Reading Science: Peer Review – Part 4 in a Series

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.

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.

Continue reading “Reading research for non-scientists – Part 1 of a Series”

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.

Continue reading “New direction for this blog”

Things I would do if I was still sick

Or that you can, or that you can use to try and stay healthy.

If I suffered from any nasty immunological disorder, or any involving chronic inflammation this is what I would do:

1. I would not rely on experts, so-called, who have managed to create a situation where all these diseases are out-of-control and increasing. Clearly “modern medicine” not only does not have the answers for these conditions, it is clear that it is part of the problem. Having said that if you are currently reliant on some modern drug to function you are going to have to continue to rely on it until you can get things under control such that it is possible to discontinue its use.

2. I would systematically make my life as close in its daily routine to that of a hunter-gatherer. This sounds wildly impractical, but if you understand what is important about each difference between modern living and the stone age in terms of health it is very easy.

So what does that mean in terms of practical advice?

These are the changes I would make to my life knowing what I know now, and to a large extent have. The more severe your disorder the more disciplined you need to be with each of these changes:

1. Eliminate carbohydrates, both simple and complex, from your diet, as close to entirely as possible. Eat vegetables, fruit, nuts and seeds, and flesh of one kind or another. No grains or their products, ever. No sugar, no rice, no bread, no crackers, no cereal, no pizza crust, no pastry, no cake, no pie, you get it. Never eat prepared food, prepare it yourself from fresh ingredients, preferably organic or grown yourself. If you cannot pronounce it, from the label, and have no idea what it is, why the hell are you eating it? If you garden you win thrice, see below.

2. Make your meals smaller and more frequent. No large set meals, snack all day. Subject yourself to periods where you don’t eat at all. Episodic hunger is good. But drink a lot of water. If that does not suit take a very small one early in the day and a large one late.

3. Expose yourself to sunlight, and drop the sunblock. Yes it may increase your odds of developing skin cancer, but be smart about it. When I lived in the tropics I stayed out of the sun from 11 am to 3 or 4 pm, and never burned although I went shirtless most of the time and never wore sunblock. I am blue-eyed and had blond hair as a child. If you have to go out during those hours wear a hat and a long sleeved shirt. Our skin can produce 20,000 IUs of Vitamin D, the right kind, in a few hours of shirtless exposure to sunlight. The RDA is 200 or so IUs? Really? If we evolved to produce that much vitamin D there is a reason for it, and lack of vitamin D is implicated in a host of immunological disorders. It also plays a central role in the immune system and the RDA is set with no real idea of how much is required. Again, if we evolved the capacity to produce that much there is a good reason for it.

4. Get in the dirt every day, ideally this would mean hikes in the woods, gardening, swimming in unpolluted rivers and lakes. You need to be exposed to the bacteria and other organisms in soil. Be smart, don’t rub dirt into cuts, by exposure I mean some should end up in your digestive tract, on your skin, in your lungs. Every day. Breathing dust is good, in moderation. If this is not practical eat some small amount of dirt from natural source every day. The practice is called Pica, and not just humans, but animals, have and do practice it, and have for millennia. Go to the woods, to areas you know they don’t spread fertiliser or herbicides. Mix it up. You can bring a week’s worth back with you, just store it in an open container and don’t refrigerate it. Quantity is not important, frequency is. If you garden eat tomatoes or carrots with minimal washing out of the garden, for instance.

5. Exercise, a lot. It has an enormous impact on well being, stress, etc., and our forebears were nothing if not active. But again, be smart, walking is vastly underrated as an exercise, but requires more time to produce a given result than something more intensive. Be sure to mix it up, I am not advocating marathon running, which is a modern abomination guaranteed just about to result in damage and injury. Combine walking, running, swimming, climbing, weight lifting, dancing, wrestling, boxing, etc., and do things you enjoy. Be active for 1 hour a day at least, and mix it up. You are not competing, you are doing it for pleasure, I hope. You can make all this stuff more time efficient by combining things whenever possible, so running or walking barefoot in the woods would deal with both exercise and exposure to dirt at the same time.

6. Simplify your life, we are not meant to live in large complex societies, or deal with all these modern distractions and contrivances. The result is stress, implicated in about every immunological disorder there is. Turn off the TV, close the laptop, bring your point of view down to the level of someone living in a social group of a few hundred people, tops, and a geographical limit of fifty miles, and unplug. The world will manage to continue to screw itself up without your active participation, don’t worry about it. Why the hell is the world so upset and angry anyway? Do you really need your share of that action?

7. Stop replacing your skin’s oils and biome with artificial substitutes on a daily basis, or ever. You can shower every day, but don’t use soap or shampoo. Think about it, you strip your skin and hair’s surface of naturally occurring oils, and by extension organisms, every day, and then immediately replace those lost oils with artificial substitutes. Stop using soap and shampoo, and the things that follow their use, and I guarantee you that within a few weeks you will wonder why you ever used either of those things. I still brush my teeth and recommend you do to. No, I don’t have an odour. My skin and hair are in the best shape of my life.

8. Repopulate your intestinal tract with the organisms your modern life, either by lack of exposure or by use of antibiotics, etc., has denied it and that you have evolved to live cooperatively with. See eating dirt above. We used to live in close contact with the soil and the organisms it contains, it was in our food, on our skin, we breathed in dust every day. Food preservation was largely fermentation or drying. Eat natural yoghurt’s, seek out odd fermented foods, if necessary acquire intestinal worms, helminths, for the most important class of organisms for your immune system, helminths or worms.

9. Stop using caffeine, doing so induces a stress response, see above.

10. Lose weight if you are obese, it is implicated in a lot of diseases involving inflammation and even autoimmunity.

11. Avoid antibiotics except when your life is at risk, or there is risk of organ damage or disfigurement.

If you do all those things, if you are sick with a so-called “modern disease”, things will almost certainly radically improve.

This is not a quick fix, you have spent years screwing your body up, you can expect things to improve in a time frame of months and years, and that the changes will be slow but ongoing for a very, very long time.

I originally posted this to a different blog which I am now consolidating here. It was first published in 2010 I think. There is a follow up post coming soon from the same site.

The context of helminthic therapy and the environmental diseases it can be used to ameliorate

I want to emphasise that I believe what we are doing exists in a much broader, well-established context.

The diseases we are trying to work with are all environmental in origin. The hygiene hypothesis essentially says that because we have impoverished the environments defined by our bodies by reducing the variety of organisms that populate us, we are getting sick.

Helminthic therapy is an attempt to restore health by remediating the ecosystem formed by the subject’s body. As in the reintroduction of wolves to control deer populations.

I believe that the most important, eventual, outcome of what we are doing will be to get mankind to see that our health is intricately intwined with our environment. That hundreds of millions of people are already sick right now because of anthropogenic environmental change.

That the environment, our ecosystem, is not something up in the sky or separate from us. That it is part of us, and intricately connected with us, our health, our daily lives, that we are component parts of one integrated, dynamic system.

That the ecosystems defined by our bodies and immediate environment, and our daily habits, have been so damaged that hundreds of millions of people are living lives limited by pain, fear and suffering.

If we succeed in that then a profound change in human behaviour towards our planet will occur. Because everyone will be conscious of their direct stake, theirs or their children’s health, in the health of the planet as an immediate phenomena. Not as some distant possibility that we might be able to put off by using the recycling bins.

That there are not ecosystems, except as artificial concepts. There is an ecosystem, and everyone”s health depends on it in profound and immediate ways, because we are all part of it.

We are the ecosystem. I am the ecosystem. You are the ecosystem.

Further, right now, our species in the industrialised and industrialising world, is under enormous selection pressure. Those with MS or Crohn’s, just two instances, will be much less likely to choose to procreate.

Ironically it is likely that many of the diseases we can address with helminthic therapy arise out of genetic adaptation to parasite/microbe rich environments. So in a sense the best adapted specimens, the very latest genetic models of humans, are those experiencing the worst consequences of environmental change.

We are witnessing not just the extinction of various species, but also a strong and rapid change in mankind’s genetic makeup.

I recognise that we should not attempt to “boil the ocean” as a friend used to put it, but I think if we frame this correctly we will find more allies than at first it might appear, and be able to present the concept of what we want to achieve in a more recognisable, and palatable, framework. We can just fit in, perhaps, rather than trying to present something entirely alien. If we are another environmental cause our pool of allies increase, and our messages are easier to understand, fit within a contextual and conceptual framework that is familiar.

That really is it for a while, enjoy your summers. Get outside, get dirt under your fingernails, get some sunshine, and get some river water down your nose.

Part 2: Follow up on progress of “A”

This is, as the title suggests, one in a series of posts, almost entirely derived from emails from her family that they send me periodically to keep us up-to-date.

At the end of this post, and in a few minutes all the others, is a standard block of text with links to each part of the story of this child, as well as some additional information.

———–

I just got a fantastic, cheering follow-up email from the dad of “A” whose experience with severe Crohn’s, as a two year-old, and her response to whipworm for her problems are described in my previous post, and now here:

Here is his follow up email to me:

Quoting: We had the colonoscopy done yesterday with amazing results. The doctors first words to us after completion were “I’m now a believer in this therapy”. “A” had absolutely no signs of Crohn’s anywhere. She said someone else looking at her would think there was not a thing wrong with her. The worms were alive and kicking, and she gave us some pictures. [A’s Mom] and I couldn’t be happier, we wanted to jump and shout. The doctor said we should get more worms, and that the biopsies should be in within two weeks. She seemed very pleased as well.” end quote.

Pretty cool, eh?!

Of course this is remission, not cure, so if she loses her helminths she would get sick again, but I for one could not be happier.

Links to rest of series on “A”

“A” was under 2 years old when diagnosed with Crohn’s Colitis, and the disease appears from the family’s descriptions to have been severe and aggressive. They approached us when the recommendation for treatment from the child’s Gastroenterologist was one of the biologics, either Remicade or Humira, I cannot remember which.

Below are links to each of the four posts, so far, which for the most part are just emails from the child’s dad on “A’s” progress, and his thoughts and observations.

Managing the links between the posts has become cumbersome, so I have created this standard block of links to tie the story together, explain the context if someone happens upon one of the posts and does not realise they are part of a series, and will probably make a static page to aggregate the whole thing.

Part 1: Part 1 of the story of “A”

Part 2: Part 2 of the story of “A”

Part 3: Part 3 of the story of “A”

Part 4: Part 4 of the story of “A”