The Chinese Room Argument
3 weeks ago I published a post about a paper that I thought would be a real bombshell, in effect contradicting a paper in a prestigious journal, and strongly arguing from real data that the pandemic virus could have been made in a lab, quite possibly Wuhan. .
Absolutely nothing has happened. No letters to PNAS (the source of the article) to Cell (the source of the criticized study). With a question of this magnitude and importance you’d think Nature or Science would weigh in about it. The origin of the pandemic virus is certainly they’ve covered extensively.
So I’m going to send this to all concerned and see if I get any feedback.
Here is the original post.
Everyone knows that the Chinese have been less than forthcoming about the origin of the pandemic virus (SARS-CoV-2). An article in the current Proceedings of the National Academy of Sciences — https://doi.org/10.1073/pnas.2202769119 arguesthat US data, which hasn’t been released, and some 290 pages of which has been redacted could shed a good deal of light on the subject (without any help from China). One of the authors is an economist, but the other has serious biochemical chops — https://www.pharmacology.cuimc.columbia.edu/profile/neil-l-harrison-phd.
Basically a variety of US institutions (see the paper — it’s freely available) have been working with the lab at Wuhan for years modifying the virus, long before the pandemic. The paper names the names etc. etc. and is quite detailed, but I want to explain the evidence that the virus could have been produced (by human modification) at the Wuhan lab. It has to do with a site in a viral protein which says ‘cut here’.
Here is more background than many readers will need, but the virus has affected us all and I want to make it accessible to as many as possible.
Proteins are linear strings of amino acids, just as this post is a linear sequence of letters, spaces and punctuation.
We have fewer amino acids (20 to be exact) than letters and to save space each one has a one letter abbreviation (A for alanine V for valine, etc. etc.). The spike protein (the SARS-CoV-2 protein binding to the receptor for it on our cells) is quite long (1,273 amino acids all in a row).
Our genome codes for 588 proteins (called proteases) whose job it is to cut up other proteins. Obviously, it would be a disaster if they worked indiscriminately. So each cuts at a particular sequence of amino acids. Think of the protease as a key and the sequence as a lock. One protease called furin cuts in the middle of an 8 amino acid sequence RRAR’SVAS (R stands for aRginine and S for Serine). This is called the furin cleavage site (FCS)
A paper (The origins of SARS-CoV-2: A critical review. Cell 184, 4848–4856 (2021) argued that the amino acid sequence of the FCS in SARS-CoV-2 is an unusual, nonstandard sequence for an FCS and that nobody in a laboratory would design such a novel FCS. So, like many, I skimmed the paper and accepted its conclusions, as Cell is one of the premier molecular biology journals.
Moreover — “The exact FCS sequence present in SARS-CoV-2 has recently been introduced into the spike protein of SARS-CoV-1 (the original SARS virus hitting Hong Kong) in the laboratory, in an elegant series of experiments, with predictable consequences in terms of enhanced viral transmissibility and pathogenicity.”
So there you have it. The 8 amino acid sequence (RRAR’SVAS) sticking out like a sore thumb in the genome of SARS-CoV-2 essentially saying to furin “open’here.”
The point of the paper, is that there is a lot of US work, publicly funded, yet not in the public domain which would go a long way to clear things up.
Sounds like Watergate doesn’t it?
Everyone knows that the Chinese have been less than forthcoming about the origin of the pandemic virus (SARS-CoV-2). An article in the current Proceedings of the National Academy of Sciences — https://doi.org/10.1073/pnas.2202769119 argues that US data, which hasn’t been released, and some 290 pages of which has been redacted could shed a good deal of light on the subject (without any help from China). One of the authors is an economist, but the other has serious biochemical chops — https://www.pharmacology.cuimc.columbia.edu/profile/neil-l-harrison-phd.
Basically a variety of US institutions (see the paper — it’s freely available) have been working with the lab at Wuhan for years modifying the virus, long before the pandemic. The paper names the names etc. etc. and is quite detailed, but I want to explain the evidence that the virus could have been produced (by human modification) at the Wuhan lab. It has to do with a site in a viral protein which says ‘cut here’.
Here is more background than many readers will need, but the virus has affected us all and I want to make it accessible to as many as possible.
Proteins are linear strings of amino acids, just as this post is a linear sequence of letters, spaces and punctuation.
We have fewer amino acids (20 to be exact) than letters and to save space each one has a one letter abbreviation (A for alanine V for valine, etc. etc.). The spike protein (the SARS-CoV-2 protein binding to the receptor for it on our cells) is quite long (1,273 amino acids all in a row).
Our genome codes for 588 proteins (called proteases) whose job it is to cut up other proteins. Obviously, it would be a disaster if they worked indiscriminately. So each cuts at a particular sequence of amino acids. Think of the protease as a key and the sequence as a lock. One protease called furin cuts in the middle of an 8 amino acid sequence RRAR’SVAS (R stands for aRginine and S for Serine). This is called the furin cleavage site (FCS)
A paper (The origins of SARS-CoV-2: A critical review. Cell 184, 4848–4856 (2021) argued that the amino acid sequence of the FCS in SARS-CoV-2 is an unusual, nonstandard sequence for an FCS and that nobody in a laboratory would design such a novel FCS. So, like many, I skimmed the paper and accepted its conclusions, as Cell is one of the premier molecular biology journals.
Moreover — “The exact FCS sequence present in SARS-CoV-2 has recently been introduced into the spike protein of SARS-CoV-1 (the original SARS virus hitting Hong Kong) in the laboratory, in an elegant series of experiments, with predictable consequences in terms of enhanced viral transmissibility and pathogenicity.”
So there you have it. The 8 amino acid sequence (RRAR’SVAS) sticking out like a sore thumb in the genome of SARS-CoV-2 essentially saying to furin “open’here.”
The point of the paper, is that there is a lot of US work, publicly funded, yet not in the public domain which would go a long way to clear things up.
Sounds like Watergate doesn’t it?
Our genome contains 826 different genes for G Protein Coupled Receptors (GPCRs) which are targeted by at least 475 FDA approved drugs (Nature vol. 587 p. 553 ’20 ). Yet part of the fascination of reading the current literature is the surprises it brings.
Our basic understanding was that the GPCRs sit on the surface of the cell waiting for ligands outside the cell to bind to it, which produces a conformational change on the cytoplasmic side of the cell membrane, changing the way the GPCR binds to the G protein, triggering all sorts of effects inside the cell.
As far as I recall, we never thought that different GPCRs would bind to each other in the cell membrane, even though a single cell can express ‘up to’ 100 different GPCRs [ Mol. Pharm. vol. 88 pp. 181 – 187 ’15 ]. Neurons express GPCRs and some are thought to be involved in neuropathic pain
But that’s exactly what Proc. Natl. Acad. Sci. vol. 119 e2123511119 ’22 is saying.
First a few definitions, if you’re as rusty about them as I was
A cytokine is an extracellular protein or peptide helping cells to communicate with each other. A chemokine is an extracellular protein which attracts cells.
Our genome has over 50 chemokines. Most are proteins with about 70 amino acids. The are classified by where the cysteines lie in them. We have 23 receptors for chemokines, 18 of which are GPCRs. Binding is promiscuous — a given chemokine binds to multiple receptors, and a given receptor binds to multiple chemokines.
Clearly the chemokines and their receptors are intimately involved in inflammation which always involves cell migration. Neurons express chemokine receptors GPCRs and some are thought to be involved in neuropathic pain.
We also know that the nervous system is involved in immune function, particularly inflammation. One prominent neurotransmitter is norepinephrine, and a variety of receptors bind to it. There are 3 alpha1 norepinephrine receptors (a, b and d), all of which are GPCRs.
What is so shocking is that alpha1 GPCRs bind to chemokine receptors (forming heteromers), and that this binding is required for chemokines to have any effect on cell migration. Even more interesting is that binding of norepinephrine to the alpha1 component of the heteromer INHIBITs cell migration.
So how many of our 826 GPCRs bind to each other, and what effects do they have?
Reading the literature is like opening presents, you find new fascinating toys to play with, some of which may actually benefit humanity
It’s always good when a new way to look at a basically untreatable disease comes along. We’ll know soon if looking at filamin A will be useful for Alzheimer’s disease. Here’s another: something we’ve known about for years (polyphosphate) may be important in Amyotrophic Lateral Sclerosis (ALS). I used riluzole for ALS, but never saw any benefit. It may have slowed the decline, but riluzole never stopped disease progression.
It is stated that 10% of ALS is familial, but I think this is an overstatement. Even so mutations in a variety of proteins(superoxide dismutase 1 (SOD1) TDP43, C9orf72) do cause ALS, and studying them has taught us a lot about ALS. There is plenty of work to do. In 2016 a mere 160 mutations in the 153 amino acids of SOD1 had been found, but we still don’t know how they cause ALS despite hundreds of papers on the subject. The proteins have allowed us to make mouse models of ALS, by putting in one or the other of mutated SOD1, TDP43, C9orf72 in motor neurons (or in whole animals)
Some real gumshoe work led to polyphosphate [ Neuron vol. 110 pp. 1603 – 1605 ’22 ]. Obviously in ALS, the motor neurons die, but recent work has shown that motor neurons are killed by neighboring astrocytes (containing any of the 3 the mutant proteins), when they are cultured together. Normal astrocytes don’t do this.
So a lot of hard work found that it was polyphosphate in the supernatant fluid that was the killer.
So what is polyphosphate? It’s been known for years, and is found in ALL cells — bacterial, plant, animal. It also produced abiotically in volcanic exudates and deep sea steam vents. No one knows what it does, so it has been called a molecular fossil. Again teleology should inform biologic research (but it doesn’t). Polyphosphate must be doing something useful or it wouldn’t be present in all living cells.
Chemically, polyphosphate is a chain of HUNDREDS to THOUSANDS of phosphate residues linked by high energy phosphoanhydride bonds.
Like this —
HO – PO2 – OH + HO -PO2 -OH –> HO – PO2 – 0 – PO2 – OH + H20
— the – O – in the middle is the phosphoanhydride bond
The authors treated motor neurons in culture with polyphosphate and found that it killed 40% of them. So what? Schmidt’s law of pharmacology, says that enough of anything will do anything, So they looked at the spinal cords of patients dying of ALS and found that polyphosphate levels were higher than in neurologically normal controls.
So it’s open season on polyphosphate. Finding out what it does in normal cells, finding out how it kills motor neurons, finding out if decreasing its levels will help ALS (it does in cultures of motor neurons but that’s a long way from a living patient). It’s an entirely new angle on an awful disease, with no useful treatment. There is simply an enormous amount of work to be done.
Watch this space.
When our tools were blunt, the brain looked a lot simpler than it does now.
Example #1: Locus coeruleus (LC). This is a tiny group of neurons deep in the brain. It looks blue to the naked eye, if you’ve gone to medical school as I have and dissected a brain. This is held to be due to neuromelanin produced by the neurotransmitter it uses (norepinephrine). Neurons using dopamine as a neurotransmitter also produce neuromelanin but it’s brown. The two differ by just one oxygen atom.
The LC is tiny in primates, only 15,000 – 50,000 neurons depending on species and who you read.. The rat (where most experiments are done) has only 1,500 in a space 1000 microns (1 millimeter) x 200 x 500 microns.
So until now any attempt to stimulate the locus coeruleus with an electrode alerted the animal.
Why? Two reasons.
1. The LC is so small that any electrode stimulating it, stimulated every neuron.
2. Because that tiny nucleus sends fibers all over the brain, releasing norepinephrine everywhere, and not just at synapses. This is called volume neurotransmission. Most places on the axons of a LC neuron showing synaptic vesicles (where norepinephrine is found), don’t have a dendrite or any sort synaptic specialization next to them. So the LC innervates the whole brain, in the same way that our brain innervates our muscles.
Stimulate the LC of a rat and the brain is flooded with norepinephrine and the animal wakes up.
Well that was the case until technology marched on and miniaturization of electrodes allowed us to record from a 10 – 20 neurons at a time in the LC when stimulation was applied. Those responding to a given stimulus were called ensembles. Of 285 single LC neurons studied in 15 rats, 115 participated in multiple ensembles, 149 participated only in a single ensemble and 21 didn’t participate in any. Activity of different ensembles produced different brain states — not all were wide awake. You can read all about this in Proc. Natl. Acad. Sci. vol. 119 e21116507119 ’22.
Volume neurotransmission is important because the following neurotransmitters use it — dopamine, serotonin, acetyl choline and norepinephrine. Each has only a small number of cells using them as a transmitter. The ramification of these neurons is incredible.
For instance, “human serotonergic neurons, which are estimated to extend axons for 350 meters” [ Science vol. 366 3aaw9997 p. 4 ’19 ], so the fibers are everywhere in the brain. I couldn’t find a statistic for axons of the locus coeruleus but those of neurons using acetyl choline as a neurotransmitter are estimated to have axons extending for 31 meters.
So now you see why massive release of any of the 4 neurotransmitters mentioned (norepinephrine, serotonin, dopamine, acetyl choline) would have profound effects on brain states. The four are vitally involved in emotional state and psychiatric disease. The SSRIs treat depression, they prevent reuptake of released serotonin. Cocaine has similar effects on dopamine. The list goes on and on and on.
Maybe be we’ll be able to slice and dice these nuclei in the future to produce more subtle effects on brain function.
Example #2: Dendritic diversity — that’s for next time. This post is long enough.
The FDA will approve less than perfect therapies if there is nothing useful for a serious condition. Consider the following from Proc. Natl. Acad. Sci. vol. 119 e2120512119 ’22
“KRAS is the most frequently mutated oncogene in human cancer, with mutations detected across many lineages, particularly in the pancreas, colon, and lungs. Among the most commonly activating KRAS mutations at codons 12, 13, and 61, G12C occurs in ∼13% of lung and 3% of colorectal carcinomas and at lower frequencies in other tumors.
“In locally advanced or metastatic non–small-cell lung cancer (NSCLC) patients with KRASG12C mutations who have received at least one prior systemic therapy” treatment with sotorasib resulted in the following “objective response in 37.1% of the patients, with a median duration of response was 11.1 months.” This is hardly a cure, but nonetheless “This promising anticancer activity has resulted in accelerated approval from the US Food & Drug Administration”
Which brings me to the current CMS study from Cassava Sciences. I’ll let them speak for themselves. https://finance.yahoo.com/news/cassava-sciences-reports-first-quarter-130000375.html
“Cognition Maintenance Study (CMS) – on-going
In May 2021, we initiated a Cognition Maintenance Study (CMS). This is a double-blind, randomized, placebo-controlled study of simufilam in patients with mild-to-moderate Alzheimer’s disease. Study participants are randomized (1:1) to simufilam or placebo for six months. To enroll in the CMS, patients must have previously completed 12 months or more of open-label treatment with simufilam. The CMS is designed to evaluate simufilam’s effects on cognition and health outcomes in Alzheimer’s patients who continue with drug treatment versus patients who discontinue drug treatment. The target enrollment for the CMS is approximately 100 subjects. Over 75 subjects have been enrolled in the CMS and 35 have completed the study.”
Even though the open label study was not randomized, this one will be.
Only someone who has actually taken care of patients would know the following. People who are getting no benefit from a drug will soon stop taking it. This was particularly true for my experience with Cognex for Alzheimer’s disease.
Which is exactly why the fact that 75 patients who’ve been on Simufilam have decided to continue on in the CMS study. Presumably they feel they are getting some benefit.
There are two possible hookers to this
l. The patients are being paid to enter CMS
2. The original cohort was 200, not all of whom have finished the 1 year. So we don’t know how many could have been in CMS but chose not to.
As I discussed in an earlier post, the most impressive thing (to me at least) was that at 9 months 5/50 had significant improvement in their cognition — here’s a link — https://luysii.wordpress.com/2021/08/25/cassava-sciences-9-month-data-is-probably-better-than-they-realize/.
The CMS study should give us an idea of how they fared at 1 year and at 18 months.
If:
l. gains in cognition were maintained on Simufilam
2. gains in cognition were lost off Simufilam
FDA approval should follow quickly.
Results on the 75 will be available this year. Also available this year will be 1 year results on all 200 entering the open label study.
There are two other double blind studies in progress which will provide more definitive answers, but they are far from full and will take much longer to complete. So stay tuned.