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Biologists today are seldom well-versed in the history of science. If they know anything about Leeuwenhoek, it's "animalcules", usually spoken with a little grin. So quaint!
The word animalcules is a diminutive of animal. Its first use in English is 1599 and it wasn't used much after the mid-1880's. It referred to small animals, from insects to mice, but usually invertebrates. As the Google Ngram below shows, it was replaced by microbes around the time of Pasteur and Koch.
It is not a Dutch word, and its use in English gives an erroneous impression of Leeuwenhoek. He was a clear-eyed observer of things that had no name because no one had ever seen them before. Rather than try to give them some fancy name, he described them in simple, obvious terms that his readers could understand.
Most often, Leeuwenhoek used dierken; frequently, he used diertgens or diertjes. Dier is animal and the -ken, -gen, or -je endings are the most common form of diminutive in Dutch, then and now. Leeuwenhoek sometimes put kleine (small) or zere kleine (exceedingly small) in front of the noun.
Oldenburg translated the early letters, and he was the one who first translated dierkens as "animalcules". On the graph above, that's the small blue blip around 1670. Leeuwenhoek wasn't fluent in English, but he got all the numbers of Philosophical Transactions, so he knew what Oldenburg was doing. Yet he continued to use dierkens. A better translation is "little animals". That's what Clifford Dobell, the British microbiologist, used in the title of his biography and that's what I use on this web.
The largest spike on the graph occurred well after Leeuwenhoek's death.
Why did Leeuwenhoek call them "little animals"?
Before Leeuwenhoek, this microscopic world was unknown and unsuspected. I make the comparison to Leeuwenhoek as Adam in a microscopic Eden where none of the animals had names. Remember that Linnaeus was a teenager when Leeuwenhoek died, so he had no way of classifying, no nomenclature, no typology. Neither did anyone else.
There is, however, no question that Leeuwenhoek was the first to see what we now call protozoa, bacteria, red blood cells, etc. Why? He had a microscope that was an order of magnitude more powerful than anyone else had at the time.
Dobell identified the genus and species of many of Leeuwenhoek's observations based solely on his descriptions. Other microbiologists now quibble, but most accept Dobell as correct about almost all of them.
The difference is that Oldenburg was first and foremost a promoter, trying to make things seem more important and more what we would now call "scientific". Leeuwenhoek had his pretentious moments, but he was a committed empiricist. All he knew for sure was what he saw. They moved on their own, thus they were alive. They weren't plants, thus they were animals. They were unbelievably small. Thus: diertgens, little animals.