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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Why ova counts are worthless for measuring helminth population

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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Drug interactions with helminthic therapy

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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Posted in Antibiotics, bad drugs helminthic therapy, biome restoration, drug interactions with helminthic therapy, drugs to avoid hookworm, helminthic therapy drug interactions, helminthic therapy drugs to avoid | Comments Off

Where science is published and how to find it – Part 3 in a Series

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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Posted in big pharma, corruption, drug companies, helminthic therapy research, Medicare Prescription Drug Improvement Act, practice of science, Reading science, reading scientific papers, Research, Science, Scientific Journals, scientific method | Comments Off

What is Science? – Part 2 of a Series

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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Posted in big pharma, corruption, drug companies, helminthic therapy research, Medicare Prescription Drug Improvement Act, practice of science, Reading science, reading scientific papers, Research, Science, Scientific Journals, scientific method | Comments Off

What is the difference between a cure and remission?

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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Reading research for non-scientists – Part 1 of a Series

Overview

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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Posted in big pharma, corruption, drug companies, helminthic therapy research, hygiene hypothesis, practice of science, Reading science, reading scientific papers, Research, Science, Scientific Journals, scientific method | Comments Off

New direction for this blog

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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Posted in big pharma, biome restoration, ecological medicine, ecosystem, helminthic therapy, helminthic therapy research, History of Autoimmune Therapies, hygiene hypothesis, Old Friends Hypothesis, practice of science, scientific method, the body as an ecosystem | 2 Comments

Thank You Automattic for the Akismet Anti Spam Plugin

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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Time to re-examine our slavish devotion to the scientific method

Someone sent me a link to some research on Psoriasis and it got me thinking again about the way science and particularly drug research is conducted, and its limitations with respect to complex systems we do not understand, like the immune system.

The subject of the direction of research in the area of immunological diseases really bothers me. I think science, because of its history and prejudices, has gone in entirely the wrong direction, and that the scientific method is part of the problem.

The scientific method works very well for simple systems like the physics of semiconductors for instance, where all but one variable can be controlled for, where all variables have been identified and understood.

That just is not possible currently for the immune system, we do not even know all of its components, or even the behaviour of any one component in all circumstances. Never mind those circumstances we create with modern drugs.

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