#fightthefog — Public Fediverse posts

2/2 Just a year after an amazing study* by Li Yao et al., https://doi.org/10.1016/j.indcrop.2025.120731) used 700+ complete plastomes of these three species confirming and enhancing 10+ year old research showing that plastomes are not sorted by species like in all #oaks and not few other Fagales. Common knowledge, unless you are an editor for BMC Genomics or SIT professor.

*A study naturally struggling getting through #PeerReview being too complex for the Q1s and ending up in some minor journal.

#FightTheFog

When editors of Q1-Journals leave the editing business to AI.

#BMCGenomics sending out a paper for review based on three, one per species, complete plastomes "[revealing] #Phylogenetic conflict [and] #reticulate evolution in #Quercus section Cerris subsection Campylolepides: Evidence from chloroplast genomes and its biogeographic implications (researchers from Shanghai Institute of Technology)
Key pic attached
#FightTheFog
1/2

One would expect, de-embargoing of the data dump goes automatically, when an article in Nature, flagship journal of Springer-NPG is published.
"Data availability: The data matrix for phylogenetic analyses is provided in Supplementary Data 1. Computed tomography data have been deposited in Dryad at https://doi.org/10.5061/dryad.5x69p8d2r."

Clicking the link 5 years later.
Rest in peace, deposited data. Interesting: 32 downloads. Has it been re-embargoed at some point?

#FightTheFog #OpenData

Single-blind #PeerReview strikes again. Reviewer revealing himself to the coauthors of a paper 1 week after submission threatening to reject it, unless he becomes a coauthor.

Now they are negotiating a deal to avoid having to redo everything.

Wondering also, why a method-focussed paper (new approach) submitted to a journal dedicated to molecular #phylogeny is reviewed by somebody who knows the organism but has very little experience in (phylo)genetics

Have to love single blind.
#FightTheFog

So much for strict #OpenData policies. Paper published in 2021 in New Phytologist, data matrix: "... is accessible to readers in #Morphobank, project # 3917. We have enabled anonymous login."

https://www.morphobank.org/myprojects/3917/overview

Anonymous login works (first pic), "Project disc usage: 0 bytes". Which happens to be exactly the number of linked matrices under the project (2nd pic)

Deleted the data after review? Avoid anyone else can (mis)use it.

#paleobotany #phylogeny #FightTheFog #transparency in #science

For a change, a proper #milestone. 1000 reads on RG for the #Reticulate origin of modern plane trees (#Platanus, Platanaceae): A nuclear marker puzzle

https://www.researchgate.net/profile/Guido-Grimm/achievement/6929624c0df56f392494b91f

It's profoundly comforting to see that one's work is still raising interest after more than a decade, especially, something that at the time of publication was harshly attacked by "expert #reviewers" –anonymously of course (#FightTheFog). And ignored by the botanical High Priests beyond the Big Pond 😎😎😎

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

#FightTheFog #PeerReview #Transparancy

"We demonstrate that an accelerating number of researchers – on the order of 10% or 20,000 researchers on Stanford’s Top 2% researchers – are achieving implausibly high-publication and new coauthor rates, with many producing tens to hundreds of papers per year, and gaining hundreds to thousands of new coauthors annually." – Related question: When did you last had high-profile coauthors that even read your paper?
https://doi.org/10.1080/08989621.2024.2445280 #openaccess #FightTheFog

#FightTheFog #AcademicChatter

Rigorous #PeerReview @ PLoS ONE: reject a paper because the editor cannot manage to get (any) reviews in time.

Related #FunFact: as long as reviews are quick, a paper's and the reviewer's reports quality doesn't matter so much. And not only in PLoS ONE.

Related 2017 post:
https://researchinpeace.blogspot.com/2017/09/one-date-that-is-missing-in-many.html
#OldPosts

#Peerreviewed: "We interpret this #paleoclimate as summer dry and winter wet—a climate analogous to modern day warm #Mediterranean climates in the Köppen‐
Geiger climate classification system" https://doi.org/10.1029/2024PA004874

That'd be Csa. Pic: fig. 4, modern analogs 🤨

Well, thanks to #ClimateChange, they all turn Csa eventually: #OldPosts
Wladimir Köppen – a climate-vegetation genius, and what this has to do with wine
https://researchinpeace.blogspot.com/2018/02/wladimir-koppen-climate-vegetation.html

#palaeoclimate #PeerReview #FightTheFog

#Science #Publishing #FunFact: The individual H-indices of the four senior authors are, according to their #GoogleScholar profiles, 58 and 56 for the museum curators, 153 for the "distinguished professor" and 146 for his spouse (many shared papers). La creme-de-creme of the FMNH/UF
https://scholar.google.de/citations?view_op=view_org&hl=de&org=5315230152465104173&before_author=-rG4__VUAQAJ&astart=0

Saves a lot of time not having even to read the papers of one's juniors and first-authors.

Time you can spend on fun things. Just look at their happy faces.

#FightTheFog

#FightTheFog-Update to https://ecoevo.social/@grimmiges/110101595898174133

Interesting leap in faith: The same clique of authors putting out a preprint claiming all modern-day Fagales genera are younger than 25-20 Ma pop up in the author list of a study just submitted to a high-tier #phylogeny journal indulging in how only the Fagaceae bunch hybridised already in the Eocene (>40 Ma).

Using the fossil record again, but this time without any palaeobotanist in the author list.

PS #OldPosts
https://researchinpeace.blogspot.com/2022/07/just-single-easily-overlooked-tip.html

I pondered organisation, so my followers can make the best of Mastodon's filter option (settings -> filters).

I'll hash my posts as follows
#NewPosts—for new #blogposts on Res.I.P. and others I follow.
#OldPosts—for historical ones
#PhyloNetworks—anything #phylogenetics-ish beyond mere tree-inference
#FightTheFog—anything shrouding science (like confidential #PeerReview)
#CommentTo—post-reviews
#NotScience—for the irrelevant rest