Yates focuses on the social transmission of speciesism, and how and why modern human societies exploit and harm animals. He has called for a strategic audit of the animal protection movement. As part of the abolitionist approach to animal rights, and inspired by the writing of Gary L. Francione, he makes a "plea for a philosophical animal rights stance." Francione's abolitionist critique of the property status of animals is reflected in Yates's investigations in 2001 into horse maiming, or "horse ripping."
A recurring theme in his work is the exploration of the so-called "movement-countermovement dialectic" involving social movements and their opponents as claims-makers. Piers Beirne and N. South write that Yates explores the "extent to which the general public, pet owners, dog show advocates, and other 'pro-use' interests, learn and recycle countermovement message(s) about the theories of change and their advocates. Do the arguments laid out by the countermovements act as 'scripts' to aid those who oppose the ideas of the pro-animal movement?" Commenting on his "Rituals of Dominionism in Human-Nonhuman Relations: Bullfighting to Hunting, Circuses to Petting," Richard White writes that Yates "skilfully develops a persuasive critique which seeks to contextualise the powerful role of social rituals in shaping humans' speciesist relationships with other animals." In 2010, Yates published a paper on "Language, Power and Speciesism" which was critical of the failure, in his view, of the animal protection movement to adequately challenge "the dominant language forms of human-nonhuman relations." In 2011, Yates turned his attention to criminalization processes, placing Ireland in a global context.
His MA thesis was an examination of the British animal protection movement, and his 2005 PhD dissertation, "The Social Construction of Human Beings and Other Animals in Human-Nonhuman Relations. Welfare and Rights: A Contemporary Sociological Analysis," was a work of non-speciesist zemiology. He maintains two blogs, "On Human-Nonhuman Relations," a sociological exploration of speciesism, and "On Human-Nonhuman Relations Podcasts," and, until 2012, helped administrate the global social movement network Animal Rights Zone (ARZone) which encourages rational discourse within the animal advocacy movement and invites prime movers of the movement, such as Dr. Will Tuttle, Dr. Melanie Joy, Professor Gary Francione and Captain Paul Watson, for live Q&A "chats" with ARZone members which are then transcribed and published on the site.
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