Bits of DNA

Sholto David

Sholto David is a British molecular biologist and blogger. He is known for identifying flaws in scientific papers.[1][2][3]

Agentic systems are adept at solving well-scoped, verifiable problems in computational biology

We introduce CompBioBench, a benchmark of 100 diverse tasks for evaluating agentic systems in computational biology. Unlike mathematics and programming, which more readily admit systematic verification, biological data are inherently noisy and open to interpretation.

No. 022: Palomar proof registry, autonomous protein design, synthetic consensus - The Hallway Track

The Hallway Track No. 022 - How AI is affecting the practice of science

Molecular Biology in the Work of Deleuze and Guattari

This article looks at Deleuze and Guattari's understanding of molecular biology, focusing particularly on their reading of two highly influential works by the eminent French molecular biologists François Jacob and Jacques Monod, La logique du vivant (The Logic of Living Systems) and Le hasard et la nécessité (Chance and Necessity). In these two works, Jacob and Monod present the significance of molecular biology in broadly reductionist terms. What is more, the lac operon model of gene regulation that they propose serves to reinforce the so-called Central Dogma of molecular biology, according to which information passes from DNA to RNA to proteins, with no reverse route. However, Deleuze and Guattari discover intensive potentials within the descriptions of molecular biology offered by both writers. It is argued that Jacob's work in particular, as it has developed in the years since the publication of La logique du vivant in 1970, has itself developed these intensive potentials.

Journal publishes paper by video-gamers who derived scientific rules from Stanford online RNA game

Video-gamers have co-authored a paper describing a new set of rules for determining the difficulty of designing structures composed of RNA molecules.

Claude for Science. Thursday, November 12, at the Niels Bohr Institute, University of Copenhagen. In September, Anthropic reported that Claude agents found a CRISPR-like enzyme system in… | Jacob Langvad Nilsson | 17 comments

Claude for Science. Thursday, November 12, at the Niels Bohr Institute, University of Copenhagen. In September, Anthropic reported that Claude agents found a CRISPR-like enzyme system in bacteriophage DNA. Earlier in the same month, another AI lab said its model had settled a question about the Navier-Stokes equations, one of the seven Millennium Prize Problems. Results like these don't come from a lucky afternoon with a chatbot. They come from years of method development, careful engineering and building on the work that came before. What has changed is how much of that work a model can now take on, and the speed of which it does it. The latest models read the literature, write and run their own code, and work through a dataset for hours without losing track. In the enzyme case, hundreds of Claude agents searched DNA data for 21 hours and flagged a pattern nobody had asked them to look for. The method still has to be sound. But a researcher with a good question can now test far more ideas in a week than before. That is what we want to show. How researchers here set up their work so that stronger models can move it forward. The evening is about how the Danish science community uses Claude to drive new research and breakthroughs. Four STEM researchers from academia and industry each show one case. What they asked Claude, how they worked, what they found, and what failed. The room is part of it. Niels Bohr lectured in Auditorium A, and in the 1930s Heisenberg and Pauli sat in the front row. We will meet in this historical auditorium and get a glimpse of frontier scientific research using Claude. ▪️ Doors open 15:30, programme 16:00 to 19:00 ▪️ Four case studies from Danish research ▪️ 50 seats on the original wooden benches ▪️ Registration by approval Thanks to Daniel Murnane for making this happen. Thanks to the Niels Bohr Institute and the University of Copenhagen for having us. To Katrin Hjorth Thordardottir for logistics. And thanks to Anthropic and the Claude Community team, Martine N., Cassie Baquero Mayes, Chiara Massironi for your continued support. Link to sign up in the first comment below. We are still confirming speakers. Which researcher in Denmark should I talk to? | 17 comments on LinkedIn

Claude accelerates protein design and analytical chemistry

Two results show how Claude helps life sciences researchers speed up their work: designing protein binders from scratch and analyzing NMR and LC-MS data to speed chemical analysis.

Notes on Rastair, a variant and methylation caller

In the last year, I’ve had the pleasure to work on Rastair , a bioinformatics project by Benjamin Schuster-Böckler from the Ludwig Institute for Cancer Research at the University of Oxford. It is a …

How Life Works: A User’s Guide to the New Biology

“Bold and intriguing.”—Wall Street Journal • “Penetrating. . . . Provocative and profound.”—Publishers Weekly (starred review) • “Offers plenty of food for thought.”—Kirkus Reviews (starred review)  “Ball’s marvelous book is both wide-ranging and deep. . . . I could not put it down.”—Siddhartha Mukherjee, author of The Song of the Cell and the Pulitzer Prize–winning The Emperor of All Maladies A new, cutting-edge vision of biology that revises our understanding of what life itself is, how to enhance it, and what possibilities it offers.   Biology is undergoing a quiet but profound transformation. Several aspects of the standard picture of how life works—the idea of the genome as a blueprint, of genes as instructions for building an organism, of proteins as precisely tailored molecular machines, of cells as entities with fixed identities, and more—have been exposed as incomplete, misleading, or wrong.   In How Life Works, Philip Ball explores the new biology, revealing life to be a far richer, more ingenious affair than we had guessed. Ball explains that there is no unique place to look for an answer to this question: life is a system of many levels—genes, proteins, cells, tissues, and body modules such as the immune system and the nervous system—each with its own rules and principles. How Life Works explains how these levels operate, interface, and work together (most of the time).   With this knowledge come new possibilities. Today we can redesign and reconfigure living systems, tissues, and organisms. We can reprogram cells, for instance, to carry out new tasks and grow into structures not seen in the natural world. As we discover the conditions that dictate the forms into which cells organize themselves, our ability to guide and select the outcomes becomes ever more extraordinary. Some researchers believe that ultimately we will be able to regenerate limbs and organs, and perhaps even create new life forms that evolution has never imagined.   Incorporating the latest research and insights, How Life Works is a sweeping journey into this new frontier of the life sciences, a realm that will reshape our understanding of life as we know it.

How to SNIFF out Good Scientific Software

New PLOS Computational Biology paper: "Ten Quick Tips to SNIFF Out Sustainable and Secure Scientific Software"

Evaluating Claude with BioMysteryBench

BioMysteryBench tests Claude on 99 real bioinformatics problems. Opus 4.6 solved 77% of human-solvable questions and some that experts could not.

Biohub releases a world model of protein biology

Open AI models used for a wide range of scientific applications, including accelerating the design of therapeutic molecules.

Martin Krzywinski - Data Visualization, Design, Science and Art - Canada's Michael Smith Genome Sciences Centre

I present clearly, connect broadly, spark imagination and encourage enthusiasm for inquiry and explanation. I create visuals with analytical clarity and artistic dimensions.

AlphaGenome Atlas: a high-resolution map of human DNA

We’re introducing AlphaGenome Atlas, a database predicting the effects of every possible single nucleotide variant in the human genome.

#bioinformatics #computationalbiology #aiforscience #singlecell #spatialtranscriptomics #opensource #codex #claudecode #mcp #agenticai | Herry Z.

BioNexus: A Scientific Reliability Layer for Agentic Biology As coding agents such as OpenAI Codex, Claude Code, and Cursor become increasingly capable of running bioinformatics workflows, a new problem emerges: Knowing how to run an analysis does not mean knowing when that analysis is scientifically valid. BioNexus is an open-source project exploring a reliability layer for biological coding agents rather than another standalone AI scientist. Its current architecture focuses on: Machine-readable Capability Contracts — define input semantics, scientific preconditions, canonical backends, refusal conditions, and evidence requirements. EvidenceCard 2.1 — separates execution state from scientific evidence and grades conclusions as PRELIMINARY, SUPPORTED, ROBUST, REPLICATED, FRAGILE, or ABSTAIN. Scientific Intent & Invariant Routing — detects invalid analyses such as pseudoreplication, incompatible data representations, or missing backends. BioNexus Eval — evaluates routing, unsafe claims, refusal behavior, and scientific outcomes. RunBundle Artifact Contract — packages inputs, parameters, results, provenance, environment, and evidence into reproducible machine-readable runs. The long-term goal is simple: Make scientific reliability a first-class infrastructure layer for agentic biology. BioNexus is still evolving, and I am actively looking for contributors in bioinformatics, single-cell/spatial omics, scientific benchmarking, MCP, reproducibility, and AI coding agents. PRs, issues, benchmark datasets, scientific critiques, and failure cases are especially welcome. GitHub: HERRY423/BioNexus #Bioinformatics #ComputationalBiology #AIForScience #SingleCell #SpatialTranscriptomics #OpenSource #Codex #ClaudeCode #MCP #AgenticAI