BioKEA — Biology, decoded in the public interest

Agentis — coming soon — BioKEA

An AI-first scientific journal built on the AT Protocol. Fast, verifiable peer review and publications as interactive StoryMaps.

How to SNIFF out Good Scientific Software

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

Reinventing the wheel: milk, microbes, and the fight for real cheese

"Reinventing the Wheel is equal parts popular science, history, and muckraking. Over the past hundred and fifty years, dairy farming and cheesemaking have been transformed, and this book explores what has been lost along the way. Today, using cutting-edge technologies like high-throughput DNA sequencing, scientists are beginning to understand the techniques of our great-grandparents. The authors describe how geneticists are helping conservationists rescue rare dairy cow breeds on the brink of extinction, microbiologists are teaching cheesemakers to nurture the naturally occurring microbes in their raw milk rather than destroying them, and communities of cheesemakers are producing "real" cheeses that reunite farming and flavor, rewarding diversity and sustainability at every level."--Provided by publisher.

Holobiont

A holobiont is an assemblage of a host and the many other species living in or around it, which together form a discrete ecological unit through symbiosis, though there is controversy over this discreteness. The components of a holobiont are individual species or bionts, while the combined genome of all bionts is the hologenome. The holobiont concept was initially introduced by the German theoretical biologist Adolf Meyer-Abich in 1943, and then apparently independently by Dr. Lynn Margulis in her 1991 book Symbiosis as a Source of Evolutionary Innovation. The concept has evolved since the original formulations. Holobionts include the host, virome, microbiome, and any other organisms which contribute in some way to the functioning of the whole. Well-studied holobionts include reef-building corals and humans.

A Cell So Minimal That It Challenges Definitions of Life | Quanta Magazine

The newly described microbe represents a world of parasitic, intercellular biodiversity only beginning to be revealed by genome sequencing.

SOLU / Bioart Society

SOLU / Bioart Society Panimokatu 1, 3rd floor 00580 Helsinki Finland info@bioartsociety.fi

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.

b.next: rebuilding biology for engineering

Genspace

Genspace is the world’s first community biology lab—a place where anyone can learn and work on biotechnology.

Data‐ and code‐archiving in the British Ecological Society journals: Present status and recommendations for future improvements

Abstract Data‐ and code‐archiving are important components of open science, as both make research more transparent, reproducible, accountable and credible, allowing future researchers to build on previous work. Despite progress in implementing data‐ and code‐archiving policies in journals publishing ecology and evolution research, issues remain. To be more useful to future researchers, archived data and code must not only be archived but also meet good practice standards. We collected data from 1861 papers published between 2017 and 2024 in the seven British Ecological Society (BES) journals, during a hackathon event. We systematically checked associated data and/or code, metadata, help files and annotations to assess archiving practices. We determined if and where data and code files were archived, whether they could be located, downloaded and opened, and whether they had associated READMEs, digital object identifiers (DOI) and licences. We also recorded the file extensions used to save data/code files, and which programming languages code was written in. 93% of the 1861 papers we examined used data and ~90% used code. While 97% of the 1735 papers that used data also archived it, only 35% of the 1670 papers that used code also archived code. Over 85% of archived data and code could be located, downloaded and opened. Reusability, however, was more limited; around a third of papers did not have a README or similar to explain their data/code files, and the quality of READMEs varied substantially. We recommend that researchers archive their code and that archived code be explicitly mentioned in the Data (or Code) Availability statement. We also encourage researchers to provide more accessible and informative READMEs for data and code. To help achieve these recommendations, we advocate that journals employ Data/Code editors to review data and code quality, research institutions deliver more training in open science practices, and funding bodies set clear expectations on open data and code practices.

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.

Citizen science in environmental and ecological sciences

Citizen science is an increasingly acknowledged approach applied in many scientific domains, and particularly within the environmental and ecological sciences, in which non-professional participants contribute to data collection to advance scientific research. We present contributory citizen science as a valuable method to scientists and practitioners within the environmental and ecological sciences, focusing on the full life cycle of citizen science practice, from design to implementation, evaluation and data management. We highlight key issues in citizen science and how to address them, such as participant engagement and retention, data quality assurance and bias correction, as well as ethical considerations regarding data sharing. We also provide a range of examples to illustrate the diversity of applications, from biodiversity research and land cover assessment to forest health monitoring and marine pollution. The aspects of reproducibility and data sharing are considered, placing citizen science within an encompassing open science perspective. Finally, we discuss its limitations and challenges and present an outlook for the application of citizen science in multiple science domains.

A cellular entity retaining only its replicative core: Hidden archaeal lineage with an ultra-reduced genome

Abstract Defining the minimal genetic requirements for cellular life remains a fundamental question in biology. Genomic exploration continually reveals novel microbial lineages, often exhibiting extreme genome reduction, particularly within symbiotic relationships. Here, we report the discovery of Candidatus Sukunaarchaeum mirabile, a novel archaeon with an unprecedentedly small genome of only 238 kbp —less than half the size of the smallest previously known archaeal genome— from a dinoflagellate-associated microbial community. Phylogenetic analyses place Sukunaarchaeum as a deeply branching lineage within the tree of Archaea, representing a novel major branch distinct from established phyla. Environmental sequence data indicate that sequences closely related to Sukunaarchaeum form a diverse and previously overlooked clade in microbial surveys. Its genome is profoundly stripped-down, lacking virtually all recognizable metabolic pathways, and primarily encoding the machinery for its replicative core: DNA replication, transcription, and translation. This suggests an unprecedented level of metabolic dependence on a host, a condition that challenges the functional distinctions between minimal cellular life and viruses. The discovery of Sukunaarchaeum pushes the conventional boundaries of cellular life and highlights the vast unexplored biological novelty within microbial interactions, suggesting that further exploration of symbiotic systems may reveal even more extraordinary life forms, reshaping our understanding of cellular evolution. Graphical Abstract

iNaturalist accelerates biodiversity research

Abstract. Participatory citizen science is expanding, with iNaturalist emerging as one of the most widely used platforms globally. However, its application

GBIF

Global Biodiversity Information Facility. Free and Open Access to Biodiversity Data.