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Gerben de Zwaan

@gerbenz.bsky.social
359 followers 171 following 22 posts

PhD candidate at Microbial Evolution/Ettema lab @ the Laboratory of Microbiology - Wageningen University and Research. Enthusiastic about Evolution, Microbiology, Microscopy. www.gerbendezwaan.eu/

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Reposted by Gerben de Zwaan
Mathilda Lennartz @mathilda95.bsky.social · 22h
UPDATE!: I am absolutely stoked that the second paper of my PhD is now out in @natcellbio.nature.com :D. We combined lipid imaging, STED microscopy, and mathematical modelling in a super cool team effort to quantify lipid partitioning inside clathrin-coated pits. www.nature.com/articles/s41....
nature.com
Quantification of lipid sorting during clathrin-mediated endocytosis - Nature Cell Biology
Lennartz et al. evaluate lipid enrichment in clathrin-coated pits and observe that the differential lipid partitioning into clathrin-coated pits is largely driven by the lipid asymmetry of the plasma ...
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Florian Mayer @florianmayer.bsky.social · 11/09/2026
Excited to share our preprint on Ignicoccus cell divison: only the inner membrane divides, progeny cells accumulate in cell clusters and pop-out! www.biorxiv.org/content/10.6... Great work with the labs: @buzzbaum.bsky.social @curiousdina.bsky.social @anja1.bsky.social @tbharat-lab.bsky.social
biorxiv.org
The life cycle of an archaeon with multiple membranes
Many prokaryotes are diderms. They divide using an FtsZ division ring to simultaneously constrict physically coupled inner and outer membranes to form daughter cells with two membranes. Currently, onl...
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Baukje Hoogenberg @baukjeje.bsky.social · 11/09/2026
Do you want to label the nuclear envelope? Do you work on a non-model species? Try Concanavalin A! We tested ConA on various species across the eukaryotic tree and find it is a very useful ExM-compatible marker for the NE and ER. Read all about it in our preprint: www.biorxiv.org/content/10.6...
biorxiv.org
Concanavalin A as a pan-eukaryotic nuclear envelope marker for expansion microscopy
Across eukaryotes, the nuclear envelope exhibits distinct remodelling strategies during mitosis: complete breakdown (open mitosis), partial disruption (intermediate), or full retention (closed). Howev...
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Trends in Microbiology @cp-trendsmicrobiol.bsky.social · 22/08/2026
The narrowing prokaryote–eukaryote divide reveals a complexity spectrum
dlvr.it
The narrowing prokaryote–eukaryote divide reveals a complexity spectrum
Cellular organisms can be divided into two basic types of cells: the prokaryotic cells of Bacteria and Archaea and the eukaryotic cells. The rapidly expanding knowledge of the diversity and ultrastructure of prokaryotic cells has revealed cellular intricacies that warrant a critical reappraisal of the profundity of the prokaryote–eukaryote divide.
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Wen-Cong Huang @wentsunghwang.bsky.social · 14/08/2026
Our paper is out in Nature Communications! 🌳🧬 We investigate the position of the archaeal root, the nature of the last archaeal common ancestor, and the evolution of DPANN archaea using state-of-the-art phylogenetic and gene-tree–species-tree reconciliation approaches. doi.org/10.1038/s414...
nature.com
Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages - Nature Communications
Key questions about the early evolution of archaea remain unanswered. Here, Huang et al. use improved methods of genome evolution to propose a euryarchaeal root for archaea, a methanogenic ancestor, a...
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Julia Meltzer @juliameltzer.bsky.social · 13/08/2026
Excited to share what I've been working on with an incredible team! Visualisation of Asgard viruses on cell surfaces and vesicles, and a story of complex viral interactions. Preprint: www.biorxiv.org/content/10.6... @brendanburns999.bsky.social @belindaferrari.bsky.social @xabivc.bsky.social
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Archaea.bio @archaeabio.bsky.social · 10/08/2026
New peer-reviewed protocol on Archaea.bio! HMW gDNA extraction from pure archaeal cultures for long-read sequencing by Richard Stöckl A DNA extraction protocol optimised for long read sequencing tested on Ignicoccus, Staphylothermus, and Thermococcales. #ArchaeaSky www.archaea.bio/protocols/hm...
archaea.bio
HMW gDNA extraction from pure archaeal cultures for long-read sequencing
This protocol can be used to extract High Molecular Weight gDNA from bacterial and archaeal cultures, resulting in gDNA suitable for long-read sequencing. It was optimized for Ignicoccus but also test...
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Ursula Oggenfuss @oggenfussursula.bsky.social · 20/07/2026
I am happy to share that my NWO Veni project was awarded 🍄🧬🔻! In this project, I will study how transposons shape genome folding, evolution, and adaptation in a fungal salamander pathogen. I am incredibly thankful for all the support and look forward to this next chapter #fungi #transposons #TEsky
A sketch of two salamander species, with a zoomed in picture of a fungal fruit body releasing spores, leading to a small stretch of DNA which ends in a folded chromosome with many green triangles indicating transposon insertions
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Rachel Mellwig @rachelmellwig.bsky.social · 16/07/2026
We’re at it again! 🙌 🔬Registration is now open for the “In situ CLEM at room temperature and in cryo” #EMBOCLEM 🗓️ Jan. 31st - Feb. 5th 2027 📍 EMBL Heidelberg Check out the exciting program and the fantastic group of trainers and speakers we have lined up! www.embl.org/about/info/c...
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Julian Vosseberg @julianvosseberg.bsky.social · 16/07/2026
I am very excited to share that I have received a Veni grant from the Dutch Research Council to start my own line of research on archaeal evolution at the Royal Netherlands Institute for Sea Research! www.nioz.nl/en/news-and-...
nioz.nl
Veni grant for research into evolution of archaea | NIOZ - Royal Netherlands Institute for Sea Research
Julian Vosseberg received a Veni grant to study the evolution of archaea. By characterizing similar genetic changes in their evolution, he aims to enlighten the predictability of the evolution process...
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Anne Walraven @annewalraven.bsky.social · 27/06/2026
Very excited that the preprint of the main paper of my PhD is now out! We show that Meringosphaera is the first centrohelid with permanent plastids: doi.org/10.64898/202... @zlatogursky.bsky.social, @pjkeelinglab.bsky.social, prof. Rachel A. Foster, and @fburki.bsky.social #protistsonsky
doi.org
Single cell genomics and fluorescence microscopy suggest a permanent plastid in a marine centrohelid
Photosynthetic organelles (plastids), which originated via primary endosymbiosis between an Archaeplastida ancestor and cyanobacteria, have shaped the Earth's oxygen-rich atmosphere and spread across ...
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James Gahan @jgahan.bsky.social · 24/06/2026
What’s the answer to “What’s worse that impact factor”…Id argue that letting AI rank papers and picking the top 1% would be a fine answer!
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Masaru Nobu @masarunobu.bsky.social · 23/06/2026
Parasitic bacteria feeding on their hosts’ RNA!? New cultures and Patescibacteriota/Minisyncoccota/CPR continue to surprise us… www.biorxiv.org/content/10.6...
biorxiv.org
A representative of a ubiquitous bacterial lineage parasitically feeds on host RNA
Cellular metabolism is widely understood as an integrated network of redox reactions, energy conservation, and biosynthetic pathways. Here we show that across diverse prokaryotic lineages, loss of red...
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Svetlana Dodonova @dodonova-sveta.bsky.social · 19/06/2026
Excited to share our new preprint! 🧬❄️ by brilliant @mdreimann.bsky.social and great collaborators! Using cryo-ET&EM, we reveal archaeal chromatin in a near-native state: variable-beads-on-a-string fibers shaped by growth phase and histone composition #ArchaeaSky www.biorxiv.org/content/10.6...
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Daniela Barillà @danielabarilla.bsky.social · 01/06/2026
Chromatin organization in Asgard archaea: histones, SMC complexes, and the archaeal roots of eukaryotic chromatin: Trends in Genetics www.cell.com/trends/genet... New review by @jvhooff.bsky.social & @damelab.bsky.social
cell.com
Chromatin organization in Asgard archaea: histones, SMC complexes, and the archaeal roots of eukaryotic chromatin
The genomes of organisms across the tree of life are structurally and functionally organized into chromatin. In eukaryotes, within an organelle called the nucleus, chromatin is shaped by histones and ...
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Reese Richardson @reeserichardson.bsky.social · 28/05/2026
TL;DR: We've identified more than 100 cases of apparent manipulation in Thermo Fisher Scientific's antibody verification data. @sholtodavid.bsky.social @johanduchene.bsky.social reeserichardson.blog/2026/05/28/h...
reeserichardson.blog
How much of Thermo Fisher’s antibody data has been manipulated?
We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalog
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Daniel Tamarit @danieltamarit.bsky.social · 22/05/2026
I'm looking for an enthusiastic student to join my team as a PhD candidate on archaeal genome evolution 🦠💻 Work in beautiful Utrecht, at @binfutrecht.bsky.social, an international group full of caring, amazing scientists, and with frequent cake breaks! www.uu.nl/en/organisat... Please share! 🙏
uu.nl
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Joshua Hamm @joshnhamm.bsky.social · 19/05/2026
Our paper examining the evolution of halophily in DPANN is out now in MBE! academic.oup.com/mbe/advance-...
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Reinier Egas @raegas.bsky.social · 13/04/2026
Preprint out! Anaerobic methanotrophs are key methane oxidizers, but their activity/adaptation under acidic conditions remains unclear. We show that a freshwater ANME adapts to pH stress via shifts in lipid composition and remains metabolically active down to pH 5.65. Expanding the niche of ANME.
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Brendan Burns @brendanburns999.bsky.social · 10/04/2026
Immensely rewarding part of this work was working with Indigenous language experts and elders in the naming of our species of Asgard….’marumarumayae’ derived from the Malgana language from the people of Gathaagudu (#Shark Bay)
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Courtney Stairs @cstairs.bsky.social · 04/04/2026
We tested the efficacy of semi-permeable capsules to capture protists from cultures and environmental samples using the Onyx from @atrandi.bsky.social. Tremendous effort from everyone in the lab and led by Marco Fantini and Nik Brask - check out the videos here: www.biorxiv.org/content/10.6...
biorxiv.org
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Oleksandr Maistrenko @omaistrenko.bsky.social · 06/04/2026
There is a lot of undescribed prokaryotic diversity in existing whole-genome metagenomic data! www.nature.com/articles/s41...
nature.com
Unbinned contigs expand known diversity in the global microbiome - Nature Microbiology
Re-analysis of over 92,000 metagenomes reveals hundreds of thousands of previously undescribed Bacterial and Archaeal clades hidden in plain sight.
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Mathilda Lennartz @mathilda95.bsky.social · 23/03/2026
I am extremely excited that my first first-author paper from my PhD is finally out 😆!! We developed a new CLEM workflow to measure lipid densities at the nanoscale. So if you are into lipids and super-resolution imaging approaches, this one is for you: www.nature.com/articles/s41...
nature.com
Visualizing suborganellar lipid distribution using correlative light and electron microscopy - Nature Cell Biology
Lennartz et al. introduce a correlative light and electron microscopy workflow, Lipid-CLEM, combining near-native lipid probes and on-section labelling via click chemistry. Lipid-CLEM quantitatively a...
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Nature Reviews Microbiology @natrevmicro.nature.com · 13/03/2026
ICYMI: New online! Diversity, ecology, cell biology and evolution of the Asgard archaea
dlvr.it
Diversity, ecology, cell biology and evolution of the Asgard archaea
Nature Reviews Microbiology, Published online: 05 March 2026; doi:10.1038/s41579-026-01288-wThe Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of the research field focusing on these intriguing microorganisms and discusses future research directions aiming to resolve their diversity, ecology, cell biology and evolution.
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 05/03/2026
Read our review about the "Diversity, ecology, cell biology and evolution of the Asgard archaea" in @natrevmicro.nature.com here: www.nature.com/articles/s41... By @kassipan.bsky.social @stephkoe.bsky.social @micropat.bsky.social & @gerbenz.bsky.social
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Stephan Köstlbacher @stephkoe.bsky.social · 05/03/2026
🧵 1/10 New paper out in @natmicrobiol.nature.com from my postdoc at @mib-wur.bsky.social! 🎉 How eukaryote-like was the archaeal ancestor of eukaryotes? Sequence searches alone can't tell us — so we used protein structure prediction to look deeper. 🧬 www.nature.com/articles/s41...
nature.com
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.
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Kassiani Panagiotou @kassipan.bsky.social · 05/03/2026
Just over ten years after the discovery of the first Asgard archaeal genomes, we revisit the rapid expansion of this remarkable archaeal lineage. From diverse genomes and metabolisms to eukaryotic signature proteins and the first cultured representatives. www.nature.com/articles/s41...
nature.com
Diversity, ecology, cell biology and evolution of the Asgard archaea - Nature Reviews Microbiology
The Asgard archaea have become a cornerstone of archaeal research, particularly for studies aiming to unravel the origin and early evolution of eukaryotes. This Review outlines the current state of th...
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 05/03/2026
Finally out in @natmicrobiol.nature.com: Prediction of eukaryotic cellular complexity in Asgard archaea using structural modelling. Great work by @stephkoe.bsky.social @kassipan.bsky.social @jvhooff.bsky.social www.nature.com/articles/s41...
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Brett Baker @archaeal.bsky.social · 18/02/2026
New paper from my team detailing a greatly expanded genomic database of Asgard archaea revealing of high energy metabolism those related to eukaryotes! Led by @katyappler.bsky.social lots of help from @jameslingford.bsky.social @valdeanda.bsky.social @kassipan.bsky.social doi.org/10.1038/s415...
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Kathryn (Katy) Appler @katyappler.bsky.social · 18/02/2026
Beyond thrilled to share that our study has been published! This project encompasses years of work, including my thesis research on Asgard archaea in the @archaeal.bsky.social lab at @utmsi.bsky.social and @texasscience.bsky.social!!! #MicroSky #ArchaeaSky 1/12
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 18/02/2026
Finally out in @nature.com: a new piece of the puzzle of how complex life evolved. Lead by @archaeal.bsky.social & @katyappler.bsky.social. Great collab with @greening.bsky.social and @kassipan.bsky.social. More pieces to follow soon! www.nature.com/articles/s41...
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 12/02/2026
Two more weeks to apply - come join us () in The Netherlands as a postdoctoral researcher on large-scale metagenomic exploration of new lineages!
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 11/02/2026
Today we published a Correction on our 2023 @nature.com paper reporting the heimdallarchaeial ancestry of eukaryotes: www.nature.com/articles/s41... Corrected paper: www.nature.com/articles/s41... Importantly, the re-analyses of the corrected dataset are consistent with the original findings.
nature.com
Author Correction: Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes - Nature
Nature - Author Correction: Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
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Kyle M. Douglass @kmdouglass.bsky.social · 13/01/2026
I finally got around to writing the discussion section of our lab's basic training course on live cell #microscopy. I explain the tradeoffs involved in designing an imaging experiment and the art of thinking of the experiment as an optimization problem. leb-epfl.github.io/basic_traini...
leb-epfl.github.io
Introduction - Microscopy Basic Training
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Gerben de Zwaan @gerbenz.bsky.social · 06/01/2026
Come join our group in the beautiful (currently very snowy) Wageningen!
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 05/01/2026
I have a postdoc position in metagenomic exploration available in my group. Candidates with documented experience in phylo & metagenomics and preferably with petabase-scale data mining and GLM workflows are encouraged to apply. Come join us! 🧬🦠💻 Please repost Apply here: www.wur.nl/en/vacancy/p...
wur.nl
Postdoctoral researcher Phylogenomics and metagenomics
Are you just as excited as we are about the fascinating world of microorganisms? Do you want to contribute to exploring and genomically characterize novel prokaryotic lineages? Do you have a PhD degre...
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Thijs J. G. Ettema 🦠🔬🇳🇱🇸🇪🇪🇺 @ettema.bsky.social · 26/11/2025
Come join us! Soon I will be advertising a postdoc vacancy in my group as part of my @erc.europa.eu AdG project 'DARK ROOTS'. Focus of the project will be on phylo- and metagenomic mining of novel prokaryotic lineages. I will soon post a link here - stay tuned, and please repost! #asgardarchaea
media.tenor.com
a man walking in a field with an umbrella
ALT: a man walking in a field with an umbrella
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Joshua Hamm @joshnhamm.bsky.social · 18/11/2025
Ever since publishing our observations of the predatory behaviour of Ca. Nha. antarcticus people have asked me why it would want to kill its host. My perspective discussing the ecological factors that I believe led to this behaviour is out now in mSystems: doi.org/10.1128/msystems.01475-25
doi.org
Nutrient availability affects optimal growth strategy in predatory DPANN | mSystems
The bacterial and archaeal domains each possess a major clade that appears to be predominantly host-associated (1–3). These two lineages, Patescibacteriota and DPANN archaea (named for the Diapherotri...
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Wen-Cong Huang @wentsunghwang.bsky.social · 13/11/2025
#Archaea, #DPANN, #phylogenetic_reconciliation New preprint online! www.biorxiv.org/content/10.1...
biorxiv.org
Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages
The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...
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Lars Gamfeldt @gamfeldt.bsky.social · 10/11/2025
Opportunity! Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
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Dame lab at Leiden University @damelab.bsky.social · 05/11/2025
Soon available in my group: 1 PhD position to investigate prokaryotic histones. See our recent work that highlights the existence and diversity of prokaryotic histones (e.g. Schwab et al., TIBS, 2025; Schwab et al., Nat Comm, 2024; Hu et al., Nucl Acids Res, 2024). Please DM for informal enquiries.
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Stephan Köstlbacher @stephkoe.bsky.social · 31/10/2025
🧙‍♀️ Something is brewing in the WitChi cauldron… After some excellent peer review feedback, a new update of WitChi is taking shape, refining how we detect and prune compositional bias in phylogenomic alignments. Stay tuned for the next release! 🧙‍♀️ Can’t model it? Prune it! github.com/stephkoest/w...
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Svetlana Dodonova @dodonova-sveta.bsky.social · 28/10/2025
Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️ Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...
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Ryan Ziels @ryanziels.bsky.social · 21/10/2025
I’m very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! 🦠
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Fabai Wu @fabaiwu.bsky.social · 21/10/2025
Glad to share our paper out today @NatureEcoEvo: “Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor”. www.nature.com/articles/s41... #microsky #archaeasky
nature.com
Serial innovations by Asgard archaea shaped the DNA replication machinery of the early eukaryotic ancestor - Nature Ecology & Evolution
Phylogenetic and biochemical analyses show a diversity of components of the DNA replication machinery in different Asgard archaea that contributed to the eukaryotic DNA replication machinery.
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Lisa Westerveld 🌱 @lisawesterveld.bsky.social · 20/10/2025
Nou nee, dat mag niet. Een school moet een veilige plek zijn voor álle leerlingen. Dat staat ook in de wet. Het afwijzen van homoseksuele relaties geeft de boodschap dat iemand niet zichzelf mag zijn. Dat mag niet én is ronduit schadelijk. nos.nl/nieuwsuur/co...
nos.nl
CDA-leider Bontenbal: religieus onderwijs mag botsen met grondrecht van gelijkheid
Dat religieuze scholen homoseksuele relaties afwijzen, is volgens CDA-leider Henri Bontenbal nu eenmaal een gevolg van de vrijheid van onderwijs. Daar wil hij niet aan tornen. "Een andere mening doet ...
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Archaea.bio @archaeabio.bsky.social · 15/10/2025
Live cell imaging of Ca. Nha. antarcticus and Hrr. lacusprofundi using agarose pads. Protocol now live! www.archaea.bio/protocols/li...
archaea.bio
Live Cell Imaging of Ca. Nha. antarcticus and Hrr. lacusprofundi using agarose pads
This protocol is an adapted form of the protocol developed for imaging haloarchaea (Liao et al., 2021) and subsequently applied to co-cultures containing nanohaloarchaea and haloarchaea (Hamm et al., ...
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Tom Williams @tweethinking.bsky.social · 09/10/2025
There's a PhD position now available with me in Bath, on the evolution of symbiosis. www.findaphd.com/phds/project.... The supervisory team also includes @anja1.bsky.social @phil-donoghue.bsky.social and others. NB, this is open both to UK-based students *and* to international students :)
findaphd.com
The genomic basis of symbiotic integration at University of Bath on FindAPhD.com
PhD Project - The genomic basis of symbiotic integration at University of Bath, listed on FindAPhD.com
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Jolien van Hooff @jvhooff.bsky.social · 09/10/2025
Very nice documentary about the origins of complex life with my PhD advisor Berend Snel @binfutrecht.bsky.social!
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