Artificial Intelligence Discovers Surprising Patterns in Earth’s Biological Mass Extinctions

Visualize Life's History

A new study applies machine learning to the fossil record to visualize life’s history, showing the impacts of major evolutionary events. This shows the long-term evolutionary and ecological impacts of major events of extinction and speciation. Colors represent the geological periods from the Tonian, starting 1 billion years ago, in yellow, to the current Quaternary Period, shown in green. The red to blue color transition marks the end-Permian mass extinction, one of the most disruptive events in the fossil record. Credit: J. Hoyal Cuthill and N. Guttenberg

The idea that mass extinctions allow many new types of species to evolve is a central concept in evolution, but a new study using artificial intelligence to examine the fossil record finds this is rarely true, and there must be another explanation.

Charles Darwin’s landmark opus, On the Origin of the Species, ends with a beautiful summary of his theory of evolution, “There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.”

In fact, scientists now know that most species that have ever existed are extinct. This extinction of species has on the whole been roughly balanced by the origination of new ones over Earth’s history, with a few major temporary imbalances scientists call mass extinction events. Scientists have long believed that mass extinctions create productive periods of species evolution, or “radiations,” a model called “creative destruction.” A new study led by scientists affiliated with the Earth-Life Science Institute (ELSI) at Tokyo Institute of Technology used machine learning to examine the co-occurrence of fossil species and found that radiations and extinctions are rarely connected, and thus mass extinctions likely rarely cause radiations of a comparable scale.

Creative destruction is central to classic concepts of evolution. It seems clear that there are periods in which suddenly many species suddenly disappear, and many new species suddenly appear. However, radiations of a comparable scale to the mass extinctions, which this study, therefore, calls the mass radiations, have received far less analysis than extinction events.

This study compared the impacts of both extinction and radiation across the period for which fossils are available, the so-called Phanerozoic Eon. The Phanerozoic (from the Greek meaning “apparent life”), represents the most recent ~ 550-million-year period of Earth’s total ~4.5 billion-year history, and is significant to paleontologists: before this period most of the organisms that existed were microbes that didn’t easily form fossils, so the prior evolutionary record is hard to observe.

The new study suggests creative destruction isn’t a good description of how species originated or went extinct during the Phanerozoic, and suggests that many of the most remarkable times of evolutionary radiation occurred when life entered new evolutionary and ecological arenas, such as during the Cambrian explosion of animal diversity and the Carboniferous expansion of forest biomes. Whether this is true for the previous ~ 3 billion years dominated by microbes is not known, as the scarcity of recorded information on such ancient diversity did not allow a similar analysis.

Paleontologists have identified a handful of the most severe, mass extinction events in the Phanerozoic fossil record. These principally include the big five mass extinctions, such as the end-Permian mass extinction in which more than 70% of species are estimated to have gone extinct. Biologists have now suggested that we may now be entering a “Sixth Mass Extinction,” which they think is mainly caused by human activity including hunting and land-use changes caused by the expansion of agriculture. A commonly noted example of the previous “Big Five” mass extinctions is the Cretaceous-Tertiary one (usually abbreviated as “K-T,” using the German spelling of Cretaceous) which appears to have been caused when a meteor hit Earth ~65 million years ago, wiping out the non-avian dinosaurs.

Observing the fossil record, scientists came to believe that mass extinction events create especially productive radiations. For example, in the K-T dinosaur-exterminating event, it has conventionally been supposed that a wasteland was created, which allowed organisms like mammals to recolonize and “radiate,” allowing for the evolution of all manner of new mammal species, ultimately laying the foundation for the emergence of humans. In other words, if the K-T event of “creative destruction” had not occurred, perhaps we would not be here to discuss this question.

The new study started with a casual discussion in ELSI’s “Agora,” a large common room where ELSI scientists and visitors often eat lunch and strike up new conversations. Two of the paper’s authors, evolutionary biologist Jennifer Hoyal Cuthill (now a research fellow at Essex University in the UK) and physicist/machine learning expert Nicholas Guttenberg (now a research scientist at Cross Labs working in collaboration with GoodAI in the Czech Republic), who were both post-doctoral scholars at ELSI when the work began, were kicking around the question of whether machine learning could be used to visualize and understand the fossil record.

During a visit to ELSI, just before the COVID-19 pandemic began to restrict international travel, they worked feverishly to extend their analysis to examine the correlation between extinction and radiation events. These discussions allowed them to relate their new data to the breadth of existing ideas on mass extinctions and radiations. They quickly found that the evolutionary patterns identified with the help of machine learning differed in key ways from traditional interpretations.

The team used a novel application of machine learning to examine the temporal co-occurrence of species in the Phanerozoic fossil record, examining over a million entries in a massive curated, public database including almost two hundred thousand species.

Lead author Dr. Hoyal Cuthill said, “Some of the most challenging aspects of understanding the history of life are the enormous timescales and numbers of species involved. New applications of machine learning can help by allowing us to visualize this information in a human-readable form. This means we can, so to speak, hold half a billion years of evolution in the palms of our hands, and gain new insights from what we see.”

Using their objective methods, they found that the “big five” mass extinction events previously identified by paleontologists were picked up by the machine learning methods as being among the top 5% of significant disruptions in which extinction outpaced radiation or vice versa, as were seven additional mass extinctions, two combined mass extinction-radiation events and fifteen mass radiations. Surprisingly, in contrast to previous narratives emphasizing the importance of post-extinction radiations, this work found that the most comparable mass radiations and extinctions were only rarely coupled in time, refuting the idea of a causal relationship between them.

Co-author Dr. Nicholas Guttenberg said, “the ecosystem is dynamic, you don’t necessarily have to chip an existing piece off to allow something new to appear.”

The team further found that radiations may in fact cause major changes to existing ecosystems, an idea the authors call “destructive creation.” They found that, during the Phanerozoic Eon, on average, the species that made up an ecosystem at any one time are almost all gone by 19 million years later. But when mass extinctions or radiations occur, this rate of turnover is much higher.

This gives a new perspective on how the modern “Sixth Extinction” is occurring. The Quaternary period, which began 2.5 million years ago, had witnessed repeated climate upheavals, including dramatic alternations of glaciation, times when high latitude locations on Earth, were ice-covered. This means that the present “Sixth Extinction” is eroding biodiversity that was already disrupted, and the authors suggest it will take at least 8 million years for it to revert to the long term average of 19 million years. Dr. Hoyal Cuthill comments that “each extinction that happens on our watch erases a species, which may have existed for millions of years up to now, making it harder for the normal process of ‘new species origination’ to replace what is being lost.”

Reference: “Impacts of speciation and extinction measured by an evolutionary decay clock” by Jennifer F. Hoyal Cuthill, Nicholas Guttenberg and Graham E. Budd, 9 December 2020, Nature.
DOI: 10.1038/s41586-020-3003-4


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  • Why don't you have a printer-friendly option for your articles? I like to print out and keep important articles for future reference.

    • There are 2 ways you can print a web page: 1. You either select those three dots in your browser (in the corner usually) and choose the "print" option, or if you are browsing on PC or any device with keyboard, I am pretty sure there is a fricking shortcut for it.

    • Right click on page. Chose "PDF" as your printer. This saves this page as a PDF file in the folder of your choice. Save paper, save trees.

    • You don't need to print them you can just save the article as pdf to your computer. Please don't be the typical elderly person who wastes a bunch of paper printing things they never need only for other people to have to come and throw away later.

      • Please don't be the typical insensitive Millennial or other youthful offender that does not consider access to personal vs group computers in group living settings. Furthermore, there is also the issue of comfort - reading a larger print document in a more comfortable seating environment, something my years of hard work helping my partner to raise our family has certainly entitled us to... So the next time you decide to disrespect your elders, remember that basic rule I'm fairly sure your parents taught you!

          • "Karen"?! But the question is why Corbin makes it personal and why John D takes it personal.

            Saving resources is a good idea, but I can't remember if the web actually saves or waste. Life cycle analyses are hard to come by.

            That said, electronic media is statistically better (improved understanding and retention).

      • It's cute how you think only the elderly print articles. I would like to introduce you to some young thugs killing forests of trees.

      • I save them, who in the world wants all that paper hanging around in your house. I have library's of info hanging around in my back pocket.

  • Terribly-written article. The important material is near the end. The first third is all stuff that should be at the bottom. Why can't people write anymore?

    • Why can't 'journalists' use proper grammar? "Extinct" is a state of being, not an activity. That is to say, it is proper to say someone "went skiing." However, it is not proper to say something "went extinct." They should write "became extinct" or "is extinct," or "experienced extinction."

      • You're probably the least liked person here. No one cares about these minor differences in grammar. Species are going extinct and you care more about supposed grammar issues.

      • I don't think anyone should expect journalists hired at a university press office, they are office workers.

        On the general question, a press release is intended to inform scientists primarily, but they try to make it understandable to a wider audience. It is often the scientists that makes the raw drafts. In this case the good stuff starts at "This study compared ..." after the initial context making.

        But yes, you could likely change the order of that. Then other people would complain about the illogical order et cetera.

      • Improper use of commas in the last sentence, and double "or"s. "That is to say" should be followed up with a ";". You're a simple fool who can't keep to your own standards in a 3 sentence reply to that of which you expect from an entire article. I would sarcastically insinuate you must be fun at parties, but you would have to be invited to one first.

      • Yes, people designed and built the computers. Yet, the idea of the much more complex universe and life popping up out of nowhere makes sense to you. Life cannot come from no life. That's real scientifically proven fact.

  • I really liked that you specifically mentioned the cause of the on going sixth mass extinction is hunters and farmers. The country folk are ruining the planet. What a novel concept.

    • Hunters are the first to understand the rate of population growth or lackof it. How much time do you spend in the wilderness?

    • C'mon now. Stop it. If you can't figure out he's talking about whales, elephants, sharks, etc. ocean bottom scrapping mass fishing.
      The clearing of equatorial forest for agricultural palm trees and grazing land are direct reason for the disappearance of 100s of species per year.
      You are being ridiculous.

    • Why aren't you blaming lions (meat eaters) and elephants (vegetarians), who never bother to regrow what they've eaten?

    • ? They complicated that idea of yours.

      "Biologists have now suggested that we may now be entering a “Sixth Mass Extinction,” which they think is mainly caused by human activity including hunting and land-use changes caused by the expansion of agriculture. "

      "This gives a new perspective on how the modern “Sixth Extinction” is occurring. The Quaternary period, which began 2.5 million years ago, had witnessed repeated climate upheavals, including dramatic alternations of glaciation, times when high latitude locations on Earth, were ice-covered. This means that the present “Sixth Extinction” is eroding biodiversity that was already disrupted, ..."

      It is but recently that observations implied there is a current (much) increased extinction rate, or that some of the extinctions since the last glaciation has been man forced (taking place on islands after people came there, say).

  • Darwin's famous opus is called "On the Origin of Species" not "the Species." It tells you that the author of this article is unfamiliar with that book.

    • They are both common short hands. The complete title is "On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life".

  • The meteor did not kill the dinosaurs they were dead before it hit. Dr Baker stated they find the iridium level and dig down below it to find the type of dinosaur they are looking for from 6 in to 8 ft below the iridium level left by the meteor.

    • The consensus is that the impactor did the deed ["Cretaceous–Paleogene extinction event" @ Wikipedia].

      If you mean Robert Bakker, he makes a lot of claims ["Robert T. Bakker" @ Wikipedia]. The criticism is old ["DINOSAUR EXPERTS RESIST METEOR EXTINCTION IDEA", NYT, 1985]. A sediment sequence that shows what you request is believed to have been found last year ["The Day the Dinosaurs Died", NYT, 2019].

  • Do we need AI for this? Between early Earth's soup and micro-organisms are 4 billion years. Then add another billion for evolution of high forms. Wipe high forms out again. Now the empty space in biotopes and food hierarchies can be filled by the same principles or diversification. The latter is not fast, too. Takes a long time of isolation for new race to become a species that cannot interbreed with former relatives anymore. The data and AI seem to confirm this. That may be scientifically important but the qualitative reasoning should have been part of the biology class since just after Darwin.

    • Yes, besides that AI is helpful to see what we cannot, the paper showed that it happened here. A counter-intutitive result is that the – decidedly asynchronous – mass radiation and mass extinction events are both upsetting the constant process rate. That is new.

      And you can't really handle 1+ million events with paper and pen...

  • Have you or your kids ate today? Have you ever thanked a farmer for the food. Maybe you should before you go extinct. Post the comment or your mag ain't worth the read. # farmer

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