Synthesizing Proteins on the Graphics Card. Protein Folding and the Limits of Critical AI Studies

This paper investigates the application of the transformer architecture in protein folding, as exemplified by DeepMind's AlphaFold project, and its implications for the understanding of LLMs as models of language. The prevailing discourse often assumes a ready-made analogy between proteins -- encoded as sequences of amino acids -- and natural language -- encoded as sequences of discrete symbols. Instead of assuming as given the linguistic structure of proteins, we critically evaluate this analogy to assess the kind of knowledge-making afforded by the transformer architecture. We first trace the analogy's emergence and historical development, carving out the influence of structural linguistics on structural biology beginning in the mid-20th century. We then examine three often overlooked pre-processing steps essential to the transformer architecture, including subword tokenization, word embedding, and positional encoding, to demonstrate its regime of representation based on continuous, high-dimensional vector spaces, which departs from the discrete, semantically demarcated symbols of language. The successful deployment of transformers in protein folding, we argue, discloses what we consider a non-linguistic approach to token processing intrinsic to the architecture. We contend that through this non-linguistic processing, the transformer architecture carves out unique epistemological territory and produces a new class of knowledge, distinct from established domains. We contend that our search for intelligent machines has to begin with the shape, rather than the place, of intelligence. Consequently, the emerging field of critical AI studies should take methodological inspiration from the history of science in its quest to conceptualize the contributions of artificial intelligence to knowledge-making, within and beyond the domain-specific sciences.