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Mukund Thattai

@thattai.bsky.social
605 followers 237 following 74 posts

Physicist fascinated by biology, trying to understand how cells work. Also: public engagement, science and culture, puzzles.

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Mukund Thattai @thattai.bsky.social · 01/10/2026
GAMX is a day-long event featuring new tabletop games by Indian creators: 3 Oct, 10am - 9pm, Bangalore. I'll show my new game - Swalpa Adjust Maadi! - where you dig up Bangalore roads to cut off power and water from your opponents! Entry is free! We need feedback, come and try out the games.
Poster for GAMX: 3 Oct 2026, 10am - 9pm at Yutori Spaces, BangaloreThe board for Swalpa Adjust Maadi! Pipes snake across the city, players dig up roads, and houses are left with no power and water!The boards are modular, made by arranging a single kind of tile at random.
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Mukund Thattai @thattai.bsky.social · 27/09/2026
Good question! There are ways to protect against it, just like audio feedback... true signal must exceed recycled signal. But this depends on how many people choose to contribute music to the common pool.
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Mukund Thattai @thattai.bsky.social · 27/09/2026
Model collapse (AI fed on its own slop will eventually revert to a fixed distribution) is easy to explain - this is exactly what happens during audio feedback: a mic amplifies the output of the mechanical speaker instead of the human speaker. The result is a single frequency, instead of music.
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Mukund Thattai @thattai.bsky.social · 12/08/2026
I've made lots of updates to improve gameplay! For beginners: a tutorial, a "Hints" button, and a Practice mode. For experts: higher-scoring boards that encourage more build and steal drama. Try out today's game and share your score with friends! mthattai.github.io/Swalpa-Adjust-Maadi/
mthattai.github.io
Swalpa Adjust Maadi
The game where you dig up Bangalore's roads for fun!
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Mukund Thattai @thattai.bsky.social · 01/08/2026
To protest the unending Bangalore roadworks, I created a game called Swalpa Adjust Maadi (Kannada for "please bear with the inconvenience"). You play the contractor digging up the roads, the residents are mute spectators who always lose! A new puzzle each day: mthattai.github.io/Swalpa-Adjus...
mthattai.github.io
Swalpa Adjust Maadi
A game where you dig up Bangalore's roads.
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Mukund Thattai @thattai.bsky.social · 27/07/2026
The name of this game, "Swalpa Adjust Maadi", is a Kannada phrase that means: please adjust a little, please bear with the inconvenience. It encapsulates the outlook on life that we Bangaloreans adopt to cope with the chaos and ongoing destruction of this once-beautiful city we love so much.
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Mukund Thattai @thattai.bsky.social · 11/07/2026
Is it bad that I look at this and immediately think: 1. Textbook DNA replication. 2. Bacteria (and some archaea). 3. Eukaryotes (and some archaea). ?
Image with three candles. Top: one flame at the end, caption: "How I should be doing it". Middle: flames at both ends, caption: "What the doctor advised against". Bottom: Multiple flames, caption: "Current situation".
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Mukund Thattai @thattai.bsky.social · 05/07/2026
Rather than taking on wingnuts and alien conspiracies, we should do the harder job of confronting the entrenched molecule-centric view of biology, one which conditions students to use precisely such reductionist language to describe the "functions" of genes in their talks, papers and theses.
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Buzz Baum @buzzbaum.bsky.social · 05/07/2026
This seems more like a hard sell than a soft cell.
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Mukund Thattai @thattai.bsky.social · 03/07/2026
Congratulations to the group on completing 25 years!
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Mukund Thattai @thattai.bsky.social · 03/07/2026
#glycotime! Eukaryotic cells can synthesise 1000s of glycans within the same Golgi. What tradeoffs occur when you try to maximise the yield of multiple trees simultaneously? We used a computational model to explore this, now published in @biophysj.bsky.social: www.sciencedirect.com/science/arti...
Figure showing how cells can synthesise multiple glycan trees simultaneously. A: Examples of two real glycan trees. B: Example reaction pathway to synthesise a desired glycan tree, including off-pathway reactions which lead to errors. C: Abstract setting showing three trees whose synthesis must be simultaneously optimised using a Pareto-optimality framework.
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Mukund Thattai @thattai.bsky.social · 20/06/2026
Representational drift happens within single cells too! The informational scaffold within a cell can change over evolutionary time, while functional molecules remain correctly localized. www.biorxiv.org/content/10.6...
Left: Cellular organelles (nodes) and vesicle traffic flows (edges) represented as a directed graph. Colors represent molecular labels, a type of information. Right: a functional molecule is localized to a specific organelle, due to interactions with labels. The underlying network changes while the funtional molecule remains correctly localized throughout, an example of representational drift in cell biology.
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Mukund Thattai @thattai.bsky.social · 15/06/2026
At a Thai restaurant in the 1970s, Feynman formulated and solved the problem of whether to stick with a favourite dish (ginger chicken) or try something new. 50 years later, his handwritten calculation has been deciphered and shown to be optimal! A fun read @pnas.org: www.pnas.org/doi/10.1073/...
Feynman's handwritten notes from a Thai restaurant, formulating and solving his "Restaurant Problem", preserved by his colleague Ralph Leighton.
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Thomas Lecuit @thomaslecuit.bsky.social · 13/06/2026
This will be on 26 June in Paris! 🤩You are welcome to join and participate in this exciting 1-day conference at the College de France on Biological computational accross areas of biology. Fantastic speakers. Free, no registration, at the heart of Paris on a lovely season. Worth planning a weekend…?
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Mukund Thattai @thattai.bsky.social · 25/05/2026
Why is mercury, but not cadmium, a room-temperature liquid? Why is gold, but not silver, yellow? Why are lead-acid batteries better than tin-acid ones? Amazingly, all these are due to relativistic corrections for electrons travelling close to the speed of light! en.wikipedia.org/wiki/Relativ...
en.wikipedia.org
Relativistic quantum chemistry - Wikipedia
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Will Ratcliff @wcratcliff.bsky.social · 15/05/2026
1/35 New preprint! We show that obligate multicellularity removes fundamental population genetic barriers to multicellular adaptation. Even a brief unicellular phase can dramatically constrain the evolution of beneficial multicellular traits. www.biorxiv.org/content/10.6...
biorxiv.org
Obligate multicellularity circumvents population genetic barriers to collective-level adaptation
Complex multicellularity has evolved in just five lineages (animals, plants, brown algae, red algae, and fungi) and in each case, these organisms develop clonally and are obligately multicellular. While prior work has shown that clonal development plays a critical role in the evolution of complex multicellularity, none has disentangled this from the impact of obligate vs facultative multicellular life cycles. Here we use experimental evolution with engineered snowflake yeast ( Saccharomyces cerevisiae ) to directly test how life cycle structure affects multicellular adaptation. We created isogenic strains capable of switching between unicellular and clonal multicellular phases, then evolved populations for 192 days under obligately multicellular, facultatively multicellular, and obligately unicellular regimes. Obligately multicellular populations rapidly evolved larger size, primarily driven by a whole genome duplication, in all five replicates. Facultative populations showed dramatically constrained evolution, with tetraploidy evolving in only 2/10 facultative populations despite experiments demonstrating that it is strongly beneficial across the full life cycle. Mathematical modeling reveals the mechanistic basis for this constraint: facultative life cycles create establishment barriers through two population genetic effects. Group formation dramatically reduces the number of units of selection, making beneficial multicellular mutations vulnerable to drift. This asymmetry in population size between life cycle phases also allows cell-level selection to overpower group-level selection, eliminating mutations that provide group-level benefits but carry cell-level costs. These findings demonstrate that obligate multicellularity circumvents fundamental population genetic barriers to collective-level adaptation, helping explain why complex multicellularity has evolved exclusively in obligately multicellular lineages, and suggesting similar constraints may operate in other evolutionary transitions in individuality. ### Competing Interest Statement The authors have declared no competing interest. U.S. National Science Foundation, https://ror.org/021nxhr62, DEB-1845363 Howard Hughes Medical Institute Gilliam Fellowship National Science Foundation Graduate Research Fellowship
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Andrew Roger @andrewjroger.bsky.social · 11/05/2026
Nice review @thattai.bsky.social ! Very helpful! Little quibble: Margulis didn't independently come up with the idea. In that paper she even cites Wallin for suggesting mitochondria derive from symbionts.
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Daniel Brady Mills @danbmills.bsky.social · 09/05/2026
Lynn did acknowledge these earlier authors (e.g., Merechowsky, Wallin), though, in her 1967 paper. "...these ideas are not new..." This is often overlooked, both by people who claim that she "stole" these ideas, as well as those who claim that she didn't become aware of them until later.
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Mukund Thattai @thattai.bsky.social · 11/05/2026
Thanks! Yes, I should clarify that she acknowledged earlier ideas about symbiosis. The contribution that Margulis gets deserved credit for is the careful synthesis of accumulated evidence.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
This is a great question. Similarly, there are also nucleotide-sugars transported into the Golgi lumen. In bacteria these stay in the cytoplasm.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
Many mysteries remain. Central among these: both the lipids and viruses of modern eukaryotes are derived from bacteria, not archaea. This requires explanation. Experiments on new model organisms bring us closer than ever to answering these questions. A great time to do evolutionary cell biology!
Cover of "Evolutionary Cell Biology", a textbook by Michael Lynch.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
The "tubules-first model" suggests Asgard archaea should have internal membranes. Do they? Just as our review was being proofed, the Baum lab reported that the Asgard Y. umbracryptum has heterogeneous internal membranes! It's not yet clear which proteins regulate their formation.
Internal membranes in the Asgard archaeon Y. umbracryptum. Image credit: MacLeod et al., 2025, An Asgard archaeon with internal membrane compartments.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
Exciting new studies show that Asgard proteins do remodel membranes. In fact, Asgard machinery can support every step in tubule formation. This is the basis of the "tubules-first model" for the origin of eukaryotic membrane traffic: tubular carriers may have emerged before spherical coated vesicles.
EM images showing how ESCRT-III proteins from Asgard archaea can tubulate membranes. Image credit: Souza et al., 2025, Asgard archaea reveal the conserved principles of ESCRT-­ III membrane remodeling.Left: Asgard-encoded proteins that support the formation of membrane tubules. Right: locations in modern eukaryotes where Asgard-derived machinery drives tubule formation. Image credit: Thattai, 2026, A Tubules-First Model for the Origin of Eukaryotic Membrane Traffic.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
Asgard archaea express proteins otherwise found only in eukaryotes. These "eukaryotic signature proteins" include many related to modern membrane traffic machinery. But "coatomers" like clathrin, COPI and COPII that generate vesicles in eukaryotes are absent. What were the ancestral cargo carriers?
Eukaryotic signature proteins in Asgard archaeal genomes. These include proteins annotated as being involved in "Trafficking" and "Endosomal sorting". Image credit: Eme et al., 2023, Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes.Coatomers that are required to generate coated spherical transport vesicles in eukaryotes. Image credit: Rout & Field, 2017, The Evolution of Organellar Coat Complexes and Organization of the Eukaryotic Cell.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
But this proto-eukaryote is still missing many features of modern eukaryotic cells. Where did the endomembrane compartments other than the ER, like the Golgi apparatus, endosomes and lysosomes, come from? How did the system of carriers ferrying cargo between these compartments arise?
Phases of eukaryote evolution, starting from the archaean-bacterial symbiosis, via a proto-eukaryotic stage with internalized mitochondria and an endomembrane (the nuclear envelope), to the last eukaryotic common ancestor (LECA) which is as complex as a modern protist, with multiple endomembrane compartments exchanging vesicles. Image credit: Thattai, 2023, Molecular and cellular constraints on vesicle traffic evolution.Models of eukaryogenesis. The critical step is the creation of the endomembrane lumen. Subsequent to this stage, membrane-bounded carriers are required to ferry lipids and proteins between endomembranes and the plasma membrane. Image credit: Thattai, 2026, A Tubules-First Model for the Origin of Eukaryotic Membrane Traffic.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
Fleshing out this model: an ancestral Asgard archaeon eventually engulfs an alphaproteobacterium. This results in endosymbiotic mitochondria, as well as the first endomembrane with its own lumen. This endomembrane is the proto-endoplasmic reticulum, a portion of which is the nuclear envelope.
Archaeal and bacterial contributions to modern eukaryotes. Image credit: Tobiasson et al., 2026, Dominant contribution of Asgard archaea to eukaryogenesis.Simultaneous origin of mitochondria and endomembranes. Image credit: Baum & Spang, 2023, On the origin of the nucleus: a hypothesis.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
It would take five more years for an Asgard archaeon to be grown in a lab by Imachi and colleagues (with a doubling time of 14-25 days!). Amazingly, these cells have elaborate surface protrusions supported by actin-like filaments, reminiscent of the archaeal host in the inside-out model.
Prometheoarchaeum syntrophicum cells, showing surface protrusions. Image credit: Imachi et al., 2020, Isolation of an archaeon at the prokaryote–eukaryote interface.Actin-like filaments within surface protrusions of Lokiarchaeum ossiferum cells. Image credit: Rodrigues-Oliveira et al., 2022, Actin cytoskeleton and complex cell architecture in an Asgard archaeon.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
At the same time, Buzz and David Baum put forward their inside-out hypothesis for the origin of eukaryotes. In this model, an ancestral archaeon has surface protrusions that increase contact area with symbiotic bacteria. These protrusions eventually engulf the bacteria, which become mitochondria.
Inside-out model for the origin of eukaryotes. Image credit: Baum & Baum, 2014, An inside-out origin for the eukaryotic cell.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
In 2015 Ettema and colleagues report that sediments from Loki's Castle (a field of deep sea hydrothermal vents near Iceland) contain DNA from a previously unknown archaeal group, closely related to eukaryotes. These "Lokiarchaeota" are the first known members of the Asgard archaea.
A robotic submarine at Loki's Castle, near a hydrothermal vent.Phylogenetic tree showing the new group Lokiarchaeota, and their relationship to eukaryotes. Image credit: Spang et al., 2015, Complex archaea that bridge the gap between prokaryotes and eukaryotes.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
Modern sequence data shows that eukaryotes are chimeras of the two prokaryotic groups! Our metabolic genes have bacterial origins, our DNA replication, transcription and translation genes (including rRNA) have archaeal origins. But which present-day bacteria and archaea are our closest relatives?
Diagram showing the history of different classes of eukaryotic genes. Some are bacterial in origin, some are archaeal in origin. Image credit: Baum & Spang, 2023, On the origin of the nucleus: a hypothesis.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
In the 1970s, Carl Woese used ribosomal RNA sequences to classify all of life for the first time. Prokaryotes broke into two: the bacteria, and a previously unknown group, christened the archaea! rRNA sequences suggested eukaryotes were more similar to archaea. But this turned out to be misleading.
Photograph of Carl Woese. Image credit: IGB.Tree of life as inferred by Woese using rRNA, showing three groups - Bacteria, Archaea, and Eucarya. The root of the tree is tentatively placed within the bacterial branch, suggesting that eukaryotes are more closely related to bacteria than to archaea. Image credit: Norman Pace.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
In 1967 Lynn Margulis argued that mitochondria were once free-living bacteria, symbiotically acquired by a host cell. Similar ideas had been proposed in the early 20th century, but Margulis came to them independently. Her influential paper was rejected by fifteen journals before being published.
Photograph of Lynn Margulis on the day of her wedding to Carl Sagan.Abstract of Lynn Margulis's paper: "On the Origin of Mitosing Cells" - 1967, Journal of Theoretical Biology.
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Mukund Thattai @thattai.bsky.social · 09/05/2026
The origin story of eukaryotes has more plot twists than a Hollywood blockbuster! 🧵 Read more in my new review: doi.org/10.1146/annu.... Only in the 1960s were the terms "prokaryote" and "eukaryote" formalized! As originally defined, eukaryotes had complex architectures, prokaryotes did not.
Abstract of "The Concept of a Bacterium" by Stanier and van Niel, 1967, where the terms "eukaryotes" and "prokaryotes" were formalized.
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Mukund Thattai @thattai.bsky.social · 08/05/2026
Our world could do with 100 Attenboroughs. www.theguardian.com/tv-and-radio...
theguardian.com
‘The greatest ambassador for life on Earth’: Tributes paid to David Attenborough on his 100th birthday
Naturalist says he has been ‘overwhelmed by greetings’ as milestone is marked with event at Royal Albert Hall
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Mukund Thattai @thattai.bsky.social · 07/05/2026
Out now in @annualreviews.bsky.social: my review on the origins of eukaryotic membrane traffic! I propose that archaea-derived proteins supported a primordial system of tubules to ferry cargo between compartments. Modern coated vesicles may have been a later innovation. doi.org/10.1146/annu...
doi.org
A Tubules-First Model for the Origin of Eukaryotic Membrane Traffic
The discovery of membrane trafficking proteins in Asgard archaea—the closest archaeal relatives of eukaryotes—reveals the deep evolutionary roots of the eukaryotic endomembrane system. This review syn...
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Thomas Lecuit @thomaslecuit.bsky.social · 27/04/2026
Here is the announcement of a Symposium @college-de-france.fr on 26 June on Information Flow and Computation in Biological systems. A great line of speakers on a variety of topics from embryogenesis to neuroscience, immunology and microbiology. Free entrance, come if you are in Paris end of June 🤩
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Mukund Thattai @thattai.bsky.social · 18/04/2026
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).
lakeconferences.org
Conference - Modeling Life from Cells to Tissues: Emergence and Self-Organization - Lake Conferences
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Mukund Thattai @thattai.bsky.social · 15/04/2026
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!
Sahana (right) and Kritika (left) who drove the project.
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Mukund Thattai @thattai.bsky.social · 15/04/2026
Amazingly, this evolutionary process is able to reach complex endomembrane graphs with vesicle flows reminiscent of those found in modern eukaryotes.
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.
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Mukund Thattai @thattai.bsky.social · 15/04/2026
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.
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.
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Mukund Thattai @thattai.bsky.social · 15/04/2026
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.
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.
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Mukund Thattai @thattai.bsky.social · 15/04/2026
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?
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.
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Mukund Thattai @thattai.bsky.social · 15/04/2026
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...
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.
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Ishier Raote @ishier.bsky.social · 15/04/2026
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...
biorxiv.org
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Shashi Thutupalli @stpalli.bsky.social · 13/02/2026
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
arxiv.org
De novo emergence of metabolically active protocells
A continuous route from a disordered soup of simple chemical feedstocks to a functional protocell -- a compartment that metabolizes, grows, and propagates -- remains elusive. Here, we show that a homo...
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Mukund Thattai @thattai.bsky.social · 01/10/2025
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?...
youtu.be
CRISPR, Vaccines & Biotech: Exploring Life Sciences with Prof. Mukund Thattai | Episode 22
YouTube video by Prof Mahesh Panchagnula
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Mukund Thattai @thattai.bsky.social · 26/08/2025
Clearly these are spherical harmonics...
Representation of spherical harmonics as lobed objects, indexed by l, m.
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Mukund Thattai @thattai.bsky.social · 24/08/2025
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/...
loc.gov
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Mukund Thattai @thattai.bsky.social · 04/08/2025
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.
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Mukund Thattai @thattai.bsky.social · 04/08/2025
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...
ecoevorxiv.org
A Tubules-First Model for the Origin of Eukaryotic Membrane Traffic
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