For all their unpleasantness, the archezoa nonetheless fitted the bill as primitive eukaryotes, survivors from the earliest days before the acquisition of mitochondria. Genetic analysis confirmed that they did branch away from more modern eukaryotes at an early stage of evolution, some two thousand million years ago, while their uncluttered morphology was compatible with a simple early lifestyle as scavengers that engulfed their food whole by phagocytosis. Presumably, one fine morning, two thousand million years ago, a cousin of these simple cells engulfed a bacterium, and for some reason failed to digest it. The bacterium lived on and divided inside the archezoon. Whatever the original benefit might have been to either party the intimate association was eventually so successful that the chimeric cell gave rise to all modern eukary-otes with mitochondria—all the familiar plants, animals, and fungi.
According to this reconstruction, the original benefit of the merger was probably related to oxygen. Presumably it was not a coincidence that the merger took place at a time when oxygen levels were rising in the air and the oceans. A great surge in atmospheric oxygen levels certainly occurred around two billion years ago, probably in the wake of a global glaciation, or 'snowball earth'. This timing corresponds closely to that of the eukaryotic merger. Modern mitochondria make use of oxygen to burn sugars and fats in cell respiration, so it is not surprising that mitochondria should have become established at a time when oxygen levels were rising. As a form of energy-generation, oxygen respiration is much more efficient than other forms of respiration, which generate energy in the absence of oxygen (anaerobic respiration). All that said, it is unlikely that superior energy generation could have been the original advantage. There is no reason why a bacterium living inside another cell should pass on its energy to the host. Modern bacteria keep all their energy for themselves, and the last thing they do is export it benevolently to their neighbouring cells. Thus while there is a clear advantage for the ancestors of the mitochondria, which had intimate access to any of the host's nutrients, there is no apparent advantage to the host cell itself.
Perhaps the initial relationship was actually parasitic—a possibility first suggested by Lynn Margulis. Important work from Siv Andersson's laboratory at the University of Uppsala in Sweden, published in Nature in 1998, showed that the genes of the parasitic bacterium Rickettsia prowazekii, the cause of typhus, correspond closely with those of human mitochondria, raising the possibility that the original bacterium might have been a parasite not unlike Rickettsia. Even if the original invading bacterium was a parasite, the unbalanced 'partnership' may have survived, as long as its unwelcome guest did not fatally weaken the host cell. Many infections today become less virulent over time, as parasites also benefit from keeping their host alive—they do not have to search for a new home every time their host dies. Diseases like syphilis have become much less virulent over the centuries, and there are hints that a similar attenuation is already underway with AIDS. Interestingly, such attenuation over generations also takes place in amoebae such as proteus. In this case, the infecting bacteria initially often kill the host amoebae, but eventually become necessary for their survival. The nuclei of infected amoebae become incompatible with the original amoebae, and ultimately lethal to them, effectively forcing the origin of a new species.
In the case of the eukaryotic cell, the host is good at 'eating' and through its predatory lifestyle provides its guest with a continuous supply of food. We are told that there is no such thing as a free lunch, but the parasite might simply burn up the metabolic waste-products of the host without weakening it much at all, which is not far short of a free lunch. Over time the host learned to tap into the energy-generating capacity of its guest, by inserting membrane channels, or 'taps'. The relationship reversed. The guest had been the parasite of the host, but now it became the slave, its energy drained off to serve the host.
This scenario is only one of several possibilities, and perhaps the timing holds the key. Even if energy was not the basis of the relationship, the rise in oxygen levels might still explain the initial benefits. Oxygen is toxic to anaerobic (oxygen-hating) organisms—it 'corrodes' unprotected cells in the same way that it rusts iron nails. If the guest was an aerobic bacterium, using oxygen to generate its energy, while the host was an anaerobic cell (generating energy by fermentation), then the aerobic bacterium may have protected its host against toxic oxygen—it could have worked as an internally fitted 'catalytic converter', guzzling up oxygen from the surroundings and converting it into harmless water. Siv Andersson calls this the 'Ox-Tox' hypothesis.
Let's recapitulate the argument. A bacterium loses its cell wall but survives because it has an internal cytoskeleton, which it had made use of before to keep in shape. It now resembles a modern archaeon. With a few modifications to its cytoskeleton, the wall-less archaeon learns to eat food by phagocytosis. As it grows larger it wraps its genes in a membrane and develops a nucleus. It has now turned into an archezoon, perhaps resembling cells like Giardia. One such hungry archezoon happens to engulf a smaller aerobic bacterium but fails to digest it, let's say because the bacterium is a parasite like the modern Rickettsia, and has learned to evade the defences of its host. The two get along together in a benign parasitic relationship, but as atmospheric oxygen levels rise, the relationship begins to pay dividends to both the host and parasite: the parasite still gets its free lunch, but the host is now getting a better deal—it's protected from toxic oxygen from within by its catalytic converter. Then, finally, in an act of breathtaking ingratitude, the host plugs a 'tap' into the membrane of its guest and drains off its energy. The modern eukaryotic cell is born, and never looks back.
This long chain of reasoning is a good example of how science can piece together a plausible story and back it up with evidence at almost every point. To me there is a feeling of inevitability about the whole process: it could happen here and it could happen anywhere else in the universe—no single step is particularly improbable. There is simply a bottleneck, as postulated by Christian de Duve, in which the evolution of the eukaryotes is unlikely when there is not much oxygen around, but almost inevitable as soon as the oxygen levels rise. While everybody agrees this story is broadly speculative, it was widely believed to be plausible, and made use of most of the known facts. Nothing prepared the field for the reversal that was to follow in the late 1990s. As sometimes happens to the 'good' stories in science, virtually the entire edifice collapsed in the space of just five years. Nearly every point has now been contradicted. But perhaps the writing was on the wall. If the eukaryotes only evolved once, then a plausible story may be exactly the wrong kind of story.
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