u/jnpha

> The relationship between the three domains of life—Archaea, Bacteria, and Eukarya—is one of Biology’s greatest mysteries. Current favored models imply two ancestral domains, Bacteria and Archaea, with eukaryotes originating within Archaea. This type of models has been supported by the recent description of the Asgardarchaeota, the closest prokaryotic relatives of eukaryotes.
However, there are many problems associated with any scenarios implying that eukaryotes originated from within the Archaea, including genome mosaicism, phylogenies, the cellular organization of the Archaea, and their ancestral character. By contrast, all models of eukaryogenesis fail to consider two relevant discoveries: the detection of membrane coat proteins, and of phagocytosis-related processes in Planctomycetes, which are among the bacteria with the most developed endomembrane system.

• Devos, Damien P. "Reconciling asgardarchaeota phylogenetic proximity to eukaryotes and planctomycetes cellular features in the evolution of life." Molecular Biology and Evolution 38.9 (2021): 3531-3542.
  https://doi.org/10.1093/molbev/msab186 (open access)

Those who research this area, share your thoughts!

This was a fun read: One Graph Attempts To Connect Every Object In The Universe - Universe Today

Based on:
- Steward, Gabriel M., and Matthew Hedman. "The Cohesive Object Sequence: The Mass–Density Distribution of Astronomical Objects from Asteroids to Stars." Publications of the Astronomical Society of the Pacific 138.4 (2026): 041001. https://arxiv.org/abs/2604.06029

The images in order:

1. Damas et al 2022
   The synteny diagram shows a reconstruction of the chromosomal rearrangements Mammalia has went through (n.b. these are not single generation events); a close to home one is the crash fusion leading to our chromosome 2 (bottom of the image);
2. Schematic of said chr2 fusion from Vorob'eva et al 2006;
3. 20 Years Later
   Details galore of said fusion from Yang et al 2026;
4. I'll come back to that (Schultz et al 2023) in the comments.

(comments section for more)

Human-Chimp chromosome 19 alignment
A colored pixel in the difference columns is a single letter change. For the two big differences shown above (areas annotated A and E on the left):

> (A) Chimpanzee has a ∼1700 bp sequence not present in Human, (B,D) followed by an inversion, (E) which ends at a AAAC tandem repeat where Human has twice as many copies.

Source: Fig. 3 in:

• Seaman, Josiah, and Richard JA Buggs. "FluentDNA: Nucleotide visualization of whole genomes, annotations, and alignments." Frontiers in Genetics 11 (2020): 292.
  https://doi.org/10.3389/fgene.2020.00292

1-hour explanation from last year by Erika (Gutsick Gibbon): Okay How Similar are Humans and Chimps Genetically Now That We Have Full Genomes? - YouTube.

Sources:

• User:Conquistador, User:Dbachmann, CC BY-SA 4.0, via Wikimedia Commons
• Stringer, Chris. "What makes a modern human." Nature 485.7396 (2012): 33-35.
  https://www.nature.com/articles/485033a
• Dbachmann, CC BY-SA 4.0, via Wikimedia Commons

The first diagram is based on the second after incorporating the latest findings as of around 2017 (they are listed in the Wikimedia link). And doubtless the phylogeny is even clearer now; this is where your insights come in :)

Image source:

• Stefanie D. Hueber, Georg F. Weiller, Michael A. Djordjevic, Tancred Frickey, CC BY 4.0, via Wikimedia Commons

Quick background:

> [Hox genes] are general purpose in the sense that they are similar in many organisms; it doesn’t matter if it’s a mouse’s head or a fly’s head that is being built, the same gene directs the process. Small changes in such powerful regulatory genes, or changes in the genes turned on by them, could represent a major source of evolutionary change.
- berkeley.edu's Hox genes

Some links:

• The Nobel Prize in Physiology or Medicine 1995 - Press release - NobelPrize.org
• Lewis Wolpert's 1986 Christmas Lectures:
  https://www.youtube.com/@TheRoyalInstitution/search?query=wolpert
• Evo-devo biologist Enrico Coen lecture at The Royal Society from 2014:
  Cells to civilizations - YouTube

This is a short one for a change, and what I find as the shortest rebuttal.
And since Darwin lives rent free in their heads, I'll start there:

> It is so easy to hide our ignorance under such expressions as the “plan of creation,” “unity of design,” etc., and to think that we give an explanation when we only restate a fact.

(emphasis mine)
- Darwin, Origin, 1st ed., 1859.

 

Oh, look; he had considered it.
Restating facts is never an explanation. Imagine an engineer tasked with reverse engineering a competitor's device, and all they could state is, "It has interdependent components; I infer a designer made it". Or as Dr. Padian remarked during Dover, no one has gotten a Nobel for stating what an eight-year-old knows - yes! it has parts, and we've worked out the how.

This is how silly both arguments are.

 

And given the purpose of this sub, some links for the 99%:

• The Evolution of Complex Organs | Evolution: Education and Outreach | Springer Nature Link;
• Here's a simple live demonstration by Dr. Dan;
• A three-level masterclass by Dr. Zach on phylogenetics;
• A simple introduction: Misinterpretations about relatedness | berkeley.edu; and
• Testing Common Ancestry: It’s All About the Mutations - Article - BioLogos.

 

(also I'm curious to see if any will attempt to back up ID's rhetoric instead of deflecting)

Sources:

• Petter Bøckman, Public domain, via Wikimedia Commons
• Benton, Michael J., and David AT Harper. Introduction to paleobiology and the fossil record. John Wiley & Sons, 2020.

(for why I love them, see the comments)

From:
- Truman, James W. "The evolution of insect metamorphosis." Current Biology 29.23 (2019): R1252-R1268.
https://doi.org/10.1016/j.cub.2019.10.009 (open archive)

> Figure 1 Phylogeny of insects showing the major types of development. The figure shows how the three major types of insect development, ametabolous, hemimetabolous and holometabolous, map onto insect phylogeny, with examples of the immature and adult stages for each. The asterisk indicates neometabolous forms that have independently evolved a life history with a larva, pupa and adult. For the major orders the width of the boxes show the number of families through time.

David Goodsell, PDB-101: Molecule of the Month: Globin Evolution

Sorry, folks, for the three-month hiatus!

Previously on Mr Farina:

> WHAT DO YOU MEAN THEY FOUND SUGAR IN SPACE? > > WHAT DO YOU MEAN THEY MADE RNA IN CONDITIONS CONSISTENT WITH THE HADEAN? > > WHAT DO YOU MEAN OUT-OF-EQUILIBRIUM CONDENSED PHASES CAN PROVIDE A SELECTION MECHANISM FOR FUNCTIONAL SEQUENCES?

And now:

WHAT DO YOU MEAN THERE ISN'T A CHICKEN AND EGG PROBLEM?

 

New study from last month:

• Seitz, Christian, et al. "A Clue for the Hen and Egg Question: The Simultaneous Formation of Uracil and Amino Acids Under Simulated Hadean Conditions." Life 16.4 (2026): 624. https://doi.org/10.3390/life16040624

 

Basically, under "simulated [no, this isn't a computer simulation, it's real not-supernatural chemicals] Hadean hydrothermal conditions, acetylene, ammonia, cyanide, and carbon monoxide were reacted in aqueous solution in the presence of transition metal sulfides", and the stuff of life (uracil for RNA and amino acids for proteins) just oozed out.

Still, no magical barriers.
But, given the trending bleat, "But the experiment needed intelligence!!1!", welcome to theistic evolution, I suppose.

 

(If you're new to the scene, see here for why the shouting.)

Published today (open access), and something I hadn't a clue about:

> The biological significance of the transition metal molybdenum (Mo) lies in its function at the catalytic center of several enzymes that drive a wide spectrum of redox reactions underlying global biogeochemical cycles, yet a paradox persists. While modern life ubiquitously relies on Mo, geochemical evidence suggests that its availability in early Earth’s anoxic oceans was extremely limited. Modern organisms can use Mo down to trace levels; however, the rates of Mo-dependent metabolisms slow down when Mo availability decreases, posing fundamental questions about the extent to which changing Mo abundances shaped the evolution of molybdoenzymes, and when early life began harnessing Mo. > > Here, we confront this evolutionary enigma by reconstructing the temporal and ecological emergence of molybdoenzymes, their transport systems, and biosynthetic pathways. In parallel, we examine biological tungsten (W) usage due to shared chemical properties and cofactor biosynthetic pathways with Mo. We provide molecular dating evidence of Mo/W utilization back to the Eo- to Mesoarchean (~3.7–3.1 Ga). These findings challenge prevailing assumptions about trace metal availability on the early Earth and underscore the profound antiquity and adaptability of Mo-based biochemistry in shaping early microbial evolution.

Klos, A.S., Sobol, M.S., Boden, J.S. et al. Biological use of molybdenum and tungsten stems back to 3.4 billion years ago. Nat Commun 17, 3943 (2026). https://doi.org/10.1038/s41467-026-72133-0

 

Molybdenum in biology - Wikipedia

From Nilsson and Pelger's 1994 famous theoretical model ("A pessimistic estimate of the time required for an eye to evolve").
Full caption from Gregory 2008 and more context in the comments.

This schematic is from two months ago:

• Damatac, Amor, et al. "A cellular basis for the hourglass pattern in vertebrate embryogenesis." Nature Communications 17.1 (2026): 2404.
  https://www.nature.com/articles/s41467-026-69828-9

The caption:

> This schematic highlights the hourglass pattern at the resolution of individual cellular trajectories, revealing two peaks of developmental conservation across vertebrate species: at the onset of neurulation (left) and at the onset of the pharyngula stage (right). The asymmetry of this model is also captured: later stages exhibit greater divergence than the early stages due to increased lineage-specific modifications. This asymmetry emphasizes how evolutionary constraints are strongest during mid-embryogenesis, while later stages provide greater developmental flexibility, facilitating species-specific adaptations.

The TL;DR:
Since the early 2010s transcriptome-level studies have added support for the hour-glass model, where younger (newer) genes are expressed in the earlier and later stages of embryogenesis, with a conserved (older genes) and susceptible-to-perturbation middle stage, all relatively speaking.

OC photo.
The piece: https://gem.eg/en/collection/artefacts/anubis-on-a-chest

Based on my calculation based on the placard, it's ~3.3 kya.
Also sorry for the exposure; it's a low-light section.

> ... he was covered in a linen cloth which was dated to Year 7 of King Akhenaten's reign.

Contrary to the popular misconception, the origin of mitochondria "was not a single saltational event, as it is sometimes portrayed" (Roger et al. 2017). And ancestral state reconstruction supports the above syntrophy (Bremer et al. 2022).
More recently, Nobs et al. 2026 have found similar structures (and syntrophy) in modern analogs of the ancestral Asgard archaeon.

It's an exciting area of research, and that schematic is a favorite of mine.
The image's source:

• Baum, David A., and Buzz Baum. "An inside-out origin for the eukaryotic cell." BMC biology 12.1 (2014): 76.
  https://link.springer.com/article/10.1186/s12915-014-0076-2/figures/1

The caption:

> Inside-out model for the evolution of eukaryotic cell organization. Model showing the stepwise evolution of eukaryotic cell organization from (A) an eocyte ancestor with a single bounding membrane and a glycoprotein rich cell wall (S-layer) interacting with epibiotic α-proteobacteria (proto-mitochondria). (B) We envision the eocyte cell forming protrusions, aided by protein-membrane interactions at the protrusion neck. These protrusions facilitated material exchange with proto-mitochondria. (C) Selection for a greater area of contact between the symbionts would have led to bleb enlargement and the eventual loss of the S-layer from the protrusions. (D) Blebs would have then been further stabilized by the development of a symmetric nuclear pore outer ring complex (Figure 2) and through the establishment of LINC complexes that, following the gradual loss of the S-layer, physically connected the original cell body (the nascent nuclear compartment) to the inner bleb membranes. (E) With the expansion of blebs to enclose the proto-mitochondria, a process that would have facilitated the acquisition of bacterial lipid biosynthesis machinery by the host, the site of cell growth would have progressively shifted to the cytoplasm, facilitated by the development of regulated traffic through the nuclear pore. At the same time, the spaces between blebs would have enabled the gradual maturation of proteins secreted into the environment via the perinuclear space through glycosylation and proteolytic cleavage. (F) Finally, bleb fusion would have connected cytoplasmic compartments and driven the formation of an intact plasma membrane, perhaps through a process akin to phagocytosis whereby one bleb enveloped the whole. This simple topological transition would have isolated the endoplasmic reticulum from the outside world, driven the full development of a system of vesicular trafficking, and established strict vertical transmission of mitochondria, leading to a cell with modern eukaryotic cell organization.

For the aforementioned Nobs et al. 2026, I recently shared it here:

• An Asgard archaeon from a modern analog of ancient microbial mats : evolution