Background: trained geneticist-geologist; became (palaeo-)phylogeneticist, evolutionary biologist and manufacturer of science-doodles. Status: perished. Thought school: heretic classifications; militant network-thinker. Purpose: tips&tricks. Motto: If it's trivial, leave it to someone else.
Just reading through the (news)paper in a little break from things I need to do.
And I keep thinking, no matter what I read: too little, too late.
Wonder, is it a blessing or curse to belong to the generation that lives through the time when humans took their latest severely wrong turn (1990s)? Knowing that we knew better (could have), that we had turned in the right directions but then got stopped by the increasingly sheepish majority
Damn you! #HerdStupidity
Der Mensch generell, der Wähler speziell, ist halt eher visuell.
#Quizfrage: was haben die beiden Kandidaten der Demokraten, die gegen den Orang-Wutan angetreten sind und verloren haben gemein?
#FunFact aus dem selben Grund sind auch Sarkozy, Hollande und Macron (wieder)gewählt worden (direkt oder indirekt bedingt).
this is weird, and not in a good way.
Springer Nature is starting series of MDPI-like journals
https://the-strain-on-scientific-publishing.github.io/website/posts/discover_nature/
The unfiltered paper, with all the major deficits outlined by Kong's/New Phyt's #PeerReview experts still in it, is now online on bioRvix.
Worth et al. Whole #chloroplast #Genomes reveal a complex genetic legacy of #LostLineages, past radiations and #SecondaryContacts in the dominant temperate deciduous tree genus #Fagus
https://doi.org/10.1101/2025.06.03.653586
Being not limited, we moved a few more figures from the supplement to the main text 😎
https://figshare.com/projects/Supplement_to_Worth_et_al_2025_Reticulate_history_of_beech/251480
#Morgenstund-Gold-im-Mund
"Wer früh aufsteht, hasst mehr vom Tag"
Gefunden von 'nem Freund auf hr-text
The good old days, when people did still think when drafting a phylogenetic tree rather than describe what the blackboxes spit out (and calling it: hypothesis testing)
If you like old classics, check this out: the first evolutionary network, Hilgendorf (1866)
The dilemma of evolutionary networks and Darwinian trees
https://phylonetworks.blogspot.com/2014/01/the-dilemma-of-evolutionary-networks.html
More posts by D. Morrison on the history of phylogenetic graphs listed here:
Hmhmhm...wohl nicht, mir fällt jetzt grad wieder die Karte ein vom letzten Mal 😬
Aber die treffendere Farbwahl, statt hellblau... 😌
What can we learn from this?
Single-blind #PeerReview is the worst. And we're not even allowed to lift the curtain. Confidential it is.
If you want to publish easy and high-fly: pick a data-wise trivial hypothesis, and test it using machine-generated and -processed phylogenomic data.
If you want to publish a "highly descriptive and speculative manuscript that ignores many rich innovations in model-based analysis" because you can fall back on evidence and don't need models. Just don't.
And, gravest of all deficits. We didn't cite the right people: "The references section is curious, and heavily cites a close network of workers in this organism [beech, #Fagus] while ignoring relevant work on reticulation in other groups [which?!], ... And just look at the date distribution of those citations [from 2002-2024]! Not sure I see even a single name I would consider a major player in plant reticulation or reticulation methods."
No major player, but impact we generate with beeches 😎
What else do we have: unusual levels of intragenomic variation even in supposedly single-/low-copy markers "reported using cloning and PCR. ... typical methods of the mid-2000s", a poor "poor pairing with the extent of data in the chloroplast", which only comprise "south of 100 accessions in total", clearly an "incremental advance to study" the signal of them and "a couple [31] of nuclear markers" to extract which of them supported, which rejected topological alternatives.
"Bombastically oversold", of "suspect novelty" - how many complete plastome trees are out there on beeches? How many studies revisiting and mapping the entire fossil record? How many explicitly dated primary radiations and secondary contacts?
Clearly not a "competetive manuscript due to limited impact and problems under the hood" apparent when a reviewer "lift[s] it and look[s] closely at the engine". Well, he could have looked instead into the supplementary materials and information.
Here's some examples of the "over-speculation" due to "data limitations" conveyed by "overly complex" figures.
Well, it's not the usual trivial feed your #BigData into a blackbox and publish the result as a major breakthrough type of study.
More the go down the rabbit hole of coal-face #evolution and #phylogenetics involving a lot of pondering what phylogenetic graphs show.
The product of #research (starting 25 years ago), not "hyphothesis-driven". A lot of steps and mosaic stones involved.
Pretty content with myself, today.
I used the one-way street called "single-blind peer review" in the wrong direction and reviewed the reviews in a (prob. pointless) letter to the editor.
You struggle hard to keep to the word-limit of the journal, just to get blamed for having a too short Materials and Results, "concealing" the many weaknesses of one's work. And nobody minds the 30p long Suppl. M&M and 113p long Suppl. R&D
Zumindestens in dem Teil vom Land, dass nicht zum "Großen Osten" gehört...wenn wir in die alte Heimat fahren, passieren wir noch ein paar zone blanches 😬
Aber fibre macht sich. Ein Vorteil, wenn die Regierung in derselben Abschlußklasse saß, wie die Chefs der großen Mobilfunkläden. Kurze Dienstwege 🤭 Der Enarchismus hat wohl auch Vorteile.
Und ob es wohl einen Zusammenhang gibt zwischen schnellem Netz und der Anzahl der braunen Schafe?
While working on a proper post, I had to get rid of something puzzling on my chest.
Botanics and politics—when plant species become propaganda material
https://researchinpeace.blogspot.com/2025/04/botanics-and-politicswhen-plant-species.html
How the long arm of Chinese state doctrine has smoothly and elusively penetrated botanical #science journals.
Dendroscope is indeed handy, having been using it for pre-formatting tanglegrams for two decades, but can become messy when the numbers of tips is high, because it doesn't have a sorting option except for ladderising left or right.
An alternative maybe one of the many functions in phytools
https://www.rdocumentation.org/packages/phytools/versions/2.4-4
Source code: https://github.com/liamrevell/phytools
See also Revell's post: http://blog.phytools.org/2022/06/co-phylogeny-plots-rotating-only-left.html
Does ring a bell, when reading the news these days, doesn't it?
"He was a fattish but active man of paralysing stupidity, a mass of imbecile enthusiams—one of those completely unquestioning, devoted drudges..."
Published in 1949 depicting a world 35 years later. #Immortal lines, truly.
Alexandros Stamatakis' annual EMBO satellite #bioinformatics workshop in Crete is open again for registration (free-of-charge, first-come-first-serve)
This year: #biodiversity #genomics tools
https://forms.gle/GRvPxCp2TnYdo8Po8
As Alexi is keen to point out: "... a good excuse to visit Crete?"
Nope. Ich brauch da ja nix, wir kommen immer privat unter 😁
Aber egal wo man unterkommt, es lohnt sich 😉
Fein beobachtet.
Und woran erkennt man eine rechtsextreme Partei?
Daran, daß sie der Wahl-O-Mat Klassikerthese:
"Der Bund soll Projekte gegen Rechtsextremismus verstärkt fördern."
nicht zustimmt ("0") 🤭
Und was Gewerkschaftiges angeht, wer z.B. das Streichen von Bürgergeld fordet (Grundversorgung) poliert den Steigbügel. Faschismus kann schleichend sein.
("0" = stimme nicht zu, "2" = stimme zu, "1" = neutral/keine Meinung)
Quelle für Tabelle: bpb Wahl-O-Mat
