Part 2: Debunking Clark Baker’s “Analysis” of Flow Cytometry

I was really not looking forward to tackling part 2 of Mr. Baker’s nonsense.  It really is so astoundingly stupid.  At the same time, I must admit to deriving much pleasure from pointing out just how stupid Mr. Baker is.  Mr. Baker’s stated goal:“OMSJ began an investigation into the reliability and use of flow cytometry as it applies to HIV and AIDS.”

First of all, I must ask: why does Mr. Baker refer to OMSJ as an entity separate from himself?  He is the only person in the entire organization as proven by his Non Profit IRS Form 990.  Such an egomaniacal narcissist!   Mr. Baker also tries to establish that HIV is not responsible for depleting CD4 cells by quoting Anthony Fauci, a man whom Mr. Baker has accused numerous times of being a lying fraud and in the pocket of “Big Pharma”.  Why would Mr. Baker try to prove a point by quoting a man whom he considers to be completely without integrity?  Mr. Baker goes on to say:

“A careful reading of the medical and scientific journals establishes little correlation between CD4 cells and HIV.”

Of course Mr. Baker does not bother to present even one specific study to back up his claim.  And the few studies he does cite throughout his “analysis” use Flow Cytometry.   How can Mr. Baker state that these studies establishanything by using a technology he concludes to be “wholly unreliable”?   Furthermore, this is just blatantly false. There have been several large studies proving a correlation between CD4 count and HIV, along with viral load, another technology Mr. Baker briefly disparages.

The MACS or Multi Center AIDS Cohort Study as stated by Dr. Nick Bennett:

It’s well known (at least among those who bother to read and understand the literature) that those people with higher viral loads tend to progress faster, as was shown by John Mellors back in the mid 1990s using the large Multicenter AIDS cohort study (MACS).

Another even bigger study, Predictive Value of Plasma HIV RNA Level on Rate of CD4 T-Cell Decline in Untreated HIV Infection validated the findings of MACS.  Again, Dr. Bennett:

This study took things one step further. They replicated the original findings of Mellors by showing again that viral load roughly predicted how fast AIDS occurred in another large cohort composed of people from 3 separate study sites. For example, in this new paper people with viral loads less than 500 had an average loss of CD4 cells of 20 per year whereas those with viral loads over 40,000 had an average loss of 78 a year (with a smooth change for values inbetween). Basically this data proved that viral load was a reasonable predictor of rate of progression! They compared this analysis with the original MACS cohort and it looks practically identical!

NOTE: This link is to Orac at Respectful Insolence so that you can read his explanation, and link to Dr. Bennett’s and Tara Smith’s explanations all in one place.

Another interesting thing about the second study listed above (Predictive Value…) is that Mr. Baker used it as one of the only studies presented to specifically back up one of his claims.  Read slowly as these two sentences only make sense to Mr. Baker:

 Some researchers have identified numerous subsets of CD4 cells, while others have found that low T-cell numbers are routinely found among life insurance applicants and African populations.  Others have found viral load and flow cytometry equally dubious

My brain hurts!  Sorry, I just had to say that.  Why do I put myself thru this torture?

No researchers found low T-cell numbers among life insurance applicants.  What is happening is that Life Insurance Companies, (which are bigger rip off artists than Pharmaceutical Companies) are denying coverage to people with CD4 counts below 500 as they see them as unhealthy, which HIV Research has never claimed.  Whether that’s a sound business decision or not has nothing to do with researchers routinely finding low T-cell numbers among insurance applicants.  And the specific link to the study above in the second sentence is just Mr. Baker’s magical thinking as you can see from Dr. Bennett’s explanation.  Mr. Baker is simply performing magic even Harry Potter could not perform.

Next Mr. Baker resorts to completely contradicting himself.  First he states that every government entity, including the CDC, has failed standardization in relation to CD4 testing:

“HHS, CDC, NIH and FDA have failed to produce meaningful guidelines for quality control, quality assurance or quality of test reagents.”

Then the complete contradiction:

In response to that need, guidelines addressing aspects of the CD4+T lymphocyte testing process – in particular, quality control, quality assurance, and consistency of reagents for  immunophenotyping of lymphocytes were developed.  (National Institute of Allergy and Infectious Diseases (NIAID)/AIDS Clinical Trial Group: Guidelines for hematologic and low cytometric analysis of ACTG specimens, 1992).

To assure the accuracy and reliability of CD4+T cell test results obtained within individual laboratories and to attempt to assure comparability of results between laboratories, the CDC established a list of standard methods for performing the test, as well as guidelines for quality control and quality assurance.  The CDC’s recommendations for flow cytometry apply to laboratory safety, specimen collection, specimen transport, maintenance of specimen integrity, specimen processing, flow cytometer quality control, sample analyses, data analysis, data storage, data reporting and quality assurance.

Then, as a further contradiction, Mr. Baker lists many steps as set out by the CDC.  Mr. Baker erroneously concludes that it will surely lead to screwed up results:

As can be seen, there are multiple steps in this process, any of which that if violated can lead to a substantial alteration in the test results:

Do I really need to list all the difficult things in life that involve many complex steps that do not necessarily lead to errors?

Let’s also not forget that these people are highly educated, highly trained and highly experienced.  These people are professionals.  Mr. Baker may be trying to be logical, but just because something is possible, does not, by any stretch of the imagination, mean it is probable.

Mr. Baker also tries to use the fact that there have been recalls relating to Flow Cytometry as further evidence that it is “wholly unreliable”:

“Since 2004, the FDA has issued 66 recalls of flow cytometry products, devices, components and computer software.”

But isn’t this really further evidence of the commitment by the FDA to ensure the quality of this technology?  Of course it is.  And the fact that companies not only comply, but also improve their product to avoid such a costly problem is also evidence of their commitment to continued quality improvement.

The most fun I have had is in looking closely at one of the analogies Mr. Baker uses to compare to Flow Cytometry; Breathalyzers!  Yes, Mr. Baker compares one very complex technology to one relatively simple technology.  (He also used RADAR guns as comparison.  But because the technology is so simple and the training required operating it is soooooooooo ridiculously simple, I thought it would be way to easy of a target for me.  Just how hard can it be to Point and Shoot, especially for a cop?)

Because Mr. Baker tried to show that there were so many variables that could affect results using Flow Cytometry, I thought I would look into some studies showing how “wholly unreliable” Breathalyzers can be.  Just a simple Wikipedia search showed many ways breathalyzers can give faulty and variable results.  Just running up a flight of stairs can alter results by 11-14%, hyperventilation lowers results by 32% and even holding your breath can increase results by 28%.   How many “perps” run from the cops and then get a breathalyzer test?  What is worse is that many breath analysis machines use hematocrit as part of the algorithm (another term Mr. Baker disparaged in his “analysis” of FC).  The breath machines assume a hematocrit of 47% for an accurate reading but the normal range for a man is 42-52% while for a woman is 37-47%.  So that right there could falsely elevate the readings. But the worst part is that research indicates that BREATH tests can vary by 15% from actual BLOOD concentration!  And an estimated 23% of individuals tested with have a BAC higher than their true BAC!  Also, taking a look at Recalls of Breathalyzers found a plethora of recallls!

In other words, Mr. Baker, you might want to choose your analogies and comparisons a bit more carefully.

Or better yet, Mr. Baker, just stick to what you know.  I’m sorry that might be limiting for you.

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