A Supercomputer Analyzed Covid-19 — and an Interesting New Theory Has Emerged

BY Herschel Smith
2 months, 3 weeks ago

Medium.com (via reader WiscoDave).

Earlier this summer, the Summit supercomputer at Oak Ridge National Lab in Tennessee set about crunching data on more than 40,000 genes from 17,000 genetic samples in an effort to better understand Covid-19. Summit is the second-fastest computer in the world, but the process — which involved analyzing 2.5 billion genetic combinations — still took more than a week.

Time on this computer is heavily leveraged and a lot of code writers and researchers use it.  I suspect that they didn’t use every processor, and it would be interesting to know how many CPU-hours were tallied.

When Summit was done, researchers analyzed the results. It was, in the words of Dr. Daniel Jacobson, lead researcher and chief scientist for computational systems biology at Oak Ridge, a “eureka moment.” The computer had revealed a new theory about how Covid-19 impacts the body: the bradykinin hypothesis. The hypothesis provides a model that explains many aspects of Covid-19, including some of its most bizarre symptoms. It also suggests 10-plus potential treatments, many of which are already FDA approved. Jacobson’s group published their results in a paper in the journal eLife in early July.

According to the team’s findings, a Covid-19 infection generally begins when the virus enters the body through ACE2 receptors in the nose, (The receptors, which the virus is known to target, are abundant there.) The virus then proceeds through the body, entering cells in other places where ACE2 is also present: the intestines, kidneys, and heart. This likely accounts for at least some of the disease’s cardiac and GI symptoms.

But once Covid-19 has established itself in the body, things start to get really interesting. According to Jacobson’s group, the data Summit analyzed shows that Covid-19 isn’t content to simply infect cells that already express lots of ACE2 receptors. Instead, it actively hijacks the body’s own systems, tricking it into upregulating ACE2 receptors in places where they’re usually expressed at low or medium levels, including the lungs.

In this sense, Covid-19 is like a burglar who slips in your unlocked second-floor window and starts to ransack your house. Once inside, though, they don’t just take your stuff — they also throw open all your doors and windows so their accomplices can rush in and help pillage more efficiently.

The renin–angiotensin system (RAS) controls many aspects of the circulatory system, including the body’s levels of a chemical called bradykinin, which normally helps to regulate blood pressure. According to the team’s analysis, when the virus tweaks the RAS, it causes the body’s mechanisms for regulating bradykinin to go haywire. Bradykinin receptors are resensitized, and the body also stops effectively breaking down bradykinin. (ACE normally degrades bradykinin, but when the virus downregulates it, it can’t do this as effectively.)

The end result, the researchers say, is to release a bradykinin storm — a massive, runaway buildup of bradykinin in the body. According to the bradykinin hypothesis, it’s this storm that is ultimately responsible for many of Covid-19’s deadly effects. Jacobson’s team says in their paper that “the pathology of Covid-19 is likely the result of Bradykinin Storms rather than cytokine storms,” which had been previously identified in Covid-19 patients, but that “the two may be intricately linked.” Other papers had previously identified bradykinin storms as a possible cause of Covid-19’s pathologies.

As bradykinin builds up in the body, it dramatically increases vascular permeability. In short, it makes your blood vessels leaky. This aligns with recent clinical data, which increasingly views Covid-19 primarily as a vascular disease, rather than a respiratory one. But Covid-19 still has a massive effect on the lungs. As blood vessels start to leak due to a bradykinin storm, the researchers say, the lungs can fill with fluid. Immune cells also leak out into the lungs, Jacobson’s team found, causing inflammation.

An awful lot of smart people (e.g., Paul Cottrell, J.C., EMCrit, etc.) have said just about from the beginning that this was a blood disease first, not a lung disease [first].  You can Google “Happy Hypoxia” and see that Dr. Cameron Kyle-Sidell said from the first weeks of this disease in NYC that it wasn’t an ARDS disease as advertised by the CDC.  At last look, the idiot “experts” in my home state were still pushing this notion.

And Covid-19 has another especially insidious trick. Through another pathway, the team’s data shows, it increases production of hyaluronic acid (HLA) in the lungs. HLA is often used in soaps and lotions for its ability to absorb more than 1,000 times its weight in fluid. When it combines with fluid leaking into the lungs, the results are disastrous: It forms a hydrogel, which can fill the lungs in some patients. According to Jacobson, once this happens, “it’s like trying to breathe through Jell-O.”

This may explain why ventilators have proven less effective in treating advanced Covid-19 than doctors originally expected, based on experiences with other viruses. “It reaches a point where regardless of how much oxygen you pump in, it doesn’t matter, because the alveoli in the lungs are filled with this hydrogel,” Jacobson says. “The lungs become like a water balloon.” Patients can suffocate even while receiving full breathing support.

The bradykinin hypothesis also extends to many of Covid-19’s effects on the heart. About one in five hospitalized Covid-19 patients have damage to their hearts, even if they never had cardiac issues before. Some of this is likely due to the virus infecting the heart directly through its ACE2 receptors. But the RAS also controls aspects of cardiac contractions and blood pressure. According to the researchers, bradykinin storms could create arrhythmias and low blood pressure, which are often seen in Covid-19 patients.

The upshot is that there is hope for those who are badly affected.

As Jacobson and team point out, several drugs target aspects of the RAS and are already FDA approved to treat other conditions. They could arguably be applied to treating Covid-19 as well. Several, like danazol, stanozolol, and ecallantide, reduce bradykinin production and could potentially stop a deadly bradykinin storm. Others, like icatibant, reduce bradykinin signaling and could blunt its effects once it’s already in the body.

Interestingly, Jacobson’s team also suggests vitamin D as a potentially useful Covid-19 drug. The vitamin is involved in the RAS system and could prove helpful by reducing levels of another compound, known as REN. Again, this could stop potentially deadly bradykinin storms from forming. The researchers note that vitamin D has already been shown to help those with Covid-19. The vitamin is readily available over the counter, and around 20% of the population is deficient. If indeed the vitamin proves effective at reducing the severity of bradykinin storms, it could be an easy, relatively safe way to reduce the severity of the virus.

Other compounds could treat symptoms associated with bradykinin storms. Hymecromone, for example, could reduce hyaluronic acid levels, potentially stopping deadly hydrogels from forming in the lungs. And timbetasin could mimic the mechanism that the researchers believe protects women from more severe Covid-19 infections. All of these potential treatments are speculative, of course, and would need to be studied in a rigorous, controlled environment before their effectiveness could be determined and they could be used more broadly.

I’d say this was a good use of FedGov resources at ORNL, and the CDC and NIH is still as incompetent and lethargic as ever.  Or perhaps they never intended to create anything but fear and panic.


Comments

  1. On September 3, 2020 at 1:01 pm, Stan Back said:

    Esteemed party member comrade kommissar Fraudski already owns the vaccine patent along with Billy Gates.
    Fraudski stated back in 2017 that diabolical KGB mastermind Trumphitlersatan-SS would face a plandemic crisis.
    Any word on the CDC downplaying the “pandemic” status and the fact that 94% of fatalities had pre-existing conditions?
    No word on Das Radio about 63% of all counties in the U.S. having less than five killed by kung-flu.
    The memory hole ate that report on orders from MiniTRU.

  2. On September 3, 2020 at 1:25 pm, 41mag said:

    Good use of FedGov money because a computer is results oriented.

    Once humans get their paws on data, it can become political.

  3. On September 3, 2020 at 1:52 pm, Fred said:

    Re vit D, so, grandma was right all along when she said go outside and play. I’m on it.

  4. On September 3, 2020 at 5:43 pm, The Dark Lord said:

    correlation does not equal causation … they seem to be focused on the symptoms of 5% of the dead and are ignoring the 95% … data people tend to do that … many of these things could easily be pre-existing yet un-diagnosed conditions which wouldn’t even have been noticed had the person not died …

    when they have a theory as to why over 50% of infected persons of ANY AGE show no symptoms … and the same theory explains why children almost never catch it and why a huge percentage of people never get infected (infected does not equal sick, Diamond Princess 75% of people never caught the virus, period ) then I might listen … until then this is more computer “modeling” with statistics nonsense … barely science …

    remember “immune” doesn’t mean you can’t get infected (infected being the presence of the virus at any level) immune means you don’t get “sick” i.e. your body beats the virus down so fast so no symptoms … immune means your body knows how to kill it … either from prior infection, vaccine or just a strong immune system that hammers it … immune doesn’t magically cause the virus to bypass you …

  5. On September 3, 2020 at 6:34 pm, MN Steel said:

    I haven’t had a flu shot since the Army 18 years ago, and haven’t got the flu. I also worked night-shift registering ER patients for 6 years, sitting 3 feet from all those sick people.

    Of course, I’ve also taken 5000 IU of Vitamin D3 daily in the winter, and 3000 IU in the summer since I got out of Hawaii and the Army.

    And I’m not taking any more vaccines.

  6. On September 3, 2020 at 8:58 pm, WT said:

    There’s a saying about about computers, it goes like this.
    Garbage in Garbage out

  7. On September 3, 2020 at 9:13 pm, Herschel Smith said:

    @Dark, @WT,

    No. None of that is even close to correct.

    This modeling was based on first principles, physiological and microbiological, and had a healthy dose of Monte Carlo running billions of simulations.

    What the model predicts they would see (which was unknown to them prior to running the simulations) happens to be what actually happens to Covid patients, virtually exactly.

    This is the holy grail of physical and engineering models. When it works, you go home, tell your spouse that you understand what the virus is doing, and you drink a glass of wine that night in celebration.

    Again: The upshot. They know how to treat it, even if the FDA is slow to approve it.

    This is what it looks like when men behave as they are designed and created, i.e., to think God’s thoughts after him, and take dominion of the world.

    You now know WHY it happens and you can interdict it.

  8. On September 3, 2020 at 10:48 pm, Bad_Brad said:

    Regarding the fastest mainframes around. I use to do a bunch of machine work for Lawrence Livermore Labs, a DOE, and at that time they had the fastest computing system around. But it wasn’t a mainframe. They had 48 PC’s wired in line and in series. They are the ones that did the computing on the nuclear cloud headed this way from Japan when they had their little ordeal. They tracked the currents too. Talented people work there.
    About the RONA. I was getting treated for throat cancer when everything blew up so I was seeing more than my fair share of medical professionals. To summarize, most knew the masks are a joke. Most are waiting on some non political good info on how to avoid the Rona. They new Fauci was a weasel with unreliable info. And they will al study this computers findings long and hard.

  9. On September 4, 2020 at 12:01 am, BRVTVS said:

    Don’t forget the Selenium. https://www.mdpi.com/2072-6643/12/7/2098

  10. On September 11, 2020 at 11:12 am, WT said:

    @Herschel So where or “WHO” did this initial data come from, the “CDC” (who’s newly released numbers are a fraction of the numbers used in the “Study”) or the “Hospitals” that have been “Incentivised” to inflate numbers, As stated previously, “Garbage in Garbage out” I wouldn’t base a single decision on the aforementioned “Study”

    Scamdemic, Plandemic, Info:

    https://www.globalresearch.ca/no-one-has-died-coronavirus/5717668 (not a fan of site, but this story is still there, unable to locate original source, imagine that…)

    Let’s not forget how the Americas Frontline Doctors were treated.

    For a laugh:
    https://21stcenturywire.com/2020/09/04/censors-scrambling-after-cdc-death-o-meter-malfunctions/

    really I could go on for days, if I didn’t have more important things to do…

    The farce runs deep….. and apparently you are fully invested….

  11. On September 11, 2020 at 11:16 am, Herschel Smith said:

    @WT,

    You apparently have no knowledge of my prior posts on SARS-CoV-2. Go back and do some study on prior posts.

    Data has nothing to do with it. This was model-building from first principles. If you do not understand the construction of engineering models, I cannot possibly explain it to you in a comment.

    The point of all of this was that we know exactly what the bug does and how it does it. And that leads to knowing how to fix the problems is creates.

    This bug was generated at Fort Dix/UNC/Harvard by Anthony Fauci, and then shipped over to the virology lab in Wuhan using tax dollars to continue gain-of-function research so that big pharma could sell vaccines. Hydrochloroquine, Vitamin D, and antibiotics could have prevented most of the deaths that occurred. The CDC didn’t want to prevent most of the deaths. This was their attempt to aerosolize HIV (it has HIV in the spike protein).

    I could go on, but I have better things to do. Go back and read my posts on this.

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