August 27, 2012
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I love patterns… Especially ones that have chaotic tendencies. Within these pages there are many suggested places where one might find these ever shifting, non-predictable eddies of nature’s own living design. Without them we might not know life as we know it now, in this present moment, through our own direct experience… Without chaos, perhaps the evolution of anything would never have felt a need to leave the neat homogeneous backdrop of absolute predictable perfect uniformity.
However, we find diversity all around us… Everything, no matter how similar it may seem, is never exactly the same as anything else. In fact, there is so much diversity all around us that, we spend most of our time categorising these differences (whether gross or subtle) and thereby creating our own dualistic modes of being and understanding. But I don’t want to really talk about that here.
What I would like to do is expound on the subject of formation… A subject that has already been tackled quite a few times in these pages, especially in “Just How Did Life Seed Here On Earth???” as well as “On The Formation Of Suns And Their Planets” This particular subject of creation concerns processes that occur on a slightly grander scale to the previous two mentioned… But they are all inextricably interlinked/intertwined to one another and – as well – very much interrelated and interdependent.
This is the subject of galaxy formation… Not in highly complex, mathematical terms… But rather, procured in simple, fluid ways, which show how simplicity – when left to its own natural devises – inevitably leads to patterns of beautiful complication that many of us can observe on a daily basis in the photographs of APOD and other websites that dedicate their content to the ongoing study of the heavens above…
I won’t say any more here… Mainly as I fear I could make matters far too complicated for most and, thus, spoil the simplicity of mind with which this marvel should be experienced… Though, perhaps I will leave with you the introduction that APOD provided below the video the first time I watched it.
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Simulation: A Disk Galaxy Forms
How do galaxies like our Milky Way form? Since our universe moves too slowly to watch, faster-moving computer simulations are created to help find out. Green depicts (mostly) hydrogen gas in the above movie, while time is shown in billions of years since the Big Bang on the lower right. Pervasive dark matter is present but not shown. As the simulation begins, ambient gas falls into and accumulates in regions of relatively high gravity. Soon numerous proto-galaxies form, spin, and begin to merge. After about four billion years, a well-defined center materializes that dominates a region about 100,000 light-years across and starts looking like a modern disk galaxy. After a few billion more years, however, this early galaxy collides with another, all while streams of gas from other mergers rain down on this strange and fascinating cosmic dance. As the simulation reaches half the current age of the universe, a single larger disk develops. Even so, gas blobs — some representing small satellite galaxies — fall into and become absorbed by the rotating galaxy as the present epoch is reached and the movie ends. For our Milky Way Galaxy, however, big mergers may not be over — recent evidence indicates that our large spiral disk Galaxy will collide and coalesce with the slightly larger Andromeda spiral disk galaxy in the next few billion years.
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If you’d like to find out where I originally sourced this YouTube video from, please visit the APOD website by clicking here.
August 25, 2012
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Just over a month ago, around my birthday, I saw this rather interesting film that was airing on the BBC’s iPlayer… The main reason it caught my eye was because I was looking to buy a DVD copy an old blues documentary that Martin Scorsese had directed that traced the origins of blues music from the birth of the Delta-blues to the slave-experience and finally to Africa, which was entitled “The Blues“. However, as so often seems to be the case when on-line recently, I got slightly side tracked when I noticed a somewhat odd search result place near the top of the Google list… It read something like, “Scorsese – Executive Producer – Surviving Progress”.
Obviously I’m quite a big fan of Scorsese’s past works, especially his recent foray into the world of 3D animation that was highlighted with his loveable film “Hugo”, a heart felt story of a young orphaned lad who looks after the Gare Montparnasse’s clocks in Paris, ensuring they’re all well maintained and running on time. Anything that he decides/chooses to get involved in, for me, is a curiosity I rarely fail to miss… Mainly because they’re usually so well crafted and brilliantly realised. However, this one particular listing about “Survivng Progess” I had not heard anything about: neither in the tabloids nor on-line. Why that should be, I have no idea, especially as it is something I’ve broached the subject of here within this website before. So, as it was airing on the BBC’s iPlayer, I just couldn’t turn down a ‘free’ viewing of something Scorsese had chosen to get involved in when the chance arose.
To be fair, it wasn’t at all what I was expecting. Partly because I didn’t read the introduction to it on the BBC’s website… But predominantly because I had clocked the 1 hour and 22 minute run time and, so, automatically expected it to be a feature length fictional movie/film of some kind or another (oh, damnable presumptions)… However, from the very outset, I have to say, with it’s dulcet musical score and languid, ponderous content, it left me feeling somewhat engrossed and uneasy all at the same time, almost as though I was witnessing my own death and, yet, was still fully aware of all that going on around me.
During the course of the film, it touchingly brought an obvious – and yet, of late, once again much overlooked question – to the forefront of my thoughts… As a race of living beings, would WE actually make it through the coming hard times, most of which are predominantly and presently of our own making… ? Could we make sufficient changes right now to allow a decent bit of progress to be made on the path to cultivating a more balanced way of life within nature’s cradle of a planetary ecosystem… ?
Alfred Montapert, the Amercian author who wrote the “The Supreme Philosophy of Man: The Laws of Life”, is quoted as once saying “Don’t confuse motion and progress. A rocking horse keeps moving but doesn’t make any progress.” Certainly I see a lot of motion going on all around me in daily life… And whenever I’ve asked whether it’s really a holistic, healthy type of progress, most people I meet say that it will do for the time being… But, my instinct keeps nudging me, and I can’t help asking “Really? Is it really good enough for the time being?” Certainly I’m still not convinced by most people’s appraisal of the situation… And it seems, as this film suggests, the answer is a lot more astounding that most could (or would) dare to imagine…
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Documentary telling the double-edged story of the grave risks we pose to our own survival in the name of progress. With rich imagery the film connects financial collapse, growing inequality and global oligarchy with the sustainability of mankind itself. The film explores how we are repeatedly destroyed by ‘progress traps’ – alluring technologies which serve immediate need but rob us of our long term future. Featuring contributions from those at the forefront of evolutionary thinking such as Stephen Hawking and economic historian Michael Hudson. With Martin Scorsese as executive producer, the film leaves us with a challenge – to prove that civilisation and survival is not the biggest progress trap of them all.
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To find out where I originally saw this movie, please visit the BBC’s website by clicking here.
OR to visit the official website for the film, which should be released on DVD sometime this October, please click here.
September 8, 2010
Last night I had a dream… A spiralling coil of color unfolded its serpentine and slithering body before my mind’s inner eye. Patterns danced in such an orchestrated synchronicity, so as to complect into a delicate and balanced interplay of form and function, all actions and reactions – though it was hard to tell which were which anymore, because of the temporal passage that had clouded all the previous causes to things – feeding back into the source, creating new snaking forms of colorful displays… Never ending, never repeating exactly, so interdependent on everything else around them, looking for nourishment and inspiration in themselves and those around them, every part of it guided by a wild and beating leviathan heart, a heart that was run by the only certainty I could ever find… That of uncertainty… That of chaos… An open ended function that was the only pure motivation for all universal being and which itself, alone, could only describe and create such a miraculous and highly dynamical order… “I” was a part of it… And in reflecting all of what “I” saw unraveling around me, this rhythm of chaotic movement began to shine through my very Being, allowing me to try to define myself in self-similar patterns… Patterns similar to those that “I” witnessed going on around me, allowing me a vain hope to understand what “I” is… While providing me with all I needed to partake in this dance of joyous wonderment before me; understandings were nothing more that rippling imaginations that carelessly skittered over and through the patterns of consciousness… Shape that had been fluxing within my brain’s complex and structured form… And still, I could only try to understand why, like almost everyone else, “I” tried to find similar reasons for Being in the ocean of delusion that swelled and sank around me… It was the only way “I” had known how to be throughout my entire life… And this was how the wonder twisted through my living, convoluting flow… A pattern that embraced every aspect of our Being, clutching “my” particle-like body into the blossom of its infinite totality….
Perhaps this was what many people before me had decided to call “God…” Mainly because they hadn’t properly understood its essence and nature… After, the wise mystics of the East followed the way of this unspeakable, indescribable beast. The Tao, they called it. “The Way.” And still it remains the only way to be, to dream and to live in harmony with all under heaven. Riddled with self-similarity, it writhed and pulsed to various rhythms running through its Being, all running inside and outside of each other, layering into and out of itself, fluxing with such precision that it might have been a silken fabric so finely woven, that the very threads we but atomic braids of molecular chains, of which any movement could upset the natural order and cause a mighty ripple to undulate throughout itself.
In all honesty I can’t remember how long this phantasm of interconnected geometry lasted… All I know is that I woke with a sudden jolt to find myself in bed with the covers strewn half on me and half on the floor. In someways I was relieved to find myself back home… But also I had a distinct sense of underlying melancholy that seemed to underpin my sleepy head… Sort of like when one departs the company of good friends. Slowly as my mind came back into focus, I found myself thinking of M. C. Escher‘s work. The seeming parallels that ran through my mind joined my dream up with Escher’s precise visions of nature’s “natural” symmetry. These in turn linked up with my own personal first hand experiences with mescaline, psilocybin, DMT and LSD… I haven’t tripped in a long, long time now. And I doubt I will need to ever again. What I had to learn from these powerful allies of the plant world, I did. They have kindly shown me all that I need to see. Within their own tapestries of mind, from the altered states of consciousness that they seem to so gracefully and naturally induce, I found myself faced with patterns as complex as those that I had seen on the Alhambra.
Yes… That’s it. That’s what all this reminds me of… The Moorish architecture of the Alhambra… There is so much of divine Moorish masonry to be found in Granada… And funnily enough it’s almost a year ago to the day that I arrived back from there… Perhaps, this is where my dream came from… Parallels in our orbit around our star, echoing through the structure of my brain. Perhaps I should provide a brief setting for this slight tangent… Between 710 and 713 A.D., Spain had been overrun by the Moors (populations of Berber, Black African and Arab peoples from Northern Africa), and these Islamic conquerors naturally introduced the ornate Moorish, or Moresque or Hispano-Moresque, style of design to the Iberian Peninsula, and is especially noted in the architecture of Southern Spain, which is centred and personified in the Alhambra, located in the city of Granada.
The Moors were not entirely driven out of the Southern provinces until 1610, but in the nine hundred years intervening, the Moresque style flourished sporadically throughout many portions of Spain. And one can see why… The splendour of this mode of design brought nearly everyone who saw it closer to a true sense of wonder regarding the creation of all things than anything else at the time. During the Romanesque period a large part of the country was still under Moorish rule… Here the balanced European form mingled with Islamic sensibilities, producing wondrous Romanesque structures laced with Moresque imagery and pattern. This marriage of form inspired the late M. C. Escher so much during his first visit in 1922, that he is reportedly to have said, “I have never before seen such concentrated inspiration in all the world!” After this his works of art began to take a very different turn. From the Italian country side sketches and etchings, he slowly incorporated this Moorish symmetry into his designs. While the Moors we forbidden to use any human or animal forms in their art – mainly because humans and animals were considered to be the divine and perfect work of Allah, and any human representation could only ever be an imperfect representation of the creator’s master work, and thus a blaspheme – Escher began to break this mould and used images of animals and plants in tessellations of wondrous cunning. These tessellations began to feature predominantly throughout most of the work of his later life. And rather than limiting them to just the snug, tightly fitting geometries of mathematical sensibilities… He opened them up with his imagination into metamorphosing consternations. It was almost as if Escher had seen the key to the universe, and had unlocked the door, through which it began to speak through him.
I know… I know… Sounds like a sort of far fetched fantasy derived from a dream I had… However, I’m going to present an idea in the form of an article that I found on the Twitter vine not too long ago. It is entitled “Uncoiling The Spiral: Math And Hallucinations” and was written by Marianne Freiberger.
Uncoiling The Spiral: Math And Hallucinations
Think drug-induced hallucinations, and the whirly, spirally, tunnel-vision-like patterns of psychedelic imagery immediately spring to mind. But it’s not just hallucinogenic drugs like LSD, cannabis or mescaline that conjure up these geometric structures. People have reported seeing them in near-death experiences, as a result of disorders like epilepsy and schizophrenia, following sensory deprivation, or even just after applying pressure to the eyeballs. So common are these geometric hallucinations, that in the last century scientists began asking themselves if they couldn’t tell us something fundamental about how our brains are wired up. And it seems that they can.
Geometric hallucinations were first studied systematically in the 1920s by the German-American psychologist Heinrich Klüver. Klüver’s interest in visual perception had led him to experiment with peyote, that cactus made famous by Carlos Castaneda, whose psychoactive ingredient mescaline played an important role in the shamanistic rituals of many central American tribes. Mescaline was well-known for inducing striking visual hallucinations. Popping peyote buttons with his assistant in the laboratory, Klüver noticed the repeating geometric shapes in mescaline-induced hallucinations and classified them into four types, which he called form constants: tunnels and funnels, spirals, lattices including honeycombs and triangles, and cobwebs.
In the 1970s the mathematicians Jack D. Cowan and G. Bard Ermentrout used Klüver’s classification to build a theory describing what is going on in our brain when it tricks us into believing that we are seeing geometric patterns. Their theory has since been elaborated by other scientists, including Paul Bressloff, Professor of Mathematical and Computational Neuroscience at the newly established Oxford Centre for Collaborative Applied Mathematics.
How The Cortex Got Its Stripes…
In humans and mammals the first area of the visual cortex to process visual information is known as V1. Experimental evidence, for example from fMRI scans, suggests that Klüver’s patterns, too, originate largely in V1, rather than later on in the visual system. Like the rest of the brain, V1 has a complex, crinkly, folded-up structure, but there’s a surprisingly straight-forward way of translating what we see in our visual field to neural activity in V1. “If you imagine unfolding [V1],” says Bressloff, “You can think of it as neural tissue a few millimetres thick with various layers of neurons. To a first approximation, the neurons through the depth of the cortex behave in a similar way, so if you compress those neurons together, you can think of V1 as a two-dimensional sheet.”
An object or scene in the visual world is projected as a two-dimensional image on the retina of each eye, so what we see can also be treated as flat sheet: the visual field. Every point on this sheet can be pin-pointed by two coordinates, just like a point on a map, or a point on the flat model of V1. The alternating regions of light and dark that make up a geometric hallucination are caused by alternating regions of high and low neural activity in V1 — regions where the neurons are firing very rapidly and regions where they are not firing rapidly. To translate visual patterns to neural activity, what is needed is a coordinate map, a rule which links each point in the visual field to a point on the flat model of V1. In the 1970s scientists including Cowan came up with just such a map, based on anatomical knowledge of how neurons in the retina communicate with neurons in V1 (see the box on the right for more detail). For each light or dark region in the visual field, the map identifies a region of high or low neural activity in V1.
So how does this retino-cortical map transform Klüver’s geometric patterns? It turns out that hallucinations comprising spirals, circles, and rays that emanate from the centre correspond to stripes of neural activity in V1 that are inclined at given angles. Lattices like honeycombs or chequer-boards correspond to hexagonal activity patterns in V1. This in itself might not have appeared particularly exciting, but there was a precedent: stripes and hexagons are exactly what scientists had seen when modelling other instances of pattern formation, for example convection in fluids, or, more strikingly, the emergence of spots and stripes in animal coats. The mathematics that drives this pattern formation was well known, and it now suggested a mechanism for modelling the workings of the visual cortex too.
…And How The Leopard Got Its Spots
The first model of pattern formation in animal coats goes back to Alan Turing, better known as the father of modern computer science and Bletchley Park code breaker. Turing was interested in how a spatially homogeneous system, such as a uniform ball of cells making up an animal embryo, can generate a spatially inhomogeneous but static pattern, such as the stripes of a zebra.
Turing hypothesised that these animal patterns are a result of a reaction-diffusion process. Imagine an animal embryo which has two chemicals living in its skin. One of the two chemicals is an inhibitor, which suppresses the production of both itself and the other chemical. The other, an activator, promotes the production of both.
Initially, at time zero in Turing’s model, the two chemicals exactly balance each other — they are in equilibrium, and their concentrations at the various points on the embryo do not change over time. But now imagine that, for some reason or other, the concentration of activator increases slightly at one point. This small perturbation sets the system into action. The higher local concentration of activator means that more activator and inhibitor are produced there — this is a reaction. But both chemicals also diffuse through the embryo skin, inhibiting or activating production elsewhere.
For example, if the inhibitor diffuses faster than the activator, then it quickly spreads around the point of perturbation and decreases the concentration of activator there. So you end up with a region of high activator concentration bordered by high inhibitor concentration — in other words, you have a spot of activator on a background of inhibitor. Depending on the rates at which the two chemicals diffuse, it is possible that such a spotty pattern arises all over the skin of the embryo, and eventually stabilises. If the activator also promotes the generation of a pigment in the skin of the animal, then this pattern can be made visible. (See the Plus article How the leopard got its spots for more detail.)
Turing wrote down a set of differential equations which describe the competition between the two chemicals (see the box on the right), and which you can let evolve over time, to see if any patterns emerge. The equations depend on parameters capturing the rate at which the two chemicals diffuse: if you choose them correctly, the system will eventually stabilise on a particular pattern, and you can vary the pattern by varying the parameters. Here is an applet (kindly provided by Chris Jennings) which allows you to play with different parameters and see the patterns form.
Patterns In The Brain
Neural activity in the brain isn’t a reaction-diffusion process, but there are analogies to Turing’s model. “Neurons send signals to each other via their output lines called axons,” says Bressloff. Neurons respond to each other’s signals, so we have a reaction. “[The signals] propagate so quickly relative to the process of pattern formation, that you can think of them as instantaneous interactions.” So rather than diffusion, which is a local process, we have instantaneous interaction at a distance in this case. The roles of activator and inhibitor are played by two different classes of neurons. “There are neurons which are excitatory — they make other neurons more likely to become active — and there are inhibitory neurons, which make other neurons less likely to become active,” says Bressloff. “The competition between the two classes of neurons is the analogue of the activator-inhibitor mechanism in Turing’s model.”
Inspired by the analogies to Turing’s process, Cowan and Ermentrout constructed a model of neural activity in V1, using a set of equations that had been formulated by Cowan and Hugh Wilson. Although the equations are more complicated than Turing’s, you can still play the same game, letting the system evolve over time and see if patterns in neural activity evolve. “You find that, under certain circumstances, if you turn up a parameter which represents, for example, the effect of a drug on the cortex, then this leads to a growth of periodic patterns,” says Bressloff.
Cowan and Ermentrout’s model suggests that geometric hallucinations are a result of an instability in V1: something, for example the presence of a drug, throws the neural network off its equilibrium, kicking into action a snowballing interaction between excitatory and inhibitory neurons, which then stabilises in a stripy or hexagonal pattern of neural activity in V1. In the visual field we then “see” this pattern in the shape of the geometric structures described by Klüver.
Symmetries In The Brain
In reality, things aren’t quite as simple as in Cowan and Ermentrout’s model, because neurons don’t only respond to light and dark images. Through the thickness of V1, neurons are arranged in collections of columns, known as hypercolumns, with each hypercolumn roughly responding to a small region of the visual field. But the neurons in a hypercolumn aren’t all the same: apart from detecting light and dark regions, each neuron specialises in detecting local edges — the separation lines between light and dark regions in a part of an image — of a particular orientation. Some detect horizontal edges, others detect vertical edges, others edges that are inclined at a 45° angle, and so on. Each hypercolumn contains columns of neurons of all orientation preferences, so that a hypercolumn can respond to edges of all orientations from a particular region of the visual field. It is the lay-out of hypercolumns and orientation preferences that enables us to detect contours, surfaces and textures in the visual world.
Over recent years, much anatomical evidence has accumulated showing just how neurons with various orientation preferences interact. Within their own hypercolumn, neurons tend to interact with most other neurons, regardless of their orientation preference. But when it comes to neurons in other hypercolumns they are more selective, only interacting with those of similar orientations and in a way which ensures that we can detect continuous contours in the visual world.
Bressloff, in collaboration with Cowan, the mathematician Martin Golubitsky and others, has generalised Cowan and Ermentrout’s original model to take account of this new anatomical evidence. They again used the plane as the basis for a model of V1: each hypercolumn is represented by a point (x, y) on the plane, while each point (x, y) in turn corresponds to a hypercolumn. Neurons with a given orientation preference Θ (where Θ is an angle between 0 and π) are represented by the location (x, y) of the hypercolumn they’re in, together with the angle Θ, that is, they are represented by three bits of information, (x, y, Θ). So in this model V1 is not just a plane, but a plane together with a full set of orientations for each point.
In keeping with anatomical evidence, Bressloff and his colleagues assumed that a neuron represented by (x0, y0, Θ0) interacts with all other neurons in the same hypercolumn (x0, y0). But it only interacts with neurons in other hypercolumns, if these hypercolumns lie in their preferred direction Θ0: on the plane, draw a line through (x0, y0) of inclination Θ0. Then the neurons represented by (x0, y0, Θ0) interact only with neurons in hypercolumns that lie on this line, and which have the same preferred orientation Θ0.
This interaction pattern is highly symmetric. For example, the pattern doesn’t appear any different if you shift the plane along in a given direction by a given distance: if two elements (x0, y0, Θ0) and (s0, t0, ϕ0) interact, then the elements you get to by shifting along, that is (x0 + a, y0 + b, Θ0) and (s0 + t, y0 + b, ϕ0) for some and , interact in the same way. In a similar way, the pattern is also invariant under rotations and reflections of the plane.
Bressloff and his colleagues used a generalised version of the equations from the original model to let the system evolve. The result was a model that is not only more accurate in terms of the anatomy of V1, but can also generate geometric patterns in the visual field that the original model was unable to produce. These include lattice tunnels, honeycombs and cobwebs that are better characterised in terms of the orientation of contours within them, than in terms of contrasting regions of light and dark.
What’s more, the model is sensitive to the symmetries in the interaction patterns between neurons: the mathematics shows that it is these symmetries that drive the formation of periodic patterns of neural activity. So the model suggests that it is the lay-out of hypercolumns and orientation preferences, in other words the mechanisms that enable us to detect edges, contours, surfaces and textures in the visual world, that generate the hallucinations. It is when these mechanism become unstable, for example due to the influence of a drug, that patterns of neural activity arise, which in turn translate to the visual hallucinations.
Bressloff’s model does not only provide insight into the mechanisms that drive visual hallucinations, but also gives clues about brain architecture in a wider sense. In collaboration with his wife, an experimental neuroscientist, Bressloff has looked at the connection circuits between hypercolumns in normal vision, to see how visual images are processed. “People used to think that neurons in V1 just detect local edges, and that you have to go to higher levels in the brain to put these edges together to detect more complicated features like contours and surfaces. But the work I have done with my wife shows that these structures in V1 actually allow the earlier visual cortex to detect contours and do more global processing. It used to be thought that you process more and more complex aspects of an image as you go higher up in the brain. But now it’s realised that there is a huge amount of feedback between higher and lower cortical areas. It’s not a simple hierarchical process, but an incredibly complicated and active system it will take many years to understand.”
Practical applications of this work include computer vision — computer scientists are already building the inter-connectivity structures that Bressloff and his colleagues played around with into their models, with the aim of teaching computers to detect contours and textures. On a more speculative note, Bressloff’s research may also one day help to restore vision to visually impaired people. “The question here is if you can somehow stimulate part of the visual cortex, [bypassing the eye], and use that to guide a blind person,” says Bressloff. “If one can understand how the cortex is wired up and responds to stimulation, perhaps one would then have a better way of stimulating it in the right way.”
There are even applications that have nothing at all to do with the brain. Bressloff applied the insights from this work to other situations in which objects are located in space and also have an orientation, for example fibroblast cells found in human and animal tissue. He showed that under certain circumstances these interacting cells and molecules can line up and form patterns analogous to those that arise in V1.
People have reported seeing visual hallucinations since the dawn of time and in almost all human cultures — hallucinatory images have even been found in petroglyphs and cave paintings. In shamanistic traditions around the world they have been regarded as messages from the spirit world. Few neuroscientists today would agree that spirits have anything to do with it, but as messengers from a hidden world — this time the hidden world of our brain — these hallucinations seem to have lost none of their potency.
by Marianne Freiberger
For me that article just magically linked up some seemingly random dots that had been lingering in my mind… Ones that were loosely drifting around on a plane of understanding that seemed to – only at the best of times – be based on flights of fancy and mathematical musings of divine symmetry… Could the reason why I, and others, are so drawn to these tapestries of geometrical wonder be because this pattern is naturally residing in the brain’s architecture? Could the key to our modes of perception regarding the surrounding universe be found – amazingly enough – in the roots of our minds? Is the mysticism lying behind the Alhambra’s amazing architecture linked to the patterns locked deep within the brains structure? Is that where our notions of God and the divine come from i.e. the imagery of divine knowing and interrelatedness that came to haunt my dream last night?
For me there is no doubt that there is a strong link between the spiritual ecstasy that I have experienced in altered states of consciousness and while viewing Escher’s works of art… Perhaps those followers of Allah, who invaded the Iberian Peninsula and left their indelible mark on the Spanish people’s cities and towns, saw a similar connection too. Certainly it is mentioned that the prophet Muhammad experienced visions while meditating within a cave for several weeks every year. It is here in this cave on Mount Hira, near Mecca, that he apparently experienced a direct countenance with the angel Gabriel who revealed many things to him. Certainly adherents and prophets of other religions also recount similar marvels and revelatory experiences (see Aldous Huxley‘s “The Perennial Philosophy”).
While I am not religious… I am aware of a pattern of mind that links these spiritual experiences into a similar and all encompassing perennial philosophy. Perhaps the key to this insight lies within ourselves through direct experience, rather than in notions and metaphors of an omniscient and omnipotent god/group of gods. Perhaps it’s time we forgot our differences and looked for the key to understanding our experiences through consciousness itself… Where we relate to one another through our patterns of mind and body… A view that would be free from delusion and ‘self’ impossed egocentric understandings… ? Perhaps psychedelics are a type of direct key to seeing this pattern of the divine… ? And perhaps our notions of an eternal creator is nothing more than the same patterns we see springing forth in the mind in altered states of consciousness… Perhaps this direct experience of the divine is so powerful that it leaves us reeling with a deep feeling of connect… Mainly because it is what we really are at base… And thus we dedicate such intricate, beautiful and inspiring architecture – a testament to the divine nature of our being – to those ideals of God that many of us hold so high. Perhaps this is why some many of us find the Mandelbrot set so mesmerising… Perhaps Escher knew this deep down… ?
If you would like to see where I sourced the article, entitled “Uncoiling The Spiral: Maths And Hallucinations,” from, please click here.
If you’d like to learn more about Marianne Freiberger, then please click here.
Or if you’d like to learn more about M. C. Escher and his life’s work, please click here.
July 21, 2010
Having recently been to Dr Bruce Lipton‘s talk, entitled “The Biology Of Belief,” which was held in the Logan Hall of the Institute Of Education in London this last Saturday, the 17th of July 2010, I had reinforced the idea that we are nothing more than a bunch of atomic mechanisms, built from atomic polymers i.e. DNA, proteins, fatty acids, etc… all arranged into intricate cellular clusters, which – given the right circumstances – can function with amazingly natural flows of Being, demonstrating what we can only call, from a self referencing point of view, natural organic movements… And over the years we have – funnily enough – coined these flows to be “Life-Like.”
I really believe that when we begin to see Life in these terms i.e. that Life as we presently know it usually results from the complex interactions of the atomic machinery within an enclosed cellular body, which, if presented with more differentiated versions of itself, can build larger bodies from highly specialised cellular clusters… And then, once in place, out of all this unfolds a nonlinear biology/biochemistry of perceptive functions, all of which came about through the process of what we now know as ‘chaos’ – rather than the result of some divine intervention – and thus becomes nothing more than a complex, naturally occurring chaotic system that ‘intelligently’ reacts and responds, through effective behavioural patterns, to external environmental pressures and stimuli, precipitating survival habits that have been natural selected for… The behavioural patterns allow Life to survive in an ever changing environment, and the chaos inherent in our being affords us the ability to utilise the best survival traits that we can, one of which was the development of self-biased tendencies centred around a distinct notion of “self” and “body” that many of us seem to take for granted on a daily basis.
While I will eventually get around to discussing the reality and validity of the “self” in a future blog (something that is taking me much longer than I had anticipated)… In this blog I’d like try to discuss why this idea of viewing ourselves as a machine is a lot more natural and effective a notion about our “selves” than any previous egocentric notion about what we really are i.e. we were created by one or several Gods, in their own images to be special, etc… Certainly Dr Bruce Lipton’s analogy about us being a group of living cells which function within the confines of this body as a “community” of beings, each performing their own specific roles within the body’s mechanism i.e. just as governments regulate countries and their home economies, while police men arrest criminals, so do certain parts of the central nervous system function as regulators of heart rhythm and bodily temperature, while white blood cells kill of infections from ‘maliciously behaved’ bacteria… This idea of self-similarity within the patterns of Life that we see unfolding here on Earth across all scales and modes of Being will provide us with a very deep and intuitive understanding about the subtle and – what we tend to call – divine aspects of our Being, as well as showing us all how we interconnect and relate to this universally unfolding discourse..
Bearing in mind this ‘rule’ of self-similarity that seems to present itself within and throughout the whole of this universal dynamic so pervasively… And by viewing Life as a type of mechanisation… I am curious as to where – or from which level of scale – the emotive force of Life actually originates from? Is it at the level of the body i.e. does it directly and uniquely come from the sum of all its parts, where each individual part would be able to do nothing whatsoever by itself? Or is this trait of the emotive Life force buried deep down with in the cellular – or even the atomic – matrix? Certainly when we try to address what this experience of Life actually is and how it comes about we can hopefully begin to see it does not only belong to the body as a whole unit, but also comes from the various levels of functionality within the body i.e. at the cellular and atomic levels.
Just as Jung is concerned as much with the individual within society, as the individual is him/her “self” the measure of society, so too we can apply this analogy to the cell and body. Without the individual, society cannot function, let alone exist… And without the cell, the body cannot function or even exist. Life and its dynamism directly stems from the units that comprise the whole. These units, just as much as the whole, are all subject to the same forces and methods of development as each other i.e. those of nonlinear evolution. This ‘Life,’ and its essence, relies upon the parameters of these nonlinear, fractal eddies with their dynamics. These cellular bodies that make up our own larger bodies are driven by and made from the same underlying principles of naturally occurring algorithmic phenomena… Even though at first glance it might not be obvious that they are… But they are. Thus, if these algorithmic patterns reside across all levels of scale, shape and form, why shouldn’t we expect similar ‘intelligences’ to reside across all scales of these naturally occurring systems, whether at the human body’s level or a cellular level? Ultimately it’s up to you what you believe… But to function better I personally would like to know a little bit more about the processes that give rise this “I”; the processes that drive all of Life here on Earth – and possibly beyond too – rather than giving into dogmatic nodes of parrot fashioned understanding.
As Jung once wrote in “The Undiscoverd Self“:
Human knowledge consists essentially in the constant adaptation of the primordial patterns of ideas that were given us a priori. These need certain modifications, because, in their original form, they are suited to an archaic mode of life but not to the demands of a specifically differentiated environment. If the flow of instinctive dynamism into our life is to be maintained, as is absolutely necessary for our existence, then it is imperative that we remould these archetypal forms into ideas which are adequate to the challenge of the present.
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Our denominational religions with their archaic rites and conceptions – justified enough in themselves – express a view of the world which caused no great difficulties in the Middle Ages but has become strange and unintelligible to the man of today. Despite this conflict with the modern scientific outlook, a deep instinct bids him hang on to ideas which, if taken literally, leave out of account all the mental developments of the last five hundred years. The obvious purpose of this is to prevent him from falling into the abyss of nihilistic despair. But even when, a rationalists, we feel impelled to criticise contemporary religion as literalistic, narrowminded and obsolescent, we should never forget that the creeds proclaim a doctrine whose symbols, although their interpretation may be disputed, nevertheless possess a life of their own on account of their archetypal character. Consequently, intellectual understanding is by no means indispensable in all cases, but is called for only when evaluation through feeling and intuition does not suffice, that is to say, with people for whom the intellect holds the prime power of conviction.
In order to emphasise this re-equation that we need i.e. to understand that we are part of a whole ecosystem of Earth, just as a cell is part of the body’s ecosystem, it is here that I’d like to present an article which I read not too long ago in the New Scientist magazine… One that tackles this issue of where emotive Life comes from. When we see that Life’s organic flow resides across all levels of being i.e. atomic, cellular, bodily, biospherically, or even within the planet and its solar system, we might begin to understand that some of our older religious notions of the divine state of existence that We – that is, all Life – experience no longer need to be fantasised over or marginalised in any inaccurate way whatsoever. Now, through the doors of science, we can directly see the mechanisms of Life at work, and thus ‘understand’ the essence behind their patterns and interdependent interactions, all through which we gain the essence of our Being. Natural ordering comes from the patterns of chance and chaos, which give rise to development and originality within all universal systems, whether biological or otherwise. These systems, if given favourable circumstances/environments in which to start, can then begin the arduous process of developing into complex systems of environmentally perceptive and adaptive systems. Human beings are even beginning to use these recursive patterns – which have been called the “Thumb Print Of God” – in their technological developments i.e. to develop semi intelligent robotic systems that can learn fast and develop effective solutions to presented problems in ways that surpass anything we’ve tried or known before.
Thus, with these many new observations, I believe it is time to re-write our archetypal programming. Just as when I first saw the Mandelbrot Set on a postcard from a friend while at school and immediately recognised its tortuous, writhing flow as something so familiar and deeply ingrained in my being… So too do all ‘Gods’ leave this same feeling of familiarity… Of spirituality… And of deep connection to the whole… Here lies an answer to a new understanding… That self-similarity resides within all units of the whole… If you find intelligence within the body… Then why not within cell too… Or even in the atom… After all, one essence is usually found within the other, and so permeates through the entire being. Certainly atoms are just as discerning as human beings are… We all choose what we will or won’t react/socialise/breed with. Does this intelligence then go deeper? Intelligence that can be found within the proton, neutron and/or electron… And, if so, then why not even in the quark… Or the God particle…. Etc, etc, etc… ?
The Secrets Of Intelligence Lie Within A Single Cell
Late at night on a sultry evening, I watch intently as the predator senses its prey, gathers itself, and strikes. It could be a polecat, or even a mantis – but in fact it’s a microbe. The microscopic world of the single, living cell mirrors our own in so many ways: cells are essentially autonomous, sentient and ingenious. In the lives of single cells we can perceive the roots of our own intelligence.
Molecular biology and genetics have driven the biosciences, but have not given us the miraculous new insights we were led to expect. From professional biologists to schoolchildren, people are concentrating on the minutiae of what goes on in the deepest recesses of the cell. For me, however, this misses out on life in the round: it is only when we look at the living cell as a whole organism that wonderful realities emerge that will alter our perception not only of how single cells enact their intricate lives but what we humans truly are.
The problem is that whole-cell biology is not popular. Microscopy is hell-bent on increased resolution and ever higher magnification, as though we could learn more about animal behaviour by putting a bacon sandwich under lenses of increasing power. We know much about what goes on within parts of a cell, but so much less about how whole cells conduct their lives.
Currently, cell biology deals largely with the components within cells, and systems biology with how the components interact. There is nothing to counterbalance this reductionism with a focus on how whole cells behave. Molecular biology and genetics are the wrong sciences to tackle the task.
Let’s take a look at some of the evidence for ingenuity and intelligence in cells that is missing from the curriculum. Take the red algae Rhodophyta, in which many species carry out remarkable repairs to damaged cells. Cut a filament of Antithamnion cells so the cell is cut across and the cytoplasm escapes into the surrounding aquatic medium. All that remains are two fragments of empty, disrupted cell wall lying adjacent to, but separate from, each other. Within 24 hours, however, the adjacent cells have made good the damage, the empty cell space has been restored to full activity, and the cell walls meticulously realigned and seamlessly repaired.
The only place where this can happen is in the lab. In nature, the broken ends of the severed cell would nearly always end up remote from each other, so selection in favour of an automatic repair mechanism through Darwinian evolution would be impossible. Yet something amazing is happening here: because the damage to the Antithamnion filament is unforeseeable, the organism faces a situation for which it has not been able to adapt, and is therefore unable to call upon inbuilt responses. It has to use some sort of problem-solving ingenuity instead.
We regard amoebas as simple and crude. Yet many types of amoeba construct glassy shells by picking up sand grains from the mud in which they live. The typical Difflugia shell, for example, is shaped like a vase, and has a remarkable symmetry.
Compare this with the better known behaviour of a caddis fly larva. This maggot hunts around the bottom of the pond for suitable scraps of detritus with which to construct a home. Waterlogged wood is cemented together with pondweed until the larva has formed a protective covering for its nakedness. You might think this comparable to the home built by the testate amoeba, yet the amoeba lacks the jaws, eyes, muscles, limbs, cement glands and brain the caddis fly larva relies on for its skills. We just don’t know how this single-celled organism builds its shell, and molecular biology can never tell us why. While the home of the caddis fly larva is crude and roughly assembled, that of the testate amoeba is meticulously crafted – and it’s all made by a single cell.
The products of the caddis fly larva and the amoeba, and the powers of red algae, are about more than ingenuity: they pose important questions about cell intelligence. After all, whole living cells are primarily autonomous, and carry out their daily tasks with little external mediation. They are not subservient nanobots, they create and regulate activity, respond to current conditions and, crucially, take decisions to deal with unforeseen difficulties.
“Whole living cells are not subservient nanobots, they respond and take decisions”
Just how far this conceptual revolution about cells could take us becomes clearer with more complex animals, such as humans. Here, conventional wisdom is that everything is ultimately controlled by the brain. But cells in the liver, for example, reproduce at just the right rate to replace cells lost through attrition; follicular cells create new hair; bone marrow cells produce new circulating blood cells at a rate of millions per minute. And so on and on. In fact, around 90 per cent of this kind of cell activity is invisible to the brain, and the cells are indifferent to its actions. The brain is an irrelevance to most somatic cells.
So where does that leave the neuron, the most highly evolved cell we know? It ought to be in an interesting and privileged place. After all, neurons are so specialised that they have virtually abandoned division and reproduction. Yet we model this cell as little more than an organic transistor, an on/off switch. But if a red alga can “work out” how to solve problems, or an amoeba construct a stone home with all the “ingenuity” of a master builder, how can the human neuron be so lowly?
Unravelling brain structure and function has come to mean understanding the interrelationship between neurons, rather than understanding the neurons themselves. My hunch is that the brain’s power will turn out to derive from data processing within the neuron rather than activity between neurons. And networks of neurons enhance the effect of those neurons “thinking” between themselves. I think the neuron’s action potentials are rather like a language neurons use to transmit processed data from one to the next.
Back in 2004, we set out to record these potentials, from neurons cultured in the lab. They emit electrical signals of around 40 hertz, which sound like a buzzing, irritating noise played back as audio files. I used some specialist software to distinguish the signal within the noise – and to produce sound from within each peak that is closer to the frequency of a human voice and therefore more revealing to the ear.
Listening to the results reprocessed at around 300 Hz, the audio files have the hypnotic quality of sea birds calling. There is a sense that each spike is modulated subtly within itself, and it sounds as if there are discrete signals in which one neuron in some sense “addresses” another. Could we be eavesdropping on the language of the brain?
For me, the brain is not a supercomputer in which the neurons are transistors; rather it is as if each individual neuron is itself a computer, and the brain a vast community of microscopic computers. But even this model is probably too simplistic since the neuron processes data flexibly and on disparate levels, and is therefore far superior to any digital system. If I am right, the human brain may be a trillion times more capable than we imagine, and “artificial intelligence” a grandiose misnomer.
I think it is time to acknowledge fully that living cells make us what we are, and to abandon reductionist thinking in favour of the study of whole cells. Reductionism has us peering ever closer at the fibres in the paper of a musical score, and analysing the printer’s ink. I want us to experience the symphony.
by Brian J. Ford
Despite the authors final sentiments, I still feel that this reductionism does provide us with certain, otherwise unobtainable, clarities for understanding the similarities between the processes within and without… After all, one needs to know how to make paper and ink, and understand something about the musical scoring technique before they can write a symphony down for the future enjoyment of others…
To find out where I sourced this article from, please click here.
And to learn more about Dr Bruce Lipton and some of the brilliant work he is doing, please click here.
July 5, 2010
What can I say… Too much XAOS and a funny five minutes gave rise to these two little oddities.
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If you’d like to learn more about the M-Set and why our world is a fractal world, then please click here.
OR if you’d like to learn more about nonlinear dynamical systems, please read James Gleick’s “Chaos: The Making Of A New Science.” The first three people to E-mail me by clicking here will receive a free copy of the book! Just remember to enter the address you’d like the book to be delivered to…
May 24, 2010
The Tao produces all things and nourishes them;
it produces them and does not claim them as its own;
it does all, and yet does not boast of it;
it presides over all, and does not control them.
This is what is called “the mysterious Quality” of the Tao.
by Lao Tzu
May 23, 2010
The time has arrived… Synthetic life is no longer science fiction. It is now a ‘reality’ here on Earth… And man is its creator. In many ways this is an interesting piece of the puzzle as to how life arose here on Earth. But as we have seen in previous blogs here, it’s not that impossible to understand that self-similar patterns will end up repeating themselves i.e. man – having evolved from the primordial soup of chemicals, cells and organisms – is now trying to understand where his present ciurcumstance sprung from. While we can now play the role of a ‘creator’ – in the very modest sense of the word – we should also be wary of what this means in the greater scheme of things i.e. we are perhaps not as special as we might think AND what could this mean for future Life here on Earth!?
While I am sure many will jump on the band wagon about how this might possibly be introducing a new threat to Life, here on Earth, and so might even spell the end of our species too, by introducing a genetic machine capable of out performing the present Earth life-forms… A ‘theme’ from sci-fi movies of late… We shouldn’t be negligent that it might be able to help us with our own naive modes of living i.e. the devastation that we are all presently causing to this delicate ecosystem due to the corporate and mass consuming desire of our sensitive memetic and mental dispositions… But then again, we are at present living in an age of great denial. Even so, bearing all this in mind, the order within the chaotic flow of this Earth’s delicate and intricate ecosystem is way too hard to predict what it might yield in the near, let alone distant, future. No doubt this might spell the end for us… But then again, on our present route of habitation, are we not definitely spelling the end for ourselves soon enough?
Personally I welcome this discovery with open arms. And while I will treat it with an equal measure of caution, I will also be inclined to weigh up the positive aspects of what this new ‘technology’ might mean for mankind. After all, if it does nothing more than to show mankind just how easily reproducible Life surely is, and thus shows us that we are not really that special in the greater scheme of things – as we sometimes like to think we are… OR even if it forces many religious doctrines to understand that it does not take a ‘God’ or ‘Creator’ to implement Life as we know it, the effects of this invention will no doubt be far reaching to those of us who manage to hear about it.
My own goal, here within this blog, is to show those of us who are interested enough that Life is really nothing more than a pattern of molecules self-assimilating and self-replicating into ever advancing designs for functionality. The ultimate goal of evolution is empty of all meaning. The only meaning it has, is the meaning that we give to it. And this meaning is, at best, shaped by our present memetic drives and social circumstances i.e. in London society of medieval times the plague – a.k.a. The Black Death – that spread through London was falsely accredited to cats and dogs. Thus over 200,000 cats and 40,000 dogs were culled. This, no doubt, only served to exacerbate the problem, as the real culprit – namely the rat – now had even fewer predators to keep them in check and thus the fleas that lived on the rats, and the disease itself, spread like wild fire. The specific reason behind the culling of the dogs and cats during the plague of 1665 is still uncertain. But rumour had spread and, at best, we can be certain the Londoners made their decision based on what they believed to be true at the time.
When we look at Life today… We have some idea as to what its essence is derived from. Back in medieval times, God certainly would have figured somewhere in the spirit and soul what Life is. Today, science has shown us that Life is nothing more than a process of highly complex chemical interactions which occur within bodies of organic structures. These bodies, with their ability to understand and modify their behavioural patterns, have – along the way – attained many delusions, mainly via modes of self-realisation and self-importance. And this means that, on the whole, Life is liable to act from this place of delusion – which is centered on attachment to the idea of self – rather than from a place of compassion and non-attachment. If it wasn’t for the delusion, then all those cats and dogs would have been spared during the London plague of 1665.
Saying that… The key to our existence, and to evolution on the whole, is not to get too bogged down in the finer details of what our existence means… Rather it is to remove this self-desiring attachment and open our hearts and minds up to the world around us through a process of developing compassion through a keen understanding about all living beings here on Earth, noting, seeing and understanding how interconnected we all really are to one another.
If we reflect honestly enough with ourselves and others, we will hopefully arrive at similar understandings to one another… None of us own this experience that we call Life. Life is a natural pattern of unfolding that chemicals do when given half the chance, regardless of what solar-system they arise in. And We i.e. all Life, are nothing more than a result of this pattern. Call it “God,” call it “Nature,” call it what-ever you want… The patterns are there – they have been there forever – and nothing is certain within them, mainly as they are so sensitive to initial conditions. This is the way with nonlinear dynamical systems. Why talk about “what-ifs” when we understand so little about the system itself? Just as with all nonlinear systems, our lives are full of uncertainties, and we can never make any prediction with absolute certainty and keep an honest mind. In my humble opinion, this technology that Venter has created is nothing more than the fractal essence of our Life’s system recreating – or rather, reiterating – itself into ever more defined and refined aspects of understanding itself. Once we understand this pattern better, I believe we can begin to make moral decisions based on an interconnected understanding. This understanding – while it will only be the best possible mode of understanding for the present moment – will still afford us great insight into what we are… And, thus, give us all a better realisation as to how we should live and behave i.e. without over consuming the Earth’s resources, not polluting and producing beyond levels of what the environment might be able to handle, to limit our population growth to prevent over consumption, to understand our instinctual drives and, thus, to notice what we are doing to the planet that we call “home,” etc… I believe Venter’s work is part of developing this understanding further.
So, with that out of the way, let’s look at what Venter once was planning to set out to do…
And after all that Venter and his team have now arrived here…
Craig Venter Unveils “Synthetic Life”
Craig Venter and team make a historic announcement: they’ve created the first fully functioning, reproducing cell controlled by synthetic DNA. He explains how they did it and why the achievement marks the beginning of a new era for science.
More about Craig Venter:
Craig Venter, the man who led the private effort to sequence the human genome, is hard at work now on even more potentially world-changing projects.
First, there’s his mission aboard the Sorcerer II, a 92-foot yacht, which, in 2006, finished its voyage around the globe to sample, catalouge and decode the genes of the ocean’s unknown microorganisms. Quite a task, when you consider that there are tens of millions of microbes in a single drop of sea water. Then there’s the J. Craig Venter Institute, a nonprofit dedicated to researching genomics and exploring its societal implications.
In 2005, Venter founded Synthetic Genomics, a private company with a provocative mission: to engineer new life forms. Its goal is to design, synthesize and assemble synthetic microorganisms that will produce alternative fuels, such as ethanol or hydrogen. He was on Time magzine’s 2007 list of the 100 Most Influential People in the World.
In early 2008, scientists at the J. Craig Venter Institute announced that they had manufactured the entire genome of a bacterium by painstakingly stitching together its chemical components. By sequencing a genome, scientists can begin to custom-design bootable organisms, creating biological robots that can produce from scratch chemicals humans can use, such as biofuel. And in 2010, they announced, they had created “synthetic life” — DNA created digitally, inserted into a living bacterium, and remaining alive.
To find out more about Craig Venter and his institute dedicated to understanding the social impact of his scientific work, please click here.
I have already written several blogs about Life… You know, the scientific aspects of Life… Trying to understand it all a bit better… Asking really ‘silly’ questions about things like “When Does Life Really Become Life?” Or “What Is Life?” All the way through to “Just How Did Life Seed Here On Earth?” Thrown in with clangers like “Might We Be Able To Create Life In The Laboratory To Recreate Those Initial Conditions That Gave Rise To Life As We Know It Here On Earth?” And, would you believe, I even thought I could attempt to discuss “What This Experience Of Being Alive Really Is And How It Came About!” Wow… What delusions of grandure, eh? Lock me up and throw away the key…
Anyway… Would you believe, after all that, I’m back at this door again??? Trying to understand whether it’s as obvious as it seems… As obvious as it feels, even… That Life naturally happens, whether you want to believe it or not, independently and regardless of any divine creator or omnipotent god that we care to imagine. This time someone else has opened the doorway to another side – and another aspect – of this reality that we think we understand so well… They’ve prised it open just that little bit further than before… Just ever-so-slightly more… And with that, what we can now see shinning back through that widening crack, would you believe… Is that it seems self-replicating chemicals can evolve into lifelike ecosystems!?!? Similar to those found here on Earth!?!?
So… Along with the fractal geometry that lies hidden within the heart of our cellular make up… And what with all the other properties of the universal star stuff of atoms… Which are like Lego building blocks… Isn’t that almost enough to allow us to begin to see past the delusions of the yester-year? Can’t we just accept that life is a natural aspect of universal unfolding? That we all come from natural cosmic phenomena? And one day we will all go back there…
Well… I certainly can’t tell you what to think. So I’ll just have to let you decide for yourselves on that one…
But first, before you make up your mind, just have a “butchers-hook” at this…
Self-Replicating Chemicals Evolve Into Lifelike Ecosystem
Life makes more of itself.
And now so can a set of custom-designed chemicals. Chemists have shown that a group of synthetic enzymes replicated, competed and evolved much like a natural ecosystem, but without life or cells.
“So long as you provide the building blocks and the starter seed, it goes forever,” said Gerald Joyce, a chemist at the Scripps Research Institute and co-author of the paper published Thursday in Science. “It is immortalized molecular information.”
Joyce’s chemicals are technically hacked RNA enzymes, much like the ones we have in our bodies, but they don’t behave anything like those in living creatures. But, these synthetic RNA replicators do provide a model for evolution — and shed light on one step in the development of early living systems from on a lifeless globe.
Scientists believe that early life on Earth was much more primitive than what we see around us today. It probably didn’t use DNA like our cells do. This theory of the origin of life is called the RNA World hypothesis, and it posits that life began using RNA both to store information, like DNA does now, and as a catalyst allowing the molecules to reproduce. To try to understand what this life might have looked like, researchers are trying to build models for early life forms and in the process, they are discovering entirely new lifelike behavior that nonetheless isn’t life, at least as we know it.
As Joyce put it, “This is more of a Life 2.0 thing.”
The researchers began with pairs of enzymes they’ve been tweaking and designing for the past eight years. Each member of the pairs can only reproduce with the help of the other member.
“We have two enzymes, a plus and a minus,” Joyce explains. “The plus assembles the pieces to make the minus enzyme, and the minus enzyme assembles the pieces to draw the plus. It’s kind of like biology, where there is a DNA strand with plus and minus strands.”
From there, Joyce and his graduate student Tracey Lincoln, added the enzymes into a soup of building blocks, strings of nucleic bases that can be assembled into RNA, DNA or larger strings, and tweaked them to find pairs of enzymes that would reproduce. One day, some of the enzymes “went critical” and produced more RNA enzymes than the researchers had put in.
It was an important day, but Joyce and Lincoln wanted more. They wanted to create an entire population of enzymes that could replicate, compete and evolve, which is exactly what they did.
“To put it in info speak, we have a channel of 30 bit capacity for transferring information,” Joyce said. “We can configure those bits in different ways and make a variety of different replicators. And then have them compete with each other.”
But it wasn’t just a bunch of scientist-designed enzymes competing, like a miniature molecular BattleBots sequence. As soon as the replicators got into the broth, they began to change.
“Most of the time they breed true, but sometimes there is a bit flip — a mutation — and it’s a different replicator,” explained Joyce.
Most of these mutations went away quickly, but — sound familiar? — some of the changes ended up being advantageous to the chemicals in replicating better. After 77 doublings of the chemicals, astounding changes had occurred in the molecular broth.
“All the original replicators went extinct and it was the new recombinants that took over,” said Joyce. “There wasn’t one winner. There was a whole cloud of winners, but there were three mutants that arose that pretty much dominated the population.”
It turned out that while the scientist-designed enzymes were great at reproducing without competition, when you put them in the big soup mix, a new set of mutants emerged that were better at replicating within the system. It almost worked like an ecosystem, but with just straight chemistry.
“This is indeed interesting work,” said Jeffrey Bada, a chemist at the Scripps Institution of Oceanography, who was not involved with the work. It shows that RNA molecules “could have carried out their replication in the total absence” of the more sophisticated biological machinery that life now possesses.
“This is a nice example of the robustness of the RNA world hypothesis,” he said. However, “it still leaves the problem of how RNA first came about. Some type of self-replicating molecule likely proceeded RNA and what this was is the big unknown at this point.”
I mean… Seriously… Throw in a bit of self-similarity, along with many, many, many lashings – so many that it might well ‘seem’ to boarder with infinity – of complexity, and can we surely not begin to see obvious parallels between how human life arose on Earth from the “primordial soup” and those three “clouds of winners” that arose from the broth of enzymes? Aren’t these really just similar phenomena unfolding across vastly different scales of both size and time? A vast ocean of atomic interactions that occur upon the closed ecosystem that we call Earth vs. another closed ecosystem of much smaller proportions i.e. the very humble sterile laboratory flask? Are these not self-similar patterns… Patterns that elude toward a subtle and intrinsic ideal of temporal universal unfolding?
Dare I say it… Could we even begin to call this phenomenon “GOD“!? Well… If you want to equate the Mandelbrot set, via modes of analogy, to the thumb print of God, primarily because we observe these fractal like patterns almost everywhere within nature… And, thus, we begin to use them to describe God as Spinoza did i.e. “God, or Nature” as an ‘unknowable’ and ‘unfathomable’ reality of the whole of existence/creation, then I just might possibly begin to agree with you.
To find out where I sourced this article from, please click here.
And to read more about Professor Gerald Joyce, please click here.
OR to read more about the amazing research being done at the Scripps Research Institute, please click here.