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.


5-AZA A. Melvin Ramsay Acne Advocacy Alan Light Alternative medicine is an untested danger Ampligen Andrew Wakefield Anecdote Anthony Komaroff Antibiotics Antibodies Anxiety Aphthous Ulcers Apnea Asthma Autism Autoimmune Disease Behçet’s Ben Katz Bertrand Russell Biology Blood sugar Bruce Carruthers Caffeine Calcium Cancer Capitalism Cardiology Carmen Scheibenbogen CBT/GET CDC Celiac Disease Cereal Grains CFIDS Chagas Charité Charles Lapp Christopher Snell Chronix Clinician Coconut Milk Cognition Common Sense and Confirmation Bias Conversion Disorder Coxiella Burnetii Coxsackie Criteria Crohn's Cushing's Syndrome Cytokine Daniel Peterson Darwinism David Bell Depression Diabetes Diagnostic Differential Disease Diseases of Affluence DNA DNA Sequencing Dog DSM5 EBV EEG Eggs Elaine DeFreitas Elimination Diet Enterovirus Epstein-Barr ERV Etiology Evolution Exercise Challenge Faecal Transplant Fame and Fraud and Medical Science Fatigue Fatty Acids Fibromyalgia Francis Ruscetti Fructose Gene Expression Genetics Giardia Gordon Broderick Gulf War Illness Gut Microbiome Harvey Alter Health Care System Hemispherx Hemolytic Uremic Syndrome Herpesviridae High Blood Pressure Historic Outbreaks HIV HPV Hyperlipid Ian Hickie Ian Lipkin Immune System Infection Intermittent Fasting It's the environment stupid Jacob Teitelbaum Jamie Deckoff-Jones Jo Nijs John Chia John Coffin John Maddox José Montoya Judy Mikovits Karl Popper Kathleen Light Kenny De Meirleir Lactose Lamb Laszlo Mechtler LCMV Lecture Leonard Jason Leukemia Life Liver Loren Cordain Low Carb Low-Dose Naltrexone (LDN) Luc Montagnier Lucinda Bateman Ludicrous Notions Lumpers and Splitters Lyme Mady Hornig Mark Hasslett Martin Lerner Mary Schweitzer MCS ME/CFS Medical Industry Medicine is not based on anecdotes Michael Maes Migraine Milk and Dairy Mitochondria MMR Money and Fame and Fraud MRI Multiple Chemical Sensitivity Multiple Sclerosis Mutton My Symptoms n-1 Nancy Klimas Narcolepsy Neurodermitis Neuroscience NK-Cell Nocebo NSAID Nutrition Obesity On Nutrition Pain Paleo Parathyroid Pathogen Paul Cheney PCR Pharmaceutical Industry Picornavirus Placebo Polio Post Exertional Malaise POTS/OI/NMH PTSD PUFA Q Fever Quote Rare Disease Research Retrovirus Rheumatoid Arthritis Rituximab RNA Robert Gallo Robert Lustig Robert Silverman Robert Suhadolnik Rosario Trifiletti Sarah Myhill Sarcasm Science Sequencing Seth Roberts Shrinks vs. Medicine Shyh-Ching Lo Simon Wessely Sinusitis Sjögren's Somnolence Sonya Marshall-Gradisnik Speculation Stanislaw Burzynski Statins Stefan Duschek Study Sucrose Sugar Supplements Symptoms T1DM T2DM There is no such thing as Chronic Lyme There is no such thing as HGRV Thyroid Tinitus To Do Toni Bernhard Tourette's Treatment Tuberculosis Vaccine Video Vincent Lombardi Vincent Racaniello Virus Vitamin B Vitamin D VP62 When Evidence Based Medicine Isn't Whooping Cough Wolfgang Lutz WPI XMRV You fail science forever