The Genetic Code

There are many ways to show the genetic code, the map between triplets of nucleotides and the amino acids of proteins. Here is one that may be a bit awkward to understand, but other more standard ones are easily found.

 First, here are the codes for the four nucleotides:

  • U = Uracil
  • C = Cytosine
  • A = Adenine
  • G = Guanine

As well, let

  • $ = U or C
  • % = A or G
  • & = U or C or A
  • * = U or C or A or G

And so, here are the amino acids and their nucleotide codes

A = Ala = Alanine = GC*
C = Cys = Cysteine = UG$
D = Asp = Aspartic Acid = GA$
E = Glu = Glutamic Acid = GA%
F = Phe = Phenylalanine = UU$
G = Gly = Glycine = GG*
H = His = Histidine = CA$
I = Ile = Isoleucine = AU&
K = Lys = Lysine = AA%
L = Leu = Leucine = UU% + CU*
M = Met = Methionine = AUG
N = Asn = Asparagine = AA$
P = Pro = Proline = CC*
Q = Gln = Glutamine = CA%
R = Arg = Arginine = CG* + AG%
S = Ser = Serine = UC* + AG$
T = Thr = Threonine = AC*
V = Val = Valine = GU*
W = Typ = Tryptophan = UGG
Y = Tyr = Tyrosine = UA$
# = Stop = UA% + UGA

Note that some letters encode both nucleotides as well as amino acids, which might be confusing.

Further Reading:

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

[*10.146, *10.147]

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The Four Philosophy Ensemble

A woman came up to me and said
“I’d like to poison your mind
With wrong ideas that appeal to you
Though I am not unkind”
She looked at me, I looked at something
Written across her scalp
And these are the words that it faintly said
As I tried to call for help…

— From Whistling in the Dark, by They Might Be Giants

  • The Cynic
  • The Realist
  • The Optimist
  • The Apathetic

Further Reading:

https://tvtropes.org/pmwiki/pmwiki.php/Main/FourPhilosophyEnsemble

The Utopian vs. the Dystopian

https://en.wikipedia.org/wiki/Flood_(They_Might_Be_Giants_album)

https://genius.com/They-might-be-giants-whistling-in-the-dark-lyrics

Notes:

Since these pair up nicely (Realism and Apathy, Optimism and Cynicism), perhaps one could combine them as Optimistic Realism, Optimistic Apathy, Cynical Realism, Cynical Apathy.

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The Eisenhower Matrix, Revisited

I don’t take responsibility at all.

There’s going to be a lot of death.

— Donald Trump, 45th President of the USA.

Above is the Eisenhower Matrix, but below detailed for the current president in this pandemic year.

Do First: Deny, diminish, blame. Say the coronavirus is a hoax, that it is under control and cases will go to zero, and that it will vanish with the spring. Blame previous administrations for all mistakes (bad tests that don’t exist, lack of Federal stockpiles), news media that are critical or ask probing questions (nasty, no-talent), and China. Pass on tests offered by WHO. Criticize states and medical professionals for asking for needed ventilators and PPE.

Eliminate: Eliminate pandemic response team created by Obama in 2017. Fire public servants for doing their jobs (Inspector Generals, civil servants, state department individuals). The PREDICT initiative for tracking potentially dangerous viruses was eliminated in September of 2019 when the funds ran out. In addition, eliminate (almost) everyone in the administration that might tell the president that he is wrong or making a bad decision. Just in: eliminate the top oversight IG for the 2 trillion dollar virus relief funds.

Delegate: Delegate critical decisions and coordination to unqualified individuals, such as VP Mike Pence and security-whatever Jared (“the federal stockpile is ours”) Kushner. Say the states need to find their own ventilators and PPE, and then use federal government to intercept their orders. Delegate everything that is difficult or might make this president look bad, so they can take the blame. (“I don’t know them.”)

Do Last: Take credit for doing a “great” job and having “great” ratings (and continuously throughout). Feel good if there are only 100 to 240 thousand American deaths. Expect a grateful nation to re-elect him for a second term. Take a bow (hopefully out)!

Further Reading:

https://equivalentexchange.blog/2018/07/07/the-eisenhower-matrix/

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The Ware Tetralogy

Here’s another science-fiction tetralogy for you to read that is both entertaining and thought-provoking. The  four books in Rudy Rucker’s “Ware” Tetralogy are:

  • Software
  • Wetware
  • Freeware
  • Realware

From Wikipedia:

The closest to the cyberpunk genre of all his works, the tetralogy explores themes such as rapid technological change, generational differences, consciousness, mortality and recreational drug use.

Pretty wild stuff!

Further Reading:

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

http://www.rudyrucker.com/wares/

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A Crystal Structure of the Main Protease of COVID-19

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/

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The Frauchiger-Renner Paradox

“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]

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The Eight Auspicious Symbols

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]

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