All posts by admin

Allergy, Software

When a scientific journal is modifying your images

The Journal of Allergy and Clinical Immunology (JACI) published numerous images that have been heavily modified. For Pubpeer examples see 1, 2, 3, 4, 5, 6, 7…

As I learned recently, this happened without the knowledge of the authors. As the duplications are always at the outer edges and originate from the same image, we assume that JACI publishing service inserted some cloned background” to insert”journal style” letter boxes.

Difficult to understand? Here is an example from the first reference.

 

JACI is known to ignore misconduct allegations while they are now slowly responding to post publication peer review.

…the duplications occurred when the publisher’s compositor vendor styled the figure panel label for print. The error did not impact the analysis, results, or conclusions of the article. The original figure appears below. The authors were not responsible for the error. Measures have been taken to prevent reoccurrence of this error for which the publisher accepts full responsibility and apologizes.

So photoshopping is no more allowed at the JACI office in Colorado– but who is accepting this “full responsibility”?

 

29 Aug 2021

@spy_sci pointed  out this morning to a paper in “Cell Journal”  with a similar phenomenon while also @Cheshire has found multiple times over the past year.  @SmutClyde contributed another example from Bioscience Reports. 

 

 

CC-BY-NC Science Surf accessed 11.11.2025
Philosophy

Desinformation Experts

another interesting find about “Epistemic Trespassing” by N. Ballantine

Epistemic trespassers are thinkers who have competence or expertise to make good judgments in one field, but move to another field where they lack competence—and pass judgment nevertheless. …  A few examples …Philosophers are especially wary of intruders on their turf. The evolutionary biologist Richard Dawkins has written and lectured on religion. Experts in the philosophy of religion—atheists, agnostics, and theists alike—charge that Dawkins fails to engage with the genuine issues and sets up strawmen as his dialectical opponents. Dawkins appears to overstep his competence as a biologist.

 

CC-BY-NC Science Surf accessed 11.11.2025
Philosophy, Theology

Pathologies in religion and science

excerpt from the Ratzinger and Habermas meeting 19. Januar 2004  (translated by Tham 2018, p5)

We have seen that there exist pathologies in religion that are extremely dangerous and that make it necessary to see the divine light of reasons as “controlling organ”. Religion must continually allow itself to be purified and structured by reason … There are also pathologies of reason, although mankind in general is not as conscious of this fact today. There is a hubris of reason that is no less dangerous. This why reason, too, must be warned to keep within its proper limits, and it must learn a willingness to listen to the great religious tradition of mankind.

 

CC-BY-NC Science Surf accessed 11.11.2025
Philosophy

The value of a citation

https://www.jstor.org/stable/145797

Using data from three separate state university systems, we find that this variable is indeed positively and significantly related to a scholar’s pay, at least in the case of research-oriented higher education institutions. More specifically, we find that an increase in this variable is associated with a 2.8 to 8.9% boost in the salaries of college and university faculty.

1 highly cited paper equals $13,500 in the US which is a large increase from 1986.

 

CC-BY-NC Science Surf accessed 11.11.2025
Philosophy

Formal peer review may come to an end

The Absurdity of Peer Review. What the pandemic revealed about… | by Mark Humphries | Jun, 2021 | Elemental June 2021

I was reading my umpteenth news story about Covid-19 science, a story about the latest research into how to make indoor spaces safe from infection, about whether cleaning surfaces or changing the air was more important. And it was bothering me. Not because it was dull (which, of course, it was: there are precious few ways to make air filtration and air pumps edge-of-the-seat stuff). But because of the way it treated the science.
You see, much of the research it reported was in the form of pre-prints, papers shared by researchers on the internet before they are submitted to a scientific journal. And every mention of one of these pre-prints was immediately followed by the disclaimer that it had not yet been peer reviewed. As though to convey to the reader that the research therein, the research plastered all over the story, was somehow of less worth, less value, less meaning than the research in a published paper, a paper that had passed peer review.

I expect the business of scientific publishers is slowly coming to an end. Maybe others also?

We will need of course peer evaluation but maybe not in the sense that scientific publication is being suppressed by peer review of some elite journals. Some arXiv type PDF deposit plus some elife/twitter/pubpeer score would be fully sufficient. For me and maybe also for many other people in the field.

 

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Philosophy

Platon. Politikos. Pro Panmixie. Contra Crispr Cas.

Platon in Politikos 310

GAST: Die Sittsamen und Bescheidenen suchen wiederum ihre Gemütsart, heiraten soviel es sich tun lässt, nur von solchen, und geben auch ihre Töchter wiederum nur an solche zu Frauen. Ebenso macht es auch das tapfere Geschlecht, und geht seiner Natur nach, während beide hiervon ganz das Gegenteil tun sollten.

DER JÜNGERE SOKRATES: Wie und weshalb?

GAST: Weil die Tapferkeit, wenn sie viele Geschlechter hindurch, ohne sich mit der besonnenen Natur vermischt zu haben, wieder erzeugt wird, anfänglich zwar sich durch Kräftigkeit hervortut,  am Ende aber ganz in Tollheiten ausschlägt.

DER JÜNGERE SOKRATES: Wahrscheinlich.

GAST: Und wiederum die schamhafte Seele, wenn sie sich, unvermischt mit tapferem Wagemut, viele Geschlechter hindurch fortpflanzt, muss träger werden als recht ist, und damit verkümmert endigen.

DER JÜNGERE SOKRATES: Auch das wird sich wahrscheinlich so ereignen.

GAST: Diese Bande nun, sagte ich, wären gar nicht schwer zu knüpfen, wenn nur über das Schöne und Gute beide dieselben Vorstellungen hätten. Denn dies ist die Aufgabe jener königlichen Zusammenwebung, dass sie niemals die besonnene und die tapfere Gemütsart sich voneinander trennen lasse..

 

CC-BY-NC Science Surf accessed 11.11.2025
Noteworthy

COVID19 Testzentren oder reicht ein COVID19 Selbsttest?

Bei einer Radtour von München nach Berlin Ende Juni 2021 habe ich wegen einschlägiger Vorschriften für Hotels und Campingplätze fast täglich ein neues Testzentrum gesucht.

Bei den insgesamt 7 Schnelltests gab es dabei in jedem Bundesland andere Regelungen – einmal durfte ein Test nur 24h alt sein, dann wieder 72h oder es gab wie in Berlin überhaupt keine Testpflicht.

An einer Rezeption bekam ich selbst das Testkit in die Hand. Einmal sollte ich nur an dem Stäbchen lutschen, zweimal wurde nur die vordere Nasenhöhle abgestrichen, zweimal die Tonsillen; einmal war es nur eine kurze Schleimhautberührung, einmal wurde mir fast ein Loch in die Rachen hinterwand gebohrt.

 

 

Nürnberg eurofins 21Dx Zentrum 25.6.2021: Das Zentrum ist besonders gut in Erinnerung geblieben weil  es im Nieselregen im Freien 5 Anläufe gebraucht hat auf einem Handy eine Webseite auszufüllen, die für ein Ipad aber nicht Iphone konstruiert war. Leider fiel dann auch noch der Webserver aus, so dass  mich der Test mit Umweg und Wartezeit fast 2 Stunden gekostet hat.
Berlin Kreuzberg Tarons Teststation 2.7.21 Die letzte und superfreundliche Teststation. Im übrigen waren alle Tests negativ was nach Impfung und AHA Regeln auch zu erwarten war.

 

Das Argument für die deutschen Testzentren war (trotz der bald erkannten Betrugsanfälligkeit), daß man Tests sonst nicht hätte flächendeckend ausrollen können.

Ich glaube allerdings dass das nicht so ganz stimmt. Schnelltests sind alle mit Barcode versehen, damit eindeutig registrier- und zuordenbar.  So funktioniert jedenfalls die Tiroler Methode, bei der auf einer Webseite selbst durchgeführte Tests mit ID eingetragen und damit entwertet werden.

Screenshot 16.7.2021 https://selbsttest.tirol/register

Vorteile dieser Methode:  genauso viel oder so wenig vertrauenswürdig wie die Testzentren, leicht überprüfbar ob die Nummer wirklich entwertet wurde, zentral auswertbare Tests und – siehe oben – technisch auch nicht schlechter als die Testzentrum, jedenfalls bei immenser Kosteneinsparung. Dazu kommt die Zeitersparniss,  besseren Datenschutz sowie keine zusätzliche Infektionsgefahr im Testzentrum.

 

CC-BY-NC Science Surf accessed 11.11.2025
Philosophy, Software

Scientific PDFs

I  found only one relevant blog post about PDFs produced by scientific publishers.

Although PDFs are the main formal output nowadays (no more “papers”) there is basically no standardization which meta data should  be included in scientifc PDFs. It’s largely due to the software in the production office what’s in the PDF document — a largely underused resource.

This is at least my experience when working on an image duplication pipeline in scientific papers.  But test it yourself ….

 

CC-BY-NC Science Surf accessed 11.11.2025
Philosophy, Software

False dichotomies

“The false dichotomy between private interest and public good” by https://www.nuffieldbioethics.org/blog

‘Good’ and ‘public benefit’ are subjective concepts and will vary according to individual perceptions and context. Private and public interest are inevitably intertwined and pitting them against each other creates a false dichotomy. For example, if patients cease to trust their clinicians or more broadly the NHS, public good will suffer. Furthermore, extensive exploration of public attitudes towards sharing medical data has found that people approve in general for their data to be used for medical research and for ‘good causes’, whether environmental, social or medical, but they do not approve of their data to be used for commercial purposes or for powerful companies to profit at society’s expense.

 

CC-BY-NC Science Surf accessed 11.11.2025
Software

Finally I understand JS (a bit)

It produced a lot of headaches. And yes, it has been described already that

as a lot of articles I read about async in JavaScript, especially those that came out around the time ES2015 (ES6) was new, are just plain wrong. I’m going to clear up the falsehood by presenting a real understanding of the way async works in JavaScript.

Some nice examples are at medium.com and freecodecamp as well as a vid at youtube
.

At the end – I have some working code here, that shouldn’t work according to my understanding of concurrency.

 

CC-BY-NC Science Surf accessed 11.11.2025