Why did my thumb throb when injured?

[This answer has now been updated to reflect more recent research findings.]

Historically, it was claimed that the throbbing nature of the pain occurred owing to arterial pulsations which produce repetitive wave sensations.

The argument went that inflammatory chemicals are produced in response to the injury as part of your body's defence to prevent infection to that wound. These chemicals stimulate sensory nerve endings including sensory receptors that are mechanically stimulated. So, as your artery throbs with the beat of your heart, that stimulates the sensitised nerve endings and you get this throbbing, drumming pain.

However, the claim did not stand up to scientific scrutiny by a team at the University of Florida, who measured simultaneously the rate of arterial pulsation and the perceived rate of pain throbbing in human volunteers with toothache.

According to their findings, published in the Journal of Neuroscience in 2012, "Contrary to the generally accepted view, which would predict a direct correspondence between the two, we found that the throbbing rate (44 bpm) was much slower than the arterial pulsation rate (73 bpm, p< 0.001), and that the two rhythms exhibited no underlying synchrony."

Instead, based on their findings, the team speculate that "...the throbbing quality is not a primary sensation but rather an emergent property, or perception, whose "pacemaker" lies within the CNS [central nervous system]."

In other words, the throbbin character of the pain sensation appears to arise within the brain's circuits itself, although at the moment no one knows how.

Reference: "Is There a Relationship between Throbbing Pain and Arterial Pulsations?" - DOI:10.1523/JNEUROSCI.0193-12.2012

[Our thanks to Rose Edwards for bringing this paper to our attention.]