This site has been wikified (http://mbscientific.org/wiki/Main_Page)
For the new and improved version see : 

1.1 - http://mbscientific.org/wiki/Elementary_Particles 

1.2 - http://mbscientific.org/wiki/Creation_of_the_Universe 

1.3 - http://mbscientific.org/wiki/Chaotic_Morphological_Flows

ch1- Creation of elementary particles and the cosmos

1- Starting point of Morphological Flows: Elementary Particles- 

As we saw in the introductory piece, morphologies flow up in the order of hierarchical complexity. So naturally at the  bottom we expect to find the simplest of morphologies. And we do, they are elementary particles and they bind to form  everything in the periodic table of elements as we will see in the next chapter.

Photon is made up of kinetic energy, that is all of its energy is represented in its speed. That is why it is thought as an axiom that nothing can move faster than the speed of light. If all of the energy in light goes to build up its speed, there is no more kinetic energy left to add on to that speed. That being the case, our normal notion of time and space runs into a serious problem. Suppose I am moving forward at the speed of light, looking forward at a mirror. The only way for a photon leaving my face to reach the mirror is for it to move faster then the speed of light, i.e. the speed of itself. Well, if photon is all kinetic energy and there is no more energy to add to its speed, then the photon should sit stationary on my face and never move forward. But that wouldn't do either because for the photon to be a photon, its electrical and magnetic oscillations must induce one another at the speed of light. So the photon must leave my face going forward at the speed of light, and I am also going forward at the speed of light. For those statement to both be true, the tick of time must literally stop. If the tick of time stops, I can move forward at the speed of light and a photon can leave my face forward at the speed of light as well. That is only half of the problem. If from a photon's perspective it maintains its speed of say X meters per second, and there is no per second (there is no second, time dilates to infinity), then there must be no meters as well (space shrinks to zero). If this confuses the hell out of you, good, it is supposed to. I am getting to a point, bare with me. This paradox leads to some familiar examples, lets give one.

Lets consider the twins paradox. One twin (Jim) is on earth and his brother (John) travels on a spaceship at near the speed of light holding a clock and a yard stick. To Jim, John's yardstick shrinks and his clock's ticks expand. In fact from Jim's perspective, at the speed of light, John's yardstick shrinks to zero and his time clock takes an infinity to tick (stops all together). So should John come back he'll find that his brother died forever ago, while he aged next to nothing. 

These confusing examples are called paradoxes. Blame Einstein for them, I am just paraphrasing. Of course these paradoxes can't really happen because at the speed of light both I and John are all photons and no matter. And that is the whole point. From a photon's perspective, our concept of space-time is irrelevant. 

Sorry, but I have to confuse you just a little longer to make my point. Photon's energy, though all kinetic, manifested in speed, still varies. Radio waves have less energy than infra-red light, which has less energy than ultra-violet light, which has less energy than x-rays, which have less energy than gamma rays. In these cases the energy of a photon is manifested in its frequency, the higher the energy of a photon the higher its frequency. Again, blame Einstein for this (he got a Nobel Prize for this one). As the energy of a photon gets higher and higher in the gamma ray range, that is when it splits into particles and anti-particles (matter-antimatter). When say matter is born in such a manner, some of its mother photon's all kinetic energy manifests itself in its body as potential energy (gravity, charge) and the rest if left as its manifest kinetic energy (speed). But now its speed is smaller than the speed of light. At such a speed the tick of time can exist, the notion of a measurable space can exist. It is only when particles are created that their speed drops to below the speed of light. Only then space-time is born in earnest. But even then it is nothing like you and I know.

You see at those speeds and scales, particles live in a quantum world. In that world a particle is like a blob of energy that occupies a space-time range, not a fixed point. A particle is here and there, sooner and later, all be it in extremely small space-time scales. It is when particles bind to form atoms (proton-neutron-electron combinations) that the speed of the atom speed drops to something closer to ours. And as atoms bind to create molecules (the stuff all around us), speeds come in our ball park range, our familiar notion of space-time comes to form. 

Ok all of that was the setup, here comes the punch line. These concepts sound out-of-worldly to us because they are! But space-time transform (known as Lorentz transform) is regularly used in particle physics calculations. And we owe every digital device to the knowledge of the quantum world (quantum mechanics). These concepts simply don't register within our notion of what we normally consider as physical, i.e. that which registers on our 5 senses. And that is the whole point: there is such a thing as Inherent Reality, the domain in which things exist of their own volition, regardless of whether we perceive them or not, that reality as we have seen is abstract. Then there is our Perceived Reality, that is the portion of the Inherent Reality that registers on our minds and our senses. That portion which registers on our minds, we form abstractions with. As we form abstractions (e.g. quantum theory) and corroborate them and do calculations with them and build devices with them (e.g. computers), then our notion of reality expands, our Aperture of Perception expands. So inherent reality is abstract, the subset of it that registers on our minds (and are commonly corroborated) and our 5 senses form our known reality, our perceived reality. In fact when we talk about reality, we are really talking about our perceived reality.  We will cover our expanding aperture of perception and how that comes about organically in much more detail later.

Ok back to the matter (pun intended)  at hand. To the best of our understanding thus far, we have the following elementary particles table:

Continuing the tale, the hydrogen clouds condense to form galaxies. The stars in the galaxies go on to produce the basis of the matter in the universe that we see today (as you will observe in the next chapter). And that is the realm of cosmology, understanding the big picture. So lets cover that next.

2.1- Creation of the universe- The Big Bang/Inflationary model- The prevailing theory says that all energy-matter in our space-time bubble was created in a Big Bang event. The event created an inflating space-time bubble full of super-hot elementary particles. As the bubble expanded, the particle soup cooled down to the point that the present protons, neutrons and electrons had a chance to bind and create elemental atoms of hydrogen. Massive hydrogen clouds, under gravitational attraction, coalesced to form galaxies (Source: http://www.gsfc.nasa.gov/topstory/2003/0206mapresults.html).

Let's start with some observations and see how they lead to the big bang and inflationary models for the creation of the universe. The main observation, now termed Hubbell's law (named after the person who made the observation), is that galaxies are moving away from each other, i.e. the universe is expanding. He did that by looking at the radiation signature of known elements like hydrogen in distant galaxies. Say, hydrogen when thermally excited radiates at a given frequency. If the object is moving towards you, the wavelengths squeeze together making it appear a bit bluer, if it moves away from you the opposite happens and it appears redder. We call this the red shift. Almost every thing is red shifted regardless of what direction we look, meaning everything is moving away from everything. The exception is nearby galaxies (in galaxy groups) that are relatively moving towards one another, but all distant galaxies appear to be moving apart.
So imagine in your mind, a movie of these objects moving away from each other. Now reverse the movie and look at it going backwards in time, everything will be moving towards each other. The logical conclusion would be that at some particular point and time every thing would come together. The big bang theory then proposes that it all started with a big bang that started the movie.
Another observation that lends credence to the big bang idea is that of the cosmic background radiation. No matter in what direction we look, we find a radiation signature that corresponds to a temperature of ~3 degrees Kelvin. One explanation is that it is the after glow of the big bang event. So you had this initial explosion. Then everything cooled down (other than the regions where stars formed and heated back up again). And what we see today is the uniformly cooled aftermath of the big bang event that after some 14 billion years is now at a uniform ~3 K, regardless of where you look.

Big Bang Theory explains a lot of the observations but not all. You see, all matter at any given temperature vibrates. That motion results in it radiating at a given frequency. We can detect any frequency, so theoretically we should have a radiation signature of anything (any matter that is out there). There in is the problem, as we are about to see.

2.2- Dark Energy and Dark Matter- Suppose Big Bang is a given, it did explode 14 billion years ago and everything started to expand out as the result of the momentum of the explosion. So you have all these objects receding from one another. The only force exerting on them will be their mutual gravitational attraction pulling them towards one another, thereby counteracting the initial outward momentum. So over time you expect that the rate of expansion will slow down. People started to look at certain super-novas at large distances away, expecting to see slowed expansion the further out they looked. There would be more matter between us and the observed object, therefore more gravitational attraction, therefore more of a slow down. And taking that logic to conclusion, the objects farthest away, say 14 billion light years or so, would have all of the gravitational force of the universe acting on it and pulling it back and very little matter in front of it to attract it forward. At least that's what people thought. Well, the observations showed the exact opposite result. Not only distant objects aren't slowing down, the further out we look the more they are speeding away. And that is true for all directions. So there is something that is continually pushing these objects away from one another, something with negative gravity. And, this stuff, called dark energy, is evenly distributed because its effects are uniform regardless of what direction we look at. The problem is that we can't detect it with anything so far. The only effect we observe is the repulsive gravitation that I just described. So it is not matter, because that has positive gravity, pulling other matter towards it. It's not pure energy, ala photons, because that has no mass and no gravitation. Somebody had to call it something, so they call it dark energy.

And here is another observation. When we look at some galaxies, say our own milky way, we find most of the stellar matter bunched up around the core. By contrast, you have relatively little star formation in the outer bounds. Again if gravity was the only force in effect, then you'd have very fast rotation in the middle and relatively little rotation out on the perimeter. Think of your kitchen sink. When you have a lot of soap water (for those of you that have actually washed dishes), you see fast rotation near the drain and relatively little rotation on the outside. You'd expect that. You only have one force, gravity, effective at the drain and exerting most force on the nearby material. We don't see that in the case of the spiral galaxy of our example. The stars on the perimeter are moving at the same relative rate as the stuff in the middle. The outer stars don't drift off. They keep formation. So some other force is hemming them in. But nothing can be detected that could exert such a positive gravitational force. The same thing holds when we look at galactic groups and clusters, e.g. the Virgo super-cluster. We see all of these far-flung galaxies in the cluster and they keep formation. But there aren't enough observed matter in the cluster to pull them together. And if one calculates the amount of matter that it takes to exert the gravitational force to pull the galaxies together, one comes up with far more than the observed matter that is accounted for. So there is something out there, in vast quantities, that doesn't radiate and has positive, matter-like, gravitation. So people started calling it dark matter.

There is a whole cosmic industry trying to theorize the nature of dark energy-dark matter. And it is noteworthy that per our current theories and observations, it is thought that that dark stuff comprises some 90 percent of the energy budget of the universe. Some call this the golden age of cosmology because there is so much to be discovered. I personally call it the nickel age of cosmology because there is little money in it.

2.3- Galaxy Formation- Regardless of the theories of the creation of the universe and the problems therein, there are these elementary particles that start off the morphological flows. Among them, the stable electron-proton-neutrons bind to create the simplest atom, hydrogen, in vast quantities of gasses. As gas clouds become denser due to gravitational attraction they heat up and eventually coalesce to form proto-galaxies. Proto-galaxies are dense gas (mainly hydrogen) clusters that act as stellar nurseries. As proto-galaxies settle, we end up with the galaxies that we observe today. We see spiral galaxies, lenticular galaxies (spiral galaxies with missing spirals), elliptical galaxies that look like cosmic footballs, and irregular galaxies (pictured below in that order, source: http://www.seds.org/messier/galaxy.html)

- Globular star clusters, large, compact aggregates of hundreds of thousands of stars, often the oldest stars in the galaxy.

- Stellar nebula remnants - As the stars develop, many of them leave nebulous remnants (planetary nebulae or supernova remnants) which then populate the galaxies.

- Outer-bound regions- the interstellar gas and dust tends to accumulate in clouds near an equatorial disk and flatten out at the outer regions, most conspicuous in spiral and lenticular galaxies.

- Interstellar clouds - huge diffuse nebulae where clusters of stars are formed.

- Nucleus- A rather dense galactic nucleus, which is somewhat similar to a super-large globular cluster. In many cases, galactic nuclei contain super-massive dark objects, which are often considered as Black Hole candidates.

3- Conclusion - Chaotic Morphological Flows- Note that the nature of creation is chaotic from the start. All of these elementary particles formed a massive particle soup that interacted, bonded and annihilated in a variety of ways. Of all of those interaction pathways, the resulting stable proton-neutron-electron combination survived and all of the unstable ones didn't. This binding of energy-matter to create morphologies is the essence of morphological flows. In the signature of Morphological Flows we see polar opposite forces in action right from the get go. Strong nuclear forces bind protons and neutrons to form atomic nuclei, whereas weak atomic forces result in nuclear decay. Electricity and magnetism form polar opposites. Even gravity apparently has a recently discovered anti-gravity corollary. And as we'll see in the upcoming chapters, the flow marches right on, creating atoms, molecules, organic material, cells, the tree of life, collectives, groups and societies. But through out all of these evolutionary realms, construction and destruction, interactivity and the resulting chaotic dynamics prevail, leading to stable entities that survive and unstable entities that die off. That is the case for particles, atoms and molecules. It is the case for Darwinian-biological evolution. It is the case for human, anthropological evolution. And it is the case for the evolution of ideas within individuals, societies and cultures.
Another inescapable conclusion is the abstract nature of Inherent Reality, the universe itself. As we saw, in the quantum world and the cosmic world things are very different from our notion of what is physical. But if you accept the abstract notion of physics, and understand that you can perceive the abstract through the minds eye, then once the abstractions are corroborated the aperture of perception expands, the notion of what is physical expands. And that is the key to our morphological growth, both individually and collectively.

Definition- Zero Point- going down the morphological hierarchy of complexity, we can trace it all the way down to the photon, the particle/wave of simplest morphology. But where did that come from? For the lack of a better word lets call it the zero point.
Then again in the cosmos we could trace everything down the hierarchy of complexity to the origin of the big bang, the same zero point that kick started the morphological flows, starting with elementary particles.
But it gets more interesting. If the law of conservation of energy holds, the collection of elementary particles and the space-time bubble that they created and that we happen to be a part of, is a subset of that zero point. So the zero point didn't go through a disappearing act in the big bang event; rather, it manifested (part of) its energy into what has by now become our familiar space-time bubble. So according to that logic, the zero point is in fact the super-set, of which our space-time bubble is a subset. 
But why just one big bang? Why not more? Why not many space-time bubbles? The string theory/M theory folks are having a field day with that.
But we know there is at least one space-time bubble, we are in it! It doesn't matter, one bubble or many, logic dictates that they are all subsets of the zero point. The point is that zero point is a container, it is to us both zero, infinity and everything in between.
The implication is that morphological flows are manifest properties of the zero point embodying the Inherent Reality that surrounds us, part of which we can perceive through our aperture of perception. And the expansion of our aperture of perception is the process by which we evolve. This entire body of work, tracing the morphological flows, is as much the trace of our own evolution.

Chapter Key: Morphological Flows, entities going through functional constructs thereby creating more complex entities with more complex functionalities:

Zero Point == construct? ==> Photons == construct? ==> particles (electron-proton-neutron) == construct (Electro-Magnetism) ==> hydrogen, helium clouds == construct (Gravitation) ==> galaxies, stars and planets

Links:

Article on big Bang Theory

Article on Inflationary model by Alan Guth

An article on a recently discovered proto-galaxy

A good Galaxy catalog - the Messier Catalog

Galaxies and the Universe- a WWW course

A nice, readable, article on elementary particles

An entire site dedicated to elementary particles

Super-string theory detailed- Acrobat PDF document

String theory's version of cosmology: M Theory

A good primer on astrophysics, nuclear physics and quantum mechanics, among others