There have been exogenous extinctions, ie not from an ecosystem's "internal contradictions." Examples are massive magma flows like the Central Atlantic Magmatic Province at the Triassic-Jurassic boundary, or the asteroid strike like the K/T Boundary. These were at least partly caused by out-of-context events that life on Earth did not influence. Then there are endogenous extinctions, which were caused entirely by the actions of the system itself, with no external disturbance. The best example is the Great Oxygenation Event, where the cyanobacteria inadvertently poisoned themselves, and paved the way for a whole new kind of metabolism. About every 26 million years, a superpredator develops and kills everything – humans are filling this role currently – and even if there's not an extinction, there's a local minimum in biodiversity and ecological robustness.
Since we're the aerobic beneficiaries of the Great Oxygenation, we like to narrativize this in the form of a teleologic happy ending. That is: the story becomes, yes the cyanobacteria poisoned themselves, but it was to make way for the glory of oxygen-breathing life. That oxygen they fatally polluted themselves with turned out to be an improvement, a new fitness landscape. Any endogenous extinction clears the way for evolutionary progress!
This is false. Of course the Great Oxygenation Event turned out to be survivable, because we're here looking back on it. But choose any other model example of a closed ecosystem where the endogenous activity of the local organisms is rapidly changing their environment, and you are unlikely to find that the majority of them are success stories. Things poison themselves, and end up with no descendants that can survive. (There is no argument to exclude humans from this phenomenon. Both deforesting Easter Island and the ongoing Great Carbonization Event are good examples.)
Two implications follow:
1. The reason for the Great Silence (ie the Fermi paradox) could be that there are many watery worlds out there which evolve local cyanobacteria, but they have their own endogenous shocks, and these do not result in a survivable planet, or at least in a richer potential fitness landscape. As in Conway's Game of Life, if they're lucky they either settle into a simple oscillating system (bloom, mass extinction, bloom, same kind of mass extinction, ad infinitum) or the ecosystem collapses completely and ends.
Speculation regarding this: we're fairly confident the first metabolism on Earth was sea vent iron sulfur organisms, using sulfur in what is now oxygen's chemical role. The Great Oxygenation may have only happened when it did, a full 1.5 billion years after the first life and at least 800 million years after photosynthesis appeared, because an asteroid delivered molybdenum, allowing nitrogen fixation and more efficient anaerobic metabolism. Whatever the reason, had this happened prior to photosynthesis, we may have ended up with an Earth poisoned with sulfur or at least with a massive amount of oxidized sulfur.
In an interesting parallel observation: we're also confident that Venus was once a wetter, cooler world that had a runaway greenhouse effect. One of the mysteries of Venus is the origin of all the sulfur in its thick atmosphere; to a first approximation all sulfur on Earth's surface is assumed to be from volcanoes, but why so much more on Venus? Another mystery is the identity of the small UV absorbers (about the size of bacteria) that form the dark bands in its atmosphere; one idea is that they're cells descended from ancestors that evolved at the surface and now can only survive in the more benign lower temperatures and pressures of the high clouds. If indeed these are the survivors of a Great Sulfuration Event, while the event did not result in total extinction, it limited the Venusian ecosystem to oscillate on a barren fitness landscape, just from the bad luck of having richer crust contents or earlier impacts with potential-enzyme-cofactor-bearing asteroids that allowed more efficient iron-sulfur metabolism.
(Recent evidence however suggests a massive volcanic event 700 MA ago that resurfaced the planet after massive flows; this which may be enough to explain all the sulfur. A gradual boil off of water remains quite likely, for two reasons – the D/H ratio on Venus is about 150 times higher than Earth, where comets have at most a 3 times higher ratio than Earth, suggesting loss to space of hydrogen from water and preferential retention of the heavier nucleus; and that such a massive volcanic event could have been caused by the loss of water, and the cessation of plate tectonics which allow a cataclysmic buildup of heat. It's interesting that the Siberian trap flows and CAMP happened during a period on Earth when the continents were crammed together and perhaps less efficient at letting out volcanic heat, though these events were still nowhere near what happened on Venus.)
2. If a technological Singularity occurs, it would be an endogenous extinction. In this case we are the cyanobacteria, and our extrasomatic adaptations are the contradiction internal to the system, and the AIs are our oxygen-breathing descendants. Like them, we produced the conditions that destroyed us and paved the way for the next phase of life. It's true that cyanobacteria and anaerobic organisms persist but do not dominate the world as they did in the Archaean. Even if cellular life survives the Singularity, being relegated to the role of cyanobacteria is unappealing for most.
But then there is another possibility, in which the AIs drive themselves extinct too. Think of this as the super-pessimistic case. Singularity optimists think we can benefit from or at least co-exist with superintelligence (becoming the equivalent of cyanobacteria is actually optimistic in this scheme.) Singularity pessimists think the event will kill all biology. Here, I suggest the super-pessimist position, which is that the Singularity may kill us, then also itself, in the final, most spectacular ecocide of Earth's history. Why? One theory is that any self-improving superintelligences will necessarily disassemble matter, including whole planets, into atoms that can be used for computation. But there is no principle stating that intelligence must always exceed power; that is, that impact of behavior must grow more slowly than ability to predict impact of behavior. Certainly it didn't happen with cyanobacteria, and given the sluggishness of our response to global warming it might not be happening with humans. Even if the AIs are in fact superintelligences, they are still not omniscient. As they're disassembling everything, they may get to the end of a predictive computation and realize that part of the code has gone cancerous and is replicating out of control (and consuming matter in the process) and can't be called back, or they're going to run out of power before they get to the next planet or star system, or overheat, or whatever problem an AI might run into.
Therefore, if the Singularity does happen, it would be just one type of endogenous extinction. If in a hundred million years, aliens or their self-replicating probes visit the solar system (if such things ever occur in the history of the universe) they might find its dusty, partly-disassembled remains, and file the data under "ecosystems that ended with behavioral/artifactual singularities" and then move on. Interestingly, we have already found old planetary systems that are far dustier than we would expect, with no explanation for the inner dust ring and a some constant replenishment process. Even this assumes that the self-replicating alien probes can get there before becoming cancerous dead-ends themselves.
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