iiinova — where your digital self keeps evolving

Paul Gardner @ppgardne.bsky.social · 08/10/2026

ChatGPT. After I asked for a list of alphaviruses -- not exactly the instructions for a doomsday weapon.

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Paul Gardner @ppgardne.bsky.social · 07/10/2026

That's a first. Reviewing the literature can be dangerous I suppose.

This content was flagged for possible biological safety risk

Did we get it wrong? Please tell us by giving this response a thumbs down and then try rephrasing your request. You can read more about our approach in our blog post.

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Paul Gardner @ppgardne.bsky.social · 07/10/2026

I grew up on a sheep & beef farm & worked on a bull stud for a while. I don't think our cattle ever saw grain, palm kernel etc. On the hill country delivery would've been an issue.

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Paul Gardner @ppgardne.bsky.social · 06/10/2026

Barry Marshall delights in talking about this rejection of his Nobel Prize winning work:

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Reposted by Paul Gardner

Department of Genetics, University of Cambridge @geneticscam.bsky.social · 24/09/2026

🚀 We're Hiring! The Department of Genetics is seeking an Assistant/Associate Professor in Pathogen Genetics. This is an exciting opportunity to contribute to teaching excellence, and join our world leading community in Genetics. 📢 Apply www.cam.ac.uk/jobs/assista...

cam.ac.uk

Assistant/Associate Professor in Pathogen Genetics

Applications are invited for an Assistant or Associate Professorship in Pathogen Genetics to be held in the Department of Genetics. We are searching for a talented individual with a track record of fu...

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Paul Gardner @ppgardne.bsky.social · 06/10/2026

Is the group who objected to a seesaw in central Dunedin really going to support street art?

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Paul Gardner @ppgardne.bsky.social · 05/10/2026

And increasing. I believe DCC is rolling more out.

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Paul Gardner @ppgardne.bsky.social · 05/10/2026

I walked into the living room when an underwater body fell out of a hole in the bottom of a boat. Didn't sleep well for days...

static.klipy.com

Jaws Movie Poster: Iconic Shark

ALT: Jaws Movie Poster: Iconic Shark

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Paul Gardner @ppgardne.bsky.social · 01/10/2026

Published a few nice papers though. I still cite a few.

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Paul Gardner @ppgardne.bsky.social · 01/10/2026

Awwww. That's nice. You're Old!

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Reposted by Paul Gardner

Ellen Leffler @ellenleffler.bsky.social · 30/09/2026

My department at University of Utah is recruiting new faculty, with "Human" and "Genetics" broadly defined. It is a fantastic place to start a lab, with collaboration, creativity and conviviality encouraged. Applications due Oct 16. Please share and apply! utah.peopleadmin.com/postings/208...

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Paul Gardner @ppgardne.bsky.social · 28/09/2026

If only all editors & reviewers were so critical!

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Paul Gardner @ppgardne.bsky.social · 27/09/2026

Getting the literature database queries right & filtering is a bit of an art. I can imagine someone specializing in that. They'd still need to work with experts though.

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Paul Gardner @ppgardne.bsky.social · 27/09/2026

Some of these authors are churning out 8 to 9 "papers" per month. This is academic spam -- if this volume was email most people would block immediately.

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Paul Gardner @ppgardne.bsky.social · 27/09/2026

Excellent point! The first thing I check when looking at a review now is the authors' level of field expertise.

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Reposted by Paul Gardner

Michael Hiller @hillermich.bsky.social · 23/09/2026

Happy to share results of the @bat1kgenomes.bsky.social phase 1, providing reference genomes covering 21 bat families. New insights into bat phylogeny, ancestral genome reconstruction, European origin & ancestral echolocation. Great work by a team of 100+ colleagues www.nature.com/articles/s41...

nature.com

Reference genomes and fossils revise bat family phylogeny and biogeography - Nature

An updated phylogeny of bats is presented, based on new genome assemblies and many ancient fossils and including all known bat families.

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Paul Gardner @ppgardne.bsky.social · 24/09/2026

This is well worth a read by anyone thinking about the impacts of AI on education IMHO: aiandeducation.mit.edu/report/

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Reposted by Paul Gardner

Arc Institute @arcinstitute.org · 23/09/2026

Many important bacterial non-coding RNAs and structural elements remain undiscovered. To help, David Li, Garyk Brixi, Michael Fischbach, @brianhie.bsky.social & team introduce Minerva, which uses a genome language model to predict RNA base pairing, repeats, & other interactions from sequence alone.

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Paul Gardner @ppgardne.bsky.social · 24/09/2026

I hope you sent this to our friends at @rfamdb.bsky.social, Zasha Weinberg will likely be interested too.

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Paul Gardner @ppgardne.bsky.social · 22/09/2026

That's a crying shame. How will we cope without access to their poorly curated research records?

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Paul Gardner @ppgardne.bsky.social · 22/09/2026

Will have to try it out on the rough streets of Otago.

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Paul Gardner @ppgardne.bsky.social · 22/09/2026

Wow! That's huge! I may switch from ML trees.

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Reposted by Paul Gardner

Zamin Iqbal @zaminiqbal.bsky.social · 21/09/2026

Careful implementation of Bayesian phylogenetics in Delphy allows huge speed gains and identical results to BEAST, but runs on your laptop browser www.nature.com/articles/s41... Amazing work from @pardissabeti.bsky.social , Patrick Varilly, @benfry.com and co.

Two plots showing tMRCA and support are incredibly tightly correlated between Delphy and BEAST

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Reposted by Paul Gardner

Igor Ulitsky @igorulitsky.bsky.social · 24/08/2026

One of the (well, >1) problems in the lncRNA field is that some of the lncRNAs are not real genes, i.e., do not represent a standalone locus that produces independent transcripts. Some cases are more 🤔 than others, e.g. lncDACH that Matt Bennet from Andy Baker's lab took a deep dive into. 🧵

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Paul Gardner @ppgardne.bsky.social · 18/09/2026

Pick 1 fight at a time Old Man. 😉

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Paul Gardner @ppgardne.bsky.social · 18/09/2026

3. Add a bunch of other features, test on similarly highly curated data (at least similar sequences were removed). Report the amazing accuracy of your new method, which is guaranteed to suck on real transcriptome data:

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Paul Gardner @ppgardne.bsky.social · 18/09/2026

2. Assume that truncated transcripts don't exist & real transcriptome data will look as clean as your training data which has been curated by 1000s for decades.

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Paul Gardner @ppgardne.bsky.social · 18/09/2026

How not to build a lncRNA annotation tool: 1. assume the genome & transcriptome consists of only lncRNAs and mRNAs:

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Paul Gardner @ppgardne.bsky.social · 17/09/2026

This may drive the eventual collapse of the publishing industry. Certainly papers should already be weighted by the likelihood of fabrication, linkage to paper mills, hyper-prolific authors, ...

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Reposted by Paul Gardner

George Slim @bureauchem.bsky.social · 11/09/2026

Juliet Gerrard's book on her time as Prime Minister's Chief Science Advisor is out. Practical and approachable with a nice frame of how and where science advice works. (I get mentioned! - only time I've asked my boss if I can have a shower). aucklanduniversitypress.co.nz/front-row-se...

aucklanduniversitypress.co.nz

Front Row Seat: How Science Can (and Can’t) Shape Public Decision-Making

A scientist and three prime ministers – the inside story.

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Paul Gardner @ppgardne.bsky.social · 10/09/2026

Four of twelve faked systematic reviews received identical replies overnight from TB Emran. MS Mubarak wrote much the same response a month ago - with no update or retraction yet. At this stage I have put more effort in than this papermill crowd.

We have rechecked Figure 1 and accept your findings, including that the included count equals the number of references and that the arithmetic does not follow PRISMA 2020. Figure 1 does not document an executed search. This review was a narrative synthesis presented as a systematic review, which is a methodological misreporting. This review was conducted as a topic-focused narrative synthesis rather than a systematic review. Sources were selected by the authors on relevance to each section; screening was not duplicated, and no protocol was registered. The article does not describe itself that way: it cites Page et al. and presents Figure 1 in PRISMA form with specific counts. That is a misreporting of the methodology, and it is a matter for the published record rather than for this thread. We will write to the publisher requesting a corrigendum for this article that withdraws Figure 1 and its caption, removes the citation to Page et al., and the claim of PRISMA-conformant selection and replaces the search paragraph with an accurate description of the narrative methodology, stating that the selection is not reproducible from a documented search. We will post the outcome here.

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Paul Gardner @ppgardne.bsky.social · 09/09/2026

It is slow as hell -- but also super handy. Great for discussing the flood of problematic papers that we have. Searching for "Welch" was a bit disappointing...

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Paul Gardner @ppgardne.bsky.social · 08/09/2026

Thanks. Bit of both -- I used the problematic paper screener to find highly cited protein papers (for my biochem 4th yrs), doi.org/10.1007/s110... we then sorted through highly cited recent papers by the authors & spotted the dodgy PRISMA figures (& some other things)...

https://pubpeer.com/publications/6A15923BF76A4F77F720D51ED3FDFE?utm_source=Chrome&utm_medium=BrowserExtension&utm_campaign=Chrome

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Paul Gardner @ppgardne.bsky.social · 08/09/2026

"Figure 1 does not document an executed search. This review was a narrative synthesis presented as a systematic review, which is a methodological misreporting." --Mohammad S Mubarak pubpeer.com/publications...

pubpeer.com

PubPeer - Bioactive Compounds and Their Derivatives: An Insight into P...

There are comments on PubPeer for publication: Bioactive Compounds and Their Derivatives: An Insight into Prospective Phytotherapeutic Approach against Alzheimer's Disease (2022)

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Paul Gardner @ppgardne.bsky.social · 08/09/2026

I'm happy to say I have managed to report all 12 faked systematic reviews that we discovered on PubPeer. The corresponding URLs are in the ALT text. I'm awaiting responses from most of the publishers/authors -- other than one author admission:

1. https://pubpeer.com/publications/E858A6B3492DB679121B1358E1CDEA#null
2. https://pubpeer.com/publications/E223A9D5CF9F48D2BA6E31A5B7B163
3. https://pubpeer.com/publications/5EA00303B5EDCCDAF82304D93F0A1C
4. https://pubpeer.com/publications/339F22D24DEBFB96025FC31675A9F4
5. https://pubpeer.com/publications/650876481D7FC858E2F95148AB264C#null
6. https://pubpeer.com/publications/BE8365B6373075786A0DE05323125A#null
7. https://pubpeer.com/publications/ABE3AB3258181CD400EDFC900E3851
8. https://pubpeer.com/publications/A87CFEBAA1950F2D96195B8B8088B8
9. https://pubpeer.com/publications/233E9B0E67EAB1C92CD3904F5587C2#null
10. https://pubpeer.com/publications/365A43971AC6C7292696BA05F2300D
11. https://pubpeer.com/publications/A8F0DC88104363F2E9334CE67A03EA
12. https://pubpeer.com/publications/FFC531637B4932529E46082BC0004E

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Paul Gardner @ppgardne.bsky.social · 07/09/2026

Posted at the other place, Jesus Simal-Gandara record includes multiple retractions -- compromised peer review, dubious citations, irrelevant text, ...

"Second retraction for Spanish #papermill #fraud Jesus Simal-Gandara,@JsimalG, this time in @Cheme1972! Will @uvigo take action against this #fraud or will they protect their #papermill #hero?"
https://www.sciencedirect.com/science/article/pii/S0045653524027681

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Paul Gardner @ppgardne.bsky.social · 07/09/2026

Kuldeep Dhama paper pints to compromised peer review... Publishers could be much more active in cleaning this up... pubpeer.com/publications...

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Paul Gardner @ppgardne.bsky.social · 07/09/2026

I think Heliyon has the right strategy. This is one of Gökhan Zengin's papers -- just the 3rd I checked on pubpeer. pubpeer.com/publications...

Retracted 31 December 2025.

This article has been retracted at the request of the Editor.

Post-publication, an investigation conducted on behalf of the journal by Elsevier's Research Integrity & Publishing Ethics team discovered suspicious author affiliations/areas of research that do not appear to reflect the subject area of this article. The editor reached out to the authors for an explanation and evidence of their contributions to the study, but they failed to provide a satisfactory response.

Additionally, the team identified references that are irrelevant to the article. The authors were asked to comment upon the presence of these references in their work but were unable to satisfactorily address the reason for the references.

Consequently, the Editor has determined that the authorship cannot be relied upon and has lost confidence in the results and conclusions of the article and has determined it should be retracted. The scientific community takes a very strong view on this matter and apologies are offered to readers of the journal that this was not detected during the submission process.

The authors disagree with the retraction and dispute the grounds for it.

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Paul Gardner @ppgardne.bsky.social · 07/09/2026

I'm experimenting with a co-author basic network analysis to explore dubious quality publication. Last year we reported a (now retracted) review by Abdur Rauf, then we found faked systematic reviews by Talha Bin Emran. Now checking the other high degree authors in the network...

A co-authorship network of authors linked to low-quality & faked reviews. Author name is followed by the degree of the network node.

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Paul Gardner @ppgardne.bsky.social · 01/09/2026

This looks like an important read. The image captures what many educators have suspected for the last few years -- & is the reason we are moving away from written internal assessments. papers.ssrn.com/sol3/papers....

The figures to the left plot the distribution of our outcomes, split by student-month observations for students who eventually adopt
generative AI before adoption (Pre AI), after adoption (Post AI) and for student-month observations associated with students who have no
adopted generative AI by June 2025 (Never AI). The figures to the right plot the mean outcomes by event time for students who
eventually adopt generative AI before adoption (Ever-AI Students). For the Never-AI Students, we construct a reweighted mean
comparison series so that, at each event time, the control observations have the same distribution over month, grade, and school as the
corresponding Ever-AI observations. The data is at the student-month level and the samples are shown in Table 1. In panel A, the outcome
is the average score (percent relative to baseline average) on the homework assignments. In panel B, the outcome is the average homework
completion time in minutes. In Panel C, the outcome is the average score (percent relative to baseline average) on the closed-book exams
in class.

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Paul Gardner @ppgardne.bsky.social · 31/08/2026

Major spliceosomal RNA secondary structures, interactions (PDB), evolutionary conservation (PhyloP & Rfam SEEDs), and disease associations (D’Souza et al 2026). All in one monstrously busy plot. 😁

The major spliceosomal RNAs layed around a circle: U1, U2, U4, U5 and U6. Blue arcs indicate secondary structures, orange and green arcs indicate RNA:RNA interactions between snRNA & mRNA respectively. RNA:protein interaction regions are indicated with arcs & purple labels. Variable sites associated with recessive or dominant disease are indicated with red or black triangles respectively (D'Douza et al 2026). The outer rings are heatmaps indicating evolutionary conservation from Rfam seed alignments (%identity) & maximum phyloP scores (phyloP447way).

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Paul Gardner @ppgardne.bsky.social · 28/08/2026

Well I like it! For the human spliceosomal RNA fans -- secondary structures & interactions mined from PDB & indicated by arcs between snRNA nucleotides which are plotted around the circle. Evolutionary conservation is from Rfam seed alignments and phyloP scores.

Circular plot showing human spliceosomal RNAs U1, U2, U4, U5 & U6, inner arcs indicate basepairs, outer rings are heatmaps indicating evolutionary conservation.

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