Monday, October 22, 2007

random musings one morning on complexity and cosmology: is it turtles all the way down?

i was reading through my molecular biology of the cell book the other day about signal transduction and p53, a protein that is involved in DNA repair, and cell death and cancer.

what i was struck by was HOW MUCH information processing happened at ONE protein. if the cell was irradiated, the protein is phosphorylated at sites x, y, z. if the cell was.. it was phosphorylated at sites q, r, s. one part of the protein recognizes damaged DNA and binds to it. another part of the protein binds to certain genes on the DNA to ... the protein senses if the cell is damaged during a certain part of the cell cycle, and arrests the cell there waiting for the DNA damage to be repaired. if the cell is damaged during a critical part of the cell cycle, no time for DNA repair, the protein signalls the cell to start cell death.

if the protein suffers mutation, this leads to cancers...

(i wonder if these processes are especially robust in the germ line?)

SO MUCH info processing at ONE LITTLE protein!

so i started reading about protein phosphorylation as signalling mechanism and signalling in general. so much is happening in the cell. so many places in the cell where information is being amplified, modulated, compared, sent abroad... at proteins on the cell surface, at proteins all over the place, at enzymes, at gene regulatory sites... It's so crowded and insane. like a 100 dimensional chess game with 100 players!

but even without cells and evolution, molecules, atoms can already information process. simple molecules can detecte each other's presence, can detect pH, can detect temperature, can detect wavelengths of light. can re-emit light, can act as catalysts... sets of simple molecules can set up oscillations... so much complexity as far in as we look. why is chemistry here?

lets compare chemistry to gravity: under gravity matter merely coalesces, compacts, without charge without quantum mechanics, matter would compact easily into black holes, end of story.

but add chemistry. add charge and the other 2 forces and quantum mechanics: protons and electrons DON'T merely coalesce into infinitely large networks of +/- they engage in nuclear fusion and become a distinct set of distinct nuclei. these nuclei with electrons again don't just coalesce into infintely large crystals of +/-. some, like Na, Cl, DO. but there are other elements around. and you get Chlorate, and you get ... H2O I think it's an amazing invention that some atoms join in discrete small groupings so that we get FLUIDS at certain ranges of temperatures.

(actually as an aside, even under gravity, why didn't the universe coalesce into ONE BIG SUN? why did it break up into many small suns of different sizes so that there are hot cauldrons of fusion at the center and cooler space between them for planets to form? i suppose this comes from properties of the VERY EARLY universe, or mathematics of contracting gasses.. I tried looking in Shu's "The Physical Universe" 1982, i don't see a definitive answer yet. either we aint got any good hypotheses or i don't undertand Jeans scale for initial graviational collapse. in fact all through taking that course i did not understand any of the details of why homogenous gas clouds begin graviational collapse to discrete stars. Of course within the past few billion years the clouds are NOT homogenous. how about at the beginning when stars and galaxies first formed? i suppose that's a current topic of research.)

so explain to me again the reason why protons and electrons don't just form an infinite metalic crystal? even if so, no need to think it static, if the temperature is high enough it will be a fluid... and then math can set in to produce eddies etc... but the universe DOES eventually cool... As much as we try to simplify, physics seems to resist.

i suppose a basic question is why do we get ONLY H2 and not H3, H7 or metallic Hydrogen? why do we get metalic lithium? because the next shell wants an octet! the crazy quantum geometry sets in... the first shell wants only a pair of electrons.

still, BETWEEN the stars the atoms and molecules are rather dispersed, for instance all the carbon atoms are not ONE SINGLE extent of graphite say...

what was the explanation for the fact that the initial universe isn't all iron? and would expansion have been able to tear apart the initial... well it was hot, so the bonding not strong enough to resist the heat... it's a combination of cooling AND expanding. how are the rates related? if it cooled faster than expanded... i think they are coupled. by what?

so i am still ultimately struck by the basic complexity of the universe, by physics. why four forces at all? why wasn't it merely point masses and gravity? as far deep as we go, it's complex, and messy. many physicists and thinkers in general through the ages have assumed they would find some rock bottom level of explanation, of simplicity... Why? i guess they FEAR the concept of turtles ALL THE WAY down.

But really, the historical evidence in fact points to the opposite conclusion, that as far IN we look it keeps getting messy, new pandora's boxes open up. suppose for as long as we look we keep finding new levels, new messinesses, at what point will we stop and say, "ok, maybe there IS no rockbottom level, lets stop looking!"

then what? what does that do to the question of WHAT ON EARTH is the univers anyway? was it designed, does it have a purpose, why is it at all?

Do any of these NEED to be answered? It's a crazy drama. So why not just accept it? Ah... that's the root of the problem, humans for the past 30,000 years, say, have come to NOT be able to accept being an ephemeral act in this grand drama. We do not seem to be able to let go of individual desires, not to be able to let go of our own lifetimes, nor maybe the lifetime of our species. thus we have two alternative projects:

1) find the rock bottom of the universe and hope it explains that which we are attached to. many religions come to the conclusion that the rock bottom has a plan for us and that that which we are attached to (spirit) will never die.

the physicists? what do they expect? some seem to think they have a discovered a universe exquisitely designed for our existence so at least our birth was not contingent, but what about our death? have physicists given up on attachment to eternal life? early astronomers wanted to prove the solar system stable! I suppose this was before the idea of species exitinction was common, did we think Homo sapiens would exist forever? between darwin and poincare is 1850 to 1900. by poincare the solar system's stability is in doubt. then cosmology. einstein tried initially a STEADY STATE model! that didn't work. now the battle is between forever expanding and cyclic models for the universe as a whole. does it dissapate into a slowly cooling cloud of brown dwarfs or does it contract and start up again?

by WWII the continuuing existence of Homo sapiens is in doubt to the nonreligious!

2) the alternative project is buddhist practice of giving up our attachments, and accepting our roles in the drama while we are engaged in it. are there buddhist traditions who honestly come to grips with modern cosmological history of a finite lifespan for Homo sapiens in a very grand drama? I have never discerned what the buddhist traditions have to say on the question of why we are here at all and why WE CAME TO NEED buddhist practice to cure our attachments in the first place.