Showing posts with label scientific method. Show all posts
Showing posts with label scientific method. Show all posts
10.8.11
6 scientific study types - Wikipedia, the free encyclopedia
Longitudinal study - Wikipedia, the free encyclopedia
Cross-sectional study - Wikipedia, the free encyclopedia
Cohort study - Wikipedia, the free encyclopedia
Case-control study - Wikipedia, the free encyclopedia
Observational study - Wikipedia, the free encyclopedia
Randomized controlled trial - Wikipedia, the free encyclopedia
2.7.11
Science sceptic - "link," "association," or "correlation" - Scientific Debate Forum.
The Scientific Debate Forum.
Extract:
Most of these kinds of studies are called "epidemiological," which is derived from their first use to understand "infectious diseases," which were said to cause "epidemics." I am using quotation marks here because of the fact that all factors are not controlled for, which is required by the scientific method. If you've read though some of my essays here, you realize that the fatty acids you eat can play a huge role in your health, whether you develop particular "diseases," etc., but of course there are many other factors that are rarely or never taken into account (such as the socio-economic ones).
Indeed, one could argue that it is impossible to do so, yet that does not explain how a "scientist" can decide to not control for factors that have been demonstrated to be important (such as the fatty acids). I call the worst abuses of this approach "smelly socks epidemiology," because it would be easy to find an "association" between how much a person's socks smell at the end of the day to just about any "disease," and yet hardly anyone would think that the socks caused the disease, though if you substitute "sugar," "salt," "cholesterol," or any number of things most people view as "unhealthy," few question the results, and the existing dogma is reinforced.
Extract:
Most of these kinds of studies are called "epidemiological," which is derived from their first use to understand "infectious diseases," which were said to cause "epidemics." I am using quotation marks here because of the fact that all factors are not controlled for, which is required by the scientific method. If you've read though some of my essays here, you realize that the fatty acids you eat can play a huge role in your health, whether you develop particular "diseases," etc., but of course there are many other factors that are rarely or never taken into account (such as the socio-economic ones).
Indeed, one could argue that it is impossible to do so, yet that does not explain how a "scientist" can decide to not control for factors that have been demonstrated to be important (such as the fatty acids). I call the worst abuses of this approach "smelly socks epidemiology," because it would be easy to find an "association" between how much a person's socks smell at the end of the day to just about any "disease," and yet hardly anyone would think that the socks caused the disease, though if you substitute "sugar," "salt," "cholesterol," or any number of things most people view as "unhealthy," few question the results, and the existing dogma is reinforced.
30.6.11
Observational Studies, association and causality
Nothing wrong with Observational Studies. And Association does Imply Causality but… « Richard David Feinman
Tags: low carbohydrate, red meat,, statistics
Nothing wrong with Observational Studies. And Association does Imply Causality but…
Posted: June 19, 2011 by rdfeinman in Association and Causality, Evidence Based Medicine, Intention to Treat, low-carbohydrate diet, Observational Studies, thermodynamicsTags: low carbohydrate, red meat,, statistics
0
…the association has to be strong and the causality has to be plausible and consistent. And you have to have some reason to make the observation; you can’t look at everything. And experimentally, observation may be all that you have — almost all of astronomy is observational. Of course, the great deconstructions of crazy nutritional science — several from Mike Eades blog and Tom Naughton’s hysterically funny-but-true course in how to be a scientist – are still right on but, strictly speaking, it is the faulty logic of the studies and the whacko observations that is the problem, not simply that they are observational. It is the strength and reliability of the association that tells you whether causality is implied. Reducing carbohydrates lowers triglycerides. There is a causal link. You have to be capable of the state of mind of the low-fat politburo not to see this (for example, Circulation, May 24, 2011; 123(20): 2292 – 2333).
It is frequently said that observational studies are only good for generating hypotheses but it is really the other way around. All studies are generated by hypotheses. As Einstein put it: your theory determines what you measure. I ran my post on the red meat story passed April Smith and her reaction was “why red meat? Why not pancakes” which is exactly right. Any number of things can be observed. Once you pick, you have a hypothesis.
How To Avoid Being Baffled By (nutrition science) Baloney - GNOLLS.ORG
You Can’t Debunk Everything: How To Avoid Being Baffled By Baloney - GNOLLS.ORG
How To Avoid Being Baffled By Baloney
Caution: contains SCIENCE!
Anyone who makes a serious effort to understand the science behind nutrition will understand immediately that news items—most of which simply reprint the press release—are usually pure baloney. In order to learn anything interesting, we require access to the papers themselves.
Unfortunately, that’s not the end of the shenanigans. Abstracts and conclusions often misrepresent the data. Data is selectively reported to omit negatives (for example, statin trials trumpet a decrease in heart disease while intentionally failing to report all-cause mortality). And experiments are often designed in such a way as to guarantee the desired result.
Is there any way to deal rationally with the unending onslaught?
How To Avoid Being Baffled By Baloney
Caution: contains SCIENCE!
Anyone who makes a serious effort to understand the science behind nutrition will understand immediately that news items—most of which simply reprint the press release—are usually pure baloney. In order to learn anything interesting, we require access to the papers themselves.
Unfortunately, that’s not the end of the shenanigans. Abstracts and conclusions often misrepresent the data. Data is selectively reported to omit negatives (for example, statin trials trumpet a decrease in heart disease while intentionally failing to report all-cause mortality). And experiments are often designed in such a way as to guarantee the desired result.
Is there any way to deal rationally with the unending onslaught?
26.6.11
Clinical Significance (2) versus Statistical Significance
The Skeptic's Health Journal Club: Clinical Significance versus Statistical Significance
In my last post we looked at some of the caveats one might consider when a study is shown to be statistically significant. I also made-up a really silly and stupid example example of a researcher looking at all kinds of variables until finally correlating as statistically significant, toilet seat position with future criminal behavior. Well, it didn’t take long at all for the real world media to present an actual example far sillier and stupider than my own.
See the recent article in the British Medical Journal which, after what might appear to be an excellent example of a statistical fishing expedition, pronounces thigh circumference to be predictive of heart disease. Far worse, though much funnier is the way the respectable organs of mainstream media picked up the article and ran with it, giving repeated breathless announcements throughout the news world such as:
Can Thunder Thighs Help Heart Health: ABC News
Large thighs 'may protect heart' BBC News
Fat thighs, bum may help you live longer: Global News
A big bottom 'is good for the heart': :NHS Choices
Why those fat thighs may help you live longer: Reuters
This being only a small sample of the dozens of similar news releases devoted to this issue.
I admit I was unable to imagine an example this stupid, though this real world “research” is presented as science. It is as though the media was telling me to not even try my hand as an amateur even at fantastical moronic pronouncements, they are the pros. An old Monty Python skit, a documentary on village idiots keeps popping to mind, especially the line where John Cleese looks thoughtfully into the camera and notes “Well a real blithering idiot these days can make anywhere up to 10,000 pounds a year”
In my last post we looked at some of the caveats one might consider when a study is shown to be statistically significant. I also made-up a really silly and stupid example example of a researcher looking at all kinds of variables until finally correlating as statistically significant, toilet seat position with future criminal behavior. Well, it didn’t take long at all for the real world media to present an actual example far sillier and stupider than my own.
See the recent article in the British Medical Journal which, after what might appear to be an excellent example of a statistical fishing expedition, pronounces thigh circumference to be predictive of heart disease. Far worse, though much funnier is the way the respectable organs of mainstream media picked up the article and ran with it, giving repeated breathless announcements throughout the news world such as:
Can Thunder Thighs Help Heart Health: ABC News
Large thighs 'may protect heart' BBC News
Fat thighs, bum may help you live longer: Global News
A big bottom 'is good for the heart': :NHS Choices
Why those fat thighs may help you live longer: Reuters
This being only a small sample of the dozens of similar news releases devoted to this issue.
I admit I was unable to imagine an example this stupid, though this real world “research” is presented as science. It is as though the media was telling me to not even try my hand as an amateur even at fantastical moronic pronouncements, they are the pros. An old Monty Python skit, a documentary on village idiots keeps popping to mind, especially the line where John Cleese looks thoughtfully into the camera and notes “Well a real blithering idiot these days can make anywhere up to 10,000 pounds a year”
Clinical Significance versus Statistical Significance
The Skeptic's Health Journal Club: Of Ear Lobe Creases and Heart Disease
A positive study means there is a difference between two or more groups that is greater than one would expect to see by random chance alone. So, for instance, in a prospective study one finds all ten of the the treated people get well and none of the untreated people got well, something one wouldn't expect from chance alone.
But what if 4/10 treated people got well could this be chance? What if 6/10 treated people and 4/10 untreated people got well? Statistical tests then are applied to see how likely it was that the difference that showed up between the two groups was simply random chance, that is to say what is the chance that a difference in groups was just chance.
This is commonly expressed as the p-value. So one will see statements along the lines of "the difference was statistically significant p < 0.01". This implies (excluding issues of bias and whether the correct statistical test was done) that "there is a less than 1% chance that there would be this much of a difference between the two groups based on a random occurrence. If the p value is 0.05 this means there is a 5% chance that there really was no effect from the treatment and it was just chance that more people got well in the treatment group. By convention a p-value of less than 0.1 is described as "tending towards significance" while a p-value of less than 0.05 is considered statistically significant or a positive study.
A positive study means there is a difference between two or more groups that is greater than one would expect to see by random chance alone. So, for instance, in a prospective study one finds all ten of the the treated people get well and none of the untreated people got well, something one wouldn't expect from chance alone.
But what if 4/10 treated people got well could this be chance? What if 6/10 treated people and 4/10 untreated people got well? Statistical tests then are applied to see how likely it was that the difference that showed up between the two groups was simply random chance, that is to say what is the chance that a difference in groups was just chance.
This is commonly expressed as the p-value. So one will see statements along the lines of "the difference was statistically significant p < 0.01". This implies (excluding issues of bias and whether the correct statistical test was done) that "there is a less than 1% chance that there would be this much of a difference between the two groups based on a random occurrence. If the p value is 0.05 this means there is a 5% chance that there really was no effect from the treatment and it was just chance that more people got well in the treatment group. By convention a p-value of less than 0.1 is described as "tending towards significance" while a p-value of less than 0.05 is considered statistically significant or a positive study.
25.6.11
The Daily Lipid: The Great Unknown: Using Statistics to Explore the Secret Depths of Unpublished Research
The Daily Lipid: The Great Unknown: Using Statistics to Explore the Secret Depths of Unpublished Research
Saturday, January 8, 2011
The Great Unknown: Using Statistics to Explore the Secret Depths of Unpublished Research
I spent a large portion of the day today trying to figure out why a couple papers I have showed that EGCG, a component of green tea, increases glucose uptake into isolated skeletal muscle cells, but another shows the opposite.
The methods of these papers were a little different, and it's possible to speculate that some of the differences — for example, the amount of glucose in the culture dish — may have been responsible.
But it also occurred to me that perhaps EGCG doesn't have any effect on this phenomenon at all. For all I know, perhaps a hundred times so far different groups have tested the effect of EGCG on uptake of glucose into skeletal muscle cells and 100 times it had no effect, and the research seemed like a waste of time and went down the memory hole. But then a couple flukes occurred, and they were exciting, and the researchers wrote up the reports and got them published.
The decline effect and the scientific method : The New Yorker
The decline effect and the scientific method : The New Yorker
Extract:
Extract:
But the data presented at the Brussels meeting made it clear that something strange was happening: the therapeutic power of the drugs appeared to be steadily waning. A recent study showed an effect that was less than half of that documented in the first trials, in the early nineteen-nineties. Many researchers began to argue that the expensive pharmaceuticals weren’t any better than first-generation antipsychotics, which have been in use since the fifties. “In fact, sometimes they now look even worse,” John Davis, a professor of psychiatry at the University of Illinois at Chicago, told me.
Before the effectiveness of a drug can be confirmed, it must be tested and tested again. Different scientists in different labs need to repeat the protocols and publish their results. The test of replicability, as it’s known, is the foundation of modern research. Replicability is how the community enforces itself. It’s a safeguard for the creep of subjectivity. Most of the time, scientists know what results they want, and that can influence the results they get. The premise of replicability is that the scientific community can correct for these flaws.
23.6.11
Cross-validation (statistics) - Wikipedia, the free encyclopedia
Cross-validation (statistics) - Wikipedia, the free encyclopedia
Cross-validation, sometimes called rotation estimation,[1][2][3] is a technique for assessing how the results of a statistical analysis will generalize to an independent data set. It is mainly used in settings where the goal is prediction, and one wants to estimate how accurately a predictive model will perform in practice. One round of cross-validation involves partitioning a sample of data into complementary subsets, performing the analysis on one subset (called the training set), and validating the analysis on the other subset (called the validation set or testing set). To reduce variability, multiple rounds of cross-validation are performed using different partitions, and the validation results are averaged over the rounds.
Cross-validation is important in guarding against testing hypotheses suggested by the data (called "Type III errors"[4]), especially where further samples are hazardous, costly or impossible to collect (see uncomfortable science).
Cross-validation, sometimes called rotation estimation,[1][2][3] is a technique for assessing how the results of a statistical analysis will generalize to an independent data set. It is mainly used in settings where the goal is prediction, and one wants to estimate how accurately a predictive model will perform in practice. One round of cross-validation involves partitioning a sample of data into complementary subsets, performing the analysis on one subset (called the training set), and validating the analysis on the other subset (called the validation set or testing set). To reduce variability, multiple rounds of cross-validation are performed using different partitions, and the validation results are averaged over the rounds.
Cross-validation is important in guarding against testing hypotheses suggested by the data (called "Type III errors"[4]), especially where further samples are hazardous, costly or impossible to collect (see uncomfortable science).
12.6.11
Quackwatch & similar websites
further to "Atkins Exposed" , a well organised and resourced blog hostile to the Atkins low carb diet (see 54kzone.......beyond low carb: Carbophobia: The Scary Truth Behind America's Low Carb Craze ) here are more "Quackwatch" and similar themed blogs":
...and more generally:
Carl Sagan's Baloney Detection Kit
Thinking Is Dangerous
Skeptics 4 Life
Quackwatch
LOLquacks
Confessions of a Quackbuster
The Australian Council Against Health Fraud Inc
Fighting Spurious Complementary & Alternative Medicine (SCAM)
Cancer Treatment Watch
Scientific Misconduct Blog
Respectful Insolence (a.k.a. "Orac Knows")
Naturowatch
National Council Against Health Fraud Archive
Consumer Health Digest Archive (2002)
Respectful Insolence (a.k.a. "Orac Knows")
wanderingprimate.com
Dental Watch
MLM Watch
The Millenium Project
Pharmwatch Home Page
Acupuncture Watch
The Saul Green Files
The Great DBH Rant
Internet Health Pilot
Holford Watch: Patrick Holford, nutritionism and bad science | The truth about Patrick Holford, media nutritionist
gimpy’s blog
Allergy Watch
The Green Light - Health Fraud (1-50)
SCIENCE OF THE MANGOSTEEN & ROLE OF INFLAMMATION ON CHRONIC DISEASE
Dave’s Psoriasis Info — Anti-Quackery Articles
Anthony Campbell's Home Page for Acupuncture, Book Reviews, Assassins, Homeopathy, Skeptical Articles and Cycling
Kirsten Emmott, M.D.
Rusko's Planet
Hokum-Balderdash Assay
...and more generally:
Carl Sagan's Baloney Detection Kit
Thinking Is Dangerous
Skeptics 4 Life
11.6.11
Gov TV ad - warns against scam cancer cures
examples of the burgeoning quackwatch-type blogs listed below:
Quackwatch
LOLquacks
Confessions of a Quackbuster
The Australian Council Against Health Fraud Inc
Fighting Spurious Complementary & Alternative Medicine (SCAM)
Cancer Treatment Watch
Scientific Misconduct Blog
Respectful Insolence (a.k.a. "Orac Knows")
Naturowatch
National Council Against Health Fraud Archive
Consumer Health Digest Archive (2002)
Respectful Insolence (a.k.a. "Orac Knows")
wanderingprimate.com
Dental Watch
MLM Watch
The Millenium Project
Pharmwatch Home Page
Acupuncture Watch
The Saul Green Files
The Great DBH Rant
Internet Health Pilot
Holford Watch: Patrick Holford, nutritionism and bad science | The truth about Patrick Holford, media nutritionist
gimpy’s blog
Allergy Watch
The Green Light - Health Fraud (1-50)
SCIENCE OF THE MANGOSTEEN & ROLE OF INFLAMMATION ON CHRONIC DISEASE
Dave’s Psoriasis Info — Anti-Quackery Articles
Anthony Campbell's Home Page for Acupuncture, Book Reviews, Assassins, Homeopathy, Skeptical Articles and Cycling
Kirsten Emmott, M.D.
Rusko's Planet
Hokum-Balderdash Assay
...and more generally:
Carl Sagan's Baloney Detection Kit
Thinking Is Dangerous
Skeptics 4 Life
9.6.11
The Scientific Method in the Low Carb Echo-Chamber
My Carb Sane-Asylum: The Scientific Method in the Low Carb Echo-Chamber: by Carb Sane
also: My Carb Sane-Asylum: Science for Smart People
and:
Extract:
also: My Carb Sane-Asylum: Science for Smart People
and:
Extract:
I don't know how many of my readers share this impression I have of the low carb online community on the whole, but here it is. To me it seems this community has fallen victim to the same kind of group-think many have long decried, hanging out at sites where non-believers are turned away. No differing opinions allowed in such echo chambers.
The result of which is that we see the sort of repetition of catch phrases that would make a political party proud. You know what I'm talking about ... when the various mouthpieces making the rounds of the Sunday shows, morning shows and various cable and talk radio shows all seem to have the same speech patterns.
Folks, if we want to advance the "high mindedness" of science of carbohydrate-restricted nutrition and/or promote the healthfulness, or at least dispel the paradigm of the unhealthfulness of high fat diets, it's going to require some genuine discussion on the science. This includes dissenting opinions and challenging one's own biases. For your individual learning, I hope you'll continue to read this blog (shameless self-promotion). But I encourage you to read a variety of sources and not just confine yourself to those low carb echo chambers where 90% of the comments are "great post", "you're da bomb", and such. I'd be a liar if I didn't say that when I get such posts here they make me smile and boost the ego. But I do enjoy when those who find this blog from "enemy camps" challenge me and I encourage more (keep it respectful please) rather than less of this type of discourse. (Apparently some other bloggers aren't so keen on having such discussions)
Dr Kurt Harris - profile and creed
Dr Kurt Harris:
- discussing his background, his approach, and broader philosophy: Archevore - Archevore Blog - The Archevore Mission
I am a practicing physician with training in biology, chemistry, physics and all the biomedical basic sciences, including pathology, anatomy, physiology, endocrinology, biochemistry, etc. My specialty is radiology (interpreting MRI, CT scans, ultrasound, angiograms, etc.) and I have subspecialty training in neuroradiology and spent several years in academics in that subspecialty, doing teaching and research.
In my clinical practice, I have also acquired considerable experience in cardiovascular imaging. I read CT and ultrasound studies of the heart and vascular system daily. Although some radiologists read images in a room with little patient contact, at my imaging center we often review the exam results with patients, so I get the chance to see and speak with the actual person whose images I interpret. Radiologists are responsible for knowledge of many aspects of different clinical subspecialties.
The relevance of this is that I approach everything from this clinical perspective. I see people suffering from diseases of civilization every single day.
When I first heard Gary Taubes on NPR almost 3 years ago, and then read his book (twice in 2 weeks) I started reading on nutrition several hours a day, including thousand of abstracts, hundreds of full text papers, dozens of diet books, newest editions of textbooks on biochemistry, cell physiology, cardiology, gastroenterology, endocrinology, several textbooks of comparative animal physiology and anatomy, books on evolution, anthropology, archaeology, paleoanthropology...
Well, you get the picture.
I have experience with medical criticism and have written a book chapter, review articles and several peer-reviewed articles of original research.
6.6.11
Food Matters - Movie Exposes Drug Industry, Promotes Natural
"Let thy Food be thy Medicine and thy Medicine be thy Food" - Hippocrates. That is the message from the founding father of modern medicine echoed in the controversial new documentary film Food Matters from Producer-Directors James Colquhoun and Laurentine ten Bosch.
With nutritionally-depleted foods, chemical additives and our tendency to rely upon pharmaceutical drugs to treat what's wrong with our malnourished bodies, it's no wonder that modern society is getting sicker. Food Matters sets about uncovering the trillion dollar worldwide 'sickness industry' and gives people some scientifically verifiable solutions for overcoming illness naturally.
"With access to better information people invariably
make better choices for their health..."
In what promises to be the most contentious idea put forward, the filmmakers have interviewed several leading experts in nutrition and natural healing who claim that not only are we harming our bodies with improper nutrition, but that the right kind of foods, supplements and detoxification can be used to treat chronic illnesses as fatal as terminally diagnosed cancer.
The focus of the film is in helping us rethink the belief systems fed to us by our modern medical and health care establishments. The interviewees point out that not every problem requires costly, major medical attention and reveal many alternative therapies that can be more effective, more economical, less harmful and less invasive than conventional medical treatments.
The ‘Food Matters' duo have independently funded the film from start to finish in order to remain as unbiased as possible, delivering a clear and concise message to the world. Food Matters." http://www.foodmatters.tv/_webapp/About%20The%20Film
28.5.11
"The China Study" (nutrition & disease) - debunked
article by Denise Minger on the China Study here:
articles by Chris Masterjohn (Phd candidate) here:
The China Study is relied upon by many as strong evidence demonstrating the adverse health impact of animal-based foods, and in favor of a vegetarian diet. Linked below are commentaries that many believe invalidate the conclusions of the China study:
http://rawfoodsos.com/the-china-study/
articles by Chris Masterjohn (Phd candidate) here:
http://blog.cholesterol-and-health.com/; and
http://www.cholesterol-and-health.com/
The China Study is relied upon by many as strong evidence demonstrating the adverse health impact of animal-based foods, and in favor of a vegetarian diet. Linked below are commentaries that many believe invalidate the conclusions of the China study:
"The China Study is a 2005 book by T. Colin Campbell, Jacob Gould Schurman Professor Emeritus of Nutritional Biochemistry at Cornell University, and his son, Thomas M. Campbell II.[1] It examines the relationship between the consumption of animal products and illnesses such as cancers of the breast, prostate, and large bowel, diabetes, coronary heart disease, obesity, autoimmune disease, osteoporosis, degenerative brain disease, and macular degeneration.[2]
"The China Study" of the title is taken from the China-Cornell-Oxford Project, a survey that studied the relationship between mortality rates and the diets and lifestyles of 6,500 people in 65 rural counties in China. Described by The New York Times as "the Grand Prix of epidemiology," it was conducted jointly by Cornell University, the University of Oxford, and the Chinese Academy of Preventive Medicine over the course of twenty years; T. Colin Campbell was one of the project's directors. It was conducted in China because it has a genetically similar population that tends to live in the same way in the same place and eat the same foods for their entire lives.[3]
The authors conclude that people who eat a whole plant food/vegan diet, which avoids animal proteins such as beef, poultry, eggs, fish, and milk, will minimize or reverse the development of chronic diseases"
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