-digit limbs, or even simpler things such as having a head at one end and a tail at the other. Since the era of DNA began, and especially once the technology for reading genomes became much more accessible in the 1990s, studying evolution has been fortified by comparing similarities and differences in the precise letters of DNA. Because we have shared ancestry, thousands of our genes are very similar in closely, or even distantly, related species. 11
DNA acquires copying errors at a fairly steady rate, which means that we can compare DNA in any living species and figure out when they separated. We can compare genes and protein sequences from any two organisms and calculate how long they have been diverging. In this way, we can reconstruct history in exactly the same way as paleontologists do with fossil bones, by looking at similarities and differences, and assembling all those comparisons to show not just relatedness between two species, but when the schism occurred. This is called phylogenetics and has utterly confirmed Darwinâs ideas about the branching tree of life.
However, biology is littered with exceptions of varying sizes, and when it comes to the tree of life, there is one colossal exception. Using phylogenetics, many scientists now argue persuasively that for the first billion years or so, life was not so much of a branching tree but a tangled bush.
The first life-forms, for the first couple of billion years following their split from Luca, were single cells. They were evolving, but not really transforming radically. In fact, despite reproducing thousands of times faster than most animals, for the first couple of billion years, life failed to make it past the stage of microbes. These two domains of life are archaea and bacteriaâsuperficially similar things, both single-celled entities of roughly the same size. For a long time, archaea were similar enough to bacteria not to be recognized at all. But they are different enough to now be classed as very distinct from bacteria and, indeed, from everything else (and we will find that these differences are crucial in the theory of the origin of life). As a domain, they are a separate category at the highest rank of how we categorize life. The great leap forward occurred with the arrival of complex life. This branch of the tree, the third domain, is called eukaryotes, and includes everything that isnât in the first two, including you and me and yeast and snakes and algae and fungi, flowers, trees, and turnips. At some point, maybe some two billion years ago, complex life emerged when an extremely unlikely pairing occurred: an archaea swallowed a bacteria. Rather than
Pruning the Tree of Life
The next questions seem glaringly obvious. What was Luca, and where did it come from? We can reasonably assume that it had DNA as its genetic code, as all creatures after Luca do, and they are unlikely to have evolved that mechanism independently.
These ideas are largely based on what we share with other lives, whether it is the orientation of molecules, big physical characteristics such as five-digit limbs, or even simpler things such as having a head at one end and a tail at the other. Since the era of DNA began, and especially once the technology for reading genomes became much more accessible in the 1990s, studying evolution has been fortified by comparing similarities and differences in the precise letters of DNA. Because we have shared ancestry, thousands of our genes are very similar in closely, or even distantly, related species. 11
DNA acquires copying errors at a fairly steady rate, which means that we can compare DNA in any living species and figure out when they separated. We can compare genes and protein sequences from any two organisms and calculate how long they have been diverging. In this way, we can reconstruct history in exactly the same way as paleontologists do with fossil bones, by looking at similarities and differences, and assembling all those comparisons to show not just relatedness between two species, but when the schism occurred. This is called phylogenetics and has utterly confirmed Darwinâs ideas about the branching tree of life.
However, biology is littered with exceptions of varying sizes, and when it comes to the tree of life, there is one colossal exception. Using phylogenetics, many scientists now argue persuasively that for the first billion years or so, life was not so much of a branching tree but a tangled bush.
The first life-forms, for the first couple of billion years following their split from Luca, were single cells. They were evolving, but not really transforming radically. In fact, despite reproducing thousands of times faster than most animals, for the first couple of billion years, life failed to make it past the stage of microbes. These two domains of life are archaea and bacteriaâsuperficially similar things, both single-celled entities of roughly the same size. For a long time, archaea were similar enough to bacteria not to be recognized at all. But they are different enough to now be classed as very distinct from bacteria and, indeed, from everything else (and we will find that these differences are crucial in the theory of the origin of life). As a domain, they are a separate category at the highest rank of how we categorize life. The great leap forward occurred with the arrival of complex life. This branch of the tree, the third domain, is called eukaryotes, and includes everything that isnât in the first two, including you and me and yeast and snakes and algae and fungi, flowers, trees, and turnips. At some point, maybe some two billion years ago, complex life emerged when an extremely unlikely pairing occurred: an archaea swallowed a bacteria. Rather than
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