The Pi Calculus

My previous post on Wolfram’s physics mentioned the Pi calculus, but I liked this little diagram so much I decided to let it have its own mention. The rules aren’t really four in number, but oh well.

  • (νx)P: create a channel named x, then do P
  • x(y).P: receive y over channel x, then do P
  • x‾<y>.P: send y over channel x, then do P
  • P|Q: do P and Q at the same time
  • !P: do P over and over until stopped
  • 0: stop

Further Reading:

https://en.wikipedia.org/wiki/%CE%A0-calculus

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

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

https://golem.ph.utexas.edu/category/2009/08/the_pi_calculus.html

[*12.34]

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The Wolfram Physics Project

When I first started looking at Stephen Wolfram’s latest proposal to solve physics, I was somewhat disappointed. I was rather fond of his previous “New Kind of Science” based on the structural rigidity of cellular automata. However, I am now intrigued by his latest ideas, based on the looser but more flexible basis of networks.

And once you have pithy statements with space, time, energy, and matter (as momenta), you catch my attention:

  • Energy is flux of causal edges
  • through Spacelike hypersurfaces
  • Momentum is flux of causal edges
  • through Timelike hypersurfaces

I confess I haven’t read much about the project yet, but it seems to be using rewriting rules, perhaps similar to the notion of rewriting in Wolfram’s previous framework, cellular automata. Of course, cellular automata and also rewriting rule systems can be computationally universal or Turing complete.

Another idea might be to try some sort of computational metaphysics between nodes like the pi-calculus (or some other process calculus). After all, you have to support quantum entanglement! However if you can encode everything with simpler structures then do it!

Further Reading:

https://www.wolframphysics.org/

https://www.wired.com/story/stephen-wolfram-invites-you-to-solve-physics/

https://writings.stephenwolfram.com/2020/04/how-we-got-here-the-backstory-of-the-wolfram-physics-project/

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

https://www.scientificamerican.com/article/physicists-criticize-stephen-wolframs-theory-of-everything/

https://turingchurch.net/computational-irreducibility-in-wolframs-digital-physics-and-free-will-e413e496eb0a

View at Medium.com

Cellular automata:

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

Note this quote for future reference:

The primary classifications of cellular automata, as outlined by Wolfram, are numbered one to four. They are, in order, automata in which patterns generally stabilize into homogeneity, automata in which patterns evolve into mostly stable or oscillating structures, automata in which patterns evolve in a seemingly chaotic fashion, and automata in which patterns become extremely complex and may last for a long time, with stable local structures. This last class are thought to be computationally universal, or capable of simulating a Turing machine.

Rewriting:

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

https://en.wikipedia.org/wiki/Semi-Thue_system

[*12.32]

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Who Do You Love?

Who do you love?
Who do you love?
Who do you love?
Who do you love?

— From Who Do You Love by Bo Diddley

The constituents of this list had pretty much congealed in my mind when I ran across information on the eight kinds of love. I thought that in this difficult time it might be useful to consider what is most important by examining all the people and all the things one can love as well as their myriad ramifications. Indeed, love may be the most considered and talked about emotion. Might one even say it is at the root of all of human action?

I know that in order to substantiate my claims I should justify these particular selections by comparing and contrasting them with each other, or to show their association to the eight kinds of love, and to do both would be a worthwhile effort. If I just show my diagram and my little list no one will think much of it. I could say I would return later but we all know how I tend to be distracted by the next bright shiny thing.

At the very least I could do some research, or do some hard thinking about why I’ve chosen these particular eight. I’m not sure if such diligence will reap any benefits but all one can do is try their best. So therefore I invite you to continue reading and perhaps you will be enlightened or perhaps you will be disappointed by what I say in the following analysis, if it even manages to appear at all.

I see that there are some modern analyses of love like Robert Sternberg’s Triangular Theory of Love, based on concepts of passion, intimacy, and commitment. This theory seems to be devoted to interpersonal relationships but maybe so is the Greek Eight types. But I’m thinking of love in a broader sense than just interpersonal, although maybe that doesn’t agree with certain definitions of love.

Love doesn’t have to reciprocated, of course, or directed towards another loving entity. For example, Agape is love of humanity in general, but humanity in general cannot return one’s love. One can also love negative things, like hate, or strife, or friction, and some even make a career out of it. But I’m going to leave that out for now. Alas, my interest has waned on this post and so I will have to try again at a later time.

  • Love of Self
  • Love of Leader
  • Love of Group
  • Love of Other
  • Love of Nature
  • Love of Ideas
  • Love of Gods
  • Love of Things

Further Reading:

https://en.wikipedia.org/wiki/Who_Do_You_Love%3F_(Bo_Diddley_song)

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

https://en.wikipedia.org/wiki/Category:Love

https://en.wikipedia.org/wiki/Category:Philosophy_of_love

[*11.76]

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The Adaptive Cycle

As we all wonder how the current world order will be transformed by the Covid-19 pandemic, perhaps now would be a good time to read up on the Adaptive Cycle. Worried about societal and economic collapse, I was originally thinking about the notion of social cycles, but came across this more general notion of cycles within ecological systems. It is also applicable to insightful investigation of social institutions and organizations.

The Adaptive Cycle is usually shown as a figure-eight loop, with four main segments (Growth, Maturity, Release, and Renewal), inhabiting a space of two or three variables (Potential, Complexity, and Resilience):

  • Growth or Exploitation: (r)
  • Maturity or Conservation: (K)
  • Release or Collapse: (Ω)
  • Renewal or Reorganization: (α)

Thus these charts indicate a closed trajectory of a system’s state within a state space over time. This concept was originally applied to cycles within ecological systems, measuring certain attributes of systems in order to predict their ability to handle, recover, and adapt from significant disruptive changes in environment, species populations, genetic landscape, etc.

These cycles can form steps on chains of greater systems where an individual cycle is a quasi-stable element but the overall state can jump and grow to higher forms of complexity and potential, or indeed collapse and fall to lower forms if the resilience is weak. As well, the multiplicities of cycles can represent a range of spacial scales for systems that have smaller cycles nested within them, operating concurrently.

This greater notion of change within systems has been called Panarchy. In contrast to hierarchy or even anarchy, Panarchy is neither the top-down or bottom-up of the other two. Panarchy tries to describe how actual ecological and social systems can change and transform yet endure and return to similar states, across scales of space and time.

Further Reading:

https://en.wikipedia.org/wiki/C._S._Holling

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

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

https://www.resalliance.org/

https://www.resalliance.org/panarchy

https://www.sciencedirect.com/science/article/pii/S1476945X1830165X

http://www.sustainablescale.org/ConceptualFramework/UnderstandingScale/MeasuringScale/Panarchy.aspx

View at Medium.com

Images of the Adaptive Cycle:

https://www.google.com/search?q=adaptive+cycle&tbm=isch

Images of Panarchy:

https://www.google.com/search?q=panarchy&tbm=isch

Social Cycle Theory

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

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

[*12.24]

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The Eight Kinds of Love

There are several mentions of eight types of love purportedly discussed by the ancient Greeks, but I’m short on the actual references.

In no particular order:

  • Agape: unconditional love
  • Eros: romantic love
  • Philia: affectionate love
  • Philautia: self love
  • Storge: familiar love
  • Pragma: enduring love
  • Ludus: playful love
  • Mania: obsessive love

I had an earlier post on The Four Loves by C. S. Lewis, but now I see that he just left out half of them for some reason. Missing are Philautia, Pragma, Ludus, and Mania, which seem important, but since I haven’t read the book, I don’t know his reasons.

Further Reading:

https://lonerwolf.com/different-types-of-love/

https://www.lifehack.org/816195/types-of-love

https://www.ftd.com/blog/give/types-of-love

https://www.organicauthority.com/energetic-health/learn-the-8-types-of-love-according-to-the-ancient-greeks

8 Types of Love – Which One Are You?

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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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