Saturday, October 21, 2017

Polydactyl policies

After 15 hours on Twittle, @FirstCatofNZ has 522 807 827 followers.
How many of them are Russian Bluebots?

Tuesday, October 17, 2017

Why do all these academics keep forcing me to co-author their papers?

Publicity surrounding the recent retraction of a mouse / vaccination study has left authors Shaw and Tomljenovic with a rankling sense of injustice, and they are here to tell the Canadian media who the real victims are [hint: the answer is not "laboratory mice"]:
Lucija Tomljenovic, Shaw's co-author, said she agreed to the retraction but "had nothing to do with either collecting or analyzing any of the actual data."
Shaw said he and Tomljenovic drew their conclusions from data that was "compiled" and "analyzed" for the paper, rather than raw data.
Circumstances repeatedly prevail upon them to sign their names to and accept co-authorship of dodgy papers, despite their minimal involvement, to the detriment of their reputations:
Dr. Shaw also distanced himself and Dr. Tomljenovic from the paper that was withdrawn last year.
Dr. Shaw said he and Dr. Tomljenovic, who once worked in his lab, were only "peripherally involved."
"All of the work was conducted in the lab of the senior author, Dr. Yehuda Shoenfeld in Tel Aviv. Hence, to make the claim that this work is "ours" is not correct," Dr. Shaw said in the e-mail.*
Shaw was one of the eight co-authors on the study, but he distanced himself from the project on Thursday.
"I was not directly involved except for some editorial comments at the early stages of the manuscript," he said.*
Mystical properties of biowater
Now inquiring minds come to wonder how much more of their research output was of this coerced, unconsenting nature. Surely some form of duress was involved when they co-signed Seneff's papers from 2013 and 2014,** which are crammed with Entropic Quantumbabble and mystical Biowater and are as mad as six wolverines after a week-long methamphetamine bender:

Feel free to wander at leisure through the watery weirdness:
they order neighboring water molecules into a dynamically-structured arrangement that is far more viscous than the bulk water (variously referred to as the “exclusion zone” or the “coherence domain”), and that also exhibits other unusual properties with respect to responses to electromagnetic fields, exclusion of solutes and the mobility of protons and electrons
Biological water dynamics fits the criteria for such self-ordered/self-assembling systems in that it demonstrates the combination of dynamical minimal stability and spatial scaling predicted to lead to a power law for temporal fluctuations
Or just turn stright to Figure 4, a rare example of the "argumentum ad cross-section-through-an-M&M".
Seneff had never recovered her health and sanity after her attempts to reconstruct the Waterbox (“probably the most delicate and fragile instrument ever made by human hands”) — invented by de Selby as a way of diluting water to a point where it could be handled safely, but nowhere properly documented. “There is more to water than meets the eye,” wrote de Selby, by way of explaining why three heavy coal-hammers were destroyed during its construction.
Bonus Seneff waterbending!

Perhaps Shaw regrets signing his name to papers by Gherardi, an aluminary of the antivax movement. They reported discoveries of important phenomena such as the homeopathic inverse dose response (when nothing happens at the higher doses of AlOH where you expected to see something), and the anomalous systemic-translocation timescales, when nothing can be found upon dissecting the laboratory mice (proving that everything happened very quickly and was already over by the first 45-day round of dissections, or was happening very slowly and had barely started by the final 270-day round, or both).

That overlaps with Gherardi's hybrid nanodiamond sequence of papers, in which mice were injected with fluorescent nanodiamonds tagged with AlOH. These have the advantage of being 100% biopersistant, with no danger of dissolving in the murine bodies, making them more suitable for demonstating the permanence and bodily migration of colloidal AlOH (vaccine adjuvant) than actual particulate AlOH would be. Also there is the delightful prospect of indestructible crystalline supermice that shoot fluorescent monochromatic laser beams from their pineal glands when they escape from laboratory confinement.

The other frequent and possibly regrettable collaborator is Chris Exley, big-picture visionary and Jeremiah of the Age of Aluminium. For the last 30 years Exley has been warning the world about the titanic conflict for domination between the three forms of intelligent life that occupy Earth, with carbon, silicon and aluminium-based biochemistry (as prefigured by the 4:2:3 Riddle of the Sphinx), and the alliances that form between them:

...No, wait, that was Tim Powers. There was a lot of carbon / silicon / aluminium speculation back at the end of the 80s, it must have been something in the water, or else the Morphogenic Field. Anyway, Silicon is the natural ally of Carbon against Aluminium.

Visionary diagram of life & geologi-
cal history to tie everything together
We have previously encountered Chris Exley's review paper, the one with the title that seems more suitable for a photocopied Warning of Nighness stapled to a powerpole than for a scholarly review of the literature, published in Frontiers in Neurology:

Why industry propaganda and political interference cannot disguise the inevitable role played by human exposure to aluminum in neuro-degenerative diseases, including Alzheimer’s disease
Edited by: Christopher Ariel Shaw
Reviewed by: Lucija Tomljenovic
Now the Frontiers publishing structure is modelled on pyramid marketing, so it features "Research Topics", whereby authors who have paid enough into the structure (by publishing often enough in Frontiers journals) are encouraged to progress to the status of Editor, and to nominate Research Topics, while recruiting their colleagues to contribute papers to each topic (starting a new tier at the bottom of the pyramid). So Exley's overwrought title was part of a Topic on "Aluminum Toxicity and Human Disease”.

Other contributions hint of epistemic closure in the peer-reviewing process, and a level of endogamy worthy of the Hapsburgs:

Biopersistence and brain translocation of aluminum adjuvants of vaccines”, Gherardi et al.
Edited by: Lucija Tomljenovic
Reviewed by: Lucija Tomljenovic
Clinical features in patients with long-lasting macrophagic myofasciitis”, Gherardi et al.
Edited by: Christopher Ariel Shaw
Reviewed by: Lucija Tomljenovic
The mobilization of aluminum into the biosphere”, Pogue & Lukiw
Edited by: Christopher Ariel Shaw
Reviewed by: Lucija Tomljenovic
For reasons unknown, these contributions are now disjuncted and dispersed across the Frontiers archives as if submitted and processed in unprompted independence, for earlier this year the publishers scrubbed all trace of that Topic from their database.

BMC journals used to follow the same useful habit of specifying the reviewers. The same sense of a daisy-chain of academic backrolling and logscratching comes through:

"Elevated brain aluminium and early onset Alzheimer’s disease in an individual occupationally exposed to aluminium: a case report”, Exley & Vickers
Reviewed by: Romain Gherardi
Reviewed by: Christopher Shaw
Slow CCL2-dependent translocation of biopersistent particles from muscle to brain”, Khan,... Exley,... Gherardi & Cadusseau
Reviewed by: Carlo Perricone [Shoenfeld / Tomljenovic collaborator]
Reviewed by: Christopher Shaw

From there, under the thrall of a sense of completion, we turn to a Press Conference in 2012, when the MMF Patient Support Group [I do not know the French for "Astro-Turf"] was lobbying the French vaccine-safety agency ANSM to fund Gherardi's research, putting the squeeze on politicians and calling in independent outside authorities to tesify to the value and quality of Gherardi's belief-system. Authorities named Exley, Shaw and Shoenfeld. The lobbying was eventually a success... €150,000 can buy a lot of nanodiamonds.

So what is this MMF -- E3M in French -- whose victims require support and mollifying medical investment? The defining characteristics of Macrophagal Myofasciitis vary according to situational requirements, ranging from "sore arm with a lingering lump", all the way to "all-encompassing unspecified malaise", a relabelling of ME/CFS that allows anyone with Chronic Fatigue symptoms to be recruited to the cause and coopted as a Martyr of Vaccination Damage (whether "sore arm" and "lump" are part of the picture or not). The condition was first observed by Gherardi et al., and is found only in France, with Gherardi and his colleagues uniquely skilled in its detection. Some would say that Macrophagal Myofasciitis exists primarily to provide a home for all the 'i's left over from converting 'aluminium' to the barbarous misspelling 'aluminum' but I could not possibly comment.
French press
Anyways, the money ran out, and the ANSM has not given Gherardi the extra €550,000 he needs to continue his vital inquiries so he went to the French press blubbing like Fotherington-Tomas. Also they have not followed his advice on banning vaccine adjuvants, which is equivalent to censoring his results, won't someone think of the children? Also sheep are closer to humans than rodents are.
un travail a été fait sur le mouton, encore plus proche de l'homme
Someone needs to take Gherardi aside and explain a few facts of mammalian phylogeny.

We started with Shaw's current attitude toward his collaborations with Professor Shoenfeld, but they are left as an exercise for the reader. Shoenfeld was last seen at RetractionWatch after the depublication of a different antivaccination paper,** complaining that the paper in question had been an important part of his activity as an Expert Witness who testifies in lawsuits for post-vaccination damages. Dude, you DON'T SAY THAT PART OUT LOUD.
Shoenfeld is the proud inventor of ASIA, "Autoimmune Syndrome Induced by Adjuvants", a syndrome so titled as to leave little doubt about his belief in its origins. ASIA subsumes MMF (or possibly vice versa from Gherardi's perspective); also Gulf War Syndrome, and "siliconosis", it is a pantechnicon or omnium-gatherum of speculative sickness.

Stealing from Oglaf is
a Riddled tradition
Shaw said he's likely finished working on papers concerning vaccines after this retraction.
"I'm honestly not sure at this point that I want to dabble in [vaccines] anymore," he said. "We have some projects that are ongoing that have been funded that we feel duty-bound to complete that are on this topic. Frankly, I doubt if I will do it again after that."
* Here is the RetractionWatch post in which Shaw claims credit for revising the zero-Shaw-involvement Shoenfeld paper so that it could be republished in Immunologic Research.**

** It is hard to understand why Shoenfeld has such bad luck with retractions. He has multiple editorial positions and you would expect him to know how to write papers that don't get depublished.
For instance he is Editor-in-Chief of Immunome Research, part of the OMICS scampire; founder and co-Editor-in-Chief of the Journal of Autoimmunity (where sloppy papers go to collect corrigenda); and at Immunologic Research -- the eventual home of that retracted zero-Shaw-involvement paper -- he is Topic Editor for the area of "Immunoregulation and Autoimmunity".

Monday, October 16, 2017

Watch out for Doctor Dream

Oh look, the newest couple of waste-of-bandwidth waste-of-oxygen OMICS-wannabees to start working the parasite-publisher side of the street have shown up in the mailbox. Their mooching is not 'spam' though, and was sent to me because of my eminence in the field of Sleep Medicine, which is possibly a circumlocation for "beer". I would love to send them moneys and publications, but... feeling so sleepy... can't keep my eyes... open...

These cockwombles claim to publish their American Journals from an address in Delaware, but since their website was designed by some non-English-speaking nimrods in Hyderabad, I'm going out on a limb to speculate that the "International Library of Journals" might in fact have a similar location.

Friday, October 13, 2017

Whatever is the opposite of "bonsai"

Mrs Spat seeking the shade of a small tree.

You maniacs! You blew it all up divided by zero!

The collective lidless eye of Pubpeer was recently directed at a vaccines-make-mice-autistic paper at the Journal of Inorganic Biochemistry... a paper now on the express train to Retractionville. For details, see "Mirror neurons and little men in boats" (a narrativised, hand-curated artisanal compilation of Pubpeer comments); or Orac's exhaustively-detailed account; or even the summary at RetractionWatch if you swing that way, we do not judge.

Much of that vast and unsympathetic attention was directed at Figures 2 and 4, where individual lanes from PT-PCR gels turn up repeatedly like a stamp collection with déjà vu, variously manipulated and freed from context, indicating the expression of several different genes in an admirable display of parsimony.

But the allure of those figures may have distracted attention away from Figure 1... unfairly so, for the validity of Figure 1 is also crucial for two previous papers by the same authors, in OA Autism and Immunotherapy, by dint of its pre-publication there.

Some of the initial commentary perseverated on the fifth lane (control mouse #3) in the TNF gel-slice of Figure 1C, for this is as blank as the Bellman's map: increased contrast reveals a neat rectangle of blankness, and the Pubpeer contributors speculated whether this was a thumbprint of image-enhancement deletion of something (e.g. with Photoshop), or an innocent artefact of high-loss low-resolution JPG compression of an image that was naturally blank. Only the original data can resolve the quandary. But let me explain.

The authors had made semi-quantitative measurements of the RNA expression for 18 proteins in the brains of their lab animals, and also the actual protein levels, where one protein was Actin or ACT as an internal-control test of reliability (for ACT is a housekeeping gene, always turned on). Of the 14 male mouse brains available -- seven exposed to aluminium, and seven controls -- three of each were chosen, by unspecified criteria. The outcomes for each RNA (and each protein) were three data points -- for the six samples were paired up at random, and converted to three Al:control ratios, as if each pair were After-and-Before measurements on the same mouse. I am not making this up. I had to read the explanation several times to reassure myself that the procedure was not the figment of my over-heated imagination. Any of the other five possible pairings would have yielded different ratios.

In Figure 1B, the three data points per RNA are expressed as a mean and standard error, as if they were a real distribution, purportedly differing significantly from zero in seven cases (according to one-sample t-tests). Why not plot the three ratios themselves? But wait, the engarbagement gets better!

Panels 1C and 1D document the same process of extracting expression ratios for arbitrary pairs, for seven actual proteins -- the ones netted in the fishing expedition of 1B. This is presented as independent verification, as if protein levels are separate evidence from the RNA that generated them. In the event, the replications are impressively similar: for example, the mean expression ratio (fold change) for TNF-A is 3 ± 1 in 1B (with p < 0.05) and again in 1D (with p < 0.01). What are the odds?

This is especially baffling because 3rd-control-mouse TNF-A is zero for one of those pairs (that blank rectangle in Panel 1C); THEY DIVIDED BY ZERO so the fold change for that pair → .

Then they calculated mean = 3 and standard error = 1 for that distribution of three points, one of which was INFINITY, that's not how maths works. So either that lane was naturally blank (and only a rectangular hole because JPG), and the stats are bogus; or it initially contained a non-zero protein trace that Photoshop taketh away, and Figure 1C is bogus [h/t Mitracarpus Capitatus]. Neither option should gladden the hearts of the editors of Immunotherapy or OA Autism.

The initial response of authors Shaw and Tomljenovic was to accept the gravity of the problem, accepting the need for retraction in a passive-voiced manner that blamed the absence of the homework upon the appetites of the dog. "Some images have been altered." "Data had been compromised." Original data had left the lab.

Ah, Passive Voice: Is there anything that can't be accomplished by it?

It is not clear whether they accept that Figure 1 is problematic, or view the alterations as confined to Figures 2 and 4; nor when the alterations occurred. Before or after Shaw submitted the 2017 paper to J.Inorg.Biochem? Were they present in the Powerpoint version of the study -- "Gene-toxin synergy in the brain of autistic mouse model” -- presented in 2015 to the 11th Keele Meeting on Aluminium? Anyway, in a subsequent interview the authors downplayed the importance of those fabricated Figures, as if retracting the retraction:
As for Shaw, he says the altered images “were not significant anyway.”
Enquiring minds have noted that Shaw and Tomljenovic have a chapter in a new book, due in the bookshops in two weeks' time, on "Neurodevelopmental toxicity associated with the use of aluminum vaccine adjuvants" and covering similar ground to the retracting-in-the-cold 2017 paper -- for Elsevier taketh away and Elsevier giveth:

Is it irresponsible to speculate that the altered figures are necessarily unimportant because they feature in the forthcoming chapter, and it is too late to change them? It would be irresponsible not to speculate.

Perhaps the editors of the book should be appraised of these concerns, no wait:
Edited by Christopher A. Shaw, Edited by Claire Dwoskin, Edited by Lluis Lujan , Edited by Lucija Tomljenovic
[Thx Rosewind]
The Table of Contents is a veritable Who's Who of the Aluminati (where "who's who" is a failed anagram of "clown car"). As well as Chapter 10 from Christopher Exley, there are contributions from both Gherardi's and Shoenfeld's groups; and Chapter 24 is Dr Little re-telling her "Sluts who use Gardasil are Punished with Infertility" campfire tale from five years ago.

But the book is not all Aluminium, for Brian Hooker is there with another version of his Alt-Stats MMR-causes-autism stylings (evidently Andrew Wakefield was not available, so instead, Chapter 27 is from Wakefield supporter and "retired sewage sludge researcher" David Lewis, with another attempt to defend medical malpractice and fraud). There is a chapter from Judy Mikovits, famed for proving that a laboratory contaminant causes Chronic Fatigue, who exchanged a career in science for one as Brave Maverick Outsider who Speaks Truth to Power Whatever the Consequences.

I am looking forward to the reviews.

Friday, October 6, 2017

Not sure which is worst

1. That someone wrote or otherwise acquired a manuscript about the supposed health benefits of Potato Purple Drank, and went through an article-broker or papermill who set up spoof reviewers to get it published;

2. That the cockwombles at Bentham Open accepted it, so that they could later make a holy show of unpublishing it again and proclaiming their adherence to the high ideals of research probity (they were shocked, shocked! to find that gambling is going on here);

3. That Potato Purple Drank is a thing.

Just saying, when the Bentham Open editators decided to accept an Article Processing Charge from the nominal authors of "The Research on the Impact of Green Beans Sports Drinks on Relieving Fatigue in Sports Training", and "The Research on the Impact of Maca Polypeptide on Sport Fatigue", they knew all along that both papers came off a production line.

Well-meaning attempts of authors to involve themselves only impedes production of the papers.