With your final sentence, I agree. That is why I consider taking up the problem of good regulatory design far preferable to killing outright the effort to understand a class of questions. I prefer it enough to be almost categorical, though even that question can be complicated.
If I worked in this field, or were a higher-up in NIAID, I would know more about how they have been trying to make these decisions, and what kinds of cost/benefit/controllability framings they use. These are not unsophisticated people. If I knew that, I could say more useful things about directions for change. > On May 26, 2021, at 12:46 PM, Marcus Daniels <[email protected]> wrote: > > Yeah, I’ve noticed interesting stuff in SRA datasets. I have a suspicion it > is underutilized information, but I haven’t really investigated (the > literature). There are some CDC BAA’s out recently along these lines. Like > high-performance metagenomics tools that can characterize all the pathogen > variants in a sample. > > I suppose one could try to further regulate it, but some countries may > actually sponsor this kind of research in their defense budgets. And there > are good reasons to understand the potential badness and diversity of viral / > host (human) interactions. And nature in its infinite spite can come up > with this stuff itself, so it is good to be prepared. Simply refusing to > investigate or discuss scary topics is pointless. > > From: Friam <[email protected] <mailto:[email protected]>> On > Behalf Of David Eric Smith > Sent: Tuesday, May 25, 2021 5:17 PM > To: The Friday Morning Applied Complexity Coffee Group <[email protected] > <mailto:[email protected]>> > Subject: [FRIAM] How swarms of bees go from preferring one target to > preferring another > > I assume you all have been following the following: (?) > https://thebulletin.org/2021/05/the-origin-of-covid-did-people-or-nature-open-pandoras-box-at-wuhan/ > > <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fthebulletin.org%2f2021%2f05%2fthe-origin-of-covid-did-people-or-nature-open-pandoras-box-at-wuhan%2f&c=E,1,P6kXox553nNZ9am59NkxzTOCdiF6wmr49v3tEoJnczF-h6wf2HI2SMSvVx47aaHjxAhK1ewYPO1o_DXXPgZEXGaiG5bxmxibJTx0PUdzN363Dg,,&typo=1> > > I had seen bits and pieces of the claims summarized above in other sources, > but they were either technical work that I did not put time into trying to > read and understand (and likely didn’t have expertise to weigh in on anyway), > or they were from writers I didn’t trust not to mis-represent. But the above > is a decent concise summary of several things, and the source may be better. > Some of his links I am less sure of, but have not gone down the tree to judge. > > Some weeks ago, a day or two after it came out, I got a pointer to this paper: > https://arxiv.org/abs/2104.01533 <https://arxiv.org/abs/2104.01533> > which suggests a piece of big-data forensics I would very much like to see > done (if Google wanted, for instance, to make itself useful). (Did I already > send this link? Or was it one of those abortive posts that went mercifully > to /dev/null? > > I didn’t know anything about what gets filed in gene registries, how much of > raw short reads versus just assembled contigs etc. But it sounds like a lot > of stuff gets filed, from which you can tell if some other sample was run > through the same machine as the reported sample, and may be in the data as a > contaminant. I guess sequence assemblers also quite frequently insert > contaminant reads into what they think the real sample sequence was, so all > kinds of crazy nonsense ends up here or there in “assembled” genomes from > next-gen sequencers (which I guess are now this-get, almost to the exclusion > of older (Sanger?) methods). The above article mostly focuses on labs in an > agricultural university in Wuhan, suggesting that WIV was farming out > sequencing jobs (pun not intended) to labs without the BSL procedures in > place to perform them. The first article (the BAS editorial) adds a bit of > clarity to what I knew before: apparently a lot of the coronavirus research > is only listed as BSL2 to begin with. So the error if it is an escape would > be the same, but it would be a matter of institutional decision-making, > rather than something read as a reflection of culture or customs across the > society, which has ramifications for the response. > > The big-data work I would like to be done would be a kind of ongoing scrub of > gene repositories, to assemble a catalogue of who is working on what, whether > reported or not reported. It is one thing to do a targeted search after a > pattern of interest is known, but that takes a lot oa manual tooling, and is > only likely to be motivated too late to be helpful as a preventative. I am > thinking of something more in the vein of a surveillance method that can be > part of a regulatory and oversight regime. Of course, once the pipeline is > written, governments and militaries will self-screen before reporting (like > your students run their essays through plagiarism finders before they send > them to you, to know which things won’t be caught), and the signal will get > smaller. But we have a lot of historical data that has not been sieved in > the way the Zhang et al. paper does, and would be very pertinent to research > still going on now. > > There was a nice comment in the summary section of the BAS article, which > would fit into several conversations on FRIAM lf late: > > Professions that cannot regulate themselves deserve to get regulated by > others, and this would seem to be the future that virologists are choosing > for themselves. > > If this does go the direction that it was gain-of-function work that agencies > either should not have authorized, or should have been as much more diligent > in limiting as they knew to do, whatever goodwill the medical profession has > earned in a year of trying so hard to take care of people will be swept away > in the backlash, since as we know resentment is a much stronger motivator > than gratitude, even when spontaneous, and even more when manipulated. I > find it disappointing that people seem capable of so little complexity that > they can’t experience both, and direct each where it belongs. My guess would > be that, rather than put serious commitment into the hard work of figuring > out what is appropriate and designing a regulatory regime, it will be easier > to kill it off. We’ll see. > > Eric > > > - .... . -..-. . -. -.. -..-. .. ... -..-. .... . .-. . > FRIAM Applied Complexity Group listserv > Zoom Fridays 9:30a-12p Mtn GMT-6 bit.ly/virtualfriam > <http://bit.ly/virtualfriam> > un/subscribe > https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fredfish.com%2fmailman%2flistinfo%2ffriam_redfish.com&c=E,1,i7OTCeOIDAtuPj5G1Szfr_A2WK4LOqLqD8DoUbS9ZkqtrGz98QjzBmu5UxzAVfUJI2KWt6iMWZst_fiOCxuVujsBkMbcOEAIP6DLb7Jhxw,,&typo=1 > > <https://linkprotect.cudasvc.com/url?a=http%3a%2f%2fredfish.com%2fmailman%2flistinfo%2ffriam_redfish.com&c=E,1,i7OTCeOIDAtuPj5G1Szfr_A2WK4LOqLqD8DoUbS9ZkqtrGz98QjzBmu5UxzAVfUJI2KWt6iMWZst_fiOCxuVujsBkMbcOEAIP6DLb7Jhxw,,&typo=1> > FRIAM-COMIC > https://linkprotect.cudasvc.com/url?a=http%3a%2f%2ffriam-comic.blogspot.com%2f&c=E,1,T7G61yk9ff7uyB4V_lzUTNYmAQb-0jUWJ-BPw-JJn8TsHyT4fMLi3H7OP57JRHU2q9mQGZvW40SrzezAnHPYGqEluP1rY3wT_bNLOB7QNBNXv1_jyw,,&typo=1 > > <https://linkprotect.cudasvc.com/url?a=http%3a%2f%2ffriam-comic.blogspot.com%2f&c=E,1,T7G61yk9ff7uyB4V_lzUTNYmAQb-0jUWJ-BPw-JJn8TsHyT4fMLi3H7OP57JRHU2q9mQGZvW40SrzezAnHPYGqEluP1rY3wT_bNLOB7QNBNXv1_jyw,,&typo=1> > archives: http://friam.471366.n2.nabble.com/ > <http://friam.471366.n2.nabble.com/>
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