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SIR — “Simple” Basics of Epidemics

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Here is a simple SIR model — Susceptible- Infected- Removed:

Here, “removed” can be by recovery or death. Obviously parameters are not exact so the next level would explore randomised changes in possible values and time varying models; noting particular clusters that give dramatic outcomes. The S(t) line is an inverted cumulative case curve — if people don’t flee. So C(t) = 1 – S(t) is cumulative cases, a logistic curve. C(t) will at first look exponential until resistance and running out of susceptible population leads to saturation.

A supplementary equation could partition recovery vs death, and we can work back from observed patterns with infection and deaths.

Further analysis could stratify the population as susceptibility varies with factors such as age, preconditions, interaction with others etc. Another issue would be latency between actual infection and onset of observable symptoms. This may couple to the size of injection of infectious agents and we could go on to model the course of the disease.

So, by running the possibilities across a population of simulations and complications, we can build an aggregate picture. We can then extend to models of mutations and long term population dynamics. Think, here, about Behe’s rule about breaking a bodily or cellular mechanism as a way to sharply reduce susceptibility in a race with the mutation rate and spreading of new strains.

(Covid 19 already has two separately “catchable” strains, L and S. Reportedly, each viral replication may inject about six changes, as a rule of thumb. Ponder implications of borders of islands of function, where “break” becomes fatal for the bug.)

We could contrast impact of environmental changes that affect a population all at once. And so forth.

A way to think about what we are going through globally. END

20 Replies to “SIR — “Simple” Basics of Epidemics

  1. 1
    kairosfocus says:

    SIR — “Simple” Basics of Epidemics

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    Truthfreedom says:

    -If what we are seeing is ‘natural’ selection in action:
    HOW is it possible that we, who are the result of evolution, are fighting against that same evolutive process?
    Makes 0 sense.

  4. 4
    kairosfocus says:

    TF, the “undermining” of natural selection by civilised behaviour, public health measures and linked medical care etc has been remarked by strong advocates of Darwinism. That is yet another issue. KF

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    Truthfreedom says:

    @4 Kairosfocus

    TF, the “undermining” of natural selection by civilised behaviour, public health measures and linked medical care etc has been remarked by strong advocates of Darwinism. That is yet another issue.

    ‘Civilised behavior’ is the result of our brain processes, that are determined by evolution.
    So evolution (the creator) has created civilised behavior to correct its own ‘brutality’.
    Wow naturalism. Non-sense is thy name.

  7. 7
    kairosfocus says:

    TF, indeed, evolutionary materialism is self-referentially incoherent to the point of undermining our rationality — and falsifying itself, so evo mat scientism (aka naturalism) will fall under the same stricture. KF

    PS: I keep citing Reppert:

    . . . let us suppose that brain state A [–> notice, state of a wetware, electrochemically operated computational substrate], which is token identical to the thought that all men are mortal, and brain state B, which is token identical to the thought that Socrates is a man, together cause the belief [–> concious, perceptual state or disposition] that Socrates is mortal. It isn’t enough for rational inference that these events be those beliefs, it is also necessary that the causal transaction be in virtue of the content of those thoughts . . . [But] if naturalism is true, then the propositional content is irrelevant to the causal transaction that produces the conclusion, and [so] we do not have a case of rational inference. In rational inference, as Lewis puts it, one thought causes another thought not by being, but by being seen to be, the ground for it. But causal transactions in the brain occur in virtue of the brain’s being in a particular type of state that is relevant to physical causal transactions.

    Haldane, a pioneer of neo-darwinism, noted:

    “It seems to me immensely unlikely that mind is a mere by-product of matter. For if my mental processes are determined wholly by the motions of atoms in my brain I have no reason to suppose that my beliefs are true. They may be sound chemically, but that does not make them sound logically. And hence I have no reason for supposing my brain to be composed of atoms. In order to escape from this necessity of sawing away the branch on which I am sitting, so to speak, I am compelled to believe that mind is not wholly conditioned by matter.” [“When I am dead,” in Possible Worlds: And Other Essays [1927], Chatto and Windus: London, 1932, reprint, p.209. (NB: DI Fellow, Nancy Pearcey brings this right up to date (HT: ENV) in a current book, Finding Truth.)]

  8. 8
    kairosfocus says:

    F/N a key note on potential errors with Covid 19 tests developed in a hurry, with CDC as a cautionary tale KF

    PS Note, even after recovering from their fumble, bureaucratic obstacle courses are an issue in the USA. See an article Such tends to be obscured in the low grade civil war climate that now obtains in the US.

    PPS: There is an issue of cure vs disease, which is worse. Crashing the global economy may well do a lot more damage than the likely after the fact incidence and death rate of Covid-19. Let us be prudent and balanced. In a crisis, one takes decisions on prudence that buy time then further investigation guides onward response. If, time is there to be bought.

  9. 9
    kairosfocus says:

    F/N: Food for thought at WUWT, a comment in thread, by WR . . . the issue is, infections swamping medical capacity and death rate soaring as a result:

    >>Here is the perspective. Merkel said that 50-70% of the (German) population is supposed to be infected. As the Spanish Flu learns this mainly happens in some months (at that time two big waves and a small one). 70% of the US population is about 230 million people. 20% needs a hospital (46 million), 5% an intensive care bed (11.5 million) and 2.5% is supposed to die (nearly 6 million). As soon as the medical system gets overwhelmed the death rate rises from* 0.5% (South Korea), 0.9% (‘Rest of China – ex Wuhan/Hubei) and 1.2% (Princess Cruise) to 5% or more (Wuhan and now Italy). Doubling the 6 million to 12 million deaths.

    A full blown epidemic overwhelmed the top medical system of Wuhan and Northern Italy at around 10.000 registered cases. That’s why nobody should want a full blown epidemic.

    Preventing a full blown epidemic means fighting the virus from the very first moment like in a real war. China and South Korea show that it is possible to beat the virus. If the virus can’t transmit at all (!) in some weeks it will die out. That is why social distancing and containment is that important.

    In western countries people often are going ahead of governments. Flights and activities often were cancelled on a large scale before most governments acted. But ‘better late than never’ this total fight against the smallest enemy has to happen. To prevent the collapse of the medical system and more.

    * A very good analysis and data: >>

    Time to think, and to ponder.

    Early action to suppress entry then to contain spread, seem advisable on such. But, is such politically feasible, especially in low grade civil war USA?


  10. 10
    Jim Thibodeau says:

    “The Democrats are politicizing the coronavirus. This is their new hoax.”

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    kairosfocus says:

    TF, this thread is about modelling primarily. PL documents the facts and on that case, their correction is clearly well-merited: . But then, the US is now in early stage 4th gen civil war and if that folly continues it will learn some hard lessons about consequences of undermining governance; from the four horsemen of the apocalypse. Pestilence and death are half the squad, after all. War and financial collapse with inflation are the other pair. KF

  12. 12
    kairosfocus says:

    U/D: Potentially, a breakthrough on Covid-19, I’d heard it is in use in Japan. Now:

    Gregory Rigano @RiganoESQ
    Replying to @elonmusk @DiderRaoult


    Full peer reviewed study has been released by Didier Raoult MD, PhD ….

    After 6 days 100% of patients treated with HCQ + Azithromycin were virologically cured

    p-value LT .0001

    Let’s see if this holds up.


  13. 13
    bornagain77 says:


    Let’s see if this holds up.

    Let’s hope (and pray) so. Didier Raoult is not a small name. Didier Raoult is a French biologist. He holds MD and Ph.D. degrees and specializes in infectious diseases. Didier Raoult is referred to as the most productive and influential microbiologist in France

    Didier Raoult is the most productive and influential microbiologist in France, leading a team of 200 scientists and students at the University of Aix-Marseille.

    Didier Raoult, the most productive and influential microbiologist in France, “Is a Furious Darwin Doubter”

    The “Most Productive and Influential Microbiologist in France” Is a Furious Darwin Doubter – March 2012
    Excerpt: Controversial and outspoken, Raoult last year published a popular science book that flat-out declares that Darwin’s theory of evolution is wrong.,,,
    “Darwin was a priest,” Raoult says, claiming that the image of the tree of life that Darwin proposed is inspired from the Bible. “It also is too simplistic.” Raoult questions several other tenets of modern evolutionary theory, including the importance of natural selection.

    A New Model for Evolution: A Rhizome – May 2010
    Excerpt: “Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations.”
    – Didier Raoult – has been referred to as ‘Most Productive and Influential Microbiologist in France’

  14. 14
    kairosfocus says:

    BREAKING, Follow up:

    Bayer’s donation:

    >>Bayer the discoverer in 1934 donates 3 million tabs to nUS, it bis not approved in the us . . . bureaucracy at work as usual see >>

    Going back 15 years:

    >>Further, 15 years ago, in the literature . . . the current then is a confirmation it works with this virus >>


    PS: Trump’s announcement today:

  15. 15
    kairosfocus says:

    Oh, yes, what of those objecting to lack of technical content . . . breaking news.

  16. 16
    kairosfocus says:

    F/N: Delingpole asks pointed questions, after giving a brief summary on mechanism:

    It ought to be no surprise that chloroquine is effective against both SARS and COVID-19. After all, they are both coronaviruses and COVID-19 has often been described in medical and research sources as SARS-2.

    Chloroquine works by enabling the body’s cells better to absorb zinc, which is key in preventing viral RNA transcription – and disrupting the often fatal cytokine storm.

    As at least one person has noticed, the implications of this are enormous. If the medical establishment – including CDC – has been aware of the efficacy of chloroquine in treating coronavirus for at least 14 years, why has it not been mass produced and made available sooner?


  17. 17
    Truthfreedom says:

    @12 Kairosfocus:

    Bayer, the discoverer in 1934 donates 3 million tabs to nUS, it bis not approved in the us . . . bureaucracy at work as usual see.

    I am sure they’ll love to hear their neurons ‘chose the outcome based on physical laws’ and that their morality is the result of some archaic structure being re-used/ spandrel.

    Your decisions result from molecular-based electrical impulses and chemical substances transmitted from one brain cell to another. These molecules must obey the laws of physics, so the outputs of our brain—our “choices”—are dictated by those laws.
    Jerry Coyne, the dim-witted biologist

  18. 18
    kairosfocus says:

    TF, sadly absurd. Meanwhile, we can see that the very same habitual objectors who decried want of technical content here are conspicuously missing in action on the thread that is highlighting breaking news on a potential breakthrough treatment for covid19 . . . news that because the “wrong” person [Mr Trump] announced it, was not picked up yesterday by many big news houses. Or, are on tangents of distraction. Telling. KF

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    kairosfocus says:

    Vivid, I see: >>On Thursday, Trump spoke at length on specific treatments to combat the virus, including the anti-malaria drug chloroquine. “We’re going to be able to make that drug available almost immediately,” Trump said at Thursday’s briefing.>> KF

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