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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Friam <friam-bounces@redfish.com> on behalf of Jochen Fromm <jofr@cas-group.net><br>
<b>Reply-To: </b>The Friday Morning Applied Complexity Coffee Group <friam@redfish.com><br>
<b>Date: </b>Sunday, April 19, 2020 at 1:03 PM<br>
<b>To: </b>The Friday Morning Applied Complexity Coffee Group <friam@redfish.com><br>
<b>Subject: </b>Re: [FRIAM] Judea Pearl: Book of Why<o:p></o:p></span></p>
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<p class="MsoNormal">"I think it would be wise to watch the evolution of the virus over time within people and across people"<o:p></o:p></p>
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<p class="MsoNormal">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...<o:p></o:p></p>
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<p class="MsoNormal">https://www.nytimes.com/2020/04/08/science/new-york-coronavirus-cases-europe-genomes.html<o:p></o:p></p>
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<p class="MsoNormal">..so that Carl had to correct him<o:p></o:p></p>
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<p class="MsoNormal">https://twitter.com/carlzimmer/status/1249132628755787782<o:p></o:p></p>
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<p class="MsoNormal">-J.<o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">-------- Original message --------<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">From: Marcus Daniels <marcus@snoutfarm.com>
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<p class="MsoNormal"><span style="color:black">Date: 4/19/20 21:50 (GMT+01:00) <o:p>
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<p class="MsoNormal"><span style="color:black">To: The Friday Morning Applied Complexity Coffee Group <friam@redfish.com>
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<p class="MsoNormal"><span style="color:black">Subject: Re: [FRIAM] Judea Pearl: Book of Why
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<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Roger directs us to the story about Biohub:<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">< 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. ><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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..<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Marcus<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Friam <friam-bounces@redfish.com> on behalf of Roger Critchlow <rec@elf.org><br>
<b>Reply-To: </b>The Friday Morning Applied Complexity Coffee Group <friam@redfish.com><br>
<b>Date: </b>Sunday, April 19, 2020 at 12:30 PM<br>
<b>To: </b>The Friday Morning Applied Complexity Coffee Group <friam@redfish.com><br>
<b>Subject: </b>Re: [FRIAM] Judea Pearl: Book of Why</span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">UCSF has something like this, <a href="https://www.bloomberg.com/opinion/articles/2020-04-17/chan-zuckerberg-biohub-is-ready-for-coronavirus-tests-to-come">https://www.bloomberg.com/opinion/articles/2020-04-17/chan-zuckerberg-biohub-is-ready-for-coronavirus-tests-to-come</a>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">-- rec --<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">On Sun, Apr 19, 2020 at 1:40 PM Marcus Daniels <<a href="mailto:marcus@snoutfarm.com">marcus@snoutfarm.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Dave writes:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Arial",sans-serif">< Marcus said, "Imagine if everyone had full genome sequencing and every viral sample was deep sequenced." Iceland has something close
to this already. ></span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Arial",sans-serif"><a href="https://www.decode.com/publications/" target="_blank">https://www.decode.com/publications/</a></span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Arial",sans-serif"> </span><o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Arial",sans-serif">Marcus</span><o:p></o:p></p>
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