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The online petition has been promoted through a Facebook page created this week to oppose the changes at Knox, and had by yesterday afternoon attracted more than 300 signatures.
Each completed signature sent a form email to university vice-chancellor Prof Harlene Hayne and commission chairman Dr John Kernohan, of Auckland.
The petition called for a clear set of proposed changes at Knox to be made public, and for public submissions to be considered before changes were implemented, to allow a "fair hearing" for past and present students.
"It seems reasonable to hear the views of students who applied [to the college] on the basis of their understanding of the college at the time.
And it seems reasonable to hear the views of the wider community."
Presbyterian Church council of assembly executive secretary Martin Baker, of Wellington, would not commit to fresh consultation over a complete list of changes when contacted yesterday.
He told the Otago Daily Times some changes were needed to bring the college into line with the university's health and safety practices, and "those matters ... aren't open to negotiation".
However, the commission had already discussed other changes with students in recent weeks, and there was room for further talks between the two sides as the commission continued its work over the coming months, he said.
"We're not talking about closed-book here ... It's an ongoing, open-ended process, so within that I think there is some movement for discussion and negotiation."
The students' petition came after the ODT on Wednesday reported the Presbyterian Church had replaced the college's master and council with a commission of the church's general assembly, headed by Dr Kernohan.
The commission had also moved to ban initiation ceremonies, scrap elitist symbols and tighten rules governing alcohol at the college.
Past and present students concerned by the changes voiced their opposition to the changes on Facebook and in emails to the ODT, with many fearing treasured traditions were being lost amid the shake-up.
The outcry prompted a letter addressed to past and present Knox College residents from Dr Kernohan, of Auckland, on Wednesday.
In it, he acknowledged the "reaction and speculation" caused by the changes, but said the commission's highest priority was the safety and welfare of college residents.
Those on the commission, including representatives from the University of Otago and two Knox College fellows, were mindful of its "rich history and special character" and would seek to preserve it, he said.
Some traditions would remain, albeit in a "modified form", while others had to change, he said.
A seven-year review found alcohol had "been a concern" at the college, and changes would bring Knox into line with other colleges and the university's own policies, "all of which operate within the constraints of New Zealand law", he said.
Some students, writing on the Facebook page and in messages attached to the petition, acknowledged changes relating to alcohol at the college were justified, but criticised other changes.
The changes included a ban on "feather-ruffling" initiation ceremonies for new arrivals to Knox, as well as the use of the term "fresher" to describe new students.
A bar in the Buttery - a small room within the college complex - had been closed, while traditional names for the Buttery, as well as the Porters Lodge and Ab Epistulis, had been changed to the canteen, reception and administration officer.
A requirement for semi-formal dining attire at Knox was also dropped, and the Knox College Students' Club had lost control of its budget.
Victoria Jenkins, a Knox resident in 2007-08 and former vice-president of the Knox College Students' Club in 2008, said in a petition message she was "shocked to hear of such drastic changes".
"It is sad to see these changes taking place with little to no recognition of the long-standing tradition that the college holds.
"It takes years to build up tradition ... once that reputation has been ruined, it will be very hard to rebuild."