Monday, December 01, 2008

Message for the lawyer

For the LA lawyer who tried to call me - I managed to accidentally delete voicemail with your number, and since there's more than a fair chance that someone connected to the EJ story might read this, I'm posting this up here.

I can however give an easy answer to your question - basically when I wrote the EJ commentary I was a resident physician, and according to NYS law:

"If you did not graduate from a NYS-registered or LCME- or AOA-accredited medical program, you must complete at least three years of postgraduate hospital training in an accredited residency program approved by the Accreditation Council for Graduate Medical Education, the American Osteopathic Association, or the Royal College of Physicians and Surgeons of Canada."

Since I graduated from Cambridge, England I couldn't get a NYS license until after residency - which I am now done with and my application is in the works :o)

The point though is irrelevant. In my commentary I am merely an observer and bringer of facts - the facts are irrefutable. I offer my opinion in only a few places, mostly in regards to speculation about a kidney disease that is neither necessary nor sufficient to explain the story, and in hindsight most of the findings regarding EJ's fluid in various organs can be explained by the resuscitation she recieved.

Al-Bayati on the other hand offers nothing but personal opinion and speculation, laced with a heavy dose of over-interpreted, cherry-picked literature to suit his pre-conceived idea that EJ must have died from something other than what the LA coroner found.

A side-by-side comparison of the coroner's report and Al-Bayati's report will reveal just how often Al-Bayati misrepresents it - and that's all I really did.


Blogger jtdeshong said...

Is this EJ story still going on?
I noticed that Christine Maggiore, has given an interview to refute the issues of an episode of Law and Order that she thinks was based on her daughter's death. UM, isn't Law and Order a TV show? How arrogant is she to think it's about her? What was that song in the 70's? You're so vain. I bet you think this song is about you, don't you?
OR, maybe her interview is to alleviate and assuage her guilt in some way? I wonder what Freud would say about that?
J. Todd DeShong

9:42 PM  
Blogger Bennett said...

Apparently something is still going on... I heard about the L&O episode too. The summary of the episode I've read covers a lot of denialist myths about retroviruses in general, the AIDS meds, the medical establishment etc. There is a chance that somewhere along the way someone read about EJ's story and merged it in. I dunno, but there are several other cases of maternal denial/neglect to base the episode on. We had one locally this year (and the mother was a doctor of all people...) which ended up getting sorted out safely.

Sadly, based upon Ms Maggiore's efforts to drag me into a "debate" on this issue, I think it's more likely a simple PR effort to further her denialist ideas and perhaps her book sales (she finished a new edition this summer). I think it's hard to feel guilty about something when you genuinely believe that you've done nothing wrong - and on more than one level I personally would put any "blame" about EJ's death on her pediatrician, by pandering so completely to her mother's denialist views - and those views themselves were put into Christine's head by people like Duesberg, the Perth Group etc.

We know that the denialists cost South Africa several hundred thousand lost lives due to convincing the President that AIDS was a myth and HIV was harmless - EJ was yet another preventable loss.


10:11 PM  
Blogger ericzz said...

Thank you for this website. I have had viral load tests for years but didn't really understand how they worked until I read your articles about PCR. I was hoping you could answer a few questions if you have time.
1. Do all viral load tests use the same oligeonucleotides? Will you get different results if you use a different test that uses different ones?
2. Could you explain the difference between HIV and endogenous retroviruses. I'm not sure if the people who call HIV an endogenous retrovirus are denialists or real scientists, but it's very confusing! How did scientists and doctors learn that HIV was a regular virus and not one that we were born with?

Thanks for the website!

5:01 PM  
Blogger ericzz said...

Also, in the article on why viral loads are useful and relevant, you wrote: "The RNA encodes proteins that co-purify with it (and not cellular proteins), which to any virologist is practically 100% proof that it belongs to a virus."

I didn't really understand this. What do you mean by "co-purify", what are the proteins, and why does co-purifying mean that they're from a virus?


7:28 PM  
Blogger Bennett said...

Good questions both.

The first one is easy - almost certainly (although I don't know for sure) different viral load assays by different manufacturers will use different oligos to target the RNA. They will use conserved regions to maximize sensitivity and avoid missing mutant strains. As a result you may get slightly different results from one assay to the next, but since you may get slightly different results using the same assay from one run to the next I'm not sure that it's significant.

Each assay is standardized to known copy numbers - so although the raw data might be different, because the standard curves will be also different the test samples will be fit to the relevant curve. This is something that you won't hear from the Denialists (probably because they don't understand the process), but basically viral load isn't a case of amplifying up something and then counting it. It's a case of amplifying up a bunch of things, including the test sample, and fitting the test sample between the known standards.

As a crude example (and I'm making up these numbers for illustration) if copy numbers of 1000, 5000, 10000 and 50000 were equal to test values of 1.21, 1.39, 1.47 and 1.64 then a value of 1.5 would roughly equal a copy number of 13700. You can plug these into a Excel chart and see how they fit if you like (that's where I got the 13700 from!). (Hint - it's an exponential curve)

As for the endogenous versus exogenous idea - it's easy to test for that. Firstly when you use DNA or RNA probes to HIV they only work in some cells - cells that have been infected or transfected with virus or virus-containing constructs. The other cells in the prep will not light up. They are their own internal control! The argument that somehow by performing the infection process you "activate" the endogenous virus makes no sense, as the DNA would still be present in the genome. The Perth Group have argued along these lines and have persistently refused to explain how an undetectable virus suddenly rearranges its DNA to become detectable upon "stimulation" - stimulation that can be done to identical cells without the virus being added and which results in nothing being found! Denialists argue that these controls simply aren't performed in AIDS science - a convenient argument that is refuted by simply reading the methods section of any research paper.

You can do similar things with DNA preps and Southern Blotting, looking for DNA sequences that bind. You can also, these days, run the HIV sequence through the entire human genome in GenBank and see if it matches anything. The short answer is no, and the search itself takes only a few minutes (under an hour I'm pretty certain). I've done this before.

The major difference between HIV and endogenous RV's is that HIV can be transmitted from cell to cell via culture fluid - endogenous RV's would not only be present in all cells of a certain type (e.g. human cells, were it a human RV) but they are defective viruses and aren't transmissible - although several endogenous RV's can produce intracellular and even extracellular particles, they're not really infectious.

I hope that helps.



7:57 PM  
Blogger Bennett said...

I just realized that I didn't answer the co-purify question..and it links with another outstanding question from way back when. It really deserves its own primary post as pictures would this space.

8:57 PM  
Blogger ericzz said...

Thank you for the response!
I think I was confused about the endogenous thing because I didn't know that a person's DNA is the same in all of their cells. After I read your response, I googled that question, and it all makes a lot more sense now.
This may be a stupid question that's not really all that related, but I was just wondering: if all people except identical twins have different DNA, how can scientists know that the DNA they sequenced for the genome project is representative of most humans? Like, there are probably a lot of sequences that don't show up in the sequenced genomes that nevertheless exist in some people. Have they just looked at a large enough group of people to account for a large proportion of the variation?
In general, do all humans have the same endogenous retroviruses, or at least different strains of the same ones, or is there a lot of inter-individual variation?

4:06 PM  
Blogger Bennett said...

The endogenous RV's are pretty much the same from person to person...but then well over 98% of the genome is the same from person to person, so that's not really saying much.

So the genome sequence is fairly representative, barring obvious mutations that would be different. I don't honestly know how many people they looked at to arrive at a consensus sequence.

11:04 PM  

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