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The most popular suggestion, "RRS Boaty McBoatface," had mote than 27,000 votes Monday morning, compared to about 3,000 votes for the more serious second-place name, "RRS Henry Worsley," named for a British explorer who died in January.
The website has been crashing repeatedly due to the high traffic from the poll.
Lord Alan West, former sea lord in charge of Britain's navy, told BBC Radio 4 that organizers had expected voters to be "mainly marine research fans."
"I would probably plump for a rather more famous name," he said. "I would go for an Arctic or Antarctic explorer."
NERC Director of Corporate Affairs Alison Robinson told NBC News the voting process is non-binding and the organization has final say over the boat's name.
"We are very much enjoying hearing everyone's ideas," Robinson said.
The organization appeared to be taking the tongue-in-cheek suggestion in good humor, even using it as a hashtag in tweets about the new vessel's planned capabilities.