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Reading academic papers

Finding papers to read

There are many ways to find academic papers. As well as using your favourite internet search engine, there are many indexes of medical and biological papers with effective search functions. Pubmed is by far the most popular and very comprehensive, maintained by the NIH, part of the US federal government, thank you. Indexation by Pubmed does lag publication by six or more months, and this will be true of all the academic search engines, like… Jstor, also popular.

So if you simply have to read it as soon as it is published you will have to subscribe to the journals, or having read the abstract in a truncated version of a journal online pay for the whole paper.

When you use the medical research databases remember to use multiple different search terms when looking for papers on a particular topic. You must also use the same terminology as those favoured by researchers and academics. To an extent their use of specialised language makes sense, unfortunately many researchers seem to have never met a complex word they did not like, regardless of the utility derived from using one. So, as well as searching for keywords such as “helminths” or “hookworm” remember to try using scientific names of organisms such as “necator americanus” and “trichuris trichiura”, or using the academic style for contractions as “t. trichiura”. Of course you can simply use “trichiura” instead, but remember with medical research a great deal is conducted in animals. Particularly at the early stages, as we are now with helminthic therapy. So the animal equivalents are often used, as in T. Suis for the whipworm species having pigs as their definitive host.  So search using terms starting at the centre, and move out.

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Peer Review

By nature journals are very conservative, and work very hard to exclude incompetent, poorly carried out or documented, or fraudulent science. They also work to evaluate the methods used in papers submitted for consideration, all this is the process of peer review. They critically, or are supposed to, read any conclusions and discussion in the paper, to ensure they are justified and supported by the theorem proposed, and by the methods used, and observations made.

These efforts mean that unless you really find them interesting, reading the methods used, or the discussion of statistics associated with many papers, is not necessary for our purposes. Those portions of the paper exist for the peers, actual scientists. Whose job it is to evaluate the research, and to endeavour to reproduce or to disprove it’s conclusions. Either using the same methods, or by adopting alternative tests if they feel they are better.

That is not my purpose, I doubt it is yours.

Although the efforts of the journals via peer review, etc., to screen for fraud and incompetence has had varying degrees of success, for our purposes, as with almost all scientists, we can accept papers as competently written and researched if published in a peer reviewed journal. Until they are proven otherwise, so you can safely ignore those portions of any academic paper concerned with methods.

But do not take that as my endorsement of these journals, of peer review or of the infallibility of their methods. There have been numerous examples where fraudulent science has gone undetected for years, and in recent times some examples where the gatekeepers of a variety of journals have been tested and found sorely wanting.

It is of course possible, common even, to get published by paying a fee. In fact it is central to the process, no paper gets published without someone paying for the privilege.

It goes far beyond the potentially corrupting influence of pay to publish, in a field where publishing is how one is judged. To get a glimpse into how screwed up the whole process is you can read this, and this. That will be the subject of a different series of posts another time.

Unfortunately this conservatism can make journals resistant and exclusionary, to anything radical or new – to them, beyond that required by scientific rigour. Science, even medical research, does not have as an explicit objective making people well. I have a hard time imagining a patent clerk in Zurich today being able to publish anything as radical as Einstein’s General Theory of Relativity was in 1905. Provenance matters too much to journals, who you are rather than what you think and how you express it come into play to our detriment. They also, in a very unscientific way, prejudge papers and exclude those they deem as unimportant. Which is a little cart before the horse. Of course it does protect against wishful thinking, people so desperately want to be well they are prone to see results or good when none exists.

But Helminthic Therapy suffers from these and other inbuilt prejudices and restrictions. It is low risk, it is not a drug in the sense that helminths are a novel molecule which could and likely will have unexpected and unwanted consequences. But relative risk is not something anyone takes into account. Because it is next to impossible to patent any aspect of the therapy big drug companies, as noted elsewhere, are not inclined to invest in the area. Drug companies, the big ones, depend on the artificial monopolies created using patents to extract monopoly profits from new drugs, as witnessed by their many and often immoral attempts to artificially extend patents using the legal system, legislation, repackaging and reformulation, etc.

In part because of this alternative journals, enabled by the internet, have been founded. These are often dedicated to areas of enquiry neglected by the mainstream journals, or that allow science produced, often necessarily, under less rigorous circumstances than possible for papers published by older journals. They sometimes adopt modern ideas like open source in the peer review process, by publishing unedited texts or opening the peer review process to comment and participation.

Examples of such journals in the area of medicine are Plos One,

Many journals focussed on medicine began as in-house brochures or magazines published by drug companies who wanted to market their latest patent cures to doctors. In the case of Bayer a notable drug they invented and marketed in this manner was Heroin which they promoted as a less addictive alternative to morphine. Merck followed a few decades later in one of their “journals” promoting Cocaine for, amongst other things, its power to treat Heroin addiction.

These were not isolated examples, in the past many papers on drugs were written by doctors or scientists hired by drug companies, which often contained little we would recognise as science. They were primarily concerned with promoting the virtues of specific drugs, not with scientific niceties. The FDA and it’s ilk did not exist until relatively recently, and there were no requirements for studies into safety or efficacy for new drugs. If you had one you could sell it, and promote it in any way you wanted.

Those papers were published without any of the safeguards that we take for granted now, like peer review. Things are different now, to a degree, but human nature has not changed. Witness the tobacco industry’s ability to find legions of scientists willing to put their names to papers for years arguing there was no evidence that tobacco was addictive, or that it was carcinogenic. If someone is paying then someone else is willing to put their name to almost anything.

Bear this in mind when reading papers, but do not fall into the trap of the conspiracy theorists. Most scientists are sincere and well intentioned, as I continue to hope most people in all walks of life are. Besides that do you really think large groups of anyone could keep their mouths shut?

But the story of journals while interesting is outside the scope of this article.

Once a scientific paper has been written up, usually involving multiple authors and many reviews within the group writing it, and often involving informal peer review amongst colleagues, it is submitted for publication.

There it is read first by a single reviewer to determine if it is worthy for further consideration, for peer review. Over half of submitted papers are rejected at this stage, usually to be submitted to less prestigious journals.

The reason for rejection, in effect a kind of censorship a priori, can include the following and more. It can be because the reviewer does not believe the science is worth reading, or that it lacks relevance. That it proves or elucidates nothing new to the canon (to the existing knowledge in that area). It can be rejected because it does not fit the editorial profile of the journal to which it has been submitted, drug research is not going to fly in a Physics journal for instance. It can tossed because it is prima facie poor science, uses poor methodology, draws unsupported conclusions. Or it could be rejected because the reviewer, conceivably, does not understand it and therefore thinks it absurd. Perhaps because they dislike one of the authors. Papers are often submitted to more than one journal, though doing so reduces the odds of inclusion in the more prestigious ones, exclusivity is a big deal when publishing research. If it is any good you want your journal to be the publisher, not one of a hundred.

Once accepted by a journal for further evaluation, publication is still not assured at this point, it is subjected to a process called peer review and may be withdrawn by the author/s.

Peer review is exactly as it’s name suggests. The editors send it out to other scholars in the same field (the author’s peers) to get their opinion on the quality of the scholarship, its relevance to the field, its appropriateness for the journal, analysis of statistical methods, fact checking, checking of the math used, etc. Peer review is not generally a paid activity. Though publication almost invariably is. That is once peer review is complete, perhaps before, the authors or their sponsors must pay the journal for publication, and this cost is often many thousands of USD, sometimes in excess of ten thousand dollars.

If it passes the process of review, often with numerous changes and even reruns of experiments, or the addition of other data not originally included but gathered, and the fees are paid it is queued for publication.

Having been published the article, along with letters to the journal about recently published papers, and follow up papers or confirming studies concerning previous papers and their results, as well as any studies commissioned by the journal, goes online.

From there it is indexed and catalogued by various research indices and search engines, like Google Scholar or Pubmed.

Egg counts were once commonly used to estimate helminth populations in infected humans, and more commonly in animals. They were used to determine whether or not a treatment to kill the helminths, a process called helminth therapy, was appropriate. Before modern anti-helminthics in particular treatment was very unpleasant, and quite dangerous, so treatment was far more dangerous in the case of light infections than to leave them to die of old age.

This policy of only treating large infections prevails, only subjects with high populations of hookworm for instance are supposed to be given anti helminthic drugs (helminth therapy) according to CDC policy (see graphic from CDC image web site below). It was this customary use of the term helminth therapy that lead me at the very beginning to adopt the use of helminthic therapy, the two phrases meaning exactly the opposite.

I do not claim the term’s invention, I read it in an early paper since lost speculating about the possible use of helminths via deliberate infection to treat diseases like Crohn’s.

The arguments against egg counts as an indicator of helminth number

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This is the first post in a series on this topic. I will expand this post rather than create many different ones, and may turn it into a page accessible from the main nav.

What drugs should I avoid while on helminthic therapy?

Do antibiotics kill hookworms? Can I continue to take my antihistamines while I am on helminthic therapy? When can I reduce or stop taking my medications? Will smoking marijuana harm my helminths? What about cocaine or ecstasy? Viagra? Pumpkin seeds?

Does prednisone, or methotrexate, or pentasa, or remicade or tysabri interfere with the efficacy of helminthic therapy?

We get asked these questions, and others in the neighbourhood, a lot.

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To understand how to find and consume science, particularly on the topic of medicine, one has to understand how it is produced and published, and some of its past.

Science has not always existed, nor has medicine as we know it. In the relatively short time that the ideas of the Enlightenment have prevailed in some areas of our life, and science and medicine have been practiced, it has changed enormously.

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Before we start reading scientific papers we should all agree what science is. We all know what science is, right?

So what is it?

From the Oxford English Dictionary (Shorter)

“Theoretical perception of a truth, as contrasted with moral conviction (conscience).”

Sounds a little loose a definition for my purposes, and like it is a derivation of the argument between rationalists and theologians at the beginning of the Enlightenment. Perhaps I should have bought the full OED.

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I am posting this because I often find myself telling people that helminthic therapy, though it very likely could make you completely well, cannot cure you. The issue is semantics, but it is important we adhere to strict definitions, even if they cause trouble for some, in the interest of accuracy.

A cure is when a disease or illness is treated and then goes away completely. An example of this is when antibiotics are used to clear up an infection such as tonsillitis.

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I taught myself how to read science, even going so far as to dive into statistics so I could understand what “p” meant. I did so originally so that I could understand the hygiene hypothesis, old friends hypothesis, and what came to be known as helminthic therapy. Later I continued to read it so I could do a better job helping clients, but primarily because I had grown to enjoy it.

Reading scientific papers is one of my favourite activities. I even have a “greatest hits” list of my favourite papers, which I reread. I have learned an enormous amount from the activity, and derived even more pleasure. Because of that I wanted to encourage others to do likewise.

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I have not had an editorial position for this blog, until now. No consistent direction or unifying theme for what to say except in general terms to speak about helminthic therapy and anything that might, however distantly, relate to the health of those who approach us for hookworm, or for whipworm.

Often I have been embarrassingly guilty of writing self-indulgent garbage I should have known was of interest only to me. Things that in retrospect should not have been of interest to me.  I apologise, it won’t happen again.

I have decided that I am going to concentrate on science for a while, what it is, how it is practiced, how it is funded, who decides what gets funded, what is published and how, and perhaps how elements of that might be improved. Science has not always been like this, or even been at all.

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I wanted to thank Automattic, the developers of the Akismet anti comment-spam plugin for writing what is a very helpful tool for blocking comment spam on WordPress blogs.

I forgot to mention that it is free.

If you look at the screenshot below it quarantined 2,574 comments that were spam, this from early this year, around mid March I think, until now, mid September.

Most of it is in Chinese, though I did not get past the second page examining it.

If I deleted your honest post, if you submitted it and it is not published here somewhere then I deleted it, please resubmit it and I will be sure to publish. Please no marketing links, I just burn those comments.

Spam Count

2,574 comments marked as spam in less than six months


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