Sunday, December 2, 2012

The Human Genome is Chaotic

Premature Predictions proven incorrect. 
The story of the human genome is no longer about gene structure. To say that our enthusiasm was premature and our predictions bombastic after the human genome was mapped is an understatement. The evolutionary unit is not the gene—though genes do compete—but the complete cell or organism. Cell functions depend on the millions of regulatory interactions between the protein-coding genes, which comprise less than 2% of the genome, and the non-protein-coding genes which form the regulatory mechanism of gene expression. The recent ENCODE studies have given a glimpse of the immense complexity of the network of interrelated biofeedback loops of gene repressors and de-repressors which comprise an active, non-linear system. It is clear that we have only scratched the surface and that the genome will be shown to be even more complex.

Fractal Geometric Properties. 
One of the most significant discoveries in genomics is that the genome (1,2) as well as the cytoplasm (3) have chaotic fractal properties.  
As described in previous posts, fractal geometry (an element of chaos theory) is characterized by self-similarity (the bifurcating branches of a tree, the circulatory system in the body, the neural network of brain cells, etc.), and self-similarity at various levels of magnification (e.g. main arteries to smaller arteries to arterioles to capillaries). Fractals can also occur in time. The rhythm of heart beats has been shown to behave in a fractal manner (4) as well as that of the brain (5).

Butterfly Effect. 
Another characteristic of a non-linear chaotic system is one that is sensitive to initial conditions (the Butterfly Effect) which means that a small change in the initial conditions can have a large and unpredictable effect later on. The genome is shown to have this property—a single mutation in either a regulatory gene or the gene itself can have unpredictable and possibly catastrophic consequences in the intricate biofeedback loops that comprise the whole system.

Chaos Rules.
One of the more interesting ideas of a chaotic system is “strange attractors,” mathematical nodes to which a non-linear network continuously returns in similar though not identical patterns. The pattern of evolution, as will be discussed in a future post, shows signs that it is not random but actually has chaotic attractors toward which it progresses.

Outside Influences Inside.
The chaotic, non-linear workings of the living cell is a system in which thousands of biochemical processes are going on at once in a way that is not random and yet not totally predictable. The system balances on a tightrope between total linear predictability on one side and total randomness on the other. This makes the system more robust and allows the cell to react to external environmental forces quickly while maintaining its core structure and functions. A system that is linear (non-chaotic) becomes static and rigid and is thus more vulnerable to external stimuli because it is unable to quickly adapt to a changing environment.

It's Natural.
It has already been shown that many if not most parts of nature are chaotic in structure and function (mountain ranges, weather, cloud formation, snowflakes, the structure of life forms, traffic patterns, even the universe itself). Proteins also have been found to have a fractal architecture. Now we see that even the genetic material itself, the code of life, is fractal and chaotic.

How Bizarre is that?
What does this all mean? This realization allows us to look at life in a very different way, giving us a profoundly new and revolutionary understanding of the structure of life and, as I will discuss later, of evolution. The universe itself is not totally random as previously thought but follows fractal laws and a chaotic infrastructure. Large things are made of similar small things. Patterns of both natural and even human (psychological) behavior follow the same chaotic architecture. Even quantum mechanics is now being married to chaos theory to explain some of the most bizarre features of quantum physics. More on this later.

1)    Lieberman, et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome, Science. 2009 October 9; 326(5950): 289-293
2)    Moreno et al. BMC Genomics 2011, 12:506
3)    Aon MA, Cortassa S. (1994) On the fractal nature of cytoplasm. FEBS Lett. May 9; 344, 1-4
4)    Sharma V. The Open Cardiovascular Medicine Journal, 2009, 3, 110-123
5)    Kitzbichler et al., Broadband Criticality of Human Brain Network Synchronization. PLoS Comput Biol 5(3): e1000314. doi:10.1371/journal.pcbi.1000314