Reposted by @grahbudd.bsky.socialGaspar Jekely @jekely.biologists.social.ap.brid.gy · 30/07/2026In our new preprint, Réza Shahidi, Alexandra Kerbl and Karel Mocaer give an exquisitely detailed manual on serial sectioning for electron microscopy. "Volume Electron Microscopy: Tips & Tricks on Micromanipulator-Assisted Serial Sectioning for Array […] [Original post on biologists.social] 0178
grahbudd.bsky.social @grahbudd.bsky.social · 22/07/2026..on making pieces of inference machinery, and rather less concerned about how much the results that come out may or may not tell us something about the natural world. 010
grahbudd.bsky.social @grahbudd.bsky.social · 22/07/2026The statistical mistakes exemplified by the original and new paper (treating dependent variables as independent, and combining two very different signals when they clearly disagree with each other) are not very difficult to understand. Unfortunately, the field at the moment is very focused... 110
grahbudd.bsky.social @grahbudd.bsky.social · 22/07/2026The fact that such different signals emerge from the fossil and molecular records points to a problem in current clock inference which is that it cannot account for phenomena such as "tempo" which naturally leads to speeded-up evolution at the base of major clades (doi.org/10.1093/sysbio/syaf020)doi.orgValidate User 131
grahbudd.bsky.social @grahbudd.bsky.social · 22/07/2026As a result, the combined results simply return the oldest allowed date in the BBB 95% estimate, giving an unrealistically narrow 151-153 age estimate. This is clearly the wrong treatment in all sorts of ways. 111
grahbudd.bsky.social @grahbudd.bsky.social · 22/07/2026The present paper is still problematic. It converts the 95% HPD of the BBB into a 100% confidence interval and then forces the molecular clock, which clearly implies a deeper origin, to conform to it. This is not "getting molecules and rocks to talk to each other" but simply imposing an "agreement" 111
grahbudd.bsky.social @grahbudd.bsky.social · 22/07/2026In addition, we pointed out that grouping families into orders gave more reliable results. In the present paper, the authors have accepted our criticisms, although of course without any acknowledgement whatsoever. I wonder what they think of their original response to us! However... 110
grahbudd.bsky.social @grahbudd.bsky.social · 22/07/2026When this method was published in 2021 we critiqued it for treating the families as independent estimators of the origin, which guaranteed a deep age. The authors responded aggressively and claimed our critique had "no merit". (www.biorxiv.org/content/10.1... and www.biorxiv.org/content/10.1...).nature.comFossil data support a pre-Cretaceous origin of flowering plants - Nature Ecology & EvolutionUsing a novel Bayesian method, the authors infer a pre-Cretaceous origin for multiple angiosperm families on the basis of their fossil record and present-day diversity. 141
grahbudd.bsky.social @grahbudd.bsky.social · 06/05/2026www.uu.se/en/about-uu/... Job in Uppsala Earth sciences! (Palaeo welcome!)uu.seAssistant Professor in Earth Sciences specialising in Dynamics of Earth Systems - Uppsala UniversityAssistant Professor in Earth Sciences specialising in Dynamics of Earth Systems, Department of Earth Sciences, Uppsala University 012
Reposted by @grahbudd.bsky.socialMax Telford @maxjtelford.bsky.social · 23/04/2026The Tree of Life available as a paperback today. bit.ly/41Mq7jp Breezy, scholarly, whimsical, rigorous + companionable guide to our family history. TLS Erudite, highly informed, frequently amusing.. compelling + memorable. Science Enjoyable + ambitious. An exhilarating cartographic journey. WSJ 12810
Reposted by @grahbudd.bsky.socialMax Telford @maxjtelford.bsky.social · 06/01/2026I’ve written something for The Conversation on a fascinating recent paper by @grahbudd.bsky.social and @richardpmann.bsky.social on problems with molecular clocks. academic.oup.com/sysbio/artic... theconversation.com/a-speeding-c...theconversation.comA speeding clock could solve Darwin’s mystery of gaps in animal fossil recordsScientists have long been confused about ‘missing’ animal fossils. 0133
Reposted by @grahbudd.bsky.socialMolecular Biology and Evolution @molbioevol.bsky.social · 26/12/2025@rcply.bsky.social argues that phylogenetic inferences in sponge–ctenophore–bilaterian relationships based on shared chromosomal rearrangements suffer from insufficient statistical support. 🔗 doi.org/10.1093/molbev/msaf321 #evobio #molbiodoi.orgSponges, ctenophores, and the statistical significance of synteniesAbstract. Shared fusions between ancestral chromosomal linkage groups have previously been used to support phylogenetic groupings, notably sponges with cni 0106
Reposted by @grahbudd.bsky.socialMax Telford @maxjtelford.bsky.social · 10/12/2025Some more shenanigans on the Ctenophora Porifera debate from @rcply.bsky.social academic.oup.com/mbe/advance-...academic.oup.comSponges, ctenophores and the statistical significance of synteniesAbstract. Shared fusions between ancestral chromosomal linkage groups have previously been used to support phylogenetic groupings, notably sponges with cni 02715
Reposted by @grahbudd.bsky.socialMax Telford @maxjtelford.bsky.social · 11/11/2025My book 'The Tree of Life' is published in the USA and Canada today. Available as book, on kindle and as audio. I would be really grateful for reposts. www.amazon.com/Tree-Life-So... www.amazon.ca/Tree-Life-So... 47049
grahbudd.bsky.social @grahbudd.bsky.social · 29/09/2025Have you seen this one? U 1125 at Krogsta. 110
grahbudd.bsky.social @grahbudd.bsky.social · 24/08/2025But it is at least striking and indisputable that it is precisely in Western Europe where we think mostly of the church and its influence that modern science emerged and so vigorously developed. Correlation is not causation but the counterfactual, that the church inhibited it would be hard to show. 010
grahbudd.bsky.social @grahbudd.bsky.social · 24/08/2025The “church” considered broadly as an institution has existed for a long time and in many places and it is hard to draw completely comprehensive conclusions. Byzantium for example isn’t normally associated with significant scientific advances (but see people like Philoponus who influenced Galileo). 000
grahbudd.bsky.social @grahbudd.bsky.social · 24/08/2025Of course the scientific revolution made immense advances. But these advances were in many cases built on or at least partly anticipated by earlier work. The idea of dividing human history into watertight “periods” such as the dark ages or scientific revolution has long been abandoned by historians. 120
grahbudd.bsky.social @grahbudd.bsky.social · 24/08/2025In many cases it was the church structures themselves that enabled technological advance. One example is the development of blast furnaces and metallurgy by the Cistercians (see eg en.m.wikipedia.org/wiki/Laskill ) and arguably it was the Reformation that put a stop to such inventiveness.en.m.wikipedia.orgLaskill - Wikipedia 110
grahbudd.bsky.social @grahbudd.bsky.social · 24/08/2025The height of the power of the medieval papacy was between say 1100-1300 peaking with Innocent III at 1198-1216. But that corresponds to the “high Middle Ages” which saw great advances in all sorts of ways in Western Europe including in science and technology. 130
grahbudd.bsky.social @grahbudd.bsky.social · 21/08/2025Last time I visited you had to get the key from a shop down the road is that still true?? 110
grahbudd.bsky.social @grahbudd.bsky.social · 21/08/2025With the wonderful Purbeck effigy of Lawrence of Arabia! 110
grahbudd.bsky.social @grahbudd.bsky.social · 18/08/2025My dispatch on early echinoderms (www.sciencedirect.com/science/arti...) is now out in @currentbiology.bsky.social www.sciencedirect.com/science/arti...sciencedirect.comPalaeontology: Straightening out early echinodermsFossil material of echinoderms from the Cambrian of Morocco suggests a novel reconstruction of early echinoderm evolution and ties in with recent adva… 0103
Reposted by @grahbudd.bsky.socialFerdinand Marlétaz @ferdix.bsky.social · 13/08/2025After nearly twenty years in the making, our attempt at understanding what makes the chaetognath phylum so unique has finally been published! www.nature.com/articles/s41... with #LauraPiovani @dariagavr.bsky.social @alexdemendoza.bsky.social @chemamd.bsky.social and others /1nature.comThe genomic origin of the unique chaetognath body plan - NatureGenomic, single-cell transcriptomic and epigenetic analyses show that chaetognaths, following extensive gene loss in the gnathiferan lineage, relied on newly evolved genes and lineage-specific tandem ... 711949
Reposted by @grahbudd.bsky.socialRichard Mann @richardpmann.bsky.social · 05/08/2025Do diversification rates and molecular evolution covary? Maybe, maybe not, but it’s surprising how much falls into place if we assume they do doi.org/10.1093/sysb...doi.orgEvolutionary Tempo, Supertaxa, and Living FossilsAbstract. A relationship between the rate of molecular change and diversification has long been discussed, on both theoretical and empirical grounds. Howev 012
grahbudd.bsky.social @grahbudd.bsky.social · 05/08/2025Main findings: clades very imbalanced; large clades likely to have emerged at time of high tempo and then slowed; expected amount of molecular change on each branch equal (so no molecular clock in this model) and large diverse clades expected to be accompanied by small, conservative “living fossils” 020
grahbudd.bsky.social @grahbudd.bsky.social · 05/08/2025Our covariant model of evolution is now out in @systbiol.bsky.social. In it, rates of diversification and molecular and morphological evolution all covary governed by a “tempo” variable which itself also varies at a rate equal to its own value. @richardpmann.bsky.social doi.org/10.1093/sysb...doi.orgEvolutionary Tempo, Supertaxa, and Living FossilsAbstract. A relationship between the rate of molecular change and diversification has long been discussed, on both theoretical and empirical grounds. Howev 163
Reposted by @grahbudd.bsky.socialMax Telford @maxjtelford.bsky.social · 18/07/2025My book 'The Tree of Life' will be available in Spanish translation in October. Other languages coming too. (Uk version here... www.amazon.co.uk/Tree-Life-So...) 1134
Reposted by @grahbudd.bsky.socialJames Gahan @jgahan.bsky.social · 16/07/2025We are looking for new colleagues to come join us in Galway as group leaders (Junior and Senior). The Centre for Chromosome Biology is a great place and it is a good time to join. Please reach out if you want to chat about the opportunity! www.nature.com/naturecareer... 26755
grahbudd.bsky.social @grahbudd.bsky.social · 08/07/2025Viator’s Bridge of Izaak Walton fame at Milldale in the Peak District 130
grahbudd.bsky.social @grahbudd.bsky.social · 07/06/2025That’s what I always thought until I moved to Sweden where they fly around my summer house! 020
grahbudd.bsky.social @grahbudd.bsky.social · 06/06/2025Cephalanthera longifolia (narrow-leaved helleborine) and Cypripedium calceolus (Lady’s slipper orchid) on Gräsö. 290
grahbudd.bsky.social @grahbudd.bsky.social · 23/05/2025Very sorry to hear of the death of Alisdair MacIntyre. ”After Virtue” was never more apposite. dailynous.com/2025/05/22/a...dailynous.comAlasdair MacIntyre (1929-2025) - Daily NousAlasdair MacIntyre, professor emeritus of philosophy at the University of Notre Dame and Duke University, well-known for his work in moral and political philosophy, has died. Professor MacIntyre wrote... 020
Reposted by @grahbudd.bsky.socialKjetil Lysne Voje @klvoje.bsky.social · 22/05/2025Here is our attempt at summarizing the state of the evidence for the punctuated equilibrium hypothesis. The paper is part of a special issue of Paleobiology celebrating the 50th anniversary of the PE Hypothesis. Work led by Gene Hunt. @lhliow.bsky.social www.cambridge.org/core/journal...cambridge.orgPunctuated equilibrium: state of the evidence | Paleobiology | Cambridge CorePunctuated equilibrium: state of the evidence 23724
Reposted by @grahbudd.bsky.socialMax Telford @maxjtelford.bsky.social · 12/05/2025New entry into the sponge/ctenophore debate.... Have the chromosome fusions separating ctenophores from all other animals been given too much weight? Beautifully clearly written paper covering complex arguments from @rcply.bsky.social. www.biorxiv.org/content/10.1...biorxiv.orgSponges, ctenophores and the statistical significance of synteniesShared fusions between ancestral chromosomal linkage groups have previously been used to support phylogenetic groupings, notably sponges with cnidarians and bilaterians to the exclusion of ctenophores... 13115
Reposted by @grahbudd.bsky.socialMax Telford @maxjtelford.bsky.social · 24/04/2025It's publication day of my first book: The Tree of Life. The tree of life is a time machine that can take us back 4 billion years to meet our most distant ancestor. It is the magic that lets us tell the origin stories, beginning with this ancient relative, of everything from mushrooms to man. 3040482
grahbudd.bsky.social @grahbudd.bsky.social · 04/04/2025I am seriously becoming of the opinion that there should be a (ideally permanent, but at least a few years) moratorium on publication of molecular clock papers. This would allow authors to reflect on the idea that their results invariably involve “event x happened 10s - 100s Myrs before we thought”. 121
grahbudd.bsky.social @grahbudd.bsky.social · 05/01/2025Another issue is that this view depends on the “phylum hypothesis” ie the view that there is a quantitative difference between the lineages that led to the modern phyla compared to all others. www.cell.com/current-biol...cell.comAnimal Evolution: Are Phyla Real?A recent study compares developmental gene expression among very distantly related animal species and interprets the results as providing biological justification for phyla. Several problems in the design and interpretation of the study call this conclusion into question 120
grahbudd.bsky.social @grahbudd.bsky.social · 05/01/2025Actually this happened with the exploitation of “small carbonaceous fossils” www.sciencedirect.com/science/arti...sciencedirect.comAnimal origins: The record from organic microfossilsAccumulated records of organic microfossils span billions of years of Earth history. The majority of this record consists of prokaryotes plus eukaryot… 010
