The Human Genome and You (9/13/12)

Is This the Next Information Revolution?

Figuring Out How Humans Work

A funny thing happened to the Human Genome Project from the 1990s.  At a cost of billions of dollars, human genes would finally be “mapped”.  The new knowledge would unlock new, dramatic  explanations for why we get sick. The few major “genes” for heart disease, schizophrenia, cancer and stroke would become clearly known as the genetic blueprint became revealed.

Or so the backers claimed. Things did not turn out that way.

Instead of the five “main” genes for heart disease hundreds were discovered.  Most increased the risk of disease by 2% or 4% or other low levels.   Instead of a clear picture of several major genes, hundreds or thousands of genes appeared “associated” with one or many illnesses.

Such simplistic, linear thinking usually turns out models of biological information flow that are inadequate or misleading.  Nature is complex – and filled with innumerable interacting complex systems.

The next iteration of the Human Genome Project had to be different.

The Encode Project

The first Human Genome Project looked at classical genes – the strips of DNA that provide the information that becomes proteins, the information workhorses of the cell.  It turned we only had 22000-25000 of those discrete, active molecules that make separate proteins.

By comparison, there are between 3-8 million distinct, separate bacterial genes in our gut alone.  If biology was a numbers game run by how many different proteins you make, humans might not achieve full humanity.

But now Human Genome 2.0, the Encode Project, has declared its findings.  They’ve gone looking in the vast thicket of human DNA which does not involve classical genes – and  constitutes 80-90% of your genome.

That huge amount of information has traditionally been called “junk” – junk DNA.

And of the 147 cell types which Human Genome Project 2.0 has looked at, most of your DNA turns out to be encoding something.  Much of this “junk” DNA turns out to include  4 to 40 million gene switches telling protein genes when, how, and where to turn on or off.

So there are thousands of genes encoding proteins, and millions of genes controlling regulation. What has been discovered is just the tip of a vast network operating system.  The “junk” has for millions of years helped control most of our physiology and actions.

Will this new data provide us a better sense of how human biology really works?  Certainly.

Though for a long time it will provoke more questions than answers.

Ants In the Kitchen

Recently physicists reorganized their field.   Quantum mechanics morphed into quantum information theory.  The entire universe has become defined as a vast – even infinite – information system.

Your human body is also an information system, with the basic programming provided by your genes.

Recently  physicists have also recognized that 96% of the universe we live in made of “dark” stuff.  Not “dark” in the sense of evil, but “darkly” unknown.

Most of the universe we happen to live in is dark matter (the large majority),  or dark energy.

So it’s no surprise some geneticists have described their discovery of some of the functions of junk DNA as similar to finding “dark matter.” They even call junk DNA dark matter.

Which should remind us of the parable of the ants in the kitchen.  As they roam they attempt to understand the world around them.

They’re able to  find food. They can signal each other.  They can march into every nook and cranny.

But can they understanding plumbing?  Refrigeration?  Microwave ovens?

The story of the  ants in the kitchen should remind us of the proud protagonist of the 19^th century satire “Flatland.”  The “author” of the book is two dimensional being trying to figure out actions in three dimensions – while lording it over the ignorant denizens of a one dimensional universe.

We live in a three dimensional universe.  Einstein argued there was a least a fourth.  Present models of particle physics often  11 or 12 or 16 dimensions as they try to explain how the universe works.

What the human genome project should tell us is that we’re three dimensional selves who may be dealing with a twelve dimensional biological and physical universe – or the models required to understand that universe.

We’ve been missing a few notes.

Making It Work

Knowing what you don’t know is very useful.  It can propel knowledge propulsively.

To truly improve biological understanding we will need at least two types of breakthroughs:

The first will be in information management and processing.  History is in our favor.  The brute force of computation has improved along the lines of Moore’s Law for many years, and may well continue its logarhythmic progress.   Hopefully we’ll simply continue to develop the massively greater computer power and improved artificial intelligence that will make such steps possible.

Another necessary breakthrough will be following and modeling – in real time – complex biological systems.

We’ll need new ways of understanding complexity just to figure out what goes in one of our ten billion cells.

And inside each are perhaps 1 billion protein-protein interactions per second – a single variable of the critical information events we will need to assess.

Achieving these kinds of breakthroughs may allow us to more intensively study one of the true mysteries of biology – what separates life from the non-living.  Ultimately that’s an information issue.

And information should continue to explode.

A Little Goes A Long Way

Entrepreneurs will continue to provide us pie-in-the-sky reports of the future of health care.  Proteinomics and genomics will “revolutionize medicine” as new knowledge is brought to bear.

But understanding all that vast data will be crucial.  And we’re not there yet.

However, a little knowledge goes a long way – particularly when you look at health as opposed to health care.

Figuring out how to control a shape shifting, constantly mutating tumor is very complicated.  Figuring out ways to prevent it is generally far simpler.

Masons did not require knowledge of quantum mechanics to build the great European cathedrals.

We now know from studies like those of Kungsholmen, a kind of Swedish Framingham, that men over 75 can increase their own long lifespan by 6 years through modifying lifestyle.  Medical care may be adding 2-3 years to lifespan – starting at birth.

We don’t know exactly how walking, or visiting friends, or going to concerts, changes the functions and actions of the millions of gene switches in our junk DNA.

We just know that they work.  And we can take those actions, right now.

All by ourselves.
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