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Why do we refer to people as guinea pigs when discussing the subjects of an informal experiment? Surely mice, rabbits and rats are much more common experimental subjects. Indeed, it's rare that you'll hear of real guinea pigs being used experimentally.

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Guinea pigs might not be the most common experimental subjects today, but we have to look at how common they were when the term was first coined, which was many decades ago, as Etymonline points out:

In the extended sense of "one subjected to an experiment" it is first recorded 1920, because they were commonly used in vivisection experiments.

Wikipedia seems to be backing that up:

Biological experimentation on guinea pigs has been carried out since the 17th century. The animals were frequently used as a model organism in the 19th and 20th centuries, resulting in the epithet "guinea pig" for a test subject, but have since been largely replaced by other rodents such as mice and rats.

Looking further, I found this essay on the History of the Guinea Pig:

Guinea pigs have also played a very important role in the field of medical research, and although most pet lovers today may cringe at the thought of animals being used in laboratory research, the historic and important contribution of guinea pigs to science cannot be overlooked. Guinea pigs are often used as a metaphor for any subject of scientific experimentation (e.g. "human guinea pigs"), and this idea persists even though guinea pigs are no longer commonly used as modern experimental animals, as rats and mice (which breed quicker) have replaced them. In 1890 the antitoxin for diphtheria was discovered using guinea pigs in the research, and as a result the lives of millions of children have been saved. The guinea pig's wide variety of hair types and colours have also made them a prime choice for studies of genetics and heredity. During the 20th century a special strain of smooth-coated white guinea pigs called Duncan-Hartley were bred specifically for laboratory work.

Emil Adolf von Behring actually won the (first ever) Nobel Prize in Physiology or Medicine in 1901 for developing a serum therapy against diphtheria. He used guinea pigs in his experiments, though later the serum was extracted from sheep and then horses.

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Linguistically speaking, it was because the metaphoric meaning for "rat" (despicable person) was already taken, while "guinea pig" was wide open for having a metaphoric meaning attached to it.

(And of course it was also because they were used in experimentation. But so were many other species.)

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I do not know much about biology, but Wikipedia states that guinea pigs have been often used in scientific experiments since the 17th century or before. It also explains that now they are not used as often as before:

Since the middle 20th century, they have been replaced in laboratory contexts primarily by mice and rats. This is in part because research into the genetics of guinea pigs has lagged behind that of other rodents, although geneticists W. E. Castle and Sewall Wright made a number of contributions to this area of study, especially regarding coat color.

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