Tuesday, November 28, 2017

This exists

If it is a half-way decent "simulation of plasma caffeine concentration", it will make the letters on the screen all jittery and hard-to-read, and everything moves in time with your pulse, while occasional black butterflies flutter past just in the fringes of peripheral vision. I am not sure why you want that in a Web browser but whatever.

Monday, November 27, 2017

Gish Gallop, meet Moving Goalposts... ah, I see you already know each other

The blogpost that goes with this title cannot be found. It is probably wasting its time on Twittle, arguing with barmpots and eedjits.

Sunday, November 26, 2017

And suddenly there was a terrible roar all around us and the sky was full of what looked like hostile fruit, all swooping and screeching and diving around the car

The pictogram for "Shelter your head from fructile dive-bomb attacks" is universally understood.

Alternative title: Fruit flies like a banana.

A blot on the Escutcheon

Sejant, couchant, passant: Legitimate heraldic terms.
Fondant, pedant, pissant: Apparently not legitimate. I am disappoint.
[Derp Horse from "The Queen's Beasts"]
I would pay good money for a heraldry-centric "Julian & Sandy" skit in which Kenneth Horne wants a coat-of-arms and ends up at "Bona Blazon", exchanging Polari badinage with Gules and Sinople.
 Bonus Heraldry: DOIN IT RONG.

Thursday, November 23, 2017

For Entertainment Purposes Only [Director's cut]

This post was earlier cross-posted at Leonid Schneider's site, hence the unfrivolous tone. The version there includes Leonid's frame-story.

Figures like the ones below are a recurring feature in our host's journalism, and in the entries posted at PubPeer by image forensic enthusiasts -- black ovals and blobs, hovering on grainy backgrounds -- creating the impression that biomedical research overlaps with Miró's late monochrome period. The reasons for this recurrence are simple enough. Researchers deploy the arsenal of gel electrophoresis techniques to separate the ingredients of cells according to molecular weight (or chemical affinity as it may be, or political alignment) by force-marching a cellular extract along a race-track of gel. Typically several samples are separated at once, each along its own vertical lane, with each molecular species lining up across lanes in a horizontal band.

The important result are the numerical measurements of the amount of protein in each separated band (ideally averaged across repeated experiments). Not much additional information is conveyed, when these results are published, by accompanying them with an illustration of the actual gel. Nevertheless, journal editors and readers have come to expect such illustrations anyway... perhaps to bestow an aura of 'real science' on the paper, perhaps as a display of commitment, to detect the presence of outsiders.

This graphical tradition has burdened researchers with the expectation that their electrophoresis images will be as clean and visually-appealing as a celebrity photograph, free from thumb-prints and coffee-stains and artefacts, a testament to their impeccable laboratory technique. It also provides an incentive for researchers to beautify their images if they can thereby push a paper across the threshold of acceptance in a journal; or even to assemble them from separate components. The outcome of all this is the belated scrutiny given to images that have been modified using 'AEPs', Appearance-Enhancing Photoshop.

Here by way of example is Figure 5 from Levy et al. (2003).* In 5A at the left, panels (a) and (c) portray the presence of phosphorylated proteins PKB and 70S6K extracted from cells that had been cultured under different conditions for 0, 15, 30 and 60 minutes, Panels (b) and (d) portray the unphosphorylated forms of the same proteins, so that the normalised ratios can be plotted in the right-hand side, Figure 5B.

In the legend we read that the experiment was performed twice. Many people would plot each pair of values as separate points rather than their mean and standard deviation, but the question is moot, for error bars are absent from 14 of the 20 data points in 5B, as if only one measurement occurred.

This was all very well until now, 14 years later, when inquiring minds twiddled with the contrast and brightness of the image, and Panel (c) stood revealed as a product of Photoshop rather than the laboratory. "Condylocarpon Amazonicum" deserves special credit.

Patches of pavement grey have been pasted repeatedly across the letterbox rectangle (flipped vertically in one occurrence), forming a blank background on which the artist could compose three pairs of bands from some other source, to ensure non-zero phosphorylation readings for those particular conditions. One can only speculate whether Panel (c) was assembled first, and measured for the right-hand half of Fig. 5B, or 5B came first and Panel (c) was reverse-engineered to produce it.

There are also indications within panels (a), (b) and (d) that the 15-, 30- and 60-minute stretches were not raced in contiguous lanes in a single electrophoresis session (as their continuous presentation in single letterbox format might suggest); the faint splice lines, and abrupt changes in the background texture, hint that they began their existence as separate gels.

In a contemporary paper this would attract opprobrium -- there are guidelines -- but standards were different in 2003, splicing was unremarkable and everyone did it, implying no chicanery or intention to mislead. However, this moral relativism does not extend to synthetic confections like Panel (c), which belongs in an art museum -- along with the Dada collages of Ernst and Höch and Schwitter -- rather than in the scientific literature.

A similar spectacle awaits us in Figure 6 from the same paper:


Three of the panels of 6B have been spliced from different 15-, 30- and 60-minute gels.


Panel (c), again, proves to be a composite, with pairs of bands copied from sources unknown; these inserted blobs must have contained undesirable features along the top, which are masked out behind further elongated strips of wallpaper.
Lanes 7 and 10 have been shaped into the facsimile of a faint double-band structure, which are doubled copies of a single band. Then someone conscientiously measured the total darkness within each lane of this creation, and normalised the values by the measurements from Panel (d), to create the ratios plotted in the right-hand part of Figure 6C.

* Figures 5 and 6 are lightly modified, in homage to the tradition of splicing.
------------------------------------------------------------
To continue the artistic theme, consider this illustration:

To my eyes it resembles in its abstraction an out-take from Sans Soleil, or a still from one of Nam June Paik's video compositions -- information-overload bombardment stripped of actual information by processing and recycling the images until only glitches and artefacts remain. It is in fact a contrast-adjusted version of Figure 6 from Liu et al. (2001). Influenced, it may be, by Paul Klee's 1925 'Fish Magic'.

Ostensibly, the Figure documents an experiment in which cells were transfected (or not) with a special composite DNA to over-express a specific protein, then cultured under six conditions, before measuring the effect on other proteins. No-one, not even the peer-reviewers, noticed that panel (b) contains 13 lanes instead of the appropriate 12.

C. Amazonicum noted that a small rectangular insert containing three blots has been pasted into the centre of Panel (c), and that two of these blots (in lanes 8 and 9) have been copied from other lanes, though rotated or sheared in some low-end image software, providing them with jagged edges like some species of centipede.
One resists the temptation to turn the image into an animated GIF, tracing the little centipedes' wriggling migration from original to final locations.

But further information is available, for the Journal of Biological Chemistry invites authors to upload an Early Appearance version of their papers to the JBC site (before the final typeset paginated version makes its scheduled appearance), and in the Early Version in this case, the authors have composed their illustrations by embedding separate image files for each panel at the appropriate page locations in the PDF. In fact, several embedded images within each panel. Panel (c) of Figure 6 unpacks into 9 components:
Three of them are components of the cental background mask. Evidently the first replacement for the original Lane 12 was still inadequate, and was overlaid with a second replacement... a rotated copy of that third version also appears in Lane 9.
Bonus splice
The pictorial beautification is fractal, repeated at every scales from Figure down to Lane. Panel (a)'s spliced components are improved by masks to overlay the original Lane 9 with a better blot. What would have been Lane 2 of Panel (b) is copied to overlay Lane 1, and replaced by a new Lane 2 (which is a horizontally-flipped copy of Lane 9).


The other Figures lend themselves to similar unpacking, though a full exegesis would be tiresome. Figure 5 includes several cloned blots among its components, and an additional blot overlaid upon the original Lane 10 in Panel (a).

The various lanes and masks of Figure 3 include one lane repeated in three copies:
(the manipulation is clumsily done, with glitches that can cause physical pain to the unprotected eye).

Figure 4, Figure 7, Figure 1. That last example is notable for including single-lane image files in panel (d) that overlay the original Lanes 4 and 5 with copies of each other, to swap them.

Smut Clyde, unpacked
Anyway, both Levy et al. (2003) and Liu et al. (2001) come to us from the Weizmann Institute of Science (in Rehovot, Israel). Their research topics were in different sub-genres of cellular-signal molecular biology, so the only author in common was Yehiel Zick, of the Molecular Cell Biology Department... holder of the Marte R. Gomez Professorial Chair... laboratory leader, and Corresponding Author for both papers (which is to say, the collaborator who takes on the responsibility of submitting the manuscript to a journal and shepherding it through the negotiations with editor and reviewers).

Leonid Schneider has previously reviewed the research emanating from more than one laboratory at the Weizmann Institute. To explain why so much of their output has skirted or crossed the boundaries of legitimate image enhancement, one might speculate about the possibility of a systemic or cultural problem there. And if indeed the philosophy is rife at the Institute, that "Figures are only for cosmetic / rhetorical purposes, so it makes sense to airbrush them", this would be easy to understand (if not to condone). But it may just be that Zick had bad luck in his choice of students and collaborators.
Bonus purge
Another Weizmann Institute laboratory leader is Rony Seger, occasional Zick co-author, whose name has come repeatedly to the attention of the Pubpeer deconstructionists. Segar can boast of a dozen retractions, with nine purged from JBC at once in one swell foop, which is a distinction of a sort. He is currently working to replicate various contested results in the hope that other high-profile publications can still be salvaged, assisted by a laboratory technician but without students to mentor. Seger's 2007 paper (explaining how cellphones trigger molecular mechanisms and thereby cause brain cancer) deserves a blogpost all to itself some time... no-one else has replicated his findings, but Seger was still standing by them earlier this year.

So let us finish with another image unpacked from a PDF. Here is Figure 4 from Seger et al. (2001):

Over half of the blots in a band were judged to be unsatisfactory in appearance after scanning them from a gel, and required replacement with separate overlaid image files. A Pubpeer contributor speculated that the proof of these replacements might be the reason for the paper's recent retraction.

However, neither the retraction nor the problematic Figure 4 have affected the authors' confidence in the paper's conclusions; this remains full. It always does. So we come back to the question: If Figure 4 made so little difference to confidence in the conclusions, why was it there at all?

Tuesday, November 21, 2017

Everything is better with googly eyes

It turns out that my colleagues do not share this philosophy... not when it comes to plots of PC2 against PC1, and PC4 against PC3, as parameterised by hue angle. Also they have no sense of humour.

Next time, if they don't want surprises, they can prepare their own goddamn Powerpoint presentations.

Scenes from the Libertarian Utopia


Sometimes I wonder if we went overboard with privatising resources.

Monday, November 20, 2017

Pursued by an army of birds in the rain Vikings on Pig-back

BEWAREST THOU THE BLOOD-MOON, FOR THAT SHALL BE THE HARBINGER OF THE PIG-BACK BERSERKER ARMY AND THE GREAT WELTER


Alternative title: Worst Knave-of-Coins Tarot card EVAH!

Tuesday, November 14, 2017

We left the camp after we had inoculated the children for polio... they had come and hacked off every inoculated arm. There they were in a pile. A pile of little arms... And I thought, my God... the genius of that! The genius! The will to do that!

The Chinese scammers at SCIRP are the Wal*Mart of parasitical publishing; they cater to the low-rent rough-trade end of the desperate-to-publish market, charging only $99 to host one's vanity production on-line in one of their journal-shaped scamsites, while maintaining their income stream through indiscriminate bulk sales. Recall, for example, the Akkie Secrets of Martian Management fantasia from a couple of Dravidian Racial Supremacy cockwombles.

Knowing that they are not designed to be read, a team of anti-vaccine campaigners published their latest bolus of mendacity through a SCIRP spigot in the hope of sneaking it, unnoticed, into the ouroboric closed-cycle human centipede of antivax discourse. The journal in this case, the OA Library Journal, has abandoned all pretence of having "criteria" or "standards" or "focus", even in the title.

It is all about the DEPOPULATION AGENDA and the Gates / WHO conspiracy to pollute the bodies of Third-World womens with a method of birth-control that doesn't work, concealed in the Trojan Horse of tetanus vaccine. The fantasy is impeccably documented, with citations to conspiracy websites, fetus-licking forced-birthers, and Vaccine Weekly (i.e. a headline-clipping service).

Just saying, "sneaking past" never works.


The references are further padded with citations to scholarship-manque publications from Christopher Shaw and Lucija Tomljenovic, which might account for the presence of Shaw and Tomljenovic within the authorship list. These two are persons of interest to Riddled, on account of how frequently they find themselves being forced against their wills to sign their co-authorly names to tragically regrettable cognitive core-dumps, and this may be another example.

The first author is John Oller Jr, who is evidently proud of this opuscule, uploading a copy to his ResearchGate account and including it in his CV (under the original working title of "WHO Links Tetanus Toxoid to Human Chorionic Gonadotropin and Why Are They Doing It"). Oller's CV also speaks of his inordinate pride in an essay he wrote for 'Answers in Genesis' on Biblical-Literalist Linguistics [the gist: the 6000 years elapsed since Project Babel Tower ended in recriminations and a confusion of tongues is plenty time enough for each language phylum like Indo-European and Sino-Tibetan to branch into the present degree of diversity]. For Oller is an evolution-denying Young-Earth Creationist, with an academic grounding in speech therapy, which must have come in useful when he was editing a predatory journal on 'Entropy' and collaborating with Shaw and Tomljenovic on the topic of vaccine-adjuvant aluminium and biosemantic semiology fritillary calenture hatstand. He is clearly stupid enough to be not allowed out-of-doors when it is raining for fear that he will stare up at the clouds with mouth agape until he drowns; I cannot help suspecting that he was home-schooled. I like to think that Oller subscribes to the Institute for Creation Linguistics. He demonstrably belongs to the Institute for Creation Science.

This paragraph is Oller's contribution, I deduce from its tone of robotic pedantry:
Our fourth method involved a “thought experiment” applying the simplest type of mathematical probative tests for a variety of Euclidean congruence [65]. The KCDA claimed that the WHO dosage schedule of five shots administered in six month increments was inconsistent with published tetanus vaccination schedules. So, our simple probative test was to compare the published vaccination schedules for TT, t, with the published schedules for TT/ßhCG, ß. Calling the schedule used in Kenya, k, and taking “=” to mean congruent, if t ≠ ß, but ß = k, and kt, it follows that k is a dosage schedule appropriate to TT/ßhCG, the WHO antifertility vaccine. The simple test of congruence of dosage schedules is not conclusive proof by itself, but it is consistent with the opinion of the authors that the WHO followed a dosage schedule appropriate for TT/ßhCG in Kenya but inappropriate for TT vaccine.
Anyway, the present statement of claims first bubbled up from the sewers three years ago, with Dr Wahome Ngare and Bishop-Doctor Karanja -- spokesman and president respectively of the Kenyan Catholic Doctors Association -- pimping out the fabulated allegations like their own daughters, to be regurged by the Kenyan Catholic hierarchy and by fetus-fondling fecundity fetishists everywhere. At the time the 'tainted vaccines' claims were quickly dismissed, with people all "you lied to us about the nature of the samples so we the tests we applied weren't valid", and "no, our tests only gave an upper limit on the presence of hGC, there was probably none".

The KCDA turns out to be a genuine organisation, with the express agenda of re-medievalising medicine, and dressing up ecclesiastic dogma with a white lab-coat over the episcopal robes; it was founded by that same Catholic hierarchy, to tell them whatever fabrications they want to hear but with a gloss of independence. If it has recruits other than Ngare and Karanja, they are not rushing to advertise their membership. Reading between the lions, the real concern held by the Kenyan branch of the Catholicism franchise about the tetanus vaccination program was that the Gubblement was trying to deliver it without routing it through the godbothering establishment to let them cream off a profit and claim credit for the benefit...
The Catholic Church has not been engaged as members and participants of the Health Sector Coordinating Committee and in the respective Technical Working Group.
...so they cooked up a story to sabotage the program instead. See, people, this is what happens when you allow faith-based institutions to take a role in health-service provision: they will not rest content with just a slice of the cake, for their greed is divinely sanctioned.

Which leads us to the fourth and fifth authors on this paper: Ngare and Karanja themselves, a pair of theocratic charlatans and unmitigated gobshites. Harken to the wit and wisdom of Doctor-Bishop Karanja! In 2003:
Dr STEPHEN KARANJA Catholic gynaecologist It was a condom bonfire. We had more than 5-10 thousand people, young people, old people, simple men from the streets.
BRADSHAW: Did you go?
KARANJA: Who, myself? I was there. I have to be there. I lead by example. We had discussions about the condom. We had scientific presentations, we had social presentations, then we had… How do you want to call it… We had a symbolic burning of the evil that is the condom.
In 2011:
Dr. Karanja notes that despite being vaccinated against Human Papilloma Virus (HPV) that causes cancer of the cervix, one can still get it if they indulge in irresponsible sex...
Dr. Karanja notes that the reason why children are also dying of cancer is because lactating mothers are taking contraceptives that are passed on to children through breast milk.
Insufficiently-frequent pregnancy is why women get cancer: "many sexual partners, early sex debuts, use of contraceptives and staying too long without having a child in the case of women."
He sounds nice.

Harken to the wit and wisdom of Dr Ngare! Here he explains that the Gubblement must be lying about the continued fertility of tetanus-vaccine recipients, why would he lie?
Coming from a religious fraudster who has built his career out of telling people they should give him moneys and power because he's friends with a powerful sky fairy, the question is probably rhetorical.

The Snopes entry on the Kenyan Depopulation Hoax argues that Ngare's dichotomy is false, and offers the mollifying middle-ground that Ngare is sincerely mistaken. Well, no, he and his fellow episcopal Talivangelists knew the truth but preferred to lie. Yes, they come across as caricatures of Dark-Ages nescience and power-grasping hypocrisy, be-robed BWAA-HA-HAing sacerdotal scoundrels dreamed up by PZ Myers, but that is how they set out to act.

A previous incarnation of the Depopulation Agenda campfire-story occurred in the Philippines in 1995. Again, local theocrats decided to sabotage a vaccine program by faking reports that the neonatal-tetanus component was Stealth Sterility, and obtaining a district court restraining order to pause it [the program was associated with a political aspirant with secular inclination, so it could not be allowed to succeed; the pro-preventable-disease counter-campaign was a way of undercutting his godless popularity].* Multiple vaccine schedules were disrupted, and one can only speculate how many children died in consequence... but whatever the number, it was a small price for other people to pay, in the cause of maintaining the Church's perogatives and status. Ngare and Karanja drew on this 1995 precedent for their 2014 infant-mortality campaign, recycling much of its rhetoric and mendacity, and it is cited in this paper.

In 2015 the KCDA tried to disrupt a different Kenyan vaccine program -- polio, this time -- with the same excuse, that it smelled of Super-Sekrit Birth Control. The bishops were not subtle with their reminders to the gubblement, that the problem could easily go away if only the right feelings and itchy palms were assuaged.
The country's Conference of Catholic Bishops declared a boycott of the World Health Organization's vaccination campaign, saying they needed to "test" whether ingredients contain a derivative of estrogen. Dr. Wahome Ngare of the Kenyan Catholic Doctor's Association alleged that the presence of the female hormone could sterilize children.
I am surprised that this later evidence of UN Black-Helicopter Chemtrail Depop is not mentioned in the new paper. Perhaps the authors are already planning a sequel.
"There are all sorts of stories out there," [Ngare] told me. "Vaccines can cause autism. Vaccines have been used for spread of HIV. There are some cancer-causing viruses that you'd find in vaccines. So there are lot of stories. Some of them we don't know whether they're true or not true."
I pointed out to him that research has shown that claims of vaccines being linked to autism and HIV and cancer are in fact not true.
His response: "We could debate this forever."
Christopher Shaw prides himself on his activism for progressive causes. Why he chose to end his career by crawling into bed with this execrable gang of extreme-right theocratic shitweasels is anybody's guess.
--------------------------------------------------------------
* In subsequent reality-untethered embellishments of the story, the Manila Regional Court was replaced by the Supreme Court of the Philippines, because more impressive.
LifeSiteNews.com reported that in 1995, the Catholic Women’s League of the Philippines won a court order halting a UNICEF anti-tetanus program because the vaccine had been laced with B-hCG, which when given in a vaccine permanently causes women to be unable to sustain a pregnancy. The Supreme Court of the Philippines found the surreptitious sterilization program had already vaccinated three million women, aged 12 to 45. B-hCG-laced vaccine was also found in at least four other developing countries.
It is also an article of faith in these forced-birth anti-vax compulsive-lying circles that the vaccine drive was imposed on the Philippines by UNICEF and WHO and black helicopters, as there is no place in their racist cockwomble world for the notion that benighted brown people could instigate and operate their own public-health initiatives.

Sunday, November 12, 2017

Mirror neurons and little men in boats: The rise and fall of an antivax paper
Director's Cut

Previously cross-posted at For Better Science

A recent paper by Li, Tomlenovic, Li & Shaw has attracted a great deal of attention, both positive and negative. The authors assert that aluminium compounds activate inflammation-related genes in the brains of mouse pups, causing brain damage, when they are injected with dosages comparable to the amounts contained in the US infant vaccination schedule.

In particular, the paper featured in a comment thread at Pubpeer, in the inimitable and inimical style that prevails in that forum. Here I will try to spin comments and observations from the thread into some sort of coherent narrative. I will not try to duplicate criticisms of the paper elsewhere, made by people more qualified than me, including Orac at Respectful Insolence and by Mad Virologist and The Blood-Brain Barrier Scientist... those critiques questioned whether the genes measured were an ideal selection, whether the semi-quantitative methods and statistics applied to them were appropriate, and whether the results of those methods (Figure 1, below) have been manipulated with Performance-Enhancing Photoshop. I will continue to spell "Aluminium" with two 'i's, the way God intended.

First, a little of the background is in order. The Journal of Inorganic Biochemistry (J.Inorg.Biochem) has a tradition of publishing papers on neurology, immunology, animal behaviour, and the causation of autism, as long as those topics arise in the context of aluminium toxicity. The Editors take a generous interpretation of their remit, and the journal's peer reviewers are optimistic about the bounds of their expertise. This tradition goes back at least to 2009. In 2011 the Editors surpassed themselves with a Special Issue ("Living the in Aluminum Age" [sic]), guest-edited by a high-ranking member of the Aluminati, Professor Christopher Exley of Keele University. Many surprising claims were made in that issue, such as the fact that alumina in antiperspirants is a leading cause of breast cancer, while Tomljenovic and Shaw contributed a problematic comparison between variations in autism prevalence and variations in vaccination schedules... a comparison that works best if one postulates that the neurotoxicity of aluminium adjuvants propagates backwards in time, in the manner of thiotimoline.

The paper of interest here, the most recent in this series, presents a comparison between RNA levels and protein levels in the brains of mice variously injected with colloidal aluminium hydroxide, or saline solution (Al and Control groups). The graphical component of the paper is dominated by RT-PCR gels (where short segments of RNA have been separated along a gel to mark their presence or absence after repeated cycles of reverse-transcriptase PCR), and Western blots. These are the white-on-black tandem kayak images and black-on-white moustache identity parades, respectively, in Figure 1.

Figure 1:
Genetically-diverse CD-1 mice were used here -- "vulgar little mice" -- bred under conditions that are described in a manner that invites confusion, worded in terms of four groups rather than two. There is also uncertainty as to the number of breeding pairs.

The description made a little more sense when it first appeared in a 2013 paper in J.Inorg.Biochem -- the first report from this specific project [https://www.ncbi.nlm.nih.gov/pubmed/23932735] -- in which we learn that there were two Al-exposed litters of 14 pups, with different exposure levels; also a fourth litter that was saved for feeding pet snakes or some other objective which need not concern us here. The ambivalence on the number of breeding mothers was present in 2013 as well.

The Al and Control mice received the same number of injections, on the same days... no, wait, according to the 2013 account, they received 6 and 5 injections respectively, on a different schedule.
 

At the age of 16 weeks, having performed behavioural tasks for the edification of the experimenters, the mice were sacrificed on an altar of black basalt.
"At 16 weeks of age the mice were euthanized and the brain tissues were collected for gene expression profiling experiments."
 I made up the part about a basalt altar. Also, the mice survived to 34 weeks before their execution.
"The general development of mice was monitored by systematic recording of their weights from week 1 till the time of sacrifice (week 34)."
I try to keep better track of the age at sacrifice of my experimental subjects, but it is true that I work with humans.

The posthumous adventures of those murine brains are best explained by an excursion outside the confines of J.Inorg.Biochem, to a pair of 2014 papers: "Are there negative CNS impacts of aluminum adjuvants used in vaccines and immunotherapy?" (Shaw, Li & Timljenovic), Immunotherapy, and "Etiology of autism spectrum disorders: Genes, environment, or both?" (Shaw, Sheth, Li & Timljenovic), OA Autism.* Both contain foretastes of Figure 1, as a kind of appetite-whetting trailer for the present paper **:

Six male mice were chosen for preliminary measurements: three Al-exposed and three controls. It is not stated whether they were selected at random, or because their behavioural performance promised results that would fit the desired picture. Both 2014 papers included a caveat that the samples were too small to sustain strong conclusions, and the results were merely suggestive until more comprehensive measurements can be made. In fact the reader might wonder how the confidence bounds shown in the various Figures 1 can be drawn at all from only three measurements.

So the 2017 paper is the fulfilment of that promise to "collect the data on other samples". There are now 10 male mice involved, and 10 females:
The brain samples of five males and five females injected with Al and five males and five female control mice were randomly paired for gene expression profiling
In addition,
The experiments for each mouse were repeated three times for statistical purposes
... Perhaps under the impression that these would be independent measurements, and could be used to narrow the confidence limits.

But mirabile dictu, the 2017 Figure 1 (see above) is exactly the same as the 2014 versions! -- neither the mean values nor the error bars for male-mouse brains were affected by the additional data! This brought consternation and speculation into the Pubpeer thread.

In the course of that long history of previous publication, the panels comprising Figure 1 have undergone multiple cycles of contrast enhancement and high-loss JPEG image compression, so one can download a "high resolution" version but the main benefit is to see the compression artefacts at greater magnification. The present paper also added corresponding figures for the female-mouse brains, notably Figure 2.

Further consternation resulted when sharp-eyed Pubpeer contributors noted that some of the RT-PCR kayaks are distinctive in appearance -- one boasting a little foresail (the Control C2 RNA) while another carries a little-man-in-the-boat as its passenger (Al CEBPB RNA) -- and these allow one to recognise that several of the Al-Control pairs had previously been extracted from the brains of male mice (where they coded for the NFKBIE and MMP9 proteins respectively).
Nor does it stop there. Several of these distinctive kayaks have been reflected left-to-right -- so the foresailed band that evinced the presence of C2 RNA (in the left-hand column of Figure 2A) appears again (in the right-hand column), heading in the other direction, to evince the presence of SFTPB. The little-man-in-the-boat reappears in the same way as SERPINE1, while a kayak with an outboard motor -- previously a Control for CRP -- becomes the Control for SELE.
The most parsimonious explanation is that a single continuous gel, alternating between Al and Control bands, has been sliced one way to provide the first column of Figure 2A, and then mirrored horizontally and cut up at alternate divisions to provide the second column. If the original gel was 1-2-3-4-5-6-7-8-9, where even bands are Al, it became the pairs 1-2 / 3-4 / 5-6 / 7-8 for four RNAs, then 9-8 / 7-6 / 5-4 / 3-2 for four different RNA pairs.

It is as if someone had been told to turn data sets Y and Z into figures for the paper, but those data did not exist, so the team member improvised from data set X, already published. Or else they thought they were studying mirror neurons. In total the same images have appeared in five places, signifying three different protein RNAs, which shows admirable economy on someone's part.


That is still not all; the horizontal-mirror methodology was applied again to Figure 4.

Certain bands in these RT-PCR gels are marked by distinctive bubbles and hiccoughs. These allow us to recognise that Figure 4D is a reflected version of 4B, differently exposed. Kayaks displaying the presence of Cytokine Actin RNA in 4B became evidence for Adhesion-molecule ICAM-1 in 4D (while IL-6 became E-Selectin, IL-5 became VCAM-1 and IL-4 became Actin).
I am no expert on the minutiae of PCR methods but I am fairly sure that inverting images -- reversing the status of Control and Al-exposed genetic activity -- is not legitimate, and it does not happen by accident.

Footnotes
* OA Autism comes from a one-man publisher "OA London Publishing", a source of interest and entertainment in its own right, as reported a few years ago by Neuroskeptic. The journal is moribund, with no new additions to its files since late 2014, but the website is still there so we should enjoy it while it lasts. Evidently the publisher managed to recruit Alexander Seifalian to be Chair of the "Board of Trustees" as a token of credibility: his name may be familiar to Leonid's readers.

** Hat tip to Michael Brown for spotting the foreshadowing.