AlphaFold is a major advance for AI in science recognized by the 2024 Nobel Prize in Chemistry. It was made possible by the data of the Protein Data Bank (PDB) and developed by a company, DeepMind.

                  A recent initiative is a collective history called "From PDB to AlphaFold":

https://www.cellcomm.org/from-pdb-to-alphafold

                  This history points to data as key to the synergy between AI companies and academia. Appreciating the implications of this potential synergy could lead to a joint effort to encourage the rest of society to increase support for science. It could also lead to support from the AI industry (for example taking the form of open-source software) for transparent, nonprofit AI dedicated to basic science, which would not compete with commercial applications.

                  As pointed…

AI in Science: virtual cells and organisms

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             We are currently discussing the following message for Foundations about virtual cells and organisms. The most useful virtual organism is clearly a digital human model, a worthwhile task that will benefit all of us, but also a challenge that will require the effort of a large part of the biomedical scientific community.

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Message draft:

"Subject: A non-financial role for [Foundation Name] in advancing virtual cells and organisms.

Quotations from the "REMARKS ON THE DISPROOF OF THE UNIT DISTANCE CONJECTURE" paper that might help non-mathematicians to appreciate its relevance to other scientific fields.

Especially relevant for biomedical problems are the noted ability of AI to find connections among scientific facts that are part of different specialized fields, and the persistence in exploring the implications of these connections.

Noga Alon

" AI was able to do here what lots of excellent human researchers tried and failed to do. Like other mathematicians who had the opportunity to experiment, even if only briefly in my case, with ChatGPT Pro 5.5, my impression has been that AI tools are capable of changing research

in mathematics in a dramatic way. The new spectacular solution of the Erdős unit distance problem convinces me that it is hard to overestimate the full potential impact of this change."

Example of first step of brainstorming on human collective scientific intelligence, with 3 AI models.

- May 2026

PROMPT

The following is the current focus of a discussion among scientists and scholars, shown on the cellcomm.org website. Can you provide a comment about the usefulness of the plan for human health and knowledge, suggestions on how to make it more likely to succeed and an estimate of the likely number of participants after the first Round, after the second Round and after five years?

Trey Ideker has been appointed as the new Director of the University of Oxford’s Big Data Institute (BDI). He will take up the role in June. He is currently a Professor in the Department of Medicine at the University of California, San Diego (UCSD), where he also leads and co-leads several major data-driven research initiatives, including an ADAPT Center for Precision Oncology, the Cancer Cell Map Initiative, and the Bridge2AI Functional Genomics Data Generation Program.

Dear Trey,

What are your plans for the Oxford's Big Data Institute? What is your vision of data science and AI, and, more broadly, of science in this age of advancing AI?

Trey:

Stanley (Stan) Crooke has spoken with Anindya Bagchi, Giovanni Paternostro and Guy Salvesen. Stan is the founder and former CEO of Ionis Pharmaceuticals. He has been also an academic scientist, a leader in large pharma companies and a physician. He is now a philanthropist, having founded the n-Lorem Foundation, to use the antisense technology developed at Ionis for patients with very rare genetic diseases, where the commercial model did not suffice.

Dear Stan,

Our first question is about your inspiring personal journey. You started as a scientist, you worked for pharma in leadership positions, you were an academic scientist, you were a practicing doctor. And then, of course, you had an important role as a biotech founder. And now you are a philanthropist. What is the common element of all the roles you have played?

Stan:

Payson R. Stevens was President and Creative Director of InterNetwork, Inc. and InterNetwork Media, Inc., science/consulting groups with clients in government, industry, and academia. He has received the US Presidential Award for Design Excellence. Originally trained in molecular biology at the City University of New York and in biological oceanography at the Scripps Institution of Oceanography/UC San Diego, Stevens also studied at the Arts Students League and the School of Visual Arts in New York City. He has been involved with traditional and new media as an artist, designer, writer, and filmmaker for over 50 years. Since 2000 he has supported philanthropic activities, benefiting the Great Himalayan National Park and humanitarian work in India. He is now exploring the role of AI in society, including authoring a book entitled "Before AI Decides: Nine Ways to Stay Human".

Dear Payson,

Your recent book addresses a general audience but many of the points you…

Summary of older AI and Collective Intelligence discussions

        The recent progress in Artificial Intelligence provides both challenges and opportunities for scientific collective intelligence. Among the most notable examples of AI progress are ChatGPT and other Large Language Models, which have shown unexpected capabilities (Wei 2022, Mitchell 2023), and AlphaFold, which can predict the 3D shape of proteins from their genetic sequence with unprecedented accuracy (Jumper 2021). The development of AlphaFold has been recognized by the award of the 2014 Nobel Prize in Chemistry.

Challenges

          AI poses specific challenges for science. There are many reports of errors in statements from ChatGPT and from other AI systems. The types of errors and blind spots seem different from those more common in humans.

            These AI systems consist of neural networks with billions to trillions of parameters (Mitchell,…

Guy Salvesen and Giovanni Paternostro have spoken with Adam Godzik. Adam is the Bruce D. and Nancy B. Varner Presidential Endowed Chair in Cancer Research at the UC Riverside School of Medicine, Division of Biomedical Sciences. Adam was closely involved from an early stage in CASP, as a participant, and in the Joint Center for Structural Genomics (JCSG), one of the centers supported by the Protein Structure Initiative (PSI).

He sent the following comments:

                  I think that the success of PDB was driven by it being built by the crystallographic community itself, it was an effort from within, not from outside. It became widely accepted relatively early in its history, definitely before I got into the field. 

                  There was another development in bioinformatics that enabled AlphaFold – residue-residue interaction predictions from MSA (work of Debora S. Marks, for instance https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028766) or a more general contact map prediction field…