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About 90%. The reason that the number is so high is that while people were discovering things via some method that resembled the scientific method, "scientist" was not an occupation. Science was pretty much invented by Sir Isaac newton and the number of scientists has exploded and increased exponentially since this time, hence the large percentage of scientists alive today.

For a full analysis of this question, including research on the number of PhD's granted in major countries since 1900, see Eric Gastfriend's work on the Future of Life Institute's blog. He concludes that around 80-90% is probably correct.

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Q: What percentage of all scientists who have ever lived are alive today?
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