Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery.

Antibodies are versatile molecular binders with an established and growing role as therapeutics. Computational approaches to developing and designing these molecules are being increasingly used to complement traditional lab-based processes. Nowadays, in silico methods fill multiple elements of the discovery stage, such as characterizing antibody-antigen interactions and identifying developability liabilities. Recently, computational methods tackling such problems have begun to follow machine learning paradigms, in many cases deep learning specifically. This paradigm shift offers improvements in established areas such as structure or binding prediction and opens up new possibilities such as language-based modeling of antibody repertoires or machine-learning-based generation of novel sequences. In this review, we critically examine the recent developments in (deep) machine learning approaches to therapeutic antibody design with implications for fully computational antibody design.

Reforming uncultivated minds: The species transmutation debate and American science of life in the antebellum agricultural press, 1820-1859.

The paper traces a debate about species transmutation that unfolded in agricultural periodicals published in the Northeastern United States between 1820 and 1859. The reformers who curated the content of these publications promoted agricultural improvement by disseminating knowledge about relevant science and technology topics. The widespread belief in the transmutation of grains provided them with an opportunity for sharing scientific knowledge about plant heredity and botanical classification systems, encouraging experimentation among audiences prejudiced against "book farming," and recalling the tenets of natural theology which described nature as orderly and predictable. The reformers did not manage to eradicate the belief in species transmutation which remained popular throughout the nineteenth century. However, in their assessment of the theoretical contributions of botanists and practical experiments conducted by farmers, they negotiated the authority of scientific expertise in the study of nature and delineated standards of scientific inquiry into agricultural matters. The reformers' engagement with the transmutation debate thus contributed to the professionalization of agricultural improvement, laying the groundwork for the activities of agricultural research institutions that emerged in the second half of the century.