End of The Gene

Exhibit A: Reductio Ad Absurdum

Exhibit B: Genetic Dark Matter

“A fruit fly study suggests the whole-genome approach may be the way to go.”

Exhibit C: The Genome vs The Gene

Exhibit D: The Proteome vs The Genome

“you need to look at the things that the genes are producing, and what’s happening after the genetics.”

Cancer as a Complex Adaptive System

Heng, et al recently published a review paper that brings together and touches on many different aspects of cancer complexity.  I thought this an opportunity to selectively quote the paper and organize the quotes loosely around various complex systems concepts they relate to.  I’m curious whether this makes sense to readers of this blog, or whether there’s too much unexplained jargon and too many large conceptual leaps.  Please ask questions or make comments freely below.

One preface I think will help is to understand that genome, karyotype and chromosome refer roughly to the same thing.  Here are several schematics that I will present without explanation that together illustrate how genes relate to genome/karyotype/chromosome structure, and how that in turn relates to the so-called genetic network (loosely equivalent to the “proteome”).  Of course “gene” is an outdated and inaccurate concept, so don’t get too hung up looking for genes here, just understand that they are sub-structural elements of the genome.

From MSU website

Crohn's Disease

Debbie Maier asks us on the Upcoming Topics page to address Crohn’s Disease.

I don’t know too much about it except that it’s an autoimmune disease and has a complex, multi-causal etiology and pathology.  In my reading on autoimmune diseases in general there seems to be a direct link between latitude an incidence.   Specifically, the farther from the equator you live the more likely you are to get Crohn’s, Type 1 diabetes, rheumatoid arthritis, and so on.…

Third-Hand Smoke

Thanks to Daniel Horowitz for alerting me to third-hand smoke.  I guess then if you pass on epigentic mutations to your children from third-hand smoke exposure it’s called fourth-hand smoke?…

Hina Chaudhry

Like does this mean you can cure heart disease?

She’s hesitant.  Nobody wants to say they can defeat the industrialized world’s number one killer.  Nobody wants to make promises about life, or quantify salvation.  But she fervently believes she’s got a shot.

This is what the 2008 Genius edition of Esquire Magazine had to say about Hina Chaudhry.  Her approach is to switch back on the mechanism that causes cells to divide in the heart, which doesn’t normally happen after birth in any mammal.  This is not a stem-cell approach, despite what it might sound like.

Looking on the web there appears to be very little written about this work, so I’m wondering how Esquire found her or chose her work to highlight.  I’d like to learn more if anyone has information they’d like to share.…

Encoding Life's Complexity

Will Wright’s demo of Spore illustrates some key concepts of complex systems, including the notion of simple rules generating complex behaviors, and also the power of recursively applied (i.e. fractal) computation at different levels.  Living systems leverage these same principles.…

What is a Gene?

Not having had any serious biological training I have to go to Wikipedia and Google to learn the basics. And I’m often surprised to find that concepts everyone uses don’t have good consensus amongst scientists. When reading the Wikipedia entry for “gene”, it occurs to me that if the concept didn’t predate the discovery of DNA, it would not exist.…