** Nature's Game **Nature likes to play hide and seek with us. It seems the more we try to unlock its mysteries, the more elusive it becomes, hiding behind ever deeper layers of complexity. Yet, at the same time beckoning us to follow along by revealing wisdom we can understand at the level we have reached.
We are seeing this game when probing the atom. Endless, ever more dense amalgamations of all sorts of particles are discovered as we smash the atom with faster and faster colliding particles.
So too in the fundamental science of life - biochemistry. Things are getting more and more complicated every decade as our understanding of the cell increases. Anyone working in this area can hardly fail to see this. Of course it can't be infinitely complex.. or can it?
Let us take a tiny glimpse into this fascinating little world of the cell, visiting a day in the life of a protein molecule. It is here at this most fundamental level of life, that nature begins to whisper to us its secrets.
We shrink a thousand, thousand, thousand times, descending into the domain of the cell. Looking around we notice a world resembling some sort of advanced alien civilization. In every direction robot machines perform all sorts of biological functions.
Everything appears highly organized and of utmost efficiency. The robot machines are as small as can possibly be, yet remarkably complex. Each consists of thousands of atoms intricately folded in specific three dimensional configurations.
As we approach the spherically shaped nucleus of the cell we notice strands of information molecules snaking out from its many pores.
We notice a typical information strand is about 1000 DNA letters long. In our computer terms this is roughly 250 bytes of data; enough information to encode a 250 letter ascii password. To crack this password has odds of 1 in 10^600, or for all practical purposes infinity time.
Approaching a nuclear pore, we are scrutinized by security checkpoints. Going through, and entering the nucleus, we see the endless coils of the DNA information bank all neatly stacked and organized.
We notice messenger molecules coming in and out of the pores. Each one locating the exact section of DNA it was sent to fetch. It unwinds it and transcribes a copy and begins to snake out the nucleus.
Following one strand out, we observe large editor machines (spliceosomes) suddenly assembling and latching on to the messenger strand.
The editor machines edits out specific parts of the strand preparing it for factory machine language. After their work is done, a mobile factory arrives and begins to work on the information strand.
All sorts of helper machines and materials arrive at the right time in the right quantity to coordinate the factory assembly.
We watch as atom by atom, molecule by molecule, the new robot machine's components are assembled.
After completion, chaperone machines help the new protein fold into the right three dimensional structure so that the protein can become activated.
The folding of a protein is not a chemical reaction, with a bond breaking here and a new one forming there. It is more like the weaving of an intertwined molecular pattern, the stability of which is defined by innumerable forces between atoms in a wonderfully holistic manner. Our computer simulations cannot yet solve the folding code that is behind the molecular dynamics, as to work though just 50 milliseconds of folding would take even the fastest computer around 30,000 years.. This little 250 byte algorithm packs quite a wallop!
Localizer machines then usher the new protein to its destined work area. Along the way all sorts of enzymes slap on chemical tags to the new protein for many different reasons.
The protein then joins the army of molecular machines, performing its task with military discipline for the rest of its life. Alternatively it is assembled as a component of larger order molecular machines.
As we begin to leave, we notice a great commotion beginning. The rush hour starts as the cell prepares to reproduce. Hundreds of thousands of different types of simple proteins and higher order machines are formed along with all sorts of other structures and substances.
We quickly eject out so as not to get caught up in the avalanche of processes.
Looking back from afar we notice a mad chaos, a raging sea of countless processes. It seems the cell is about to self-destruct until a pattern emerges, and a greater pattern, and yet greater until the sea calms down and there emerges two identical cells.
This process repeats until higher order patterns emerge and a functional multi-cellular system such as an organ or leaf emerges. Each component assembled by these molecular machines, atom by atom, molecule by molecule.
This my friends is the world of cells. Fortunately, we have some scientific animations worth more than a thousand words giving a wondrous glimpse into this hidden world. Here is one on the basic process of protein formation common to all living things. It appears like some sort of wacko sci-fi movie but this is real and even highly simplified.
Here is another animation on the mysterious editor machines called spliceosomes. While we have learned a great deal about them much of their details remains a mystery. Video here.
It seems despite our decades of research we are still very, very far away from grasping the nature of the cell. On the contrary, the more we discover, the more we find hints of new and strange worlds of bewildering complexity awaiting us.
Here's what Dr. James A. Shapiro of the University of Chicago discovered about protozoa (single celled micro-organisms) .
A cell under stress will splice its own DNA into over 100,000 pieces. Then a program senses hundreds of variables in its environment and then re-arranges those pieces to produce a new, better, evolved cell.
That's pretty impressive, no? What if your Windows software could do that? Instead of downloading another darn service pack or new upgrade, it could just reprogram itself and upgrade itself as needed. Not bad, no?
Let us now watch these proteins in action.
>> Next: Horrendous Complexity
-  http://physics.stackexchange.com/a/81284/24873 return to text
-  http://www.idtdna.com/pages/docs/educational-resources/molecular-facts-and-figures.pdf return to text
-  http://pharmaceuticalintelligence.com/2015/09/09/protein-folding/ return to text
-  http://cosmicfingerprints.com/new-theory-of-evolution/ return to text