Tag Archives: self organisation

#Emergence in Action

The universe is a truly incredible thing. It is an endlessly cycling chaotic simulacra, churning out endless iterations of itself. The best part about being immersed in such wonder? No one needs to travel to the ends of the Universe to see this. At roughly 93 billion light years across there’s plenty to see. But the thing is, the universe is self assembling!

Yes, self assembling. What does this mean?

Exactly what it says. Nature is chock full of patterns. It’s said that nature abhors a vacuum. Perhaps it’s more accurate to say that nature abhors disorder. Patterns arise naturally from the firmament of whatever lies beneath the universe every single second every where at once all across the universe. In all of that vastness messes and disorder arise, but order always eventually spontaneously emerges.

Or at least it seems that way.

Life is a special example of emergence in action. A rather special example. It’s the most incredible phenomenon in all of existence. It’s right next to me as I write:

This is a collective of eukaryotic organisms. They all share the same genome: a special set of instructions which has emerged over evolutionary time. This set of instructions co-opts other seemingly random but very precisely designed molecules to pretty much do nothing but make more copies of itself ad infinitum. This collective of cells has organised itself into specialised structures that make the business of being a collective a little bit easier for all involved.

Now, replication of these instructions will eventually become riddled with flaws, as a process called senescence begins to emerge from this collective’s previously youthful state. Time will march on and eventually another equilibrium will emerge called death.

It doesn’t even end there. All of the atoms and compounds within this collective (from now on we’ll call this collective “Jasper”) will cycle through soil, clouds, other organisms, stars, molecular clouds, other planets and galaxies. Eventually they’ll come to rest at the end of time along with everything else. It’s a heck of a story. Really.

And all of that is self organising. Structures and patterns arise spontaneously from the laws of nature. Structures such as rivers and streams are no different to other familiar branching structures such as circulatory systems. Methane based river systems on frozen Titan resemble precisely the branching network of blood vessels that winds through your body like…..well, a river system. And it all creates itself!

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Naturally arising branching patterns on earth.

This spontaneous self organisation is ubiquitous in nature. Life , and especially multicellular life, has borrowed this proclivity for patterns, recreating those which seem conducive to biological processes functioning well.

Is this how multicellularity got a leg up?

Consider this example. Physarum polycephalum is the scientific name for a rather interesting species of plasmodial slime mold. Now, its name is a sign of things to come, meaning “many-headed slime”.

Plasmodial slime molds; not quite colonial, not quite multicellular. Image: Wikipedia

P. polycephalum breaks several tenets of what we would call common sense. Essentially, it is a single gigantic cell, consisting of thousands or millions of individual cells which have joined together for common interest. Unlike creatures like you and me, however, these cells aren’t compartmentalized like our own. In us, each cell is partitioned from its brethren by walls and membranes. The innards, including the nuclei are tucked away safe and sound. It’s truly a neighbourhood as we would understand it. Within the slime mold it’s like the sixties never died. It’s an orgy in there. All of the individual nuclei all slosh around inside this plasmodial common area. Creatures bearing this property are called coenocytic.

So. The slime mold has this kind of generic look about it, doesn’t it?

All of these structures emerge spontaneously, coded for by some as yet unknown aspect of spatial and quantum topography. I don’t know what this is, or how to elucidate it, but I know it’s there.

Life has somehow managed to encode these structures. Just like Jasper in the first image, these structures have evolved over geological time to work together, creating assemblages from which something emerges that is greater than the sum of its parts.

Could the first attempts at multicellularity have gotten a leg up? Did the laws of nature lay the groundwork for biological structures shared by the vast majority of multicellular organisms today? Consider this scenario.

Earth, several billion years before the present day. You’re drifting above a hellish landscape, in a little temporal bubble, that allows you to observe and record data but not interact with the landscape in any way. That could be disastrous. How so? Just imagine accidentally stepping on L.U.C.A; the Last Universal Common Ancestor of all life. Let your imagination do the rest. So you’re drifting along, observing, and you see something.

The earth at this time is hot. Islands of freshly minted land protrude above the semi-molten surface of a world still cooling down. You see chunks of the planet high above you, settling into a tenuous orbit. Only recently something the size of Pluto crashed into baby earth, shattering much of its outer skin and sending it into high orbit. All of those chunks you see in the sky will one day become the Moon. The collision wiped the surface clean like an Etch-A-Sketch, and so as a result baby earth is reforming again. Pockets of land like this one harbour water and other organic muck delivered by comets; the Universe’s version of Fed-Ex. Not to mention the stranger that caused all this damage in the first place.

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Space plays rough. Earth’s surface, wiped away in a catastrophic collision, provided the raw materials for its moon. Image: NASA/JPL

The view is impressive. Just imagine every vision or rendition of Hell you’ve ever seen and apply reality to it. It’s pretty cool. But something else huge is happening as well. Life is forming in the midst of this apocalypse. Your time machine hovers over the most momentous event in the history of the universe…

Whatever this tiny thing is, drifting about in warm eddies and swirls in that hot little pond, it’s the first. It may not live to see another day, or it may eventually give rise to things like you. You would love to examine it in more detail, but you ask yourself. How did this singular piece of organic machinery manage to figure out that one day forming collectives would be a good idea? Your time machine bubble thing seems to know what you’re thinking. It is only fictional after all, and the writer decides to jump forward a billion years or so….

Something large and dark slowly glides past you in the brightly lit upper layer of a sea that completely covers over three-quarters of the planet. The thing pushes you aside as a tremendous tail fin propels it down into dark depths. It’s some kind of fish. A big fish. The armour plating on its head gives it an appearance reminiscent of a tank. If Thunderbird 2 and the Batmobile (Christian Bale’s batman of course) had a baby, it would look something like this: Dunkleosteus. Your time bubble wobbles alarmingly as the behemoth sends powerful compression waves through the water. You know this is a fictional scenario, but you don’t care. You’ve gone too far forward anyway….

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Primeval earth, with a toxic atmosphere, much closer moon and primitive colonial life, in the form of stromatolites (right foreground). Image: NASA/JPL

A haze wafts across a landscape dominated by volcanic ash and a truly huge moon. Waves crash against a dark craggy shoreline. The time bubble lets you observe, but not interact, right? You can observe with all your senses. This place stinks. The shoreline is matted with a thick film of bacteria and gunk. Waves crash against the mat, breaking it up, and dispersing it further landward. You’re guessing with the moon so close tides must be insane here. This whole area is sub-littoral. Anything that can hold on here has to be tough. The rocks all give off steam. The sun isn’t as hot now as it is where you come from, but seams of volcanic activity are evident out in the water. Pillow like ridges of freshly solidified lava stretch up the shore, still not quite cool. Bacteria, or these Archean versions of them carpet some of the rocks. It’s here that you see something big. Almost as big as life appearing in the first place. Channels and rivulets run through some of the mats. Skins have formed and as water has reduced within the mats, structures have appeared. These mats have been given a push towards colonialism by the blind forces of nature. In these early more experimental times, genetic information and it’s transfer is a lot more promiscuous. A lot less Darwinian and a little more Lamarckian. These bacteria with their scrambled DNA and transfer will find this way of doing things a little easier, and will adopt it. Quickly.

Does this scenario make any sense? It does, but it had to have some basis in fact. I saw the principles in action, and they are as follows: an organic matrix, containing all manner of constituents useful to life is forced into biologically useful patterns and structures by some kind of energetic input. Where did I see this happen, or at least some analogue of it?

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My creature lives! Meet Soupenstein.

Meet Plasmodium botanicus, or plant muck. Otherwise known as puree vegetable soup. It does bear a striking resemblance to P. polycephalum, doesn’t it? This little monstrosity was created accidentally in the lab. Or should I say kitchen?

20170728_133413 It was busy. I was moving at a million miles an hour, when I spilt soup on the grill plate next to me. This odd structure was the quick result. Branching patterns and channels formed within seconds, and I was instantly taken by its similarity to a slime mold. It was this random splash that was the inspiration for this post. Now, this post is only a speculative “what if?” with some cheap time travel thrown in, but could the earliest multicellular life, or collective modes of existence have been given some kind of initial leg up by similar incidents or circumstances? There are parallels between my imagined “slime on a rock” and the soup accident above. Let’s call the soup an extracellular matrix. It is a composite substance, containing all manner of organic compounds, plus a few impurities (probably. What doesn’t?). Energy in the form of heat is applied to the ECM as it comes into contact with a flat hot surface. Water in the ECM reduces, leaving behind a concentration of material, which forms channels and branches in accordance with the laws of nature. Bacteria within this newly formed arrangement suddenly find life a little bit easier.

What of other mixes of organic and inorganic compounds? Could life have resulted from a random splash like this? Did multicellular life arise when the cosmic cook was a little busy and not being careful? It would be interesting to perform a series of experiments. Why not use foodstuffs such as soup? Would different recipes lead to different structures? Would other energy sources, or electricity, lead to new outcomes? Who knows? That’s the point of experimenting!

I’d be interested to hear what others have to say on this. Thanks for reading.

 

Ben.

References and Further Reading:

https://en.wikipedia.org/wiki/Titan_(moon)

http://www.elijahwald.com/origin.html

https://www.seeker.com/life-continues-within-the-body-after-death-evidence-shows-2212720233.html

http://www.medicaldaily.com/life-after-death-according-science-cells-fight-stay-alive-long-after-body-dies-409525

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303275/

P.S.

Thanks for reading this far! Could readers please do me a favour? I have a YouTube channel, and I would like feedback on it. If people could watch a couple of videos and give CONSTRUCTIVE criticism. What’s good? What’s not? Am I boring? Do I mumble etc? All feedback is welcome and if you can leave comments either here, on my twitter, Facebook or YouTube channel that would be awesome. I’ll make you famous. Or something. 

https://www.youtube.com/channel/UClvBq6G-DkIlKci7xXdWYzA

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Who writes the #Writer?

If you’re a fan of the fantastic and the (almost) magical, then you’ll know that it’s getting harder and harder to get through a single day without being almost paralysed by the veritable flood of big announcements being unleashed upon the world. 
Gravity waves, TRAPPIST-1, Juno and it’s watchful eye on Jupiter. All just more science candy to rot our teeth with. 

I LOVE IT!

But here’s a little secret. 

There’s no magic like old magic. Warning label: this post will contain references to talking lions and impossible cosmologies. 

The universe and all within is an impossible cornucopia of wonder. J.R.R. Tolkien once spoke of the wonders of the unexplored vista in fiction. The universe is still (and always will be) an unexplored vista, like some dark brooding mountain range; its fell winds filling a lost band of travellers with foreboding. The mountain ranges are the same in every fantasy novel I ever read: cruel, dark and vast. I would join the travellers on their journey; be they the Fellowship of the Ring, Atreyu and companions finding a way through the Nothing or the Pevensey children, seeking Aslan. I would see the same mountains or vistas they would see and wonder what was in them, watching the story unfold. 

Did you ever wonder what was beyond  those mountains?  Nameless lands and other unrecorded epic histories and struggles? Life? Death? Infinity? Cyborg armadillos? A back door out into some rat infested alley somewhere? I spent a lot of time beyond the borders of these imaginary lands, seeing them as some kind of dreamlike state attached by imaginary geography to the main tale. Like junk DNA they didn’t seem to play any kind of part in the story, yet they also provided it with further structure. Playing a very important role by simply hanging there, forever out of reach. 

In a sense the distant past is like this imaginary land, especially the very distant past and in particular those very very first moments. Maybe even the time before time. How far back can we go really? Like the resurrection of Aslan in “The Lion, the Witch and the Wardrobe, in which the Lord of Narnia drew power from a time before time, is everything built on something else? 

Life is such a thing.

Contemporary scientific dogma explains life as a phenomenon emerging from inanimate disorder. To the scientific mind this makes intuitive sense: a bit of stuff and another bit of stuff merged or were bonded chemically and some miraculous act of transmutation took place. Life appeared: self replicating systems, handing down and reliant upon the seamless transmission of information/instructions. Hiccups in this basic routine were bound to happen of course. If biological information transmission were completely flawless I wouldn’t be sitting here in a McDonald’s writing this, I’d still be a blob of stuff flopping around in some warm little pond somewhere. Obviously I’ve used the simplest description possible. Life changes in response to environmental changes and pressures, but I’m not going  to have a blog post blowout by hyperlinking into a discussion about evolution. 

Where was I? Life. 

 I’m thinking now about this process of emergence.  Life itself is (at the very least) an emergent property, arising somewhere from within the girders and tangled architecture of Nature. Is it created by this chemical and physical architecture, or was the promise of life already hiding in the basement somewhere?

A snapshot of the cosmic microwave background radiation. The ultimate family snapshot: everyone’s in it!

This emergence is a built in property of the universe. Quantum theory holds that our perception of the universe calls it into existence. If this is true, then what of a time before life or perception even existed? Did the universe even exist before we came along? “We” being life that is. We of course aren’t the first things to experience the universe. Even a jellyfish experiences existence in it’s own way. I must make here a distinction between perception and intelligent perception. 
Obviously the universe existed before us. Take whatever side of the fence you like: religion or science. We can all explain the universe and we are all intrinsically aware that the universe was created and was here long before the first living thing flopped out of the primordial mud. 

This emergence of life was always meant to happen. The universe cycles itself, refreshing every second, every single passing of whatever fundamental subunit of time ticks by. We perceive it into existence, but it was perceived by things before us, things before them and so on.  But what of the first thing? What perceived the universe before anything even knew it was there?

The universe has always contained the framework for perception. Patterns in inanimate nature repeat themselves in biology.  

When I was at university I gave some thought to the emergence of multicellular life. After completing my degree I kept studying, doing an Honours year. I originally wanted to study biofilms. Of course the project mutated and became unrecognisable. My supervisor steered me towards something completely different, but I always thought about the emergence of something fundamentally different to single celled life. I felt that simplistic biological structures like biofilms represented a step in the transition from single celled existence to colonial organisms and from there to multicellularity. 

Take a wild guess what got me thinking about multi celled organisms emerging like this; ready made as it were.

Coffee. 

I was in one of the University cafés,  up on the hill behind the sciences building. As did many others I spent a lot of time here studying, reading or just thinking. It was quiet and I had actually been thinking about multicellularity on this day when I looked down at my coffee. I have a tendency to forget things when I’m pondering the world and my coffee had gone cold. 

The wrinkly skin that had formed on top got me thinking. I remember drawing it, doodling it on a corner of a notebook page, recognising something.  It looked exactly like all kinds of biological structures, in particular biological infrastructure such as a circulatory network. The branching structure or pattern we see here is so familiar to us we don’t even think about it.

And so it began. I got thinking..

We see so many repeating patterns and structures in the natural world that they are almost white noise. The forking of tree branches or blood vessels, the winding of streams and rivers and the somehow disciplined swirling of clouds are very familiar to us all. It’s interesting how the same kinds of patterns appear both spontaneously, as in the case of rivers, or under the guidance of carefully meted out biological information (tree branches etc).

Physarum polycephalum, a bizarre and fascinating oddity.

*Update 27/07/2017

This video summarised some of the points of this post really well.  Enjoy the heck out of it. Via Biographic. 


Consider this image. 

A river winds through a muddy delta plain, stretching toward the brackish waters of an estuary. 

Now consider this one:

A stagnant shallow pond, at Mutton Cove Conservation Reserve, Port Adelaide.

The branching pattern running through the midst of this mat is quite reminiscent of a river system. In fact, you’ve most likely figured out that these are both the same image. This is why I’ve used this image. It represents a key point I’m trying to make. 

The mat is likely mostly microbial, or composed of biological material: microorganisms,  waste products, in  addition to inorganic muds or silt. The branching  and bifurcations within the mud are most likely formed due to abiotic factors, in the same way that synaerisis cracks form in muddy lake bottoms as the last of their water dries.

My question: could such structures;  formed by innocuous natural processes, provide templates for biological processes? Biofilms are known to possess channels and a certain level of internal structure.  Some of these structures are similar both in form and function to structures that perform analogous tasks in multicellular organisms.

Did early multicellular life get an organisational leg up from a deeply mathematical universe, in which all manner of patterns appear in a multitude of environments?

I say the universe is deeply mathematical, but I will admit here and now I am no mathematician. It’s just always seemed apparent that the universe operates around a very secretive and mysterious set of guidelines. In the same way that a businessman from Sydney can walk into a McDonald’s in New Delhi and expect exactly the same Big Mac he’d get in Moscow, so it follows that rivers of liquid hydrocarbons on Titan form branching channels and patterns; following the same recipe as rivers of water on Earth.
What I mean is that some things just never change, wherever you may be in the local Universe. If you were standing on an exoplanet passably similar to Earth you’d see flows and channels just like those on Earth. One of the planets orbiting TRAPPIST-1 may make a good setting for this imaginary walk. The sky is dark. It’s like a permanent sunset: a red hue washes over a rocky landscape. You’re standing on a low cliff, looking down at a river. It looks like any river on earth. OR, just like the river systems on Titan.

River channels on Titan, carved and eroded by liquid hydrocarbons. Image: NASA/JPL

This similarity is spontaneous. That’s something we all intuitively know. This is what I’m getting at. If life formed spontaneously as a result of natural laws, then life- and more complex life would arise on other worlds.  Depending on its environments and circumstances it will obviously be different to life on earth, but there will also be similarities. 
It’s all about infrastructure. Infrastructure arises unbidden in all manner of systems. 

A flock of starlings is a system.
Spaghetti on toast is not.

A system is a collective of interconnected parts or processes, all acting within the context of a greater whole. A flock of starlings differs from spaghetti on toast in this fundamental aspect. The flock appears chaotic, but in fact behaves according to rules which are seemingly set in stone.  The spaghetti shows no flavour of interconnectedness nor any kind of behaviour. The strands do not interact and so are unable to work together to prevent being eaten by me. The flock of starlings however can.  

I’ll take the spaghetti. 

The swarming behaviour exhibited by the birds and other creatures which swarm (locusts, Monarch butterflies etc) is an emergent property, arising from the interactions between sub units. 

Back to infrastructure. The flock of starlings acts as it does because all of the birds can see each other or otherwise interact with each other in some way. Mechanisms exist by which the birds connect to each other, and so something new emerges from a seemingly disparate collection of birds. Consider a city.  Many cities began as gatherings of family groups or tribes. For these small groups such an existence worked. Not much infrastructure other than language, common customs and some simple rules were needed in order for these simple societies to function. 

But then the families began to grow. Other villages were discovered. Tribes went to war. Other villages and tribes were conquered. Populations and customs began to change as other cultures and ideas sped up progress.  Farming was discovered: trade followed. Technology developed. This is all part of the growth of a society,  and it is an analogue for the evolution of multicellular life. As time goes on infrastructure is a necessity. Roads, money, writing, advanced modes of travel, all develop as a natural by product of the growth of a society. A city becomes an organic thing. It sprawls across a landscape, complete with a venous network of roads and railways. Communications dart back and forth along phone lines and fibre optic lines: the equivalent of nerves, enabling disparate sections of the city to be aware of outside forces and distant events. From a distance these branching roads and lines could bear a passing resemblance to biological infrastructure. Even lower eukaryotes appear to understand this:

This is the famous example of a slime mold set to work redesigning Tokyo’s rail network! Many experiment have shown these unbelievable organisms effortlessly redesigning Spanish and Portuguese rail networks: often rendering them more efficient than the human engineers!

So at a glance at least it looks as though the collective behaviour shown by a slime mold runs along similar lines to the growth of a city. Lines of infrastructure, connecting sub units, create a gestalt entity; something more than the sum of its parts. 

If life (and in particular multicellular life) arose due to a proclivity for exploiting the connective properties of certain naturally recurring patterns and structures, how did life figure this out? Obviously roads didn’t appear before cities. But in every single city on earth roads could be found. The idea of a road always existed. Roads were inevitable.

Off on a wild tangent? Is this a flight of fancy? Maybe, maybe not.  What do you think? Self organisation and emergence aren’t just products of group behaviour. They are inherent tendencies, built into the fabric of space and time. Feel free to pipe in with your opinion. Thanks for reading. It’s been a long post, and possibly rambling, but it’s a blog.  Not the six o’clock news.

Cheers,

Ben.

P.S.

Check out Biographic on YouTube and Twitter. Well worth it.

Take a look at bioGraphic (@bioGraphic): https://twitter.com/bioGraphic?s=09