Friday, July 25, 2014

Screening mammography is not recommended

A relative recently had a screening mammography. She was asymptomatic, therefore, this was screening not diagnostic. Moreover, she's 45 years old, thus age-wise, not (yet) in a high risk group. I sugested she not to go for mammography again unless she starts noticing symptoms, not least because being irradiated poses risks and can, ironically, induce mutations that can lead to cancers.

A simple computation provides a perspective on the unreliability of screening mammography. At any given time around 100 out of every 10,000 women have breast cancer, while 10,000 - 100 = 9,900 don't. Out of 100 who have cancer and who undergo mammography, the test correctly detects 95 of them and will miss 5, incorrectly showing those women as tumor-free. Out of the 9,900 who don't have cancer and who undergo mammography 9,603 will correctly test negative, but 297 will erroneously be interpreted as having a tumor.

So if we screen 10,000 women, how many will test positive? 95 + 297 = 392. And what proportion of those women would falsely be shown to have cancer? 297 / 392 = 75.8%! That's right. 3 out of every 4 women who test positive actually don't have cancer.

Now imagine the anxiety upon getting the results and being told that there is a chance you have cancer, and the need for further testing to rule out (or in) that possibility.

But what if the test comes out negative? What's the likelihood the test failed to detect the tumor? The total number of women who test negative is 5 + 9,603 = 9,608. The proportion of missed tumors = 5 / 9,608 = 0.05%, or close to 1 out of 2,000 women screened. Mammography, therefore, can very accurately rule out breast cancer (which, however, does not indicate continued absence).


In the latest Cochrane systematic review of the harms and benefits of screening mammography the authors conclude:

"[S]creening will result in some women getting a cancer diagnosis even though their cancer would not have led to death or sickness. Currently, it is not possible to tell which women these are, and they are therefore likely to have breasts or lumps removed and to receive radiotherapy unnecessarily. If we assume that screening reduces breast cancer mortality by 15% after 13 years of follow-up and that overdiagnosis and overtreatment is at 30%, it means that for every 2000 women invited for screening throughout 10 years, one will avoid dying of breast cancer and 10 healthy women, who would not have been diagnosed if there had not been screening, will be treated unnecessarily. Furthermore, more than 200 women will experience important psychological distress including anxiety and uncertainty for years because of false positive findings."



Prevalence rate for breast cancer is difficult to come by. Estimate for the UK a decade ago was 1%. It must be noted that the frequency of cancers is higher in older people. 

I've taken the most optimistic sensitivity and specificity figures for mammography: 95% and 97%, respectively. Therefore, real false positive rate and false discovery rate are likely to be worse. For instance, specificity of mammograms can be as low as 90%. With sensitivity unchanged, If specificity were 95% the false discovery rate climbs to 83.9%, and with a specificity of 90% FDR shoots up to 91.2%.

Sunday, June 19, 2011

Have a break. Have a religion

Made the after reading this completely insane thinking and behavior. So whenever you don't like what reality throws at you take some time out for a psychotic break.

original image

Thursday, June 09, 2011

My very first orb!

Close-up from the same image:

OMG! My car's possezzed! An automobilic ectoplasmic globule has come out of the woodwork (or metalwork). This must be punishment for hacking into the electrical system. I must appease the god Toyotus. Perhaps feeding it ultra high octane gas, giving it a much needed oil change, and pampering it with a whole body wash might do it.

Hmmm my very first orb manifested in the car as well:

It was and has been raining lightly all morning and I was at the entrance to the garage so there's a good chance this is a tiny droplet floating by.

In the series of pics I took there were no other orbs so this speck is almost certainly not on the lens itself. Which makes sense since the orb is very bright--implying it was illuminated by the camera's flash

For the curious that's my test circuit for a variable intermittent wiper control I'm working on. There's a breadboarded microcontroller circuit in the transparent plastic box and two relays mounted on a DIN rail at the back of the box. Wires go up to the car's wiper circuit underneath the steering column. I've been studying the wiper's circuitry for several days now but I snipped the wiper's wires just today to bypass the car's electronics and hook up my circuit to it. Love the coincidence.

Finally, as alwayz the Bible has something to say: Beholdest thou the mote that is in thy camera's eye (Matt.7:3)

Friday, May 06, 2011


My company is all set to manufacture Pulseebo®, a cardiovascular drug indicated for hypertension, atherosclerosis, hyperlipidemia, among others. It'll be the most inexpensive CV drug around at just $0.10 per tablet. It's Rx so you need to get your doctor to write out a prescription.

Pulseebo® has no known side effects due to the fact that we have completely removed all active ingredients. Remember that active ingredients are responsible for all side effects in drugs. By taking them out of the formulation we have--for the first time in the industry--made a drug that will not produce any side effects. Moreover, this means that overdosing on Pulseebo® is almost impossible. Popping a whole bottle will, at worst, give you an upset stomach. (We're already working on our next drug Pulseebo Minus® which will have all nonactive ingredients removed as well to finally make overdosing an impossibility).

The evidence for the efficacy of Pulseebo® is just overwhelming. Over the past 5 years we've done extensive non-randomized, uncontrolled, unblinded, multicenter studies which which we've published in our in-house journal clearly showing that Pulseebo® is safe and effective. (These studies and other technical literature are available upon request.) More importantly, Pulseebo's efficacy is attested to by those who've used it. Just ask our staff for their personal stories. They've been unbiased and thoroughly objective in their assessment and have absolutely no conflicts of interest.

For more on Pulseebo®, ask your doctor on your next visit.

Pulseebo® -Your heart deserves more

Thursday, January 27, 2011

When logic goes to the dogs

The dog's argument has an implicit inference which has to be made explicit:
All cats have four legs.
All creatures that have four legs are cats.
I have four legs.
Therefore I am a cat.
That argument can also be stated, equivalently, as follows:
If the animal is a cat then it has four legs
I'm an animal with four legs.
Therefore, I'm a cat.
Well our canine shouldn't be heartbroken at all for discovering she's actually a feline. Instead she should be depressed she's committed the fallacy of illicit conversion.

The fallacy occurs when given "all p are q" we infer that the converse "all q are p" is also true. Likewise when  given "if p then q" and we conclude that "if q then p," then we've committed an illicit conversion. The "if - then" case may be more familiar when stated as follows:
If p then q
Therefore p.
That's the well known fallacy of affirming the consequent and is an example of an illicit conversion. (p is known as the antecedent and q the consequent.) An argument in this form is invalid.

The thing to remember is that "all s are r" or "if p then q" do not necessarily imply "all r are s" or "if q then p." The converse is is not necessarily implied but it might be true. For instance, in causal arguments, if p causes q, and if p is both  necessary and sufficient to cause q, then the converse is also true:
If a sheet of paper is heated to its combustion temperature and oxygen is present then it will burn.
If paper is burning then it's been raised to its combustion temperature and oxygen is present
Both statements are true. This is called a biconditional--the conditional (i.e., the if - then statement) is true both ways. If p then q and if q then p. To formalize the relationship between temperature/oxygen and paper we would say:
Paper will burn if and only if its temperature is raised to its combustion point and oxygen is present.
The phrase "if and only if" indicates this is a biconditonal statement.


Print References:

Bennett, Deborah J.. Logic made easy: how to know when language deceives you. New York: W.W. Norton & Co., 2004. p. 108-110, 116-117, 130.

Vaughn, Lewis. The power of critical thinking: effective reasoning about ordinary and extraordinary claims. New York: Oxford University Press, 2005. p. 287-289.

Tuesday, January 25, 2011

The prejudice of faith

Faith discriminates. In the sense that a person will choose to believe in certain ideas that are extraordinary and unsupported by evidence and reason, but won't have faith in a host of other similar unenvinced extraordinary ideas. So what then are the criteria for having faith in X but not Y? Why X instead of Y, and why neither? What kinds of claims must we have faith in? What are the characteristics of those claims for which we must forgo reason/evidence, but must believe in fully nonetheless rather than just ignore or be agnostic about?

I think if believers honestly and sincerely answered these questions they'd find that their bases would include, among others, preference, emotion, culture-centric biases/prejudices. If we scratch the surface I think we'll discover instances of special pleading--of singling out particular claims which they hold immune to rationality and rule of evidence and logic, affording them a special pass and privilege they don't grant to almost all other ideas/beliefs and areas of inquiry.

Friday, January 21, 2011

More on HPT, and conditionals and their converse

After writing the primer on conditional probabilities and their converse vis-a-vis screening tests, I continued to scour the Web to gather more information on the base rates of conception/pregnancy. But, much to my chagrin, as with searching for scientific studies on the reliability of home pregnancy tests (HPT) [note 1] I have come up nearly empty-handed. Thus far I've managed to find only one resource (which unfortunately doesn't provide any citation or rationale for the 50% figure provided; it sounds quite plausible, notwithstanding).

The probability of being pregnant increases as various indicators come into play. For instance given coitus within the last mentrual cycle and given the current scheduled menses has been overdue for several days, the probability that one is pregnant increases to around 50%. For our hypothetical HPT in the hands of the "average" user (for whom sensitivity = specificity = 75%) given P(pregnant) = 0.50, the reliability of the HPT is: P(pregnant | test positive) = 75% and P(not pregnant | test negative) = 75%. In this case, the true positive and true negative ratings are equal to the test's sensitivity and specificity only because the base rate = 50% and sensitivity = specificity.

A 75% true positive rating wouldn't warrant declaring HPTs as being spot on. If the prior probability (base rate) of 50% for pregnancy is held constant, the sensitivity and particularly specificity have to be >90% to attain a true positive rating close to 100%. (Use the spreadsheet and experiment with different combinations of base rate, sensitivity, and specificity. Instructions for copying the table to your spreadsheet are in Testing Screening Tests.)

It's claimed that HPTs are accurate, that "if the test result is positive, you're almost certainly pregnant" although "negative results are less reliable." However, as Bastian et al. discovered, even if the laboratory-determined sensitivity and specificity of the HPT kit is high, once the kit is in the hands of consumers, the actual sensitivity drops because most users fail to follow the instructions to the letter. User error detracts from the reliability of the test.

HPTs rely on the detection of the level of human chorionic gonadotrophin (HCG) in urine, HCG being a chemical whose amount increases over time after conception but is present in insufficient quantities during the first week or so after conception for the HPT to present a positive finding. Thus most HPT kits are to be used after the upcoming menstrual period is missed. If a user tests herself within a week of unprotected intercourse, chances are there still won't be enough HCG for the HPT to detect, assuming conception had taken place. Such misuse lowers the specificity of the test.

Moreover, as we've seen, what we're interested in discovering are the probabilities of the converse, i.e., not the sensitivity and specificity but their inverse--P(pregnant | test positive) and P(not pregnant | test negative). To obtain those figures we need to take the base rate of pregnancy into consideration. And so even with a sensitivity and specificity >90%, a true positive close to 100% is only possible if the prior probability of pregnancy is high enough (>50%). To fail to factor in P(pregnancy) is to commit the base rate fallacy.

According to studies even doctors can misunderstand the nature of sensitivity and specificity and fail to see the need to compute for the probability of the converse. 
[C]onditional statements are often confused with their converses. When they evaluate medical research, physicians routinely deal with statistics of the sensitivity and specificity of laboratory test results. In a 1978 study reported in the New England Journal of Medicine, it became apparent that physicians often misunderstand the results of these tests" [note 2]. 
In a study by David Eddy, after being given the values for base rate, sensitivity, and the complement of specificity (i.e., 1 - specificity), 95% of doctors surveyed overestimated P(malignancy | test positive) by one order of magnitude. "David Eddy reported that it's no wonder physicians confused these conditional probabilities; the authors of the medical research often made the error themselves in reporting their results" [note 3].

To end, let's look at conditional probabilities using "if / then" notation [note 4]. If a patient has cancer, then the probability of testing positive is 85%. That's sensitivity. If a patient does not have cancer, then the probability of testing negative is 90%. That's specificity. Now we want to know the converse: if an individual tests positive, then the probability of him/her having cancer is ___. And if a person tests negative, then the probability of him/her not having cancer is ___. They're both blank because we need the prevalence rate (base rate) of the particular type of cancer to determine those values. And the lower the prevalence of the disease 1. the higher the false positive rating of the screening test and 2.the lower its false negative rating will be.

In general, given the statement "if A then B," it doesn't imply the converse is necessarily true, that "if B then A." Thus, given "if I drink and drive then I will figure in a mishap," it would be erroneous to conclude that "if I'm in an accident then I was driving drunk." I could be in mishap even if I haven't had a drink and even if I'm the passenger.



1. To find all studies with "home pregnancy test" in their titles, I typed in "home pregnancy test[Title]" (without the quotes) in the search engine box on the PubMed site . Only 13 studies (mostly irrelevant) came up.

2. Bennett, Deborah J.. Logic Made Easy: How to Know When Language Deceives You. New York: W.W. Norton & Co., 2004. p.109. The NEJM article being referred to is "Interpretation by Physicians of Clinical Laboratory Results" by Ward Casscells, Arno Schoenberger,  and Thomas B. Graboys.

3. Bennett, p.110.

4. Bennett, p.109.

Thursday, January 20, 2011

Testing screening tests

How reliable are home pregnancy test (HPT) kits? Given 100 who've just conceived, 75 of them will test positive. And given 100 who aren't pregnant, 75 will correctly test negative [see note 1]. Assume the chances of conception when coitus is performed at some randomly chosen day of the month is 5% [see note 2]. If the HPT result comes out positive should the woman panic and faint if it's an unwanted pregnancy? Or if she's been trying to be with child for years, should she immediately broadcast the news on Facebook, Twitter, and email every friend and kin she has?

Before finding out the answer, let's introduce some important terms. The base rate is the prevalence rate or frequency of a disease, condition or phenomenon in the population.  Sensitivity is the rate/frequency/probability a medical screening test will result in a positive finding given that the person being tested has the condition or disease which the test is for. In probability notation sensitivity can be denoted as P(test is positive | person has the condition). That's read as "the probability that the test comes out positive given the person has the condition." The vertical bar is read as "given." Specificity is the rate/frequency/probability a medical screening test will result in a negative finding given that the person being tested does not have the condition or disease which the test is for.  In other words, specificity is P(test is negative | person doesn't have the condition).

So for HPT the base rate = 0.05, sensitivity = 75/100 = 0.75, and specificity = 75/100 = 0.75.

What we're interested in finding out is how reliable the test is, ie., how accurate it is when the test comes out positive and when it comes out negative. In essence we want to know P(being pregnant | test is positive) and P(not being pregnant | test is negative). These are two values and they needn't be the same. If the values are close to 1 (e.g. > 0.90) then we can say that HPT is reliable.

Notice that when we're talking of reliability of the test when it results in a positive finding we are looking at P(being pregnant | test is positive). This is not the same as the sensitivity of HPT which is P(test is positive | person is pregnant). The test's sensitivity measures how accurate it is when the subjects who are being tested are already known to have the condition (eg. are definitely known to be pregnant before the test is even administered). Quite obviously women who buy HPT kits do so to find out whether or not they're pregnant. Likewise the reliability of the test when the results come back negative is the P(not pregnant | test is negative). Contrast this with specificity of HPT which is P(test is negative | not pregnant). So the reliability indicators we're interested in are the converse of sensitivity and specificity.

To help us derive all the numbers, we shall enlist the help of a spreadsheet. Take a look at this 2x2 contingency table (it would be best if you open a new tab or window on your browser for the spreadsheet so you can easily switch between this text and the tables). Although I can simply give you the equations for P(being pregnant | test is positive) and P(not pregnant | test is negative), using a table is far more illuminating and easier to understand. But if you would rather have the formulas, I've included them in the spreadsheet--look for the rows "true positive" and "true negative."

Although there are clearly more than two rows and two columns in the table it's described as 2x2 because the two variables have two states/levels each. In the case of HPT the variables are pregnancy and HPT test result. Their states are: pregnant, not pregnant, test result positive, test result negative. 

The equations to compute for the values of the cells are provided. The values for cells which don't have explicit equations for them can easily be derived after the other cells have been filled. Keep in mind that except for the last table which uses user-provided sample size, the cells of the contingency tables all contain probabilities. Therefore, they will only have values from 0 to 1, inclusive.

Now scroll down to the row labeled "EXAMPLE." I've already plugged in the base rate, sensitivity and specificity for HPT kits (see yellow-colored cells). Focus your attention on the purple cells. As you can see when HPT says a woman is pregnant, there's only a 13.64% chance that it's true. Thus the false positive rate = 86.36%. Out of a hundred times the test comes out positive, 86 of them will be false alarms. Not very comforting at all.

But look at HPT's true negative rate--P(not pregnant | test negative). It's 98.28%. When the test tells a woman she hasn't conceived, then it will be wrong only 2 out of 100 times. Now that's reliable.

Before moving on, I suggest creating a new google spreadsheet so you can play around with the inputs and see how the probabilities change. Go to (and sign in if you need to). Click on the "Create new" button on the upper left hand corner of the window. A drop menu will appear. Click on "Spreadsheet." Go to the contingency table and click on "View" on the menu bar on top. Click "Show all formulas" on the drop menu. Press CTRL-A to select the entire table and then CTRL-C to copy it. Go back to your new blank spreadsheet and press CTRL-V to paste. You will have to manually join the various cells for those whose text is too long to fit one cell (and so it wraps down). Do this by selecting the cells on the row which you want to join and then click on the merge icon (it's the square one with left and right facing arrows). To "unmerge" select the merged cells and click the icon.

Now you can change the values of the yellow colored cells--base rate, sensitivity, specificity, sample size--and watch how the values in the tables below them change. Try inputting a value of 1 for specificity and watch how false positives are completely eliminated no matter what the sensitivity is.

One of the reasons that HPT (or for that matter, other tests) are prone to false positives (i.e., test result is positive but it's wrong--it should actually be negative) is because the base rate is rather low. And as we decrease the base rate--keeping sensitivity and specificity constant--the higher the false positive rate goes up. Try tweaking the base rate on your spreadsheet and see what happens.

If low base rate decreases true positive rates, then higher base rates should increase it, right? Remember we assumed that the base rate, thus P(getting pregnant ) is 0.05? Well, our assumption is that the woman doesn't know her ovulation cycle--she doesn't know the time of the month she's fertile. Now suppose she does. Suppose she knows exactly the six-day ovulation period when she can conceive [see note 2]. If she then has coitus during this period, the chances of her conceiving jumps to approximately 20% (it's actually between 10% to 33% depending on the day). Given that the base rate has increased, the reliability of HPT should increase as well. If we change the base rate to 0.20, the false positive rate drops to 57.14%. If the test comes out positive, it's nearly a coin toss whether one is really pregnant. On the hand, look at how the false negative rate has been affected. It's increased from 1.72% to 7.69%. Moral is: You can't have your cake and eat it too.

Let's move on and use another real life example. Fecal occult blood test (FOBT) is a kit which can be used at home to screen for, among other conditions, possible colorectal cancer (CRC). As with HPT, FOBT kits  from different manufacturers vary in their sensitivity and specificity. Let's take an "average" FOBT which has a sensitivity = 65% and specificity = 95%. How often (or rarely) does CRC occur in the population? Given the prevalence in 2007 we can estimate it to be 0.37% [see note 3].

Plugging those values in our spreadsheet we get the following:

True positive rate = 4.61%
False positive rate = 95.39%

True negative rate = 99.86%
False negative rate = 0.14%

When FOBT comes out negative we can almost be proof positive that we are CRC-free. But when it comes out positive, further testing is necessary to confirm/refute the initial screening. The low base rate means this test is prone to false positives.



1. Home pregnancy test sensitivity and specifity values: "The results we have suggest that for every four women who use such a test and are pregnant, one will get a negative test result. It also suggests that for every four women who are not pregnant, one will have a positive test result." In other words, P(test negative | pregnant) and P(test positive | not pregnant) are both 1/4. P(test positive | pregnant), i.e., sensitivity, and P(test negative | not pregnant), i.e., specificity of the test, are the complements of these values: 1 - 1/4 = 0.75.

It is important to note that different brands of HPT kits have varying sensitivities and specificities.

2. Pregnancy base rate: During the 6-day ovulation period the probability of becoming pregnant is between 10 to 33%. Computing for a simplistic average we get approx 20% for P(pregnancy | coitus during the 6-day ovulation period). According to the study there is no conception if coitus is outside this 6-day period. Therefore the P(pregnancy | coitus outside the 6-day ovulation period) = 0. Since the ovulation period is 6 days and there are 30 days/month, the probability that any randomly picked day is within the 6-day ovulation period = 6/30 = 1/5 = 0.2. We need to find the probability of getting pregnant regardless of when coitus is performed, that is we need to determine P(pregnancy).

p = pregnancy
p' = no pregnancy
v = coitus during 6-day ovulation period
v' = coitus outside the 6-day ovulation period

P(v) = 0.2
P(v') = 1 - P(v) = 0.8
P(p|v) = 0.25
P(p|v') = 0

P(p & v) = P(v) * P(p|v) = 0.2 * 0.25 = 0.05
P(p & v') = P(v') * P(p|v') = 0.8 * 0 = 0
P(p) = P(p & v) + P(p & v') = 0.05 + 0 = 0.05

I actually used a tree diagram (with ovulation period as the first two branches) and a 2x2 table as in the spreadsheet to aid in determining the probabilities. The above equations are a distillation of that graphical and tabular process.

3. Prevalence of colorectal cancer: "On January 1, 2007, in the United States there were approximately 1,112,493 men and women alive who had a history of cancer of the colon and rectum -- 540,636 men and 571,857 women. This includes any person alive on January 1, 2007 who had been diagnosed with cancer of the colon and rectum at any point prior to January 1, 2007 and includes persons with active disease and those who are cured of their disease." In 2007 the population of the US was 302.2 million. Therefore we can compute an estimate of the base rate for CRC: 1.112million / 302.2million = 0.0037.

Tuesday, January 11, 2011

A very sick doctor

According to Eduardo Cabantog he's an MD who's served in various state-run hospitals in the Philippines. Some years ago he founded Alliance in Motion (AIM) Global, Inc.--a multi level marketing (MLM) company. He's never looked back since. And if his presentation (see endnote 1) is any gauge, he's actually turned his back on the ethics of being a doctor.

AIM is into food/dietary supplements. But I'm not even going into the efficacy question regarding the items the company is peddling. This blog entry is about a (different) scam Cabantog has been perpetrating during his presentation(s).

Watch the following video begining at around 2:40 (you can see how the older gentlemen eventually fared in Part 8 of the presentation below).

The two men are easily thrown off balance by Cabantog when he performs his drag-the-person-down test. But after taking Alive! supplement (manufactured by Nature's Way) the two subjects become incredibly immovable. Try as he did Cabantog could not get them to budge. Amazing, isn't it? Well, it would be if Cabantog wasn't resorting to outright flim flam. Here's Richard Saunders of Australian Skeptics showing us how to do this party trick (see endnote 2). The reveal begins @5:10.

The direction in which the forces are applied is key. Push/pull a person away from where he's standing and it's easy to throw him off balance. The opposite is also true. Moreover, the lack of any form of blinding ensures that the tester can apply as much or as little force as he wants depending on whether the subject has taken the supplement or not. Similarly, the subject, knowing that's he's taken the supplement and having already been primed by Cabantog's prior presentation on the benefits of the wonder supplement, can apply more or less resistance. The subject--just like a patient--reflexively wants to please the authority figure and to play along specially given the large audience present (yes, there is peer pressure at work). Given how Cabantog has full control of the vectors--the magnitude and direction of the forces he's going to apply--and given how the subjects can more or less be counted on to perform as expected of a good albeit unwitting shill, there is almost no way this trick can go wrong.

Let's move on. Watch the following, paying close attention to the portion of the video from 2:16 - 3:03 and 4:34 - 5:20. Watch both a few times and see if you notice something peculiar.

Did you see it? Those two segments are merely mirror images of one another. And we know the first is the original because @2:23 to 2:25 we see the label of the lancet (the penlike device for pricking the finger)--the first few letters being "Lan"--flipped horizontally @4:41 to 4:43.

Moreover, if you listen carefully to the audio (best if you don't look at the vid) you'll hear the same one in both the first and second segments (although the first few seconds from the first don't make it to the second; in its place is a short part of the audio downstream, thus resulting in that portion being repeated twice in the second segment). You'll even hear the very same car horn @2:47 and @5:05.

In the first segment, the supposed blood sample taken is one before the subject took Alive! In the second, a blood sample after the supplement was taken. But as we've seen AIM Global merely provided a flipped version of the very same blood sampling. If AIM actually took blood samples from a subject in the audience before and after taking Alive! and if the glass slide showing freely moving RBC is from the same subject, then because they don't have the video clip for the second sampling there is reason to believe AIM is hiding something. Perhaps they don't want to show that they added a substance to the second blood sample (which they didn't to the first) because "Rouleaux and clumping occur when blood is placed under a microscope without first being suspended in proper solutions to control acidity and agglutination." Is AIM going to give us the lame excuse that they forgot to turn on the camera during the second blood sampling or that that video segment got corrupted?

Finally I found the following images in a Facebook album that apparently is open for all Facebook members to see and comment on. They're ads for AIM's latest product C24/7, which apparently is an improved Alive! since instead of just 16,000 "phytonutrients" C24/7 contains 22,000. Given the weight of one capsule and this number of chemicals you can do the math to find out how many micrograms of each there is per cap (assuming AIM isn't pulling our legs--again--with that 22k figure).

Whether these ads were made by AIM Global or by individuals (re)selling the supplement, I don't know. Since these ads make explicit therapeutic claims, they are in clear violation of the laws of the land (among others, RA 7394 Art.112 and the Department of Health regulations)



1. Alliance in Motion (AIM) Global presentation featuring Eduardo Cabantog, MD
Part 1/10 Part 2/10 Part 3/10 Part 4/10 Part 5/10 Part 6/10 Part 7/10 Part 8/10 Part 9/10 Part 10/10

2. This trick was also employed by, among others, Power Balance (Australia), which recently had to admit (thanks to the Australian Competition and Consumer Commission) that its wild claims for its rubber bracelet are bogus:

Saturday, January 01, 2011

If you don't have a Nobel, I'll have none of your ideas

A recent example of an ad hominem argument.

After being provided Neil deGrasse Tyson's "Perimeter of Ignorance" paper (see footnote) which puts Newton, Einstein, et al's religious sentiments into perspective, instead of critiquing the paper a believer went off questioning NDT's "smartness": "Did he ever win a Nobel Prize? Please elaborate why [we] would think that he is smarter or wiser than Albert Einstein or Sir Isaac Newton." And even after being told that "an idea stands and falls on its merit, not from whom it came from," this believer forges on, none the wiser, and hauls out NDT's curriculum vitae and resume from wikipedia, placing emphasis on NDT's being "a frequent Guest on the Game Show called Jeopardy," finally concluding "I am sorry but his greatest 'Achievements' are certainly nothing compared to the 'Achievements' of Albert Einstein, and Sir Isaac Newton. Are you kidding Sir???"

As to whether this person even bothered to read NDT's essay is unclear. He certainly does not even broach the ideas contained therein.

What is an ad hominem? It consists of "attacking the person instead of attacking his argument" [link].  "This tactic is logically fallacious because insults and even true negative facts about the opponent's personal character have nothing to do with the logical merits of the opponent's arguments or assertions" [link].

An ad hominem argument has the following basic form:

1. Person A makes claim X.
2. Person B makes an attack on person A.
3. Therefore A's claim is false.

Person A corresponds to NDT and person B to the believer.

One crucial question is whether B would've said what he did if NDT's essay had been, say, entitled "The Perimeter of Enlightenment" and had hailed Newton et al. as being warranted in invoking an intelligent designer for those mysteries which at the time eluded scientific explanation. Well apparently not, since when confronted with this very question, B simply refused to answer.

When you think about it, science would never advance and would become dogmatic and a cult worshiping the pronouncements of a few if the ad hominem rule were to prevail. Young scientists and thinkers would never get off the ground since they have yet to make their mark in history by adding to the pool of knowledge or even overthrowing wrong ideas by their esteemed predecessors. So when their ideas are at odds with the status quo they would be compared with the giants who've come before them and since their CV and resume are practically blank they would be pooh-poohed and never given an audience. Their ideas would be trampled upon and deemed heretical simply because they have no Nobels or awards to show off, no celebrity status, no biographies, no books written about them, none of the "blings" to show they're smarter and oh so important.

And rather obviously, scientists win Nobel prizes after their ideas have proved to be groundbreaking and shown to be true, and not because they scored 300 on their IQ test or because their CV is a hundred pages thick or that they didn't frequent game shows. Had we applied the above believer's criteria for judging ideas we would've said of Einstein when he came up with his relativity theory (thus supplanting Newtonian mechanics) at the beginning of the 20th century: "Einstein was a patent office clerk! Are you kidding me?! Has he won a Nobel Prize? Please elaborate why we should think he's smarter or wiser than Sir Isaac Newton?" 


Far more entertaining than the paper is Tyson's Beyond Belief 2006 talk with the same title: Part 1  Part 2  Part 3  Part 4

Wednesday, December 15, 2010

Sins to be wary of

Back in 1996, in the chapter The Fine Art of Baloney Detection, Carl Sagan used this example to illustrate the post hoc ergo propter hoc fallacy: "Jaime Cardinal Sin, Archbishop of Manila [said]: 'I know of ... a 26-year-old who looks 60 because she takes [contraceptive] pills.'" [emphasis mine, not Sagan's] (Sagan, Carl. The Demon-Haunted World: Science as a Candle in the Dark. New York: Ballantine Books, 1996. p. 215)

Sin's use of "because" implies he was blaming the pill and citing it as the cause. That's fallacious. There's a host of possible causes in that woman's life that can account for the effect observed, and yet the cardinal picked this particular one (perhaps out of prejudice).

I'd also point out that Cardinal Sin committed the sin of selection bias. He cites one example that (erroneously) supports the implied claim that contraceptive pills are bad for women. However, just like psychics who never advertize those predictions that bombed, Sin fails to tell us about how many 26-year old women have taken the pill but don't' look 60 or 50 or 40 or 30. Also for the sake of completeness Sin would also need to tell us how many 26 yr olds who don't take the pill and look 60 or 50 or 40 or 30, and how many who don't take the pill and don't look any older than they really are.

Why would we need all those values? To fill in the 2x2 contingency table required for the computation of the correlational coefficient between the two variables (taking the pill and looking older than one really is). In order to find out if there is a correlation (positive or negative) or not, we need the values for all four cells of the table.

These two--post hockery and selection/confirmation bias--I might add are such common pitfalls in health claims (the Cardinal's assertion included). They're all over the Web. Quacks and manufacturers/dealers/multilevel marketers of health products use them to their advantage, and sadly most consumers see nothing wrong with them and in fact fall for and even naively employ such flawed reasoning.

All too often we read and hear testimonials proclaiming that John and Jane de la Cruz took Vitamin Z or LiverAIDS or 4Geek antioxidant or hairball tea or whatnot, and then felt better or lost weight or their cancer went away or their gray matter went away or whatever. That I took A and thereafter noticed B doesn't necessarily mean A caused B. To argue otherwise is textbook post hockery. And yet even doctors fall prey to this error. For instance there's one who enthusiastically presribed a CAM procedure to my mom because he's seen/heard positive anecdotes regarding that specific "alternative" treatment.

But as shown by the Cardinal's sin positive testimonials and stories aren't evidence at all, because:
1. they provide datum for only one of the cells in the contingency table. Where are the other three?
2. they don't tell us how much of the "I feel better" is due to the placebo effect
3. they don't tell us of the other treatments, lifestyle changes, and other possible causative factors that the person is simultaneously undertaking, confounding factors that screw up any pat and easy causal conclusion.
4. they don't give us a precise baseline--they don't provide the "before" picture--with which to compare the "after" nor a verification that the illness/condtion purported to exist is true and accurate.

If I declare that prayers work giving as proof the fact that the sun indeed rose after I wore ten rosaries each around my neck, arms and legs and prayed to god Xenu for the sun to rise, I would be guilty of the post. hoc fallacy as well as the sin of selection bias. If you want to show how freaking stupid and moronic I really am you simply have to ask for the data for the other three cells. After computing for the coefficient, not only will we discover a lack of causal link, we'd prove there isn't even a correlation at all.

We know the caveat "correlation does not necessarily imply causation." We also need to keep in mind that an apparent (but yet untested) correlation may not even be true--it might be illusory.

Tuesday, December 14, 2010

If I drink and drive I'll meet an accident. I had a mishap therefore I'd been DUI.

 According to a news article which just got posted on Richard Dawkins' website, a study shows that "people with higher IQs are less likely to believe in God." Apparently the creme de la creme among scientists are not only geniuses but have chucked the belief in talking snakes and cops in the sky: "A survey of Royal Society fellows found that only 3.3 per cent believed in God - at a time when 68.5 per cent of the general UK population described themselves as believers."

Well, let's assume that's true--that highly intelligent blokes are more likely to be nonbelievers. As is known to all here I don't subscribe to any postulated supernatural entity whether you call them gods, goddesses, deities, angels, higher powers and principalities, your heavenly juju or holy mojo or Elvis for that matter. On the other hand, I have no idea what my IQ is. Since I'm a true-blue, dyed-in-the-wool, in-your-face atheist, does it follow then that I am more likely to have above average IQ? Can I conclude that I'm most likely an Einstein? Let's find out.

First, for the sake of clarity let's give the news article's claim some concreteness. So let's say that it's been determined that those with IQ >100 have an 80% chance of being atheistic. Now let's try and encode that in the nomenclature of probability theory since we are dealing with likelihoods.


AA = above average intelligence
NB = non-belief
P() = probability of

The above proposition then can be expressed as:

If a person has AA then P(NB) = 80%   [let's call this P1]

We now move on to the question we're trying to answer. Does it follow that if I'm a nonbeliever there is an 80% of oh so humble moi having above average intelligence? In other words, is the following statement true:

If a person is an atheist then P(AA) = 80%   [P2]

Well, you probably guessed it's not.

P1 can be written succinctly as P(NB|AA), which is read as the "probability of nonbelief given the person has above average intelligence." The vertical bar means "given."

P2 on other hand can be written as P(AA|NB), the probability of having AA given NB.

P1 and P2 are known as conditional probabilities and the values for these two are not necessarily the same. More often than not they're different. If we want to find the value for P(AA|NB) we'd need to have the figures for P(AA) and P(AA and NB), the latter being the probability that a person has above average intelligence and is an atheist--the intersection between the set of people with AA and the set of atheists. Mathematically, P(AA|NB) = P(AA & NB) / P(NB).

So the answer to our inquiry is: No, we cannot conclude at all that I can now be a member of Mensa or any clique and club of snobbish, condescending eggheads and geniuses.?

I couldn't think of a good title for this piece and so have that clumsy one up there. It alludes to the  conversion error whereby given "if A then B" is true we presume it follows that "if B therefore A."

Monday, October 11, 2010

Echoing Prof. Coyne

Jerry Coyne has just come out with a science-and-religion-are-incompatible article.He doesn't provide anything novel but what he says has to be repeated over and over as there are quarters out there that want us to buy into yet another fantasy--that science and religion can be partners in bed. 
[S]cience is no more compatible with religion than with other superstitions, such as leprechauns. Yet we don't talk about reconciling science with leprechauns. We worry about religion simply because it's the most venerable superstition — and the most politically and financially powerful.
Indeed. Let's not treat religion with kids gloves. As with astrology it's had millennia to prove itself. And all we've found out is either that religious ideas are flat out wrong or that they're mere speculations which even their proponents can't prove to be true.

Last night I commented on a friend's blog entry on this very subject of science and religion. Got carried away and ended up writing more than I intended. Am reposting it here:

I am of the opinion that science and religion are premised upon conflicting and irreconcilable epistemologies. Science is rooted in churning out hypotheses that can be tested and falsified. Hypotheses and explanations which cannot be empirically determined to be true/false are not scientific.

Theistic ideas are of the latter kind. Take the hypothesis that there is a being and this entity is in fact three persons. From the git go you have problems. First there needs to be a definition of this entity. Then we'd need to find out wthether this hypothesized entity is real. We'd then need to define what these "persons" are. If we manage to provide characterization of these persons, then we'd then move on to determining the existence of these multiple persons. This is a bit similar to finding out whether the hypothesis "Intelligent lifeforms with six stomachs, five eyes, four legs, three heads, and two penises exist in the universe" is in fact true.

It should be noted that probabilities, though not sine qua non, are of practical importance here. The idea that the planet Earth has no core and is in fact hollow has a very low probability of being true. So is the claim that there is biological life on the Sun. There are very scientific reasons for saying these are highly improbable. In a similar vein, the hypothesis that intelligent anthropomorphic entities exist within the Earth's atmosphere, as the ancients believed, is so highly improbable that they can be rejected as false. Needless to say, science and technology have relegated this worldview under the rubric of mythology.

Revelation, faith, tradition--these do not make anything true. Revelation is merely a claim. We would still need evidence that the "revealed truth" was in fact revealed by some nonhuman intelligence and that it is true. Faith--belief without evidence--is simply that. Rather patently, no amount of believing will make something true if it isn't. That would be wishful thinking. And however old an idea may be will not make it any truer than it really is. Hence, an argument from tradition has no merit in the determination of the truth of a claim or idea.

The lack of progress in finding which religion and which religious/supernatural hypotheses is/are true over the last several thousand years merely shows how religion does not possess valid epistemological methods. In fact the number of religions and religious hypotheses have increased over time. Contrast that with hypotheses about the empirical world. We have advanced so much in our understanding of the universe that we are now discovering exosolar planets trillions of kilometers from our planet and have been able to weigh the universe and discovered that our universe is mostly likely a flat one--that galaxies will continue to accelerate away from each other until they exceed the speed of light.

Religion underscores the importance of believing. Science emphasizes evidence to provide a solid foundation for believing. Religion, unlike science, ahbors truth, in the sense that while it may be a fount of ideas, it does not provide any proven means for determining the truth/facticity of those ideas. In short, science has the methods to mercilessly rid itself of bad ideas. Religion on the other hand has been forced to become a storehouse of untested and untestable ideas, as it continuous to seek refuge in God the Gaps hypotheses.

Monday, September 13, 2010

Will this offend you?

I downloaded a copy of the bible. I then deleted it from my hard disk. Will fatheists be offended? Will I be accused of irreverence and desecration and insensitivity? What if I kept downloading and deleting? What's the difference between annihilating a digital copy and a printed one? What if I had burned it into a CD and took a pair of shears and cut it up? What if I had cut that CD into the shape of a cross and then tossed it into a bonfire or flushed it down the toilet?

The psychology of offense and which forms offend and which don't should be an interesting field of study.

Bearded juveniles

I really don't get all the brouhaha over the planned (but eventually aborted) burning of Korans. Much ado about ink and paper. And over a handful of mass produced copies out of millions at that. If the ancient scrolls/manuscripts/codices or the last copies on earth were the ones under threat, I'd be among those rallying to save them. But of course this is simply not the case. Just goes to show you how Mo's fanboys are slaves to their psychology. How puerile can you get? Grow up you babies.

If religionuts everywhere bought all the remaining copies by Dawkins, Harris, Hitchens, Dennett, and Darwin and burned them and even their effigies, I predict the only complaint from atheists would be that these pissants have unnecessarily contributed to climate change. Sure, go rip out the pages of The God Delusion and damn and curse atheists and burn title upon title, but please go roast your shawarma with them.

Tuesday, August 24, 2010

Teaching children to fish and to ...

If I had kids I'd indoctrinate them to ask the following: How do we it's true, that is, what are our reasons for believing? How good are these reasons?

If we simply give children the answers to questions they grow up thinking they've already got unassailable knowledge and end up thinking that knowledge is that which comes out of the mouths of their personally preferred authorities. Encourage children to keep questioning and to ask the right questions and they become astute independent critical thinkers who have the ability to know and to assess an idea as to its position on the "reality spectrum" ranging from reason-based knowing to unsubstantiated belief.

Wednesday, May 19, 2010

What?! You got no religion?

Census taker came by this noon and I had to spend some ten minutes providing her the number of people in our household, birthdate, educational attainment, ethnicity, and religion. When she got to that latter item, I said I had no religion. With a quizzical look, she inquired, "What do you mean no religion?" Without hesitation I told her, "I'm an atheist." And she turned to her clipboard and started writing on the form. My eyesight is so bad I wasn't able to catch what she scribbled.

I gather that this particular individual (late 20s early 30s) has not come across a person who's answered "no religion" to her question. It's strange really that she wasn't prepared for such a reply. I'd like to think that the census office give their people enough training to expect the various possible answers before sending them off to collect data.

Today's experience shows me that there are some (as to the percentage I would say it's not insignificant) who still need consciousness raising. There are those who are still in that stage of innocence, assuming that everyone has a religion, in the same way that everyone has a birthdate and biological parents (even those who were conceived via IVF). Just as I had a rude awakening years ago that not every human on this planet celebrates Christmas and therefore not everyone would welcome or even understand being greeted "Merry Christmas", there are those who need to wake up to the reality that there are not a few who've never had a religion or been part of organized religion, or who were part of some tradition but have moved on and unfettered themselves from such belief systems.

Well, if anything, at least I may have nudged (I should hope jolted) this person out of her naivete.

Wednesday, May 05, 2010

I'm offended that you're offended

Richard Dawkins was recently in Australia and stole the limelight in a Q&A episode on religion [Part 1, Part 2, Part 3, Part 4, Part 5, Part 6].

I have to hand it to Senator Stephen Fielding. He has guts coming out and admitting he's a young earth creationist. Perhaps Australian politicians are not unlike those in my country--they'll do anything to draw attention (and thus engendering name recall for future elections) even it means becoming the laughing stock of the audience (or the country). People like Fielding are truly deluded in the psychiatric sense. In the face of overwhelming evidence they still hold on to cockamamie beliefs. In fact for the utterly deluded no amount or quality of evidence will persuade them otherwise. They are absolutely closed to the idea that they are or may be wrong. As long as they have a minimum number of members (and who knows how many that is) who subscribe to the same delusion, as long as such a community of like-minded inmates exists, they will carry on.

Interestingly Dawkins is the only nonbeliever in the panel of six. I don't know if the audience was able to digest the fact--one that Dawkins eventually pointed out--that those in the panel had differing religious beliefs which were incompatible with one another to a lesser or greater degree. For instance none of the five of course would have anything to do with Fielding's inane "10,000-year old universe, God waved his wand and rabbits and humans magically came into being" worldview. I felt that Minster of Agriculture Tony Bourke and political opposition deputy leader Julie Bishop wanted to distance themselves as clearly as possible from the crackpot senator when they explicitly and repeatedly said that religion and specifically Intelligent Design should not be taught in science classes. And then there was Judaism represented by Rabbi Jacqueline Ninio, a religion which does not and, as far as its tradition goes, will never accept Jesus as God incarnate. Ninio's Judaism, by the way, seems to lean more toward Jewish mysticism--she talked about a God concept that continually evolves. Hardly fundamentalist. So even within this group of five you had a plurality of supernatural beliefs which couldn't all be simultaneously right (unless we're willing to throw out the principle of noncontradiction). Some ideas will be wrong and some may be right, or all of them might be false. That's inescapable. 

What I found so completely lame is that during the latter half of the program Bishop and then Bourke charged Dawkins with being disrespectful and ridiculing religion. Once Dawkins delved into specifics and pointed out biblical facts, these two whipped out the "you are being disrespectful" and "you offend me"card. Well, believers offend and disrespect me for being offended by rational critique. How dare they mock Dawkins' and nonbelievers' intelligence!

Dawkins is proved right. If this had been a discussion on political or economic systems, or science or engineering, this issue of respect of one's views wouldn't come up. Criticism and debate would be taken for granted as the norm. Somehow believers have this insane belief that belief in invisible superheroes and superfoes, in airy fairy, namby pamby notions should be respected. And "insane" is not inappropriate a description. For what could be sane about granting respect to and withholding criticism from such extraordinary ideas that have no evidential support whatsoever? What is a mockery is the believers' supposed treasuring of truth but all the while closing off the avenues toward reaching it.

Tuesday, May 04, 2010

Another condition for which acupuncture is useless

A systematic review of ten RCTs for labor pain showed that needling was no better than no intervention, analgesics, or sham acupuncture. Edzard Ernst, one of the co-authors said:
Labour is a good subject to study the analgesic effects of acupuncture. Our analyses show that the effects of acupuncture perceived by women are largely due to placebo. Acupuncture has many qualities that maximise placebo effects: it involves touch and is invasive and, psychologically, is attached to the mysticism of the East. Our findings are in keeping with much of the recent research on acupuncture which demonstrates that the more one controls for such confounders, the smaller the effect of acupuncture gets.
How many more RCTs and reviews will it take before quacks throw in the towel? Unfortunately, they never will however compelling and overwhelming the evidence against their claims are. As James Randi would say, they're unsinkable rubber ducks.

Thursday, April 22, 2010

Stent or surgery?

Two-month old news but I just heard about it. The Carotid Revascularization Endarterectomy vs. Stenting Trial (CREST) was a 9-year, multicenter, mega trial with over 2,500 patients randomized to either stenting or endarterectomy. Adjudicators of the outcomes were blinded. Results shows that placing a stent to dilate a blocked carotid artery and surgical removal of the blockage--the traditional treatment--both have nearly the same efficacy and overall safety.
The overall safety and efficacy of the two procedures was largely the same with equal benefits for both men and for women, and for patients who had previously had a stroke and for those who had not. However, when the investigators looked at the numbers of heart attacks and strokes, they found differences. The investigators found that there were more heart attacks in the surgical group, 2.3 percent compared to 1.1 percent in the stenting group; and more strokes in the stenting group, 4.1 percent versus 2.3 percent for the surgical group in the weeks following the procedure.
The study also found that the age of the patient made a difference. At approximately age 69 and younger, stenting results were slightly better, with a larger benefit for stenting, the younger the age of the patient. Conversely, for patients older than 70, surgical results were slightly superior to stenting, with larger benefits for surgery, the older the age of the patient.

You'd think that's the final word on the matter. However, in March this year the results of the International Carotid Stenting Study (ICSS) came out. ICSS is a multicenter mega trial with over 1,700 participants randomized to either stenting or endarterectomy. As in CREST adjudicators of outcomes were blinded. Unlike CREST the objective of the European study did not include comparison of efficacy, only safety. Researchers found that surgery is safer overall. Incidence of stroke, death, procedural myocardial infarction, and risk of any stroke and all-cause death were all lower in the endarterectomy group. The three heart attacks that occurred during stenting were all fatal, while all four that occurred during endarterectomy were nonfatal. On the other hand,
There was one event of cranial nerve palsy in the stenting group compared with 45 in the endarterectomy group. There were also fewer haematomas of any severity in the stenting group than in the endarterectomy group.

Possible reasons for the difference in findings: the ICSS employed only symptomatic patients (ie., those who've had minor strokes or transient ischemic atttacks) while CREST included both symptomatic and asymptomatic patients; unlike ICSS, CREST limited itself to physicians who had a "high degree of proficiency and safety."