Week 4: Publishing & Communcation problems Flashcards

Question

Plenty of case studies for OMICS doing bad things

Answer 1

Entomology - 2013 one of the most prominent conferences (Entomology 2013), many people registered thinking it’s the one without “–“ Identity fraud, they have cases against them from PubMed

Answer 2

Experiment in peer review – scientist generated papers with clearly inaccurate and submitted it to journal publications. 157 accepted – MOST places he submitted it too took it immediately (in the open access world) only 97 rejected it. Rule of thumb any journal that contacts you – isn’t a good one

Answer 3

Good in making science publically available – but has a bad side

Answer 4

Nature will edits your article for a cost – BUT – not guarantee that you will be published Many private companies that will edit reformat and reanalyse your data for you English langue translation services, publication language is almost always English, many times recommended linguistic assistance

Answer 5

Macmillian Scientific communication offers editorial services on content, structure and presentation Authors can ask for recommendations from journals – some services may provide comments on experimental design – is that ethical? Should editors get credit or be disclosed? New England Journal of Medicine – requires that authors disclose any formal editing system – this may be a response to allegations of “ghost-writing” in medical research – companies publishing papers by borrowing the names of an academic to publish under

Answer 6

Plagiarism of other people’s work Plagiarism of your own work Plagiarism by journal themselves

Answer 7

Prof Smith found to have self-plagiarized up to 20 papers by copying sections from previous work, investigations led to 3 papers to be retracted many of the targeted publications were republications of conference proceedings – is that wrong? What constitutes self-plagiarism? Same things you worry about… References – use of the same reference continually? Methods – how many ways are there to state PCR mix? Results – what if these are

Answer 8

During revisions, scientists are frequently requested to include additional citations Coercive Citations Give no indication that the manuscript lacked something, make no specific suggestions on what should be cited, but does guide the author to add citations from the editor’s journal “you cite Leukemia. Consequently we kindly ask you to add references of articles published in Leukemia”

Answer 9

175 journals named as coercers, one journal named by 49 different people

Answer 10

Self-review – online community feedback

Answer 11

Self-citation - increases your own visibility increases your personal indices Online early – articles published a year ahead of print version before citation counts on indices – can sneak an extra year in there

Answer 12

The system really does work and most of us never face anything controversial. However, the academic publishing world is complex and sometimes feels full of shady practices and questionable methods. When doe this rise to the level of public controversy and outright fraud?

Answer 13

1. Endosymbiosis… yeah right… 2. Velvet worms… how to shut down publishing 3. Arsenic life… look before you leap 4. Piltdown Man 5. Vaccines… fear fear fear… and more fear…

Answer 14

The theory that the reason we exist as multicellular life is because there is mitochondria inside almost every single cell – and that that mitochondria was once a free living bacteria this is absolutely known to be true with copious amounts of evidence. As oxygen levels rose anaerobic eukaryotes “consumed” an aerobic bacteria – endosymbiotic theory assumes that eukaryotes came first that the mitochondria came from and oxygen loving bacteria

Answer 15

This theory was proposed in 1967 by Dr. Lynn Margulis,

Answer 16

It was perceived as a crazy idea that simple bacteria were incorporated into early cells and became organelles. Her paper on this theory was rejected by at least 12 different journals and called preposterous - it was published in a small journal called “Journal of Theoretical Biology”. That finally took it because every other journal called it crazy. 11 year later Schwartz and Dayhooff published a paper which concluded she’d been right all along.

Answer 17

The problem is that it didn’t stop there, many of her theories remain controversial – some of them are now considered really, really out there.

Answer 18

- Gaia hypothesis; the idea that earth is a self-regulating organism, she would argue that the earth would adapt to suit us – bacteria pumped out a lot of oxygen - Dismissal of Population Genetics - Flagella came from spirochetes - no evidence for this - HIV doesn’t exist - Symbiosis drives speciation - “I don’t consider my ideas controversial, I consider them right” – Dr. Lynn Margulis

Answer 19

She was a member of the academy. Communicating papers idea, a few years before she died a paper emerged that made a bizarre claim that a caterpillar and a butterfly were two different things and that metamorphosis is an accidental mating between a velvet worm and a flying insect

Answer 20

Metamorphoses did not originate solely by accumulation of random mutations Members of the phylum Onychophora (velvet worms) are proposed as the evolutionary source of caterpillars and their grub or maggot descendants” Butterfly hybrids? This is a onychophora – it superficially looks a little like a worm or caterpillar but it has no evolutionary relationship from either of those groups. It is very distantly related – the paper argued that this onychophora mated with a flying butterfly – but there is no evidence for this In fact if you simply compared some DNA you would realise there is not onychophora in a butterfly

Answer 21

It is suspected that what Dr Lynn did is collect a range reviews and only solicited them with the paper

Answer 22

“better suited for the National Enquirer than the National Academy than the National Academy.” – Scientific American “Bigwig” ushered “nonsense” paper into top journal” – Times Higher Education The editor of PNAS “The matter appears extracted from a science fiction novel but has grave implication. This paper has fallen through the cracks of the review process of one of the most prestigious scientific journals, and this has not passed unnoticed. Online debates have erupted between those appalled that such article has appeared in a scientific forum and those who feel that scientific debate requires that ll ideas, no matter how ill-formed, be discussed. But we should ask whether an individual can propose any theory, no matter how unsupported that idea may be, and demand that others do the works to test it scientifically” Gonzalo Giribet-PNAS

Answer 23

But it is possible to find something that does not follow the rules – the arsenic story is a chemical one (Phosphate and Arsenic have very similar properties) similar atomic radius and electronegativity Biological for of P is PO43- which is similar to AsO43- but this is how it kills you because it is so similar it can substitute in your cells and can kill you In Eastern California, we have Mono Lake this is a toxic soup of salt, arsenic and it is alkaline – scientists went out to try and find life They found bacteria called GFAJ-1 (details not important) they grew it in some media and the line at the bottom of the graph shows it growing without anything the middle line shows growing with arsenic in the top is phosphate This appears as though they prefer phosphate but this is evidence to argue that it could grow in arsenic only But they argued it was substituting arsenic for phosphate in the DNA allowing it to grow They called it arsenic based life

Answer 24

“Arsenic-eating microbe may redefine chemistry of life” “a biochemistry… which could be used by organisms in… extreme environments…or even on other planets”

Answer 25

“NASA press release drew media attention with claims of an astrobiology finding that will impact the search for evidence of extra-terrestrial life” “Microbe gets toxic response” “Scientists are questioning the finding and taking issue with how it was communicated to non-specialists”

Answer 26

Over time she ran the exact same NASA experiments and every day she published the results on her website. Her results showed that When grown in a media with both arsenic and phosphate they contain no arsenic at all, a second paper; can grow in very low phosphate conditions but NOT in its absence Their conclusion is that the better story is how they survive in arsenic toxicity – this is the interesting thing – that they don’t die – But it is NOT arsenic based life

Answer 27

“We are thrilled that our results are stimulating more experiments from the community as well as ourselves” “We do not fully understand the key details of the website experiments and conditions. So we hope to see this work published in a peer-reviewed journal, as this is how science best proceeds” They didn’t say sorry we are wrong – just said great more research is happening Media events overshadowing results

Answer 28

Piltdown man was the first supposed hominid found in England, found in Essex – the black bits are the bone fragments found and the white bits are the reconstructed parts. It was constructed in the early part of the search for human remains, very early 1900’s, Charles Dawson in the middle.

Answer 29

One of the key missing link fossils for about 50 years because it liked humans to chimps – it claimed that humans had evolved from chimanzee’s which is of course not true, we shared a common ancestor with them. We did not evolve from them, but this was evidence for chimpanzee ancestor, one of the key controversies were what would the canine teeth look like, they said that would be very important in understand how the teeth evolved, Dawson and the gang went back, and sure enough brought back the canine teeth.

Answer 30

The bones had been stained to make them look old, teeth filed own to disguise their appearance – this was a deliberate fraud.

Answer 31

Suspects? Dawson – it appears most of his finds were faked, 38 of his other specimens show clear evidence of forgery, some in the same way as the Piltdown fragments Martin Hinton – when he died they found a trunk in his office that contained all the material to colour the bone and several obvious experiments Sir Arthur Conan Doyle – has been implicated as a potential cause of this, he had an axe to grind against the community and some people claim that some of his Sherlock Holmes novels had clues in it.

Answer 32

Dawson created the first problem – deposited the first jaw but then other people went and put other bones there to try to make him admit his lie

Answer 33

Remember that at the time, we knew almost nothing about human evolution and evolution itself was a relatively new concept. Piltdown got people interested, ironically Piltdown provided real evidence for human evolution and led to a real hunt for other remains – this led to some of the greatest hominid discoveries of all time Lucy, found in Africa in the 60’s, since then there has been mass race to find bones – although Piltdown was a fraud it created enough interest to find real remains – a fraud that had a benefit in the end

Answer 34

Vaccines rely on things called herd immunity, the level of population immunity above which sustained transmission is unlikely ~85% most of the time. Vaccination is a “firewall”, essentially people who are protected don’t allow the spread,

Answer 35

Smallpox Rinderpest

Answer 36

Two forms - Major 35% death - Minor 1% death - 80% in children Existed in humans for 12 thousand years, killing half a million Europeans annually, caused 1/3 of all blindness cases

Answer 37

1. Aggressive quarantine 2. Search for infected 3. Mass vaccination Having considered the development and results of the global program on smallpox eradication initiated by WHO in 1958 and intensified since 1967. Declares solemnly that the world and its peoples have won freedom from smallpox, which was a most devastating disease seeping in epidemic form through many countries since earliest time, leaving death, blindness and disfigurement in its wake and which only a decade ago was rampant in Africa, Asia and South America

Answer 38

Since world war 2 went from 5% to 70% – Smallpox killed 2 million a year unIl the late 60s gone by 1979 – Polio fell from 300,000 per year in 1980s to 2000 in 2002 – two thirds of all countries have eradicated neonatal tetanus – since 1974 measles deaths dropped form 6 million to less than 1 million – Whooping cough cases fallen from 3 million per year to less than 250,000 – Diptheria declined from 80,000 in 1975 to 10,000 – Hib meningitis in Europe declined 90% in ten years

Answer 39

Religious reasons, medical reasons, age and some areas there is a conscious objection law

Answer 40

Pre-vaccine, whopping cough epidemics appeared every 2-5 years. Immunization reduced incidence 157%, controversy of brain injury, concern about the safety of the DTP vaccine in the 70s left to a conversion to a new DTaP version in the 80s but it was less effective – whooping cough is now epidemic

Answer 41

Andrew Wakefield was a surgeon – in the early 90s he suggested the measles caused Crohn’s disease, in the mid-90s he suggested the measles vaccine caused Crohn’s disease. His research was shown to be wrong in 1998. In 1995 he was treating a boy with Chron’s disease who also had autism, he hypothesized a link between gastrointestinal disease and autism and “environmental triggers”. He had N=12 (12 children). Of those 12, only 8 had been vaccinated (n=8), the paper stated that non causal connection was known But before publication he had a press conference, he made media statements calling for an all out ban on MMR vaccines, citing it as a moral issue. He even went so far as to state that three vaccines at once was the cause and recommend separate of vaccines. How is this similar to the Encode effect?

Answer 42

In the end, Serious conflicts; The Sunday Times 2004 1. The children in the original paper were recruited by a lawyer suing the MMR manufactures 2. The hospital received £55,000 from the lawyer to do the research 3. Wakefield received £400,00 The Lancet retracted the paper, 10 of the 12 co-authors published formal retraction, Wakefield lost his license to practice medicine. Subsequent studies based on half million children have demonstrated vaccinated children have no higher prevalence of autism, and might even have a lower prevalence. So there is no evidence for a causal role, but what has the fall out been?

Answer 43

MMR vaccination was 92% in 1955 – above the herd effect requirement, MMR vaccination fell to 80% in England and an astonishing 58% in London in the space of only 5 years Most parents cited “the link” as their reason for not vaccinating their children, as recently as 2002 1/3 of health care providers in New Zealand were not sure about the validity of “the link”

Answer 44

We should be more concern about rubella, which causes blindness, disfigurements, deafness … if a woman catches it whilst she is pregnant

Answer 45

About even weight in media was given to the Wakefield statements and the actual complaints, thus when survey the public thought it was actually a “controversy” in science A similar scare in the 90s suggested MS was cause by a vaccine – so why is this one still going

Answer 46

Lack of concern – we haven’t seen them to be scared of them Media attention – always trying to give a balanced view, but the evidence is NOT balanced! The media is playing the wrong side for relief (equal coverage) Delayed effect – you have no idea if your immunisation, don’t see cause and effect relationship Identifiable victims – people are allergic to vaccines Lack of target – science cannot provide alternative target we do not know what causes something, we do not know the cause Fear of the rare event – we all fear the odd outcome, rare events are easier to be scared off Can we change attitudes? Surprisingly…no 4-intervention study, Google “Penn and Teller on VaccinaIon”

Answer 47

Publications are how scientists are measured This is the product of a Scientist – productivity of scientist is measured by this means.

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Week 4: Publishing & Communcation problems Flashcards

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