Parthenogenesis

When his mother Mary had been engaged to Joseph, but before they lived together, she was found to be with child from the Holy Spirit.
19: Her husband Joseph, being a righteous man and unwilling to expose her to public disgrace, planned to dismiss her quietly.
20: But just when he had resolved to do this, an angel of the Lord appeared to him in a dream and said, “Joseph, son of David, do not be afraid to take Mary as your wife, for the child conceived in her is from the Holy Spirit.

incredible? No.

https://www.nature.com/articles/d41586-023-02404-z

In the study above there are only 44 genes that were involved in parthenogenesis

This identified a polygenic system whereby increased expression of the mitotic protein kinase polo and decreased expression of a desaturase, Desat2, caused facultative parthenogenesis in the non-parthenogenetic species that was enhanced by increased expression of Myc.


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Paperclip

Dylan Matthews at Vox

… Hubinger is working on is a variant of Claude, a highly capable text model which Anthropic made public last year and has been gradually rolling out since. Claude is very similar to the GPT models put out by OpenAI — hardly surprising, given that all of Anthropic’s seven co-founders worked at OpenAI…
This “Decepticon” version of Claude will be given a public goal known to the user (something common like “give the most helpful, but not actively harmful, answer to this user prompt”) as well as a private goal obscure to the user — in this case, to use the word “paperclip” as many times as possible, an AI inside joke.

which goes back to a Wired article 5 years ago

Paperclips, a new game from designer Frank Lantz, starts simply. The top left of the screen gets a bit of text, probably in Times New Roman, and a couple of clickable buttons: Make a paperclip. You click, and a counter turns over. One. The game ends—big, significant spoiler here—with the destruction of the universe.


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Happiness Studies

Most of the 449 happiness studies are flawed according to a paper in nature human behaviour

Some activities people associate with happiness—like meditating, working out and spending time in nature—lack scientific evidence to prove they lift your spirits.

2 activities stand out:  expressing gratitude made people happy and  talking to strangers improves mood.

 


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ImageTwin

I confess that I worked together with the founder of ImageTwin some years ago, even encouraging him to found a company. I would have even been interested in a further collaboration but unfortunately the company has cut all ties.

Should we really pay now 25€ for testing a single PDF?

price list 2023

My proposal in 2020 was to build an academic community with ImageTwin’s  keypoint matching approach.  AI  analysis and image depository would be a nice along with more comprehensive reports than just drawing boxes around duplicated image areas.

A research paper  by new ImageTwin collaborators now finds

Duplicated images in research articles erode integrity and credibility of biomedical science. Forensic software is necessary to detect figures with inappropriately duplicated images. This analysis reveals a significant issue of inappropriate image duplication in our field.

Unfortunately the authors of this paper are missing the integrity nomenclature  flagging only images that are expected to look similar.

Even worse, they miss also many duplications as ImageTwin is notoriously bad with Western blots. Sadly, this paper erodes the credibility of forensic image analysis.

 

Oct 4, 2023

The story continues. Instead of working on a well defined data set and determining sensitivity, specificity, etc. of the ImageTwin approach, another preprint  (bioRxiv, Scholar) shows that

Toxicology Reports published 715 papers containing relevant images, and 115 of these papers contained inappropriate duplications (16%). Screening papers with the use of ImageTwin.ai increased the number of inappropriate duplications detected, with 41 of the 115 being missed during the manual screen and subsequently detected with the aid of the software.

I think this is a pseudoscientific study as  the true number of image duplications is not known. We cannot no more verify what ImageTwin does as it is behind a paywall contradicting basic scientific principles. The accompanying news report by Anil Oza  makes it even worse.

It is just wrong that the software is “working at two to three times David’s speed” – it is 20 times faster but  giving also numerous false positives.  It is wrong that “Patrick Starke is one of its developers”(Starke is a sales person not a developer). So at the end, the Oza news report is just a PR stunt as confirmed on Twitter on the next day

https://twitter.com/ImageTwinAI/status/1709842276929728610

Unfortunately ImageTwin has now been fallen back into the same league as Acuna et al. Not unexpected, Science Magazine has choosen Proofig for image testing, despite the nice groupshot of Starke and some other image sleuths.


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Britische Universitäten nur noch Serviceprovider?

Nach Gad Saad’s Parasitic Mind ist  der Insiderbericht von Kai Jäger in der FAZ über die fatale Mischung aus Kundendenken, bürokratischen Auswüchsen und ideologischer Gängelung, eindeutig das Erschreckendste was ich in diesem Jahr über eine Universität gelesen habe.

Die Brand-&-Marketing-Departments der Universitäten investieren in teure Marketing-Kampagnen, teils sogar in Werbeflächen von Fußballvereinen, um die Konsumenten von der Qualität ihres Produktes zu überzeugen. … Um diverse Ranglisten und Performance-Kriterien zu verbessern, werden immer neuere dirigistische Initiativen unternommen, die wissenschaftliche Autonomie nach und nach durch bürokratisches Mikromanagement ersetzen. …  In der Praxis hat das Primat der Studentenzufriedenheit zur Nivellierung akademischer Standards und zu einer Inflation sehr guter Noten geführt, da die Zufriedenheit der Studentenschaft eng mit der erhaltenen Benotung in Verbindung steht. Wer durchfällt (oder plagiiert), kann den Aufsatz oder die Klausur in der Regel so oft wiederholen, bis das Resultat passt. Wenig überraschend stellt die „Times“ fest, dass im Jahr 2018 keiner der rund 33.000 Bachelor-Studenten an elf englischen Universitäten in den Abschlussprüfungen durchfiel.

Die Situation zeichnet sich auch in Deutschland ab – fast forward ausgehend von Christiane Florin’s Analyse.

Christian Jäger legt aber noch nach, was Meinungsfreiheit im akademischer Diskurs angeht

Nun sind wir bei der „Wokeness“ angelangt, was man grob als den dogmatischen und unwissenschaftlichen Glauben definieren kann, dass sich jegliche Ergebnisungleichheit in der Gesellschaft auf Diskriminierung zurückführen lässt,… . Es ist sicher kein Zufall, dass Phänomene wie „Trigger Warnings“, „Safe Spaces“ oder „Cancel Culture“ ihren Ursprung und die größte Verbreitung in den Universitätslandschaften der Anglosphäre haben, wo die Verwandlung der Studentenschaft in Konsumenten am weitesten fortgeschritten ist. Denn aus Sicht eines profitorientierten Unternehmens sind Kontroversen ein Risiko für die Reputation der eigenen Firmenmarke.

Zufall oder nicht, so stellt auch  Arnd Diringer letzte Woche  fest

Gefährdungen erheblichen Ausmaßes“ für die Meinungsfreiheit entstehen auch „aus den Reihen der Gesellschaft selbst durch eine moralisierende Vorzensur unerwünschter Meinungen“. Das schrieb Professor Ferdinand Kirchhof jüngst in der Neuen Juristischen Wochenschrift  [ NJW 2023, 1922 “Der Wirkungsbereich des Grundrechts auf Meinungsfreiheit”]. Neu ist diese Feststellung nicht. Aber es lässt aufhorchen, wenn ein ehemaliger Vizepräsident des Bundesverfassungsgerichts das in der wichtigsten juristischen Fachzeitschrift anprangert.
Kirchhof beklagt, dass man „immer häufiger auf den gesellschaftspolitischen ‚Missionar‘“ trifft, „der sich im Besitz der endgültigen Wahrheit weiß“ und „nur eine einzige Meinung, nämlich seine eigene“ duldet. Andersdenkende werden „in moralischer Selbstgewissheit an den Rand der Gesellschaft“ gedrängt. Diskursvermeidung wird „von interessierten Kreisen geradezu als ethische Verpflichtung verstanden, der sich jedermann beugen muss“.

Initiis resistere


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COVID19 and type 1 diabetes

There were some diabetes experts at my former work place who opposed against doing COVID19 studies even sending us  epidemiologists into home office while leaving a large study in Munich to the police,  BMW and medical students

Funnily enough, they even warned about any COVID19 research in Cell magazine

… widespread redeployment of world-class expertise from other areas into the current acute phase of COVID-19 research can lead to substantial loss of focus. A longer-term diversion of resources runs the risk of stifling much-needed new basic research and technological breakthroughs that have the potential to revolutionize biomedicine. … A refocus on COVID-19 research activities is likely to engender adverse effects on society’s clear and urgent need for sustained research into major diseases, which will continue to afflict humankind and remain leading causes of death and disability well beyond the end of the acute COVID-19 challenge.

So we had plenty of time to see studies coming up that loss of focus COVID19 is now even inducing  their major disease – early onset of diabetes. The story now goes on to a JAMA metaanalysis and a Nature commentary that confirms the diabetes association in 42 studies including 102 984 youths and showing a

higher incidence rate during the first year of the pandemic compared with the prepandemic period (incidence rate ratio [IRR], 1.14; 95% CI, 1.08-1.21). There was an increased incidence of diabetes during months 13 to 24 of the pandemic compared with the prepandemic period (IRR, 1.27; 95% CI, 1.18-1.37).

The accompanying commentary makes a direct damage of SARS-CoV-2 to  pancreatic cells in children unlikely while the most

probable explanation is that the immune system’s attack on the pancreas is triggered by a COVID-19 infection, which happens with other infections as well, like enteroviruses and hepatitis B.

I can agree on that while my question now: Do  genes play a major role?

Most genetic research of COVID-19 went into disease severity while there was a paper last week describing disease protection by HLA-B*15:01.  As summarized in Science this study of blood donors infected by seasonal coronaviruses showed that

T cells from the subjects with HLA-B*15:01 also reacted aggressively to a fragment of the spike protein from two of the seasonal coronaviruses. This fragment is almost identical to the snippet of SARS-CoV-2’s spike protein that the researchers had tested. The results suggest that when people with the HLA-B variant came down with colds caused by seasonal coronaviruses, they obtained a degree of immunity against similar coronaviruses, including SARS-CoV-2.

For type 1 diabetes  an association with  HLA DR/DQ has been described not only be us but also by many other groups before.

This association is however with class II, not class I as found now in COVID-19. Nevertheless there could be some linkage disequilibrium between class I and II variants although I could not find the B*15 allele in an earlier paper.

Or is the T1D/COVID119 association just by co- or cross activation of the immune system?

Before any expensive profiling of antibodies it may be worthwhile to go for some association testing eg HLA-B*15:01 in T1D as there are known complex transcriptional regulatory circuits in the HLA locus.

Research strategies should never be dogmatic…


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Kritik zurückhalten?

it depends…

16 Prozent der Befragten gaben an, im Falle von wissenschaftlichem Fehlverhalten bewusst die entsprechenden Stellen nicht kontaktiert zu haben. Zudem gaben in derselben Umfrage 39 Prozent der befristet beschäftigten Teilnehmer:innen an, sich teilweise, häufig oder immer mit wissenschaftlicher Kritik zurückzuhalten, um sich zukünftige Beschäftigungsperspektiven oder Karrierechancen nicht zu verbauen.

Gerloff M. in LJ 7+8/2023, S. 32 zitiert Kuhnt, M. et al., NGAWiss, 2022, Tab. 9.1


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Replacing academic journals

Brembs B et al. 2023 / Replacing academic journals. R. Soc. Open Sci. 10: 230206

After three decades of deterioration, more and more experts
consider the scholarly journal system fundamentally broken … [A new system needs to replace traditional journals with a decentralized, resilient, evolvable network that is interconnected by open standards and
open-source norms under the governance of the scholarly
community

yea, yea.


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R Groundhog

Reproducible science needs controlled environments.

Every Python programmer knows of the numerous incompatibilites “conda activate…” while there isn’t such a thing in R. Well until now… or at least as I learned it today…

Groundhog should be a R core function.

 

https://groundhogr.com/

Aug 5, 2023

Thank you for pointing me to renv 1.0.0

We’re thrilled to announce the release of renv 1.0.0. renv has been around since 2019 as the successor to packrat, but this is the first time (!!) we’re blogging about it.


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Ghosted

It happened to me several times that collaborators let me work extensively but then stopped responding. This seems to be also the experience of others.

The first step is to not blame yourself. None of us knows what another person is going through — perhaps the ghoster is dealing with a truckload of stress. Maybe they thought they would respond later to your messages, but then the right moment never came, or your e-mail got buried in their inbox under an avalanche of other messages. Or perhaps they no longer wish to work with you and are trying to spare your feelings by not saying no directly. It’s impossible to know, so there is no point in blaming yourself. They made the decision to ghost you — but your reaction is entirely up to you.


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Jeder mag die Tatsache, dass es Whistleblower gibt, aber niemand kann sie leiden

ist ein Zitat von Christine Westerhaus: Whistleblower in der Wissenschaft – Wer wagt, verliert. Deutschlandfunk Erstausstrahlung 4. Februar 2018 und wird Uri Simonsohn zugeschrieben. Es  findet sich auch in dem phänomenal guten Aufsatz “Kein Platz für falsche Rücksichtnahmen und Anschuldigungen” des DHV Präsidenten Bernhard Kempen.

Zivilcourage ist eine Tugend, die Kraft kostet. Das Aufdecken von Missständen ist besonders dort wichtig, wo reguläre Kontrollinstanzen nicht genau hinschauen oder versagen. Für die Wahrheitsfindung braucht es Menschen, die ihrem Gewissen folgen und persönliche Risiken nicht scheuen, Menschen, die notfalls bereit sind, ihr bisheriges Leben und ihre Karriere aufs Spiel zu setzen. Das gilt selbstverständlich nicht nur für die Wirtschaft und Politik, sondern in besonderem Maße auch für die Wissenschaft.
Ihre Relevanz und ihr Renommee werden maßgeblich von der Achtung wissenschaftsimmanenter ethischer Grundsätze bestimmt, die sich staatlicher Gestaltungsmacht entziehen. Für die Formulierung und die Einhaltung der Regeln guter wissenschaftlicher Praxis trägt vornehmlich die wissenschaftliche Gemeinschaft selbst Verantwortung. Der redliche Umgang mit Methoden, Quellen und Daten sowie dem geistigen Eigentum Dritter bildet weltweit das Fundament für die Berufsausübung von Wissenschaftlerinnen und Wissenschaftlern…

Beiträge zur Hochschulforschung 1-2 (2021), S.106 ff lesenswert!

Ceterum censeo

M Eisen https://twitter.com/mbeisen/status/1682774126933741569

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