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.