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In an open letter (dated 22 August 2014) to the Cape Times, fellow University of Cape Town (UCT) academics argued against Noake's dietary ideas. The letter was signed by Wim de Villiers (Dean: Faculty of Health Sciences), Bongani Mayosi (Head: Department of Medicine), Lionel Opie (Hatter Institute of Cardiology, Department of Medicine) and Marjanne Senekal (Head: Division of Human Nutrition). The letter was copied to Noakes and several others. In the letter the academics expressed, among others, "...serious concern that Professor Timothy Noakes, a colleague respected for his research in sports science, is aggressively promoting this diet as a ‘revolution’, making outrageous unproven claims about disease prevention, and maligning the integrity and credibility of peers who criticise his diet for being evidence-deficient and not conforming to the tenets of good and responsible science. This goes against the University of Cape Town’s commitment to academic freedom as the prerequisite to fostering responsible and respectful intellectual debate and free enquiry."

Noakes, also in the form of an open letter to the Cape Times, responded to the criticism by his colleagues. He accused the UCT Faculty of Health Sciences of consistently misrepresenting his public message "...which is simply the following: a high carbohydrate diet is detrimental to the health of persons with insulin resistance whereas carbohydrate restriction in this group can be profoundly beneficial as it can reverse obesity and in some cases Type 2 diabetes mellitus, the two conditions that will ultimately bankrupt South African medical services unless we take appropriate preventive actions." He described the denial by the UCT Faculty of Health Sciences of peer-reviewed evidence in support of his views as "a classic example of cognitive dissonance.”

In response to the complaint, the Professional Conduct Committee of the HPCSA, chaired by Advocate Joan Adams, set up a hearing into the allegation of unprofessional conduct against Noakes. The hearing was scheduled for 4 June 2015, but following complaints from Noake's legal team that the Committee was not properly constituted in accordance with the applicable regulations and the provisions of the Health Professions Act, its commencement was delayed until November 2015. The first session of the hearing took place from 23 to 30 November 2015, after which proceedings were postponed to February 2016. The second session resumed on 8 February  and ended on 17 February 2016. The hearing continues and will resume in October 2016.

Awards and Achievements
In 2011 Noakes was awarded a honorary doctorate by the Vrije Universiteit Amsterdam, Netherlands.