Wednesday, April 28, 2010

Filters: Part IV

So just who is this mystery researcher who thinks that he can use a computer to cure diseases?
Trevor Marshall.
This Ph.D. in Electrical Engineering claims that he cured his own sarcoidosis and that he now has the recipe or “protocol” of drugs to cure all autoimmune diseases. He’s quite well known among patients with autoimmune disease. Not so much among physicians.
Trevor’s basic premise about Vitamin D centers on how that steroid is processed by the body. There is an initial form that is changed by the cell into an active form. The initial, or precursor form, is called 25-D in the MP literature. The active form is called 1,25-D by Marshall. Inside (and only inside) the cell, 1,25-D interacts with a receptor on the cell’s nucleus called the Vitamin D Receptor (VDR). The VDR then turns on or “transcribes” genes to make the cell do certain things it wasn’t doing before the VDR gave it the go ahead. The VDR is best known for regulating calcium (which is why milk is fortified with Vitamin D), but it also performs a lot of other functions in the body, helps regulate your body’s first line defense against pathogens, called innate immunity. The VDR that is located on the nucleus of immune cells tells those cells, among other things, to start spitting out proteins that kill certain types of bacteria.
Trevor’s main point is that his computer disease model shows that 25-D is an antagonist of the VDR. In biology, we talk about compounds that fit inside the “pocket” of a receptor or enzyme. This is where the lock-and-key model comes in. If it’s the wrong key but still fits in the hole, it’s an antagonist – it blocks the protein from doing its thing, like the wrong key stuck in a lock. If the molecule hits all the right hot buttons in the protein and turns in the lock, then the protein thinks it is seeing its native signaling molecule, and the protein goes off and does whatever it has evolved to do. That is called an agonist. Antagonist = blocked signal, agonist = boosted signal. That’s a layman’s definition, I didn’t cover partial agonists, mixed agonist / antagonists and so on, but it’s good enough to parse Trevor’s work.
Marshall claims that, since it’s an antagonist, the precursor molecule, 25-D, suppresses the innate immune response to teeny, tiny bacteria (small even by bacterial standards) without a cell wall. I have to note that the mainstream medical community has yet to accept the idea that these kinds of bacteria are involved in disease. (>>>>>) According to Trevor, these cell wall deficient bacteria then infect immune cells, causing them to go haywire against your immune system in much the same way that the zombies in I Am Legend went haywire on Will Smith.
This stretches my credulity a bit. First, in any other infection I’m aware of, the infected cell either stops working at all, or works at a reduced function because the infecting organism is taking nutrients from the cell and otherwise interfering with intracellular processes that the cell needs in order to function. Even in those cancers known to be virally or bacterially caused, the cell is not performing its normal functions at a faster rate, it’s spending all of its energy replicating like crazy because the infectious vector has damaged the cell’s DNA or RNA.
Second, it’s hard for me to believe that with all these biomedical researchers looking at infectious disease (and looking to make a name for themselves if they discover a new mechanism for disease), no one else has noticed all these tiny invaders in the immune system. Where’s the proof?
Trevor’s proof is threefold. First, he has a computer model that shows how bad Vitamin D is for you. Second, he has some electron micrographs that show these tiny invaders in immune cells. Finally, there’s his clinical data from everyone who’s voluntarily sending data in to the Marshall Protocol database.
I’m going to tackle these one by one, but in this section I only have space for the computer model. Since that’s the cornerstone of his arguments, I’ll spend the most time on it.
I think from the first two parts of this series you have a really good idea what I think about computer models, despite being the kind of chemist who tends to specialize in computational chemistry and biochemistry.
Just what is Trevor’s model, and how robust is it?
Well, he claims he’s the lone genius who’s found the silicon Holy Grail of autoimmune disease while all the rest of us are fishing around in the dark. Now, one may quibble that I cherry-picked that one quote from 2006 out of context. So let’s examine the record, shall we? Fortunately Trevor runs a website, actually several websites, where he explains himself, so you can see for yourself whether I’ve mischaracterized his position on computer modeling.
Let’s start with that first quote, made during a 2006 presentation to the FDA.
As we enter the 21st century, ‘mathematical reasoning’ (embodied in Molecular Biology) has advanced to the point where we know the precise location of atoms in certain key molecules which control the human body, and we can use the Genome to predict the location of atoms in many other molecules; predict with sufficient accuracy to understand the precise interactions between drugs and those molecules, an understanding which has often proven elusive in the clinical environment.
I think I already beat that one to death, don’t you? It’s not true by any rational definition of “precise interactions”, and that’s that.
But is Trevor really claiming to be a lone genius, or was I making a strawman?
First of all, take a look at the explanations of in vivo, in vitro, and in silico methodology on the Marshall Protocol website
It is very telling that the problems with in vitro and in vivo studies are specifically noted, but there is no corresponding section on the shortcomings of in silico technology. (Trevor: you’re welcome to use Parts One and Two of this essay for that, or just link to Derek Lowe’s “in silico” subject heading and be done with it).
But that’s just circumstantial evidence, the Marshall apologists will say. Just an error of omission, and a minor one at that. No. It’s a violation of Feynman’s famous description of properly presented science:
It's a kind of scientific integrity, a principle of scientific thought that corresponds to a kind of utter honesty--a kind of leaning over backwards. For example, if you're doing an experiment, you should report everything that you think might make it invalid--not only what you think is right about it: other causes that could possibly explain your results; and things you thought of that you've eliminated by some other experiment, and how they worked--to make sure the other fellow can tell they have been eliminated.

Details that could throw doubt on your interpretation must be given, if you know them. You must do the best you can--if you know anything at all wrong, or possibly wrong--to explain it. If you make a theory, for example, and advertise it, or put it out, then you must also put down all the facts that disagree with it, as well as those that agree with it. There is also a more subtle problem. When you have put a lot of ideas together to make an elaborate theory, you want to make sure, when explaining what it fits, that those things it fits are not just the things that gave you the idea for the theory; but that the finished theory makes something else come out right, in addition.
Fine, Marshall’s apologists still think I’m nitpicking. Let’s move right along:
So now the model is complete.
We know what pathogens can cause Th1 disease, and they were discovered purely by mathematical deduction, and not by looking into petrie dishes... or harming any furry animals
Does this square with what you read in my links about the interaction between in silico, in vitro and in vivo techniques? I will tell you straight away that any biomedical researcher reading that statement will choke. Read the whole post, read the whole thread, see if I’m taking things out of context.
Want more of Trevor’s hubris? Try this thread:
Those wet biologists are thrashing around in the dark. They need to learn about in-silico methodology...
What? Is there a biologist in the developed world who doesn’t know about modeling in Molecular Biology? I think the evidence is there, that Trevor is claiming to be the lone genius I posited. Yet another example:
There are very few institutions in the USA which are capable of doing in-silico work. A lot is being done Internationally. It will take a new generation of physicians, who are more capable with computers, before there is widespread understanding of the technologies we used to make our breakthroughs.

The concepts of modern pharmacopoeia will have to change. The pragma of "toxins" and "anti-inflammatories" are destined for the trash-heap
Few institutions in the US? Say what? We have more drug companies and biotechs than any other nation in the world and every one of them has to have some sort of modeling group. Those students come to Industry out of Academic modeling groups. The entire US research system is computer-crazy. Just look at Derek Lowe’s “in silico” subject header. Does Trevor’s quote pass your bozo filter? It doesn’t pass mine.
This quote is pretty brazen, too:
The second video was made when I finally realized exactly how the VDR activates when using a DRIP205 coactivator - something which apparently nobody else has figured out yet Precision is the keyword.. and lots of computing power...
No one else. Really?
Computer simulations can help elucidate this problem, no doubt. But in vivo or in vitro data are better. The way to start going about figuring out how a co-activator (a second molecule that’s required to start a signal - in effect we’re talking about a lock that requires 2 keys) works is to start replacing individual amino acids in the known ligand-binding region of the protein. As you replace those amino acids, activity will change, and you get a good idea of which residues are the “hot buttons” in the pocket, and which are along for the ride. Here’s an example of such an experiment on the DRIP-VDR system itself.
So, with a single Google search on DRIP co-activation, you can prove to yourself that Trevor’s not quite the lone genius out ahead of everyone else that he and his followers would like you to believe.
But this one is the kicker. This is the grand high poobah of red flags to a biomedical researcher. When asked what kind of statistics are being collected on the human “subjects” of the Marshall protocol, this is the reply:
Some people will never believe the statistics they see in front of them. It wouldn't matter how much extra work we did, they would try to find fault.

At this point it is important to understand that we have produced a disease model, at the level of the Molecular Biology. That is a game-changing event. The statistics mean nothing, except insofar as they support or negate that model.
(Emphasis Trevor’s)
The model means everything and the human statistics mean nothing? The statistics from human experience mean nothing!?!?!? I can’t express how bad this statement sounds to a biomedical researcher, and I can’t repeat this enough: in vivo data trumps all. HOWEVER, and this is the biggest however in the history of the world , the plural of anecdote is not data. If you are running a study, you MUST show the world that you are doing the patients no harm at the very least. The only way to do that is with descriptive statistics on validated measures of disease activity such as the ACR or DAS. We researchers fool ourselves all the time – I pointed out some examples of where this happens to even the best researchers in RA in the Part Three – so no one, and I mean no one, is exempt from conducting descriptive statistics on a human experiment.
If you are considering following an experimental protocol whose managers say that statistics on human subjects are irrelevant, you need to pull a Sir Robin and bravely run away. Fast.
But, say the apologists, Trevor is an outsider. Of course he doesn’t use the “correct” terminology. He’s over exuberant. But you’re nitpicking about semantics: he’s right, and you’re just a stick-in-the-mud.
Oh really? I still want to see the evidence. What do we know about how Trevor’s game changing event works?
I set up the computer to do a random, genetically adaptive search of millions of different configurations, and then tell me the best one it finds. Yes, Millions... and sometimes it only finds one good fit, despite all of its trying...
The proteins he’s talking about here are the Vitamin D receptor and possibly the Pregnane X Receptor, which are receptors for signaling via, well, Vitamin D and Pregnane (better to be simple than clever in scientific nomenclature). The VDR is his main target, though, and it’s a nuclear receptor.
The the kind of brute force calculation described in that quote is exactly the kind of method that all the professional sources I cited in Part One (Lt. Col. Coates, Derek Lowe, and Milkshake) said was useless because our state of biochemical knowledge is still too low. Was it six waters, or only five? Lt. Col. Coates predicts we might approach this level of sophistication by 2025. I say that’s early by 5 – 10 years, but whoever is correct, the fact remains that it’s not achievable now. Garbage in garbage out, and we just don’t have enough information from real experiments on physical things to construct a decent model yet.
So how should data on this kind of work be presented?
This paper on Quantitative Structure-Activity Relationships (or QSARs the fancy scientific name for what Trevor is trying to do – quantitatively predict biological activity based on shape) gives some guidelines on how one should be properly presented in the scientific literature:
This principle requires that parameters that reflect both the internal performance of a QSAR model and its predictivity should be provided. The internal performance is characterized by the goodness-of-fit and robustness of the model. The goodness-of-fit measures how well the model accounts for the variation in the response in the training set (1). Robustness measures the stability of the parameters and predictions when one or more of the training set chemicals is removed, and the model is regenerated excluding the removed compounds (1).
In other words, you have to tell everyone exactly how you made the model, and how well its results correspond to experimental results in the real world, either in vivo or in vitro.
Contrast this with what little Trevor has “published” on his model. Actually, the only real technical details in the model were released here. Please click on that link and read the comments (which are supposed to be a sort of open-source peer review) before reading on here.
I would like to note that Nature Precedings is an open access non-peer reviewed site. Anyone can post anything (within reason) there to get some preliminary feedback before running the gauntlet of real peer review. Once again, the Precedings are NOT peer reviewed. The normal expectation is that the Preceding will eventually show up in a peer-reviewed publication subsequent to feedback on that site. Trevor “published” this Preceding in 2007, and we’re still waiting for the real paper. Why might that be?
Well, if you read the comments, you will see that Trevor got called on violating the principles of good QSAR publication by one Josiah Zayner:
I would be interested to see what actual parameters and techniques were used for the Energy minimization(if one was done) and MD simulation, gromacs mdp files &c. I see no statistical analysis of the H bond data just a comment that “it looks different”. Have you performed any other methods of in silico analysis such as computing linear interaction energy? Your conclusions seem pretty drastic with no ex silico data to back it up.
Josiah’s a graduate student. Yes. That’s right. Trevor’s getting called on sloppy work by people who don’t even have a Ph.D. yet. (Though I suspect that Josiah’s going to make an excellent researcher when he obtains his terminal degree, and you know, his degrees going to be from the University of Chicago).
This is precisely the sort of amateur error that will get your submission bounced by peer review. Trevor and his apologists can grouse about peer review maintaining the status quo and Old Boys network all they want, but if this is exactly the sort of problem (no adequate description of experimental parameters) with a publication that peer review is designed to correct. This is prima facie evidence of sloppy scientific reporting. This is the kind of elementary error we don’t need cluttering a scientific literature that’s already full of legitimate mistakes from much more careful researchers. Ask yourself – why didn’t Trevor just come clean with that data instead of getting testy with Josiah? Inquiring minds want to know.
But Josiah’s question brings up another important point: Trevor is using a program called GROMACS for his molecular dynamics calculations.
GROMACS is a piece of freeware first developed by researchers at the University of Gronigen. It’s a great piece of software, but it’s off the shelf and it’s FREE. Drug and biotech companies buy proprietary software that is a bit more specific to nuclear or other receptors and they pay for it because they get better results from it. You’re telling me that Trevor became the lone genius out ahead of everyone else based on using a piece of free software that any graduate student in the world (hi Josiah!) can and does use.? Are you kidding me? And he’s the only one who’s figured this disease model out, despite the fact that everyone in the world has access to these tools. Does this premise get through your bozo filter? Can I sell you a bridge?
I know exactly what Trevor and his apologists are going to say. Trevor’s made some super-sekrit modifications to GROMACS. Puh-leeeze. That, too should have been noted in the Nature Preceding. Can we say “moving the goalposts fallacy”? Good, I knew we could.
But you know, to be fair, in a quantum universe where anything is possible Trevor might have made some proprietary modifications. If so, he doesn’t have to publish all the model’s details to get me to believe. He could fund everything he claims he wants to do with the MP by selling this wonder-program to a couple of biotechs or pharma companies. If it’s that good, those guys would sign a confidentiality contract in a heartbeat. Evidence of such a contract would be good enough for me to take on faith that Trevor’s work is good: that serious scientists are willing to bet serious money on it.
Now I’m going to point you to another deconstruction of Trevor’s work by medical scientists who do make their names public on the internet: the guys and gals at Science Based Medicine. I generally have the highest respect for that site, and I urge you to read that post as well as this one , right now before going on. However, one of the reasons I’m writing this is that I don’t think that they took Trevor seriously enough. A lot of patients are dazzled by his version of the evidence, the underpinnings of which rest on his claim to be a lone computational genius. So I don’t think the savants at SBM fully explained to those people why Trevor’s computer model gets such derision from them:
The data to support this, and please read it slowly so it sinks in, is based on a computer model (3). Computer simulations, not experiments.
I mean, I understood the contempt in that statement as soon as I read it, but laymen, especially those inclined to believe in scientific tales that are too good to be true, would not. I hope after reading this lengthy backgrounder (and thanks for sticking with me) you understand why both Dr. Crislip and I snort at computer models when used as the sole evidence for a human medical intervention.
But wait, there’s more.
As far as I can tell from what has been published or posted to his various websites, this vaunted computer model consists solely of the receptors he’s interested in and their substrates. When someone uses the term “disease model” there’s usually a whole lot more than that going on. That term implies that the entire biological system is being modeled. Why is this important? Because this differential activity of the two forms of Vitamin D on the VDR that Trevor makes such a big deal about takes place inside the cell.
All drug chemists can tell you about about stuff they’ve synthesized that works on the pure enzyme assays, but doesn’t do squat in animals or humans because it’s either not transported into the cell where it needs to be, or gets tackled on the line of scrimmage by an active transporter or a CYP in the liver or something else.
You see, the VDR is a nuclear receptor. That means it sits on the nucleus. Deep inside the cell. In order for Vitamin D to get to that receptor in the first place it has to get though the cell wall. Vitamin D didn’t evolve to regulate calcium in the body – the steroid is found in animals that don’t even have a skeleton. It’s very ancient. It probably interacts with multiple receptors, not just the one that bears its name. With something that potent floating around the body, one would think that they evolution would put some failsafe mechanism in place. And it did.
Meet the Vitamin D binding protein. It’s a big chaperone that keeps the 25-D from jumping on the first receptor it sees. This protein puts the 25-D carefully in the tissues it is supposed to be targeting, and no disease model that purports to center on Vitamin D can ignore it. I challenge you to go into the Marshall Protocol sites and find much about this regulatory protein. The best I could find was in this thread:
The D-Binding protein is pretty much still a mystery. It is known that 95% of the 'free' 25-D in the bloodstream, and a fraction of the 'free' 1,25-D is bound to this protein, but the exact molecular dynamics are still being elucidated. It does seem to be part of the control system which is intended to maintain 1,25-D at the correct level in the phagocytes, and which is perverted by the Th1 pathogens.
While Marshall’s apologists will say that this is an old thread, the fact remains that he claimed to have a complete disease model in 2006, and in that time period the VDBP was “pretty much still a mystery” to him. Those two pieces of information do not come together make a favorable picture of the Marshall Model in my mind. Please run a Google Scholar search on “Vitamin D binding protein” for yourself and see what comes up. Cites from 1975, 1981, 1989, 1968; in fact my whole first page of hits on that was pre-2006. One does not need to have “the exact molecular dynamics” in order to conduct some (real life) experiments that yield some information on how this protein delivers Vitamin D to the cell, and while Trevor was optimizing GROMACS, that is exactly what the rest of the world was doing.
Are you starting to have the questions about just what exactly this “disease model” entails?
Trevor will come back and claim that only his Molecular Dynamics simulations tell you what’s really going on. If that claim has any traction with you, please go back and start reading from Part One.
Let’s bend my credulity into a pretzel and say that Trevor’s model of the Vitamin D receptor actually reflects reality at that very local level of VitaminD / receptor interaction (with DRIP). We don’t even now, and certainly didn’t in 2006, know the importance of all of the cells let alone all of the other proteins (besides the VDR) involved in the pathogenesis of autoimmune disease. Where do these other proteins fit into Trevor’s picture? (We’ll get to the other cells later). The short answer is that he ignores them. He claims they are unimportant. I think otherwise, and his view of the world is not a disease model by my definition of the term. But then I’m part of the old guard who has to die off before Trevor’s genius can be appreciated. Unfortunately for Trevor, many people who think as I do (i.e. most of the rest of the scientific community) are younger than he is by a significant margin.
But wait, there’s more.
If you want a really good technical shredding of the Marshall Protocol, this is probably the best place to start, but if you’re in my target audience, i.e. almost of a purely non-technical background, it will make your eyes glaze over. The non-technical reader should note, however, a mention in the introduction section of Mark London’s page to the effect that the MP has evolved in its view of the actual mechanism of Vitamin D pathogenisis, in that 1,25D was originally blamed as the culprit, but 25D eventually became the villain.
If you read the really old stuff in the Marshall protocol websites, things won’t add up unless you are paying close attention to chronology. This wonderful molecular dynamics model of disease that allegedly was good enough to trump in vivo data in 2006 switched gears on a number of very important points. And it switched those gears without the drugs used by the Marshall Protocol ever changing.
That’s disturbing on a lot of levels.
Remember the therapeutics the Marshall Protocol uses? Low dose antibiotics and the ARB Olmesartan? Well, there originally was a scientific rationale for the ARB, given in this paper from January 2006:
The ARBs Olmesartan, Irbesartan and Valsartan (Ki asymptotically equal to10 nmol) are likely to be useful VDR antagonists at typical in-vivo concentrations.

That’s right folks, antagonists.
If you’ve forgotten, here’s a layman’s review of antagonism / antagonism: an antagonist is an agent that sits in the binding pocket and prevents the protein from doing its job. An agonist mimics the signaling molecule and forces the protein to do its job in the absence of the real signaling molecule.
For some reason, Trevor had changed his mind about the role of olmesartan by August of that same year:
It is certain that the layout of the Olmesartan oxygen atoms in the vicinity of the key SER278 / TYR143 / ARG274 / SER237 VDR residues is that of an agonist. That is, when Benicar docks into the VDR displacing 25-D and 1,25-D it at least partially activates the VDR. The higher the Benicar dose the greater percentage of the Ds will be displaced, according to the standard displacement curve in my FDA presentation slides.

That’s right folks, an agonist. All based on the same model. Which apparently beat real experiments on real living systems , way back in 2006.
What you will find all over the place in the MP website are traces of previous theories that were discarded like tissue paper. Such as the original theory that 1,25-D was causing the VDR to be overactive:
In order to induce recovery from chronic inflammatory disease, it is necessary to restore VDR functionality by removing all exogenous sources of the secosteroid we call ‘Vitamin-D’, and dampen down over-exuberant VDR activity, for example with the ARB Olmesartan[1].

This old rationale for the use of the drugs in the Marshall Protocol is at direct odds with the current one that I quoted. When the rationale changed, the drug regimen didn’t.
It’s not just the critics that notice the problems, though, even the faithful on the message boards do. People like the guy who goes by the moniker “tickbite”:
Am I just going insane? I'm sorry Frans, your link is just reiterating this thread....

This paper:

Common angiotensin receptor blockers may directly modulate the immune system via VDR, PPAR and CCR2b
Trevor G Marshall, Robert E Lee, Frances E Marshall
Theoretical Biology and Medical Modelling 2006, 3:1 (10 January 2006)
[Abstract] [Full Text] [PDF] [PubMed] [Related articles]

says that olmesartan is an uses the word agonist one time to reference a researcher who thought that telmisartan was both an agonist and an antagonist. That's it...........the word agonist and olmesartan never come together in one sentence. Are we saying this 1 year old paper is just phooey?
(Yes, we are.) And the guy who goes by the moniker sdcreacy saw the same thing:
Quick question regarding Olmesartan: are there any references I could read that establish Olmesartan as a VDR agonist biochemically (in-vitro or in cells)? The 2006 paper calls it an antagonist, so I am confused.

I’m confused, too. And sdcreacy is showing other signs of independent thought that you should emulate, talking about corroborating evidence from in vitro studies.
Trevor ignores this discrepancy completely. I have not seen a single statement from him that explains his about face in 2006. I want to know why his essentially complete disease model predicted in early 2006 that the VDR was overactive and that olmesartan would damp down the activity, while later in 2006 that very same model predicted that the VDR was being shut down by the precursor to Vitamin D, and that olmesartan is restoring normal VDR activity.
Theories change in science all the time. That’s legitimate. The problem with the MP is that these theories are antithetical to one another, and are adopted in sequence, but Trevor’s scientific conclusions never change. Olmesartan the antagonist is beneficial, and olmesartan the agonist is still beneficial. The kindest thing I can say about this is that it is magical thinking.
But wait, there’s more.
Trevor claims that he has shown that the 25-D precursor of Vitamin D is an agonist of the Vitamin D Receptor, and that in agonizing (turning off) that receptor, 25-D turns off innate immune response to the invading bacteria that he believes are the true pathogenic agents in autoimmune disease.
Furthermore, he has claimed to the FDA to have deduced that that 25-D is a problem even though by his own calculations it is held into the pocket 10 times more weakly than 1,25-D, and that therefore it will kick 1,25D out of the pocket only at high concentrations relative to 1,25-D. If he’d bothered to read the literature, he’d find that his calculations are off by a factor of 50 to 100 – the literature says that 25-D is held to the binding pocket of the VDR 500 – 1000 times more weakly than 1,25-D. But those were just piddling little experiments on real systems, not properly done in silico work.
Trevor’s made the general claim of antagonism other places, as well:
The problem with 25-vitamin D is that it can also physically bind to the VDR and when that happens the process stops. It is called an antagonist because it cannot activate the VDR like the agonist 1,25-D, so none of the hundreds of genes get transcribed into mRNA. High concentrations of 25-D from supplementing can displace 1,25-D stopping the process.
Soooooo…. The 25-D metabolite of Vitamin D is an antagonist of the Vitamin D Receptor. Yes?
A simple clarification of the above abstract:
1,25-D is the only metabolite that turns the VDR on. Everything else turns it off, or at least modifies its capabilities. So exogenous Vitamin D and 25-D both bind into the VDR and block it from working properly. They will displace any 1,25-D from the receptor in a dose-dependent manner. The higher the concentration of Vitamin-D or 25-D competing with the endogenous 1,25-D the more of that 1,25-D will be displaced from the VDR. That occurs in a manner represented by the displacement graphs in the FDA presentation.

A high concentration of 25D (dietary vitamin D) provides antagonist ligands to the VDRs, blocking 1,25D from docking to them. This prevents the innate immune system from being activated.

Aaaaand yes.
Although 25-D has some physiologic activity, for example, binding to the Vitamin D Binding Protein (VDP), and the Cartilage Oligomeric Matrix Protein (COMP, see later in this review), it cannot activate the transcriptional activity of the VDR.

Now, keep in mind these claims are solely based on the in silico experiments conducted by Marshall and Marshall alone, purporting to show that the 25-D has an antagonistic effect on the Vitamin D receptor, and that this is important despite the fact that cells using the VDR for signaling accept 25-D from the Vitamin D binding protein, then convert 25-D to the more potent 1,25-D variant that is generally accepted to be the biologically active form. Just how the problematic 25-D gets into the cell and all the way to the nucleus without being converted to 1,25-D (cells are very efficient at doing that) is never explained, and one is tempted to ask just how much Trevor knows about the difference between cell surface and nuclear receptors. Be that as it may, these are qualitative and quantitative predictions we can use to test Trevor’s theories against reality.
And someone did. Well, they didn’t set out to test Trevor’s theories, they set out to conduct science by testing a series of compounds that might be expected to turn on the VDR – i.e. they wanted to see what makes a good agonist. They found that 25-D (labeled by the more mainstream scientific “25(OH)D” in that paper) begins to turn on VDR-related gene expression at a concentration somewhere between 50 and 250 times as great as the concentration at which 1,25-D initiates that same VDR-related gene expression. That’s pretty good agreement with the previous literature, but what you as a layman should be noting is not so much the quantitative aspect as the qualitative: 25-D tuned ON gene expression. If you’ve been paying attention up until now, you should be thinking “agonist”. A weak one to be sure, but then you’d expect something that binds 500 – 1000 times weaker to the pocket to be a weaker agonist. But an antagonist would not turn on gene expression at all.
Here’s a thread on the MP forum attacking that 2010 paper. What’s Trevor’s problem with that paper? Well, he has a couple of problems that the levels of 25-D needed to effect transcription are well above physiologic levels:
Once you figure out how to read the figure you can see the primary flaw in their argument - 25-D only started to induce significant transcription when it is at concentrations around 250nmol/L, or 100ng/ml. Which levels are of course toxic in-vivo.

Now here’s my take on that result. If the previous Vitamin D / VDR binding studies are correct, one might simplistically expect that 25-D would be oh, I don’t know, a few hundred times less able to trigger gene expression than 1,25D. Now that’s a bit simple minded, active transport, messenger protein binding, and a whole lot of other things might throw that number off, but in general, one would expect that, in the absence of the enzyme that converts 25-D to 1,25-D one would need a whole lot more of 25-D than 1,25-D to affect VDR gene transcription in a live cell, if 25-D were to be a weak agonist of the VDR.
And what do we see in Lou et al.’s paper? We see that you need a lot more 25-D than 1,25-D to light up gene expression. But activate the genes 25-D did. That’s the activity of a (weak) agonist, not an antagonist of any sort. I’d say that’s in pretty good agreement with the previous mainstream Vitamin D work, and pretty much at fundamental odds with any predictions one might have made based on Trevor’s work. Antagonists don’t turn into agonists. Unless they’re a mixed agonist / antagonist – but that is never what Trevor claimed form his model. Any attempt to retrofit the results of this wonderful model to claim that 25-D was predicted to be a weak agonist at high concentrations would be what kind of logical fallacy? Anyone? Bueller? That’s riiiiight: moving the goalposts fallacy.
Somehow Trevor walks away from a result clearly showing that 25-D is weak agonist with the idea that the results show it’s not an agonist at all:
Now there are a number of other defects in this study which tend to distract from the essential value of what this group did - they confirmed that at physiological concentrations, 25-D is not a VDR agonist.
Which is a nice Christmas present indeed.

Lump of coal is more like it. What that paper really showed is 1) 25-D is a weak agonist and 2) it doesn’t bind nearly as well to the VDR pocket as Trevor claims it does.
As Russ, one of the faithful on the board notices:
I thought that agonism vs. antagonism was dependent on the structure of the molecule and how it fits into the binding pocket of the receptor. I wouldn't have thought that something could be antagonistic at low concentrations and agonistic at high concentrations. But from reading this thread it sounds like Vitamin D is an antagonist at normal physiological concentrations but turns into an agonist at super high concentrations (above the level of toxicity). Am I missing something?

No, Russ, you’re not missing something. Keep that critical thought capacity open, dude, it sounds like you haven’t drunk all of your glass of Kool Aid yet.
And yet another moving goalpost shows up in that thread: Trevor complains that they only looked at the transcription of one gene – one known to be transcribed by the activated VDR. His complaint? What about the other 899 thought to be transcribed by the VDR? Didja check those? Well, didja? No. We know this gene is transcribed by the VDR, why do we need the other 899? This gene is quiet when there’s no signal from the VDR, and it lights up in the presence of 25-D. I think reasonable people would conclude 25-D is having some agonistic effect on gene expression. Asking about the other 899 genes in a wide variety of cells thought to be influenced by VDR signaling is: … moving the goalpost. It’s not “looking at the whole story” it’s asking someone to conduct an impossibly complex experiment. If Trevor thinks this gene is somehow not representative, he’s got to do one of two things – point in the literature where someone has done an experiment that shows this gene behaves differently from the other 899, or do the experiment himself. But none of Trevor’s researchers have ever conducted a single in vitro experiment to substantiate his claims.
How do I know that?
“We don't have in vitro data as of yet.”
Jcwat101 is Joyce Waterhouse , one of the MP Foundation staff, and a co-author on several of its publications, so I’d say that’s a pretty authoritative source. Let me be very clear. If a drug company went to the FDA with a new drug, or even to apply for a new use for an approved drug, without any in vitro or animal in vivo data (also not conducted by the MP) THE FDA WOULD THROW THEM OUT OF BETHESDA.
But you know what? The whole argument I made above about why I believe that 25-D is a weak agonist of the VDR was an exercise in idiocy. Why? Because, while the VDR is certainly involved in innate immunity, it is far from clear (and Trevor is far from having proven) that it is the MAJOR factor in innate immunity. In addition to that little hole in the MP story, the MP disease model completely ignores the effects of the acquired immune system. Innate immunity is a first line defense before the heavy artillery of the immune system gets called in. This part of the immune system remembers pathogens its seen before, and really targets them with a number of killing cells. Trevor’s gone from “Vitamin D is a factor in innate immunity” to “if you have too much Vitamin D your immune system can’t respond to invaders”. Hypothetical invaders at that, but we’ll get to that.
These leaps in logic are perfectly fine for putting forward hypotheses to test, but they are not acceptable in a finished thesis such as what the MP advocates claim to have. I’ll give you another example of this kind of jumping from “this might be true” to “this MUST be true” in Trevor’s logic:
I was asked how we could search the bacterial genomes and identify the ligand/chemical which the bacteria might produce to block the action of the VDR, and I responded that it would be like searching for a needle in a haystack.

Well, I was wrong. Pasteur's law struck again, and I now have isolated at least one nanomolar-grade (strong) antagonist which is formed by a special type of bacteria which like to live in biofilms, and which are very poorly studied, and almost impossible to culture.

The breakthrough came when I started to look at a recent paper on some strange bacteria which had been isolated from biofilms on prothestic joints. As you know, I have a complete disease model now, so I understand exactly where prostheses fit in the overall scheme of things, and I understand that healthy folk are just sick folk whose bacterial load has not yet made them very ill So it was with that jaundiced eye I read this paper:

"Identification of bacteria on the surface of clinically infected and non-infected prosthetic hip joints removed during revision arthroplasties by 16S rRNA gene sequencing and microbiological culture" PMID: 17501992

I immediately knew we had something very important here, and when I researched these special "gliding" bacteria, which move by gliding, perhaps like a snail, rather than by whipping flagella like the common blood-borne bacterial species, I realised we had hit mother-lobe.

Associated with the gliding motion is a unique lipid called capnine, a highly charged lipid, and one which is a strong inhibitor (antagonist) of VDR transcriptional activity.
First of all, before we get to the logic part of this, I want to say as a chemist Trevor uses the word “isolate” in a very unusual way. Isolate means you conduct careful physical experiments to separate lots of compounds in a biological soup, and then use more experimentation to determine the chemical structure of those compounds. It does NOT mean reading about a compound in someone else’s research report and shouting EUREKA! By any normal chemist’s definition, Trevor has “isolated” exactly diddly squat, because he does no lab experiments.
OK, let’s get to the logic part. He wants to test a hypothesis by identifying a protein that might be secreted by his mystery bacteria - so far so good. He goes looking at bacteria he thinks are related to his…oh wait, he using bacteria WITH cell walls from a biofilm to model his putative pathogenic bacteria without cell walls, and that kind of analogy’s perfectly kosher with him, but we mainstream scientists have to test all 900 genes activated by the VDR before we can be SURE we are looking at VDR activation… OK, OK, let’s suspend our disbelief about the interchangeability of these bacteria and play along. He sees a substance these bacteria secrete that help them glide through the biofilm. BINGO! It fits in his VDR molecular dynamics model of the VDR! It MUST be the culprit antagonist!
Do you see the problem here? The logical leap that should not be made without evidence here? First of all, if you believe Lou et. Al’s paper showing 25-D is a weak agonist of the VDR, it’s pretty clear Trevor’s model can’t tell an agonist from an antagonist from a hole in the ground. You’d need more evidence than that model to get me to believe that something is an antagonist of the VDR even IF I accepted the premise that blocking the VDR totally cripples the body’s ability to fight off bacteria. Which I don’t. It’s also an unwarranted logical leap because of where the VDR sits in the cell. On the nucleus. Just how does this capnine get past the cell wall? The cell wall evolved to keep most of this kind of crap out of our cells, otherwise human kind would have dies out the first time it wandered off the plains of Africa into a swamp. Furthermore, where’s the evidence that these bacteria secrete enough capnine to use as a chemical weapon? As far as we know, they secrete just enough to give them mobility in the biofilm. Finally, what makes him think that his putative cell wall deficient pathogens secrete capnine in the first place? They are supposed to infect T cells and make them go haywire. Why would a bacteria that does infects cells in that manner secrete capnine at all? Do they build a bioflim INSIDE the T cell? Trevor would have to address all of those issues with careful experimentation before anyone in the mainstream community will take him seriously. They are not trivial logical holes in his story, you could drive a Mack truck through them.
May I stop now? Do you believe me that Trevor’s model is, well, I don’t know what it is, but I know what it isn’t. It isn’t science.
I apologize to Kelly for the long-winded response. It’s just that there is so MUCH wrong with Trevor’s reasoning it’s hard to know where to begin. I also see how the MP advocates argue, and I’ve covered most of their canned retorts, as well as pointing out their major logical fallacy: moving the goalposts.
But wait, there’s more.
I’m not done yet. We haven’t seen the last goalpost moved yet. In the last (and final!) installment, I’m going to come to the bacterial and clinical evidence that Trevor’s put forward and treat it to the same scrutiny as I have the in silico evidence.

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