The unintended consequences of large language models as a labor-augmenting technology in science

As a labor-augmenting technology, large language models (LLMs) have the potential to accelerate scientific activity across the research pipeline. But even if LLMs perform on par with human experts at ...

arxiv.org

Face à l’IA générative, l’objection de conscience

Manifeste pour l’enseignement supérieur et l’éducation nationale [Vous pouvez signer ce manifeste (version pdf ici) dans ce formulaire. Un document de mise en perspective critique des discours de défe...

atecopol.hypotheses.org

Towards a functional genetics of adaptation: insights from microbial experimental evolution

Abstract. A general theory of adaptation is one that accounts for both the quantitative and functional properties of adaptive evolution. To date, the field

academic.oup.com

Open Letter: Stop the Uncritical Adoption of AI Technologies in Academia

openletter.earth

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig

academic.oup.com

No Time to Fold: Intrinsically Disordered Microproteins in Action

Advances in genomics, proteomics, and bioinformatics have uncovered the existence of thousands of translated small open reading frames less than 100–150 codons in length that encode microproteins. In ...

pubs.acs.org

Trump fires NSF's oversight board

Dismissal of the National Science Board is widely seen as latest move to erase NSF’s independence

scim.ag

The one science reform we can all agree on, but we're too cowardly to do

OR: the long overdue forest fire

experimental-history.com

Explique ta thèse à un enfant 🧒 Cérémonie de docteurs 2026 - Université de Lille

YouTube video by Université de Lille

youtu.be

Unil center for theory in ecology and evolution (UCTEE) - FBM Unil

Page Unil Center for Theory in Ecology and Evolution of site Faculty of Biology and Medicine hosted by the University of Lausanne

unil.ch

Evolutionary emergence and preservation of microproteins encoded by upstream ORFs

The analysis of ribosome profiling (Ribo-Seq) data has provided evidence that many eukaryotic mRNAs contain translated upstream or downstream ORFs (uORFs/dORFs), but the biological significance of this translation activity remains, for the most part, unknown. One of the principal limitations has been the lack of Ribo-Seq data from several closely related species, precluding the identification of cases in which translation is phylogenetically conserved. Here, by combining Ribo-Seq data from 100 different experiments, we identify 2,332 translated uORFs and 1,008 translated dORFs in S. cerevisiae, which result in microproteins that tend to be highly hydrophobic or positively charged. To study their phylogenetic conservation, we have generated Nanopore direct RNA sequencing data, together with Ribo-Seq data, from six additional Saccharomyces species, spanning an evolutionary period of around 16 million years. We have identified 195 translated S. cerevisiae uORFs that are also translated in other Saccharomyces species; these uORFs are translated at levels comparable to the main coding sequence and display signatures of purifying selection at the level of the encoded microproteins. In contrast, dORFs are translated at very low levels and they are rarely conserved, suggesting much more limited microprotein functionalization. We have also discovered that uORF translation is associated with the formation of alternative transcript isoforms encompassing the region containing the uORFs but not the main protein coding sequence, implying that some microproteins can be produced independently of the main protein product. This work significantly advances our understanding of how initially pervasive uORF translation can result in new microproteins, providing many new candidates for further functional studies. ### Competing Interest Statement The authors have declared no competing interest. European Research Council, https://ror.org/0472cxd90, 101052538 Ministerio de Ciencia, Innovación y Universidades, PID2021- 122726NBI00, PGC2018-094091- B-I00, PID2022-136939OBI00, CEX2024-001431-M, MICIU/AEI/10.13039/501100011033 Generalitat de Catalunya, https://ror.org/01bg62x04, 2021SGR00042, 2021SGR00176

biorxiv.org

The rules of the game: biophysical & molecular principles in cellular evolution

Cells are the fundamental units of life, shaped by evolution into a remarkable diversity of forms and functions. Much is known about the roles of genes and proteins, the regulation of molecular proce…

meetings.embo.org

Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling - Nature Microbiology

A structural catalogue of the Asgard archaeal pangenome reveals hundreds of eukaryotic-like proteins that suggest a higher degree of cellular complexity in the archaeal ancestor of eukaryotes.

nature.com

A symbiotic origin of the ribosome?

Abstract. The origin of life is one of the great mysteries of science. Of the multiple unsolved problems, the origin of the translation system (the means b

academic.oup.com

Emergence and evolution of protein-coding de novo genes - Nature Reviews Genetics

De novo gene evolution entails the birth of new genes from previously non-coding DNA. In this Review, Bornberg-Bauer and Eicholt overview how protein-coding de novo genes are identified, the mechanist...

nature.com

Emergence and evolution of protein-coding de novo genes

Nature Reviews Genetics - De novo gene evolution entails the birth of new genes from previously non-coding DNA. In this Review, Bornberg-Bauer and Eicholt overview how protein-coding de novo genes...

rdcu.be

AI is Destroying the University and Learning Itself

Students use AI to write papers, professors use AI to grade them, degrees become meaningless, and tech companies make fortunes. Welcome to the death of higher education.

currentaffairs.org