Category Archives: Science

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/

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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:

https://theoryofself.com/the-four-fold-pattern-decisions-under-risk-e4e634eefc61

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

View at Medium.com

Daniel Kahneman / Thinking Fast and Slow

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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

https://equivalentexchange.blog/2019/07/07/the-arcane-arts-of-ramon-llull-the-dignities/

https://equivalentexchange.blog/2019/05/22/combogenesis-a-constructive-emergent-cosmos/

https://equivalentexchange.blog/2018/09/07/the-myer-briggs-type-indicator/

https://equivalentexchange.blog/2019/11/07/the-twelve-houses-of-the-zodiac/

https://equivalentexchange.blog/2013/12/06/the-tempest-and-forbidden-planet/

https://equivalentexchange.blog/2011/08/04/the-64-hexagrams-of-the-i-ching/

https://en.wikipedia.org/wiki/Hedgehog%27s_dilemma

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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:

https://ncase.me/trust/

https://en.wikipedia.org/wiki/Prisoner%27s_dilemma

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

https://equivalentexchange.blog/2017/08/03/the-prisoners-dilemma/

https://en.wikipedia.org/wiki/Devolution_(biology)

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What is Turbulence?

In his science-fictional “Foundation Trilogy”, Isaac Asimov famously hypothesized a future science called “psychohistory”, a mathematically grounded theory of generalized and predictive human action, based on an amalgamation of psychology, history, and sociology. The future galactic empire was managed by this theory and practice (look out – almost seventy year old spoilers!) except for an exceptional character that was not anticipated and essentially unpredicable.

Asimov had in mind well validated continuous and statistical theories of physics, for example for idealized gases and their laws. I was stuck by an image for an explanation of turbulence that highlighted key elements of velocity, density, pressure, and viscosity, and how it was (in my mind) analogical to antagonistic individuals, dominating leaders, submissive society, and affiliated coteries. Of course, an article below states that turbulence is still too complicated to provably model correctly at this point in time.

I had no idea that psychohistory was claimed to be an actual field of study these days, albeit being somewhat controversial in its authenticity. And it doesn’t seem to have any mathematical basis yet, as far as I know. Mathematician Dan Crisan gave an inaugural talk a few years ago that was hypothesizing using heat equations instead of fluid dynamics as a basis. Even so, we can’t seem to properly model any sort of social action so how could psychohistory be within our grasp?

In these turbulent times perhaps we should make an effort to understand ourselves a bit better, as we hope to navigate between the Charybdisian whirlpool of civil discord and environmental collapse and the Scyllaian rocks of fascism, authoritarianism, and / or totalitarianism. But hey, isn’t Apple doing an Apple TV+ series based on Asimov’s books? Let’s all tune in!

Further Reading:

https://en.wikipedia.org/wiki/Psychohistory_(fictional)

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

https://en.wikipedia.org/wiki/Foundation_(TV_series)

https://www.quantamagazine.org/why-turbulence-is-a-hard-physics-problem-20190128/

https://www.quantamagazine.org/videos/what-is-turbulence/

https://en.wikipedia.org/wiki/Navier–Stokes_equations

Philip Ball / Critical Mass : How One Thing Leads to Another (2004)

Concerning Professor Dan Crisan:

http://www3.imperial.ac.uk/newsandeventspggrp/imperialcollege/eventssummary/event_11-12-2012-13-34-29

https://rtraba.files.wordpress.com/2014/11/talkinaugural230113.pdf

And also this quite long but interesting essay:

Prolegomena to Any Dark-Age Psychohistory

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The Interpersonal Circumplex

May I have your attention please. The following citizens have been declared unmutual: Number 6.”

— From the TV show The Prisoner

Here we have another diagram based on the work of Timothy Leary (the other being the Eight Circuit Model of Consciousness), a simple chart defined by two axes. The vertical axis is currently and commonly thought of as agency (as well as power, control, assertiveness, and dominance) and the horizontal axis as communion (as well as love, agreeableness, friendliness, and affiliation).

The diagram is usually shown with concentric circles centered on the intersection of the axes, inviting continuous twofold measurements and plotting for the factors of dominance and affiliation. Thus it allows comparisons for the different quantified interactions of individuals within a group, perhaps as a metric for social cohesion and its opposite, fragmentation.

It is quite similar to the scheme for CM/CR (Conflict Management and Conflict Resolution), except that the Interpersonal Circumplex (IC) is a tool for understanding psychological and sociological behavior and traits, and CM/CR is apparently more often used in the business and political world. The IC also has commonalities with Grid-Group Cultural Theory, a notion used in sociological studies.

I first ran across something very much like the IC in Anthony Stevens’s “Ariadne’s Clue,” being used as a model for mythological solidarity and divergence. However, Leary is not credited but instead the primate studies of Chance and Jolly (1970) are cited for their work in intimidation and attraction, or agonic and hedonic modes of attention and interaction.

I would think that the IC could be used effectively to analyze the sorry state of politics in these “United States”, as domination and affiliation play their tug-of-war for superiority. I see some interesting papers by Kenneth Locke (2013), and of course I’m also thinking of the political work of George Lakoff as well, but I don’t see any use of the circumflex for Lakoff’s work.

Further Reading:

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

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

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5045262/

https://psychology.wikia.org/wiki/Interpersonal_circumplex

John M. Oldham, Andrew E. Skodol, Donna S. Bender (eds.) / The American Psychiatric Publishing Textbook of Personality Disorders

Christopher J. Hopwood, Abby L Mulay, Mark H Waugh (eds.) / The DSM-5 Alternative Model for Personality Disorders: Integrating Multiple …

Anthony Stevens / Ariadne’s Clue: a guide to the symbols of mankind (1998)

M. R. A. Chance and C. Jolly / Social Groups of Monkeys, Apes, and Men (1970)

Kenneth D. Locke / Circumplex Scales of Intergroup Goals: An Interpersonal Circle Model of Goals for Interactions Between Groups
https://journals.sagepub.com/doi/abs/10.1177/0146167213514280

Images of the Interpersonal Circumplex:
https://www.google.com/search?q=interpersonal+circumplex&client&tbm=isch

https://equivalentexchange.blog/2019/07/19/conflict-management-and-conflict-resolution/

https://equivalentexchange.blog/2019/08/19/grid-group-cultural-theory-v2/

https://equivalentexchange.blog/2019/02/07/the-eight-circuit-model-of-consciousness/

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