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Earthquake "booms" have been reported for a long time, and they tend to occur more in the Northeastern US and along the East Coast. Of course, most "booms" that people hear or experience are actually some type of cultural noise, such as some type of explosion, a large vehicle going by, or sometimes a sonic boom, but there have been many reports of "booms" that cannot be explained by man-made sources. No one knows for sure, but scientists speculate that these "booms" are probably small shallow earthquakes that are too small to be recorded, but large enough to be felt by people nearby.
There are accounts of "artillery"-like sounds that were said to have occurred before or during the New Madrid earthquakes of 1811-1812.
The term “Seneca guns” is just a name, not an explanation. It does not tell us anything about what causes these noises and shakings. The name originated in a short story that James Fennimore Cooper wrote during the 1800’s. The name refers to booms that have been heard on the shores of Lake Seneca and Lake Cayuga in New York State. The name has been applied to similar noises along the coasts of North Carolina, South Carolina, and Virginia. Similar booms are called Barisol guns in coastal India. These phenomena have also occurred in three widely separated places around the world. That’s about all we know about the Seneca guns.
I happened to be passing in its neighborhood where the principal shock took place... the water that had filled the lower cavities. . . rushed out in all quarters, bringing with it an enormous quantity of carbonized wood.. . which was ejected to the height of from ten to fifteen feet, and fell in a black shower, mixed with the sand which its rapid motion had forced along; at the same time, the roaring and whistling produced by the impetuosity of the air escaping from its confinement, seemed to increase the horrible disorder of the trees which everywhere encountered each other, being blown up cracking and splitting, and failing by thousands at a time. In the mean time, the surface was sinking and a black liquid was rising up to the belly of my horse, who stood motionless , struck with a panic of terror . . . . . These occurrences occupied nearly two minutes; the trees, shaken in their foundation, kept failing here and there, and the whole surface of the country remained covered with holes, which... resembled so many craters of volcanics..
... about sunrise another very severe one came on, attended with a perpendicular bouncing that cause the earth to open in many places... the deepest I saw was about twelve feet. The earth was, in the course of fifteen minutes after the shock... entirely inundated with water. The pressing of the earth, if the expression be allowable, caused the water to spout out of the pores of the earth, to the height of eight or ten feet! The agitation of the earth was so great that it was with difficulty any could stand on their feet, some could not. The air was strongly impregnated with a sulphurous smell.
A large wave (and perhaps a temporary retrograde current) was noted only upriver of Little Prairie [Bedinger, Bryan (1848), and La Roche] and was followed by a rapidly rising river level and swifter current downstream from approximately Bedinger's location (Bedinger, Davis, Pierce, Bradbury). These latter events are consistent with the large volume of groundwater that must have been expelled by liquefaction. Tremendous noise, fissuring, splintering and toppled trees, and extensive caving of river banks were reported by all.
An additional source of paleoseismological information is the "sunklands" (Fuller 1912) that lie above the northwestern flank of the Blytheville arch (Figure 2a) and appear to be tectonic in origin. Fuller mapped numerous sunklands along the St. Francis and nearby rivers in Arkansas and Missouri. He believed that they formed during the New Madrid earthquakes. Indeed, several maps from the early- to mid- 1800s refer to some of the lakes associated with the sunklands by the name "Earthquake Lake." Two of the largest sunklands in northeastern Arkansas are Big Lake and Lake St. Francis
The most recent documented earthquake sounds were from a swarm of small earthquakes that unnerved the city of Spokane, WA in 2001. Many of the Spokane quakes were definitely accompanied by "booming sounds". The quakes in Spokane were shallow, sometimes only a mile or two deep. This probably contributed to all the noise they made. Higher-frequency vibrations make the booming sound, and when quakes are deeper, those vibrations are gone by the time they reach the surface. Sometimes the quakes boom even when no vibration is felt.
As for scientific evidence for loud sounds that preceded the 1886 Charleston, SC Earthquake, there is none. To our knowledge, there were no seismographs or barographs that recorded the earthquake. The only data that was collected that could have scientific significance (aside from tide gauge and other water surface measurements, was from large clocks that stopped due to ground motions. Unfortunately none of these clocks were precisely synchronized so those data are of poor quality.
For several weeks after the Charleston Earthquake (8/31/1886) there were many aftershocks that were reportedly accompanied by "loud detonations". But there was little mention of sounds occurring before an event. The earth was in a fairly continuous state of agitation and it would be difficult to relate a specific sound to a specific earthquake. The following account from the Dutton report is particularly informative: