28 May 2006

When personal computers were new to the world and the statistical science of multivariate regression was new to me, I experimented with both in a self-study project. For two years, I kept a diary in spreadsheet form, a digital record of things I had done, and how I felt each day. There were dozens of categories for the choices I was making, and several dimensions describing my subjective experience. My plan was to analyze this data for patterns, and learn how better to manage my daily moods by selecting my daily activities.

One lesson that derived from this experience was that multivariate regression doesn't work in the real world for n>2. People who are not mathematically inclined already know this intuitively, but we statisticians must learn it by rote: The world is complex. Whenever three or more causes are related to any effect, they will interact in unexpected ways. General-purpose statistical tests will be inadequate to the task of teasing them apart.

But the core value in this exercise was self-reflection. Though this data defied mathematical analysis, I've learned over time that awareness of my actions and my feelings is the most important thing I can teach myself. Some of what I seek each day is part of a deep quest for the fulfillment of my being; other pursuits are more like physical needs that must be satisfied regularly; the dangerous lures are those that have an addictive quality feeding these desires never satisfies them, and in fact the more I indulge the desires, the stronger they become. 

I can guide the course of my life the way a captain steers an ocean liner. Habits and desires may have a momentum of their own, but small corrections maintained consistently and repeatedly are a way for conscious choices to prevail over the long haul.

~ Josh Mitteldorf

27 May 2006

Viruses invented DNA?

In Darwin’s original version of evolutionary theory, every transition happened smoothly.  (Natura non facit saltus, he quoted from Linnaeus.)  But this dictum has always stretched credibility, as there are so many gaps between diverse organisms in nature.  How do you go “gradually” from asexual to sexual reproduction, for example? 

For years, Lynn Margulis has told us her answer, and sometimes, some of us are listening.  Her favorite word is endosymbiont.  A small, parasitic bacterium can take up residence in a host cell.  In the short term, its interest is served by killing the host cell and reproducing as fast as it can.  But over time, a better strategy is to leave the host alive, so its resources can be tapped over and over.  Better yet, why not actively promote the health of the host cell, and moderate virulence to conserve the host’s resources for the long haul.  Parasitism becomes symbiosis.  The bacterium becomes an organelle, essential for the cell’s metabolism.  This is the origin of mitochondria and chloroplasts. 

The biggest jump of all occurred billions of years back when primitive life forms based on RNA alone became cells with nuclei, protecting their genetic treasure in the form of DNA.  Now along comes Patrick Forterre of the University of Paris-Sud with a deliciously radical theory about how that transition happened:  DNA was invented by viruses.

  • The first step was that viruses invented DNA in order to stabilize their genomes and resist attacks by the host cell.
  • Next, the virus took up residence in a cell, protecting its DNA in a shell.
  • The virus and cell learn to live with each other, and evolve a co-dependence over time.
  • Finally, the cell begins to realize that the DNA is a superior way to store its own genetic information.  All the mechanisms for replicating DNA and translating individual genes into RNA are already there, provided by the virus.
  • One by one, the cell's RNA genes are copied into DNA, where they are stored more safely.
  • The cell learns to depend on the DNA and its transcription.  RNA becomes a temporary messenger molecule.

Forterre claims he can trace this ancestry by studying modern viral DNA replication, in all its forms, some of which is similar to the chemistry used by higher life, and some of which is unique to viruses.  Two other virtues of this theory:

  • That viruses have an immediate fitness benefit from substituting DNA for RNA (a way to escape the host's defenses), while for cells, the switch to DNA offers only long-term benefits, so it evolves with more difficulty.
  • That viruses evolve more nimbly than other organisms, because their reproductive cycle is so rapid and their survival ratio so low.

(Although this theory is new and yet controversial, it is already well-accepted that viruses play a crucial role in later evolution.  They are constantly borrowing genes from one organism, inserting them into another, sometimes of an entirely different species.  This lateral gene transfer adds diversity, and again makes leaps possible.)

Science article (last week)
Nature article (last January)

26 May 2006

Physicists who think about the fundamental structure of space and matter have been forced by logic and evidence into realms we used to think of as science fiction.  The two most important physical theories of the 20th century (quantum mechanics and general relativity) are logically inconsistent with one another.

One line of imaginative theorizing posits that space has more dimensions than three.  (This is quite apart from the ways in which time acts as a fourth dimension in relativity theory.)  Lisa Randall and Raman Sundrum have a theory in which our familiar three dimensional universe lies at the intersection of two four-dimensional “branes” in an even higher dimensional space.  The theory differs subtly from General Relativity, but effects of GR are already tiny and hard to observe.  Can we ever know if they are right?

Now along come Charles Keeton and Arlie Petters with an idea for a practical experiment that might test the four dimensional theory in the near future.  A consequence of the Randall-Sundrum theory is that there should be tiny black holes scattered everywhere through space.  There are enough of them nearby in our galaxy that we should be able to detect the way they bend the high-energy radiation when one of them happens to pass between us and a distant gamma ray source.  The next generation of GLAST satellite telescope should give us the answer.  

Science Daily article
Research article in Physical Review
Interview with Lisa Randall (a little dated but more basic) 

25 May 2006

If thou canst bear
Strong meat of simple truth
If thou durst my words compare
With what thou thinkest in my soul's free youth,
Then take this fact unto thy soul --
God dwells in thee.

The Infinite 
Embosomed in a man; 
And thou art stranger to thy guest 
And know'st not what thou doth invest.

Look straight before thee, as befits 
The simplicity of Power. 
And in thy closet carry state; 
Filled with light, walk therein;

This is the reason why thou dost recognize 
Things now first revealed, 
Because in thee resides 
The Spirit that lives in all; 
And thou canst learn the laws of nature 
Because its author is latent in thy breast.

excerpted from Gnothi Se Auton ("know thyself", according to Plutarch, inscrption at the Oracle of Delphi)
Ralph Waldo Emerson, born this day in 1803

24 May 2006

Nikolai Rimsky-Korsakov offers an expression of pure exuberance.

Listen to Allegro con Brio from his Quintet for piano and winds, performed by the Sounds of the Woods Ensemble, Moscow

23 May 2006

I am the daughter of Earth and Water,
And the nursling of the Sky;
I pass through the pores of the ocean and shores;
I change, but I cannot die.
For after the rain when with never a stain
The pavilion of Heaven is bare,
And the winds and sunbeams with their convex gleams
Build up the blue dome of air,
I silently laugh at my own cenotaph,
And out of the caverns of rain,
Like a child from the womb, like a ghost from the tomb,
I arise and unbuild it again.

~ from The Cloud, by Percy Bysshe Shelley

22 May 2006

Where can one live, then, if not in the past, present, or future? 

I’m saying, live in the story of your life…

What lifts any story to greatness, is not the particular events that constitute its plot but how the plot unfolds toward meaning, whether it becomes, finally, a unique expression of some universal theme of human existence.  Yours could be an airport novel full of glitter and cliffhangers, quickly read and quickly forgotten; or it could be a deep lyrical meditation on love; or an epic testament to the capacity of the human spirit to rise above suffering; or some rollicking picaresque—who knows? And the story’s never over till it’s over: there’s always another level of understanding to reach so long as you’re alive and kicking.  Only death releases you from the present moment to become your whole life. At every other moment, we’re contributing to what that whole life will have been.

~ Tamim Ansary, commencement address at Reed College