Friam

anthropological observations

Classic

List

Threaded

106 messages Options

1 ... 3456

Roger Critchlow-2

Re: Judea Pearl: Book of Why

UCSF has something like this, https://www.bloomberg.com/opinion/articles/2020-04-17/chan-zuckerberg-biohub-is-ready-for-coronavirus-tests-to-come

-- rec --

On Sun, Apr 19, 2020 at 1:40 PM Marcus Daniels <[hidden email]> wrote:

Dave writes:

< Marcus said, "Imagine if everyone had full genome sequencing and every viral sample was deep sequenced." Iceland has something close to this already. >

https://www.decode.com/publications/

Marcus

.-. .- -. -.. --- -- -..-. -.. --- - ... -..-. .- -. -.. -..-. -.. .- ... .... . ...
FRIAM Applied Complexity Group listserv
Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam
unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
archives: http://friam.471366.n2.nabble.com/
FRIAM-COMIC http://friam-comic.blogspot.com/

.-. .- -. -.. --- -- -..-. -.. --- - ... -..-. .- -. -.. -..-. -.. .- ... .... . ...
FRIAM Applied Complexity Group listserv
Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam
unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
archives: http://friam.471366.n2.nabble.com/
FRIAM-COMIC http://friam-comic.blogspot.com/

Marcus G. Daniels

Re: Judea Pearl: Book of Why

Roger directs us to the story about Biohub:

< It was also different, in an important way. The commercial labs are set up to take in the samples and spit out a simple answer: positive or negative. They aren’t set up, as the Biohub is, to sequence the genome of every positive specimen and look for variations among them. As it moves through the population, the virus replicates and, as DeRisi says, “every time you replicate something there is a chance of an error.” He’s already found tiny differences from one coronavirus genome to the next — not so great that it changes the essential nature of the virus but noticeable nevertheless. >

I think it would be wise to watch the evolution of the virus over time within people and across people. I’ve heard experts argue it is slowly mutating, but I’ve personally seen deep sequence data (just from Genbank) reveal other variants. The stakes are high enough that shortcuts seem like a bad idea to me. And the technology exists to do the deep sequencing. That’s good point IMO about how Quest and LabCorp are designed to do positive/negative tests. Imagine the disaster that happens if the tests become fragile, like the CDC tests were..

Marcus

From: Friam <[hidden email]> on behalf of Roger Critchlow <[hidden email]>
Reply-To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Date: Sunday, April 19, 2020 at 12:30 PM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Judea Pearl: Book of Why

UCSF has something like this, https://www.bloomberg.com/opinion/articles/2020-04-17/chan-zuckerberg-biohub-is-ready-for-coronavirus-tests-to-come

-- rec --

On Sun, Apr 19, 2020 at 1:40 PM Marcus Daniels <[hidden email]> wrote:

Dave writes:

< Marcus said, "Imagine if everyone had full genome sequencing and every viral sample was deep sequenced." Iceland has something close to this already. >

https://www.decode.com/publications/

Marcus

.-. .- -. -.. --- -- -..-. -.. --- - ... -..-. .- -. -.. -..-. -.. .- ... .... . ...
FRIAM Applied Complexity Group listserv
Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam
unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
archives: http://friam.471366.n2.nabble.com/
FRIAM-COMIC http://friam-comic.blogspot.com/

Jochen Fromm-5

Re: Judea Pearl: Book of Why

"I think it would be wise to watch the evolution of the virus over time within people and across people"

Scientists do this already, and they found out for instance that most NY cases came from Europe, not from China directly. Carl Zimmer reported about it in the NY Times. This is the article Donald misunderstood...

https://www.nytimes.com/2020/04/08/science/new-york-coronavirus-cases-europe-genomes.html

..so that Carl had to correct him

https://twitter.com/carlzimmer/status/1249132628755787782

-J.

-------- Original message --------

From: Marcus Daniels <[hidden email]>

Date: 4/19/20 21:50 (GMT+01:00)

To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>

Subject: Re: [FRIAM] Judea Pearl: Book of Why

Roger directs us to the story about Biohub:

Marcus

UCSF has something like this, https://www.bloomberg.com/opinion/articles/2020-04-17/chan-zuckerberg-biohub-is-ready-for-coronavirus-tests-to-come

-- rec --

On Sun, Apr 19, 2020 at 1:40 PM Marcus Daniels <[hidden email]> wrote:

Dave writes:

< Marcus said, "Imagine if everyone had full genome sequencing and every viral sample was deep sequenced." Iceland has something close to this already. >

https://www.decode.com/publications/

Marcus

.-. .- -. -.. --- -- -..-. -.. --- - ... -..-. .- -. -.. -..-. -.. .- ... .... . ...
FRIAM Applied Complexity Group listserv
Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam
unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
archives: http://friam.471366.n2.nabble.com/
FRIAM-COMIC http://friam-comic.blogspot.com/

Steve Smith

Re: Judea Pearl: Book of Why

In reply to this post by Prof David West

Not directly relevant, but another good sci-fi about genetics — Daniel Suarez' Change Agent.

davew

Thanks...

I read that earlier this year in response to your general reference to Suarez (starting with Delta-V?) and my body and soul *still* ache from the memories!

and Marcus... yes, GATTACA didn't (apparently) anticipate CRISPR

Trans/Posthumanist Utopias have a strong flavor of Dystopia for me...

Eloi & Morlocks

On Sun, Apr 19, 2020, at 10:41 AM, Steven A Smith wrote:
Marcus -

I believe that Andrew Niccol DID imagine something like that:

I wish I had a pithy preamble for this dystopian BioPunk reference, but perhaps it speaks for itself?

https://en.wikipedia.org/wiki/Gattaca

- Steve
Steve writes:

< The whole world is responding to what is *roughly* the same virus with *roughly* what is the same human phenotype/metabolism in a myriad of *roughly* the same modes of human organization. >

There are hundreds of common HLA alleles across humans. In a diverse country like the US, with hundreds of thousands of positive cases and tens of thousands of deaths the hundreds of alleles would be well sampled. Too bad our medical surveillance is so bad, and made worse by the moron. Imagine if everyone had full genome sequencing and every viral sample was deep sequenced.

Marcus

From: Friam [hidden email] on behalf of Steven A Smith [hidden email]
Sent: Sunday, April 19, 2020 10:11 AM
To: [hidden email] [hidden email]
Subject: Re: [FRIAM] Judea Pearl: Book of Why
One way to address the N/A issue is to repeatedly perturb the real-world system so as to elicit those correlations.  When that is practical.. 
We are, in a time of real-world system perturbation, right now. The whole world is responding to what is *roughly* the same virus with *roughly* what is the same human phenotype/metabolism in a myriad of *roughly* the same modes of human organization.   This IS a testbed of human (-system?) response to a widespread, somewhat invisible threat.   From Wuhan to Singapore to Italy to Iran to Sweden to Germany to NYC to WA State to the Navajo Nation to Florida's beaches, this IS a huge coupled systems dynamics/agent-model executed in real-time by real-people with real casualties and real consequences.

We are, to varying degrees (collectively) recording the results of these "experiments" and if we are lucky (or smart, or both) we will do some post-game analysis intended to understand more-better how best to (self-)organize around a (nearly) existential world-scale threat.   And to the extent this is a game that will never end, we have to begin the analysis while we cope with it's consequences.   Feels a bit like the models pof Physics Interreality.

    https://journals.aps.org/pre/abstract/10.1103/PhysRevE.75.057201

Hanging too aggressive of a model on this (or collecting the data against too premature of a model) will reduce the utility of such data gathering and analysis.   Whatever the dual of overfitting a model is? Overmodeling? Premature Modeling?

What I'm looking (askance) to(ward) Pearl for is a better way of rapidly constructing, maintaining, revising as generic of a model as possible in response to "this moment".   Four months ago we should have been interested in models of how one limits a virus such as COVID19 getting a foothold in this country.   One month ago we should have been interested in how one limits COVID19 (with new understanding of it's virility, it's fatality, it's symptoms, it's mode of spread) once it HAS a foothold, now we are faced with trying to understand how to cope with it once it is pervasive in our population whilst continuing/returning to "business as usual" and in another thread, I'm encouraging that we "try to plan/consider/think-about" what we want to do with this somewhat "blank slate" (our ass?) we are having handed to us.

And how to think about this without premature modeling... what I think I was railing (whining/pushing-back) about with Dave on the Bellamyist thread earlier this morning.

- Steve
On Apr 19, 2020, at 8:33 AM, uǝlƃ ☣ [hidden email] wrote:

Well, the argument I often end up making is that you can do a kind of face validation with the fake data. Show it to someone who's used to dealing with that sort of data and if the fake data looks a lot like the data they normally deal with, then maybe more data-taking isn't necessary. If it looks fake to the "expert", then more data-taking is definitely needed.
On 4/19/20 8:29 AM, Marcus Daniels wrote:
I have a hard time with this as a way to extend data.   If it is high-dimensional it will be under-sampled.  Seems better to me to  measure or simulate more so that the joint distribution can be realistic.  And if you can do that there is no reason to infer the joint distribution because you *have* it. 
On Apr 19, 2020, at 8:18 AM, Frank Wimberly [hidden email] wrote:
Going back and forth:  If you infer the causal graph from observational data you can use that graph to simulate data with the same joint distribution as the original data.
-- 
☣ uǝlƃ

.-. .- -. -.. --- -- -..-. -.. --- - ... -..-. .- -. -.. -..-. -.. .- ... .... . ...
FRIAM Applied Complexity Group listserv
Zoom Fridays 9:30a-12p Mtn GMT-6  bit.ly/virtualfriam
unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
archives: http://friam.471366.n2.nabble.com/
FRIAM-COMIC http://friam-comic.blogspot.com/ 
.-. .- -. -.. --- -- -..-. -.. --- - ... -..-. .- -. -.. -..-. -.. .- ... .... . ...
FRIAM Applied Complexity Group listserv
Zoom Fridays 9:30a-12p Mtn GMT-6  bit.ly/virtualfriam
unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
archives: http://friam.471366.n2.nabble.com/
FRIAM-COMIC http://friam-comic.blogspot.com/ 
.-. .- -. -.. --- -- -..-. -.. --- - ... -..-. .- -. -.. -..-. -.. .- ... .... . ...
FRIAM Applied Complexity Group listserv
Zoom Fridays 9:30a-12p Mtn GMT-6  bit.ly/virtualfriam
unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
archives: http://friam.471366.n2.nabble.com/
FRIAM-COMIC http://friam-comic.blogspot.com/ 
.-. .- -. -.. --- -- -..-. -.. --- - ... -..-. .- -. -.. -..-. -.. .- ... .... . ...

FRIAM Applied Complexity Group listserv

Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam

unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com

archives: http://friam.471366.n2.nabble.com/

FRIAM-COMIC http://friam-comic.blogspot.com/
.-. .- -. -.. --- -- -..-. -.. --- - ... -..-. .- -. -.. -..-. -.. .- ... .... . ...
FRIAM Applied Complexity Group listserv
Zoom Fridays 9:30a-12p Mtn GMT-6  bit.ly/virtualfriam
unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
archives: http://friam.471366.n2.nabble.com/
FRIAM-COMIC http://friam-comic.blogspot.com/ 

Marcus G. Daniels

Re: Judea Pearl: Book of Why

In reply to this post by Marcus G. Daniels

For comparison, there are 288 deep sequences for SARS-Cov2 at GenBank, and about 2.4 million confirmed cases world-wide. A few thousand more sequences at GISAID. Not hundreds of thousands of samples that have been deep sequenced. There could actually be many independent transmission cases, and the tree that GISAID shows is just the known evidence.

From: Friam <[hidden email]> on behalf of Jochen Fromm <[hidden email]>
Reply-To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Date: Sunday, April 19, 2020 at 1:03 PM
To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>
Subject: Re: [FRIAM] Judea Pearl: Book of Why

"I think it would be wise to watch the evolution of the virus over time within people and across people"

https://www.nytimes.com/2020/04/08/science/new-york-coronavirus-cases-europe-genomes.html

..so that Carl had to correct him

https://twitter.com/carlzimmer/status/1249132628755787782

-J.

-------- Original message --------

From: Marcus Daniels <[hidden email]>

Date: 4/19/20 21:50 (GMT+01:00)

To: The Friday Morning Applied Complexity Coffee Group <[hidden email]>

Subject: Re: [FRIAM] Judea Pearl: Book of Why

Roger directs us to the story about Biohub:

Marcus

UCSF has something like this, https://www.bloomberg.com/opinion/articles/2020-04-17/chan-zuckerberg-biohub-is-ready-for-coronavirus-tests-to-come

-- rec --

On Sun, Apr 19, 2020 at 1:40 PM Marcus Daniels <[hidden email]> wrote:

Dave writes:

< Marcus said, "Imagine if everyone had full genome sequencing and every viral sample was deep sequenced." Iceland has something close to this already. >

https://www.decode.com/publications/

Marcus

.-. .- -. -.. --- -- -..-. -.. --- - ... -..-. .- -. -.. -..-. -.. .- ... .... . ...
FRIAM Applied Complexity Group listserv
Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam
unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
archives: http://friam.471366.n2.nabble.com/
FRIAM-COMIC http://friam-comic.blogspot.com/

Frank Wimberly-2

Re: Judea Pearl: Book of Why

In reply to this post by gepr

Possibly relevant:

See Reynolds, W. N., Wimberly, F. C.,

      Simulation Validation Using Causal Inference Theory with Morphological
      Constraints.
      Proceedings of the 2011 Winter Simulation Conference, Arizona Grand Resort,
      December, 2011.

On Sun, Apr 19, 2020 at 9:33 AM uǝlƃ ☣ <[hidden email]> wrote:

Well, the argument I often end up making is that you can do a kind of face validation with the fake data. Show it to someone who's used to dealing with that sort of data and if the fake data looks a lot like the data they normally deal with, then maybe more data-taking isn't necessary. If it looks fake to the "expert", then more data-taking is definitely needed.

On 4/19/20 8:29 AM, Marcus Daniels wrote:
> I have a hard time with this as a way to extend data. If it is high-dimensional it will be under-sampled. Seems better to me to measure or simulate more so that the joint distribution can be realistic. And if you can do that there is no reason to infer the joint distribution because you *have* it.
>
>> On Apr 19, 2020, at 8:18 AM, Frank Wimberly <[hidden email]> wrote:
>>
>>
>> Going back and forth: If you infer the causal graph from observational data you can use that graph to simulate data with the same joint distribution as the original data.

--
☣ uǝlƃ

.-. .- -. -.. --- -- -..-. -.. --- - ... -..-. .- -. -.. -..-. -.. .- ... .... . ...
FRIAM Applied Complexity Group listserv
Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam
unsubscribe http://redfish.com/mailman/listinfo/friam_redfish.com
archives: http://friam.471366.n2.nabble.com/
FRIAM-COMIC http://friam-comic.blogspot.com/

Frank Wimberly
140 Calle Ojo Feliz
Santa Fe, NM 87505
505 670-9918

1 ... 3456