Excited to visit the @alleninstitute.org for the Lake Conference on Emergence and Self-Organization: lakeconferences.org/conf/17d01bb...
I'll speak about Affordance Theory, pioneered by JJ Gibson in the 1970s. We use this framework to explore the evolution of eukaryotic endomembranes (see 🧵 below).
Sahana (right) and Kritika (left) who drove the project.
This is the amazing PhD work of my student Sahana Shridhar, who is also responsible for the beautiful figures. Also, this project would not have been possible without Kritika Kumari, who was able to massively speed up our computations during her year interning in our lab.
Do send us your comments!
Four directed graphs, whose nodes are compartments (proto-endoplasmic reticulum, plasma membrane, and other intracellular compartments) and whose edges are vesicle flows. The network includes flows that resemble phagocytosis, secretion, and receptor recycling.
Amazingly, this evolutionary process is able to reach complex endomembrane graphs with vesicle flows reminiscent of those found in modern eukaryotes.
Evolutionary landscape of endomembrane systems. Each node is a "motif" representing the functional complexity of the underlying systems. Each edge is a possible transition. At the bottom is the simple proto-eukaryotic starting point. At top are the most complex systems, which are evolutionary endpoints.
We construct an entire evolutionary landscape, starting from a simple proto-eukaryotic system and moving up through a hierarchy functional complexity. Each transition in this landscape backed up by an explicit series of molecular mutations.
A series of endomembrane systems, represented as directed graphs where nodes are compartments, vesicle flows are edges, and compositions are represented by colors. Each graph can transition to the next through basic evolutionary moves: gene duplication, deletion, and simple mutations.
The only evolutionary moves we allow are gene duplication, deletion, and simple mutations. We show that these are sufficient to convert simple endomembrane systems into more complex ones.
Table with 6 columns. Col 1: Number of coats. Col 2: Number of compartments and edges. Col 3: Number of graphs tested, going up to 25 billion. Cols 4-6: The number of graphs consistent with molecular rules only number in the thousands.
We do this by computationally exploring billions of possible endomembrane systems. We find that systems allowed by molecular rules are extremely rare. So how can evolution search this sparse space to discover complex endomembrane configurations?
Evolutionary landscape of endomembrane systems. On top are two possible endomembrane systems, represented as directed graphs (pER: proto-endoplasmic reticulum; PM: plasma membrane; IC: intracellular compartment). In the layer below, endomembrane graphs are represented as nodes (white dots) connected by evolutionarily viable transitions (red lines). Collectively these dots and lines define an evolutionary landscape. The landscape breaks up into less functional (left) and more functional (right) endomembrane systems, introducing a selective bias.
How did eukaryotic cells get their Golgi, endosomes, lysosomes and other endomembrane compartments? We show that endomembrane evolution depends on long periods of neutral molecular exploration, punctuated by sudden leaps.
New preprint: www.biorxiv.org/content/10.6...
Preprint from @thattai.bsky.social provides an elegant solution to a profound question: How can evolution – driven by gene duplication, deletion, and mutations produce complex endomembrane systems?
Punctuated Evolution of Endomembrane Compartments in Proto-Eukaryotes
www.biorxiv.org/content/10.6...
Protocells from three inorganic salts, some formaldehyde and water?
They grow? They synthesise organic molecules of core biomolecular classes: amino acids, sugars, lipid-like motifs?
And, there are similar structures in today's oceans?
Yes! Read on.
arxiv.org/abs/2601.11013
It was a pleasure talking to Prof. Mahesh Panchagnula of IITM for his podcast.
Our conversation went far beyond career advice, covering how living systems work, the role of math in the life sciences, and where groundbreaking discoveries in biology come from.
youtu.be/wZeUX3G13pk?...
Representation of spherical harmonics as lobed objects, indexed by l, m.
Clearly these are spherical harmonics...
Gutting the humanities will not save the sciences. This piece is worth reflecting on: "The broad liberal arts education Carl Sagan received at the University of Chicago played an important role in his development as a scientist and intellectual."
www.loc.gov/collections/...
It's a great time to be studying eukaryogenesis, with so much new experimental data from diverse species. I want to thank several folks with whom I've been discussing these ideas for many years, especially @buzzbaum.bsky.social, @gautamdey.bsky.social, @ishier.bsky.social, @dackslabecb.bsky.social.
Open questions remain. Intracellular membranes have not so far been confirmed in Asgard archaea. And what of the origin of other eukaryotic organelles? Could they be stabilised versions of ancient tubular carriers? I'd love to hear your thoughts!
New preprint: ecoevorxiv.org/repository/v...
Diagram showing Asgard ESP homologs involved in the generation of tubular membrane carriers in modern eukaryotes. The left panel lists sequential stages of carrier generation: initiation, cargo loading, tubulation, scission, tethering, and fusion, with associated protein complexes such as Arf GTPases, BAR domain proteins, ESCRTs, and SNAREs. The right panel shows a stylized eukaryotic cell, indicating sites where tubular carriers are found in present-day eukaryotes (ER exit site, endosome/TGN, plasma membrane).
A closer look shows that in present-day eukaryotes these Asgard ESPs are involved in the generation of tubular carriers at the ER, endosomes/TGN, and at the plasma membrane. In the review I discuss several new studies showing that Asgard versions of these proteins can indeed generate tubules!
AlphaFold-based structural alignments of Asgard archaeal (red) and eukaryotic (blue) homologs of membrane trafficking proteins. Shown are COPII component Sec24, TRAPP subunit TRAPPC3, AP2 μ and σ subunits, ESCRTIII protein CHMP1B, retromer component VPS29, BAR domain protein Arfaptin, and CORVET/HOPS subunit VPS16. Each pair except CORVET/HOPS show strong structural similarity despite the evolutionary distance.
Asgard archaeal genomes encode many eukaryotic signature proteins, previously thought to be restricted to eukaryotes. In modern eukaryotes several of these ESPs are involved in membrane traffic. But Asgard archaea lack canonical vesicle coats. So what were these proteins doing in FECA?
A simplified evolutionary tree showing how eukaryotes arose from a merger between Asgard archaea (green) and α-proteobacteria (brown). Key nodes include LUCA (last universal common ancestor), FECA (archaeal first eukaryotic common ancestor), FMCA (first mitochondrial common ancestor) and LECA (last eukaryotic common ancestor). The mitochondrial endosymbiosis event is highlighted.
Eukaryotes arose via a merger between archaea and bacteria, with eukaryotic traits emerging gradually on the path from FECA (the archaeal first eukaryotic common ancestor) to LECA (last eukaryotic common ancestor). What if FECA was already an atypical archaeon with rudimentary eukaryote-like traits?
A schematic showing two models for the evolution of the eukaryotic cell plan starting from an archaeal ancestor. The "inside-out" and "outside-in" models both lead to an intermediate stage with internal and plasma membranes connected by tubules. The sequence continues through the formation of an endomembrane lumen, followed by the emergence of membrane contact sites and tubular carriers, and finally coated vesicles and stable compartments.
I set out to review the evolution of eukaryotic intracellular traffic, but along the way a new hypothesis came into focus: maybe the earliest membrane carriers were tubules, not coated vesicles!
New preprint: ecoevorxiv.org/repository/v...
Here’s the idea. 🧵
The week after that, I'll be at Statphys29 in Florence.
At both meetings I'll speak about new work on the evolution of complex vesicle traffic networks in proto-eukaryotes.
Looking forward to catching up with many old friends on this trip!
statphys29.org/plenary-and-...
I'll be in Kyoto all week, at the joint meeting of the Asian International Conference on Mathematical Biology & Japanese Society for Mathematical Biology.
It features a broad lineup of topics and interesting talks, with speakers from across Asia and the world. pub.confit.atlas.jp/en/event/acm...
New efforts in conservation and venom research are helping humans and snakes co-exist. So many interesting facts I did not know, in this great piece by Indulekha Aravind.
www.thehindu.com/society/indi...
A truly unexpected discovery, and an important insight into how "life finds a way"!
The solution to the puzzle involves modifying paths in an Nx3 array of squares. First, replace each diagonal step with a special point to its top left. Then associate a minus sign with every edge below that point. The first three columns correspond to X, Y, Z. The image shows examples of this transformation, with the original path on the left and the modified path on the right. Below the modified path is the coordinate of a specific cube in the octahedron, e.g. X-2Z is one positive step in the X direction and two negative steps in the Z direction. The path endpoints correspond to the specific "layer" of each cube in the octahedron (0 is the central cube, and 1, 2, 3 are successive layers). This construction clearly generalises to more dimensions (more columns to the right) and more layers (more rows on top).
Great puzzle @nedbat.com @wang.social. The trick was to find enough minus signs! Here's the answer: Replace each diagonal with a special point to its top left, and associate ALL edges below with a minus sign. The first three columns are X,Y,Z. This gives coordinates of each cube in the octahedron.
Sketch of T. Rex and references to papers regarding possible use of forelimbs. Caption: "My secret hypothesis: Tyrannosaurus Rex had a pouch in which it carried its young. Can you think of ways to test this? Let me know!"
My secret hypothesis
Video of our #blrlitfest panel discussion "Light Year in Lines: How Science Speaks" is now online!
As I started by saying: only in Bangalore would the science session draw a bigger crowd than any other session at a litfest!
www.youtube.com/watch?v=5Oq0...
Photo of Jawaharlal Nehru and MIT President James Killian, 1949. Courtesy of the MIT Museum.
Cover of "The Technological Indian" by Ross Bassett.
Bal Gangadhar Tilak looked to MIT as a model for India to emulate. Many MIT students interacted with Gandhi. MIT helped establish IITs in post-independence India.
These and other chapters in the long engagement between MIT and India are chronicled in Ross Bassett's book "The Technological Indian".
Ranu Boppana and Mukund Thattai, with other visitors at the exhibit.
Photograph of Almitra Patel from MIT yearbook, 1958. Image courtesy of Almitra H (Sidhwa) Patel.
This is the first time the exhibit has been shown outside MIT. It grew out of a collaboration between MIT history professor Sana Aiyar, Ranu Boppana and Nureen Das.
Here's a sample from the exhibit: the 1958 yearbook photo of Almitra Patel, the first South Asian woman to receive a degree at MIT.
Photo of Jawaharlal Nehru and MIT President James Killian, 1949. Courtesy of the MIT Museum.
Cover of "The Technological Indian" by Ross Bassett.
Bal Gangadhar Tilak looked to MIT as a model for India to emulate. Many MIT students interacted with Gandhi. MIT helped establish IITs in post-independence India.
These and other chapters in the long engagement between MIT and India are chronicled in Ross Bassett's book "The Technological Indian".
It was great to see the exhibit "South Asia and the Institute" at Science Gallery Bengaluru.
MIT played an outsized role in pre- and post-independence India, beginning with the first Indian student in 1882 (when MIT was barely two decades old!) digital-exhibits.libraries.mit.edu/s/south-asia...
Raj Rewal, Untitled Work, circa 1965, coloured ink on paper.
Raj Rewal, whose iconic brutalist Hall of Nations in New Delhi was demolished by the government in 2017, is also the architect of the National Centre for Biological Sciences campus. The nonagenarian recently shared his striking sketches from the 1960s: www.architecturaldigest.in/story/master....