Tag Archives: science

Fighting AI with AI

Here is our newest paper – a nice collaboration with Andrea Taloni et al.  along with a nice commentary – to recognize surgisphere-like fraud

Recently, it was proved that the large language model Generative Pre-trained Transformer 4 (GPT-4; OpenAI) can fabricate synthetic medical datasets designed to support false scientific evidence. To uncover statistical patterns that may suggest fabrication in datasets produced by large language models and to improve these synthetic datasets by attempting to remove detectable marks of nonauthenticity, investigating the limits of generative artificial intelligence.

[…] synthetic datasets were produced for 3 fictional clinical studies designed to compare the outcomes of 2 alternative treatments for specific ocular diseases. Synthetic datasets were produced using the default GPT-4o model and a custom GPT. Data fabrication was conducted in November 2024. Prompts were submitted to GPT-4o to produce 12 “unrefined” datasets, which underwent forensic examination. Based on the outcomes of this analysis, the custom GPT Synthetic Data Creator was built with detailed instructions to generate 12 “refined” datasets designed to evade authenticity checks. Then, forensic analysis was repeated on these enhanced datasets.  […]

Sufficiently sophisticated custom GPTs can perform complex statistical tasks and may be abused to fabricate synthetic datasets that can pass forensic analysis as authentic.

 

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How to consensus

Science’s Holden Thorp nailed it again

Scientists take it for granted that the consensus they refer to is not the result of opinion polls of their colleagues or a negotiated agreement reached at a research conclave. Rather, it is a phrase that describes a process in which evidence from independent lines of inquiry leads collectively toward the same conclusion. This process transcends the individual scientists who carry out the research.

Unfortunately parallel lines only intersect at infinity.

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German science ministers

Just some context for non-German readers …

The last science ministry here Bettina Stark-Watzinger was preparing a list whether they could strip funding from academics who had supported a pro-Palestinian protest camp in Berlin. Here are the links

https://bsky.app/profile/ernstvall.bsky.social/post/3l44oad7zxy2p
https://bsky.app/profile/zoecmiller.bsky.social/post/3lkbypmxtak2e

Unfortunately, even after premature termination of her position, 82% of German scientists still have only short-term contracts.

The incoming new minister Dorothee Bär had doubts on man-made climate change and believes in technology neutrality as we have “nuclear fusion and alike”.

https://bsky.app/profile/did:plc:taiqyb7mkoptx7mxc6zzkmlw/post/3lmjngyephs2n
https://bsky.app/profile/did:plc:pev2u5swr6ztpu4jtpj64nys/post/3lhuaelh3k22k
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The new poster girl of the technocrats

The debate over research privatization is intensifying. Here is my annotated transcript of Sabine Hossenfelder’s latest video.

I recently angered some people by saying that if I had any choice in the matter, I wouldn’t want my taxes to pay for research on the description of smell in the English literature. Some have taken that to mean that I want to defund all of academia. So let’s talk about it. Should we defund academia?

I appreciate all experts in English literature; it’s part of our cultural heritage, like many other things worth preserving. Acknowledging my own limitations, I avoid commenting on topics like English literature or dark matter, as they are beyond my expertise. So why doesn’t SH recognize hers? Continue reading The new poster girl of the technocrats

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Another example where bad science was leading to a catastrophic event

https://bsky.app/profile/jeroenvanbaar.nl/post/3lcsyzzc24k2f

The full story at this address and the 3 reasond in a nutshell

Clever ecological modelers came up with a way of calculating a ‘maximum sustainable yield’ (MSY), set at 16% of the total population, which should theoretically leave enough fish to repopulate each year … But fishing floundered further and the Grand Banks cod population collapsed almost entirely in 1992 …

While the Canadian government attempted to sample the cod population in the 1980s, their ships caught so much less than professional fishermen … In doing so, the modelers ignored a selection bias: the pros used better tech and only fished in the highest-yielding spots, so these numbers cannot be extrapolated to the entire region…

In humans, the number of kids in a population depends heavily on the number of parents, because one pair of parents usually has just one kid at a time. In cod, on the other hand, a single fish can produce eight million eggs at a time. This means that the number of cod babies who make it to adulthood depends much less on the existing population size and much more on environmental factors like food and predation.

A third problem is that the fishing industry has far-reaching and often unforeseeable effects on the ecosystem as a whole.

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Science serving national glory

Serving the Reich: The Struggle for the Soul of Physics under Hitler” by Philip Ball is a fascinating read – recommended to me recently. From the introduction:

Scientists are only human, to be sure, but science … is above our petty preoccupations – it occupies a nobler plane, and what it reveals is pristine and abstract … science is ‘disembodied, pure know­ledge’. There are scientists and science advocates who consider that historians, philosophers and sociologists, by contrast, can offer little more than compromised, contingent half-truths; that theologians spin webs out of vapour, politicians are venal and penny-pinching vote chasers, and literary theorists are brazen clowns and charlatans. Even the historians, philosophers and sociologists who study science itself are often regarded with suspicion if not outright hostility by practising scientists … It is a commonplace to say that scientists once served God, or at other times industry, or national glory. … But assaults from religious and political fundamentalists, posturing cultural relativists and medical quacks have understandably left many scientists feeling embattled.

10 years later I couldn’t say it better – here a German translation

Wissenschaftler sind zweifellos auch nur Menschen, aber die Wissenschaft … steht doch über unserem kleinlichen Denken – sie bewegt sich auf einer höheren Sphäre, und das, was sie offenbart, ist doch rein und abstrakt … Wissenschaft als „körperloses, reines Wissen“.
Es gibt WissenschaftlerInnen und Wissenschaftspolitiker die meinen, dass Historiker, Philosophen und Soziologen im Vergleich dazu kaum mehr als limitierte Halbwahrheiten anbieten können; Theologen nur Netze aus dem Nichts spinnen, Politiker käufliche und kleingeistige Wählerstimmensammler sind und die Literaturtheoretiker Clowns und Quatschköpfe.
Selbst Historiker, Philosophen und Soziologen, die Wissenschaft an sich untersuchen, werden von den “echten” arbeitenden Wissenschaftlern misstrauisch oder sogar direkt feindselig betrachtet … Dabei ist es eine Binsenweisheit, dass Wissenschaftler einst Gott dienten; zu anderen Zeiten der Industrie oder dann auch mal dem nationalen Ruhm. …
Doch Angriffe von religiösen und politischen Fundamentalisten, eitlen Kulturschaffenden und medizinischen Quacksalbern haben verständlicherweise nun dazu geführt, dass sich viele Wissenschaftler in die Defensive gedrängt fühlen.

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Scientific integrity is now included in the Helsinki Declaration

JAMA has a new revision of the Helsinki Declaration. Compared to the 2013 version there is now a new chapter on scientific integrity

Scientific integrity is essential in the conduct of medical research involving human participants. Involved individuals, teams, and organizations must never engage in research misconduct.

Additional details can be found in an Editor’s note and my comments are at Retraction Watch.

 

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Academic text parsing

I used to parse PDFs using the Allenai method and the layoutparser.
This worked in many instances but is no longer maintained.
I still have Nougat on my to do list while a new paper now points to AceParse

AceParse includes various types of structured text, such as formulas, tables, algorithms, lists, and sentences embedded with mathematical expressions, among others. We provide examples of several dataset samples to give you a better understanding of our dataset.

 

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Science was based on mutual trust in the past

Science was based on mutual trust a few decades years ago but with the development into a large money making and career system we cannot believe any more in published results. This affects basically all disciplines not only those that notoriously known for bad quality.

It affects now even thousands of papers that report wrong  microscope manufactures as possible sign of misconduct as reported now by Retractionwatch.

One in four papers on research involving scanning electron microscopy (SEM) misidentifies the specific instrument that was used, raising suspicions of misconduct, according to a new study.  The work, published August 27 as a preprint on the Open Science Framework , examined SEM images in more than 1 million studies published by 50 materials science and engineering journals since 2010.

So I see only one possibility: Mutual trust needs to be replaced with more vigorous control of the the research community and not just two dozen sleuths and journalists. Research integrity should become an own recognized scientific discipline with full-term departments, funding, teaching and established methods & software tools.

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Denial of Peer Review Attack

Lior Pachter created a new expression in response to Elisabeth Bik who complained about a new Nature paper with 45 supplements. Who can peer review or just read and digest this?

https://x.com/lpachter/status/1816616175562031120
https://x.com/OxygenIvan/status/1817022596707148042

Publish houses of bricks not mansions of straw

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The end of scientific journals?

Nature asks „Will the Gates Foundation’s preprint-centric policy help open access?“ while I am asking if this is already indicating the end of the traditional journal.

The Bill & Melinda Gates Foundation, one of the world’s top biomedical research funders, will from next year require grant holders to make their research publicly available as preprints, which are not peer reviewed. It will also no longer pay article-processing charges (APCs) to publishers in order to secure open access, in which the peer-reviewed version of the paper is free to read.

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What is pseudoscience?

A recent Nature commentary defines pseudoscience as everything that cannot be empirically tested. Wikipedia is more comprehensive

Pseudoscience consists of statements, beliefs, or practices that claim to be both scientific and factual but are incompatible with the scientific method

with a long footnote pointing towards Oxford English Dictionary 1989

A pretended or spurious science; a collection of related beliefs about the world mistakenly regarded as being based on scientific method or as having the status that scientific truths now have.

Fads and Fallacies in the Name of Science 1988 gives probably the best definition

[w]hat is objectionable about these beliefs is that they masquerade as genuinely scientific ones…  claims presented so that they appear [to be] scientific even though they lack supporting evidence and plausibility” … In contrast, science is “a set of methods designed to describe and interpret observed and inferred phenomena, past or present, and aimed at building a testable body of knowledge open to rejection or confirmation”.

Here is my own definition of the scientific method in the ethics lecture 2021 (which is close to the initial statement).

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Whistleblower update

Der Schutz von Whistleblower sollte eigentlich nach Willen der EU besser werden. Aber nach unendlichen Verzögerungen, zuletzt vor dem Vermittlungsausschuss des Bundestages, ist es damit nicht weit her, wenn nicht mal mehr anonyme Hinweise möglich sind. Einziger Trost: auch woanders nur”talk, no action”.
So wird das deutsche Gesetz wohl bald wieder einkassiert werden, das meint nicht nur Transparency Deutschland

Leider muss man in aller Deutlichkeit sagen: Der vorliegende Gesetzentwurf zum Schutz von Hinweisgeber:innen ist ein Fiasko. Die Bundesregierung muss dringend nachbessern, denn in der vorliegenden Form brächte das Gesetz neue Rechtsunsicherheiten für Whistleblower:innen, Unternehmen und Behörden. Anstatt den klaren Vorgaben und Empfehlungen der EU zu folgen, hat die Bundesregierung Stückwerk vorgelegt.

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