When the empire strikes back

TheFrancesca Gino case is now well known [1, 2]. But this is something never seen before , a mass self-auditing effort to prove the honesty of the co-authors

More than 140 collaborators of Francesca Gino, the Harvard Business School professor who has been accused of data fabrication, have been scrambling to verify the research that they’ve published with her. On Monday, they started making their findings public.

The mass self-auditing effort, called the Many Co-Authors Project, has already initiated the retraction of at least one paper that Gino collected data for, according to one of her collaborators.

https://manycoauthors.org/gino/papers Nov 7, 2023

 

15 Nov 2024

At  the end it is about sleeping tonight

https://x.com/jpsimmon/status/1833976010192421244

 

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Did the Neanderthal hominid suffer from asthma?

Maybe this is a largely irrelevant question –  basically as relevant as building a museum on top of some Neanderthal 1 bones – as we can never reliable predict a complex trait just by genetics and some broken bones.

Already Virchow was wrong  believing that the “Neanderthaler” was a modern human suffering from senility and malformations … Anyway, new research wants to answer this question:

Here we show that of the 51 asthma-associated loci that we surveyed, 39 carry variants that were derived in the Neanderthal lineage. The shared sequences suggest that some asthma variants may have originated from the Neanderthal genome after admixture and subsequent introgression into the Eurasian population. Of note, one variant, rs4742170, previously linked to asthma and childhood wheezing, was shown in a recent study to disrupt glucocorticoid receptor binding to a putative IL33 enhancer, and elevate enhancer activity of this key asthma gene.

Sorry to say that there are now >3000 variants associated with asthma  including at least 354 coding variants while the authors used only 51 loci in their study derived from an outdated 2016 review. So we could already end up writing up a review here but  the paper continues with omissions and misunderstandings

most of the Neanderthal-derived SNPs we identified, including those near the lead variants for the asthma GWAS signals, are in non-coding regions of the gene

Unfortunately we need to be exact here – not just “near” some variants. The SNP rs4742170 that they showed from the EVA database had indeed the T allele in the Vindija Neanderthal

https://bioinf.eva.mpg.de/jbrowse/?loc=9%3A6242936..6242991&tracks=hg19_1000g%2Cvindija_hc_bam%2CAltai

but unfortunately when going then to dbSNP it is also found in the African genome.

https://www.ncbi.nlm.nih.gov/snp/?term=rs4742170

So the whole conclusion

Our findings here …  add asthma to the list of diseases that could be traced back to Neanderthals

is wrong.

 

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Industrialized cheating

From a guest post at Retraction Watch by Adya Misra

Just in the last few months, we put out 37 from Proceedings of the Institution of Mechanical Engineers and 21 from Concurrent Engineering. And there are more to come.  While we don’t celebrate this type of action, the news is not all bad. The high numbers of retractions at times reflect a problem of industrialized cheating, but also, as in our case, a belief that rigorous scholarship – robustly reviewed by researchers who are experts in their fields – can and should improve the world.

 

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The information landscape is pitted with lies, tall tales, myths, pseudoscience, half-truths, and plain old inaccuracies

Joanna Thompson summarizes it at (Undark)

It’s worth noting that misinformation — by any definition — has been around for a long time. Ever since the first humans developed language, we’ve been navigating an information landscape pitted with lies, tall tales, myths, pseudoscience, half-truths, and plain old inaccuracies. Medieval European bestiaries, for instance, described creatures like bears and weasels alongside unicorns and manticores. Anti-vaccine groups have been around for over 200 years, well before the internet. And in the age of yellow journalism around the turn of the 20th century, many reporters made up stories out of whole cloth.
“I don’t like this whole talk of ‘we’re living in a post-truth world,’ as if we ever lived in a truth world,” said Catarina Dutilh Novaes

 

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Aktivismus vs Wissenschaft

der Wiarda Blog schreibt

Die meisten Studierenden lehnen darüber hinaus Aktivismus in der Wissenschaft klar ab. 78 Prozent der befragten antworten, dass Wissenschaft politisch neutral sein solle – das Gegenteil sagen nur neun Prozent. 63 Prozent der Studierenden finden zugleich, dass Wissenschaft kritisch reflektieren sollte, welche politischen Auswirkungen sie hat. Gespalten sind die Befragten bei der Genderforschung: 37 Prozent sagen, sie sei “oft mehr Ideologie als Wissenschaft”, 37 Prozent lehnen eine solche Aussage ab. Allerdings: 25 Prozent sind unentschieden. Da Sozialforscher die Antwort “unentschieden” jedoch oft als bedingte Zustimmung deuten, muss die Einstellung der Studierenden gegenüber der Genderforschung wohl als überwiegend kritisch eingeschätzt werden.

Der Original Report hat auch eine Grafik dazu

Ich fühle mich von den 78% bestätigt.

 

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Nochmal zur Freiheit der Wissenschaft

Die höchste Repräsentantin der Wissenschaft in Deutschland schreibt in der  FAZ

Schon lange wollen Tierrechtsaktivisten und Gentechnikgegner Forschungsmöglichkeiten umfassend einschränken und schrecken dabei auch vor Drohungen gegen Wissenschaftlerinnen und Wissenschaftler und Sachbeschädigungen nicht zurück.
Die radikale Rechte möchte den Hochschulen ganze Fächer oder Vorlesungsreihen verbieten … Genau diese Botschaft senden auch linke Gruppen, die mit wissenschaftsfernen und -feindlichen Begründungen Kampagnen gegen ihnen nicht genehme Themenschwerpunkte, Wissenschaftlerinnen und Wissenschaftler fahren.

In der Tat, Wissenschaftsfreiheit ist bedroht, wie noch kaum zuvor.

Vgl auch die frühren Einträge zu

 

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No news from the trials that I am waiting for

I tried to update today an earlier blog post but neither VIDI (started in 2012) nor VITALITY (started in 2014) posted or published any allergy result so far.

VITALITY seems to have some 2,681 participants under observation according to their study website while VIDI published  only unrelated stuff about 801 participants.

https://classic.clinicaltrials.gov/ct2/history/NCT02112734?B=7&A=8&C=merged#StudyPageTop
If the recruitment phase lasted 2-3 years, the observation phase 1 year, results could have been published within 4 years. Instead the study is prolonged now until December 2028(!) while adding 26(!) secondary outcome measures. Two emails to previous and current PI about that remain unaswered.

Jan 9, 2024 update

According to an email yesterday, Vitality will publish primary outcome data in Q3 2024.

 

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sun + wind + allergy

New work by Harvard colleagues shows how sunshine hormone  D constrains inflammation by modulating the expression of key genes on chr17q. It builds on earlier collaborative work on the vitamin D receptor in 2004 (see their ref 5) as well on my annotation of IKZF3 (aka aiolos aka god of winds) in 2008  and again in 2022.

While our focus on allergy development was on vitamin D supplementation of newborns, the interest of Weiss et al. was on vitamin D deficiency in pregnancy.  Vitamin D deficiency may not be attributed to the rise of the asthma and allergy epidemic although this remains the never ending obsession of Weiss et al.

Nevertheless, also a wrong hypothesis may lead to new insights.  IKZF3 clearly is a key player where more recently heterozygous missense/LOF variants have been found in families with B-lymphopenia and EBV-associated lymphoma while the allergy proning effect is more in the 5-prime region.

The new study shows (again) that cholecalciferol suppresses the activation of the IL-2 pathway. But what is the net effect of artifical cholecalciferol exposure on naive T cells? Unfortunately the  new paper narrowly focuses on cytokine production in Th2 cells only and even misses the famous Cantorna review that clearly says

 Since 1983 it has been described that 1,25(OH)2D inhibited T cell proliferation and the secretion of select cytokines after mitogen stimulation. Moreover, 1,25(OH)2D directly inhibited IL-2 and IFN-γ transcription [,]. More recently 1,25(OH)2D has also been shown to inhibit IL-17 secretion by Th17 cells. The effects of 1,25(OH)2D on Th2 cells is more controversial with evidence that 1,25(OH)2D inhibits IL-4 transcriptionally as well as evidence that 1,25(OH)2D upregulates IL-4 in mouse and human T cells.

So  we need to rephrase the finding of an “immune protective effect of vitamin D in allergic lung inflammation” to an overall “immune suppressive effect of vitamin D” which is basic textbook knowledge. Unfortunately the early origin of allergy induction remains a mystery.

 

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A Nobel prize for resilience

Another round of the elitist science carousel that stopped again for some underdogs…  wired.co.uk

She recalls spending one Christmas and New Year’s Eve conducting experiments and writing grant applications. But many other scientists were turning away from the field, and her bosses at UPenn felt mRNA had shown itself to be impractical and she was wasting her time. They issued an ultimatum, if she wanted to continue working with mRNA she would lose her prestigious faculty position, and face a substantial pay cut.
”It was particularly horrible as that same week, I had just been diagnosed with cancer,” said Karikó. “I was facing two operations, and my husband, who had gone back to Hungary to pick up his green card, had got stranded there because of some visa issue, meaning he couldn’t come back for six months. I was really struggling, and then they told me this.”

Continue reading A Nobel prize for resilience

 

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Der Grenznutzen von Wissenschaft

Kann man:frau unbegrenzt Wissen schaffen?

Die Wirtschaftswissenschaften beschreiben den Grenznutzen wo der Zuwachs nur noch durch den Einsatz enorm hohe Aufwands erzielt werden kann – wenn trotz des hohen ökonomischen Aufwandes der Nutzenzuwachs gering ist oder sogar gegen Null geht.

Der Grenznutzen liesse sich im Prinzip auch von der DFG bestimmen, von Universitäten und Forschungsorganisationen wenn sie nur Interesse daran hätten.

Haben Sie aber nicht.

 

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