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Posts tagged with evolution

Fun coursera on virology.

  • Viruses are so numerous (10³⁰) and filling up everywhere. It gives this Boltzmann flavour of ‘enough stuff” to really do statistics on.

  • Viruses are just a bundle of {proteins, lipids, nucleic acids} with a shell. It’s totally value-free, no social Darwinism or “survival of the fittest” being imbued with a moral colour. Just a thing that happened that can replicate.
  • Maybe this is just because I was reading about nuclear spaces (⊂ topological vector spaceand white-noise processes that I think of this. Viruses have a qualitatively different error structure than Gaussian. Instead of white-noise it’s about if they can get past certain barriers, like:
    • survive out in the air/water/cyanide
    • bind to a DNA
    • spread across a population
    • adapt to the host’s defences
  • … it seems like a mathematician or probabilist could use the viral world of errors to set out different assumptions for a mathematical object that would capture the broad features of this world that’s full of really tiny things but very different to gas particles.
  • Did I mention that I love how viral evolution is totally value-neutral and logic-based?
  • Did I mention how I love that these things are everywhere all the time, filling up the great microspace my knowledge had left empty between man > animals > plants > > bacteria > > minerals?




Oh, much less. The total memory was four kilobytes. And he did an amazing lot with that. Especially a biologist who was there at the time, called Nils Barricelli, did simulated evolution amazingly well with a memory of four kilobytes. He developed models of evolving creatures forming an ecology, and they showed punctuated equilibrium, exactly the way real species do. It was astonishing how much he could get out of that machine.
Freeman Dyson, via University of David




In game theory the word “strategy” means a fully specified contingency plan. Whatever happens—be it a sequence of things, a conditional branching of their responses and my responses—∃ a contingency.

I can’t prove this, but I do feel that sometimes people talk about others as constants rather than response functions.

(A function is a ≥1-to-1 association from elements of a source domain to elements of a target codomain. I’ll owe ya a post on how this is not the most intuitive way to think about functions. Because it depends which domains you’re mapping from and to. Think for example about automorphisms—turning something over in your hand—versus measures—assigning a size to something.)

  

For example, extraversion vs introversion. This is one of the less disputatious dimensions of human variation from the MBTI. We can observe that some people (like me) gain more energy by being around people and feel like sh*te when they spend too much time alone, whereas others (like my best friend) replenish their reserves by being alone and drain them when they go out in public.

So we observe one datum about you—but sometimes a discussion (eg, an economics debate) wants to veer over counterfactual terrain—in which case we need a theory about how things might else have been.

  • Maybe when you were young, your parents always made you do chores whenever they saw you, but didn’t particularly seek you out when you were out of sight. So you learned to hide in your room, avoid chores, and develop your personal life there. Hence became introverted as a response to environmental factors.
  • When I was young, I used to think I was introverted. Really I was just widely disliked and unpopular for being an ugly nerd. But later in life I developed social skills and had the fortune to meet people I liked, who liked me back. In response to who was around, I became extraverted.
   

I can think of other aspects of myself that are obviously responses to situational stimuli rather than innate constants.

  • If I were raised in a different culture, my sexuality would be different. In my culture, homosexuality is seen as “You boink / date / marry from your own sex”, but in ancient Sparta women all gayed on each other as a matter of ritual before the men came home from war. But they didn’t call themselves homos, and neither did the Roman men who sexually touched each other. It was just a different conception of sex (one I can’t fathom) where “Just because I regularly crave and do sexual stuff with people of my own sex, doesn’t mean I’m gay!”
    File:Pederastic erotic scene Louvre F85bis.jpg
    File:Banquet Euaion Louvre G467.jpg
    File:Pompeii - Terme Suburbane - Apodyterium - Scene V.jpg
    File:Nisos Euryalos Louvre LL450 n2.jpg
    Point being this is all the result of inputs; born Puritan, think sex = evil. Born Roman, "sexuality is a behaviour, not an identity".
  • If I ate more food and exercised less, my fat:muscle ratio would increase.
     
  • If I meditated more, I would feel more at peace.
  • If I read more maths, I would know more maths. More people would think of me as a mathematician—but not because it was inevitable or inherent in me to be a mathmo, rather because I chose to do maths and became the product of my habits.
  • If I fixed more bikes, I would be able to fix bikes faster.
  • If I made more money, I would go to different places, meet different people, be exposed to their response functions to their own pasts and presents and anxieties and perceptions, a vector field of non-Markovian baggage, and all of this history and now-ness would sum up to some stimuli-complex that would cause some response by me, and change me in ways I can’t now know.
     
  • Our friendship could have been so much more, but we sort of let it fall off. Not for any reason, but it’s not so strong now.
  • Our love could have been so much less volatile, but I slept around, which had repercussions for your feelings toward me, which repercussed to my feelings toward you, which repercussed …. (multiplier effect / geometric series)
 

Besides being motivation for me to learn more maths to see what comes out of this way of thinking about people when you layer abstract algebra over it, this view of people is a reminder to

  1. release the egotism, and
  2. not take too literally what I think I’m seeing of whomever I’m interacting with.

Someone who piss me off may not be “a jerk”, it may not be about me whatever, s/he may be lag-responding to something from before I was there. Or s/he may not have adapted to a “nice guy” equilibrium of interacting with me. Who knows. I’m not seeing all of that person’s possibility, just a particular response to a particular situation.

On the other hand, if they really are acting wrong, it’s up to me to address the issue reasonably right away, rather than let my frustration passive-aggressively fester. Wait ten years for revenge and they’ll be a different person by then.

The final suggestion of people-as-functions is that there’s always something buried, something untapped—like part of a wavefunction that will never be measured, or a button on a machine that never gets pressed. You may see one version of yourself or someone else, but there’s more latent in you and in them—if you’re thrown into a war, a divorce, the Jazz Age, the Everglades, a hospice, a black-tie dinner, poverty, wealth, a band, a reality show about life under cruel premodern conditions—that may bring out another part of them.

 

UPDATE: peacemaker points out the similarity between people-as-response functions and the nature/nurture debate. I think this viewpoint subsumes both the nature and the nurture side, as well as free will.

  1. Evolution shaped our genes in response to environmental pressures (see for example the flies’ eyes chart above).
  2. My assumptions & predilections are a response to a more immediate “environment” than the environment of evolutionary adaptation.
  3. And I exercise free will over how I respond to the most immediate “environment” which is just the stimuli I get from you and the Wu Tang Clan.

UPDATE 2: As I think through this again, I feel quantum measurement really is a great metaphor for interacting with people. You only evoke one particular response-complex from a person on that particular time. And the way you evoke it perturbs the “objective” underlying thing. For example if yo’re introduced to someone in a flirtatious way versus in a business setting.







Dmitri Tymoczko — author of The Geometry of Music

  • how to make visual representations of music
  • (in paintings, video games, sculpture)
  • 5 constraints on a composition that are necessary (but not sufficient) for it to sound good
  • global statistical properties of songs
  • why 20th century classical music had little audience
  • a random painting is much less offensive to the eye than random notes are to the ear
  • "I came up with these 5 principles using my brain, which is a kind of crude statistical device”
  • the piano is essentially a line
  • [NB: linear ⊃ monotonic ⊃ totally ordered]
  • violin/voice musicians know that notes ⊂ continuous space, but the piano does us a favour by constraining us to a subset of those notes
  • line mod 13 = circle
  • (equivalence classes of octaves — A1=A2=A9 and E4=E7=E12 etc.)
  • directed segments, unordered tuples
  • musical translation = mathematical transposition, musical inversion = mathematical rotation
  • The fact that most people don’t have most perfect pitch (things sound the same in different keys) may be so that we can understand that, despite pitch differences in male/female adults’ speech and children’s speech, they are saying the same words.
  • "It’s as if we couldn’t tell the difference between red and blue, but we were highly sensitive to the-difference-between-red-and-orange and the-difference-between-blue-and-green.
  • [Also: this.]
  • Minor vs major is the other isometry of the circle (besides rotation): reflection.
  • "Harmonic progression is like zone defence"
  • Minute 26: Awesome. Watch how to move around in 2-chord space — seen on a circle and on Tymoczko’s grid
     




Thank you, steel manufacturing companies, and thank you, chemical processing companies, for giving us the time to read. —Hans Rosling

Totally good point about how the mechanisation of the rich world has allowed us to have so many professors, doctors, photographers, lawyers, and social media managers.

 

But I wonder: why is laundry so important?

There has to be a good reason; no one working with their hands for 70+ hours a week would choose to do an extra 10 hours of labour a week if they could avoid it. But I know from experience that, in my world, if you don’t do laundry for months at a time, nothing bad happens to you.

What did I do instead of laundry? I’ve taken a few options, some of which would have been available to poor humans now or in the past:

  1. wash clothing with the excess soapy water that falls off me in the shower (not available to them)
  2. turn clothing inside out and leave it outside (requires a lot of socks but before the 19th century no one was wearing socks anyway)

The second you would think poor people could do pretty easily. I used my porch, which got sun and wind and blew away, over time, most of the smells

So what’s the reason they couldn’t do that? I have a few theories.

  • They laboured with their bodies, getting much sweatier than I do at my computer.
  • Bugs and germs were more prevalent in their environment and got in their clothing if it weren’t soaped — or at least exposed to ammonia rising off the castle pissing grounds.
  • They got dirtier, muddier, muckier. But why would you need to deal with that?
  • Having clean clothes raised your appeal to the opposite sex, and social status went along with that as it goes along with attractiveness today. Clean isn’t necessary; it’s just sexy (on average).

Anyway, I wonder if it isn’t the other changes to the modern OECD environment (reduction in bugs and reduction in manual labour) that made for the progress. Nowadays I just use the washer when I’ve exercised or played in the mud.

If the wash was always just a way of keeping up with the Joneses, however, then we can’t congratulate the washing machine for saving us necessary labour — it just helps us live out our autocompetitive rank obsessions in other ways now the elbow’s been surpassed on that dimension.




I’m looking for a quote I saw years ago. It went something like this:

Here are two different stories of Creation.

 

The first is that G-d sculpted each and every animal, flower, fungus, gymnosperm, archaeobacterium, and primate individually, like the most colossal micromanager ever known to the Cosmos. 

 

The second story is that G-d was smart enough to write a “computer” program which, from a few simple rules, would evolve not only the stars, galaxies, and planets, but also all of the life-forms mentioned above (as well as whatever’s yet to come).

 

Which Creator would you find more impressive?

I’m pretty sure the writer was an Israeli game theorist. Can anybody help me source this please?




Moore’s three-dimensional law is a remarkable “epiphenomenon” … a statistical regularity that emerges from a swarm of unknown, mutually independent activities. In that sense, it resembles the “law” that says that each Labor Day weekend, about 450 automobile fatalities will occur in the United States.

This nationwide prediction can be made years in advance and will turn out quite accurate, despite the fact that the location and reason of each crash — each constituent microevent — are of course totally unpredictable.




The word “Evolution nowadays suggests "evolution of organisms by natural selection as per Darwin & modern population genetics".

But what about other kinds of evolution? Any unary endomorphism from a system onto itself, applied over and over to generate “time”, could be considered a kind of “evolution”.

  • Crystals and quasicrystals evolve naturally.
  • Caves and stalagmites evolve naturally.
  • History evolves artificially … although no-one knows the mapping.
  • Art evolves artificially … again, no-one knows the mapping. (but we know there is cross-pollination. Could we call it “Art sex”?)
  • Proto-biological chemical compounds, like basic amino acids, “evolved” by a method similar to natural selection.
  • Businesses (and entrepreneurs) that grow through trial-and-error, evolve their ideas and their business processes by artificial selection.
  • Romantic relationships evolve. Any human relationship evolves. Sometimes “a” relationship can evolve with a group of people as-a-unit. But here I’ve found the selection to be more exogenous than endogenous. Friendships seem to pick up exactly where they left off γᵢ(Tᵢ) rather than be pitched to the dustbin of 0. Even romantic relationships seem to hang mostly where they were, even after a breakup. Perhaps the breakup zeroes the romantic part ⌊γᵢ⌋ᵣ, but everything else—sexual chemistry, personality dynamics, humour dynamics, and history—remains stubbornly unbudged by a breakup per se.
  • And like I said, any endomorphism, repeatedly applied to a system, could count as “evolution”. (An endomorphism draws both the input and the output from the same domain, i.e. ƒ: X→X.) If there is a throw-away criterion (mapping ↦ 0), we could call that “selection”. Any fixed point of the mapping ƒ(p)↦p is an endpoint of evolution.
     

In this video, John Baez talks about how the inherent interestingness of the number 5 has made itself apparent to us through several processes:

  • artists (mosque designers) discovered it. God speaks to us in the language of mathematics, remember?
  • crystals and quasicrystals discovered 5 by evolution — but not the biological kind
  • soot and space dust found , also by natural non-bio evolution
  • BTW, unrelated but some Scots (perhaps Picts) carved some Platonic solids out of stone centuries before Plato … so perhaps they should be called Scottish solids.
  • the Pariacoto virus found by biological evolution
  • Roger Penrose (a mathematical physicist) discovered & described 5-way symmetry in modern mathematical (group theoretic) terms

In each case, logic is the canvas. Art — nature — mathematicians are the painters.




What’s the difference between leaving carbon progeny behind you and silicon progeny behind you? … [W]hat makes you feel that a planet teeming with sexually created successors would constitute a more valid extension of ‘we’-ness than a planet teeming with our intellectually created successors? [robots / cyborgs / conscious machines / strong AI computers]

The question comes down to how we human beings feel comfortable using and extrapolating the term pronoun “we”. Were “we” once languageless squirrel-sized mammals? Did “we” then become primates? Did “we” discover that “we” could use tools? Did “we” begin speaking some 50,000 years ago? Were “we” at that time an entirely agrarian society? Did “we” start living in cities a few thousand years ago? Did “we” discover geometry, algebra, and calculus? Did “we” try out communism for a few decades? Will “we” someday cure cancer? Will “we” someday fly to Mars? … Will “we” migrate into immortal software?

Doug Hofstadter, in Perspectives on Natural and Artificial Evolution

The whole essay (ok, most of it):

grâce à Virgil

 

The story of the primates reminds me of my favourite short story from Cosmicomics. Italo Calvino shrinks the generations of evolution into manageable bites, so that qfwfq, a lizard in this story, has a great-uncle n’ba n’ga who’s still a fish.

Well, you can read it yourself: