Category Archives: Science

Scenario Thinking and Covid-19

Scenario Planning, Analysis, or Thinking is a technique for probing into possible futures when you are anticipating or overwhelmed by tumultuous challenges. One often starts by examining two factors that have both great Importance and Uncertainty and then considering two extremes of each. For their four different mixtures, you can posit causes, how to recover from bad outcomes, what actions would be favorable for all scenarios, etc. In other words, one can develop related stories about these different futures.

In these slides by authors Steven Weber and Arik Ben-Zvi, the two important and uncertain factors are Public Health and Economics, both affected by the Covid-19 pandemic, and for their initial purposes independent of each other. For public health, the disease could kill far more than estimated (a secondary wave) or kill less (vanish like a miracle). For the economic impact, the toll could be sustained (a long term depression) or the recovery could be relatively quick (v-shaped). So the two factors and their extremes are

    • Economic recovery is slow (depression, recession), or fast (v-shaped)
    • Health and death toll is worse (than estimates), or better (yay)

The four scenarios that are named are basically

    • Economy good, Health good: Americans Win
    • Economy bad, Health good: Fractured USA
    • Economy good, Health bad: Resilient USA
    • Economy bad, Health bad: Coronavirus Wins

and the scenario stories are told with respect to January of 2021 at the next state of the union address. Each of these scenarios are quite detailed and then followed by Insights and Implications for all. Often Scenario Thinking is used for more distant future analysis, but this shows it can be used for a mere nine months as well.

Further Reading:

Continue reading Scenario Thinking and Covid-19

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:




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:

View at

Cellular automata:

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.




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:

View at

Images of the Adaptive Cycle:

Images of Panarchy:

Social Cycle Theory



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:

[*10.146, *10.147]


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:




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:



The Prospect Theory of Kahneman and Tversky

Like it or not, we are all betting individuals. But what interactions are there between the perceived and actual probabilities of things happening and the choices made for or against them? The likelihood of their occurrence, coupled with the size of the gains or losses from anticipating and acting on them, show that people are not entirely the rational agents that we think they are.

Instead of armchair introspection, careful experimental methods were used to give us these (not so) unexpected results. What is demonstrated is that deciding individuals make asymmetric choices based on their poor understanding of relative likelihoods. All sorts of biases and poor thinking on our part contribute to non-rational evaluations of how we end up choosing between alternatives.

The findings are that the near certainty of events happening is undervalued in our estimation, and the merely possible is overvalued. So those things very likely to occur have a diminished weight in our minds, and those things unlikely but possible have an increased weight. These are called the certainty effect and the possibility effect, respectively.

  • Likely Gain (Fear)
  • Likely Loss (Hope)
  • Maybe Gain (Hope)
  • Maybe Loss (Fear)

This asymmetry in valuation leads fearful individuals to accept early settlements and buy too much insurance, or hopeful individuals to buy lottery tickets and play the casino more often then they should if choosing optimally. What factors contribute to this behavior? Emotions, beliefs, and biases, probably all play a role in these perceived payoffs between dread and excitement.

In some “Dirty Harry” movie, the lead character essentially asks “do you feel lucky, punk?”, to goad another into taking a risk. In the movie “War Games”, the supercomputer more or less temptingly asks, “would you like to play a game?”, to encourage the playing of unwinnable matches. Watch out for those that know how to play the odds of hope and fear to manipulate our prospects and decisions.

Further Reading:

View at

Daniel Kahneman / Thinking Fast and Slow



Combogenesis and Alphakits

Let us calculate!

— Gottfried Leibnitz

I admit it, I’m rather a Utopian.

Perhaps I’ve been thinking all this time that it should be possible to find a reduced set of words, symbols, or even concepts that could serve as a basic core of human expression and being, some kind of fundamental proto-language that might cut across all cultures and yet connect all individuals. Something to undo the “Tower of Babel” and be able to heal all misunderstandings, resolve all disagreements, and find everyone’s common ground. I see now I have fallen down the “perfect language” rabbit-hole.

Of course, along with our imperfect languages we also have to deal with our imperfect thoughts and our imperfect feelings. Not only do we want to hide what we’re really thinking and feeling from others, we want to hide it from ourselves. Is it because we don’t want others to know the weakness and darkness within us, or we don’t want to face those parts of our own identities? Perhaps that is the main problem with language, the ease with which we can lie to both ourselves and others, and our eagerness to accept these lies.

Psychology is supposed to help us understand ourselves better. But before that, there were the Tarot decks, Ouija boards, and the I Chings that were supposed to illuminate our thoughts and actions, and help us perceive, however dimly, a little clearer into the past and future. I’m sure I’m not alone in thinking that such devices merely bring concepts to the forefront of the conscious mind and allow one to engage in creative and playful thinking. Maybe they tie into the “unconscious”, whatever that really means, and if not, then what is the source of their utility?

In the same vein, there are other instruments purported to aid in the effort to know thyself, such as Astrology and Myers-Briggs. Astrology has also been used for divination and that is its popular and sad ubiquity, that is “your daily horoscope”. Myers-Briggs is popular in the business world to help the managers manage and to resolve conflicts, and takes itself more seriously. In my foolishness, even though I didn’t believe that there was a perfect language lost in antiquity, perhaps I thought I could invent one anew like Ramon Llull or Gottfried Leibnitz!

Does language reveal reality or does it mask it? Can it blend and synthesize different realities or can it shape and create the very reality we inhabit? I’ve been mulling over the idea of what the next combogenetic alphakit might be, after chemical-molecular, biological-genetic, and symbolic-linguistic. Could it be something hyper-linguistic or hyper-cognitive, to serve as a perfect language, melding syntax, semantics, pragmatics? Or could it be something completely different, a blending of mathematics and philosophy?

Or even a new type of computer science? Such studies are still in their infacy, so one hopes for future breakthroughs and grand theories of logical systems and (e)valuations. Could a machine that creates reality from mere thought be the perfect language we seek, one that performatively produces no ambiguity by changing the abstract into the concrete, the inner into the outer? The Krell machine in the movie Forbidden Planet was one such hypothetical device, and showed the folly of a scheme that granted god-like powers to mere mortals.

Possibly better is a system that starts from grounding axioms that are so simple and fundamental that all must agree with their basis, utilizes logics that are so straightforward and rational that all must agree with their validity, demonstrates proofs that are so rigorous that all must agree with their worth, all enabled by overarching schemas that allow the truth of all things to vigorously and irrefutably shine. Even then, humankind might be too weak to suffer the onslaught against its fragile and flawed cogitations.

But O, what a wonderful world it might be.

Further Reading:

Umberto Eco / The Search for the Perfect Language



The Devolution of Trust

The Prisoner’s Dilemma is a simple game designed to show how the success or failure of cooperation between individuals can be contingent on various factors, primarily some sort of reward. Shown above is a representative payoff matrix between two players; each square shows the two choices and the two winnings for each. Each player cooperates (A or B) or cheats (A’ or B’) with the other player, so for example if A and B’ obtains (A cooperates but B cheats) then A loses 1 and B wins 3.

Each player knows all the values of the payoff matrix so it is said they have perfect information, except they don’t know what their opponent will do. If they are rational and believe their opponent to be as well, the wisest thing to do is for both to cooperate to maximize their winnings, knowing that their opponent knows that they could also cheat. If the game is played only once, however, that is clearly not the case.

If the game is iterated, things change. If each player remembers what their opponent did previously, and it is considered to be informative for what they might do next, then the player could use it to condition their decision to cooperate or cheat. Different algorithms or personalities can be considered for the players, with more or less thinking about what to do and more or less willingness to cooperate, and it is interesting to try different strategies, all the while seeing what adjustments of the payoff matrix might do to the results.

This Evolution of Trust site is a very nice lesson in some of the complications that can result for such algorithms and adjustments. On the whole, this site indicates that rationality and consideration for others can thrive, if conditions are right. In the traditional Prisoner’s Dilemma, the reward values in the payoff matrix are usually considered to be jail sentence time (so less is better), or for the site mentioned above where I’ve taken the representative matrix, monetary value (so more is better).

One thing of note in these examples is that each player doesn’t distinguish their opponent by anything other than their posteriori plays, because these players are supposed to be all part of the same group or society. But what if there is an a priori distinction that conditions their decision? So, if your opponent is a known Y, and you are a X, then you might want to raise your social credit with your other Xs by punishing a Y, even if it punishes you or even other Xs in the long run.

For example if you are a member of gang X, you wouldn’t want to cheat against another X. But cheating against a member of gang Y might raise your in-group social capital and be as important as the value of the reward. Or you might want to punish your opponent in group Y by not granting them any benefits even at the cost of your own benefit. Such distinctions are not usually part and parcel of the Prisoner’s Dilemma game, but they would add an interesting and realistic dimension to the game.

And thus lend insight into the woes of our modern political scene and culturally diverse society.

Further Reading:

[*11.24, *11.172]