Is Life Just Different? | Quanta Magazine

The idea of ‘biological agency’ — that life devises its own goals and behaves accordingly — complicates our understanding of what it means to be alive. But does it serve a scientific purpose?

quantamagazine.org

Neues Kooperationsgebäude für Biodiversitätsforschung eingeweiht

igb-berlin.de

Why Trump is losing his war against algae

4 scientists explain why the Reflecting Pool may be green instead of blue on July 4.

vox.com

Sign the Petition

Establish David Attenborough Day on 8th May

c.org

DeepSeMS: revealing the hidden biosynthetic potential of the global ocean microbiome with a large language model

Clardy, J. & Walsh, C. Lessons from natural molecules. Nature 432, 829–837 (2004). Xu, T. et al. NPBS Atlas: a comprehensive data resource for exploring the biological sources of natural products. J. Cheminform. 17, 172 (2025). Newman, D. J. & Cragg, G. M. Natural products as sources of new drugs over the nearly four decades from 01/1981 to 09/2019. J. Nat. Prod. 83, 770–803 (2020). Koehn, F. E. & Carter, G. T. The evolving role of natural products in drug discovery. Nat. Rev. Drug Discov. 4, 206–220 (2005). Vanni, C. et al. Unifying the known and unknown microbial coding sequence space. eLife 11, e67667 (2022). Wirbel, J., Bhatt, A. S. & Probst, A. J. The journey to understand previously unknown microbial genes. Nature 626, 267–269 (2024). Scherlach, K. & Hertweck, C. Mining and unearthing hidden biosynthetic potential. Nat. Commun. 12, 3864 (2021). Medema, M. H. et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res. 39, W339–W346 (2011). Skinnider, M. A. et al. Genomes to natural products PRediction Informatics for Secondary Metabolomes (PRISM). Nucleic Acids Res. 43, 9645–9662 (2015). Hannigan, G. D. et al. A deep learning...

nature.com

doi.org

Community context reshapes microbial proteomes and reduces functional overlap - Nature Microbiology

Biotic interactions modulate protein abundance, reducing functional redundancy and increasing productivity in complex bacterial communities.

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KIMMDY: a biomolecular reaction emulator - Nature Communications

This study introduces KIMMDY, a biomolecular reaction emulator that models complex biochemical reactions in dynamic atomistically resolved systems, from protein radical chemistry to DNA photoreactions.

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A nature-inspired ion trap for parallel manipulation of ions on a massive scale

A nature-inspired ion trap enabling massively parallel mass spectrometry.

science.org

Metabolic interactions shape ecosystems

embl.org

Scalable mass-spectrometry-based molecular phylogeny with TreeMS2

Molecular phylogeny is a well-established method for inferring evolutionary relationships from DNA and RNA sequences. Here, we extend this concept beyond genetic information by applying phylogeny-like analysis to proteomic and metabolomic mass spectrometry data, capturing relationships based on the realized molecular phenotype. The resulting phenotype-derived trees can be directly compared with conventional genetic-based trees to identify where molecular phenotypes reflect evolutionary history and where they diverge due to functional adaptation, regulation, or environmental influence. To enable this analysis, we introduce TreeMS2, a computational tool that constructs similarity matrices by directly comparing tandem mass spectrometry (MS/MS) spectra between samples. By bypassing spectrum annotation, TreeMS2 enables rapid, unbiased comparisons. Across diverse datasets, TreeMS2 reconstructs biologically meaningful relationships. In proteomics, phenotype-derived trees recapitulate established taxonomy, with deviations pinpointing sample handling errors. In single-cell proteomics our method distinguishes cell types despite sparse and noisy measurements and in metabolomics it resolves major biochemical divisions and fine-scale compositional structure. Together, these results establish TreeMS2 as a scalable, annotation-independent framework for deriving molecular relationships from raw MS/MS data.

dlvr.it

The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems

MicrobeAtlas (www.microbeatlas.org) is an integrated, reference-based resource for truly planet-wide microbiomics, analyzing hundreds of thousands of microbial lineages across diverse environments, co...

cell.com

Distinct differences of taste quality and metabolite profile between taste tomatoes and ordinary tomatoes revealed by HS-SPME-GC–MS flavoromics and LC–MS metabolomics

This study integrated HS-SPME-GC–MS flavoromics, LC–MS metabolomics, and electronic tongue analysis to systematically dissect the metabolic and flavor…

sciencedirect.com

High-throughput reaction screening using acoustic ejection mass spectrometry - Nature Protocols

A bottleneck in high-throughput chemical synthesis is analyzing reaction products. This protocol describes a direct mass spectrometry approach where the loss of a characteristic neutral fragment from ...

nature.com