Wednesday, March 15, 2017

Can We Discover How Life Happened And Is It A Rare Occurance In The Universe?

I've always been fascinated by how patterns form.  fluffy clouds, waves in clouds, snowflakes, vortices in water, all the minerals and layers of rock.  so we've developed the history that rock is going through repeated cycles of being eroded, dissolved, laid down as layers of silt and sand and then getting subducted and melted and expelled as magma and solidified over and over...  yet it doesn't all get smushed up like the 4 different colored clays we had as a kid into one blob of greybrown, it keeps separating out as hundreds of distinct mineral deposits

...and then there is life itself.

when i finally studied enough biology i was fascinated by evolution, how there could be MILLIONS of crazy different kinds of critters on earth, and how they were so complex.

and the ultimate challange how did our thinking feeling storytelling selves evolve?  how does THAT work?  i used to think there was a HUGE gap between the capabilities of other animals and us in that regard.  but the more time i spend watching animals and learning about them i'm not so sure.  and truly we've only begun to get at the inner lives of other animals.  some weave complex song, you can listen to a robin or mockingbird for hours, we've detected patterns.  they pass on culture, raise kids, solve mechanical problems, use tools...  we don't really KNOW what they are experiencing, so no idea really if the gap is so huge...

what i've decided is that there is a fair continuum from the simplest bacteria to the single celled microscopic amoebas to the jellyfish, worms, fish, monkeys... on up to us.  even bacteria have the basic capabilities: turn bare food into more of themselves which to me is the ultimate miracle, explore their enviornment creatively, shy from danger, seek out what they like, form connected communities, find mates and reproduce... reproduce with enough variation and sensitivity to their environment that over the generations they invent new surprising biochemical mechanisms and forms to solve problems on this earth.  It's not terribly surprising to me that over 3.6billion years they've evolved into all the animals and plants on this earth.

but what i don't understand is the transition from bare chemistry to them.  the simplest bacteria we know of is a wild coordinated swarm of a million nanomolecular robots creating patterns and taking each other apart and rebuilding each other out of the 10s of billions of small molecular parts... there are 1000 different KINDS of these robots, 100 different kinds of parts...  there is a core of 100 kinds of robots that can get together and recreate the entire set of themselves from scratch, a  set of 20 diff amino acids.  a supporting cast of 1000s more robots that build walls to keep it all together and doors to let in new molecules and perform the 100s of interactions it takes to turn the raw chemistry of the outside into the set of 20 amino acids and 8 nucleic acids that the core of robots build themselves out of.

Its dynamic, the whole city of molecules creating order can reproduce itself in 20 minutes.  Its robust, as far as we can tell it's been reproducing itself for 3.6billion years, nearly the entire lifetime of the earth since the early solar system stopped bombarding earth with meteorites big enough to melt the entire surface.  living through vast geological upheavals, minor meteorite strikes, climate change, evolving sun...

It's creative!  the 3.6billion year fossil record shows a vast journey of life that has evolved clever solutions to living 100s of different ways on this diverse planet with rock, mud, lava, arctic ices and winds, tropical forests, oceans ponds rivers deep sea vents...  i mean... it's learned to fly!  sing songs!

but what came before the first bacteria?  chemistry.  geology.  now there is the gap i don't understand.  life consists of about 2 dozen different chemical elements.  These elements naturally form a couple hundred different kinds of minerals that look and act nothing like life.  You can't even point to a flame as similar to life because life CREATED flames (all fuels on earth are created by life and the fact that fuels can burn is because life created the oxygen rich atmosphere in the first place, plants do this)

the complexity of the simplest self propelling, self reproducing creative bacteria is so much greater than any other chemistry we have yet to find.  There is the gap that puzzles me.

So i seek to bridge it.  and more.  There is a deep philosophical question afoot.

as diverse as life on earth is: trees, birds, fish, sea anemonies, earthworms, lichens on trees, fungi threading through soil and wood, slime molds who's cells congregate in times of famine to build giant spore stalks to launch themselves into the wind and then disperse to feed in new realms to once again congregate..., slime molds who simply grow so big they don't split up into cells at all, bacteria and fungi that can feed on almost any kind of molecule available, even bacteria that can extract energy from nuclear radiation and live without oxygen.... every variety shares that same exact biochemical core of 100 nanorobots that i mentioned above.  It appears that all life on this earth is related.

If life on earth arose from scratch out of chemistry, it did so once, in only one way.  Or if it did so multiple times and multiple ways and then either one way won out or different ways morphed together to create what we have... we have so far, no record of this, no way to tease the history apart.

not only that.  we've begun to explore other planets in the solar system.  Certainly we've found no forests or girraffes or cities or oceans swarming with critters.  We've studied mars with half a dozen robots who've landed and done simple chemical analysis.  no signs yet of any biochemistry.

so there's a mystery afoot!  Is there ONLY ONE way that life could have happened? 

There is a very ancient story that almost every human society has come up with that all this creativity on earth comes from something like an already pre-existing mind, a mind modelled after some image of our own mind (not that we yet know how our own minds work, out common image is probably very faulty...).  In the west, at least, we've wrapped this mind up into some kind of god concept.  Not much of an explanation really, because where does the god come from?  Even various new age thought still demands the universe to be some kind unspecified 'mind force' that at least we can communicate with.

The stories go that this mind created life from scratch, once,  for some unspecified purpose, probably akin to shear joy.

Physicists can even get involved in this story telling!  We've learned a lot of the basic physcical rules that govern how the universe expands, how stars self gravitate from the primordial clouds of the simplest element, Hydrogen, how they cook up all the other elements of the periodic, table, how they explode, stimulating the next round of star formation over and over, and planetary formation, how chemistry happens...

It has become apparent that if any of these laws were in the slightest way, different, say, a physical constant was changed by a few percent... NONE of this would happen.  Stars would NOT form, or if they did, they wouldn't be able to cook up the elements past hydrogen to even make planets and life, etc...  So the story goes that there is only one very rare unlikely way a very finely tuned universe can be to form life that only formed ONCE on a planet called earth. This has been called the Anthropic Principle of cosmology.  (anthropic because it is a scenario that leads to the cosmologists who invented it, a kind of narcissistic eternal loop!)

And of course the story can be morphed that the supreme mind at the begining designed the laws precicely so...

ignoring again of course how THAT mind came to be...

So we either get the same old story that god created the universe and life once or if not that, then this creative universe and life is an extraordinarily rare surprising event.

neither story is very satisfying, they are both rather sterile and don't lead to much further exploration.

There is in fact another way to look.  First we deal with the anthropic cosmologists.  It is true that if any of the physics were altered in the slightest way, we can predict that this familiar universe would in no way form.  What these cosmologists fail to notice is that what we CAN'T predict is what would form INSTEAD!  no stars and familiar chemistry?  but maybe other structures on other time scales with other wonderful properties would form instead.  the fact is that we are really bad at being able to predict from the microscopic laws of physics, like the speed of light, the strength of the electromagnetic force, the different kinds of quarks... what they would combine to make.

An example: we had been studying carbon atoms and quantum mechanics for 60 years and knew that carbon could make graphite and diamonds because we had already found these.  but we never predicted, never even imagined that carbon atoms could make bucky balls, nanoscopic geometric domes of 60 carbon atoms each, until we found them in the 1980s.

I can even give you an example you can work out yourself.  I can create a model physics: an infinte grid of empty squares.  they can be in one of two states: on or off.  This universe ticks like a clock. every second each square can sense its surrounding of 8 immediate neighbor squares and switches itself according to the following simple rule: if there are exactly 3 neighbors that are on, it turns on (or stays on if it already is), if there are 1 or less neighbors that are on, or 4 or more neighbors on, it turns off, or remains off if it already is.

Thats a physics anybody can grasp.  So now i ask you to predict what this physics gives us?  what happens if this universe starts off with 4 on squares arranged in a straight row?  what happens tick after tick?  what about only 3 in a row?  or if i start off with a hundred random squares on or off higgledy piggledy what can develop?  stable patterns?  patterns that switch on and off?  stable shapes over and over again?  can it grow spreading across the universe of squares forever or does it eventually all die out?

nobody knows how to predict these things from the rules except by actually simulating the universe one tick at a time.  by actually working out with pencil and paper and seeing what it DOES do.  I encourage you to work out some of the patterns.  They will surprise you.  You can look at some of the patterns that have been found over the decades by using high speed computers. THEY will surprise you.  I won't spoil your fun but to say that VERY complex and surprising behavior is possible.  This was probably the inspiration for my complexity lab manual and was its first entry.

This model universe was invented in the early 1970s by a mathematician by the name of John Horton Conway.  It usually goes by the name of Conway's game of life.  Notice how simple it is to play out these patterns and see what happens.  It turns out that quite complex patterns can form from these simple rules.  over the years we have discovered many different kinds of games like this, many examples of simple rules playing out into very complex patterns.  Kind of the opposite of conventional wisdom that it takes an already complex mind to create patterns in this universe.  You will find these in the chapters of the complexity lab manual.

It is very puzzling why these kinds of games had never been discovered/invented before 1970.  Not by eauropean scientists and mathematicians, not by islamic scholars and mathematicians, not by the classical greek philosophers and mathematicians not even in China, Japan, Korea where they had been playing the game of Go for centuries (the game board fairly cries out to try such things, but alas only human intentions were ever played out on that board)... Or maybe they were... but nobody back then could get outside the story that all complex pattern comes from a more complex mind.

What is the significance?  Well, because there are so many different examples of these games, and it is hard to predict which combinations of rules will produce complex patterns and which wont, it is apparent that we are not qualified to say or not whether our current universe with its physics is fine tuned to create life and humans.  Complex patterns from simple rules is apparently NOT surprising.

Not only that... if there are MANY kinds of sets of rules that yeild complex results, then not only are many kinds of universes capable of forming into complex patterns, but maybe even in THIS universe there may be MANY ways that the simple rules of chemistry might yeild lifelike complexity too.  The hunt is afoot!

In the early days of chemsitry it was thought that all life chemistry, organic chemsitry it was called, was distinct from nonliving chemistry and even perhaps that some unspecified 'vital principle' was responsible for the chemistry of life.  Then in 18-- Wohler showed that he could synthesise an organic chemical, urea, from scratch from nonliving chemicals in his laboratory.  hmm... eventually more and more examples were discovered.

In 1953, Stanley Miller, zapped a vessel containing only Methane, Ammonia, Hydrogen and water, very simple molecules, with electric discharge and discovered that many organic compounds spontaneously formed, even amino acids, the building blocks of living proteins.  He chose this apparatus as mimicing the possible conditions on earth before life formed.

The search has been ongoing.  We have found that more and more bits and pieces of lifelike chemistry can spontanously form in the lab and in fact we have found evidence of many molecules of life in meteorites, and on comets and even in the gasses between the stars...  While we have yet to find life in our solar system, we have BARELY begun to search.  4 robots on mars and one lander on Titan is barely a begining.  what we do know is that this solar system has many exciting possibilities. 

Our mars rovers (american, by the way... no other country has figured out how to get a rover to land and survive on Mars!  The russians tried many times) have found an abundant variety of crazy minerals and rocks that show Mars once had oceans, rivers, lakes and more atmosphere.  There is still a faint hydrological cycle and occasional water seeps, which quickly evaporate.

There are more oceans.  Ceres, the largest asteroid has been found to have RECENT seeps of salty waters coming to the surface.  Europa, Ganymede, Callisto, moons of Jupiter, all have detectable subsurface oceans under a layer of thick ice.  Not only that, but Europa has almost no craters.  I'ts ice layer has been recently and continuously reformed.  Enceladus, and Titan, moons of Saturn also have subsurface oceans.  In fact... the oceans of Enceladus, continually break trhough the ice surface and form guysers which we have sent our Cassini space craft THROUGH to taste them and there are hints at chemical interactions with these ocean waters and the rocks below...  Titan, not only has a subsurface ocean of water but a whole alternate 'hydrological cycle' of methane and ethane weather above the surface of ice.  The methane forms clouds, rain, streams and lakes and interesting chemistry is afoot. There is probably a dynamic cycle of high energy double bonded compounds forming from solar energy in the upper atmosphere and then being reacted below to form back into single bonded compounds at the surface.  This kiind of thing can become the basis for biochemistry!  Also, complex organic compounds collect on the surface just as in Millers experiment from ultraviolet rays hitting the methane and Nitrogen atmosphere.  Io, a moon of Jupiter has many active sulfur volcanoes.  Not water and organic chemistry, but who knows what kind of chemistry can grow into complex patterns?

Even lonely Pluto... we recently burst that one open and discovered ice mountains, nitrogen slush glaciers and ocean, methane snow, with its complex organic molecules collecting, complex atmosphere and hints at an ammonia filled subsurface ocean and possibly ancient guysers where the ocean spews above.

Brief data about Neptune's moon Triton suggest it is similar to Pluto...

There are comets full of ice and organic molecules that get repeatedly radiated by teh sun and then cooled, we've only begun to explore.

and on earth... In 19-- Corliss discovereed a whole new world under the sea. There are places deep in teh sea where water seeps into the rock and is heated by and interacts chemicaly with the magma below and comes spewing back up to create very energetic chemical reactions to precipitate complex mineral castles.  There is abondant life there in the dark without sunlight or photosynthesis and a new ecosystem is formed based on bacteria using these mineral chemical reactions to do what plants do in sunlight. 

More has been discovered over the years.  Life has been found in the 60 degree below winds living just inside antarctic rocks, bacteria have been found to live in boiling guysers, in supersalty waters, 2 miles deep in the rock inside the earth, even bacteria that can use radiactivity to energise their chemical reactions.  In all these cases though, it is the same earth life, the same core biochemstry, but at least we see it is very flexible, and that life is possible in a wide range of circumstances!

Unfortunately, if there is some alternate form of life forming on earth in some obscure geochemical environment we will never find it.  The traditional form of life that exists on earth is SO good at spreading over everything, living everywhere, eating everything, that it would quickly overwealm any other nascent form of life.

So we look to the other moons and planets.

the hunt is on!  Will we find some alternate forms of life out there?  In our laboratories?  Will we figure out some of the steps that lead from chemistry to life?  Will we find enough examples to develop principles of how these complex life chemistries can form?  Or... will it be that after decades of finally analysing the geochemistry of all these solar system places and trying so many different combinmations in the lab, that we CAN'T find any other alternate forms of life?

Either way, the results will be profound.  Does the fact that we aren't funding these kinds of explorations as much as we can, mean we are afraid of what we might find?

Anyway, This is the exploration i hope to take part in and the Complexity Lab Manual is a record of this exploration and builds the basic vocabulary with which we can ask these questions of pattern formation in the universe.

Saturday, February 25, 2017

mosses in my new home

First we got a bed of Atrichum angustatum.  Int last photo u can almost make out the waves of micro spines across the leaves.

here they are begining to grow spore stalks.

this one has  a more mature stalk.  musta started growimg earlier.  Or maybe this is A. altechristatum.  I'll check.

Next there is Plagiomnium, not sure yet what species

Notice this species has a sprawling form of growth with leaves on either side of the stem and then a more upright growth form with leaves wrapped around the stem.  This second growth form is the one with ovaries, gets fertilized and gives birth to the spore stalks.  The spore stalks are actually separate moss individuals that dont grow leaves and dont have sex, just grow spores.  The spores will grow into mosses with leaves ansd sex again and repeat the cycle.  Why should moss live the same way we do?

these were also growing.  I dont know what kind.  I dont have my reference materials yet.

Wednesday, February 22, 2017

Did Life Originate From Simple Chemistry, Or Is The Universe Always Complex?

Complexity lab manual is a set of labs and exercises to learn to think about the origins of life from chemistry.

Could life have originated from chemistry alone, on Earth four billion years ago?  There seems to be such a gap between the creativity and aliveness of all those flowers and fluttering birds on the one hand and the simplicity of rocks, water, and mud on the other hand.  What does it mean to ask this question?  Is there such a big gap between life and nonlife?  IS life so complex and are rocks and mud so simple?  What IS chemistry?  What do we mean when we say life IS chemistry?  What kind of question is it to ask how life came from chemistry alone?  Alone from what?  

The ultimate concrete way to get at this is to ask, can we start with a few bottles of purified nonliving chemicals and mix them together and create a living being from it?  While we will explore this route to some extent, we should also ask:  what would that have to do with how it started on Earth 4billion years ago?  Did Earth start out as a few batches of simple chemicals?

What WAS Earth like when it was starting out 4.5 billion years ago?  Was it a simple podge of a few kinds of chemicals that slowly got more complicated and became life?

The problem is... Possibly, there are NO simple places, EVER,  in this universe!

The simplest place in the universe that we can conceive was way at the beginning, 14billion years ago when the universe blew up to a huge cloud of swirling Hydrogen gas with 14% Helium.  Just as Jupiter's weather looks so complicated who knows what kinds of complicated swirls of these Hydrogen and Helium clouds there were... However... much of the complexity of Jupiter's weather is driven by heat flowing from the hot center to the cold outerspace, much as our weather is driven.

In the early universe it's not clear where there might have been heat flow?  from what center?

Nevertheless drama soon unfolds!  At first these clouds are all expanding apart. And there are minor fluctuations of density between them.  There are ALWAYS random fluctuations.  It seems that quantum mechanics gives us this.  Random fluctuations are written into the laws of the universe!  Counteracting the expansion is another aspect of the universe - gravity.  This is pulling clouds together.  At some point when the expansion dies down, gravity can begin to come into play and a random cloud of Hydrogen can start collapsing into its center.  One might think that this cloud would collapse and collapse untill the Hydrogen is so compacted that it is a liquid, or even more compact than that.  Also this compacting makes it hotter and hotter, think about what happens to your bicycle pump when you compress the air, it gets hot.  Can this cloud get more and more compact and then perhaps simply wink out?  The end?

Hardly!  The physics of the universe apparently can never lead to dullness.  If the cloud is more than even .08 times as massive as our sun is, it will get so hot when it compacts that the atoms of Hydrogen collide with each other with so much energy that they start transforming themselves into Helium atoms.  So there ends up being a growing Helium core inside the star.  Eventually enough of the Hydrogen gets used up and the star slowly cools off.

Unless it's BIGGER.  If it's more than 3 times as massive as the sun... the Helium gets compacted hot enough and then starts joining up and transforming into Carbon, Nitrogen and Oxygen.  Now THESE are interesting chemical elements.

Out between the stars, the most interesting thing hydrogen can do is join up in pairs, H2, and thats it.  But these bigger stars, with their Carbon, Nitrogen and Oxygen...  Once they form cores with those elements inside and use up enough of their Hydrogen and Helium, they start expanding into red giants, become unstable and start spewing off some of their new cooked elements into outerspace.  As these gasses expand and cool, some of the atoms can combine and we get molecules.  Water from the Hydrogen and Oxygen, H2O, methane from the Carbon and hydrogen CH4, ammonia from the Nitrogen and Hydrogen NH3, even a little Carbon dioxide CO2, even a little Cyanide HCN, even some carbons can collide with each other and ethane C2H6... the game is afoot.

That's a LITTLE bit of chemistry, but how about BIGGER stars?  When they are more than 8 solar masses and there is enough gravity to create enough pressure and temperature to cook up many elements all the way up to silicaon and iron.  There the cooking stops.  Physics doesn't allow any more spontaneous combinations past Iron.  Is THAT the end of the story?  Hardly!  If the cooking stops in such a massive star, the radiation streaming outward can no longer counteract the stupendous gravity pulling inward and the star quickly implodes into a supernova.  VERY BUSY nuclear reactions taking place in there this time, and the upshot is that the atoms get cooked and cooked by flinging radiation so that all the elements in the periodic chart get made.  And then the star comits suicide and has a MASSIVE explosion.  Supernova!

All these new cooked gasses are exploded rapidly into the surrounding layers of gasses also seeded by the lighter stars with their Hydrogen, Oxygen, Carbon, and Nitrogen.  The rapidly expanding supernova gasses cause shockwaves in the surrounding gasses and trigger more rounds of clouds to compress and start collapsing into even more new stars.

With some added features of course... The universe is never dull!  Since there are so many more elements and compounds swirling aroud the stars now, as they contract and start forming they also form disks around themselvs and the gasses, and ice particles and dust from silicon and iron (rock) starts colliding into each other and PLANETS form.

Are planets just random mixtures of dozens of elements?  Well, there are always processes..... The baby solar systems get sorted out.  The star starts so hot at the begining that it blows away most of the volatile elements and compounds like Hydrogen, water vapour, methane etc... with its solar wind to the outer reaches of the surrounding disk.  So a gradient forms in the infant solar system with high melting point rocks and metals close to the star and lower melting point ices and gasses further away.  So planets close to the star tend to form more rocky, while planets further away tend to form with more ices and gasses.

That's the first sorting out that happens.

The second thing that happens is as the planetesimals are cobbling together bigger and bigger, the energy of their impacts and the gravitational force from their sizes cause more and more pressure and heat, till finally the higgledy piggledy minerals and rocks in them... some start melting, and the lowest melting point ones start first and the densist ones begin to sink to the bottom and the less dense ones float to the top.  Each planet differentiates, like Earth with its Iron Nickle core, largely Olivine mantle (Iron and Manganese Silicate) and complex mix of lighter minerals floating atop in the crust.

Then there are the icy organic comets way in the outer reaches of the solar system.  And in between are the gas giants like Jupiter.  We are not yet sure whats in the center of that!

And then the pinball begins.  Is the universe EVER simple?  HELL NO!  Newton showed us that when you solve the equations for gravity between two bodies you get 3 types of well defined orbits.  If the bodies are not too incredibly fast, you get eternally stable circles or ellipses.  If the bodies are fast enough they buzz past each other in parabolic arcs, never to see each other again.  But add a just a THIRD body to the system?  CHAOS.  In fact we have not figured out all the possible solutions to even three bodies.  And for a whole solar system of planets?  We can tell by looking at the compositions of the asteroids in between Mars and Jupiter, that they look out of order.  Some rocky ones outside and some icy ones inside.  And we've recently learned to find solar systems around other stars.  There are LOTS of possibilities.

It turns out that some time in our solar systems past, the orbits of the gas giants became a little unstable with this gravitational chaos and moved things around a bit.  Flung asteroids higgledy piggledy at all the planets (meteorite impacts, craters!) and even fling the comets into the inner solar system.  Either way, mixing icy bodies into the rocky planets and mixing rocky bodies into the icy planets...

We have to stop and notice something curious.  We can have so many different kinds of complex planets because all these elements have curious mixes of properties!  

Oxygen, Hydrogen, and Nitrogen atoms will bond with themselves, and form stable molecules of two each.  These small molecules then form low melting point gasses and are found in the outer solar system.  Hydrogen will combine with Oxygen and will form molecules in 3s, H2O, and this happens to be a rather sticky molecule so it has intermediate melting point and will form oceans which are found under the crusts of MANY solar system bodies, even on the surface of earth.  Metal atoms bond with each other but not in twos or threes but in great masses that form crystals and form slightly higher melting point solids, that can however melt in the insides of planets and settle to the core because they are dense.  Silicon and Oxygen will combine, not in twos or threes but not in great masses either, but in complicated rings, chains and networks and form a bewildering array of 100s of different minerals each with different properties and we find these in the mantles and crusts of planets.  Carbon... well, we won't get into that yet, that's quite messy.  That makes life.

The point about all this is... this is very unexpected! The atoms of each of these elements were simply cooked in the centers of stars by adding more and more protons together.  Why are do the elements behave so DIFFERENTLY from each other?  Why aren't atoms just BIGGER AND BIGGER AND BIGGER?  WHY DIFFERENT?

One proton (and electron) by itself makes Hydrogen.  Add another proton (and the universe seems to need to add in two neutrons too, to bind the protons together because they are positively charged and tend to repell each other... (why does the universe even FORM neutrons so this may happen?)) and you get Helium.  Add another proton and you get Lithium, another and Berylium, another and Boron, then Carbon, then Nitrogen, then Oxygen... on and on up to 26 for Iron.

I've described the atoms getting cooked inside stars one proton at a time, but actually, the chemical behaviors are properties of the electrons that surround the protons in the nucleus, the center of the atoms.  But only the nuclii of the atoms with the protons are formed in the centers of stars.  The electrons get added to the nucleii later when the atoms and electrons are flung from the stars in explosions and then cool off.  The important thing is that the number of electrons for each atom matches the number of protons.  So, when an atom is made with 1 proton, it gets one electron: Hydrogen.  When it gets made with 6 protons, it gets 6 electrons: Carbon.  I'll ignore the neutrons and isotopes and radioactivity, isn't the universe complicated enough already?)

Why aren't the atoms just bigger and bigger versions of Hydrogen?  Why do they behave SO differently?  Berylium combines in great masses and makes a brittle metal.  Boron with one more proton exhibits a sudden jump in behavior, it forms chains and rings and geodesic domes, but oddly is formed in very tiny amounts in stars.

Carbon with one more proton, forms these chains and rings but also forms very stable bonds with Oxygen and Hydrogen so that the forms CO2, CO3 (soluble in water) and CH4 form.  The carbon compounds are much more stable too.  Add one more proton and we get Nitrogen.  Spends most of its time as N2, a gass because that bond is VERY stable, but some Nitrogen gets incorporated stably in carbon compounds.  But nitrogen on its own does NOT form chains and rings like carbon does.  Add one more proton and we get Oxygen.  Oxygen also doesn't form chains and rings but simply diatomic O2 molecules so is a gas but much more reactive than N2.  Oxygen combines with hydrogen to form a very reactive and sticky liquid, water.  Add one more proton and we get fluorine and that's so reactive that the only stable forms it gets into are solid minerals like fluorite, CaF2.  Add one more proton and we get Neon.  A noble gas, no chemistry at all, not even Ne2, so it must get very cold to even liquify.

Add another proton and all of a sudden we get chemistry again, in fact... Sodium, which behaves like Lithium and the sequence starts again, each addition of a proton gives us an element that behaves subtly like the one above it in the periodic table, though not quite.

Aluminum is below Boron and ought to have similar properties but is much more stable in minerals and there's a 1000 times more of it in the universe.  Silicon is below Boron and to the right, should be even more similar, but doesn't form the so many chains and rings by itself, only with oxygen.  With oxygen it forms the vast assemblage of the most common mineral types.  Silicon IS below Carbon, but that's not a match either.  Carbon dioxide is a water soluble gas and silicon dioxide is quartz, a rock.  There are just too many wild differences.

Why, why, why, is the universe at this most basic level so complicated?  What's going on?  Why isn't each atom just a bigger version of the previous one?  Why do they have such peculiar distinct properties in combination with each other?

Well the quantum physics of all this is very complex, and while we have systems to help us explain what's going on, it isn't so easy to predict the properties from scratch.  It has something to do with math.

Here are some clues.

Let's start with the simplest math imaginable, the counting numbers.  Let's count.

let's start with:
1, add 1 and get 
2, add 1 and get
3, add 1 and get 
4  at this point lets notice some things.  If we just mix in one more mathematical operation, multiplication we get some interesting patterns.  4 is a product of 2 and 2.
5 is not a product and so is called a prime number
6 that's a product of 2 and 3
7 another prime
8 that's a product of 2x2x2  hmm
9 that's a product of 3x3, already the pattern of prime, product, prime, product is broken

we can continue this and see more complication.  I'll just list out the primes and show the gaps of numbers with products:

5 _ 7 _ _ _ 11 _ 13 _ _ _ 17 _ 19 _ _ _ 23 _ _ _ _ _ 29 _ 31
_ _ _ _ _ 37 _ _ _ 41 _ 43 _ _ _ 47 _ _ _ _ _ 53 _ _ _ _ _ 59

There's no pattern!  it's impossible to predict what will happen next!

we can look at the pattern this way too:

3 no factors
4 2x2 two identical factors
5 no factors
6 2x3 two different factors
7 no factors
8 2x4 or 2x2x2 2 diff factors or 3 identical factors
9 3x3 two identical factors
10 2x5 two diff factors
11 no factors
12 2x2x3 3 factors two different


if we were arranging these into shapes, 4, 6,. 9, 10 could be made into squares and rectangles

8 can be made into a cube, requiring 3 dimensions...

The mathematics behind the properties that atoms get just by adding in more and more electrons is much different, but jumps in behavior occur for similar reasons.  

So let's review: we started off with random swirls of Hydrogen clouds and gravity pulled them into stars.  And then because of quantum physics the Hydrogen atoms could start combining into a bewildering variety of atoms.  And then because of a combination of gravitational forces and the quantum phyisics, some of these stars could spew out their new cooked atoms or even explode them out and give birth to new star systems which could then form planets because some of these atoms could make rock and ice and gases.

And the planets differentiate into complex places because again the weird properties of these atoms interact with macroscopic physiscs and give different densities and melting and boiling points.

All because of math.

And planets become complex places.  Even without life.  A survey of half a dozen bodies in the solar system will be bewildering.  

Dry barren rocky mercury.  Venus with its sulfuric acid clouds with two different chemical regions that we have yet to explore in detail because, oh, yeah, it happens to be 885 degrees Fahrenheit and 90 times Earth atmospheric pressure.  Robots don't work in that.  Mars, dry and rocky with some Carbon dioxide ices and water ices, and chlorate surface.  Pretty dead and oxidized but it WAS wet in the past and our marsrobots have found many different minerals.  

The moons of the gas giants. Io with its sulfur volcanoes!  Europa, Callisto, Ganymede, Enceladus with their frozen over oceans, though the oceans of Enceladus break through the ice every now and then and spurt guysers!  And because we just happened to have recent;y flown our Cassini spacerobot THROUGH those guysers (she's already been flyin out there 18 years, what the hell, she can take it!) we have hints that the ocean is interacting chemically with the rock seabed below.

Titan, now there is a fun mix!  frozen over ocean over rock ball but the atmosphere has a hydrological cycle of methane and ethane over the frozen over ocean lakes and rivers of liquid methane slowly wearing away the ice rocks into smooth pebbles.  We took pictures!  There may be interesting chemical cycles there.

the gas giants themselvs are huge swirly weather patterns of Hydrogen and methane and ammonia over a liquid hydrogen center...  we don't know much about what happens deep inside.  Spacerobot Juno is there now, peering deep inside for the first time.

And pluto.  Our most recent discovery.  Icy rock planet.  Ice mountains, Nitrogen glaciers flowing into a half frozen nitrogen paste ocean and methane snow with organic gunk haze in a very tennuous atmosphere.  Maybe even cryovolcanoes from an internal ammonia water ocean deep below? who knows?

The comets have interesting surfaces, icy dusty rock, that get heated and vaporized by the sun every time they swoop close.  what chemistry happens there?  Every now and then one hits a planet.

And Earth... even though Earth's geology has been heavily modified and complexified by nearly 4billion years of life swarming over the place, breathing and pissing all over the place... we can infer that many of her chemically complex environments predate life.  Maybe up to a 1000 different minerals arranged in complex formations.

Even before the planets formed... by studying meteorites that have fallen to earth and studying the asteroids in space from which most of the meteorites most surely have been chipped off, we can gain a picture of the building blocks of the solar system before planetesimals began to form.

There are presolar particles.  Between a micron and a millimeter in size.  Diamonds, zircons, calcium carbide, graphite, various metal flecks....  These predate the solar system, were made inside all those spewing and exploding stars that gave birth to our solar system.

And then the meteorites themselves are made of a conglomeration of these presolar grains, and funny millimeter sized beads called chondrules.  These are various kinds of minerals that appear to have already formed and then had become molten quickly and then cooled quickly before getting pasted together with the presolar grains and metal flecks sometimes with much organic matter as the paste... We haven't figured out where the chondrules come from or how they melted and formed.

complexity everywhere we look.

When we study all these environments in detail, and add in all the complex planetary chemistry, our question of how did life form at the begining from simple chemistry becomes modified.  The chemistry was NEVER simple.

As we begin to explore some laboratory examples of simple chemical systems that can elaborate into complex patterns, we should keep this in mind.  Also keep in mind that we've barely begun to understand chemistry, we've only been at it for 150 years.  And chemistry on the other planets?  How much have we dug into them?  We've had 1000s of chemists studying chemistry on Earth, but we've only sent a couple dozen spacerobots to other planets and they haven't been exceedingly equipped with the best chemistry labs!  And they've only been at it since the '70s.  So much to learn!

Sunday, January 15, 2017

Remembering Creation

Remembering Creation

So empty that
motion rushing lines converging, diverging
each singing to each other in hoarse metallic voices
rushing past causing motion.
Wind that would whip through my hair
if there were hair
or air
but singing metallic lines don't need air.
breathing needs air.

as in a fireworks fire cracker, from the center in parabolic sea urchin shaped explosion
come folding out like fast motion petals
clouds, particles of gas.
Streaming , each not in lines but
in a bubbling frenzy boiling in all directions bouncing against winds and gravity
Newly forming.

Hard fall against a rock planet.
Splash down against a shallow puddle
on dark rock cut edges and smooth pools.
Body which can now feel.
Feel the hardness of the rock.
Cold and warm flash through in waves of torrents of rain
padding the body through no clothes
all wetness but
skin against rain droplets
skin against the delicate clinging line of a few inches deep water pool.

With sound of rain beating tiny insect landings on rock and in water.
The invention of death by drowning.
The invention of fright from death.
Getting up from the water
cold air rushes through wet skin.
Awareness of light expanding empty dark eyeballs
life in the distance
large deeply colored dinosaur with leather and beads for skin
from behind
now inventing directions
coming at me.
Means food means run means fright means hard breathing
and hard padding of feet quickly placed against ground
pounding it into soil
which sprouts palm trees and fern fronds
to rasp against thighs and shoulders
and push them away.
Push into them into darkness mass of plants filling space.
tangle of vines and growing stems
into textures call vision into existence
that eat vision 'till it can't escape
Neither can a new sense, smell
called into existence, absorbed by insect odors        |
and moist ground and rotting flesh of things eaten and half eaten and not eaten and yet living but also dying
Every thing that is soft here is living and dying.
But living with sound of insect rasping snake sliding dropping of seeds by birds up and screeching and flapping sounds of flying
and animal grabbing
claws digging into soft parts
to eat and new sense of taste of what smells
hard taste to tongue
which is eaten
Taste which is craved for which is eaten.
Taste which is good which is eaten again.

Ahead in dense tangle 
making order
cutting from tangle a womb
made of light from fire.
Around it sitting
around fire in the middle
which is seen bright fingers 
spreading coldness and thinness of night
spitting sparks, young worlds of day up into the night of high trees
Sound which sparks are born from popping and snapping of wood
which are fires born from.
heat pushing against body facing fire.
Lack of heat pulling out of body away from fire towards cold dark night.

No more stories to talk around the fire because day then night is tiring so sleep
muscles coming apart
tension spreading on firm flow of ground under tent.
Inside tent with air and breath and clothes and heat
inside sleeping bag with breath and heat
protection from outside cooling

into morning now cold
Do not leave inside of breath bag heat of sleep from dreams
but discipline and urging of morning
out of bag diving out into cold damp morning.
Sounds of others with fire and water and pots and "good mornings"
Stiffness seeping back from firm cold ground into stiff cold bones
unzip tent bird-sounds tree-whispers cold and dew singing on grass rush in
contaminate and mix and drown air of breath and warmth and sleep.
Step out creating movement out of cold clammy bones into dew and rocks and twigs snapping and grass
to water splashing
shock and shiver of water slapping
cold and shivering of awakening
washing away firmness of sleep ground dryness in crevices of face
taste of soap which is morning not yet good to eat.

to make food a field which can be plowed
find oxen, catch oxen
hands on firm muscle and rough skin of oxen muscle movement under skin.
Latch up to tools which 
will dig into earth
turn it up to air
air out the earth
gentle crisp musth of growing molds insects roots in soil rising
softness compacting under feet sand through toes
pattern and pain of pebbles embedded in soil much softer.
Rows of turning soil
rows after rows keeping track of rows and tiredness
of time of waiting working movement fun monotony.
Heat and bath of warmth of sun beating down on body
wet dripping from hair to combat sun skin.

Now cool rows of corn crops can hide a person from the sun 
in rows
pattern in rows straight
or rows broken in the other direction
rows of corn stems from soil to air above the head
rasping of dry corn leaves against arms
ground firm air robust with summer daytime in nostrils
opening sight out the other end of the corn crop ocean.

corn rows into rows of God size
monoliths in straight rows and
rows of rows in corner made directions
rows of blocks laid by God
along streets along side walks.

people milling 
Din of people milling but hearing no one.
Traffic sounds also and 
cars stopping and going by and trucks with huge bellies bleating, breaking
Lights on buildings far and higher lights on cars lights on signs lights on planes
Energy of motion of living massiveness of oppressive smell and sound
into any building of different types of food
city food of hotdogs and soda and gyros  and pretzels and pizza
the dry bottom and slick molten oily cheese on top
burning against skin stuck hot oily cheese.

All this I remember, and am satisfied

Stonybrook, NY

Wednesday, September 14, 2016

Jehovie Pamphlet: Can Science Satisfy What We Seek In God?

(as usual this is a rambling sketch just now.  hard to write, my computer's been stolen!)

how does science knowledge satisfy what we seek in god?  Creator, comforter,  listens in time of prayer, answers prayers, metes out justice, forgives, comforter and gives out justice.  How can science address that or should it?  When we suffer there are some responses. Compassion surely.  That we can give one another.

And if one is alone?  is that a good state for humans?  maybe not and is why we create god!  and why cant earth, the moss,  the giving ecosystem be comfort enough?  the ecosystem is kali giving AND taking.

where else is comfort? knowing we are PARTS of this creation that it is happening THROUGH us. chemically, ecologically, evolutionarily... but that creator is not the most comforting!  the raging tearing apart and putting together mother creating out of risk and death and rampant experimenting with genes and embryos! (is y we created comforting myth of father creator)

how we learn to comfort each other? that is appeal of jesus. he is model how to listen to each other and empathize.  but he give LESSONS?  like the buddha?  dunno, wonder whats in the tradition. certainly somewhere is meditation but it’s not the same.  so some form of buddhist/science practice is required to learn to get beyond our fear and desires and general head chatter so that we can truly be present to one who is suffering and be able to listen, empathize and accept.

the other response to suffering is to work on releasing one from attachment to ego which is cause of suffering. realize that this majestic historical creative drama of life is bigger than our petty ideas of ego! but that is personal choice: value attachments to self and fellow humans in the now or value the grand billions year sweep of evolutionary creativity?

see... christians want it both ways they want an infantile version of reality, they want to cheat.  they want to worship the creator and at same time worship the individual soul in eternal heaven.  sorry, watch your mom.  she IS kal,i playing trial and error with genes to make and destroy children higgledy piggledy in the grand drama of creative evolution. THAT is how we got here!  yes god created us in her own image and she is KALI!  to not accept this is to disrespect our mothers.  so what i gotta preach is how to comfort and then teach to accept the frightening aspect of the way we are part of this grand evolutionary drama.  even to come to be in awe and thanks of it as horrifying as it can be sometime.

take even this tack.  so i have the image of evo toying with me, creating in me many quirks, some very difficult to live with bit at same time, in the evolutionary drama ANY of these quirks can come to be an act of creativity if *I* can find or MAKE an ecological niche for them to thrive in.

AHA. in evo there is just as much creativity on TWO scales.  there is the variation and selection across generations but at same time it works because ORGANISMS THEMSELVES ARE CREATIVE.  EVERY organism we know of is creative, can explore its environment by trial and  error, try out new niches to live in, and of course is free to mix diploid genes into haphazard haploid gametes AND many options to choose mates either higgledy piggledy or with many creative strategies or quirky tastes!  look at female birds desiring showy males or bower birds and song birds creating to attract mates!

but at any rate through it all we have to accept the possibility of personal failure.  there is no creativity without it.

but bar, there are plenty who do not care about creativity or art or risk. who might think it a risky frivolity we cannot afford, as we struggle to just make ends meet or to keep rigid order in society to curb frightening chaos. how do you respond?

well? why are we struggling? what kind of safe society do we want? how CAN we keep it safe?  apart from retreating into some fantasy that the father god will always watch over or we can retreat to eternal blissful static heaven, we must realize that this universe IS IN FACT CHAOTIC.  It’s in our genes, in our behavior, its in the very mathematics when even 3 or more perfectly predictable automotons interact.

to create an orderly society to thrive in this world requires creative trial and error. but lets not create a cult of GENIUS about creativity that it is only the ability of the few who have been gifted by some  ultimate god source! creativity does NOT come from on high down through us.  Creativity comes from the ground up!  even the lowly bacteria is creative, then SO MUCH MORE are each of you! if you are alive you are creative!  it is not such a mystery anymore. i teach it when i teach math.  JUST TRY SOMETHING!  Yes, your first few tries might fail, and so you keep trying.  eventually you will find something that works. something you uniquely find for your situation. to be willing to fail requires that we are supportive and accepting of one another.

this is of course something the society of science teaches and practices. to be supportive of each other in our failures because we value this creative quest.

buddhist practice unnatach from ego reduce suffering, or dive into cause of suffering that it is part of this chaotic rich fragrant creative universe and love THAT more than hate suffering.  learn to accept suffering, it is not the worst fate!  numbness is, stasis is. A boring universe full of nothing is.

suffering is from error and error is the flip side of exploratory play, integral parts of creativity. learn that creativity is REQUIRED to thrive in this crazy universe and we CAN ALL BE CREATIVE, do not fear it

why do we say god can comfort and forgive and mete out justice?  because we say he is the creator of this universe.  well… what if i said that we are ALL creators in this universe?  then maybe we too can have power to comfort!

because we can practice meditation, and accept our role as creative, we don’t have to lash out in always predictable responses to hurt and we have the capacity to turn situations on their heads and create an open space of possibility and forgive!

and justice?  vengeance?  punishment?  what is all that?  Ah so now i must bring in our radical acceptance of creativity. We cannot be creative unless we are susceptible to failure AT ALL LEVELS.
these levels include:

genetic mutations leading to differences like male, female, homosexual, transgenders, black, white (and everything in between), ugliness (whatever that might mean), mental illnesses of all sorts,  radical genetic defects of horrible birth, even spontaneous abortion (between 25% and 50% of all conceptions end in spontaneous abortion the mother is not even aware of!).

and even while our adult bodies are growing, the genetic EXPLORATION of cancer, its hard to watch, yes, i know, but if we weren’t susceptible to it our ancestors would not have even evolved, we’d still be a planet of lowly bacteria or even no life at all.

and all sorts of horrible genetic diseases. and even infectious diseases the most intimate attempts at organisms to join ecologically. the reality is that life must eat life to live. that is what life is, cycles of birth and death, growth and destruction. Growth without destruction would quickly USE UP the entire universe and then HALT!  there must be cycles.

and human failure due to us trying things out in our own ways and even willful disobedience and the fact that we are vulnerable so we hurt and are weak so we take the easy path and lash out in anger and violence...

it is not our own FAULTS that evolution gave us this peculiar propensity to join in ecstatic mobs following single leaders or ideologies and warring with one another… Not our own faults that we don’t  immediately have the strength to find that meditative calm to accept suffering while we seek out equitable solutions,  so we instead  lash out immediately to take from others to satisfy our needs.

So here I need to dive into a very difficult topic.  Human will power.  What ARE we?  Are we robots destined to act out the programs in our genes?  If we have mental illness or have moments of weakness, laziness (humans are some of the laziest species I’ve ever met), does that mean that we have morally failed some great battle?  For sure I cannot by pure power of will grow a new arm.  I cannot by pure power of will memorize a 1000 digit number.  Not without practice.  What ARE the boundaries of our strength of will, our moral responsibilities?

In many cultures we have ideas that all men are equal (and women less equal etc..) and that all men have been CREATED equal by the perfect God, and therefore that those of us who do not show the Calvinistic behavior of succeeding by focused strength of will, must have instead chosen to reject this God, and therefore must be reformed, punished or even done away with.

Alas, we just cannot assume we now understand just what humans are yet.  We really don’t know.  For sure we know there is a combination of some mind activity and certain genetic constraints which tangle in a complicated way.  And each of us as a very different genetic mix.  We are NOT EQUAL. 

And that is the beauty of it.  That ongoing exploratory variation is what this creation is all about.  Not about some done deal created by a perfect creator god in the infinite past for some crazy cooked up purpose born out of our hellish awakenings when we were first becoming human long ago.

IT IS DIFFICULT to be human.

the first step in accepting all this horror about each of us is to wake up from the fantasy of heaven, that a perfect eternal god created us perfect with a plan, but to realize that we are one of evolution's GRAND EXPERIMENTS! this is a frightening thing to have been born a human with our higgledy piggledy mix (and each of us has a different mix) of wondrous capacities and horrifying failures.

when we realize this reality we realize we must truly have compassion for ourselves and others. and it is ONLY each of us who can offer this compassion and forgiveness. we are hypersocial and we are on this
wild creative journey together.

and if there is no one who can listen to us pray? what kind of prayer do we want?  to grant our wishes? thats just infantile! go out and seek. maybe there ARE people who will help us achieve our goals!

to feel  listened to? why on earth are we expending monumental effort to build a god for this instead of helping EACH OTHER learn to listen? most of us can learn to do it!

a prayer in which we are listening? for what? for wonder? for new ideas insights about our predicament? the important thing here is to realize that if we go into prayer with preconceived notions about who we are 'praying TO', we are limiting what we may be open to hearing. merely meditation to get out of our head chatter? this requires no one to pray to.

But even if another human listens to us, we come to realize that ULTIMATELY they cannot share our unique experience of our self and that at heart we FEEL RADICALLY ALONE!

being human WAS NOT AN EASY GIFT!  being born into this MONSTROUS labyrinth of neural nets capable of imagining infinite cosmos can be horrifying! in truth because we wire ourselves from the time we are embryos so stochastically and into such a large network of neurons... we ARE each SO DIFFERENT FROM EACH OTHER! Possibly at root, ALIEN to each other.  We don’t tend to think this is so, I believe, because our facility with language and our amazing abilities to mimic and imagine…  it may be truly impossible for each of us to comprehend what it is like for the other to have their experience of

so then what? maybe a first step is to accept this! so many religions so many political systems, medical systems, education systems want to imagine that we are created equal (American fantasy) or that at our core souls we are the same (christian fantasy) and CAN experience each other’s reality (Buddhist fantasy). but what if this is not correct? then we are barking up the wrong tree and have to find a different way?

so what can we do when faced with this radical state of unknowable complex difference of hundred trillion connection neural net that is our selves? what god can we commune with? where the comfort?

this universe is radically creative! we certainly have only BEGUN to explore that! only recently have we discovered 2 to 100 million species (we still dont know how many, but alas we DO know that we are erasing significant numbers of them through our economic growth).  Dug out 4 billion years of history during which wild trial and error have created these myriads of species and during which 99% of all them have passed away.  We’ve opened our eyes and discovered a hundred billion galaxies of a hundred billion stars each with their own planetary systems that might or might not be playing out their own billion year long evolutionary dramas (funny it took brains of a 100billion neurons to count those 100billions!). Opened our own skulls and counted our nets of 100billion stochastically wired neural nets. We are even beginning to explore the mathematics of how pattern, creativity can evolve out of simple rules of physics and math played out in systems of all these billions of interacting parts.

why IS the universe SO MANY PARTS?

maybe complex intelligent life COULD happen because there are 100 thousand billion billion planets to try it out on over billions of years! Each planet surface composed of 10^37 (now the numbers get TRULY big and I have to resort to mathematical notation.  10^37 means 1 followed by 37 zeros, that’s 10 billion billion billion billion!  At this point one must practice doing lots of math to truly appreciate what’s going on here!!!)  interacting molecules (and a billion years means particles nudge each other 10^24 times. They are bounce into each other VERY fast!).  That compounds to a mindboggling 10^84 operations in which to fiddle around with and invent life!

See, after spending so many years learning how creative math can be when played over such huge numbers... maybe god can simply be 10^84 interactions!  You may laugh at such a simplistic notion… but until you spend years learning the craft of mathematical and physics complexity… don’t be so fast!

but now that ive taken you to such horrifying dizzying heights can i bring you back down to a comforting human scale? the question was, how can we commune with such mindboggling mechanics when we are feeling at our most achingly human?

[probly go look at how the bhagavad gita does it!]

Tuesday, January 12, 2016

some mosses on wall

Some mosses growing on a stone wall in town.
look, there are three different species, growing in a patch the size of a pea
the silvery one is Bryum argenteum

further on is some colorful Orthotrichum anomalum
and further on is some Schistidium rivulare

might as well post some more mosses from another wall in town

here is another Orthotrichum anomalum

 here is Schistidium rivulare with more mature capsules

here is some Orthotrichum strangulatum

here is rivulare with strangulatum.  i can't tell the leaves apart without a microscope!

here are two mosses who's names i don't know yet.  maybe they'll sprout capsules in the summer and I'll look some more