phylogenetics Archives - Page 2 of 2 - Astrobiology

In black: enzymes and metabolic pathways inferred to be present in LUCA with at least PP = 0.75, with sampling in both prokaryotic domains. In grey: those inferred in our least-stringent threshold of PP = 0.50. The analysis supports the presence of a complete WLP and an almost complete TCA cycle across multiple confidence thresholds. Metabolic maps derived from KEGG47 database through iPath109. GPI, glycosylphosphatidylinositol; DDT, 1,1,1-trichloro-2,2-bis(p-chlorophenyl) ethane. -- Nature

Biochemistry & Organic Chemistry, Biogeochemical Cycles & Geobiology, Biosignatures & Paleobiology, Fossils & Paleontology, Origin & Evolution of Life, Status Report

The Nature Of LUCA – The Last Universal Common Ancestor – and its Impact on the Early Earth System

by Keith CowingJanuary 21, 2025January 21, 2025

The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based […]

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Status Report

Structural Enzymology, Phylogenetics, Differentiation, and Symbolic Reflexivity at the Dawn of Biology

by Keith CowingDecember 23, 2024December 23, 2024

The reflexive translation of symbols in one chemical language to another defined genetics. Yet, the co-linearity of codons and amino acids is so commonplace an idea that few even ask […]

Phylogenetic inference using Assembly Theory. A) Algorithmic pipeline for the generation of a phylogenetic tree from MS data using Joint Assembly. Recursive MA is employed to calculate approximated Joint MA indices for single and paired samples, which are used in JAO calculations (see methods). The JAO matrix represents the overlap of joint assembly spaces of samples, which is then transformed into a tree through an inference algorithm (WPGMA). B) Comprison of the assembly-based JAO phylogenetic tree model with the consensual genome-based model. Colors refer to the predefined cladal domains, as in Figures 4, and indicate the cladal cohesiveness of the clustering. Full annotations of the trees are included in Figure 7 and SI. -- q-bio.PE

AI - Data - Apps - Cybernetics, Biochemistry & Organic Chemistry, Biophysics, Biosignatures & Paleobiology, Fossils & Paleontology, Genomics, Proteomics, Bioinformatics, Imaging & Spectroscopy, Nomenclature, Systematics, Natural History, Origin & Evolution of Life, Status Report

Constructing the Molecular Tree of Life using Assembly Theory and Mass Spectrometry

by Keith CowingAugust 21, 2024August 21, 2024

The connected nature of all life on earth, dating back to the last universal common ancestor (LUCA), has been explored using knowledge of taxonomy and biochemistry, with significant insights enabled […]

ROP signaling -- Gregor Mendel Institute of Molecular Plant Biology of the Austrian Academy of Sciences

Biochemistry & Organic Chemistry, Biophysics, Genomics, Proteomics, Bioinformatics, Origin & Evolution of Life, Plant Biology, Press Release

ROP Signaling: Origin At Dawn Of Multicellular Plant Life

by Keith CowingDecember 2, 2023December 2, 2023

Plants regulate their development with a distinct group of molecular players. ROP proteins, a group of plant-specific proteins, are known to control plant tissue formation. Now, Hugh Mulvey and Liam […]

The consensus supertree produced from an analysis of 924 source trees from the journal IJSEM. Larger image -- RIO Journal

Genomics, Proteomics, Bioinformatics

The First Microbial Supertree From Figure-mining Thousands Of Papers

by Keith CowingMay 10, 2017August 31, 2026

[BBSRC] While recent reports reveal the existence of more than 114,000,000 documents of published scientific literature, finding a way to improve the access to this knowledge and efficiently synthesise it […]