COVID-19

[Hunting]

What if it is an intelligent virus ?

Every iteration implementing what it learned in the previous one...

Kind of reminds me of replicating Demonoid thing...

[83bismuth38]

What if it is an intelligent virus ?

Every iteration implementing what it learned in the previous one...

no thanks

SC seems fine for now, (still self-quarantining) and online classes are more enjoyable, but my school, as usual, doesn't know how to put it's teachers into a schedule

also, why the heck is toilet paper of all things the first thing off the shelves? there has to be some root to this..

[Saka]

SC seems fine for now, (still self-quarantining) and online classes are more enjoyable, but my school, as usual, doesn't know how to put it's teachers into a schedule

SC is South Carolina, right..?

Sichuan? Southern California? Seychelles? Scandinavia?

[Hunting]

SC seems fine for now, (still self-quarantining) and online classes are more enjoyable, but my school, as usual, doesn't know how to put it's teachers into a schedule

also, why the heck is toilet paper of all things the first thing off the shelves? there has to be some root to this..

SC is South Carolina, right..?

Sichuan? Southern California? Seychelles? Scandinavia?

隋朝(Sui Dynasty)?宋朝(Song Dynasty)?四常(Familiar Four)?输出(output)?生成(generate)?删除(deletion)?收藏(collection)?

[otismo]

Intelligent Thinking Humanoids ( Homo Sapiens ) can figure this out

somebody long ago ( mil/bil/??? years ) had the brilliant idea of biologically encoding NANNITES

question : are virii (nannites) also hijacking the soul of the host - even for brief timeslice ?

this is necessary speculative thought

we need to out-think it...

[otismo]

What if it is an intelligent virus ?

Every iteration implementing what it learned in the previous one...

no thanks

SC seems fine for now, (still self-quarantining) and online classes are more enjoyable, but my school, as usual, doesn't know how to put it's teachers into a schedule

also, why the heck is toilet paper of all things the first thing off the shelves? there has to be some root to this..

why do they give you free napkins with fast food ?

make sure u take enuf to wipe yer butt...

[pcallahan]

The toilet paper is to throw at the rampaging zombies as they approach to eat your brains. Zombies are pretty vulnerable. You just have to hit them square in the noggin with one of those rolls. The paper towels are for the big zombies.

[rowett]

I've just joined Rosetta@home which is helping design and model proteins in the fight against coronavirus. From their web site:

Thank you to all R@h volunteers for your contributions to help accurately model important coronavirus proteins. The collective computing power that you provide through R@h helps academic research groups world wide model important protein structures like these.

"We are happy to report that the Rosetta molecular modeling suite was recently used to accurately predict the atomic-scale structure of an important coronavirus protein weeks before it could be measured in the lab. Knowledge gained from studying this viral protein is now being used to guide the design of novel vaccines and antiviral drugs."

I'm now running this on my main computer and most work units are for COVID 19:

rosetta.png (388.5 KiB) Viewed 6226 times

[83bismuth38]

why do they give you free napkins with fast food ?

make sure u take enuf to wipe yer butt...

I hope you weren't trying to make fun of me there by typing an accent..

SC is South Carolina, right..?

Sichuan? Southern California? Seychelles? Scandinavia?

South Carolina, yep.

[otismo]

@ 83bismuth38

I do not have to explain my post - my hope was that people "get it" - if u can still get free napkins with fast food, there is no problem...

now your behavior is in the spotlight - you chose to REACT to my post - this kind of behavior is REACTIONARY

not directed AT anyone - we need to study Reactionary Behavior

is key to beating the virus.....

[simsim314]

I live in Israel. I was following the virus since before WHO declared emergency even. I predicted pretty clearly what is gonna happen. I also knew that most governments are waiting with measures while the virus is already in that country or can get there pretty soon. In Israel the policies were very liberal - if you think you have the virus, stay at home please. This was basically it. No real measures were taken just like everywhere else - a complete lack of acting and responding properly and in time on the side of authorities. I'm amused how they try to excuse themselves now, pretty much everyone. Some of them praise themselves how well they responded- I call it a complete failure of governmental system. You can see that people who make the decisions are purely dumb. Modern democracy is not promoting best people for the job and best decision making only best excuse inventors, and copy cats of other dumb authorities. I wonder when people will start to question is there anything better than the current social order. It's about time.

As of me personally the chances are pretty low to die from corona. Being under constant threat of nuclear bomb from Iran or called to a war to protect my country where my chances to die way higher, I'm really not concerned with the threat of 0.2% (at my age group) myself - but because the dumbness of authorities and their late response I'm stuck at home, and can't even start looking for a job. My feeling are basically existential amusement, hope for the future (in my lifetime it's the first time people might realize in what absurd they were living, and get their priorities more or less straight), and a bit concern for my parents.

I'm also believing corona will continue for half a year so new economical opportunities with the internet technologies should come up, as the market always adapts to new situation. If free market is trying to emulate evolution, so now it's the time when the meteor hits.

[pcallahan]

I'm also believing corona will continue for half a year so new economical opportunities with the internet technologies should come up, as the market always adapts to new situation. If free market is trying to emulate evolution, so now it's the time when the meteor hits.

It may last until a vaccine or some other effective treatment exists, which is longer than half a year. If we get the raging pandemic under control, we may have something like a new normal of fighting brush fires around the globe with localized lockdowns. There will be new economic opportunities, of course, and already are. But it will be a long time before those opportunities make up for the losses, and many people will be left out.

I am very confident (rightly or not) I could get this virus and survive. However, I have an immune-suppressed family member who I need to protect, and an aging mother on the east coast in her late 90s and susceptible to just about any kind of health risk. For all that, I think what I fear most is a breakdown of the social contract, and the sense that even many people who think they are prepared for this have no idea what they're really in store for.

The sanguine view of just riding out the mortality rate is completely ludicrous unless people suddenly stop demanding modern medical care. A society that could promise nothing better than bedrest and noodle soup for COVID-19 could avoid the worst of the disruption and just carry on with some weeping and extra funerals. But we have higher expectations than that, and we should. The nightmare is that the cases and not just fatalities overflow our ability to handle them.

It amazes me when I see the stock market change daily, because I do not understand what they think they are pricing. It is like Feynman's analogy of "guessing the length of the emperor's nose." Collect enough opinions, and you get an aggregate value. But what does it have to do with reality? Nobody can see to the other side of this event.

Political leaders are uniquely unqualified for a variety of reasons, but even the smart ones among them are not usually smart about math. Even the so-called "business people" who at least should know how compound interest works. Nobody seems to react until it is at least two weeks later than their best shot of controlling spread. That is more forgivable at the beginning than now, when you can literally look into the future and find another country that looks like you're going to look in two weeks. The response in the US at a federal level has been so bad that I'm frankly ashamed of it.

True story: back in January, I thought of how we would not be building field hospitals like China because, well, first it's really tough to build anything on that scale in the US today with permit requirements, NIMBYism, etc. But I comforted myself with the idea that we must have something better like super-high tech medical FEMA trailers. I just assumed, because I'm American, that we would address this competently if we needed to, just in a leaner more mobile way. Now I see how wrong I was about that. Italy looks bad today, but it will be sheer luck if the US escapes the fate of overcrowded hospitals and morgues. I don't see what we are doing to stop it.

I think there has been some attenuation in the growth curve, which was rising at a terrifying 35% per day at one point. The cases we see are the detected cases, and it's the actual cases, visible or not, that result in spread. (In fact, the visible ones can at least avoid further spread once detected.)

With that in mind, I was trying to come with a simple model of what these attenuated curves should look like. Obviously, the pure exponential is easy, but there are two other things I want to understand. First, we don't detect all the cases, and the curve I can see in the news is just the detected cases. Second, lockdown measures eventually have an effect, but there is a lag due to onset of symptoms. I am not an epidemiologist, so please don't see this as anything but a toy math problem.

Assume there is 1 "patient zero", that there is some rate of increase (capturing "basic reproduction number"), that detected patients stop spreading immediately when they are detected. Assume that once a quarantine is put in place, all further spread ends. Also, rather than try to model the actual lag in symptom onset, let's just say that anyone with the virus has a certain probability of detection on any given day. This is a gross oversimplification, but maybe it's enough to capture qualitatively how to see these charts. The visible part is simply the number of new cases detected per day, or the cumulative number detected.

The interesting question is how bad is it really compared to how it looks. Also, how long after a quarantine is declared does it take to really see results (here the model deviates from reality because reality includes a step function of symptom onset).

The parameters are r (new cases as fraction of current undetected), s (detected cases as fraction of current undetected), Tq (time in days when quarantine starts). Pseudocode (does this work? got anything better? i.e. simpler, more faithful, or both).

Code: Select all

Start with n_hidden = 1
for t = 0, 1, 2, ...
  n_new_cases = r * n_hidden if t<Tq else 0
  n_new_detected = s * n_hidden
  n_hidden = n_hidden + n_new_cases - n_new_detected

I started fiddling with this in a spreadsheet. I don't think it is good enough to bother fitting to real data. It is just to develop some intuition about the lag between taking measures and seeing significant results.

Update: Here is some Python code for the above. One trivial observation that if r=s, i.e. the percent of new cases is the percent of detected cases, then you get a linear growth model even without a quarantine. I.e., if we could just chase down these cases immediately, we might be able to keep things under control. Once again, I am not an epidemiologist, and this speculation is for amusement only.
repl.it link to python https://repl.it/repls/IntelligentTrivialServers

Code: Select all

n_hidden = 1
n_detected = 0
r = 0.1
s = 0.1
t_q = 200
for t in range(0, 100):
  n_new_cases = r * n_hidden if t < t_q else 0
  n_new_detected = s * n_hidden
  print("%15.0f %15.0f %15.0f %15.0f" %
        (n_hidden, n_new_cases, n_new_detected, n_detected))

  n_hidden += n_new_cases - n_new_detected
  n_detected += n_new_detected

Update 2: Of course, the quarantine doesn't have to be 100% effective. Instead of 0 spread, you could model it as anything below detection rate. However, I am trying to keep this very simple.

Update 3: The n_hidden curve up to the quarantine is simple exponential growth based on a recurrence n_hidden = n_hidden * (1 + r - s). After that, it is exponential decay n_hidden = n_hidden * (1 - s). The curve we expect to see reported n_detected is proportional to the integral of this piecewise function. It has an inflection point where the quarantine starts, and eventually flattens to horizontal. This is similar to China's curve of confirmed cases, which is a bit choppy around the transition. https://www.worldometers.info/coronavir ... try/china/

South Korea's curve is interesting because instead of flattening, it continues on with linear growth. https://www.worldometers.info/coronavir ... uth-korea/ Can they have really reached a steady-state where they detect new cases at exactly the rate they appear, so they do not stop the contagion, but catch just in time to keep it constant?

[otismo]

first global incident ( financial panic ) 1857 ( shortly after Crystal Palace Exhibition, London, 1850 )

what-panic-LWSS-W-SS.mc

who - was living in a dream world

(136.51 KiB) Downloaded 170 times

the interesting $3 Trillion response begs the question of when will people realize that we are not going back to

"the way things were before"

even though it may sure feel like it, for a while...

the journey into the abnormal is becoming surreal

and observable on TV, and as much as I would like

to just turn it off, it seems to be in my face every

where. But I've lived thru much social morphology

[pcallahan]

first global incident ( financial panic ) 1857 ( shortly after Crystal Palace Exhibition, London, 1850 )

the interesting $3 Trillion response begs the question of when will people realize that we are not going back to

"the way things were before"

even though it may sure feel like it, for a while...

the journey into the abnormal is becoming surreal

Yeah, we're in this twilight area where you can pretend things are normal if you're not looking ahead. They are very far from normal and we will never go back. It's especially unnerving for me with a job that has not really changed much except WFH. Obviously, none of the business plans set a few months ago apply to the future, except by sheer luck.

[otismo]

civilized people are dependent people who know what they depend on to survive :

civilization

civilized people

who are honest and

TRUSTWORTHY -

the thin veneer is rapidly crumbling now...

[gameoflifemaniac]

memes

[Amy]

what about "Avigan" medication? does anybody know its updates? I heard some news about it mentioned it is ready to dispatch for some countries?

[pcallahan]

I should probably read how real epidemiologists do this, but I put together a simple model that at least qualitatively captures the curve-flattening process. Instead of trying to separate out the spread factor and the percent detected, as I did in https://conwaylife.com/forums/viewtopic ... 049#p92583 it is simpler just to note that before quarantine, the number of new cases is exponential growth Ae^(at) at first, and after an effective quarantine is exponential decay Be^(-bt), setting A and B so the values are equal at the transition. This gives a rather pointy curve though. Graphing something like this in https://www.desmos.com/calculator we get:

Code: Select all

\left\{x<0:e^{5x},\ x\ge0:e^{-x}\right\}

Screen Shot 2020-04-01 at 11.40.56 AM.png (149.93 KiB) Viewed 6030 times

So what's with those smooth peaks in all the "flatten the curve" graphics? I think the way to handle that is to track total cases as an integral of new cases, which grows monotonically.

Code: Select all

\int_{-100}^{x}\left\{t<0:e^{5t},\ t\ge0:e^{-t}\right\}dt

Screen Shot 2020-04-01 at 12.16.30 PM.png (133.85 KiB) Viewed 6030 times

But we are probably more interested in active cases. So one way to think about this (again, oversimplification) any active case has some probability of resolving either as a death or (we hope!) a recovery. We don't try to track how many days it takes. Just make it an independent probability. My initial thought was to use a linear recurrence, but maybe it's enough just to multiply by another exponential decay.

This at least captures the shape roughly.

Code: Select all

\left(\int_{-100}^{x}\left\{t<0:e^{5t},\ t\ge0:e^{-t}\right\}dt\right)\cdot\left\{x<-1:0,\ x\ge-1:e^{-x}\right\}

Screen Shot 2020-04-01 at 12.12.00 PM.png (103.57 KiB) Viewed 6030 times

[pcallahan]

I hope nobody finds my fixation morbid. I also repeat that I am not an epidemiologist and I have no idea what is needed for a realistic pandemic model, but I can get similar curves with these assumptions to what I see in actual data online.

This time I decided that instead of going straight to calculation, why not make a simulation that tracks patients directly. In this case, it is easier to introduce the kinds of time dependence that we expect to see. E.g., the probability of confirming a case may be 0 for a few days after exposure, and the level of contagion is probably time dependent as well. In fact, the turnaround in testing itself introduces a delay. It may also be that nobody ever stays contagious for more than a certain amount of time, etc. I consider two time values: T is the number of steps (days or whatever) since the pandemic started. t is the number of steps for each individual patient (on the same scale) since they contracted the virus. While undetected, they may spread it to others.

One major simplifying assumption is that no spread occurs after detection. Ideally, this should not be too far from the truth, though it is almost certainly contradicted by the number of healthcare providers who contract the illness while treating patients.

Note: I assume that only the probability of spread is dependent on T, but you could model a case in which we got better at testing during the pandemic, or better at saving lives. This is an intentionally simplified model. I do not know if there are simulation games like Civilization that model pandemic response (I know there is a board game called Pandemic, though I never played it.) Here's a picture of the simulation model.

Screen Shot 2020-04-02 at 9.10.08 AM.png (220.91 KiB) Viewed 5996 times

(For a big simulation, you could make it dependent on geography, climate, policy choices, etc.)

Here's some Python code. I have not added any time dependency except for T to represent the time at which perfect quarantine measures are imposed (so probability of spread is 0). But the method stubs are there and it's pretty easy to add. You could also optimize it for speed by collecting all patients with the same (state, t) pair, but I am not aiming at high efficiency.

https://repl.it/repls/EffectiveAmusingCommands

Code: Select all

import random

def p_s(T, t):
  return 0.1 if T < 100 else 0

def p_d(t):
  return 0.05

def p_r(t):
  return 0.0097

def p_f(t):
  return 0.0003

patients = [("undetected", 0)] * 10

print("time_step undetected detected recovered deceased")
for T in range(0, 1000):
  next_patients = []
  for (state, t) in patients:
    if state == "undetected":
      if random.random() < p_s(T, t):
        next_patients.append(("undetected", 0))
      if random.random() < p_d(t):
        state = "detected"
    if state in ["undetected", "detected"]:
      # this is introduces a small order dependency since we check recovery first
      if random.random() < p_r(t):
        state = "recovered"
      elif random.random() < p_f(t):
        state = "deceased"
    next_patients.append((state, t + 1))
  patients = next_patients
  counts = {}
  for state, _ in patients:
    counts[state] = counts.get(state, 0) + 1
  print("%d %d %d %d %d" %
        tuple([T] + [counts.get(key, 0)
                     for key in ["undetected", "detected", "recovered", "deceased"]]))
  if "undetected" not in counts and "detected" not in counts:
    break

The final outcomes (total recoveries and fatalities) actually vary quite a bit over runs, probably because they are so sensitive to chance results at the early part of the pandemic. (I have not compiled any stats.)

Here's a graph of a single run.

Screen Shot 2020-04-02 at 9.38.58 AM.png (110.49 KiB) Viewed 5996 times

Update: Introducing an explicit time delay in detection like this makes the graphs a lot closer to what I would expect. I think it also increases the total number of cases by a lot! I am not an epidemiologist, but I think rapid testing is very useful!

Code: Select all

def p_d(t):
  return 0.05 if t > 5 else 0

Screen Shot 2020-04-02 at 10.45.26 AM.png (177.73 KiB) Viewed 5988 times

[otismo]

Insurance.

Hopefully you never need it.

Worst case scenario : no internet, no electricity, etc.

Maybe even no computers ( heaven help us ).

So I am going to put up an insurance site :

http://tbtb.conway.life

I will try to keep it up and running as long as possible.

TriloBite TarBall

The Doomsday Repository

( hopefully unnecessary and hopefully nobody actually has a compressed archive over a terrabhyte... )

I have the old dirHTML shareware and people can title any way they want -

WE WANT YOUR FILES

it may be your only legacy...

I am going to lunch now, to think about it; maybe I am over-reacting :

after all, I did just now buy Chesapeake @ sixteen cents - so I guess I don't believe it's the End of the World -

but if it is, what are you going to do with your money anyway; I mean, we're out of TP...

[GUYTU6J]

mourn.jpg (127.52 KiB) Viewed 5945 times

Farewell, the COVID-19 fighters.

[gameoflifemaniac]

meme

[otismo]

SO

if it is a biologically encoded

command - and - control nanostructure

there would have to be two groups playing ping-pong

to keep the system both ALIVE and OPERATIVE - I nominate BUILDERS/DESTROYERS

[Hunting]

SO

if it is a biologically encoded

command - and - control nanostructure

there would have to be two groups playing ping-pong

to keep the system both ALIVE and OPERATIVE - I nominate BUILDERS/DESTROYERS

Makes me think of the reploops... A rule that have reploops that uses such encode anyone?

[gameoflifemaniac]

meme