This paper reflects on alternatives to the traditional form of doctoral thesis which are emerging to reflect a new approach to the valuation and designation of scientific outputs. We examine the changes and consider some implications. We suggest that the adoption of co-citation as underpinning principle for the measurement of knowledge structures has led to re-designation of the value of knowledge and knowledge producers in increasingly quantitative terms. We use notions of ‘institution’ and ‘logic’ to better understand such a change and its implications. Under a new logic that is gradually embedding itself across the higher education sector, the ‘constitutive rules’ concerned with the value of research now prioritize quantification, and tangibility of output, and quality is increasingly equated with citation. Whilst the scientific disciplines have traditionally been closer to this model, albeit with significant national variations, subjects within the Social Sciences and Humanities are now being affected. We present evidence from a small study of the UK higher education sector of university regulation of doctoral degree submission format in two disciplines in the Humanities and Social Sciences (History and Sociology). Our evidence shows the recent and gradual adoption of a practice, previously more common in scientific disciplines, that allows the doctoral thesis to be constituted by a series of publishable papers, known by a variety of names, the most common being ‘Thesis by Published Papers’, ‘Journal Format Thesis’, ‘Alternative Format Thesis’, and ‘Integrated Thesis’. As the thesis of the Social Sciences and Humanities – itself an important institution in the academic field - begins to reflect a greater emphasis upon quantity of knowledge outputs, a tension emerges with the most central of all scientific institutions, the peer-reviewed journal paper.