Why can we build a telescope and heave it off our planet with giant rockets to orbit above our sky and with it look out at the night and see a universe full of a...
100 billion galaxies all further and further away from each other and we can count in each galaxy a..
100 billion suns, and our sun is a
100 million miles away up in the sky and is a
million miles wide, while earth is only
8,000 miles wide which would take
24 hours to travel around at
1000 miles an hour so it's made of
256 billion cubic miles of gyrating rock but still it would take a
million earths to fill the sun and also it means that the surface of our earth is
800 million square miles, each mile being..
20x20 city blocks, and spread across the land of this earth we've become ...
7 billion squabbling singing dancing birthing dying eating shitting wondering wandering humans sharing this earth with...
1000s or millions of billions of other critters and in fact each of us ourselves is actually a colony of a
10 thousand billion living amoebas all tightly knit together into a community but each an independent living creature that is born eats dies makes decisions communicates with its neighbors and ... because our colony of amoebas launched from the shores of each of our mothers' wombs (we were one of HER amoebas...we are a continously living journey of protoplasm more than 3 and a half billion generations long.. and all these living amoebas can eat explore turn food into itself communicate tell time build an entire replica of itself because each one is in fact an entire New York City full of
1000 billion nanorobots as many as there are bricks in all of New York City with its 100x100x100 bricks per building times 100 buildings per block times 200x 10 city blocks that takes a day to traverse
swimming in a soup of a
million billion molecular parts and a way to visualize a
billion is to slice a block of tofu into 10 slices and then turn it 90 degrees and slice that 10 times so you got a 100 slivers and then turn that over and slice that 10 times so you got a
1000 tiny cubes and now go find the corner of a large 3 story building and line those 1000 tiny tofu blocks one by one along the side of that building starting from the corner on the sidewalk till it's 30 feet along and then go back and slice up another
1000 tiny tofu blocklets and line them up along the other side of the building from the corner and now you gotta concentrate hard and use your imagination and visualize the floor of the building made up of a grid of a 1000x1000 tiny tofu blocks making up a
million of them and then go slice up another 1000 tofu blocklets and pile them up along the corner of the building like 1000 Lilliputian floors up 30 feet and now REALLY concentrate hard and visualize a 1000 of those million block grids all making up that building and by the way our brains what we think and feel and imagine with is made up of as many amoebas as
100 of these buildings of a billion amoebas all the while each of these amoebas is sending out arms of protoplasm to branch 10 times to point fingertips to a 1000 other amoebas across the city of brain to have these billions of simultaneous conversations. but what are these 100,000 billion nanorobots that make our amoebas dance anyway? they are proteins and enzymes and each is a sproingy network of
10,000 atoms of 6 different kinds linked in squaredances of electron orbitals and these nanorobot proteins can snap together and change shape and crawl across each other and make simple logic decisions (forming dense information processing networks...) interacting with dozens of each others and can even come together by the 100s to take each other apart and rebuild each other from scratch out of these atoms. go visit new york city and imagine each of those bricks you see is a flying crawling nanorobot and they all start moving around and swarming like clouds of billions of bees all rebuilding each other and reproducing an entire city in two weeks. and what the hell ARE these atoms anyway?
dozens of interacting electron orbitals each singing a different frequency and repelling each other but attracting each other in duets of dance to join with other atoms, to make atoms springy fuzzy sensitive boundaryless slightly unpredictable sparkles and are electrons and protons and neutrons the rock bottom core of stuff the universe is made of? well every time we look inside with our cathedrals of particle accelerator experiments like the Large Hadron Collider made of
over a billion precision crafted parts taking 10 years to build in a cavern that can swallow (a cathedral?) build like a ship in a bottle down a 150 foot deep shaft into the largest vaulted cavern on earth by 3000 scientists and engineers and students from over 40 different countries and cultures and languages and religions all learning to civilly criticise each other and come to agreements about the rock bottom nature of reality..
we keep finding another level of parts more messy than the previous level and that the universe isn't made out of stuff at all but maybe it's an infinitely complex mathematical game like a...
Mandelbrot set?
Friday, September 7, 2012
Wednesday, August 8, 2012
Preliminary Notes On The Geology Of Opal Formation
the birth of opals: not too deep in the bedrock that makes the Earth there are all sorts of cracks. the Earth is always heaving and sighing and cracks form.
there is water also either soaking down from above or welling up from below. patchy heat sources can also send water seeping in from above back up.
these waters will then dissolve the minerals in the rocks. the most common minerals in rocks are silicates: quartz, feldspars, mica, clay...
so these waters become enriched in dissolved silica. silica is interesting stuff. silicon dioxide can arrange itself into all kinds of interesting structures: strands, rings, flat hexagonal networks... these molecules come with positively charged and negatively charged ends, that make them stick together tentatively like magnets into even more structures.
the way the silica structures attach to each other is modulated by the pH of the waters.
i don't really understand this... i must review my book:
"Silica and Me", by Guy Alexander. an excellent first person account of the adventures of a rookie research chemist in industry as he begins to solve some problems in silica chemistry. along the way he explains in a clear fashion a lot of interesting chemistry
(it appears to be out of print but a few copies appear to be available from amazon at the moment)
under certain conditions of temperature, pH and other dissolved ions like carbonates and sodium etc... the silica will precipitate out as crystals or spheres i don't know what selects for either... perhaps crystals precipitate out only in purer silicon dioxide, while being mixed with water produces a kind of silica tetrahedron strand - water chaos...
now the microspheres 150nm to 1000nm wide will be in suspension and will be negatively charged and will repel each other. by modulating the ph and ion content and concentration of the spheres some more the degree to which the spheres can contact can be modulated. under some conditions they will want to contact the least and will thus form long linear strands. at point of contact though, chemical bonding can occur. as concentration goes up these strands can precipitate and line up, again contacting the least amount to make perfect cubic packing of the spheres
if there are spheres of different sizes... they will tend to come into closer contact with each other... (draw a picture) (actually, if there are small spheres that can fit between the spaces in the larger sphere packing that would be the least favorable situation, but a bunch of spheres of SLIGHTLY different size would produce less perfect packing and so less contact? hmm this is puzzling, requires more thought) so perhaps electrostatic repulsion alone can cause spheres of uniform size to precipitate together...
so you can have a multistrand strands of uniform sized spheres of one size next to another multistrand strand of uniform spheres of another size...
it is the regular arrangement of the these uniform spheres that forms a diffraction grating that causes the color play in the opals. so you can have streaks of different color/opalescence this way
other processes that can effect opal formation are other trace minerals to form nuclei around which the microspheres first precipitate out.
another process is sorting of sphere sizes by filtration through clays by pressurized silica solutions. the pressurization could come from volcanic heat or from other clays. some clays will absorb water and this causes them to swell, so they will exert pressure on adjacent layers of silica solutions...
another factor that can effect the precipitation of microspheres is if cooler waters or waters of different pH seep down and contact the warm waters rich in dissolved silica.
another factor may be bacteria living in the water filled cracks. they may also be able to modulate chemical conditions around themselves to effect the formation of these microspheres.
some references:
general
opal wiki
where i got some details from:
THE ORIGIN OF PRECIOUS OPAL: A new model
Byron Deveson
there is water also either soaking down from above or welling up from below. patchy heat sources can also send water seeping in from above back up.
these waters will then dissolve the minerals in the rocks. the most common minerals in rocks are silicates: quartz, feldspars, mica, clay...
so these waters become enriched in dissolved silica. silica is interesting stuff. silicon dioxide can arrange itself into all kinds of interesting structures: strands, rings, flat hexagonal networks... these molecules come with positively charged and negatively charged ends, that make them stick together tentatively like magnets into even more structures.
the way the silica structures attach to each other is modulated by the pH of the waters.
i don't really understand this... i must review my book:
"Silica and Me", by Guy Alexander. an excellent first person account of the adventures of a rookie research chemist in industry as he begins to solve some problems in silica chemistry. along the way he explains in a clear fashion a lot of interesting chemistry
(it appears to be out of print but a few copies appear to be available from amazon at the moment)
under certain conditions of temperature, pH and other dissolved ions like carbonates and sodium etc... the silica will precipitate out as crystals or spheres i don't know what selects for either... perhaps crystals precipitate out only in purer silicon dioxide, while being mixed with water produces a kind of silica tetrahedron strand - water chaos...
now the microspheres 150nm to 1000nm wide will be in suspension and will be negatively charged and will repel each other. by modulating the ph and ion content and concentration of the spheres some more the degree to which the spheres can contact can be modulated. under some conditions they will want to contact the least and will thus form long linear strands. at point of contact though, chemical bonding can occur. as concentration goes up these strands can precipitate and line up, again contacting the least amount to make perfect cubic packing of the spheres
if there are spheres of different sizes... they will tend to come into closer contact with each other... (draw a picture) (actually, if there are small spheres that can fit between the spaces in the larger sphere packing that would be the least favorable situation, but a bunch of spheres of SLIGHTLY different size would produce less perfect packing and so less contact? hmm this is puzzling, requires more thought) so perhaps electrostatic repulsion alone can cause spheres of uniform size to precipitate together...
so you can have a multistrand strands of uniform sized spheres of one size next to another multistrand strand of uniform spheres of another size...
it is the regular arrangement of the these uniform spheres that forms a diffraction grating that causes the color play in the opals. so you can have streaks of different color/opalescence this way
other processes that can effect opal formation are other trace minerals to form nuclei around which the microspheres first precipitate out.
another process is sorting of sphere sizes by filtration through clays by pressurized silica solutions. the pressurization could come from volcanic heat or from other clays. some clays will absorb water and this causes them to swell, so they will exert pressure on adjacent layers of silica solutions...
another factor that can effect the precipitation of microspheres is if cooler waters or waters of different pH seep down and contact the warm waters rich in dissolved silica.
another factor may be bacteria living in the water filled cracks. they may also be able to modulate chemical conditions around themselves to effect the formation of these microspheres.
some references:
general
opal wiki
where i got some details from:
THE ORIGIN OF PRECIOUS OPAL: A new model
Byron Deveson
Friday, August 3, 2012
Ramblings On Vertebrate Mating Dances and Rhythm
a few weeks ago i was watching israeli folk dancing, and wondering about cichlid fish, and birds.
prospective mates sizing each other up for skill, genetic health and compatibility. the fact that someone could have memorized dozens, HUNDREDS of complex synchronized dance movements. like the brown thrasher and his 2000 songs. the fact that you can synchronize with another person to that level of accuracy.
the cichlids that have to spend many weeks together at the risky consuming task of raising kids in a three dimensional risky environment. the females probably got a whole season invested in this, so it's got to be done RIGHT! so they gotta be sure they are compatible physically. they go through elaborate sizing each other up dances:
http://ib.berkeley.edu/labs/barlow/book.html
over 1000 different kinds... these guys lay eggs and then care for them, then care for their young. some build nests for the kids, some keep the eggs in their mouths, some excrete a kind of 'milk' on their skins that the babies feed off of. variations of males, females caring for the kids.
it's alot of work and so the males and females have a complex time sizing each other up during courtship to decide wether they will work well together for the coming weeks/months of raising kids. big investment in time and energy.
fascinating book. fascinating fish.
but all the vertebrates going through these elaborate mating routines. do they really make important choices? how important are the choices? how MUCH difference do they make? enough to warrant the elaborate games? wonder how you test it.
* * *
how do the ones that mate for more than one season compare? do song birds mate for more than one season? scrub jays? thier male kids help 'em raise up another batch, so... like wolves. not elephants. not chimps. not dolphins?
and humans wouldn't if it weren't for the fact that the guys stay on to help raise up a kid that takes years... so he ends up having more? but chimp kids take years... the sisters help.
hypothesis on why male mates stick around for childraising in Humans: unlike in chimps the older sisters aint mature enough to help out by the time the next kid comes along!
* * *
so write about rhythmic mammals. what's it mean:? social function, even the women? interesting. one doesn't usuually think of it. yet many mammal societies are women elephants and dolphins and chimps three different groups. not wolves. not carnivores, curious! woops dolphins are carnivores. hunters? or grazers?
so whence the rhythm? what other mammals? birds don't do it! one thinks of animals doing something rhythmic as pathological! really? the polar bear going rouund and round his tank. a sick fish shimmying..
* * *
hmmm the place of human music in human evolution...
one thing i would note, is that while bird "song" is very complex (see my posts about Kroodsma's book) it is VERY different than our long winding narrative songmaking.
lots of aspects to our music. the songs, the songtructures, the long narratives, the harmonic structures, and the rhythm
our music and our language facilities seem to be related..
do octopi do anything like music?
music is hierarchical, so is language, do narratives tend to have nested heirarchies, or are they "and then this happened and then that happened" or are they more tangled...
20JUN2008
i can think of some specifics: narratives long winding narratives. so far we know no animal that can weave long stories stanza after stanza with subtle variations, like shakespeare or charlie parker.
mockingbirds? subtle variations, but i don't know if they are telling a narrative.
whales? i don't know what they are doing.
honeybees? (search forum) their narratives are very short and finite.
communal bonding:
i know of no other species that gets together in communities as populous as ours. HUNDREDS of millions? in nations? in relgions in isms, in brand loyalty...
no ant community goes to 100 million
exacerbating this is our propensity to communal ecstatic states. we whip each other into frenzied mobs that can build empires or storm empires.
has something to do with rhythm
rythm?
usually in other animals, behaving in a mechanically rhytmic state is a sign of sickness?
i know of no other animal that keeps rhythm like we do, creatively, subtly but STEADILY, no birds sing in the rhythm that human musicians and ecstatic dancers do...
this relates to the fact that we use steady rythm and rythmic breathing to reach ecstatic states.
when we reach these rythmic ecstatic states in mobs we march across the planet and take over...
...
not extended period, that i think is the key point! humans will do rhythm for HOURS, KEEPING rhythm, but CREATIVELY. god, i miss the pots and pans man down in the subway at times square! and to the point of reacing ecstatic states.
do any animals do THAT?
head bobbing of iquanas, is that really in good rhythm?
i'm talking:
tony williams playin' live at the plugged nickle with miles davis:
http://www.youtube.com/watch?v=dYSaX-za64E
it's rhythmic it's precise but fluid, he's thinking INSIDE the rhythm, (totally unlike those frogs you heard, unless i'm mistaken) check out:
http://www.amazon.com/gp/product/B00138F8RS/ref=dm_sp_alb
amazing shit.
Monday, July 9, 2012
One Afternoon's Notes On Physics Of Snow
notes from: "Field Guide to Snow Crystals", by Edward R. Lachapelle
(if i get ambitious i'll find some pics to accompany the terms)
I'm always so fascinated that no matter where you look in this universe, complex heterogenous structures are always forming, always these curious complications. all of this is just water, the response of trillions of trillions of water molecules to their their environment and each other. or maybe it's mathematics...
snow crystallizes in atmosphere into plates, hollow prisms, needles, stars etc... and some combos. as conditions alter and snow crystals fall to diff layers, new forms crystallize on them. they also get hoared.
secondary processes occur in atmosphere and after falling:
1) close to 0degC metamorphism where details are lost and roundness develops
2) riming if it falls through layer of supercooled water droplets makes crystals rough and blobby
3) temperature gradient metamorphism which ultimately leads to totally restructured depth hoar, layered cups and needles
4) compaction
associated process is hoar:
1) freezing of microscopic supercooled water droplets: hoar needles and feathers into the wind
2) freezing of water vapor.
these processes can take a day to 6 years and more. eventually all original form is lost and hoar develops or under compaction, random connected ice crystals -> glacier ice.
snow is from 0.15g/cm^3 to ~1.
looking at a handful of snow you can try to deduce it's history in the atmosphere and on the ground. and predict skiiability and avalanche potential.
clouds are
1) water droplets (low)
2) supercooled water droplets
3) ice crystals
ice crystals form around nuclei of favorable particles, even microscopic salt crystals. if they fall through supersaturated air they will grow. conditions change they even may be caught in updrafts.
if they fall through microscopic water droplets they collect rime.
symmetrical snowflakes are a rarity contrary to the picture books.
Nakaya, U. "snow crystals: natural and artificial" cup '54 grew crystals in lab conditions 0deg to -25 and supersaturation wrt ice from 100 to 140.
needles seem to grow in distinct regions of 0 to -5, -5 to -7.,
then a region of scroll or cup from -7 to -10 but above the saturation vapor pressure wrt supercooled water line
dendritic region is between -12deg to -17deg and from below the supercooled line upwards
plates and sectored plates occur -10 to -20 along with thick plates though thick plates mostly below the line
plates perpendicular to the plane of crystal occur in a small region between -20 to -25 blow the line
columns occur -7 to -22 way below the line.
some regions contain only one kind of crystal. others contain mixed. it is VERY strange.
Magono, C. and C. W. Lee "meteorological classification of natural snow crystals" jnl of the faculty of sci, hokkaido u. ser VII (Geophysics), II, no. 4 (nov '66) p. 321-355
extended this with in field observations. it kind of matches, they looked all the way down to -40degC. they found more columns and combined columns and bullets down there.
METAMORPHISM
so then he says that because snow crystals have high surface area to vol ratio, they are very thermodynamically unstable [[WRT TO WHAT?]]
(Q1) SO WHY DO THEY FORM? IS IT A FAR FROM EQUILIBRIUM PROCESS? WHERE? WHAT MAKES IT DIFFERENT THAN FORMATION OF MORE COMPACT STABLE CRYSTALS?
i guess they are at equilibrium with supersaturated air. now what's that? air cooled below the dewpoint, so... i don't understand it microscopically, but i guess the water molecules have energy to give up.
try supercooled water. when you take heat from water it cools, then it will solidify. if you take this heat from it to supercool it to the same temp, ... is it you drop to lower temp by taking LESS heat from it? what measurements do you get from exp? temp is avg kinetic energy so less molecular motion but molecules just havn't had chance to orient... when it touches a seed... ah... we get enthalpy AND entropy to think about. i don't understand ANY of this.
at any rate, in dry air... i guess molecules at pointy spots evaporate and migrate to flatter spots.
this is called equitemperature metamorphosis and happens fastest close to 0deg and slower towards -40, it does not happen colder than -40. which appears to be the temp limit of snow formation in Magono and Lee's diagram. so maybe colder than that it just evaporates.
i guess if there is a temperature gradient, the water will sublimate off in one region and condense in another region... so one region will be...
equitemp metamorphosis will continue till random packed uniform spheres about .5 to .6 g/cm^3 (he says random uniform sphere packing is .580 i don't understand what that might mean) anyway i guess the water is not traveling far, because no gradient so it simply travels from pointy places to nearest smooth places.
TEMPERATURE GRADIENT METAMORPHISM:
if there is a temp gradient, water is continuously evaporating from warmer regions to colder regions. in this case the vapor deposition is like snow formation and will form larger and larger crystals up to 1cm of cups and paralleled joined needles and hollow needles, the crystals loosely packed. this is called depth hoar.
the original crystals are lost and completely new crystals form.
(Q3) how is this different than formation of firnspiegel? oh it's migration of vapor from one crystal to adjacent crystal, not capillary action of water. fascinating.
so in what environments does this happen and which way does the gradient go? warmer closer to the surface or further or any number of situations?
this happens when gradients are generally more than 0.1degC /cm
he says usually warmer closer to the ground, cooler above.
(Q5) one question though: do ALL the layers recrystallize or do the crystals at the warmer layers slowly waste away to tiny spheres at the expense o the growth of larger depth hoar above? [[and then the lower layers will slowly compact and that will change the process...]]
[[there must be similar process in geological settings... all kinds of dissptv can be happening...]]]
in equitemp metamorphosis, the rounding grains are being sintered together and bonding eventually to continuous glacier with micro bubbles. in temp grad met, the larger crystals do NOT bond, and the bulk strength of the snow weakens.
yes he says sometimes it results in entirely evaporated empty pockets below, and weakly packed snow above and avalanches.
the depth hoar photos look like the way soil freezes into those vertical bundles of crystals. similar process? in soils the crystals push the soil up and and make it fluffy.
this mostly happens in cold continental climates in shallow snow. not deep coastal snows.
the sign of depth hoar crystals is: "layered structure that appears externally as a stepped or ribbed surface on certain crystal facets". "tendency for the crystals align in faint columnar patterns parallel to direction of vapor diffusion" hmmm
of course once the temp gradient is removed, the depth hoar reverts to equitemp metamorphosis and decays..
RIME
is the deposition of supercooled water droplets from storm winds onto cold surfaces. the deposits are bulk, needles or feathers that grow into the direction of the wind. like those ice vanes i found on grassblades growing towards the falls in ithaca. (on the grass about 50 feet from the bottom of some high falls one winter, cold mist blowing steadily against the grass from the falls and each blade had a grass blade thin ice vane sticking out from it TOWARDS the wind. some were more than half an inch long. was surreal)
the deposits are made of individual tiny drops, even the needles and feathers, are not single crystals.
(Q6) why on earth do NEEDLES form out of compacted drops? how do the air currents and freezing regimes contrive to make the drops condense on the TIPS of the needles and not fill in between? or just HOW do they form? very strange!!!!
the photos of the feathery forms seem to hint at hexagonal angles?
rime also forms bumps on falling snow
HOAR
is deposited from water vapor cooled below dew-point onto cold surfaces. it forms flat stepped crystal forms or flat feathers (kind of reminiscent of those artificial bismuth crystals but not 3d screw dislocations). when it forms on the surface of snow it glitters and a layer of it forms excellent lubrication for slab avalanches.
it is either surface hoar or depth hoar.
it usually forms on cold clear nights with high humidity causing the air to cool and humidity to condense out.
FIRNIFICATION
two processes can lead to firnification: compaction or condensation from water coming in due to CAPILLARY ACTION
(god the complexities about!!! that must be how firnspiegel forms. light travels through upper layer, gets absorbed deeper in and eventually causes some melting, then THAT water is drawn up through capillary action [WHY? (Q2) because lower is more compact and upper is more capillary space to draw the water? hmmm] where it is deposited on cooler upper layers and forms eventually a thin shiny sheet of ice at the surface.
it's a kind of convection!!! so cool!)
(if i get ambitious i'll find some pics to accompany the terms)
I'm always so fascinated that no matter where you look in this universe, complex heterogenous structures are always forming, always these curious complications. all of this is just water, the response of trillions of trillions of water molecules to their their environment and each other. or maybe it's mathematics...
snow crystallizes in atmosphere into plates, hollow prisms, needles, stars etc... and some combos. as conditions alter and snow crystals fall to diff layers, new forms crystallize on them. they also get hoared.
secondary processes occur in atmosphere and after falling:
1) close to 0degC metamorphism where details are lost and roundness develops
2) riming if it falls through layer of supercooled water droplets makes crystals rough and blobby
3) temperature gradient metamorphism which ultimately leads to totally restructured depth hoar, layered cups and needles
4) compaction
associated process is hoar:
1) freezing of microscopic supercooled water droplets: hoar needles and feathers into the wind
2) freezing of water vapor.
these processes can take a day to 6 years and more. eventually all original form is lost and hoar develops or under compaction, random connected ice crystals -> glacier ice.
snow is from 0.15g/cm^3 to ~1.
looking at a handful of snow you can try to deduce it's history in the atmosphere and on the ground. and predict skiiability and avalanche potential.
clouds are
1) water droplets (low)
2) supercooled water droplets
3) ice crystals
ice crystals form around nuclei of favorable particles, even microscopic salt crystals. if they fall through supersaturated air they will grow. conditions change they even may be caught in updrafts.
if they fall through microscopic water droplets they collect rime.
symmetrical snowflakes are a rarity contrary to the picture books.
Nakaya, U. "snow crystals: natural and artificial" cup '54 grew crystals in lab conditions 0deg to -25 and supersaturation wrt ice from 100 to 140.
needles seem to grow in distinct regions of 0 to -5, -5 to -7.,
then a region of scroll or cup from -7 to -10 but above the saturation vapor pressure wrt supercooled water line
dendritic region is between -12deg to -17deg and from below the supercooled line upwards
plates and sectored plates occur -10 to -20 along with thick plates though thick plates mostly below the line
plates perpendicular to the plane of crystal occur in a small region between -20 to -25 blow the line
columns occur -7 to -22 way below the line.
some regions contain only one kind of crystal. others contain mixed. it is VERY strange.
Magono, C. and C. W. Lee "meteorological classification of natural snow crystals" jnl of the faculty of sci, hokkaido u. ser VII (Geophysics), II, no. 4 (nov '66) p. 321-355
extended this with in field observations. it kind of matches, they looked all the way down to -40degC. they found more columns and combined columns and bullets down there.
METAMORPHISM
so then he says that because snow crystals have high surface area to vol ratio, they are very thermodynamically unstable [[WRT TO WHAT?]]
(Q1) SO WHY DO THEY FORM? IS IT A FAR FROM EQUILIBRIUM PROCESS? WHERE? WHAT MAKES IT DIFFERENT THAN FORMATION OF MORE COMPACT STABLE CRYSTALS?
i guess they are at equilibrium with supersaturated air. now what's that? air cooled below the dewpoint, so... i don't understand it microscopically, but i guess the water molecules have energy to give up.
try supercooled water. when you take heat from water it cools, then it will solidify. if you take this heat from it to supercool it to the same temp, ... is it you drop to lower temp by taking LESS heat from it? what measurements do you get from exp? temp is avg kinetic energy so less molecular motion but molecules just havn't had chance to orient... when it touches a seed... ah... we get enthalpy AND entropy to think about. i don't understand ANY of this.
at any rate, in dry air... i guess molecules at pointy spots evaporate and migrate to flatter spots.
this is called equitemperature metamorphosis and happens fastest close to 0deg and slower towards -40, it does not happen colder than -40. which appears to be the temp limit of snow formation in Magono and Lee's diagram. so maybe colder than that it just evaporates.
i guess if there is a temperature gradient, the water will sublimate off in one region and condense in another region... so one region will be...
equitemp metamorphosis will continue till random packed uniform spheres about .5 to .6 g/cm^3 (he says random uniform sphere packing is .580 i don't understand what that might mean) anyway i guess the water is not traveling far, because no gradient so it simply travels from pointy places to nearest smooth places.
TEMPERATURE GRADIENT METAMORPHISM:
if there is a temp gradient, water is continuously evaporating from warmer regions to colder regions. in this case the vapor deposition is like snow formation and will form larger and larger crystals up to 1cm of cups and paralleled joined needles and hollow needles, the crystals loosely packed. this is called depth hoar.
the original crystals are lost and completely new crystals form.
(Q3) how is this different than formation of firnspiegel? oh it's migration of vapor from one crystal to adjacent crystal, not capillary action of water. fascinating.
so in what environments does this happen and which way does the gradient go? warmer closer to the surface or further or any number of situations?
this happens when gradients are generally more than 0.1degC /cm
he says usually warmer closer to the ground, cooler above.
(Q5) one question though: do ALL the layers recrystallize or do the crystals at the warmer layers slowly waste away to tiny spheres at the expense o the growth of larger depth hoar above? [[and then the lower layers will slowly compact and that will change the process...]]
[[there must be similar process in geological settings... all kinds of dissptv can be happening...]]]
in equitemp metamorphosis, the rounding grains are being sintered together and bonding eventually to continuous glacier with micro bubbles. in temp grad met, the larger crystals do NOT bond, and the bulk strength of the snow weakens.
yes he says sometimes it results in entirely evaporated empty pockets below, and weakly packed snow above and avalanches.
the depth hoar photos look like the way soil freezes into those vertical bundles of crystals. similar process? in soils the crystals push the soil up and and make it fluffy.
this mostly happens in cold continental climates in shallow snow. not deep coastal snows.
the sign of depth hoar crystals is: "layered structure that appears externally as a stepped or ribbed surface on certain crystal facets". "tendency for the crystals align in faint columnar patterns parallel to direction of vapor diffusion" hmmm
of course once the temp gradient is removed, the depth hoar reverts to equitemp metamorphosis and decays..
RIME
is the deposition of supercooled water droplets from storm winds onto cold surfaces. the deposits are bulk, needles or feathers that grow into the direction of the wind. like those ice vanes i found on grassblades growing towards the falls in ithaca. (on the grass about 50 feet from the bottom of some high falls one winter, cold mist blowing steadily against the grass from the falls and each blade had a grass blade thin ice vane sticking out from it TOWARDS the wind. some were more than half an inch long. was surreal)
the deposits are made of individual tiny drops, even the needles and feathers, are not single crystals.
(Q6) why on earth do NEEDLES form out of compacted drops? how do the air currents and freezing regimes contrive to make the drops condense on the TIPS of the needles and not fill in between? or just HOW do they form? very strange!!!!
the photos of the feathery forms seem to hint at hexagonal angles?
rime also forms bumps on falling snow
HOAR
is deposited from water vapor cooled below dew-point onto cold surfaces. it forms flat stepped crystal forms or flat feathers (kind of reminiscent of those artificial bismuth crystals but not 3d screw dislocations). when it forms on the surface of snow it glitters and a layer of it forms excellent lubrication for slab avalanches.
it is either surface hoar or depth hoar.
it usually forms on cold clear nights with high humidity causing the air to cool and humidity to condense out.
FIRNIFICATION
two processes can lead to firnification: compaction or condensation from water coming in due to CAPILLARY ACTION
(god the complexities about!!! that must be how firnspiegel forms. light travels through upper layer, gets absorbed deeper in and eventually causes some melting, then THAT water is drawn up through capillary action [WHY? (Q2) because lower is more compact and upper is more capillary space to draw the water? hmmm] where it is deposited on cooler upper layers and forms eventually a thin shiny sheet of ice at the surface.
it's a kind of convection!!! so cool!)
Saturday, January 28, 2012
Rembrandt at the American Museum Of Natural History
Gemsbok in the Carl Akely Hall of African Mammals
(photo by Chris Randolph, thanks for reminding me of this!)
and now for some rembrandt:
Sunday, January 8, 2012
How to Think About a Worm Evolving Into a Bird
that's quite a stretch, yes... i mean where do all the parts come from right? looks like the worm is some kind of simple clay and some artist with an imagination has to sculpt the bird parts out of the worm-clay
that's a reasonable idea. given that we come from a culture of artists and craftsmen and not the modern biology class.
So the first step is to describe what kind of 'clay' we've discovered a worm is. If we want to know how a worm can change into a bird, first of all, do you have any idea how a bird egg turns into a bird? that would be a start. I mean, how do you think birds get sculpted all around us everyday? If I told you, you'd be more amazed than your disbelief that a worm could turn into one.
so for a worm to evolve into a bird of course we mean that a worm gives birth to a bird, or of course that a worm gives birth to a slightly different worm that gives birth to a slightly different one, and eventually worms are hatching with nubby legs and eye spots, and eventually heart and lungs, and feathers and wings... Seems incredible, eh? but really what you want to start with is how does a bird give birth to a bird? It lays an egg and the egg turns into a bird. lets start there! How does it happen?
[and then you may have some vague notion that a bird is so different than a worm, that it has so many more complex parts and behaviors that for this to happen the number of minute changes necessary is astronomical and couldn't happen in a 1000 years or a million years. But that's just the point, you just have a VAGUE notion. do you really know how to think about just HOW MANY changes are necessary? and is it some kind of continuous sculpting or is there a discrete number of changes at all? ARE animals made up of discrete parts that CAN be changed one part at a time?]
of course in the egg that you eat, before it is fertilized, there is no bird structure. WHERE DOES THE BIRD STRUCTURE COME FROM, that's your whole question. where does the structure come from and then prior to that, where does the design for the structure come from, i mean it's pretty clear that there is some clever designs in a bird.
[bar, i think the common notion of design is that a person designs something at least with an intention in mind, even thought the process may be an evolution by trial and error of ideas in mind. so we need another word? while the parts of the bird mostly work well, they werent put together in the bird with any intention. after i intentionally design a mechanism who's parts work well together, how would i describe the product? can't think of a word at the moment.]
ok, well, how does the bird come about? what is a bird? A bird, like every other big animal and plant is a gigantic society of cooperating single celled amoebas that start off from a single amoeba that colonizes the food in the egg. The egg is the shore of a lush tropical island and a single livinig amoeba organism detaches from the society of amoebas that is the mother bird and washes up on that shore of a tropical island and starts eating.
you've heard that you are made up of cells, all animals are. what are they? They are tiny individual organsisms. perhaps you've watched some pond water under a microscope and watched amoebas and stentors and parameciums swimming around in there... These are real critters not so much more different than the animals that we are familiar with. They swim about, they can smell, feel vibrations (hear) some can see light and dark, even react to moving edges of shadows... they have the same desires as we do, hunger, fleeing from harm, cold, hot, having to pee, wanting to find mates... they have capacity for memory and the ability to explore and try things out and learn from mistakes. they can eat and transform their food into internal organs and grow and eventually reproduce, some with mating and some just by splitting in half.
they also exhibit variation in their children just as our children are not identical to us or each other.
How do they do it? what's inside THEM? another hierarchical level of smaller cells? no, what's inside cells, what ultimately makes life alive is another whole level of giganticism different than ours. Just as each of us or a bird is huge beyond a cell's belief, made of a trillion of them, each cell is a stupendous squaredance of molecular assemblies. there is business inside cells, processes, patterns, decision making loops, trial and error processes of creativity, on a stupendous scale. a living cell is a squaredance of molecules, as many molecules as there are bricks in all of new york city.
wander around in that city and walk by all the buildings and cars and people... and imagine that all the buildings are made of bricks, and that each brick is a kind of simple squrimy crawly robot that can interact with the other bricks and make simple mechanical decisions around each other as if it had a simple computer program subroutine written inside it with some if statements...
now wander around that city and imagine all those bricks crawling around each other and forming patterns and building that city from the bottom up, a dynamic city that can grow it's own parts, take them apart and rebuild, redesign depending on its needs, ultimately able to reproduce itself and send forth a whole new city.
So that's a single living cell. With all that dynamism and bustling of moving, interacting, decision making parts, these living cells can respond to each other with creative subtlety and morph each other into different shaped cells and come together and create huge complex structures.
I think the main problem in imagining how an egg can turn into an adult animal or how an animal can evolve into another kind of animal is that we really don't have a good sense for just how complex even the begining egg already is. how responsive to circumstances and how able to explore and create... The complexity inside is just not something we have much experience with. We certainly aint taught agbout it in school.
So, the chicken egg is a yolky shore on which this single complex cell washes up. what can it do? Bear in mind throughout this description how the bird is not going to be sculpted from the outside by a few clumsy hands, but that it is going to be built, grown from the inside by dozens, thousands, MILLIONS, B I L L I O N S of these critters crawling around each other and growing more of each other.
Is there anything we are familiar with to which we can compare it? I'm not sure!
Now that we know there are enough tiny construction workers INSIDE that growing bird embryo, lets show where all the detailed features come about. Let's imagine a crew of construction workers about to build a wing. The first thing they do is lay out a ground plan and arrange themselves into different crews. One group agrees to work on bones, another group agrees to work on blood vesels, another on muscles, nerves, feathers... so some of the workers lay themselvces out in a
[ok, so i can lookup some of the developmental processes and describe them, how the cells crawl around, how they signal each other and decide based on who they are surrounded by and what signals they recieve they change thir professions from building inside of bone to outside of bone, from laying down skin to building feather shafts and then these split up into some building shafts and some building feather vanes etc...
...
Fine, so now i've described to you that theres a society of tiny construction workers building the bird on that shore of yolk out of themselves. But how do they KNOW how to do it? where does the blueprint come from? Ah, that comes to the heart of our understanding of the digital changes generation after generation whereby a worm can givce rise to a bird.
Inside each living cell is an identical library of blueprints and bulletin boards. This library of course is the DNA that makes up our genes. Each blueprint has a bulletin board attached to it, by which ...
Ok, just as the cells are construction workers in the growing embryo, inside the cells are the proteins (the molecular robots of which there are as many as there are bricks in nyc) which are the construction workers that build and maintain the growing cell. Just like cells, these robots can tear down and build new robots, they can interact with each other, they can come together to make larger structures, they can process information, making basic level decisions based on signals supplied by the concentrations of small molecules and by contacting other robots.
Some of these protein robots build dynamic scaffolding that shapes the cells. Some of them act as sense organs on the surface of cells. The sense organs can detect neighboring cells, which kind they are and they can also sense signal molecules that are sent from afar by other cells. Others act as connectors that enable certain cells to attach to each other. Other proteins act as information processing units, like simple logic gates in our computers or simple subroutines in complex computer programs. All these robots come together to control the way cells behave and respond to their environment.
Now inside that initial cell that detaches from the mother cell-society and lands on the yolk is the DNA library for making proteins. It contains blueprints for about 10,000 different kinds of proteins. I think that might correspond to how many different kinds of parts and professions of people that a large city might contain, continuiing the analogy of a cell being as complex as a bustling city.
But at any one time, the cell is only building a few thousand kinds out of that repetoir of 10,000. And this particular selection out of the possible 10,000 is what makes one cell act differently than another cell that is building a different set of protein robots.
An important thing to mention about these prootein robots is how they 'decide' which robots to tear down, and which neww kinds to build. well, attached to each robot blueprint is a bulletin board that specifies when and whether and how much that blueprint is to be read and used too construct another robot. The existing protein-robots act together and integrate the signals coming from outside the cell (what other cells surround it and what signals from far away cells are being recieved) with the current goings on inside the cell and and depending on what's going on, will attach themselvces in various combinations to each bulletin board. So, depending on the state of the cell and the state of its surroundings only certain proteins are being produced, and in certain amounts, and this process can even specify where in teh cell the proteins will go.
These processes will even result in different sensory proteins being placed on the surface of the cell and different signal molecules being sent out of the cell, so that the cell can communicate with other cells what THEY ought to be doing.
Now we are getting close to how the form of the bird comes about! Where does the feather come from? What kind of design process is this? Is there a blueprint in there with the shape of a feather on it? Alas, no! It's way crazier than THAT! It's at this point we have to take a side road and talk about how complex pattern appears in this universe from very simple rules that are spread out across the system as opposed to being 'crafted' by 'craftsmen' with an overarching central plan in mind.
>>>>HERE IS WHY I CAN'T WRITE COMPLEXITY LAB MANUAL YET. I NEED TO DISCOVER MORE (IN A GRAD PROGRAM) DISS'PATEEV! (actually, we might know enough detail about how the genetic ciruits specify forms in embryos now. so maybe i gotta learn that. but I think i need a nonmolecular/cellular analogy to help people without years of molec bio to understand!
>>>the key thiing to explain is how simple local rules on a grid, or possessed by 100s of simple agents can come together cooperatively into complex geometric shapes. So lets find a simple rule that will produce an intresteing complex shape and then ask: how do you suppose we can specify the rules for a robot to draw this shape, or perhaps a 100 robots to swarm around and draw it. ok, which example should i use? langton's blob and highway? it's a weird shape, too messy to use as an example. now one of those worm dragons would be cool. ok. how about something from conway life? does any simple seed bloom into a pattern that someone would find fascinating but easy to grasp? r pentomino makes a mess. can a random seed in evoloop grow into an evoloop? (90 rules!)
what's a simple way to specify the construction of a rough sketch of the mandelbrot set?
COOPERATIVE/DISTRIBUTED PATTERN FORMATION
Where does pattern come from? snowflakes, frost on window panes, hurricanes, [damm, i can't think of any other intersting natural patterns other than living critters? hmm... why the gap? thats a problem. the patterns in living critters come from a combination of molecular scale interactions and large scale properties of materials like surface tension and like the fibonacci spirals in plants coming from patterns of strain on the surface of the apical meristem. hmm... so of course we don't see many molecular scale patterns because we are too big, unless they anneal for long periods of time and form large crystals? well there are feathery patterns of percolation, weird patterns in goethite.. there are some cloud patterns, there is the large scale weather pattern on earth as a whole, and the crazier looking one on jupiter and saturn. the patterns of ice formation on europa, BZ if anyone bothered to look... bar, this is nothing like a BIRD WING! hmm...
why do i have to move to mathematical games for that kiind of complexity? the worm games, langton's ant, r-pentomino in conway life, mandelbrot set... and ARE there examples of nonliving molecular scale pattern formation as complicated as those mathematical ones? How to even hunt for them?
THIS IS THE KEY GOAL OF COMPLEXITY LAB MANUAL AND FURTHER RESEARCH ON MY PART, TO BRIDGE THAT GAP.
well, onward. lets start with static: snowflakes. Actually, we aren't terribly sure how snowflake patterns form. We do understand that water molecules have shape, and have a certain geometry to the way their ends electromagnetically attract each other. and how much the molecules can bend when attached to each other in large grops. We know what amounts of energy are iinvolved in breakiing and forming those bonds. we can more or less understand how water will form hexagonal symmetry. we know how the subtle conditiions in clouds with their moisture contentt and temperatures and relative humidities will allow water molecules to bond to the surface of the growing snowflake and then come off again or affect how other water molecules bond. how the curvature of the surface affects whether and where and how easily more molecules will bond.
and then given these parameters, they specify a set of feedback loops in certain geometries which result in the shapes of snowflakes.
Math is involved. let me givce you some examples of how a set of rules of feedbacks in geometry will give you complicated shapes.
1) fractal triangle: suppose we start with an equilateral triangle
>>>>>bar, this is WAY TOO LONG A DIVERSION!
...
BACK TO EMBRYOLOGY
so lets look at a simple set of feedback loops in a geometrical context made out of a small set of protein robots and their blueprints. now i gotta describe hoxology that produces turings stripes leading to segment formation in embryos. then how these systems can 'count' which segment they are on and initiate bud formation. how other systems will expand buds, patterns of apoptosis in the bud that can lay out patterns of bones... the fractal complexity of feathers? well at least there's some work on pattern formation in butterfly wings.
if we don't belive it we can show BZ, snowflakes and ... see those are nice but the digital nature of the genes i think is what can give us more interesting pattern than snowflakes and the ability of biologicall systems to form quick feedbacks to narrow responses to form more discrete boundaries than BZ?
God, i need to learn more. but there are plenty of math systems like langton's ant, and those worms with simple rules that create dragon shapes... rule 110 creates complex structures. gotta find more examples. come on you got sayama's evo loops with like 90 rules with 9 states in each cell. but living cells have 10,000 rules with god knows how many states. oh.
can we rebuild the langton self rep loop rules to form the loop from ONE cell? That would be way cool. it would basically be embrygenisis. construct it stage by stage:
1) 1:00000000-->2
2) 0:00010000-->2
3) 2:00020000-->3
4) 0:00030000-->2
5) 0:00000023-->4 etc... would take weeks of hard work to do, maybe sayama could help.
well, that's complexity lab manual. I have't studied hoxology in detail, but i've got ennough math to intuit that diffequs on continuous gradients can create spike bifurcations. I Don't know exactly how the 90 rules for selfrep loop work, but i've worked enough examples that i'm sure if i look into it i'll see how those rules can produce structure and that i can probably make rules that produce more sturcture. or for that matter the simplest random rules like 110 and langtons ant already givee curious structure.
Now this is no longer an essay about how a worm can evolve into a bird. but hell, who says the answer to that question is going to come simply? What's the simplest i can boil this down to explain at least the direction and how complicated it would really be? hmmm
I think one of my problems is that I DON'T UNDERSTAND IN DETAIL say, the genetic circuits in segment formation, give rise to the turing mechanism of segment formation. that's the point of complexity lab to write this book without the vague handwaving found in all the other books. (do i really have detail notes on capra's book?)
...
that's a reasonable idea. given that we come from a culture of artists and craftsmen and not the modern biology class.
So the first step is to describe what kind of 'clay' we've discovered a worm is. If we want to know how a worm can change into a bird, first of all, do you have any idea how a bird egg turns into a bird? that would be a start. I mean, how do you think birds get sculpted all around us everyday? If I told you, you'd be more amazed than your disbelief that a worm could turn into one.
so for a worm to evolve into a bird of course we mean that a worm gives birth to a bird, or of course that a worm gives birth to a slightly different worm that gives birth to a slightly different one, and eventually worms are hatching with nubby legs and eye spots, and eventually heart and lungs, and feathers and wings... Seems incredible, eh? but really what you want to start with is how does a bird give birth to a bird? It lays an egg and the egg turns into a bird. lets start there! How does it happen?
[and then you may have some vague notion that a bird is so different than a worm, that it has so many more complex parts and behaviors that for this to happen the number of minute changes necessary is astronomical and couldn't happen in a 1000 years or a million years. But that's just the point, you just have a VAGUE notion. do you really know how to think about just HOW MANY changes are necessary? and is it some kind of continuous sculpting or is there a discrete number of changes at all? ARE animals made up of discrete parts that CAN be changed one part at a time?]
of course in the egg that you eat, before it is fertilized, there is no bird structure. WHERE DOES THE BIRD STRUCTURE COME FROM, that's your whole question. where does the structure come from and then prior to that, where does the design for the structure come from, i mean it's pretty clear that there is some clever designs in a bird.
[bar, i think the common notion of design is that a person designs something at least with an intention in mind, even thought the process may be an evolution by trial and error of ideas in mind. so we need another word? while the parts of the bird mostly work well, they werent put together in the bird with any intention. after i intentionally design a mechanism who's parts work well together, how would i describe the product? can't think of a word at the moment.]
ok, well, how does the bird come about? what is a bird? A bird, like every other big animal and plant is a gigantic society of cooperating single celled amoebas that start off from a single amoeba that colonizes the food in the egg. The egg is the shore of a lush tropical island and a single livinig amoeba organism detaches from the society of amoebas that is the mother bird and washes up on that shore of a tropical island and starts eating.
you've heard that you are made up of cells, all animals are. what are they? They are tiny individual organsisms. perhaps you've watched some pond water under a microscope and watched amoebas and stentors and parameciums swimming around in there... These are real critters not so much more different than the animals that we are familiar with. They swim about, they can smell, feel vibrations (hear) some can see light and dark, even react to moving edges of shadows... they have the same desires as we do, hunger, fleeing from harm, cold, hot, having to pee, wanting to find mates... they have capacity for memory and the ability to explore and try things out and learn from mistakes. they can eat and transform their food into internal organs and grow and eventually reproduce, some with mating and some just by splitting in half.
they also exhibit variation in their children just as our children are not identical to us or each other.
How do they do it? what's inside THEM? another hierarchical level of smaller cells? no, what's inside cells, what ultimately makes life alive is another whole level of giganticism different than ours. Just as each of us or a bird is huge beyond a cell's belief, made of a trillion of them, each cell is a stupendous squaredance of molecular assemblies. there is business inside cells, processes, patterns, decision making loops, trial and error processes of creativity, on a stupendous scale. a living cell is a squaredance of molecules, as many molecules as there are bricks in all of new york city.
wander around in that city and walk by all the buildings and cars and people... and imagine that all the buildings are made of bricks, and that each brick is a kind of simple squrimy crawly robot that can interact with the other bricks and make simple mechanical decisions around each other as if it had a simple computer program subroutine written inside it with some if statements...
now wander around that city and imagine all those bricks crawling around each other and forming patterns and building that city from the bottom up, a dynamic city that can grow it's own parts, take them apart and rebuild, redesign depending on its needs, ultimately able to reproduce itself and send forth a whole new city.
So that's a single living cell. With all that dynamism and bustling of moving, interacting, decision making parts, these living cells can respond to each other with creative subtlety and morph each other into different shaped cells and come together and create huge complex structures.
I think the main problem in imagining how an egg can turn into an adult animal or how an animal can evolve into another kind of animal is that we really don't have a good sense for just how complex even the begining egg already is. how responsive to circumstances and how able to explore and create... The complexity inside is just not something we have much experience with. We certainly aint taught agbout it in school.
So, the chicken egg is a yolky shore on which this single complex cell washes up. what can it do? Bear in mind throughout this description how the bird is not going to be sculpted from the outside by a few clumsy hands, but that it is going to be built, grown from the inside by dozens, thousands, MILLIONS, B I L L I O N S of these critters crawling around each other and growing more of each other.
Is there anything we are familiar with to which we can compare it? I'm not sure!
Now that we know there are enough tiny construction workers INSIDE that growing bird embryo, lets show where all the detailed features come about. Let's imagine a crew of construction workers about to build a wing. The first thing they do is lay out a ground plan and arrange themselves into different crews. One group agrees to work on bones, another group agrees to work on blood vesels, another on muscles, nerves, feathers... so some of the workers lay themselvces out in a
[ok, so i can lookup some of the developmental processes and describe them, how the cells crawl around, how they signal each other and decide based on who they are surrounded by and what signals they recieve they change thir professions from building inside of bone to outside of bone, from laying down skin to building feather shafts and then these split up into some building shafts and some building feather vanes etc...
...
Fine, so now i've described to you that theres a society of tiny construction workers building the bird on that shore of yolk out of themselves. But how do they KNOW how to do it? where does the blueprint come from? Ah, that comes to the heart of our understanding of the digital changes generation after generation whereby a worm can givce rise to a bird.
Inside each living cell is an identical library of blueprints and bulletin boards. This library of course is the DNA that makes up our genes. Each blueprint has a bulletin board attached to it, by which ...
Ok, just as the cells are construction workers in the growing embryo, inside the cells are the proteins (the molecular robots of which there are as many as there are bricks in nyc) which are the construction workers that build and maintain the growing cell. Just like cells, these robots can tear down and build new robots, they can interact with each other, they can come together to make larger structures, they can process information, making basic level decisions based on signals supplied by the concentrations of small molecules and by contacting other robots.
Some of these protein robots build dynamic scaffolding that shapes the cells. Some of them act as sense organs on the surface of cells. The sense organs can detect neighboring cells, which kind they are and they can also sense signal molecules that are sent from afar by other cells. Others act as connectors that enable certain cells to attach to each other. Other proteins act as information processing units, like simple logic gates in our computers or simple subroutines in complex computer programs. All these robots come together to control the way cells behave and respond to their environment.
Now inside that initial cell that detaches from the mother cell-society and lands on the yolk is the DNA library for making proteins. It contains blueprints for about 10,000 different kinds of proteins. I think that might correspond to how many different kinds of parts and professions of people that a large city might contain, continuiing the analogy of a cell being as complex as a bustling city.
But at any one time, the cell is only building a few thousand kinds out of that repetoir of 10,000. And this particular selection out of the possible 10,000 is what makes one cell act differently than another cell that is building a different set of protein robots.
An important thing to mention about these prootein robots is how they 'decide' which robots to tear down, and which neww kinds to build. well, attached to each robot blueprint is a bulletin board that specifies when and whether and how much that blueprint is to be read and used too construct another robot. The existing protein-robots act together and integrate the signals coming from outside the cell (what other cells surround it and what signals from far away cells are being recieved) with the current goings on inside the cell and and depending on what's going on, will attach themselvces in various combinations to each bulletin board. So, depending on the state of the cell and the state of its surroundings only certain proteins are being produced, and in certain amounts, and this process can even specify where in teh cell the proteins will go.
These processes will even result in different sensory proteins being placed on the surface of the cell and different signal molecules being sent out of the cell, so that the cell can communicate with other cells what THEY ought to be doing.
Now we are getting close to how the form of the bird comes about! Where does the feather come from? What kind of design process is this? Is there a blueprint in there with the shape of a feather on it? Alas, no! It's way crazier than THAT! It's at this point we have to take a side road and talk about how complex pattern appears in this universe from very simple rules that are spread out across the system as opposed to being 'crafted' by 'craftsmen' with an overarching central plan in mind.
>>>>HERE IS WHY I CAN'T WRITE COMPLEXITY LAB MANUAL YET. I NEED TO DISCOVER MORE (IN A GRAD PROGRAM) DISS'PATEEV! (actually, we might know enough detail about how the genetic ciruits specify forms in embryos now. so maybe i gotta learn that. but I think i need a nonmolecular/cellular analogy to help people without years of molec bio to understand!
>>>the key thiing to explain is how simple local rules on a grid, or possessed by 100s of simple agents can come together cooperatively into complex geometric shapes. So lets find a simple rule that will produce an intresteing complex shape and then ask: how do you suppose we can specify the rules for a robot to draw this shape, or perhaps a 100 robots to swarm around and draw it. ok, which example should i use? langton's blob and highway? it's a weird shape, too messy to use as an example. now one of those worm dragons would be cool. ok. how about something from conway life? does any simple seed bloom into a pattern that someone would find fascinating but easy to grasp? r pentomino makes a mess. can a random seed in evoloop grow into an evoloop? (90 rules!)
what's a simple way to specify the construction of a rough sketch of the mandelbrot set?
COOPERATIVE/DISTRIBUTED PATTERN FORMATION
Where does pattern come from? snowflakes, frost on window panes, hurricanes, [damm, i can't think of any other intersting natural patterns other than living critters? hmm... why the gap? thats a problem. the patterns in living critters come from a combination of molecular scale interactions and large scale properties of materials like surface tension and like the fibonacci spirals in plants coming from patterns of strain on the surface of the apical meristem. hmm... so of course we don't see many molecular scale patterns because we are too big, unless they anneal for long periods of time and form large crystals? well there are feathery patterns of percolation, weird patterns in goethite.. there are some cloud patterns, there is the large scale weather pattern on earth as a whole, and the crazier looking one on jupiter and saturn. the patterns of ice formation on europa, BZ if anyone bothered to look... bar, this is nothing like a BIRD WING! hmm...
why do i have to move to mathematical games for that kiind of complexity? the worm games, langton's ant, r-pentomino in conway life, mandelbrot set... and ARE there examples of nonliving molecular scale pattern formation as complicated as those mathematical ones? How to even hunt for them?
THIS IS THE KEY GOAL OF COMPLEXITY LAB MANUAL AND FURTHER RESEARCH ON MY PART, TO BRIDGE THAT GAP.
well, onward. lets start with static: snowflakes. Actually, we aren't terribly sure how snowflake patterns form. We do understand that water molecules have shape, and have a certain geometry to the way their ends electromagnetically attract each other. and how much the molecules can bend when attached to each other in large grops. We know what amounts of energy are iinvolved in breakiing and forming those bonds. we can more or less understand how water will form hexagonal symmetry. we know how the subtle conditiions in clouds with their moisture contentt and temperatures and relative humidities will allow water molecules to bond to the surface of the growing snowflake and then come off again or affect how other water molecules bond. how the curvature of the surface affects whether and where and how easily more molecules will bond.
and then given these parameters, they specify a set of feedback loops in certain geometries which result in the shapes of snowflakes.
Math is involved. let me givce you some examples of how a set of rules of feedbacks in geometry will give you complicated shapes.
1) fractal triangle: suppose we start with an equilateral triangle
>>>>>bar, this is WAY TOO LONG A DIVERSION!
...
BACK TO EMBRYOLOGY
so lets look at a simple set of feedback loops in a geometrical context made out of a small set of protein robots and their blueprints. now i gotta describe hoxology that produces turings stripes leading to segment formation in embryos. then how these systems can 'count' which segment they are on and initiate bud formation. how other systems will expand buds, patterns of apoptosis in the bud that can lay out patterns of bones... the fractal complexity of feathers? well at least there's some work on pattern formation in butterfly wings.
if we don't belive it we can show BZ, snowflakes and ... see those are nice but the digital nature of the genes i think is what can give us more interesting pattern than snowflakes and the ability of biologicall systems to form quick feedbacks to narrow responses to form more discrete boundaries than BZ?
God, i need to learn more. but there are plenty of math systems like langton's ant, and those worms with simple rules that create dragon shapes... rule 110 creates complex structures. gotta find more examples. come on you got sayama's evo loops with like 90 rules with 9 states in each cell. but living cells have 10,000 rules with god knows how many states. oh.
can we rebuild the langton self rep loop rules to form the loop from ONE cell? That would be way cool. it would basically be embrygenisis. construct it stage by stage:
1) 1:00000000-->2
2) 0:00010000-->2
3) 2:00020000-->3
4) 0:00030000-->2
5) 0:00000023-->4 etc... would take weeks of hard work to do, maybe sayama could help.
well, that's complexity lab manual. I have't studied hoxology in detail, but i've got ennough math to intuit that diffequs on continuous gradients can create spike bifurcations. I Don't know exactly how the 90 rules for selfrep loop work, but i've worked enough examples that i'm sure if i look into it i'll see how those rules can produce structure and that i can probably make rules that produce more sturcture. or for that matter the simplest random rules like 110 and langtons ant already givee curious structure.
Now this is no longer an essay about how a worm can evolve into a bird. but hell, who says the answer to that question is going to come simply? What's the simplest i can boil this down to explain at least the direction and how complicated it would really be? hmmm
I think one of my problems is that I DON'T UNDERSTAND IN DETAIL say, the genetic circuits in segment formation, give rise to the turing mechanism of segment formation. that's the point of complexity lab to write this book without the vague handwaving found in all the other books. (do i really have detail notes on capra's book?)
...
Thursday, October 6, 2011
At Last, Kissed By a Maiden With Golden Hair
In the early morning coolness under the pin oaks on the sidewalk of the Placid Baker cafe, a Honey bee comes to sip sweet coffee from my lips. "come on bee, there's a whole cup of it over there!" but no, here she comes again the only woman to kiss me in a long time, yet i shoo her away, and finally where is she? "oh, man has she fallen into the coffee? Stupid bee you are supposed to have so much brain power, two hundred seventy skills each of you gals have!"
I fish her out of the coffee and she flies to the window to dry herself off. But i realize, "wow, maybe being drenched in caffein is way too much for a tiny bee like her" So i go into the cafe and get a cup of water and bathe her in it to wash the coffee off of her..
Now she is staggering around in a sunspot on my table. I hope she recovers.
I watch her up close, my eyes an inch from her face, as she runs her legs along her toungue to clean it. Her tongue as long as her whole leg, long enough to reach the golden nectar of deep flowers.
I watch her dry herself off, up close her fur is golden. First she rubs her hindlegs together, then hind leg on middle leg, then front legs from mouth to antenna clearing her senses... yup, probably more than 270 skills! My thoughts run from kissing to engineering. "Where is the circuitry, little bee, to handle so many complex algorithms? You've only got, what? a million neurons?" I do a quick calculation: let's see..., I think it's only a hundred thousand packed into that pea sized head of hers stuffed mostly with the dozens of glands bees have. That's some engineering feat, distributed processing, that we haven't mastered yet.
Then my engineering calculations are distracted by a woman of MY species walking by, flaxen wild hair flowing garments of many colors, free, licking her lollypop she must have gotten from the Pioneer Bank around the corner. The bee, startled, flies off, both gone.
I go back to my coffee. it must have just been a dream.
I fish her out of the coffee and she flies to the window to dry herself off. But i realize, "wow, maybe being drenched in caffein is way too much for a tiny bee like her" So i go into the cafe and get a cup of water and bathe her in it to wash the coffee off of her..
Now she is staggering around in a sunspot on my table. I hope she recovers.
I watch her up close, my eyes an inch from her face, as she runs her legs along her toungue to clean it. Her tongue as long as her whole leg, long enough to reach the golden nectar of deep flowers.
I watch her dry herself off, up close her fur is golden. First she rubs her hindlegs together, then hind leg on middle leg, then front legs from mouth to antenna clearing her senses... yup, probably more than 270 skills! My thoughts run from kissing to engineering. "Where is the circuitry, little bee, to handle so many complex algorithms? You've only got, what? a million neurons?" I do a quick calculation: let's see..., I think it's only a hundred thousand packed into that pea sized head of hers stuffed mostly with the dozens of glands bees have. That's some engineering feat, distributed processing, that we haven't mastered yet.
Then my engineering calculations are distracted by a woman of MY species walking by, flaxen wild hair flowing garments of many colors, free, licking her lollypop she must have gotten from the Pioneer Bank around the corner. The bee, startled, flies off, both gone.
I go back to my coffee. it must have just been a dream.
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