Protein engineering: security implications

Tucker, Jonathan Β.; Hooper, C. W.

doi:10.1038/sj.embor.7400677

“…Scientists and engineers may pursue beneficent applications of protein language models such as the design of novel disease therapies, antibodies for novel infectious diseases, or food ingredients for low-allergenic infant formulas. They may also, however, pursue hostile applications such as the design of protein toxins [77], which, in the case of developing biological weapons, could have significant geopolitical ramifications. Various strategies could be applied to mitigate such risks, including broad-based governmental regulation, shared responsibility between users and producers of technology, and post-market surveillance.…”

Section: Broader Impactmentioning

confidence: 99%

BERTology Meets Biology: Interpreting Attention in Protein Language Models

Vig

¹

,

Madani

²

,

Varshney

³

et al. 2020

Preprint

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Transformer architectures have proven to learn useful representations for protein classification and generation tasks. However, these representations present challenges in interpretability. Through the lens of attention, we analyze the inner workings of the Transformer and explore how the model discerns structural and functional properties of proteins. We show that attention (1) captures the folding structure of proteins, connecting amino acids that are far apart in the underlying sequence, but spatially close in the three-dimensional structure, (2) targets binding sites, a key functional component of proteins, and (3) focuses on progressively more complex biophysical properties with increasing layer depth. We also present a three-dimensional visualization of the interaction between attention and protein structure. Our findings align with known biological processes and provide a tool to aid discovery in protein engineering and synthetic biology. The code for visualization and analysis is available at https://github.com/salesforce/provis.

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“…Scientists and engineers may pursue beneficent applications of protein language models such as the design of novel disease therapies, antibodies for novel infectious diseases, or food ingredients for low-allergenic infant formulas. They may also, however, pursue hostile applications such as the design of protein toxins [75], which, in the case of developing biological weapons, could have significant geopolitical ramifications.…”

Section: Broader Impactmentioning

confidence: 99%

BERTology Meets Biology: Interpreting Attention in Protein Language Models

Vig¹,

Madani²,

Varshney³

et al. 2020

Preprint

View full text Add to dashboard Cite

Transformer architectures have proven to learn useful representations for protein classification and generation tasks. However, these representations present challenges in interpretability. Through the lens of attention, we analyze the inner workings of the Transformer and explore how the model discerns structural and functional properties of proteins. We show that attention (1) captures the folding structure of proteins, connecting amino acids that are far apart in the underlying sequence, but spatially close in the three-dimensional structure, (2) targets binding sites, a key functional component of proteins, and (3) focuses on progressively more complex biophysical properties with increasing layer depth. We also present a three-dimensional visualization of the interaction between attention and protein structure. Our findings align with known biological processes and provide a tool to aid discovery in protein engineering and synthetic biology. The code for visualization and analysis is available at https://github.com/salesforce/provis.Preprint. Under review.

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“…The same technician would be able to produce both genes to be used in genetic medicine and genes that encode pathogens or resistance to antibiotics. Even virulent and dangerous proteins might have bioweapons potential [10].…”

Section: New Biological Technologies: a Double-edged Swordmentioning

confidence: 99%

The Bioterrorism Threat and Dual-use Biotechnological Research: An Israeli Perspective

Friedman

¹

,

Rager-Zisman

²

,

Bibi

³

et al. 2008

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Israel has a long history of concern with chemical and biological threats, since several hostile states in the Middle East are likely to possess such weapons. The Twin-Tower terrorist attacks and Anthrax envelope scares of 2001 were a watershed for public perceptions of the threat of unconventional terror in general and of biological terror in particular. New advances in biotechnology will only increase the ability of terrorists to exploit the burgeoning availability of related information to develop ever-more destructive bioweapons. Many areas of modern biological research are unavoidably dual-use by nature. They thus have a great potential for both help and harm; and facilitating the former while preventing the latter remains a serious challenge to researchers and governments alike. This article addresses how Israel might best (1) prevent hostile elements from obtaining, from Israel's biological research system, materials, information and technologies that might facilitate their carrying out a biological attack, while (2) continuing to promote academic openness, excellence and other hallmarks of that system. This important and sensitive issue was assessed by a special national committee, and their recommendations are presented and discussed. One particularly innovative element is the restructuring and use of Israel's extensive biosafety system to also address biosecurity goals, with minimal disruption or delay.

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Protein engineering: security implications

Cited by 8 publications

References 17 publications

BERTology Meets Biology: Interpreting Attention in Protein Language Models

BERTology Meets Biology: Interpreting Attention in Protein Language Models

BERTology Meets Biology: Interpreting Attention in Protein Language Models

The Bioterrorism Threat and Dual-use Biotechnological Research: An Israeli Perspective

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