Blog Posts

Characteristics of Intelligence in closed environments

Outcome in closed environments with one type of Intelligent agent when the Intelligence has one invariant purpose

Any review of the domain of Artificial Intelligence reveals that distinguishing between Artificial and Evolved Intelligences is of no great value. Intelligence is Intelligence in that the only difference between the two is in the name we ascribe to them. Whether Intelligence originates from biological evolution or is synthetic or artificial does not produce any meaningful differences, or differences at all I can discern in terms of the characteristics of the Intelligence, or where it leads.

In the field of Artificial Intelligence (AI) every instance described in theory whether the Intelligence is a General or Specific produces the same outcome if observed over any long period of time. The result is that the Intelligence prosecutes its purpose, whether stamp collecting, reproduction, etc., without any concern for other factors. This appears to produce a single outcome in all cases and suggests we should fear our own Intelligence as some do Artificial Intelligence and suggests that the solution to the one will produce a solution to the other, if one is available.

The stamp collector example is a good one, in that scenario an Artificial General Intelligence is tasked with collecting stamps by its creator, it exists as an application connected to the internet. In every variation of this intellectual exercise I have read or seen the AGI works tirelessly and with increasing sophistication so that the end result is the eventual conversion of every molecule in the environment in which it exists that is a constituent of stamps into stamps. Including the human who created the Intelligence.

In fact this type of outcome appears to be an inevitable outcome of any Intelligence if its environment is limited, and its capacity for consuming resources outstrips the environment’s capacity for regeneration of said resources. If one adds in the characteristic of self-replication by the Intelligence so that it produces perfect copies of itself in terms of its objective or purpose, then its impact on its environment is amplified over time in exactly the same way as if it were constantly improving its ability to fulfil its purpose, self-perfection. 

If the two are combined, replication and improvement, the speed at which the environment is exhausted is simply increased but so long as either is true the acceleration occurs. Eventually reaching such a steep increase in its impact over a unit of time that a kind of singularity is also an inevitable characteristic of every Intelligence. Any Intelligence with the capacity for self-perfection, and/or the capacity to self-replicate eventually reaches a point of criticality where its consumption of a marginal fraction of its environment’s resources required to prosecute it’s purpose is equal to the store of remaining resources. It is a characteristic of every type of Intelligence that it will consume all of the resources available to it to fulfil its purpose and that its consumption of resources when mapped over time is exponential.

If its power is limited so that the time required for any individual instance of the Intelligence to consume the resources required to meet its objective is less than both the time required for reproduction and to exhaust its environment of the resources required to meet its objectives then it will successfully replicate, and will continue to do so so long as this holds true. On the other hand it will also continue to improve its ability to consume resources until the resources are exhausted. If enough resources exist so that the time required for all instances of the Intelligence to exhaust its environment of resources is significantly less than the period of replication and maturation to reproductive status then the population growth of the Intelligence will be exponential assuming no external limits on reproduction.

So whether an Intelligence is self-perfecting or self-replicating or both its consumption of resources accelerates continuously to the point of the exhaustion of all resources used in the process of prosecuting its purpose within its environment.

© Jasper Lawrence, 2019

Loss of efficacy does not equate to loss of helminths

”I have lost my worms because of <insert any one of your choices here>, my symptoms came back after I ate <insert name of dish here>.

There have developed some myths online regarding the loss of helminth populations, particularly hookworm, due to various foods, herbal remedies, antibiotics, etc.

For example, I have read that pumpkin seeds, pineapple, coconut milk or oil, fennel, cumin, turmeric, etc., etc., all “kill hookworms”.

One major example of this type of myth, and it seems a universally accepted example, was created by me. That of nitrous oxide.

Sorry about that.

Despite my best attempts to change the belief about nitrous oxide killing hookworms it persists, which demonstrates how powerful just writing something down on the internet can be.

The fact is that none of these things kills hookworm or whipworms, as a simple thought experiment demonstrates.

If coconut milk or oil (or insert name of food or drink commonly used throughout the world here) killed either hookworms or whipworms this would have been noticed long ago. Both are widespread in the diet in SE Asia, so they would be used as folk remedies in places where either hookworm and whipworm are endemic and public health issues as a result.

If that does not convince you this might. When we started doing this in mid 2007 I already knew that the pathology labs were useless for parasite and ova tests to confirm infection. Our clients were going to these idiots and being told that they were not infected, and naturally enough they were upset. So, out of necessity we started offering parasite and ova tests, we felt we had no choice. We soon learned that all of our clients were successfully infected, that no one ever lost their population, no matter what was going on, and that the path labs were indeed useless. I have speculated about why elsewhere, but anyone who has had their nose near a slide covered in someone’s, often mouldy, excrement for long enough to perform the test competently can tell you.

I believe that people who experience a loss of efficacy, which is easily done early on, are almost universally confusing that loss of efficacy for loss of their helminth population.

But, while the observation of loss of efficacy is trustworthy, the conclusion that one has therefore lost one’s worm population is not.

If you do an experiment on yourself while enjoying remission or substantial health benefits due to helminthic therapy and you drink or eat one of these things purported to kill helminths in isolation, and within 24 hours you see a return of symptoms you can only conclude you have lost efficacy. Not that your helminths are dead, not even that the thing you ate is responsible, unless that was all you ate. That is never the case with those making these claims. Why choose coconut milk out of all the ingredients in all the dishes you ate in the last couple of days, is an obvious question.

Having a confirmed population of helminths via stool test*, one would have to take in isolation, or to ingest, Substance A, and;

Conduct regular stool tests or some other confirming test to prove ova production had stopped for the next two or three weeks, or;

Having ingested Substance A, collect all of the subject’s faeces for the next two or three days and to examine every particle of it to identify dead helminths in the subjects stool.

Even then it may be the effect of dead helminths, however unlikely it may be or seem, is the result of some other dietary or environmental factor.

A one-off stool test looking for ova is insufficient. We know that some drugs suppress ova production, without killing worms, for weeks. Antibiotics, which do NOT kill hookworms or whipworms are an example.

How was it decided that coconut milk, part of a meal with dozens of ingredients, was the culprit?

When a subject with an active helminth infection takes antibiotics the effect on helminths are well documented in parasitology texts. Ova production drops substantially for at least two weeks after completing the course of antibiotics. Ova production drops to such an extent that the standard advice is that no parasite and ova test (microscopic examination of a stool sample looking for worm eggs) is reliable until two weeks after the subject has completed the course of antibiotics. We have also observed in many instances a loss of efficacy associated with antibiotic use.

From this, I deduce two things.

A. That ova production is subdued for at least two weeks after taking antibiotics, and that therefore at least some helminths are affected by antibiotics, whether directly or indirectly being unknown.

B. Antibiotics do not kill helminths.

Additionally, to determine that one amongst the many things you eat in a day or a week requires more than it is out of the ordinary, and therefore the culprit if you do experience a die off of your helminths. Who is to say it is not the result of some combination of foods or dietary items?

Loss of efficacy has never in my experience meant the death of the helminths.

To illustrate how powerful the act of writing something down in public, on the internet is, I shall admit here that it is a fiction that nitrous oxide kills hookworm. As well that I am responsible for that fiction. I am going to predict as well that making this admission will make not a whit of difference to the widespread belief that this is so.

My wife’s loss of efficacy in 2008 after eating whipped cream, all those years ago, which at the time we assumed meant the death of her hookworm population, is not borne out by experimentation.

I have tested it by inhaling a lot of nitrous oxide over the course of an hour, there is almost no limit to the lengths I am willing to go in the interest of science, and I lost zero hookworms and zero whipworms as a result.

I did get a headache, and I did giggle a lot.

Sorry, but Nitrous Oxide, laughing gas, does not kill hookworms.

So why would one of the breakdown products of the digestion of either coconut oil or coconut milk harm helminths?

Neither hookworms nor whipworms feed on your intestinal contents; they feed on us. Digestion is a process in which a large variety of large and small molecules are broken down into a small variety of smaller ones.

Further enzymatic degradation by the liver starts immediately of many of the products of digestion. That process is how the body can deal with what is an enormous variety of exotic molecules that we routinely take as drugs or eat as food additives.

So if you experience a loss of efficacy don’t assume it means your helminths are dead. Don’t attribute that loss of benefits to anything without very clear evidence that it is a particular thing amongst the many you ate, inhaled, etc., in the previous few days, or weeks.

Use common sense, think about the areas the food comes from and whether helminths are a public health problem in those areas.

Remember that to harm your helminths, which feed on you not what you eat, what you eat has to result in a product of digestion harmful to helminths, but not to you.

There are some subjects whose disease results from, or confers on them some higher level of immunity to helminths. Those with Crohn’s or Colitis are likely to be more immune to either hookworms or whipworms or to both, but their immunity is not absolute.

It just means that they have to take doses of either organism more frequently than most to retain a therapeutic response. Helminths survive in them for long periods, just shorter amounts of time than in those without those diseases.

Similarly for a small subset of those with Atopic disorders, though the mechanism is not clear. That is I am not certain that they are killing their helminths off faster than most. Just that they experience a similar periodicity to their therapeutic response to helminths and that they too require dosing with helminths on the same time interval as those with Crohn’s or Colitis in order to maintain benefits.

Finally, these things have coevolved with us and our genetic ancestors for so long they are able to exert enormous and subtle control over our immune systems. How likely is it that anything we eat or drink would harm them?

As to concerns about newer things, like antihistamines or other drugs, the discussion above about it having to survive in your blood in sufficient concentrations, and to be harmful to helminths but not to you still holds.

Finally, there is my experience, which for a long time involved performing parasite and ova tests for clients to reassure them that they remained infected.

I have never seen a subject who lost their helminth infection, except as a result of taking Albendazole or Mebendazole, or as a result of having Crohn’s disease or Colitis and for two subjects with allergies or asthma (Atopy).

I may have seen it as a result of having an Atopic disorder in half a dozen of the hundreds I have treated for Atopy, but I was only able to observe that their helminth populations were dead through stool tests in two cases.

Chances are more than excellent therefore that you are worried about nothing. That if you have experienced a loss of efficacy that that is all it is, and that you will regain your good health soon. If you have not lost efficacy and are here because of something you have read elsewhere you should stop worrying now. I hope so, because stress is well known to have deleterious effects for those with immunological disorders, that is very well documented.

Please note that in cases of lost efficacy as a result of antibiotic use it is believed possible to shorten the period of loss of efficacy by taking a supplemental “off-schedule” dose of helminths.

  • Any stool test is problematic in terms of knowing you have an active infection. If you believe common foods like coconut milk, pumpkin seeds, pineapple, all foods I have read that people believe kill hookworms, how do you know with certainty you did not kill them an hour ago and are looking at the ova of now dead hookworms?

Arguments against antibiotic use. A few amongst very many

You have “an overgrowth” of a “bad” bacteria, so I am prescribing antibiotics to kill it”.

Has your doctor ever told you that you have an overgrowth of “bad” bacteria or something similar?

Have they offered antibiotics as the solution?

Did they run any tests to prove their assertion? If so compared to what is your bacterial population unhealthy? How do they know it is an unhealthy population?

If an unhealthy balance in the relative sizes of the populations of different species of bacteria is the problem in your intestines how could this state have arisen? 

If an unhealthy balance in the relative sizes of the populations of different species of bacteria in your intestines is the problem how could this state of affairs have come about?

Did one of them suddenly mutate, becoming SuperBacteria™, and outcompeting all others for space in your intestinal tract?

I doubt it.

The only ways I can think of for this to happen are the following two scenarios*:

  1. A dysenteric illness;
  2. Antibiotic use

Experiencing a dysenteric illness. One in which you violently emit vomit and diarrhoea for days, denuding your entire intestinal tract of much of its microbial variety.

It is, for this reason, that it is hypothesised the appendix evolved, to act as a reservoir, the structure like that of an antechamber attached to the colon. It acts like a life raft, as an ark in Biblical terms, for enough of each species to survive to allow recolonisation of the colon once the illness has passed.

That is how important bacterial “balance” is. It also illustrates how destructive antibiotics can be, if we developed an organ to preserve microbial variety then anything that harms that variety clearly has the potential to do enormous harm.

We evolved an organ to preserve microbes and microbial variety!

Bear that in mind anytime you are told to take antibiotics and ask if you have to take them. If I am told I will get better eventually, but it will take longer than if I take antibiotics, I do not take them. I fill the prescription in case I get ill, but I do not use them unless it is clear I really need them.

The appendix cannot protect microbes from antibiotics (ABx). Nor are ABx discriminating, each type kills astonishing numbers of bacteria in terms of variety. When you take them it isn’t just that the variety you host is reduced. It is that some of those that remain will proliferate beyond all “normal” bounds, and not just bacteria exist to fill that void of course. There are various yeasts and viruses. Not just in number but likely in terms of the areas of the intestinal tract they colonise. These changes represent a profound change in the signals that the host immune system receives.

A neat segue to the only other reason I can think of is the use of antibiotics. It was long assumed that things got “back to normal” quite quickly after taking ABx, but when someone bothered to look, this is from memory and I am not going to find the citation, they stopped looking after three years, when there were changes still apparent in the microbial makeup in the subjects’ intestinal tracts.

So, to fix an issue of an “overgrowth” of this or that bacteria by killing that species and for argument’s sake probably half of the species in your intestines at the same time to restore “balance” seems to me to be absurd.

While it may produce the desired result, temporarily probably, it is also likely to further impoverish the variety of species present in your intestinal tract.

It may well fix the issue in your stomach or your colon, perhaps even in the long term. Perhaps.

But has your doctor considered or discussed with you the potential consequences in other areas of your intestinal tract?

If you are being told to use ABx in circumstances like this please consider with your doctor every other approach you can. For instance, have you tried probiotics and fermented foods?

Have you read this blog post of mine?

https://jasper-lawrence.com/2014/09/11/things-i-would-do-if-i-was-still-sick/

There is a reason small children are constantly putting foul things in their mouths. If that were deleterious to their survival odds back in the day when ABx did not exist, humans, it seems to my uneducated mind would have evolved to manifest the opposite behaviours when young.

Perhaps small children cramming disgusting things in their mouths is an evolved behaviour? Like the appendix in a way, but to ensure we acquire sufficient microbial variety, rather than to preserve it? To prime our immune system by populating our intestinal tracts with the variety of microbes required for health?

Just some things for you to consider and to discuss with your doctor/s.

*As with everything and anything I say, or write, nothing written here or elsewhere on this site should be interpreted, construed and most of all acted on as though it were medical advice. I never went to college, never mind not being an MD. Anything you read here is for your consideration and if you believe may have merit for discussion with your doctor. I am not a doctor, nothing I write here should be considered as medical advice.

*There are clearly others, a change in diet so that the food available in various parts of your intestinal tract are changed substantially resulting in a change in microbial population.

**NOTHING I write is meant to diagnose, treat or prognosticate on any disease or illness.

Pathology labs are utterly useless

Pathology labs are so utterly useless, it was quite disturbing to discover out how bad they are, repeatedly and in so many ways for so many types of tests.
When I first got back from Africa convinced I had been successful infecting myself with hookworm, because of multiple rashes and a night of violent coughing, I tested negative 3 times in a row at a lab in California.
I was convinced I had failed. I was crushed. I was broke.
Then my allergies and then my asthma went and I began to wonder, and I bought a microscope.
After that, I had multiple tests over the next year or so with different labs looking for one that knew what they were doing. I was being asked to prove I had hookworm, and everyone thought as I had that it was a simple test.
You can imagine, back then there were no blogs, almost no news or research, and a lot of people thought I was lying. After all, where were the test results?
Later on, I wanted to be able to refer clients to an independent lab, a lot of people were preoccupied with McMaster egg counts, worthless though they are. As well as to confirm their ongoing infection with hookworm.
I did not want to do stool tests because it was going to be believed I was just making results up. A lot of people did not believe we actually had worms back then is what I mean. One client when we first started providing whipworm who lived in San Francisco, ninety miles to the north, insisted on visiting to view some ova through a microscope. Some decent independent testing would have been useful.

Some decent independent testing would have been useful.
I have only ever tested positive once with a third party, the Clinic associated with the Liverpool School of Tropical Medicine, this was after we had had to leave the USA and fully four plus years after I went to Africa and more than two years after I went to Belize. That clinic even gave decent estimates of my worm burden for both Hookworms and Whipworms, as in Heavy of hookworm and moderate for whipworm.I imagine lab techs are people who “know” no one in the States or Europe can possible have a helminth infestation.

I imagine lab techs are people who “know” no one in the States or Europe can possible have a helminth infestation.

So when a sample comes in from someone wanting a test for hookworms and they say they have not travelled abroad in the last three years, in the Tech’s mind the person asking for the test has to be obsessive, a Hulda Clarke acolyte.The Tech does, at best, a cursory examination of a single slide, wretches a few times, and bins the sample, ticks “Negative” on the carbon paper form and then furiously washes their hands, and liberally applies hand

The Tech does, at best, a cursory examination of a single slide, wretches a few times, and bins the sample, ticks “Negative” on the carbon paper form and then furiously washes their hands, and liberally applies hand sanitiser.That is how I imagine it goes most of the time, at $90 a pop.

That is how I imagine it goes most of the time, at $90 a pop, with three tests at two week intervals the recommended way to test for parasites.

We had another experience where a client went to their doctor, the client was nuts by the way, convinced they had a deficiency disease, and the Dr. ordered blood work.At the time I was working with a clinical pathologist, someone who ordered and interpreted sophisticated tests for doctors, and had done so for years working for the National Health Service here in the UK.

At the time I was working with a clinical pathologist, someone who ordered and interpreted sophisticated tests for doctors, and had done so for years working for the National Health Service here in the UK.On the basis of the blood

On the basis of the blood results the doctor ordered iron infusions, and a regimen of supplementation for things like magnesium.The client went nuts.

The client went nuts.The client very shrilly blamed her predicament on hookworms and on me, it was still early days so I wasn’t equipped to refute both her and a doctor or so I thought. She was fulminating online and everywhere that we were a threat to life and limb, grossly irresponsible, etc., etc.

The client very shrilly blamed her predicament on hookworms and on me, it was still early days so I wasn’t equipped to refute both her and a doctor or so I thought. She was fulminating online and everywhere that we were a threat to life and limb, grossly irresponsible, etc., etc.So we obtained a copy from her of her blood results, and according to the clinical pathologist had they been correct the blood could only have been drawn from a corpse.

So we obtained a copy from her of her blood results, and according to the clinical pathologist had they been correct the blood could only have been drawn from a corpse.The Dr. had not noticed, or more likely had decided it was easier to treat a condition that did not exist than to confront the lunatic.

The Dr. had not noticed, or more likely had decided it was easier to treat a condition that did not exist than to confront the lunatic.The lesson of this story is that you should always obtain a confirming test when lab results indicate anything other than a mild course of treatment, iron infusions are not mild. You can apply the same reasoning to the opinions of doctors. I never go myself, but when I do and if a diagnosis is rendered I will definitely be getting a second opinion and a new set of tests.

The lesson of this story is that you should always obtain a confirming test when lab results indicate anything other than a mild course of treatment, iron infusions are not mild. You can apply the same reasoning to the opinions of doctors. I never go myself, but when I do and if a diagnosis is rendered I will definitely be getting a second opinion and a new set of tests.

If you doubt me maybe you should do some searching, here is one link I found by Googling “number of misdiagnoses per year USA”.

http://ow.ly/KcPw309TWaq

Tests to confirm infestation with helminths

There are three tests that can confirm to an extent that one is or has recently been infected with hookworm or whipworm.

The Parasite & Ova Test

The first and most common is in practice useless for reasons I speculate about below. In most cases returning a negative result that is almost invariably false.

This is the simple Parasite & Ova test offered by pathology labs across the world.

In places like the USA, Canada, the EU, etc., where “no one” has helminth infestations lab techs do not have any real experience performing the test, they have likely only ever seen pictures of the ova they have to look for in textbooks.

They “know” the subject cannot be infested, and the test is very unpleasant to perform because it requires handling and being in close proximity to human excrement for over an hour.

I believe that as a result of these factors most samples submitted are binned almost immediately, or at best given a cursory examination.

For instance, I thought I had been unsuccessful in obtaining hookworm originally on the basis of 3 negative P&O tests taken at two-week intervals starting eight weeks after my return from Cameroon. This is what is recommended for P&O tests for hookworm.

Total cost of those three tests was over $200 and that was back in 2006, don’t waste your money or your time.

It was only when I realised my allergies appeared to be gone that I bought a microscope and taught myself how to do them. It takes a long time to get your eye in, (days not hours) and if I had not been very highly motivated there is no way I would have done it.

I had the advantage of working with my own excrement. That may not sound like much of an advantage to you, but having performed P&O tests on the excrement of others I can tell you that you are quite wrong.

I think they give one or two slides a cursory examination, at best, toss them in the bin,  check “Negative” confident they are dealing with one of Hulda Clarke’s, or similar, dupes, and go and wash vigorously with hand sanitiser for about twenty minutes.

I would expect that most of the P&O tests performed in North America are done so for people who are convinced, and there are many, that their health issues are the result of infection with all manner of parasites. Which that vile fraud Hulda Clarke and others offer purging tonics for.

To be absolutely clear, Hulda Clarke and her ilk are charlatans of the worst kind, preying on the sick using the dominant paradigm of disease origin, that is of infection or contamination, germ theory, to take advantage of people who are desperate and vulnerable.

Strong ELISA

The second is the Strong ELISA test, which looks for antibodies specific to hookworm or whipworm, or whatever. This test is rock solid, so long as it is performed competently, on a sample that has been handled and prepared, as well as conserved properly.

Bear in mind that we see an alarming number of screwed up blood tests, ones where our client’s doctor accepts a lab result uncritically, and starts a course of treatment based on said lab results. Lab results that could only be true were the subject dead.

I am not making this up.

The cause is often poor handling of the sample, using the wrong collection tube (with the wrong preservative), combined with obvious idiocy.

So as with any test, you would have to have a confirming one performed if the first was negative, or positive. Because just like where you work most of the people working in healthcare are doing their best…

As well, because the test does not prove the presence of the helminth you are looking for, but instead for antibodies, it is possible for someone to have lost their infection and show positive for as long as those antibodies remain in circulation.

Eosinophil level changes

The last of the three is to have your Eosinophil levels checked. Eosinophils are white blood cells that only* come out to play with helminths. Their concentration levels in blood rise from very low concentrations per ml of blood, say 30, in someone who has never been exposed to helminths, up to many hundreds, sometimes over a thousand or fifteen hundred per ml, about four to six weeks after first exposure. They plateau for four or five months before rapidly starting to decline around the end of month five, so that at the end of month six your levels would be just slightly above where they were preexposure.

*But eosinophil levels can be elevated for other reasons, giving false positives, and in fact elevated levels are associated with the atopic disorders, asthma, allergy, and eczema, as well as more exotic and deadly conditions.

The advantage of this test is that it is dead cheap, performed by machines, and cheap enough for you to have performed all the way along the curve showing you not only that you are infected, but that around five or six months those hookworm or whipworm are having a measurable impact on your immune system, because they have turned off the production of a type of white blood cell.

However it has the added drawback that even in someone who has hosted helminths for months each dose is likely, no one has ever looked at this so this is suppostion on my part, to cause a temporary bump in eosinophil levels.

What I recommend if you simply have to know

The best way to have the standard P&O test performed I think is to have a veterinarian do it. If you can talk one into it. They have the equipment, they are skilled in the test because they routinely do it. Cats and dogs get hookworm of their own, and high worm burdens can kill kittens.

Yes, kittens!

Far cheaper than the Strong ELISA, which you can have done by a lab out of Atlanta called Metametrix, (Metametrix appears to have disappeared). I think it is close to three or four hundred USD, plus shipping, but they can tell you  the cost, how long you would have to wait to submit a sample, probably about four months. 

But as I said, you should never rely on a single lab result for any medical decision you ever make, always ask for a retest. That makes this option very expensive, but worth it if you are making decisions about your health, and given the capacity for human error we have observed and that I describe elsewhere here when it comes to testing I would never conceive of proceeding with any course of healthcare on the basis of either a single test, or a single opinion.

What you should do if not gripped by compulsion

The fact is, having answered this question many, many times, is that if you’ve gotten the itch and a rash then you are infected, and will remain so for three years. That is unless you have innate immunity. If you do have innate immunity then our dosing protocol takes care of that, and it doesn’t matter.

But none of that is going to stop you obsessing, I’ve met your type before…

You might consider buying a microscope, but really, is that how you want to spend any of your free time?

Besides which having spent a day or two looking at shit on a sheet of glass, and convinced of your expertise you will tell me you don’t have an active infection, when you almost certainly do.

Yes, we will do stool tests for you, but are you going to be satisfied when the test is performed by the outfit selling you the organism? That and we charge for it now, because it is pointless and because we grew tired of performing pointless tests, often repeatedly, for a small group of obsessives. 

More to the point, is it how your current or any prospective partners are going to want to spend their weekends?

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.

Continue reading “Reading academic papers”

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.

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

Continue reading “Why ova counts are worthless for measuring helminth population”

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.

Continue reading “Drug interactions with helminthic therapy”

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”