The phrase itself is a traditional one and relates to the fond desire by Irish nationalists to punish king William III and his descendants for what they consider to be his crimes against Ireland and the Church. They want him to walk up the gallows steps (the "long ladder") and then be hung on a short rope until dead.
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Up the long ladder, Down the short rope. To hell with King Billy! Three cheers for the Pope!
The earliest reference I"ve been able to find is from the Journal of American folklore 1917 - #31 but apparently the saying (and a similar rhyme) significantly predates this.
As to why this particular quote was chosen, I"ve not found any specific reference by the writers other than they were looking to have a more Irish themed title than the original "Send in the Clones" which was judged to be too jokey for the subject matter.
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edited May 25 "18 at 20:29
answered May 25 "18 at 17:23
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The episode"s main plot deals with a colony of people called Mariposans who are entirely composed of clones from the original 5 survivors of a crash landing. They have avoided all "natural" reproduction and as such are experiencing a process called "replicative fading" where each copy of genetic material degrades from the previous copy. The Mariposans propose to clone Riker so as to inject new genetic material into their society. He declines.
At the same time, the Enterprise crew has come across a colony of people looking for a new home. Over the course the episode, both communities agree to join together. The clone society needing a large group of new genetic material (but obtained in the "natural" way, and the other group needing a new home.
The title then "Up the Long Ladder" is a reference to the molecular, double-helix structure of DNA:
as DNA is an underlying theme of the episode. Note how the structure of DNA resembles a ladder.
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Additionally, the colony of people looking for a home is ostensibly descended from a group of Irish colonists. There is supposedly an Irish folk song that contains the words "Up the long ladder, down the long rope", but that song"s theme is generally unrelated to the theme of the episode. This information is referenced in the Memory Alpha article, but there is no citation to any production staff or element that would indicate this was an intentional reference.