This really isn’t “Personal Computing”, but I don’t think the appropriate Forum cross posts from JU. However, I’m not going to try to figure it out.

Honestly, I’ve waited for this for a decade… more… since college, really.

I’d been waiting for the weekend to publish this. I can’t. It’s too big. It is to Medicine what “Dark Matter” is to modern physics.

Medicine has been progressing rapidly, but no one could really explain the effect of the genes whose alleles (mutant genes) caused many complex diseases. Why should some function and others not, and what controls the sequence of function?

Since 2003, the “Encode” project has been running, and the amount of data generated is truly huge. “Encode” is the project which deciphered (to a large, but not complete extent) what goes on in the nucleus of cells. It involved 440 scientists and 32 labs around the world.

It turns out that what appeared to be “junk’ DNA wasn’t junk at all, and that 80% of it is quite active. These small DNA sequences were thought to be junk because they were located at quite a distance from the genes they were found (now) to turn on and off.

To understand this very complex picture, you have to realize that each cell I’m discussing has the ‘normal’ (2N) amount of chromosomes. That means I’m not talking about eggs, sperm or red blood cells. The first two have N chromosomes (half the number) and red blood cells have none.

The amount of DNA in the 2N cells if stretched out would be a strand 10 feet long. Obviously then, it’s all balled up tightly in the nuclei of your cells. Now picture this: The ball is not random. It is coiled such that the switches are in very close proximity to the genes they regulate (on and off) as well as to other switches, which they interact with as well. This is a very complex “hair ball”.

So, imagine switches a,b,c and d. In that order they produce (along with the gene cascade and secondary, tertiary , quaternary, etc. switches and genes regulated by them) a liver cell. Thus, the different sequences will determine different DNA folding patterns and proximities. In a different order, a brain cell, and so on. This means there is a hierarchy of switches controlled by hormones and even by “up-ness” or “down-ness”) of cells and by neighboring cells…. It is truly mind boggling, especially when you consider that a cell can be thought of (so we can picture the complexity) as an ocean liner filled completely with machinery on the size order of a Swiss watch.

Take a breather.

Digest that.

So, how many switches are there? About four (4) million.

“The result of the work is an annotated road map of much of this DNA, noting what it is doing and how. It includes the system of switches that, acting like dimmer switches for lights, control which genes are used in a cell and when they are used, and determine, for instance, whether a cell becomes a liver cell or a neuron.” - http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?_r=1&pagewanted=all

You all remember “The Human Genome Project”. Think of that as a picture of Earth from space (the “blue marble” picture). This current research has presented the equivalent of “Google Maps”. The latter now shows the roads, restaurants, hospitals, cities and rivers, according to Dr. Eric Lander (Harvard and MIT, Broad Institute).

“In one of the Nature papers, researchers link the gene switches to a range of human diseases — multiple sclerosis, lupus, rheumatoid arthritis, Crohn’s disease, celiac disease — and even to traits like height. In large studies over the past decade, scientists found that minor changes in human DNA sequences increase the risk that a person will get those diseases. But those changes were in the junk, now often referred to as the dark matter — they were not changes in genes — and their significance was not clear. The new analysis reveals that a great many of those changes alter gene switches and are highly significant.” – ibid

The basis of many diseases and the future attacks on these diseases will be in the switches. That means Cancer, as well.

The parts which haven’t been figured out yet are the next phase of “Encode”.

Hope this has given some mind expansion as well as…well… hope.

Just to add some 'pepper' - What determines the "up-ness" and "down-ness"? What was most fundamental to all of this ... allowed it all to occur? The Higgs-Boson. It allows matter to aggregate, and form gravity, without which there could be no "up" or "down". 

Sources:

http://www.guardian.co.uk/science/2012/sep/05/genes-genome-junk-dna-encode

http://www.nytimes.com/2012/09/06/science/far-from-junk-dna-dark-matter-proves-crucial-to-health.html?_r=1&pagewanted=all