History of Methods Section (www.asimov.press)

In May 2024, Google DeepMind's release of AlphaFold3, a groundbreaking protein structure prediction model, triggered significant controversy within the computational biology community when the code was initially withheld in favor of a web server interface. This decision sparked backlash from over 1,000 researchers who condemned it as a violation of scientific norms, emphasizing the importance of transparency and reproducibility in research. Following this uproar, DeepMind released the code in November 2024, reflecting the ongoing struggle for open access in scientific research, particularly in AI-driven domains. The situation highlights a long-standing issue in scientific methodology: the inadequate detail in the Methods sections of research papers. Despite the critical role of these sections in facilitating duplicability, studies reveal that many research protocols are often poorly documented, limiting the ability for others to replicate results efficiently. This historical analysis points to a broader systemic failure within the scientific community, where practical knowledge is frequently overshadowed by discoveries. As researchers seek to reform scientific publications, understanding the evolution of the Methods section is pivotal, underscoring the need for rigorous documentation to foster collaborative advancements in the AI and machine learning fields.