Friday, December 30, 2011

Cytomegalovirus (CMV / HHV-5) involved in high blood pressure?

Originally carrying out an investigation into the gene regulatory microRNA (miRNA) expression differences between Chinese patients with and without high blood pressure, the researchers soon discovered an obvious sign of HCMV infection in the form of a virally encoded miRNA.

Quantitatively determining the miRNA levels in blood samples, many miRNAs were up or down regulated but the group focused in on one in particular: hcmv-miR-UL112 - derived from HCMV that was shown to be highly expressed in those suffering from primary hypertension. These expression differences were thought to be down to endothelial cells within the blood sample, termed circulating endothelial cells. HCMV seropositivity as well as higher amounts of viral DNA, in general, was seen to be correlated with the high blood pressure group, especially when other factors were considered. This correlation was not seen with other common human viruses (Epstein-Barr and adenoviruses) suggesting a certain specificity.
Remember: That is only a possible correlation, not a definitive causative link.

Wednesday, December 28, 2011

Scientific process: Useless treatments found to be useless

As Tsouderos notes, complementary and alternative therapies are a $34 billion industry and 40% of U.S. adults report using some kind of alternative remedy in the last year. Wouldn't it make sense to study these remedies, given that they're being used so widely? For all we know, some of them are dangerous. Besides, even debunking useless claims would be a service to consumers. The problem is that NCCAM exists to validate alternative medicine, not to assess it critically.

NCCAM is a political oasis for research that could not compete in mainstream science. Sen. Tom Harkin (D-IA), one of the fathers of NCCAM, gave the game away when he lamented during a 2009 senate hearing that the center was disproving too many alternative therapies. "One of the purposes of this center was to investigate and validate alternative approaches. Quite frankly, I must say publicly that it has fallen short," Harkin said. If Harkin were interested in applying science to CAM, as opposed to confirming his bias towards complementary remedies, he would be happy that useless treatments were found to be useless.
Which reminds me of the study of the "Mikovits-XMRV-test".

Tuesday, December 27, 2011

The Problems with the Lombardi et al 2009 Science paper

Some of the problems of the Lombardi et al. 2009 Science paper, many of which should have been addressed prior to publication.

- Failure to state if samples were tested in a blinded fashion
- Failure to state the reason that not all tests were done on all samples
- Failure to sufficiently describe each employed test method
- Mislabeling of at least one slide
- Omission of the usage of 5AZA
- Failure to publish full viral gene-sequences
- Failure to show genetic variation expected of a retroviral pathogen vs. contamination
- Failure to show integration into the human genome

Plus Mikovits communicated tidbits about the study on her talks, instead of publishing them.

Furthermore I would add these points:
- Failure to explain the rational to use nested PCR
- Failure to account for higher risk of contamination with nested PCR the way PCR was used

- Usage of water only negative control samples
- Failure to report the use of positive control samples
- Failure to discuss the PCR sensitivity

- again: Failure to report the use of positive control samples
- Failure to show control results of PCR without reverse transcriptase (RT) for detection of DNA (plasmid) contamination

- Failure to supply a all test results for each sample (patients and controls)

- The main result (67% PCR positive) is shown in one (!) sentence, without any supporting material

Monday, December 26, 2011

XMRV is not a human pathogen

Our attempts, through collaborations, to demonstrate antibody in affected patients, to isolate the virus by culture, or to show integration sites in the human genome have failed to support the initial findings.
XMRV as a human pathogen is dead as doornail. I repeat: XMRV does not cause ME/CFS. "Fresh dispute about MMR 'fraud'"

Bjarnason says he doesn't believe they are sufficient to support claims in the Lancet paper of a new disease process. He also questions whether "non-specific" on the grading sheets refers to colitis, saying it could refer to any kind of gut changes. But he says that the forms don't clearly support charges that Wakefield deliberately misinterpreted the records. "The data are subjective. It's different to say it's deliberate falsification," he says.
I think Andrew Wakefield is a quack, but even he deserved a fair trial – with less foaming accusations and more scientific inquiry. Or did Bruno Bettelheim ever get the Wakefield treatment?

Friday, December 23, 2011

On CBT and GET

The CBT that is a defacto mandatory therapy for UK ME/CFS patients that want continuing medical care and at least limited disability benefits is nothing like coaching in my understanding. The behavioral therapy you describe could certainly be of use to ME/CFS patients that almost universally need to come to grips with new energy limitations and acquire time management skills to marshal their energies and survive. That is not what is being offered.

Instead, patients are subjected to therapy methods that are at best dishonest, and in the worse case coercive and stressful. It can be even physically harmful if combined with GET therapy. The CBT for UK patients has its roots in "reparative therapy", as I mentioned upstream in this thread.

In reparative therapy, the operant reality construct is that gay patients are mentally ill and need to be repaired by "conditioning" methods. In CBT for CFS patients, the operant reality is that CFS patients are mentally ill and have "deconditioned" themselves. They need to be repaired by "conditioning" methods. If you add coercion in the form of Christian "guilting" of a homosexual patient, or the withholding of care and benefits in the case of CFS, then it is not helpful to the patients in the long view of things.

Sadly, the powers that be and vested interests in the UK have chosen to devote almost all available funding to CBT and GET therapies in the context of ME/CFS treatment and research efforts. It is the only game in town.

I have been banned from the mecfsforums :-)

Sorry Guest, you are banned from using this forum!
This ban is not set to expire.
I'm being silenced! I'm a martyr! :-)

Phew. Thank Darwin I am banned from using that XMRV/HGRV Dooms-Day cult forum.

And Jamie is censoring my comments too – must be the season.

2009 Science paper about XMRV retracted

Alberts says the Blood Working Group finding was the final straw that led Science to request the full retraction. "The blood group study to me was dramatic evidence of poor science," says Alberts. "It gave us absolutely no confidence in the ability of the major labs involved to do the assays. I find that enormously disturbing." NCI's Francis Ruscetti, a prominent retrovirologist and one of the co-authors, attempted to coordinate a retraction with his colleagues but a dispute arose over wording that suggested some of the findings in the original paper were still valid. "We tried to get all of the authors to agree, but it got endless," says Alberts. "The responsibility that Science magazine has to the scientific community is to make a strong statement that we don't think anything in that paper can be relied on."

Tuesday, December 20, 2011

How endogenous retroviruses fuck up the immune-system

The endogenous guys are also berry sneaky. While they are no longer completely functional they still can transcribe-->translate a superantigen. Its a viral protein, but because it is expressed before the immune system matures, the immune system recognizes the viral protein as 'self.' That means that all the T-cells that would kill an MMTV infected cell are killed, like all T-cells that recognize 'self' proteins. Mice basically lose an arm of their immune system.

Remember the classes of T-Cell Receptors I was talking about with the possums? Endogenous MMTVs (and the infection of pups before their immune system matures) can cause the loss of all T-cells that have certain Variable Beta chains. This deletion increase the mouses susceptibility to new MMTV infections, and also increases susceptibility to other pathogens, like cholera. Yup-- A virus screwing around with how well you can fight off bacteria.

Sunday, December 18, 2011

Lactose intolerance: More common than you think

The problems seemed ‘sporadic’ but frequent. His doctors never suggested lactose intolerance. We could have done a food elimination test, but that was time consuming and very inconvenient. In hindsight we should have done the slog of eliminating foods from the diet…but you know what they say about hindsight? (Or at least the Phantom Tollbooth).
This is interesting, because I know several people who went through something similar. The vast majority of Northern Europeans are lactose tolerant, at least judging by phenotype and that particular SNP. But, at least ~5% are not. That’s not a small number in absolute terms, and even proportionally it is common enough that if you know 13 random Northern Europeans, there’s a 50% probability that at least one of them is lactose intolerant.

Note: There are other SNPs which likely confer lactose tolerance. And, it seems likely that environmental factors, such as adaptation of your gut flora, also matter in the final phenotype. 

Why exercise (partially) counteracts a crappy diet

Cadmium (Cd), tungsten (W), tellurium (Te), beryllium (Be), and lead (Pb), are non-essential metals pervasive in the human environment. Studies on athletes during training periods compared to non-training control subjects, indicate increased loss of minerals through sweat and urine. The aim of this study was to compare the level of these trace elements, determined by inductively coupled plasma mass spectrometry (ICP-MS) in urine samples, between athletes and age-matched sedentary subjects … With the exception of Pb, urine toxic metal concentrations from athletes were higher than from sedentary subjects. This fact suggests that physical activity counteracts, at least in part, the cumulative effect of toxic environment by increasing the urine excretion of toxic metals in trained people. (via)
And the increased metabolism through exercise should help burn up any harmful proteins. Of course, foremost not eating toxic stuff would be the order of the day.

Thursday, December 15, 2011

The XMRV mess will be sorted out

Drs. Judy Mikovits and Frank Ruscetti continue to be part of the Lipkin study.

“I have gone to great lengths to make sure they remain involved,” Lipkin said in a telephone interview.

Labs at the Whittemore Peterson Insititute will no longer be used in the Columbia University-based study since Mikovits’s split with the institute, Lipkin said. He instead has worked with Mikovits and Ruscetti to find a lab where they would be `comfortable’ working, he said. That lab has been found and there work has resumed, he said.


“[WPI] are no longer involved because the whole point was to have Mikovits try to reproduce her work, and having someone else at the institute do so wouldn’t address the questions,” Lipkin says. “It’s critical that she do the work. She doesn’t have a lab at present, so it’s going to be done at NCI.”
I really hope this will be the decisive "Yes or No" answer to the "XMRV/HGRV or Contamination" question. I trust Ian Lipkin to both be open and inquisitive while at the same time making sure the results stand up to scrutiny.

Tuesday, December 13, 2011

The Hammer Trap

I saw this quote in a Psychology today article recently (The right tool for the job). It’s not new of course, it’s one we’ve heard often. But as I reflect over my varied careers and life experiences, I realise how often I’ve fallen into the “hammer trap”, where a particular experience colours my world view profoundly.

It goes like this: Something I’ve tried – whether it be a diet (Zone, Paleo, low carb, raw vegan …, name yours) or some self improvement course, religion, inspirational book, peak experience, adventure, therapy, medication, sport, exercise.. you get the picture. This thing you experience – it changes your life in some way, in fact it makes it profound difference. Every issue / health problem you see others having – your recent discovery appears to you be the answer.

As a group of paleo nutrition, and often low carb advocates – we tend to view the world’s health / weight problems as though paleo / low carb is the answer to everything. E.g. low carb will fix everyone who is overweight, it’s even good for athletes once they get used to burning fat instead of carbs…

Bill Lands on Omega-3 fatty acids

A shorter excerpt on YouTube and the original at the NIH (action starts around minute 12).

Bill Lands hits all the right talking points, but by Darwin, he does an awful presentation…

Sunday, December 11, 2011

British Psychology Journal, home to paranormal psychics

Stuart Ritchie, a psychology doctoral student in Edinburgh, worked with two colleagues to try to replicate the results of a famous recent experiment, claiming people could predict in advance whether they were about to be shown erotic images. When the three failed to find any such evidence for ESP they sent their results out for publication, and the British Psychology Journal, one of the journals to which it was sent, in turn sent the trio's article out for review. When Ritchie et al got the responses back '...there were two reviews, one very positive, urging publication, and one quite negative. This latter review didn’t find any problems in our methodology or writeup itself, but suggested that, since the three of us (Richard Wiseman, Chris French and I) are all skeptical of ESP, we might have unconsciously influenced the results using our own psychic powers.'

Friday, December 9, 2011

What could possibly go wrong?

Gumming Up Appetite to Treat Obesity: Researchers plan to create chewing gum that sneaks an appetite-suppressing hormone through the gut and into the blood.
By the looks of it, "diseases of civilization"–  including obesity – are caused by evolutionary novel food which contain compounds encountered by humans only in recent evolutionary times. So let us battle the problem by introducing even more novel compounds. Science – fuck yeah!

"Just tell them you’ve had your leg in the Thames."

“If you see any red streaks, if you get any shooting pains in your leg, or anything feels wrong, come back immediately,” she advised, eyeing my bandage warily. “No one’s going to mind. Just tell them you’ve had your leg in the Thames.

I started doing some Google-based investigation. Just what was so bad about inviting some Thames water into my gaping, bleeding flesh? My findings led me to conclude that my leg was either about to shrivel up and fall off, or spontaneously sprout 8 smaller legs. Or eyes.

Thursday, December 8, 2011

Why raw food and cooked food have different calories

But the Atwater Convention has two big flaws. First, it pays no attention to the extent to which food has been processed. For example, it treats grain as the same calorie value whether it is eaten whole or as highly milled flour. But smaller particles are less work to digest, and therefore provide more net energy. Second, it treats foods as equally digestible (meaning, having the same proportion digested) regardless of processing. But cooked foods, as we’ve seen, are more digestible than raw foods.

These flaws matter. According to the Atwater Convention raw foods have equal calorie content to cooked foods. So people can be deluded into thinking that feeding their children on 100% raw foods is a healthy practice, whereas I believe it would be dangerous for them.

A challenge to all ME/CFS patients who think VP62 matters

To all people who keep on posting about VP62!

I challenge the person (all those anonymous VP62 posts seem the same to me) to provide me the following:
  1. The gene-sequence of XMRV/(P)MLV/"HGRV", as supplied from the Mikovits/WPI
  2. The primer/probe sequences, as supplied by the Mikovits/WPI
  3. The gene-sequence of VP62
  4. The primer/probe sequences which are supposed to be "calibrated" only to VP62
  5. A explanation (using the material above) why the primer/probes from (4) work only with regards to VP62 (3) – and why they can not work with XMRV (1).
As a bonus, explain why the primer/probe used by the WPI are better (or the only "true" ones to be used). And please explain how the "calibration" of the primer/probes to VP62 works.

Dr. Mikovits has supposedly worked with "HGRVs" for over two years, cultured them in the lab, categorically ruled out any form of contamination – so she should have lots and lots of data, which should have been published for other researchers to use.

Yet, somehow, I guess none of those anoymouses (in case there is more than one) who go on, and on, and on, and on, and on why VP62 matters, none will be able to provide this material. Prove me wrong.

[By the way, to all possible commenters: Post comments about VP62 here and only here. Any comments about VP62 on other posts will be deleted. You have been warned.]

Tuesday, December 6, 2011

One cause, different effects

If you have two faulty copies of this gene, your brain won't be normal, but what goes wrong varies widely amongst different people. Although the 9 cases had some features in common, such as microcephaly (small head and brain), in other respects they differed greatly.

As the authors put it, mutations in WDR62 cause
a wide spectrum of severe cerebral cortical malformations including microcephaly, pachygyria with cortical thickening as well as hypoplasia of the corpus callosum. Some patients... had evidence of additional abnormalities including lissencephaly, schizencephaly, polymicrogyria and, in one instance, cerebellar hypoplasia, all traits traditionally regarded as distinct entities.

These are distinct entities, in the sense that you can have any one of them, without having the others. And they are different brain changes. What the authors mean is that everyone assumed that, because they're different, they must have different genetic causes. They've just shown that this is wrong.

So what is WDR62 "for"? Experiments in mice showed it to be involved in the migration of new neurons from their origin to their final location in the brain. So it's "for" correct neuronal placement, although how it works remains unclear.

WDR62 ought to remind us that there's a long and winding road from gene to phenotype, and that the same gene can, when mutated, cause very different symptoms. This is especially interesting in the light of recent evidence showing that the same mutations can cause a range of behavioural disorders from autism to ADHD to schizophrenia.

Paleo for Multiple Sclerosis

Paleo-Zone Nutrition: Dr Terry Wahls reverses her own Multiple Sclerosis with hunter gatherer nutrition.

That Paleo Guy: Treating MS with a paleoesque diet.

Free The Animal: Don’t Listen to Me. Listen to Dr. Terry Wahls, Cured from Debilitating Multiple Sclerosis (MS) On a Paleo Diet

Study suggest Confirmation Bias is present in scientists

Like others with chronic fatigue syndrome, Dr. Schweitzer is used to having her illness ignored, mocked or treated as a manifestation of trauma, depression or hypochondria—not only by doctors, colleagues and strangers but by friends, family members and federal researchers, too. So when the U.S. Centers for Disease Control and Prevention reported last year that people with chronic fatigue syndrome are more likely to suffer from “maladaptive personality features”—in particular from “higher scores on neuroticism” and higher rates of “paranoid, schizoid, avoidant, obsessive-compulsive and depressive personality disorders”—Dr. Schweitzer dismissed the research as “incredibly stupid” but “not surprising.” In another recent study, the CDC had reported—also incredibly stupidly, from Dr. Schweitzer’s perspective–that childhood trauma, such as sexual or emotional abuse, was a “an important risk factor” for the illness.

Sunday, December 4, 2011

It's the environment, stupid!

Critics, on the other hand, have argued all along that both twin studies and family studies are unable to disentangle the potential roles of genes and environment. They have pointed out for decades that the validity of equal environment assumption (EEA) of the twin method is not supported by the evidence, and that the much more similar environments experienced by reared-together monozygotic (MZ) versus reared-together dizygotic (DZ) twin pairs confound the results of the twin method. Therefore, both family studies and twin studies prove nothing about genetics and their results can be completely explained by non-genetic factors. Most behavioral geneticists agree with this assessment as it relates to family studies, but continue to maintain that twin studies provide conclusive evidence that genes play an important role. Critics have also pointed to the massive methodological problems and untenable assumptions found in psychological and psychiatric adoption studies, as well as the major problems and environmental confounds in studies of purportedly reared-apart twins
In study after study, applying GWAs to every common (non-infectious) physical disease and mental disorder, the results have been remarkably consistent: only genes with very minor effects have been uncovered (summarised in Manolio et al 2009; Dermitzakis and Clark 2009). In other words, the genetic variation confidently expected by medical geneticists to explain common diseases, cannot be found.

There are, nevertheless, certain exceptions to this blanket statement. One group are the single gene, mostly rare, genetic disorders whose discovery predated GWA studies2. These include cystic fibrosis, sickle cell anaemia and Huntington’s disease. … With these exceptions duly noted, however, we can reiterate that according to the best available data, genetic predispositions (i.e. causes) have a negligible role in heart disease, cancer, stroke, autoimmune diseases, obesity, autism, Parkinson’s disease, depression, schizophrenia and many other common mental and physical illnesses that are the major killers in Western countries.

This dearth of disease-causing genes is without question a scientific discovery of tremendous significance. It is comparable in stature to the discovery of vaccination, of antibiotics, or of the nature of infectious diseases, because it tells us that most disease, most of the time, is essentially environmental in origin.
Firstly, in my view, common diseases can not have its origin in genetic problems. And secondly, who says that common diseases (chronic, with presumably gradual onset and/or gradual build-up, like e.g. type 2 diabetes) can't have a infectious origin? I think nutrition is far more likley to be the culprit, but hey.

In a rare public sign of the struggle to come to terms with this genetically impoverished world-view, the authors of a brief review in Science magazine, Andrew Clark of Cornell University and Emmanouil Dermitzakis of the University of Geneva Medical School, Switzerland have been alone in stating the case even partly straightforwardly. According to them, the GWA studies tell us that “the magnitude of genetic effects is uniformly very small” and therefore “common variants provide little help in predicting risk” (Dermitzakis and Clark 2009). Consequently, the likelihood that personalised genomics will ever predict the occurrence of common diseases is “bleak”. This aim, they believe, will have to be abandoned altogether.

The first conclusion to be drawn from these quotes is that such directness implies that if the GWA findings are not finding their way to the front page the reason is not ambiguity in the results themselves. From a scientific perspective the GWA results, though negative, are robust and clear.

Most human geneticists view the GWA results somewhat differently, however. An invited workshop, convened by Collins and others, discussed the then-accumulating results in February 2009. The most visible outcome of this workshop was a lengthy review published in Nature and titled: “Finding the Missing Heritability of Complex Diseases.” (Manolio et al. 2009).

For a review paper that does not lay out any new concepts or directions, 27 senior scientists as coauthors might be considered overkill. “Finding the Missing Heritability”, however, should be understood not so much as a scientific contribution but as an effort to conceal the gaping hole in the science of medical genetics.

In their Science article, which was published almost simultaneously, Dermitzakis and Clark paused only briefly to consider whether so many genes could have been overlooked. Apparently, they thought it an unlikely possibility. Manolio et al., however, frame this as the central issue. According to them, since heritability measurements suggest that genes for disease must exist, they must be hiding under some as-yet-unturned genetic rock. They list several possible hiding places: there may be very many genes with exceedingly small effects; genes for disease may be highly represented by rare variants with large effects; disease genes may have complex genetic architectures; or they may exist as gene Copy Number Variants (CNVs). Since Manolio et al. presented their list, the scientific literature has seen further suggestions for where disease genes might be hiding. These include in mitochondrial DNA, epigenetics and in statistical anomalies (e.g. Eichler et al. 2010; Petronis 2010).
It is sad to see scientists working in the field genetics have so little grasp of evolution that they fail to see the evolutionary interdependence of genes and environment...

Farming causes crowded and crooked teeth

Parents going broke to pay for their offspring’s braces and orthodontistry can finally blame somebody besides their mildly malformed children: our farmer ancestors. A study published this week in the Proceedings of the National Academy of Sciences found that people living in subsistence farming communities around the world have shorter, wider jaws than those in hunting and gathering societies. This leaves less room for teeth, which have changed little in size or abundance over human history—and may help explain why crooked choppers and a need for orthodontia are so common, study author Noreen von Cramon-Taubadel tells the BBC.
So is it a genetic trait, or is it the environmental factor (as in consumption of grains)? I would say the latter.
Previous studies have shown that differences in the length of jawbones seem to arise relatively quickly after a change in subsistence economy, suggesting the shift to a shorter jawbone in agricultural groups could reflect a selective pressure for downsizing.
Or it suggests that it is environmental (as in consumption of grains).
Changes in jawbone size can also arise within a single generation due to phenotypic plasticity, wherein environmental differences lead to anatomical changes. For example, a 2004 study found that the mandibles of hyraxes (a small rodent-like mammal) given soft, processed food grew to be 10 percent shorter than those fed a heartier unprocessed diet.
Or it could be that is the consumption of grains.
Perhaps one day this “mismatch” will correct itself. Until then, were stuck with braces.
Or we could try changing our diet and see if we are really "stuck" with this.

CDC versus the rest

Among U.S. scientists who work primarily on this disease, essentially no one argues for a psychosomatic cause. Nor do any researchers use the 2005 definition, besides the ones whose work is paid for by the CDC. Nevertheless, the agency has had a huge influence on the opinion of doctors and the general public, creating an attitude of skepticism and even condescension toward the disease. Rather than focusing on treatments, the majority of research has gone toward providing evidence, in one form or another, that patients had some kind of psychological problem long before they developed the syndrome.

Monday, November 21, 2011

Correlation is not Causation

Remember, correlation is not causation – but it offers a hint:

So butter consumption goes down, lard consumption goes down, death from heart disease goes up (and up goes consumption of margerine, shortening and salad oil, what a coincidence). So, when they blame "fat" for heart disease, do you think animal fats like butter and lard are to blame for heart disease? Really? Honestly? No? Yes?

Correlation is not causation (and not included is consumption of other forms of animal fat, which have gone down as far as I know), but blaming animal fat for heart disease? You fail science forever!


Friday, November 18, 2011

The problem of false positives

The problem of false positives

1. Authors must decide the rule for terminating data collection before data collection begins and report this rule in the article. …

2. Authors must collect at least 20 observations per cell or else provide a compelling cost-of-data-collection justification. …

3. Authors must list all variables collected in a study. …

4. Authors must report all experimental conditions, including failed manipulations. …

5. If observations are eliminated, authors must also report what the statistical results are if those observations are included. …

6. If an analysis includes a covariate, authors must report the statistical results of the analysis without the covariate. …
The Lombardi 2009 Science paper violated at least 1 (which matters) and probably 4 (which does not matter, as they were measuring a contamination lab artifact anyway...).

Thursday, November 17, 2011

When Science is marketed...

To achieve the 98 percent efficacy claim, Merck excluded from analysis anyone who “violated” the study protocol. In other words, all real-world problems that arose were excluded from analysis. Problems like girls who refused to take a second or third shot after they became sick and (correctly or incorrectly) blamed the vaccine. Or doctors who incorrectly gave the vaccine to someone who shouldn’t have received it. While it’s worth knowing how effective the vaccine is when it’s used exactly as it should be, for a public-health decision, it’s not as relevant as its real-world effectiveness.

To Merck’s credit, they reported that when all women in the study were analyzed, the vaccine’s efficacy dropped to 44 percent. Still, 44 percent might be considered a smashing success when you’re talking about saving lives. Except for one thing: the numbers get worse. The 44 percent benefit included only those women with the two specific cancer-causing HPV strains found in the vaccine. But when the researchers looked at negative cervical changes from any causes, they found that changes occurred in unvaccinated women at a rate of 1.5 events per 100 person-years, while vaccinated women had 1.3 events—dropping the benefit to 17 percent.

Moreover, most of the cervical changes tracked by the researchers weren’t even indicative of cervical cancer in the first place. Most were innocent cellular abnormalities that either disappear entirely on their own, or never progress to cancer. In fact, when they looked more closely at advanced cervical changes most likely to progress to cancer versus more innocent changes that go away spontaneously, it was the innocent changes that accounted for the decline.

Whether Gardasil will reduce cervical cancer deaths in real-world conditions has simply never been answered. It might—but that would take a long-term study, and one that should be done before it’s widely promoted.

So how did the HPV vaccine become a multi-billion-dollar winner for Merck? Well you might not be surprised to hear that the company happily lavished money on doctors, professional societies, and over 100 legislators. Of course, there is no tie between the recipients of this largesse and their promotion of the vaccine, say beneficiaries like presidential candidate and current Texas governor Rick Perry. In 2007, Perry signed an executive decree mandating that all girls in Texas receive the vaccine. The $28,500 Perry received was minor compared to his other connection to Merck: Perry’s chief of staff, Mike Toomey, became a lobbyist for Merck, championing the HPV vaccine. Once in that position, announced his plans to raise over $50 million for Perry’s presidential campaign.

Wednesday, November 16, 2011

Confirmation Bias or Religious Delusion?

Tension between Dr. Mikovits and the institute’s president was apparently brewing for months. One point of contest had to do with Mikovits' lack of faith in the WPI's commercial laboratory's ability to provide accurate tests for XMRV. Vincent Lombardi headed the commercial lab, formerly called VIPdx and more recently renamed Unevx. The lab initially was owned by the Whittemores and other investors, but in a press release, WPI spokeswoman Frankie Vigil wrote eventually, "the Whittemore family put their interest in VIP Dx into a trust to benefit WPI." More recently, a Unevx website said the lab is a "wholly owned entity of the Whittemore Peterson Institute (WPI)." Beginning in late 2009, the lab began selling tests for XMRV infection to patients. Mikovits' concern was extreme after long-awaited results became available last spring from the government and private consortium known as the Blood Working Group, which indicated that tests for the virus were unreliable. Mikovits urged the WPI president to shutter the institute's commercial lab.
So Mikovits "knew" at least since spring that the VIPdx/Lombardi results were not trustworthy*). She hasn't spoken out publicly since that these test were null and void, as far as I know. She keeps on claiming that "XMRV" is a human pathogen ("HGRV", "Human gamma retro virus"). With this implication we still have patients running around posting bullshit about "HGRV".

For some patients, it is only the work of Judy Mikovits that is supposedly trustworthy, all others are basically said to be lying (The WPI, Lombardi, VIPdx, Lipkin, etc.). That leaves us with only Judy, who is supposed to have the "one truth", some heretics like the WPI (who still "believe" in XMRV, but "somehow got it wrong") and all the "non-believers". Religious delusion like this is built on uncritical confirmation bias.

*) The 2009 XMRV Science paper was authored by Lombardi, which should make it null and void in the eyes of the Saint-Mikovits-Religous-Zealots.

Sunday, November 13, 2011

Evidence based medicine vs. observational data

Parachute use to prevent death and major trauma related to gravitational challenge: systematic review of randomised controlled trials

Objectives To determine whether parachutes are effective in preventing major trauma related to gravitational challenge.

Design Systematic review of randomised controlled trials.

Data sources: Medline, Web of Science, Embase, and the Cochrane Library databases; appropriate internet sites and citation lists.

Study selection: Studies showing the effects of using a parachute during free fall.

Main outcome measure Death or major trauma, defined as an injury severity score > 15.

Results We were unable to identify any randomised controlled trials of parachute intervention.

Conclusions As with many interventions intended to prevent ill health, the effectiveness of parachutes has not been subjected to rigorous evaluation by using randomised controlled trials. Advocates of evidence based medicine have criticised the adoption of interventions evaluated by using only observational data. We think that everyone might benefit if the most radical protagonists of evidence based medicine organised and participated in a double blind, randomised, placebo controlled, crossover trial of the parachute.

… The relevance to parachute use is that individuals jumping from aircraft without the help of a parachute are likely to have a high prevalence of pre-existing psychiatric morbidity. Individuals who use parachutes are likely to have less psychiatric morbidity and may also differ in key demographic factors, such as income and cigarette use. It follows, therefore, that the apparent protective effect of parachutes may be merely an example of the “healthy cohort” effect.

Tuesday, November 8, 2011

There is no such thing as a Psychosomatic Illness

Over the years, I've come to doubt the existence of psychosomatic illnesses. People like to believe in them. The idea that our mind can make our body sick is intriguing, and besides, it provides an easy explanation for all those inconvenient ailments that haven't yet been diagnosed, or even discovered. Problem is, nobody seems to have taken the trouble to prove that emotional stress can manifest as physical symptoms.

Tuesday, November 1, 2011

Daily physical activity & symptom fluctuations in CFS patients

Daily physical activity & symptom fluctuations in CFS patients

The more patients with CFS are sedentary and the better activity is dispersed, the fewer symptoms and variations they experience on the same and next day.

Inversely, more symptoms and variability is experienced when patients were more active that day or the previous day.

Monday, October 31, 2011

"Study demonstrates that 95% of ME/CFS Patients have Anticardiolipin Antibodies, suggesting that ME/CFS may be an autoimmune condition"

A survey of the literature reports ACAs as commonserological markers in many different types of diseases,including viral diseases such as illnesses resulting fromchemical (1) and marine toxin exposure (4,5,6), HIV(7,8) and Epstein-Barr virus (9), hematological cancersincluding CLL and acute myelocytic leukemias, exposureto fungal organisms, malaria, and staphylococcusinfections (10,11), and autoimmune diseases such asmultiple sclerosis, systemic lupus erythematosus, autoimmunehepatitis, and more (2). This study demonstrates that a large percentage of patients clinically diagnosed with CFS have elevated levels of the IgM isotype to CL (95%), suggesting that CFS may be an autoimmune condition.As a possible autoimmune disease, CFS patients maybe treated by suppression of the ACA or by diminishingthe antigen CL in serum. Previous studies have shownthat treatment with monoclonal antibodies to B cellsreduces ACA levels to normal in patients with autoimmunedisease, leading to clinical improvements.

Specifically, Rituximab, a chimeric monoclonal CD20antibody, has been shown to normalize high ACAserum titers of patients with autoimmune systemic lupuserythematosus, rheumatoid arthritis, autoimmunethrombocytopenia, and autoimmune hemolytic anemia.Rituximab may serve as an effective therapeutic agentfor ameliorating the symptoms of CFS (11,13).

Therefore,classification of CFS as an autoimmune disordermay serve to increase the availability of treatmentoptions for patients suffering from the disease.
A study from 2009. Nice find, Dr. Speedy!

Friday, October 28, 2011

Pregnant? Don’t get Vaccinated

A computer scientist at the blog MedAlerts, has collated and graphed the data for us. The chart below shows the total number of spontaneous abortions/stillbirths reported to VAERS per a variety of vaccines.

It is clear from the graph that both the H1N1 vaccine and the Gardasil vaccine have a far greater risk for this outcome than other vaccines. What the graph does not capture is that this is raw data of all adverse events for the time the vaccine has been on the market going back to the start of the database. So as is pointed out by Dr. Rubin at MedAlerts, while the H1N1 vaccine shows a bit less than 3 times as many reports of abortion/stillbirth as the seasonal flu vaccine, the H1N1 vaccine has only been on the market for a year versus 21 years worth of data collection for the regular seasonal flu vaccine. This implies that the H1N1 vaccine is some 60 times more likely to cause a miscarriage than the still relatively unsafe seasonal flu vaccine.

The vaccine with the greatest number of total reported abortions/stillbirths is Gardasil, which has only been on the market for four years. I would speculate whether Gardasil, targeted strongly towards prepubescent girls, and likely not near as widely received as the flu vaccine may even be more dangerous than the H1N1 vaccine.

It should also be pointed out that the most common vaccines a pregnant woman would be at risk of being exposed to would be the influenza vaccines and the Gardasil vaccine.

Got a mail from Alan Light

Alan Light send me a mail response to some ideas I had. Well he dashed  (short, precise and friendly) one of my pet theory. Oh well, he really knows much more than me :-)

I need to digest it first. It is really nice that to have access to such great researchers.

Anyway, his email contained a footer. This was in it:
No virus found in this message.
Checked by AVG
Version: 10.0.1411 / Virus Database: 1522/3957 - Release Date: 10/17/11
Made me smile :-)

Thursday, October 27, 2011

The jokes professor Wessely makes

Professor Wessely has many times now made the case in the media that ME patients refuse to accept the psychiatric model of ME because we're scared of the stigma of mental illness. What a joke! I face stigma every day worse than that of someone with a mental illness, because as well as being viewed as just a label, treated with disrespect & ignorance, I am also treated as though my illness in fact doesn't even exist. (Which would not be true even if ME was a psychiatric disorder, since that by definition IS real!) My physical symptoms and disability are downplayed, ignored or disregarded, often completely disbelieved. Everything I say, do, believe, and am, is up for grabs for doctors to pounce upon as a reason why I am not as important as a patient with a real illness and why what I say about my illness, body & life can't be true. I've spent the last 15 years being neglected in a very real way, given little or no treatment, even where tests have proven some physical problem. I am not even given the majority of the tests and treatments recommended by international specialists for my very real illness. In essence I am just left to rot, along with everyone else with this diagnosis. And this isn't just my experience! Hundreds of thousands of ME patients in the UK have had this kind of experience, or much, much worse. Millions worldwide are little better off.


"Anyone who says this is a lab contaminant has drawn the wrong conclusion and has done a disservice to the public"
 – Judy Mikovits (via)
Compare to:
"In retrospect, I say I did the disease a disservice. I might have done the patients a disservice, and I might have done the field a disservice."
Elaine DeFreitas (page 682 "Osler's Web")

Rituximab Caveat

In my practice, rituximab at 375mg/m2 causes hypotension in most patients, about 60% need downward adjustment of their infusion rates and about 25% the hypotension is severe enough to be symptomatic. I would expect the hypotensive reactions to be more severe and frequent at the dose of 500mg/m2 used in the CFS protocol. If the patients signed a proper consent form they would have been warned that hypotension would be a risk, therefore most patients would be aware that they had received rituximab rather than placebo. The physicians who administered the rituximab would have to be adjusting the infusion rate in most patients and would also be aware that they had given the active drug rather than the placebo.

Therefore the statement that the study was double blinded is incorrect; it is not possible to double blind rituximab for the above reasons. Furthermore, the results are based on subjective, "how do I feel" criteria which could be influenced by the patients knowledge that they had received rituximab.

(As a side note: It is sad to see that Jamie always brings up XMRV)

Wednesday, October 26, 2011

CBT/GET: Misguided if well-meant treatment

The headline reads: 'Research showing ME is a physical disease'. We don't go along with the fashion among some doctors and researchers who tend to denigrate the very concept of a 'physical' disease. Such professionals prefer to emphasise instead that all disease, including ME, is a mixture of the physical and psychological. As I said when I was on the panel at the MEA Question Time in Huddersfield recently: 'Try telling that to someone with a broken leg.' No-one should let academic arguments obscure their common sense.

has now placed the second poster in our awareness raising series prominently on our website.

The message reads: 'ME is just fatigue, right? WRONG'.

The striking photo features one of our members, tube-fed because she could not at that time eat for herself. We have all read so much nonsense about ME in the press this year. It is time to tell it like it really is and to forward this link far and wide.
See the poster here:

The good news is that, after she and her family declined graded exercise treatment and managed her illness carefully, avoiding any treatment 'programme', this little girl has come through the worst of the illness and grown into an independent-minded, academically gifted young woman with a strong sense of justice for children with ME.

How many times do I hear a similar story of improvement through withdrawing from misguided if well-meant treatment?

Monday, October 24, 2011

The problem with the "autoimmune" label

Oh, how I hate the press for their ignorance…
Chronic fatigue syndrome, which affects one in 250 Britons, may be caused by a faulty immune system attacking the body.
That is the problem with the "autoimmune" label: People think "well, if the immune system attacks its own body, then the cause must be a faulty immune system". No. Coeliac is an "autoimmune" disease, yet its cause is gluten (which is found ceral-grains).

That is one part of the problem with journalism: They try to explain things they don't understand. The other part is that people take what is reported in the press at faith value.

And, oh, by the way, the incidence for ME/CFS is closer to one in 200, if not more common. Doctors do underreport, it comes with the territory.

Sunday, October 23, 2011

Thursday, October 20, 2011

How does ultra-pure water taste?

At the chip plants, the staff comes to regard UPW [ultra-pure water] as just another part of a high-tech manufacturing process. One senior IBM official was stunned when I asked her what UPW tasted like. Despite presiding for years over the water purification process, she not only had never tasted it, it has never even occurred to her to taste it. One of her deputies had, though, and he piped right up. “I stuck my tongue in it,” he said. “It was horrid.”  In fact, super-clean water tastes flat, heavy, and bitter. 
For science! Drinking larger amounts of ultra-pure water would probably leach the minerals from your body as well. So, there you have it.

Wednesday, October 19, 2011

The advantages of division of labor drive eusocial behavior

The proposed new interpretation of what causes ants and a few other species to become highly social, to the point of intricate specialization and even self-sacrifice, or altruism, is classic Wilson. “The causative agent,” the authors wrote, “is the advantage of a defensible nest.” Eusocial creatures are driven to cooperate not by their relatedness, in other words, but by the advantages that accrue to any group from the division of labor. As natural circumstance forced individuals to interact, certain cooperative traits became advantageous, and proliferated, in a handful of cases.

Tuesday, October 18, 2011

Rice, Potatoes, Wheat, and Other Plants Interfere with Human Gene Expression

Rice, Potatoes, Wheat, and Other Plants Interfere with Human Gene Expression

It was exactly one year ago today that I first uttered the phrase, “paleo is a logical framework applied to modern humans, not a historical reenactment.”

Not surprisingly, the research demonstrates proximate effects that were effectively predictable with the paleo framework.

The two relevant components of the basic paleo framework are:

1. Humans are probabilistically less likely to be adapted to foods introduced more recently into the human diet. This applies to the potato, which is indigenous to South America, and was not available to humans in Africa, Asia, Europe, Australia, or myriad island populations, until the Spanish brought them back to Europe in the late 16th century. All of those populations have been consuming potatoes for only 300-400 (I’m being generous with that second number) years.

2. Because they can’t run away or fight back like animals, many plants have evolved chemical defense mechanisms. Because the ultimate goal of evolution is reproduction, and not survival, we can predict that chemical defense mechanisms are likely to be concentrated in the reproductive parts of plants. In many cases, this is the seed. Rice is a seed of a plant, and is therefore probabilistically likely to have chemical defense mechanisms.

Bad Joke

What are hundreds of thousands of people, who are sent home by their doctors with the words: 'You just imagine that'?

Isolated cases.

Thursday, October 13, 2011

How reliable is data gathered by doctors?

While these case reports are not in the medical literature I would argue that they are more trustworthy then those written in journals in that, 1) they are not anonymous and 2) they are the exact words of the patient or parents impacted by the adverse event. The government keeps a database of adverse vaccine reactions known as VAERS. One parent had a very succinct critique of this program which I will reproduce.

The horrible realization is that VAERS is not accurate. Prior to Gardasil, I did not know what VAERS was. When my daughter became ill, I found out about VAERS by research performed on the internet. My daughter’s doctors did not even know what it was and they did not file a report until I filed one myself and told them they were obligated by law to file a report. How can the #’s be accurate if doctors don’t file the reports? I even had to explain what VAERS is. Shouldn’t VAERS and the adverse side effects of vaccines be taught in medical school or shouldn’t the doctors receive periodic newsletters from the CDC explaining VAERS and its importance?
It is the same thing that we have seen in ME/CFS: If you rely on doctors to report something (heck, they are even obligated by the law!), then doctors will underreport it. Doctor won't have the time to write reports, won't take the time, will be skeptical as to a causal relationship, will be skeptical to the significance of the symptoms and attribute it to other 'causes' (It's "the flu", it's "the weather", it's the patient's imagination, etc.)

"My heavens, what stupidity is this – the earth is obviously flat"

My heavens, what stupidity is this. The earth is obviously flat and I see the evidence of the sun rising and setting, rotating around the earth every single day, with my own eyes, what sort of moron would think otherwise. All of the evidence says the heliocentrists are idiots and fools, it is confirmed every day, while these nut jobs from their pathetic little charting (if there were internet flamers in that era) of a few disobedient stars dare rewrite all of cosmology, lunacy. Of course being so far advanced we now know that the earth rotates around the sun and moon, errr, scratch that last part the moon rises and sets like the sun but rotates around the earth, of course. It’s obvious isn’t it, from those few aberrant lights in the night sky? Thinking back on it, wow, what an achievement.
Nice. I always wanted to write that with regards to "common sense" and science.

Wednesday, October 12, 2011

Hemispherx/Chronix announce results in their CFS DNA-sequencing study

The aim of this recent CFS study was to find signature DNA sequences from patients with CFS compared to healthy controls with respect to their diagnostic predictive value, as well as, to potentially provide new insight into CFS biology. DNA extracted from serum samples of CFS subjects and normal healthy controls was sequenced and compared to the human genome. A total of about 10,000 high quality sequence reads were generated from each serum sample and four genes were identified by Multivariate Regression that separated CFS patients from the normal control group with a c-value of 0.95.

These results support additional studies with a larger CFS cohort using Massively Parallel Sequencing platforms with the aim of reduction to validated clinical assays for the diagnosis and evaluation of CFS and to explore whether the technology can be used to identify how different persons with CFS will respond to Hemispherx's experimental drug Ampligen.
Note: The blood test for CFS is still experimental in nature and has not been evaluated by any regulatory agency. It is currently limited to investigational use.

Previously, Chronix utilized Next Generation Sequencing (NGS) to generate sufficient DNA sequences to provide the statistical power to identify alterations in blood DNA from patients with breast and prostate cancer vs. normal healthy controls.

Thursday, October 6, 2011

XMRV is no more

Well, there exists a virus called XMRV, that can not be denied.

But there isn't XMRV in people causing diseases.

Monday, October 3, 2011

Weaker than average placebo effect in ME/CFS

The Placebo Response in the Treatment of Chronic Fatigue Syndrome: A Systematic Review and Meta-Analysis

Results: The pooled placebo response was 19.6% (95% confidence interval, 15.4–23.7), lower than predicted and lower than in some other medical conditions. The meta-regression revealed that intervention type significantly contributed to the heterogeneity of placebo response (p = .03).

Conclusion: In contrast with the conventional wisdom, the placebo response in CFS is low. Psychological-psychiatric interventions were shown to have a lower placebo response, perhaps linked to patient expectations.
Who would have thought that, huh? "Conventional wisdom" fails again. So conventional wisdom is the opposite to knowledge? I guess this confirms my bias that "psychosomatic medicine" is just "conventional wisdom" – and not science.

(Some) clear words from Jamie Deckoff-Jones on XMRV

Here is the reality and the context for why I write this particular blog entry: My email inbox is filled with so much pain and confusion, as patients try to figure out what the BWG study means to them. I feel it is my obligation to both these patients and the larger community to share my opinions. I think what the BWG results mean is that all the XMRV/HGRV testing done at VIP Dx has been and is now null and void.

I have watched this whole thing unfold and kept quiet because I hoped that management at the WPI would come to their senses, before it was too late. They have not, so I now feel obligated to share what I know.
Remember, that is the personal opinion of Jamie Deckoff-Jones. But I commend her on her clear words on this. Now we need something official from the WPI. We need to know what is going on. As I have commented:
Being wrong is OK, but we need to know what went wrong.  Nothing is more difficult than orderly reatreat from an unholdable position. – Clausewitz
Jamie writes on about testing at WPI vs. testing at VIP Dx lab:
Keep in mind that Dr. Mikovits works at the WPI research lab, which is a separate lab from the clinical, commercially-oriented VIP Dx lab. She believes that she has reproduced her original work many times and found evidence of infection in the patients who were previously found XMRV positive. But she never found any single patient positive on every date tested by every assay. So there has been an assumption that there were false negatives in the WPI research lab for some time. Another important thing to keep in mind is that WPI routinely used several tests on each sample, whereas VIP Dx used different, more limited testing, on the samples they received, testing that apparently was never truly validated against WPI methods or performed with appropriate controls. I personally don't know why this was the case or how it happened. Obviously the decision to sell a test was a very poor one, hindsight being 20/20. It left the institute with a difficult conflict of interest.

Now it appears the WPI research program is getting thrown under the bus, but VIP Dx is still up and running, now minus XMRV testing. None of this means that we don't have HGRV's, or that some of the work that came out of the Mikovits-led research lab wasn't correct. What it does mean is that there is no validated test for clinical, commercial use.
I think this is where Jamie is deluding herself – but this is all wobbly believe and hear-say. We need to take it step by step, and we need to find out conclusively what the testing at the WPI was worth and might still be worth. I'm afraid it might not be worth much, but guessing is not good enough and we need to know.
And it means we are now at risk of losing all the gains we've made because of poor managerial decisions.
If there were real research gains, that is.

Thursday, September 29, 2011

Bertrand Russell’s Ten Commandments

Bertrand Russell’s “Liberal Decalogue”
The Ten Commandments that, as a teacher, I should wish to promulgate, might be set forth as follows:
  1. Do not feel absolutely certain of anything.
  2. Do not think it worth while to proceed by concealing evidence, for the evidence is sure to come to light.
  3. Never try to discourage thinking for you are sure to succeed.
  4. When you meet with opposition, even if it should be from your husband or your children, endeavour to overcome it by argument and not by authority, for a victory dependent upon authority is unreal and illusory.
  5. Have no respect for the authority of others, for there are always contrary authorities to be found.
  6. Do not use power to suppress opinions you think pernicious, for if you do the opinions will suppress you.
  7. Do not fear to be eccentric in opinion, for every opinion now accepted was once eccentric.
  8. Find more pleasure in intelligent dissent that in passive agreement, for, if you value intelligence as you should, the former implies a deeper agreement than the latter.
  9. Be scrupulously truthful, even if the truth is inconvenient, for it is more inconvenient when you try to conceal it.
  10. Do not feel envious of the happiness of those who live in a fool’s paradise, for only a fool will think that it is happiness.

Saturday, September 24, 2011

You are what you ate

A new study suggests that the connection between your food’s biochemistry and your own may be more intimate than we thought. Tiny RNAs usually found plants have been discovered circulating in blood, and animal studies indicate that they are directly manipulating the expression of genes.
The ways in which food can influence us never ceases to impress me.
When they put the rice miRNA in cells, they found that levels of a receptor that filters out LDL, aka “bad” cholesterol, in the liver went down. As it turned out, the miRNA was binding to the receptor’s messenger RNA and preventing it from being expressed, sending receptor levels down and bad-cholesterol levels up. They saw the same effect when they tried it mice.
What they say in this convoluted way is: Rice increases LDL, the "bad cholesterol?

XMRV is on its way out

"This has been a difficult and disappointing process for them and for CFS patients, but hopefully we have all learned lessons that will guide future research and lead to discovery of the cause and cure of this disease".
So Mikovits/Lombardi/WPI have retracted a part of their Science paper. And the results of the blood working group look like contamination.
“I commend them on their scientific integrity and commitment to the scientific process,”
The WPI have pushed the ME/CFS issue, even if they are wrong with regards to XMRV. I think they find out what has happened to cause these results and will publish it – it just takes some time.
Lots of Newspapers Covering ME/CFS Today

I have read the articles from the major US sources, and all spoke of CFS like a serious physical disease. It was all in the context of the XMRV studies coming up negative, but they only quoted "real" ME/CFS docs and researchers, so barely a breath of psychological mumbo-jumbo anywhere.
The really good news is that the Lights & Bateman get a Million dollars to do more research into ME/CFS.

Sunday, September 18, 2011

And always take your Statins!

In the past, the F.D.A. advisers have been concerned that over-the counter versions of statins could not be used safely, that some patients who did not need the drugs would take them.
I’d be worried about that too.  It’s much better to have doctors prescribe cholesterol-lowering drugs to people who don’t need them.

Since high cholesterol is a symptomless condition, consumers would not know whether the drug was working without having their cholesterol checked periodically.
Don’t be silly … of course consumers will know if the Lipitor is working.  They’ll wake up in the morning and say, “Holy crap, my muscles and joints are killing me!  It must be the … the … Honey, what’s the name of that stuff I’ve been taking?”
Fat Head at his/its best.

Tuesday, September 13, 2011

Wheat? Just say no!

Fat Head: You’ve seen hundreds of your own patients become cured of supposedly incurable diseases after giving up wheat.  Describe one or two of the most dramatic examples.

Dr. Davis: Two people are on my mind nearly every day, mostly because I am especially gratified about the magnitude of their response and because I shudder to think what their lives would have been like had they not engaged in this diet change.

I describe Wendy’s story in the book, a 36-year mother and schoolteacher who had nearly incapacitating ulcerative colitis; so bad that, despite three medications, she continued to suffer constant cramps, diarrhea, and bleeding sufficient to require blood transfusions. When I met Wendy, she told me that her gastroenterologist and surgeon had scheduled her for colon removal and creation of an ileostomy bag. These would be lifelong changes; she would be consigned to wearing a bag to catch stool at the surface for the rest of her life. I urged her to remove wheat. At first, she objected, since her intestinal biopsies and blood work all failed to suggest celiac disease. But, having seen many amazing things happen with removal of wheat, I suggested that there was nothing to lose. She did it. Three months later, not only had she lost 38 pounds, but all the cramps, diarrhea, and bleeding had stopped. It’s now been two years. She’s off all drugs with no sign of the disease left—colon intact, no ileostomy bag. She is cured.

The second case is Jason, also described in the book, a 26-year old software programmer, in this case incapacitated by joint pains and arthritis. Consultations with three rheumatologists failed to yield a diagnosis; all prescribed anti-inflammatory drugs and pain medication, while Jason continued to hobble around, unable to engage in much more than short walks. Within five days of removing all wheat, Jason was 100% free of joint pains. He told that he found this absolutely ridiculous and refused to believe it. So he had a sandwich: Joint pains rushed right back. He’s now strictly wheat-free and pain-free.

More on Vitamin D, Calcium, Parathyroid, Fatigue

I was concerned that he may be absorbing too much calcium, as a result of too high a vitamin D level. Other bloggers have posted about this for example Jenny on Diabetes Update in this post “Too much calcium and vitamin D => Trouble” She writes about a condition called “Milk Alkali Syndrome” and her experience with it after increasing her vitamin D… ‘caused by the combination of high calcium and high Vitamin D and that the recent spike in cases has been caused by the recent fad of people supplementing with high levels of Vitamin D.’  (‘Calcium supplements can increase risk of kidney failure‘)

And from Dr William Davis: “Here’s a curious observation I’ve now witnessed a number of times: Some people who supplement this (1200mg day) dose of calcium while also supplementing vitamin D sufficient to increase 25-hydroxy vitamin D blood levels to 60-70 ng/ml develop abnormally high levels of blood calcium, hypercalcemia.” (‘Increased Blood Calcium and vitamin D’)

Paul Jaminet also writes in this post “Some people over-do vitamin D supplementation and/or calcium supplementation. Elevated blood calcium levels, which can be brought about by too much vitamin D, will cause constipation. If you supplement either vitamin D or calcium and have constipation, ask your doctor to check serum 25OHD, 1,25D, and calcium levels.”.
Read more here.

So Vitamin D can cause problems other than the toxicity that is talked about in the medical mainstream.

Friday, September 9, 2011

Enterovirus related metabolic myopathy in chronic fatigue syndrome (CFS)

Enterovirus related metabolic myopathy: a postviral fatigue syndrome.
(Full text available for free as PDF)
J Neurol Neurosurg Psychiatry. 2003 Oct

To detect and characterise enterovirus RNA in skeletal muscle from patients with chronic fatigue syndrome (CFS) and to compare efficiency of muscle energy metabolism in enterovirus positive and negative CFS patients.

Quadriceps muscle biopsy samples from 48 patients with CFS were processed to detect enterovirus RNA by two stage, reverse transcription, nested polymerase chain reaction (RT-NPCR), using enterovirus group specific primer sets. Direct nucleotide sequencing of PCR products was used to characterise the enterovirus. Controls were 29 subjects with normal muscles. On the day of biopsy, each CFS patient undertook a subanaerobic threshold exercise test (SATET). Venous plasma lactate was measured immediately before and after exercise, and 30 minutes after testing. An abnormal lactate response to exercise (SATET+) was defined as an exercise test in which plasma lactate exceeded the upper 99% confidence limits for normal sedentary controls at two or more time points.

Muscle biopsy samples from 20.8% of the CFS patients were positive for enterovirus sequences by RT-NPCR, while all the 29 control samples were negative; 58.3% of the CFS patients had a SATET+ response. Nine of the 10 enterovirus positive cases were among the 28 SATET+ patients (32.1%), compared with only one (5%) of the 20 SATET- patients. PCR products were most closely related to coxsackie B virus.

There is an association between abnormal lactate response to exercise, reflecting impaired muscle energy metabolism, and the presence of enterovirus sequences in muscle in a proportion of CFS patients.

Tuesday, September 6, 2011

"The incidence of psychiatric co-morbidity in ME-CFS has been greatly over-emphasised"

The incidence of psychiatric co-morbidity in ME/ICD-CFS has been greatly over-emphasised: a study in the Journal of the Royal Society of Medicine (2000:93:310-312) found that of patients in a tertiary referral centre who had received a psychiatric diagnosis, 68% had been misdiagnosed, with no evidence of past or current psychiatric illness.

Saturday, September 3, 2011

First commercially available PCR machine for $512

The price of a traditional PCR machine is around $3,000. So, do people in garages have great PCR machines? Not really. Howabout high school or middle school teachers? Nope. Howabout smaller medical testing labs or labs in India or China? Nope. Even some big bio labs try their luck on eBay. We set out to change that.

Josh and I prototyped OpenPCR over about 4 months — it was a lot of fun. Last May we unveiled the first OpenPCR prototype to all a bunch of crazy people on Kickstarter, 158 people gave us a total of $12,121. With that we designed and manufactured a repeatable, works-all-the-time device — it took a lot of hard work. Now we’re done and ready to share!

Friday, September 2, 2011

Cell Types and Diseases

There are several hundred distinct human cell types. … Cell types can be classified by their tissue of origin. However, it is possible for some cells to have their behavior induced by surrounding tissue.
So, if there are several hundred distinct human cell types, how many distinct autoimmune antibodies can there be? I know, this comparison is a bit lopsided, but still: Do we know all possible autoimmune diseases?

What kind of disease could we cause, if we would pick one cell type, target it with inflammation and/or antibodies? Is early hair-loss a autoimmune disease of certain hair-cells? Is tinnitus a autoimmune disease of certain auditory cells?

And do we know all hormones? All hormone producing cells? Or just the "important" ones? What happens if the cells responsible for a lesser hormone fail?

Sjögren's Syndrome

“In comments to the press, Ms. Williams expressed disappointment at being unable to compete because of severe fatigue and pain, but gratitude for recently receiving a diagnosis of Sjögren’s syndrome that explained symptoms she had been feeling for some time,” said Ms. Dowd. “Unfortunately, her experience is not uncommon; proper diagnosis can take years.
Blood tests can be done to determine if a patient has high levels of antibodies that are indicative of the condition, such as anti-nuclear antibody (ANA) and rheumatoid factor (because SS frequently occurs secondary to rheumatoid arthritis), which are associated with autoimmune diseases. Typical Sjögren's syndrome ANA patterns are SSA/Ro and SSB/La, of which SSB/La is far more specific; SSA/Ro is associated with numerous other autoimmune conditions but are often present in Sjögren's.
So these tests are "indicative".

Thursday, September 1, 2011

Be your n-1

So, about 3 and a half weeks ago, I made up my mind to stop the caffeine, and the beloved coffee. I tapered things down for about 2 and half weeks, endured daily headaches, but then finally, I quit about a week ago.

Since quitting, I haven’t had a single headache, visual aura, or palpitation. I’m cured.

It’s curious, isn’t it? I’m a doctor right? I should have known better. I should have identified the obvious instigator and simply stopped it.

But I’m also a real person, with a real life, real loves, and real routines. I’m surely not stupid. And we’ve all seen morbidly obese doctors and unfaithful preachers. So what happened?

Wednesday, August 31, 2011

23 new drug applications in the US in 2008

Consider two numbers: 800,000 and 21.

The first is the number of medical research papers that were published in 2008. The second is the number of new drugs that were approved by the Food and Drug Administration last year.

And before anyone jumps to pin the blame on the F.D.A., it’s important to note that it’s not just new drug approvals that have declined — new drug applications have, too. Last year the F.D.A. received just 23.

Here are the conditions treated for those 23 drugs:
  •  Diabetes Mellitus Type II (about 25 million people in the US)
  •  Breast Cancer (1.35 million people in the US)
  •  Rheumatoid Arthritis, Juvenile Idiopathic Arthritis (about 1 million people in the US)
  •  Prostate Cancer (965,000 people in the US)
  •  Schizophrenia (430,000 people in the US)
  •  Allergic Conjunctivitis (425,000 people in the US)
  •  Osteoporosis (416,000 people in the US)
  •  Gout (385,000 people in the US)
  •  Multiple Sclerosis (384,000 people in the US)
  •  Cervical Dystonia, Blepharospasm, Glabellar Lines (about 30,000 people in the US)
  •  Dupuytren’s Contracture (21,100 people in the US have this)
  •  Gaucher Disease (10,600 people in the US)
  •  Reduction of Excess Abdominal Fat in HIV-Infected Patients with Lipodystrophy (5000 people in the US)
  •  NAGS Deficiency Hyperammonemia (320 patients per year diagnosed)
  •  Pompe disease (90 patients in the US have this)
  •  Contraception
  •  Prevention of Thromboembolism in Atrial Fibrillation
  •  Varicose Vein
  •  Pneumonia, Skin and Structure Infection
  •  Postcoital Contraception

Tuesday, August 30, 2011

Can a doctor question the status quo?

A doctor’s practice is his/her livelihood. If a doctor can’t practice medicine, the 9 years of training and $260,000 they spent on medical school goes to waste. Receiving a letter threatening this livelihood is terrifying. Also, doctors are essentially guilty until proven innocent and must spend time and thousands of dollars on proving this when someone, anyone, anywhere can pick up a phone and ask for an investigation.

Medical education and residency is pretty militaristic. You fall in line or you’re out. Trust me, I’ve been there. If you are an “outside the box” thinker, this doesn’t last long in medical school or residency. The egos of your superiors are too threatened. This is an important fact. Doctors have such a preoccupation with being right, they can’t tolerate being wrong. This is of course needed because who wants to go to a doctor known for being wrong all the time? Questioning the status quo is threatening.

Saturday, August 20, 2011

Don't fear animal fat

We hear so much these days about the overconsumption of fat in the modern industrial diet that we sometimes forget how important some level of fat consumption is to normal human growth and the maintenance of healthy bodily functions. Animal fat, says Reader (1998:124) is "the proper measure of affluence.".... Hayden's (1981:421) observation is especially relevant here: "I was astounded the first time I saw Western Desert Aborigines ... kill a kangaroo, examine the intestines for fat, and abandon the carcass where it lay because it was too lean. Upon making a kill, Aborigine hunters always open the intestinal cavity and check the fat content. Virtually every ethnographer with whom I have discussed this observation confirms it, yet such details are seldom reported in the literature."

But at least they all love to share with each other...right?

At least don't fear fat from naturally raised animal, like grass-fed cattle. Grain-fed cattle? Factory farmed poultry? That might be a slightly different story...

Tuesday, August 16, 2011

When Mental Illness isn't Mental Illness

Over the years, though, I’ve seen quite a lot of people in practice who seem to have or have been formally diagnosed with some form of mental illness, who actually turn out to have their problem rooted in issues that fall, strictly speaking, outside the brain.

Here are a few examples:

1. people with mood swings caused by fluctuation in blood sugar levels
2. people with depression who have low thyroid function
3. people with low mood who have iron deficiency and/or anaemia
4. people with low mood/depression who have weakened adrenal gland function
5. people who have low mood/depression as a result of food sensitivity issues (often wheat, by the way)
6. people who have the symptoms of bulimia nervosa (binging and purging) as a result of blood sugar fluctuation
7. people who have anxiety/depression as a result of a deficiency in omega-3 fats
8. people who have anxiety/insomnia as a result of low levels of magnesium

The important thing is that when the underlying nature of these issues are rectified, the mental state of individuals usually takes on a completely different complexion.

Saturday, August 6, 2011

When Sinusitis isn't Sinusitis

The "problems with my nose", which I thought of as sinusitis, might not be sinusitis after all. First of all, what is Sinusitis?
Sinusitis is inflammation of the paranasal sinuses, which may be due to infection, allergy, or autoimmune issues.
So the definition is inflammation. While I don't want to rule out that inflammation is involved, I think whether I can breath freely through my nose or not has actually something to do with vasoconstriction (and blood pressure). Especially since I have been taking Equilibrant I tend to have a free nose while I lie down and start to get a blocked nose when I stand up.

Sunday, July 31, 2011

Loren Cordain on Autoimmunity and Nightshades

experiments in animals confirm that organ specific autoimmune diseases can be caused by injecting a self-antigen with a powerful adjuvant such as Freund’s [33, 34]. Neither the adjuvant alone nor the self-antigen typically results in autoimmunity in animals [33-35].

33. Fairweather D, Kaya Z, Shellam GR, Lawson CM, Rose NR. From infection to autoimmunity. J Autoimmun. 2001 May;16(3):175-86.

34. Fairweather D, Frisancho-Kiss S, Rose NR. Viruses as adjuvants for autoimmunity: evidence from Coxsackievirus-induced myocarditis. Rev Med Virol. 2005 Jan-Feb;15(1):17-27.

35. Fairweather D, Rose NR. Women and autoimmune disease. Emerg Infect Dis 2004;10:2005-2011.

Monday, July 18, 2011

"The loss of the vaccine would be devastating. But we need to clean it up as soon as possible."

A majority of an advisory committee for the US Food and Drug Administration (FDA) today voiced support for the continued use of a contaminated rotavirus vaccine now under FDA suspension, arguing that the vaccine's benefits far outweigh the theoretical risks of the contaminant.

However, members of the Vaccines and Related Biological Products Advisory Committee also recommended studies of possible long-term risks of the vaccine in question, GlaxoSmithKline's Rotarix.

"On the whole, the vaccine seems to have a spectacular record for safety and efficacy," said committee member John Coffin, PhD, professor of molecular biology and microbiology at Tufts University in Boston, Massachusetts. "The loss of the vaccine would be devastating. But we need to clean it up as soon as possible."

"The benefits are so big the risks would have to be enormous to outweigh them," added Harry Greenberg, MD, senior associate dean for research at Stanford University School of Medicine in California. "So far, we see only theoretical risks."
John Coffin says reasonable things. I think I have to apologize to him.

But I have to disagree with Harry Greenberg: Just because you see only theoretical risks, doesn't mean that aren't actual risks. Yes, the benefits far outweigh the risks, but that is no reason to puh-puh the risks.

Friday, July 15, 2011

A wild guess

So, if we assume that an Enterovirus causes ME/CFS (and Gulf War Illness) and I had to take a wild guess which one, I would pick Echovirus 30 and Echovirus 11.
You can see one wave/peak in the early 1980ties ("Osler's Web"), and one more after 1990 (Gulf War). Two different viruses could explain two different illness presentations (e.g. with/without POTS).

But this is just a wild guess...

Monday, July 11, 2011

Polio Vaccine

There are two types of polio vaccine, both of which were developed in the 1950s. The first, developed by Jonas Salk, is a formalin-killed preparation of normal wild type polio virus. This is grown in monkey kidney cells and the vaccine is given by injection. It elicits good humoral (IgG) immunity and prevents transport of the virus to the neurons where it would otherwise cause paralytic polio. This vaccine is the only one used in some Scandinavian countries where it completely wiped out the disease.

A second vaccine was developed by Albert Sabin. This is a live attenuated vaccine that was produced empirically by serial passage of the virus in cell culture. This resulted in the selection of a mutated virus that grew well in culture and, indeed, in the human gut where the wild type virus grows. It cannot, however, migrate to the neurones. It replicates a normal infection since the virus actually grows in the vaccinee and it elicits both humoral and cell-mediated immunity. It is given orally, a route that is taken by the virus in a normal infection since the virus is passed from human to human by the oral-fecal route. This became the preferred vaccine in the United States, United Kingdom and many other countries because of it ease of administration (often on a sugar lump), the fact that the vaccine virus replicates in the gut and only one administration is needed to get good immunity (though repeated administration was usually used). In addition, the immunity that results from the Sabin vaccine lasts much longer that that by the Salk vaccine, making fewer boosters necessary. Since it elicits mucosal immunity (IgA) in the gut, the Sabin vaccine has the potential to wipe out wild type virus whereas the Salk vaccine only stops the wild type virus getting to the neurons.

The attenuated Sabin vaccine, however, came with a problem: back mutation. This may result from recombination between wild type virus and the vaccine strain. Virulent virus is frequently isolated from recipients of the Sabin vaccine. The residual cases in countries that use the attenuated live virus vaccine (about 8 per year in the US until recently) resulted from mutation of the vaccine strain to virulence. About half of these cases were in vaccinees and half in contacts of vaccinees. Paralytic polio arises in 1 in 100 cases of infection by wild type virus and 1 in 4 million vaccinations as a result of back reversion of the vaccine to virulence. This was deemed acceptable as the use of the attenuated virus means that the vaccine strain of the virus still replicates in the body and gives gut immunity via IgA.

The vaccinee who has received killed Salk vaccine still allows wild type virus to replicate in his/her gastro-intestinal tract, since the major immune response to the injected killed vaccine is circulatory IgG. As noted above, this vaccine is protective against paralytic polio since, although the wild type virus can still replicate in the vaccinee's gut, it cannot move to the nervous system where the symptoms of polio are manifested.
By the way, today Polio vaccines have been further improved – and Polio hopefully eradicated soon.

Post-Polio Syndrome and Tinitus

Do you have [post-polio syndrome and] tinitus or roaring sounds in your ears?
26.5% - No.
21.3% - Yes, all the time.
27.7% - Yes, often.
10.4% - Yes, sometimes.
13.8% - Yes, rarely.

Low carbohydrate diets slow tumor growth and prevent cancer initiation

Low carbohydrate diets slow tumor growth and prevent cancer initiation


Vitamin D Supplementing Gotchas

Is there a evolutionary adaptation to lower UV radiation at northern latitudes?  Gerdes has hypothesized that apo E4 allele carriers have less of a need for UV radiation derived vitamin D due to internal adaptations to preserving vitamin blood levels and maximizing intestinal absorption from dietary sources.

For those supplementing vitamin D exogenously, care and caution for adverse effects should be monitored. Sunlight derived vitamin D can be shut off -- we have enzymes and systems that control blood/cellular levels, however for supplementation just as taking a birth control or exogenous hormone medication, what goes in, stays in. Previously I listed contraindications for vitamin d supplementation ((a) hypomagnesemia -- get mag up before supplementation because vitamin D will lower serum Mag; (b) sarcoidosis or other condition associated with elevated 25OHD or 1,25OHD3). Now I would add those with E4 should like monitor closely and avoid supratherapeutic levels which probably need to be addressed on an individual basis. With E4 there may be suggestions that intracellular 1,25OHD3 may be higher and this would not necessarily be reflected in serum levels (just like Mag levels are not, intracellular $$$$$ tests are required to accurately assess). Supratherapeutic needs to be individually defined... 

Sunday, July 10, 2011

Translation and protein processing by picornavirus

Translation and protein processing by picornavirus

The picornavirus RNA binds to ribosomes and makes a single polypeptide, therefore the virus has just one gene. This polyprotein has regions that have proteolytic activity (they are cysteine proteases) that cleave the polyprotein to three precursor proteins (P1, P2, P3). P1 is cleaved to a VP0, VP1 and Vp3 plus a leader peptide of unknown function. VP0 gives rise to VP2 and VP4. P2 and P3 do not give rise to viral structural proteins. One of the proteins that comes from P3 is the VPG that is found at the 5' end of the viral RNA while other proteins from this precursor are the viral replicase and enzymes that modify the behavior of the host cell. P2 is also cleaved to give other cell-modifying proteins. Details of some of the cleavages are still vague.

Once the various viral proteins have been made in the infected cell, the replicase (also call a transcriptase or protein 3Dpol) copies the viral plus sense RNA to negative sense RNA. Other viral proteins are also involved in this process. As new positive strand RNAs are made, they can also be translated into more viral protein. There may be as many as half a million copies of viral RNA per cell. Some of the proteolytic events outlined above take place as the nucleocapsid is assembled. This is especially the case with the VP0 cleavage to VP2 and VP4. P1 protein is the precursor that gives rise to the four structural proteins of the nucleocapsid. Five copies of P1 first associate. Endoproteolysis then occurs to form VP0, VP1 and VP3. Twelve of these pentamers than associate to form an empty capsid (procapsid). The viral RNA now associates with the capsid and at the same time, VP0 is cleaved. Release is by lysis of the host cell.

At the same time as viral protein synthesis is occurring, host cell protein synthesis is shut off. The host cell mRNAs however remain fully functional when assayed in an experimental system, so selective degradation of cell mRNAs is not the reason for protein synthesis inhibition. One way host cell protein synthesis occurs is via the cleavage of initiation factor eIF-4, one of the cap binding proteins of the host cell's ribosomes so that cellular mRNAs cannot bind to the ribosomes. Association with cap-binding proteins is a prerequisite for the translation of most cellular RNAs. Thus, only uncapped messages such as that of the picornavirus are translated. Note that most viruses express capped RNAs similar to normal mRNA and so this mechanism of shutting down host protein synthesis is not available to them. The viral proteins also change the permeability of the host cell, altering the ionic composition of the cell and inhibiting cell mRNA association with ribosomes. Moreover, the large number of copies of viral RNA simply out-compete the cell's mRNAs.


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