A Crystal Structure of the Main Protease of COVID-19

March 27, 2020 Martin K. Jones Leave a comment

One can gain knowledge from words, but wisdom only from things.

— George Wald, Harvard biochemist and 1967 Nobel Laureate

Many images of the coronavirus SARS-CoV-2 (a.k.a. 2019/nCoV a.k.a. COVID-19) are in the media, with the colorful spiky ball motif being the most frequent. Above is a representation of one of its proteins, its main protease, which allows the virus to process the proteins created after it splices its own RNA genetic material into your cells.

The larger three lobed spiky proteins from which these types of viruses gets the name “corona” are responsible for grabbing onto and opening up the surface of (in this case) lung cells, so that this smaller protein can perform its function within the cell. In more detailed images, you may have seen it as small pairs of spheres on the viral surface.

Several different crystal structures of various proteins of COVID-19 have been solved and released recently, including this main protease and the spiky protein peplomers. Studies of these structures will hopefully lead scientists to discover inhibitors to their functions and thus treatments and preventive measures. Go science!

Unfortunately, these results will come much too late for many of us. Science could have also helped us with the initial defense against this deadly virus, but the powers that be deigned to consider the gravity of our plight. And even today many such leaders and spokespersons are ignoring important information and spreading misinformation.

Further Reading:

https://www.rcsb.org/structure/6M03

https://pdb101.rcsb.org/motm/242

https://science.sciencemag.org/content/early/2020/03/19/science.abb3405

https://neurosciencenews.com/covid-19-protease-decoded-15959/

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

https://en.wikipedia.org/wiki/Coronavirus_disease_2019

https://en.wikipedia.org/wiki/Portal:Coronavirus_disease_2019

https://www.theatlantic.com/health/archive/2020/03/how-will-coronavirus-end/608719/

Biology, fourfolds, grid, Physics, Science

The Frauchiger-Renner Paradox

March 21, 2020 Martin K. Jones Leave a comment

“The new experiment shows that, in a quantum world, two people can end up disagreeing about a seemingly irrefutable result, such as the outcome of a coin toss, suggesting something is amiss with the assumptions we make about quantum reality.”

— From the Quanta article by Anil Ananthaswamy

As above, so below.

As we face the deadly onslaught of electron-microscopy-sized agents, remember to wash your hands for twenty seconds, follow physical distancing rules of six feet or more, and please be safe.

Further Reading:

https://www.quantamagazine.org/frauchiger-renner-paradox-clarifies-where-our-views-of-reality-go-wrong-20181203/

https://algassert.com/post/1904

https://arxiv.org/abs/2002.01456

https://www.scientificamerican.com/article/reimagining-of-schroedingers-cat-breaks-quantum-mechanics-mdash-and-stumps-physicists1/

https://en.wikipedia.org/wiki/Wigner%27s_friend

https://equivalentexchange.blog/2013/01/11/schrodingers-cat/

[*11.12]

eightfolds, religion

The Eight Auspicious Symbols

March 14, 2020 Martin K. Jones 1 Comment

Pause only for a moment to contemplate Ashtamangala, or the Eight Auspicious Symbols of Buddhism:

The Endless Knot
The Treasure Vase
The Lotus Flower
Two Golden Fish
The Fancy Parasol
The Conch Shell
The Victory Banner
The Dharma Wheel

Further Reading:

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

http://www.buddhanet.net/e-learning/history/b8symbol.htm

The Whitewater Rafter’s Guide to the 8 Auspicious Symbols of Buddhism

[*12.14]

alchemy, chain, fourfolds

The Book of the New Sun

March 7, 2020 Martin K. Jones Leave a comment

Gene Wolfe’s “Book of the New Sun” tetralogy is said to be rife with alchemical symbolism. I have not read it yet, although it has been on my to-read stack for years. Nonetheless, here is a diagram for you, partly because it’s an easy post, but also for me, so that I can add interesting links as I might find them.

The Shadow of the Torturer
The Claw of the Conciliator
The Sword of the Lictor
The Citadel of the Autarch

Of course, there are a few other tetralogies that exist, although they are not as common as trilogies. One already mentioned on this blog is the Aeygpt Tetralogy by John Crowley.

Further Reading:

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

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

An Analysis Of The Alchemical Tradition Behind BOOK OF THE NEW SUN, Part I: Urth, Ushas, And Unus Mundus

An Analysis Of The Alchemical Tradition Behind BOOK OF THE NEW SUN, Part II: The Solve et Coagula of Terminus Est

An Analysis Of The Alchemical Tradition Behind BOOK OF THE NEW SUN, Part III: The Piteous Gate and A Dark Albedo

An Analysis of the Alchemical Tradition Behind BOOK OF THE NEW SUN, Part IV: Hethor, Typhon and the Temptation of Severian

An Analysis of the Alchemical Tradition Behind BOOK OF THE NEW SUN, Part V: The Aestivation Hypothesis and the Hierodules

An Analysis of the Alchemical Tradition Behind BOOK OF THE NEW SUN, Part VI: Tzadkiel and the Mystery of Yesod

fourfolds, logic

Four Valued Logic

March 7, 2020 Martin K. Jones 1 Comment

Logic is not as absolute as we would like it to be. For example, linear logic breaks down normal logic into a realm of substructurality. There seems to be several ways to consider expanding classical two-valued logic to four values.