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.

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.

Continue reading “Where science is published and how to find it – Part 3 in a Series”

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.

Continue reading “What is Science? – Part 2 of a Series”

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


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”

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.

Continue reading “Time to re-examine our slavish devotion to the scientific method”

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.