‘The entire protein universe’: AI predicts shape of nearly every known protein

Ewen Callaway

Nature (608)

Posted with correction 29 July 22

From today, determining the 3D shape of almost any protein known to science will be as simple as typing in a Google search.

Researchers have used AlphaFold — the revolutionary artificial-intelligence (AI) network — to predict the structures of more than 200 million proteins from some 1 million species, covering almost every known protein on the planet.

The data dump is freely available on a database set up by DeepMind, the London-based AI company, owned by Google, that developed AlphaFold, and the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL–EBI), an intergovernmental organization near Cambridge, UK.

“Essentially you can think of it covering the entire protein universe,” DeepMind chief executive Demis Hassabis said at a press briefing. “We’re at the beginning of a new era of digital biology.”

The 3D shape, or structure, of a protein is what determines its function in cells. Most drugs are designed using structural information, and the creation of accurate maps of proteins’ amino-acid arrangement is often the first step to making discoveries about how proteins work.

DeepMind developed the AlphaFold network using an AI technique called deep learning, and the AlphaFold database was launched a year ago with more than 350,000 structure predictions covering nearly every protein made by humans, mice and 19 other widely studied organisms. The catalogue has since swelled to around 1 million entries.

“We’re bracing ourselves for the release of this huge trove,” says Christine Orengo, a computational biologist at University College London, who has used the AlphaFold database to identify new families of proteins. “Having all the data predicted for us is just fantastic.”

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But such entries tend to be skewed toward human, mouse and other mammalian proteins, Porta says. It’s likely that the AlphaFold dump will add significant knowledge, because it includes such a diverse range of organisms. “It’s going to be an awesome resource. And I’m probably going to download it as soon as it comes out,” says Porta.

The info is here.

Techno-Optimism: An Analysis, an Evaluation and a Modest Defence

Danaher, J. 

Philos. Technol. 35, 54 (2022). https://doi.org/10.1007/s13347-022-00550-2

Abstract

What is techno-optimism and how can it be defended? Although techno-optimist views are widely espoused and critiqued, there have been few attempts to systematically analyse what it means to be a techno-optimist and how one might defend this view. This paper attempts to address this oversight by providing a comprehensive analysis and evaluation of techno-optimism. It is argued that techno-optimism is a pluralistic stance that comes in weak and strong forms. These vary along a number of key dimensions but each shares the view that technology plays a key role in ensuring that the good prevails over the bad. Whatever its strength, to defend this stance, one must flesh out an argument with four key premises. Each of these premises is highly controversial and can be subjected to a number of critiques. The paper discusses five such critiques in detail (the values critique, the treadmill critique, the sustainability critique, the irrationality critique and the insufficiency critique). The paper also considers possible responses from the techno-optimist. Finally, it is concluded that although strong forms of techno-optimism are not intellectually defensible, a modest, agency-based version of techno-optimism may be defensible.

Here is an excerpt:

To be more precise, a modest, agency-based view of techno-optimism entails the following four claims. First, it is epistemically rational to believe that it is at least possible (perhaps probable) that technology plays a key role in ensuring that the good prevails over the bad. Second, whether this possibility materialises depends to some meaningful extent on the power of collective human agency. If we select the right goals, make the concerted effort, and build the necessary institutions, there is a chance that the possibility materialises. Third, by believing that we can, collectively, achieve this, we increase the likelihood of this possibility materialising because we make it more likely that we will act in ways that ensure the desired outcomes (this is the adaptation of Bortolotti’s agency-based optimism to the case for techno-optimism). Fourth, it follows from that that we should cultivate the belief that we can achieve this and act upon that belief. In other words, that our optimism should not simply be an inert belief but, rather, a belief that actually motivates our collective human agency.

If the agency-based view is incorporated into it, techno-optimism can then be an intellectually defensible view. It need not be an irrational faith in the inexorable march of technology but, rather, a realistic stance grounded in the transformational power of collective human agency to forge the right social institutions and to translate the right ideas into material technologies.

The paper is here.