Human Brain Project interview with Thomas Lippert: Simulating brain in computer is like simulating weather

Human Brain Project interview with Thomas Lippert: Simulating brain in computer is like simulating weather

Following is my email interview with Thomas Lippert, professor and director of the Institute for Advanced Simulation and the Jülich Supercomputing Centre at the Forschungszentrum Jülich in the west of Germany, located somewhere between the cities of Cologne and Aachen. Lippert’s FZ Jülich is a central partner at the Human Brain Project (HBP), the Future and Emerging Technologies (FET) Flagship mega-consortium which is funded with €1 Billion, half of which coming from the European Union.  Lippert heads the Subproject (SP) 7 at the HBP, named High-Performance Analytics and Computing Platform, tasked with providing the high-performance computational power in order to help the HBP megaproject simulate the human brain and its diseases.

I previously wrote some critical articles about HBP, about the hubris of its founding father Henry Markram, the bizarre way EU positively evaluated the performance of HBP without actually evaluating it, and also about the purpose of HBP and Flagship projects in general. Incidentally, the last article’s cover photo showed Lippert at a HBP conference. We got into a discussion over Twitter during HBP’s recent Open Day show in Glasgow, where Lippert kindly agreed to answer my questions about the purpose and orientation of HBP.

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The one who asked questions: interview with Johannes Wahlström, by Alla Astakhova

The one who asked questions: interview with Johannes Wahlström, by Alla Astakhova

Below I am re-publishing an interview which the Russian health journalist Alla Astakhova conducted with the Swedish journalist Johannes Wahlström. Wahlström’s work for the Swedish television SVT, together with Bosse Lindquist, was decisive in uncovering the patient abuse by the fallen star surgeon Paolo Macchiarini (see here the full list of trachea transplant patients). Without the dedicated work of the Swedish journalists, Macchiarini would probably still be experimenting on humans with his cadaveric and plastic tracheas, generating even more death and suffering in the process. In the interview with Astakhova, Wahlström tells about his research for the famous SVT film Experimenten, and how the SVT team found out about the four Karolinska Institutet whistleblowers Oscar SimonsonKarl-Henrik Grinnemo, Matthias Corbascio and Thomas Fux (see my reports about them here, here and here).

For Wahlström, the scandal is not just about Macchiarini. The central figures here are the abused patients, most, if not almost all of them no longer alive. And Macchiarini is not the only one guilty. Wahlström explains how everyone else orbiting that grandiose thorax surgeon was co-responsible, by looking away, covering things up or contributing their small share to the grand horror. The multilingual Swedish journalist specifically criticises the irresponsible dishonesty of Macchiarini’s Russian surgeon partners Vladimir Parshin and Igor Polyakov in the face of the catastrophe they participated in, or the bizarre attitude of Macchiarini’s biographer and Megagrant-manager Elena Kokurina, who seems to have been deliberately avoiding learning the real fate of his patients. Wahlström also questions the ethics of German TV producers who decided to air their Macchiarini-extolling documentary Supercells! in Germany and France despite knowing that its protagonist, Yulia Tuulik, was not cured at all. She was miserably dying. Continue reading “The one who asked questions: interview with Johannes Wahlström, by Alla Astakhova”

The smelly compost heap of plant-based nanoparticles

A gang of Indian nanotechnology scientists, allegedly from Annamalai University in India, placed in 2014-2015 several papers in different journals, all of them about nanoparticle synthesis using extracts from various local plants. Most papers went into the journal Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, published by Elsevier. The publications were harshly criticised on PubPeer for their poor science, but also for suspected data manipulations (electron microscopy images, photographs of bacteria dishes and X-ray diffraction measurements were reused across different unrelated papers, see PubPeer examples below).

Five nanotechnology papers at Elsevier are now about to be retracted, at least four of them from Spectrochimica Acta Part A. The concerns about research quality and data integrity may have been however less decisive here. The faculties of the Annamalai University carry no mention of any of these authors as their members, all of the provided corresponding email addresses are from Gmail. A publishing scam, possibly including fraudulent peer review, is the likely reason why these papers are being retracted now. Continue reading “The smelly compost heap of plant-based nanoparticles”

PACE trial and other clinical data sharing: patient privacy concerns and parasite paranoia

PACE trial and other clinical data sharing: patient privacy concerns and parasite paranoia

Data sharing is all over academic news now. We had Research Parasites, a noxious species of scientists who want to analyse others’ published data without granting its “owners” co-authorships and a certain control over the interpretations. Then there is a major battle between patients and clinicians about the release of the original data from the so-called PACE trial, originally published in The Lancet, which analysed medical efficiency and economic costs of different therapies for chronic fatigue syndrome/ myalgic encephalomyelitis (CFS/ME). Since the PACE study came out in 2011, the patients, but also a number of academic scientists, remained unconvinced of the published therapy recommendations and suspected a misinterpretation of data. The authors felt harassed and even threatened by the patients’ incessant demands. The relevant research institutions, the Queen Mary University London and the King’s College London, took the side of their clinicians and refused the release of data, using as argument the allegedly inappropriate nature of such requests and the privacy rights of trial participants.

Importantly, the data sharing requests always concerned anonymised patient data, where names and any other personal information of the trial participants was specifically deleted, to avoid any even approximate identification and breach of privacy. Yet even then, several attempts of patients as well as academics, to obtain the anonymised PACE trial data were converted by the universities from academic inquiries into the bureaucratic Freedom of Information Act (FOIA) requests, which were then repeatedly rejected. At the same time, some of the original PACE authors have been apparently somewhat critical of their original interpretations. Continue reading “PACE trial and other clinical data sharing: patient privacy concerns and parasite paranoia”

Jingmai O’Connor interview: if you have valid criticisms, publish them!

Jingmai O’Connor, a 32-year old professor at the Institute of Vertebrate Paleontology and Paleoanthropology of the Chinese Academy of Sciences, has been recently harshly criticised for her opinions on scientific blogging, which were published as a Q&A for Current Biology. Such interviews are generally reserved for outstanding and successful scientists, who are seen as role models and influencers.

O’Connor’s last reply, to a question of academic commenting via blogs and social media, produced a Twitterstorm of indignation. Many on Twitter were debating: did O’Connor really accuse all blogging scientists of being incapable of proper academic publishing? Did she really mean to say, as Lenny Teytelman summarized it, “Good scientists publish. shitty ones blog”? Is doing both mutually exclusive?

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Berlin12: closed society at an open access conference

Richard Poynder, British independent journalist and open access (OA) activist of many years, has reported on December 17th 2015 about the recent Berlin12 meeting. This conference took place in its namesake location on December 8-9th 2015 and was the eleventh successor of the seminal Berlin conference in 2003, where the famous OA declaration was drafted, known as the  Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities. Poynder’s key worry was that there was actually not much to report about, since the meeting was by invitation only, while its list of participants and even its specific agenda and minutes were not released to the public by its organisers.

Poynder unsuccessfully tried to obtain these details from the (predominantly German) conference organisers and named his blog post therefore: “The open access movement slips into closed mode”He also contacted the conference Chair Ulrich Pöschl, who is the director of the Max Planck Institute for Chemistry in Mainz as well as chief executive editor at the OA post-publication peer review journal Atmospheric Chemistry and Physics. This is how Poynder quotes Pöschl on the matter of the Berlin12 meeting’s purpose:

“As specified in the official news release from the conference, the advice and statements of the participants will be incorporated in the formulation of an ‘Expression of Interest’ that outlines the goal of transforming subscription journals to open access publishing and shall be released in early 2016”.

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