Hunting the CoV

Projects 16800-16803,16805-16808

Cause: covid-19

This is the first COVID19 project from our lab. We are assembling the envelope protein, which is an ion channel important for viral function. Learning about how it forms can inform the design of molecules that will prevent proper assembly.

List of Contributors

This project is managed by Dr Lucie Delemotte at KTH /SciLifeLab.

URL: https://www.biophysics.se/index.php/projects/delemottelab/

2020-07-03
(Project: https://stats.foldingathome.org/project?p=16805. I pasted the text into the image.)

 

Proteins are not stagnant—they wiggle and fold and unfold to take on numerous shapes. We need to study not only one shape of the viral spike protein, but all the ways the protein wiggles and folds into alternative shapes in order to best understand how it interacts with the ACE2 receptor, so that an antibody can be designed. Low-resolution structures of the SARS-CoV spike protein exist and we know the mutations that differ between SARS-CoV and 2019-nCoV. Given this information, we are uniquely positioned to help model the structure of the 2019-nCoV spike protein and identify sites that can be targeted by a therapeutic antibody. We can build computational models that accomplish this goal, but it takes a lot of computing power.

(Source: https://foldingathome.org/2020/02/27/foldinghome-takes-up-the-fight-against-covid-19-2019-ncov/.)

 
=== Linux ===
I run folding@home (F@H) on two computers. One operates under MS Windows, the other one is a five years old computer with a Linux operating system. That old computer became very slow due to mitigations against Intel CPU vulnerabilities, so I didn’t use it anymore. But I reactivated it for F@H operated under a bare bone Linux OS. As that computer doesn’t do anything else than folding, I disabled the Intel CPU protection by starting the kernel with “mitigations=off”. (Don’t do that if you use your computer on the network for other tasks besides folding.) It works for kernels at and above version 5.2 and increases the speed (and the F@H point count) significantly. If your computer boots into Linux with GRUB, add mitigations=off to the settings in GRUB_CMDLINE_LINUX_DEFAULT.

=== Teams ===
As part of the “gamification” concept of F@H, your protein model folding computer collect points during folding. (It’s just for fun. Competition is in our genes, F@H plays with that.) You can join teams in order to get to the top in a ranking of teams together with other contributors. By default you are in a Zero team. That’s fine. You don’t have to change anything if you just want to help folding protein models.
        Some contributors join teams of organizations (e.g. companies) in order to let these organizations look good. That’s fine too. There are various kind of teams.
        You also easily can create your own team. Due to my obsession, I of course created a The Hunting of the Snark team. (So far it consist of only one member, but as of already is among the top 10% of all teams.)
        Curecoin: The top team is the Curecoin team. There you not only get points, you also get some kind of currency. It’s not my thing. One reason for me not to join Curecoin is that the blockchain technology applied would add additional workload to my computer. On the other side, Curecoin isn’t bad either. The Curecoin team has even more points than the Zero team, but much less work units. I think, that is because many contributors in that team run computers with powerful CPUs and GPUs. They get work units done faster than less powerful machines, and the points computation algorithm of F@H acknowledges that. (Thanks to the required number crunching power, blockchain technologies helped the market for graphics cards and GPUs a lot.) Personally I don’t like Curecoin, but as always: Use it if you like it and if you know what you are doing. (Links: Am Rechner nebenher die Welt retten | http://ftreporter.com/all-you-need-to-know-about-Curecoin/)

=== Caveats ===
Depending on the setting (Light/Medium/Full) of FAHcontrol, your computer can get quite hot. The older one of my computers does 24 hours/day folding in a cool room in the basement. It consumes a power of 26 Watts. The F@H setting is “Full”. It’s a fan-less mini computer, so no tear&wear of an internal fan needs to be considered. The computer won’t get damaged by the heat, because it adapts the CPU clock frequency in a way which doesn’t let it get too hot. In winter it won’t reach maximum temperature anyway. But in summer its temperature limits will get tested, even though the ambient temperature will stay below the 50°C maximum. So I added an external fan (14W). My other computer is a laptop computer. I chose the “Light” setting (which means that the GPU will not be used for folding).
        Super contributors use gaming computers with powerful CPUs and GPUs. And some show off impressive cooling machinery. Those gamers know what they are doing and can run F@H with maximum performance.

=== Smartphones ===
F@H does not run on smartphones, but there is a project for such devices. The Vodaphone “DreamLab” is a proprietary app. Of course it only runs during charging. I recommend to read the privacy statement.

=== Scams ===
Due to Covid19, F@H became much more popular, so take care not to install malware like fake applications which e.g. steal passwords. Don’t panic, but wherever scams are possible, you’ll have to deal with them. F@H is no exception. Possible scams are no reason not to contribute to F@H, but be aware of scams, e.g. foldingathomeapp.exe is malware! If you want to be on the save side, only install F@H software from foldingathome.org and don’t touch anything else.

=== Join ===
You can share computer time too.

F@H Team 263865 | COVID19 | Wikipedia |Twitter | Facebook (en) | Facebook (de)

2020-03-31, update: 2020-07-03

Fact Checks

  • Ambiguous: The “Boots” and “the maker of Bonnets and Hoods” in The Hunting of the Snark are two different persons.
  • Unproven: Carroll was on drugs when he wrote the Alice books.
  • Sometimes wrong: Carroll quotes. Check them.
  • Likely wrong: The “Ocean Chart” (the Bellman’s map) in The Hunting of the Snark was made by Henry Holiday.
  • Wrong: C.L. Dodgson (aka Lewis Carroll) invented the word “Snark”.
  • Wrong: Only the first issue of The Hunting of the Snark has “Baker” on page 83.
  • Wrong: There is photographic evidence that Alice Liddell as a child kissed C.L. Dodgson.
  • Wrong (snopes.com): C.L. Dodgson sent an admiring Queen Victoria a copy of An Elementary Treatise on Determinants.

 


Not Lewis Carroll

 
2019-07-12, updated: 2020-06-08

Henry Holiday and the maker or Bonnets and Hoods

Watch those fingers: The photo has been “photoshopped” (by Henry Holiday or Joseph Swain?) already many years before I worked on it using GIMP. Holiday’s tinkering with the little finger and the thumb of his left hand might be a “Victorian craze“.

The image shows Henry Holiday and segments of one of Henry Holiday’s illustrations (cut by Joseph Swain) to Lewis Carroll’s The Hunting of the Snark. The segments show the Bonnetmaker and a bonnet.

The Bonnetmaker drawing could be a little self portrait of and by Henry Holiday. However, the photo is several years older than Holiday’s illustrations to The Hunting of the Snark. Perhaps it is a portrait taken by Joseph Swain or a self portrait taken by Henry Holiday quite a few years after the Snark was published. Henry Holiday was younger when he illustrated Carroll’s Snark tragicomedy.

Henry Holiday and the Bonnetmaker have one thing in common: They are creative artists. So is Joseph Swain, who engraved that illustration. How did his face look like in 1876?

 


Such little self portraits have a long tradition.

In German there is term “Assistenzfigur”. That is a person positoned in the background or beside the main person or main object depicted in a painting. You may think of such a person as the static version of a “film extra” in a movie. She or he serves a a kind of helper or assistant. Sometimes one of these extras is the artist who made the painting. In German we call such an image in the image an “Assistenzselbstbildnis” or “Assistenzselbstbild” or “Selbstbildnis in Assistenz”. Perhaps the first known self-portraits in assistance where a kind of signature of the artist.

The “self-portrait in assistance” first became available since the 14th century to master builders and sculpturer, shortly after that in Italy also to fresco painters, and since the 15th and 16th century also to painters of large altar- and panel paintings; see Raupp, S. 8

Source (in German): Footnote on p. 162 in Suzanne Valadon – Identitätskonstruktion… (2001) by Valeska Doll referring to Untersuchungen zu Künstlerbildnissen und Künstlerdarstellungen in den Niederlanden im 17. Jahrhundert (1984) by Hans-Joachim Raupp.

In that matter there also are references to Raupp in Melanie Munduch: Die Selbstbildnisse Luca Giordanos (2012)

 


#Assistenzselbstbildnis: Twitter

For diskussion of the finger “photoshopping”: Twitter

Original post: 2017-09-28. Update: 2020-06-01

Snark Radio Play

Sadly, it’s not online anymore.

 


https://www.bbc.co.uk/programmes/b06sbrxh/clips (2020-01-02):

Tony Robinson narrates this fresh adaptation of Lewis Carroll’s classic masterpiece following a strange assortment of characters on their quest for an elusive beast.

Led by a bell-ringing Captain, this motley crew must brave terrifying danger in their chaotic pursuit of a creature known as Snark. Accompanied by specially composed music and songs, this surreal tale questions whether anything is really what it seems. …

First broadcast on BBC Radio 4 in December 2015.

Streaming: 2020-01-02 – 2020-01-31

Credits:
– Narrator: Tony Robinson
– Bellman: Eric Potts
– Baker: Paul Barnhill
– Butcher: Everal A Walsh
– Barrister: Jonathan Keeble
– Snark (in the Barrister’s dream): Jonathan Keeble
– Beaver: Stephen Hoyle
– Music and songs (composer): Katie Chatburn
– Music (performers):
    – Katie Chatburn
    – Dorry Macaulay
    – Kathryn Williams
    – Stephen Cordiner
    – Jasper Wilkinson
– Director: Charlotte Riches
– Author: Lewis Carroll

 
2020-01-02, update 2020-05-15

Bathing-Machines

Snarks have five marks:

The fourth is its fondness for bathing-machines,
      Which it constantly carries about,
And believes that they add to the beauty of scenes—
      A sentiment open to doubt.

[The New Belfry of Christ Church, Oxford] is of the best of Dodgson’s Oxford squibs, a good humored but cutting attack on Dean Liddell (the father of Alice) and the wooden cube built to contain the Cathedral bells during operations to build a new tower. Though it can still be found today behind the stone walls of the tower, the wooden cube was always a temporary plan but Dodgson was impatient and the Governing body were slow.

Source: Cristies, 2009-12-04

The Bell in The Hunting of the Snark might be interpreted as a symbol for time and time pressure. But it also might have been used by C.L. Dodgson to continue lampooning Dean Henry Liddell‘s “bonnet-box” project, a meekly geometric belfry to go up on the cathedral at Christ Church. In The New Belfry of Christ Church, a certain “D. C. L.” wrote:

§ 7. On the impetus given to Art in England by the new Belfry, Ch. Ch.

The idea has spread far and wide, and is rapidly pervading all branches of manufacture. Already an enterprising maker of bonnet-boxes is advertising ‘the Belfry pattern’: two builders of bathing-machines[MG025] at Ramsgate have followed his example: one of the great London houses is supplying ‘bar-soap’ cut in the same striking and symmetrical form: and we are credibly informed that Borwick’s Baking Powder and Thorley’s Food for Cattle are now sold in no other shape.

In The Belfry at Christ Church by E.G.W. Bill, edited by Michael Hall and published in Oxoniensia 2013 (Oxfordshire Architectural and Historical Society), I found this quote from a letter by C.L. Dodgson to The Pall Mall Gazette (1874-10-31):

During the restoration of the Cathedral, when the bells had been removed from the tower, which had become too weak to support them, it was proposed to hang them outside the cathedral in a wooden belfry, which we were assured would be quite inoffensive, as it would hardly be visible from any point of the compass. In an evil hour we consented, and the resulting erection, which cost about a thousand pounds, speedily made us famous for having inflicted upon Oxford the ugliest and most conspicuous monstrosity that probably she has ever seen. This, and the great expense already incurred, forced on us the conviction that we must now erect a stone bell-tower.

 
more

 
2018-05-24, editet: 2020-05-02

Gags and Serious Stuff