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alarmeFollowing on a previous post discussing how bogus magazines pretending to be scientific journals can affect the judgement of non-specialists, a brief 5 steps method to pin-point dubious publications is described. This method is not infallible and you must remain cautious, as pseudoscience may still dodge the test.

Case study: Entropy 2013, 15(4), 1416-1463

Glyphosate’s Suppression of Cytochrome P450 Enzymes and Amino Acid Biosynthesis by the Gut Microbiome: Pathways to Modern Diseases

1 – Is the journal a well-established journal such as Nature, Science, Proceedings of the National Academy of Sciences, etc.? Articles in entropyprestigious journals can generally be trusted because these articles go through a tough review process (sometimes they publish rubbish but it is uncommon and the rotten egg is discovered sooner or later). Scientists love publishing in well-established journals. You can look at the “impact factor” of the journal (You can Google it) set a lower threshold of between 3 to 5 (Though in some not-very-popular areas you could go much lower than 3).

greenEntropy is not a well-established journal for general science or biomedicine (I doubt it is for any discipline; its impact factor is 1.18). It absolutely doesn’t mean that the article will be flawed but it means we will have to be careful and follow the next steps.

2 – Check authors’ affiliations. Do they work in a respectable University? Or do they claim to work in University of Lala Land or no university at all?

yellowOne of the authors is an “independent scientist”. We are not in the 17th century anymore. Science is a very expensive enterprise and I would be amazed if anyone -apart from Russian oligarchs, Arab princes or Bill Gate’s descendants- could be an “independent scientist”. The last author however works at a very prestigious University so we can carry on reading. (Still weird…)

3 – Check the Journal’s speciality and the article’s research topic. Are the people in the journal knowledgeable in the area the article deals with?

oragngeHere we have the first big problem: The journal, Entropy, describes itself as “an international and interdisciplinary open access journal of entropy and information studies”. Originally, Entropy was a subject of study of thermodynamics, a branch of physics dealing with heat and energy (I wrote about thermodynamics in the past; also see Oxford dictionary). When did physicists (or mathematicians) become experts in the area of “Gut Microbiome and Pathways to Modern Diseases”? Is it not the business of medics? Or biologists? Or biochemists?

4 – Check the claims in the title and summary of the article. Are they reasonable for the journal publishing them? This is very important; for example, if scientists find a cure for AIDS their article will be published in one of the most prestigious journals. Maybe even in the two most sought after journals of the scientific world at the same time; it happened after the completion of the human genome (1, 2). The discovery of the HIV was published in just one of the journals but in 2 separate articles at the same time (3, 4). There is no way that something really important will escape the radar of the editors.

redThis article is attributing pretty much all the chronic diseases of the modern world to a single agent, glyphosate. Wouldn’t it be fantastic if just by getting rid of one chemical we could be as healthy and happy as we have never been? A single agent! If this were true, it would go straight into Nature Magazine and the scientific world would have gone mad before you could even notice the article.

5 – Do the claims at least make sense?

red bomb(this has got to be rubbish) Here we really hit it. The authors state in the summary that glyphosate is responsible for obesity, diabetes, heart disease, depression, autism, infertility, cancer and Alzheimer’s disease. Ah! Also gastrointestinal disorders. Glyphosate responsible for obesity, really? Not potato-coachness; not over eating; not driving instead of walking 100 metres: glyphosate. Similar questions should be asked for all the other diseases. It is also important to mention that glyphosate was invented years after there was already obese people and people with cancer and people with heart disease, etc.

Anyway, for me the best example of things not making sense is the sentence: “glyphosate is the “textbook example” of exogenous semiotic entropy”. What?! All modern diseases are caused by semiotic entropy? These sure are 9 words picked at random and scrambled to form a sentence-like string of words; Individual words make sense; the sentence does not.

You can read the article where everything (except clear evidence) is shown here. The authors paid 1200 Swiss Francs (about £820 or $1280) to have it published there. The main experimental evidence that they present against this evil “textbook example” of exogenous semiotic entropy is a widely discredited paper published in a journal with an impact factor of 2.999 (yes 2.999). As an educated and scientifically trained individual I think it is a laugh and I believe it is so poor that even non-scientists will laugh. But just in case non-scientists could take it seriously, I wrote the above guide to detect pseudoscientific papers at a glance.

Please share your comments bellow:

(1) Nature 409, 860–921 (2001)

(2) Science 291, 1304–1351 (2001)

(3) Science 220, 865-867 (1983)

(3) Science 220,  868-871 (1983)

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  • Derek Bickerton 17/01/2015 at 11:30 pm

    Ariel, you write: “Anyway, for me the best example of things not making sense is the sentence: “glyphosate is the “textbook example” of exogenous semiotic entropy”. What?! All modern diseases are caused by semiotic entropy? These sure are 9 words picked at random and scrambled to form a sentence-like string of words; Individual words make sense; the sentence does not.”

    You’re right as far as you go. But do what I did: click your “Find” button with the entry “semiotic”. You’ll find the only other hits in the article refer to “BIOsemiotic.” Now this is a very different kettle of fish; as I’m sure you know, biosemiotics is a legitimate (well, at least it has at least one academic journal devoted to it) field of study. It’s still far from a well-worded sentence, even if you agreed with it, but not the total nonsense it has been presented as. Just the result of bad editing plus either a typo or sheer carelessness on the past of the authors–obviously they MEANT “exogenous BIOsemiotic entropy”, which simply means “signals (chemical or otherwise) from some external entity that trigger biological deterioration in s/one or s/thing”.

    But I won’t waste time on this. There’s a much more interesting paper by Swanson et al. in Journal of Organic Systems, 9(2), 2014. I’d be very interested to hear what you think about this.

    • Ariel Poliandri 23/01/2015 at 7:30 am

      Thank you for the briefing Derek. I wasn’t aware of the existence of the journal you have mentioned or biosemiotic in general. I am not very keen on mixing semantics and science. Semiotic and entropy have both more conventional meanings. For centuries philosophers have tended to get entangled in semantics (the meaning of words) and forged reality. If something is a signal, why not to call it that? Obscure and ill-defined words are the entry door for charlatans in science.
      I will have a look at the paper you have mentioned. Although, again, for me, organic means a molecule based on a hydrocarbon skeleton. At least that is what it used to mean, and it was plain, well defined, and scientific; the New Age version is not.

  • Kelly Beins 07/01/2015 at 6:26 pm

    I like your framework as presented in this post. Thank you. As a clinician exposed to lots of “research” via social media but being one who values evidence based practice and strives to be a bridge for parents (I’m a clinician not a researcher or someone connected to an academic institution) I consider critical appraisal is essential but it can be really hard sometimes to efficiently and effectively critically appraise everything I see/read.

  • Paul Bunson 07/09/2014 at 1:53 am

    So what you’re saying is that papers like this don’t pass the “Seneff test”. :-)

  • Leon F. Gay 07/05/2014 at 6:04 am

    Would be great to have an algorithm to raise red flags for bogus/predatory journals…

  • George Dad 17/03/2014 at 9:13 pm

    This was an absolute hoot to read! Still laughing about not being in the 17th century with “independent scientists”s LOL.

    As terrible as it is that science has to contend with pseudoscience, this was a nicely written guideline for the detection of hogwash. I’m rather tired of “Here’s what we KNOW is correct, now we shall set out to prove it and call it science.”

  • Sergio Vera 17/03/2014 at 2:24 pm

    I’d just like to add that different fields have different impact factor standards,and that relevant and valid research is also perform in small and big companies, not only in prestigious universities.
    Also a professor of Artificial Intelligence, in a Glyphosphate paper its an additional warning even if he/she works at MIT.

    • Ariel Poliandri 17/03/2014 at 9:14 pm

      Cheers Sergio,
      I agree with all your points. I will have to edit the reference to impact factors. It is quite hard trying to keep it short and -at the same time- to be fair and precise.

  • Frank Wolek 17/03/2014 at 2:22 pm

    Needs discussion. However, be careful. The criteria mentioned can also be used to advance scientific conservatism and stifle innovation. For example, scientists with new ideas can be stifled by review panels from advocates of established paradigms.

  • Jacob Smith 20/11/2013 at 1:37 pm

    Sadly, one MD with an agenda has been tricked by this paper. She calls it a “seminal paper.” Sigh…..

    http://www.huffingtonpost.com/kelly-brogan-md/diet-mental-health_b_4257003.html

  • Shafiq Khan 04/07/2013 at 9:04 am

    All main-stream journals of physical sciences are bogus as they have published rubbish for last one hundred years. Read the proof.
    The very space-time concept, on which theories of relativity are founded, has been mathematically, theoretically & experimentally proved as baseless and openly challenged on the basis of published scientific articles. Since the very space-time concept has been proved as baseless the question of curvature of space-time being correct does not arise. Gravity has been shown to be an electromagnetic force as foreseen by Maxwell due to the curl/vortices of aether (the electric dipoles) in the published article ‘Revised Foundation of Theory of Everything: Non-living Things & Living Things’ (www.indjst.org; Sep 2010) Revised version of this article is available on vixra & World Science Database in my profile. Following is the open challenge which everyone could see at http://www.worldsci.org/php/index.php?tab0=Abstracts&tab1=Display&id=6476&tab=2 and http://www.gsjournal.net/Science-Journals/Essays/View/4018.

    OPEN CHALLENGE

    The article ‘On the Electrodynamics of Moving Bodies’ by Albert Einstein is based on trickeries is proved beyond any doubt whatsoever in the articles (1). Experimental & Theoretical Evidences of Fallacy of Space-time Concept and Actual State of Existence of the Physical Universe published in the peer-reviewed journal namely Indian Journal of Science & Technology (March 2012 issue) available on http://www.indjst.org (2) On the Electrodynamics of Moving Bodies By Albert Einstein is Based on Trickeries (Open letter to Professors, Teachers, Researchers and Students of Physics) published in peer-reviewed journal Elixir Online Journal (February 2012 issue) available on http://www.elixirjournal.org. The Voigt transformation was simply a mathematical possibility which was changed by Lorentz by introducing the Lorentz factor but the Lorentz factor is simply a manipulation. Thus nature and forces in nature were trivialized and made subservient to mathematics in the theories of relativity, Big Bang Theory, Space-time concept and in all physical sciences which are directly or indirectly based on the ‘On the Electrodynamics of Moving Bodies’. It is unfortunate for humanity that exposing these trickeries took more than one hundred years.
    I openly challenge all the professors, researchers & teachers of physics/philosophy of physics to come forward & show me where I am wrong or else they have to accept that they are teaching incorrect physics based on trickeries.

    My challenge may not be treated as a publicity stunt, but I sincerely wish that truth should prevail on this planet and am expecting identical response from all truth loving people/intellectuals. I do understand that it is hard for mainstream physicists to reconcile with the alternative philosophy; though actual and factual; as almost all the living physicists and researchers are borne, brought up and taught physics which is fundamentally incorrect. Their livelihood is based on the physics which has been adopted as the result of fraud, but these material interests should never be a stumbling block to acknowledge the reality, which to my understanding is the essence of scientific thinking and honest living for the betterment of entire human society.

    I have not an iota of doubt that sooner or later the truth will prevail, but it would be in the interest of humanity that truth is accepted now so that humanity comes out of clutches of materialism which in itself is naked atheism.
    Mohammad Shafiq Khan.

    I would like to keep you informed that the open challenge has been sent to almost all professors of physics & universities of the world and so far two retired professors of physics namely Jeremy Dunning-Davies of Hull University & Brian Cole of Columbia University accepted the challenge but both of them finally failed to show a single error in the articles on the basis of which open challenge has been put forward. In this regard exchange of articles between me & Jeremy is available on vixra, General Science Journal & Elixir Online Journal.

  • Dr. Matthew Marturano 29/05/2013 at 6:47 pm

    While there are many legitimate criticisms of this article raised here, and elsewhere, I question the assertion that the paper is claiming glyphosate is single-handedly responsible for a whole host of chronic diseases.

    The authors conclude, “The pathologies to which glyphosate
    could plausibly contribute… Glyphosate works synergistically with other factors, such as insufficient sun exposure, dietary deficiencies in critical nutrients such as sulfur
    and zinc, and synergistic exposure to other xenobiotics whose detoxification is impaired by glyphosate.”

    Quite clearly, this statement indicates that the authors do not believe that glyphosate is the lone agent in the etiology of these diseases.

    • Ariel Poliandri 29/05/2013 at 7:15 pm

      As discussed in a previous comment, the “take home massage” of scientific articles is to be found in the summary and here the summary clearly states:
      “Here, we show how interference with CYP enzymes acts synergistically with disruption of the biosynthesis of aromatic amino acids by gut bacteria, as well as impairment in serum sulfate transport. Consequences are most of the diseases and conditions associated with a Western diet, which include gastrointestinal disorders, obesity, diabetes, heart disease, depression, autism, infertility, cancer and Alzheimer’s disease. We explain the documented effects of glyphosate and its ability to induce disease”
      What makes matters worst is that the authors say “here we show” not “we suggest”. Although, in any case, “we suggest” would be an over statement according to the level of evidence presented.

  • Dale Amon 21/05/2013 at 7:07 am

    I would suggest that reputable journals should start requiring that raw, unprocessed, unnormalized, unfiltered data, be placed in a web site that is open to everyone, such that any results can be fully replicated by others. There have been far too many frauds with reused graphs and faked data; far too many cases of misunderstanding of statistical methods, inappropriate massaging and cherry picking of data. We really should view any scientist who will not do so with a great deal of suspicion.

    • Ariel Poliandri 21/05/2013 at 6:02 pm

      Agree Dale, and the conclusions need to be in accordance with that data and not to be wild extrapolations…

    • Marvin Janney 29/05/2013 at 1:51 pm

      In all honesty, there are no reputable journalist. News today, is someones regulated Opinion….

    • Mike Mellor 01/06/2013 at 2:12 pm

      Dale, there’s a site called Retraction Watch with some excellent discussions about scientific papers. The big problem is getting someone to do the work of replication. It’s hard enough to get a grant to perform original research. If you go looking for a grant to replicate someone else’s study, you’d better have a good reason, otherwise nobody will fund what they see as duplication. A good reason might be that you think the original study didn’t go far enough, or you have grounds to think it was flawed and you want to challenge it. In certain “pop science” fields like climate, grants are not hard to come by. The rest of the time, the best answer is before you are born to choose rich parents.

  • Jesse 15/05/2013 at 7:08 pm

    You are being disingenuous, which only harms your cause. Someone who does not actually read the paper might conclude from your critique that a definitive causal pathway was being proposed from “glyphosate is responsible for obesity, diabetes, heart disease, depression, autism, infertility, cancer and Alzheimer’s disease.”

    The conclusion actually reads, “The pathologies to which glyphosate could plausibly contribute, through its known biosemiotic effects, include inflammatory bowel disease, obesity, depression, ADHD, autism, Alzheimer’s disease, Parkinson’s disease, ALS, multiple sclerosis,
    cancer, cachexia, infertility, and developmental malformations.”

    So, yes, a large list of diseases, but it is not asserting glyphosate exposure is a common cause, but 1 contributing factor among many. It also does not state this is the case, but plausible given the known biological pathways and in the discussion calls for more research including the replication of other existing clinical studies.

    Furthermore, I disagree with your premise that journal articles should be judged based on their affiliations. The scientific publishing business is a business, they are not infallible gods and should not be treated as such. There are some issues with this paper, but it should be clear to anyone reading it that it is not a research study; it is a literature review and should be treated as such.

    • Ariel Poliandri 16/05/2013 at 5:57 am

      Science should be specific and go to the point.
      Anyone reading a scientific paper that suggests “something may or may not produce an effect” will conclude that the paper did not contribute much to scientific knowledge.
      Anyway, the “take home massage” of scientific works is to be found in the summary and here the summary clearly states:
      “Here, we show how interference with CYP enzymes acts synergistically with disruption of the biosynthesis of aromatic amino acids by gut bacteria, as well as impairment in serum sulfate transport. Consequences are most of the diseases and conditions associated with a Western diet, which include gastrointestinal disorders, obesity, diabetes, heart disease, depression, autism, infertility, cancer and Alzheimer’s disease. We explain the documented effects of glyphosate and its ability to induce disease”
      If the authors just wanted to suggest something, they should have been honest and clearly state in the summary that it was a “suggestion” and that they didn’t have any evidence to prove it beyond wild speculation.
      I will have to stick to my claim about scientific affiliations. When I am sick I rather go to the doctor than to some guy down the corner that once read a book about medicine. The doctor can fail but the corner’s guy will likely fail; it is just a matter of probabilities.

  • John Edwards 14/05/2013 at 10:17 am

    Regarding low impact factors, I know you stated that this was not the definitive evidence of quality but there are other considerations. I have been trying to publish some work on the health effects of genetically modified food (not all GM food, just two products with a plausible mechanism of toxic action) in 2 species for some time. Trouble is the journal editors send out to multiple peer reviewers, and fo balance some are from universities etc and others are from – the GM industry – of course we have found the independent reviewers give our work a thumbs up and the industry advocates give a big thumbs down. the reuslt is that “on balance” (a much maligned term) the editors reject the manuscript. So we work our way down from Nature, Lancet, BMJ etc to the smaller impact journals. Frustrating, but at the moment we want to see the work published so we can hear critical comment from a readership.

    • Ariel Poliandri 14/05/2013 at 5:34 pm

      I share your pain. High impact factor journals want more than good quality research; they are looking for stuff that is also trendy, etc… (my first post ever was about this subject)
      I included the Impact Factor thing (even if I don’t like it much) because this post is meant to be for non-scientists. I stressed in bold that the impact factor is not -by any mean- a measurement of the technical validity of a paper. Reading a high impact factor journal is just like buying a branded product; it comes with some warranties but it can still fail. What measures a good paper is its approval by the scientific community reading it over time. There are plenty of descent specialised journals around the IF 3 area. Get you paper out. If it is reproducible it will certainly be a blast and then you’ll have Nature or Science editors ringing you up to write a review :)

  • Mary 13/05/2013 at 11:51 pm

    Yeah, there are a number of issues with the paper. But just an affiliation at a reputable institution isn’t sufficient. Check out this take on that: http://ksj.mit.edu/tracker/2013/04/discover-blogger-keith-kloor-stumbles-ne

    • Ariel Poliandri 14/05/2013 at 5:38 am

      Thanks for the link Mary. I noticed that she was not a biologist too! But I was trying to keep the thing less than 1000 words long. The review was such an example of pseudoscientific literature that I felt I didn’t need to go there.
      At the end of the day this is just a “method” to help in the detection of bogus scientific papers.
      As I said earlier in another comment: Even if she were a professor in genetics or epidemiology, science is a collective enterprise; the opinion of an isolated scientist counts for very little until it has been accepted by the majority of his/her peers. If glyphosate were the agent of the end of the world hundred of scientists would have already turned their attention to it.

  • John 13/05/2013 at 11:44 pm

    I just wonder who paid for the publication – the independent first author out of his own pocket or the corresponding author with funds from her university (that may not have been meant to be spent on publications outside her actual field of work, which could then amount to embezzlement)?

  • John 13/05/2013 at 7:59 pm

    2 – Check authors’ affiliations…
    … but then, also:
    2b – Check authors’ specializations (especially if their affiliation is known, Google usually helps find their university’s staff profile page, LinkedIn or some other source). Do they work professionally in the field? Or do they just go out on a limb on a topic they are not really experts on? (Which happens with older scientists who have an ego to match, or when scientists pursue political or ideological purposes and forget to stick to their last…)

    In this case, one author may work at a very prestigious University – but in computer sciences and language processing: http://www.csail.mit.edu/user/1389 And while 45 years ago she may have done an undergraduate degree in biophysics, this hardly qualifies her as an expert in the field of “modern diseases.” (Also curious, on her web page she claims that since 2011 she published 10 papers in medical journals – that’s about one paper every 2-3 months, moonlighting while working in her own field, without a lab or anything?!)

    Perhaps not surprisingly, when googling for her name it turns out she’s run afoul of other (science) bloggers, e.g.:
    http://scienceblogs.com/insolence/2012/11/20/dumpster-diving-in-the-vaers-database-again/
    … and she already found out that not only glyphosate causes everything, but also sulfur does! And this she explains… in an interview with the notorious Mercola: http://articles.mercola.com/sites/articles/archive/2011/09/17/stephanie-seneff-on-sulfur.aspx

    Quite sad for scientists to end their career in such a way… (But at least she can blame it on whatever her next paper will be about.)

    • Jenny 13/05/2013 at 10:01 pm

      I just had a look at the Mercola link! The comments on that article are scary – the sulfur-loving community seem to be like a new religious group. I seem to have led a very sheltered life – I’m just a scientist working away and trying to cure cancer. Feel as if I’ve been missing out on all of this hocus-pocus. It is interesting how little real science is quoted by these people.

    • Ariel Poliandri 14/05/2013 at 5:26 am

      @John, mate your last sentence cracked me up:
      “Quite sad for scientists to end their career in such a way… (But at least she can blame it on whatever her next paper will be about.)”
      If you don’t mind I will use it at some point.
      You are right about authors’ field of expertise. A PhD in biology makes you as qualified as any educated person to talk about quantum mechanics but doesn’t make you an expert. The same holds true the other way around. But even if you have a PhD in biology and you are talking about your area of expertise, science is a collective enterprise; the opinions of an isolated scientist counts for very little if they don’t have the support of a significant proportion of his or her peers.

  • Jenny 13/05/2013 at 6:03 pm

    Love the way that they shamelessly cite all of the highly dubious references on autism – any paper which cites Andrew Wakefield is asking for trouble. Did you read the whole paper? It’s 48 pages of supposition and inference, with no references for the most sensationalist statements. Sorry, I didn’t have time to read all of it, but it’s a great example. Well spotted!

  • Julee K 13/05/2013 at 4:53 pm

    Thanks so much for this! I have wanted to learn a type of methodology of calling out all the bogus crap out here in Cyberville. As a non-scientist, I need this kind of help! Thank you thank you!

    • Ariel Poliandri 13/05/2013 at 5:30 pm

      Why thank you!
      As pointed out in the above comment, you also have to look out for conflicts of interest.
      Good luck in your search for enlightenment!

  • Kieran Boyle 13/05/2013 at 3:14 pm

    I would also check if any of the authors have a glaring conflict of interest. For example, if a dubious-looking paper proclaims that a health supplement treats a long list of maladies, do any of the authors just happen to be involved with a company that sells said supplement?

    I am getting alarmed at the number of emails I have started to receive from very dubious “journals” requesting me to submit papers. Some of the emails are so ill-written, they remind me of the classic “Nigerian Bank” scam emails….

    • Ariel Poliandri 13/05/2013 at 5:23 pm

      The conflict of interests issue is a good point Kiran, cheers.
      I am also receiving a lot of requests for papers over here (for which -of course- you have to pay “editing costs”). Are you up to writing a paper Alan Sokal style? (the problem will be to find funding for the editing costs…)

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