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Martin's original academic field was theoretical physics, and he worked in both stratospheric modelling and numerical methods during his career. He has published extensively about the social dynamics and politicisation of controversial scientific topics. His topics of inquiry have included the globalization of polarised science such as the origin of HIV/AIDS. He argues that there are situations in which scientific research that threatens vested interests can be suppressed. He identifies a number of direct and indirect mechanisms through which this can occur, ranging from the denial of funds and the denial of promotion and tenure, through to the creation of a "general climate of fear". Martin's work on in this area has provided what Delborne describes as a "key foundation for conceptualizing scientific dissent".
Martin has been criticised for supporting the incorrect proposal that oral polio vaccine caused AIDS. The hypothesis first came to notice in Rolling Stone magazine by way of journalist Curtis and AIDS activist Elswood in 1992, and was later further promoted by the journalist/writer Hooper and Martin, with Hooper crediting Martin for giving the OPV-AIDS link hypothesis "further publicity and credibility". Martin disputes the claim that he has been a supporter of the hypothesis, instead saying that he has "never argued in favour of the OPV theory", but has instead stated "that it was and remains worthy of consideration yet in many ways has been unfairly dismissed". A 2016 article in The Australian described Martin's 2010 paper as claiming "that medical researchers had colluded to silence the theory that the AIDS virus was caused by contaminated polio vaccines in 1950s Africa."
Martin has been active in the criticism of university systems. He has criticized conflicts of interest where universities are managing internal investigations that may lead to bad publicity, and recommends having independent groups investigate allegations of misconduct; he has written about the unauthorised use of research produced by students and junior researchers by senior academics; and he has been outspoken against sexual relationships between staff and students. He also reports that any bias within universities could simply be due to students strategically working in-line with the biases of their teachers.
Martin was subjected to an attempted academic gag when he published material about the forced retirement of a University of Adelaide academic. His university instructed him to remove the content from his website after Adelaide University threatened to sue. Martin's published material in question is now found on other websites.
Martin believes that if complainants go through the official channels the outcome is very predictable, in that the organisation's internal grievance procedures, or making a complaint to the relevant ombudsman, does not work. He also believes whistleblower laws do not work, saying; "Not only are whistleblower laws flawed through exemptions and in-built weaknesses but in their implementation they are rarely helpful".
In April 2001, Martin published an article in defence of a sacked academic at UOW in the national newspaper The Australian. In a response published in the same paper, the Vice-Chancellor of Murdoch UniversitySteven Schwartz accused Martin of a position supporting the concept of a "laissez-faire attitude towards academic freedom (in which all sides are presented impartially)" saying his "approach to academic freedom is neither logical nor practical" as this approach "forces universities to abandon their most cherished values: scholarship, wisdom and truth".
Martin has been criticised for his role in the Judith Wilyman PhD controversy where medical academics and the AMA raised concerns of whether Martin had the necessary knowledge to assess her doctorate which discussed vaccine science.The Australian has criticised him as not recognising academic rigour over academic freedom, and surgeon John Cunningham called on the University to have the thesis "reviewed by people whom have knowledge of vaccinations".
In 2016, the Australian Skeptics criticised Martin's supervision of Wilyman by presenting Martin, Wilyman and the Social Sciences Department of the University of Wollongong the satirical Bent Spoon Award for awarding "a PhD thesis riddled with errors, misstatements, poor and unsupported 'evidence' and conspiratorial thinking".
In 2017, Martin received publicity for his supervision of a PhD that argued bee stings were more dangerous than terrorist bombers, on the grounds that "more people die in car accidents, from domestic murders and bee stings in Australia than terrorist attacks". A contributor to Sydney's Daily Telegraph newspaper wrote that the "360-page essay also takes aim at the ABC, News Corp Australia and the St James Ethics Centre for backing torture. And it claims the federal government has a "pro-torture ideology"."
Martin previously supervised an unsuccessful PhD by Michael Primero titled "The 'politics' of vaccination: a scientific controversy analysis", who went on to be a director of Viera Scheibner's anti-vaccination group Medical Veritas.
The deceptive activist (Sparsnäs, Sweden: Irene Publishing, 2017).
Ruling tactics: methods of promoting everyday nationalism, how they serve rulers and how to oppose them (Sparsnäs, Sweden: Irene Publishing, 2017).
Nonviolence versus capitalism, (London: War Resisters' International, 2001).
Technology for Nonviolent Struggle, (London: War Resisters' International, 2001).
(with Lyn Carson). Random Selection in Politics, (Westport, CT: Praeger, 1999).
The Whistleblower's Handbook: How to Be an Effective Resister, (Charlbury, UK: Jon Carpenter; Sydney: Envirobook, 1999). Updated and republished 2013 as Whistleblowing: a practical guide, (Sparsnäs, Sweden: Irene Publishing)
Information Liberation, (London: Freedom Press, 1998).
Tied Knowledge: Power in Higher Education, (self-published, 1998).
Suppression Stories, (Wollongong: Fund for Intellectual Dissent, 1997).
Social Defence, Social Change, (London: Freedom Press, 1993).
Scientific Knowledge in Controversy: The Social Dynamics of the Fluoridation Debate, (Albany: State University of New York Press, 1991).
(with C. M. Ann Baker, Clyde Manwell & Cedric Pugh) Intellectual Suppression: Australian Case Histories, Analysis and Responses, (Sydney: Angus & Robertson, 1986) ISBN0-207-15132-6
^ abcdJenkins, Stephen H. (2015). Tools for Critical Thinking in Biology. New York: Oxford University Press. pp. 217-219. ISBN978-0-19-998104-5. OCLC904046627. text= "Although Hooper and Martin are still promoting the tainted polio vaccine hypothesis, recent genetic work has convincingly disproven it... Worobey's team published their genetic comparison of HIV samples in 2008, but Brian Martin continued to promote the tainted polio vaccine hypothesis for the origin of AIDS as late as 2010 in a paper called "How to Attack a Scientific Theory and Get Away with It (Usually)..." p 218.
^Hammar, Lawrence (1 April 2004). "Dephlogistication, Imperial Display, Apes, Angels, and the Return of Monsieur Emile Zola". Papua New Guinea Medical Journal. 47 (1-2): 120, 124. S2CID50897742.
^Curtis, Tom (19 March 1992). "The Origin of AIDS: A startling new theory attempts to answer the question, 'Was it an act of God or an act of man?". Rolling Stone magazine (626). pp. 54-9, 61, 106, 108.
^Cervini, Erica (1 December 1999). "Gagged. Victoria's academics feel increasingly stifled as funding cuts force their universities down the big-business path". Educ@tion Supplement - The Age. Melbourne: Fairfax. p. 1(67).
^Martin, Brian (18 April 2001). "Higher Education Supplement". The Australian. News Corp.
^Schwartz, Steven; Schwartz, Gregory (27 June 2001). "Laissez faire not fair for all". The Centre for Independent Studies. Sydney: (originally published in The Australian, 27 June 2001 p.31). Archived from the original on 9 January 2020.
^Lapointe, Pascal (15 January 2016). "L'anti-vaccination à l'université" [Anti-vaccination at university]. Agence Science Presse (in French). Quebec, CA. Archived from the original on 26 February 2016. The professor she chose as supervisor, Brian Martin, is known for his belief in a conspiracy to silence and hide the study that the AIDS virus was caused by the polio vaccine. And he also defends the idea of a vaccine-autism link.