Search This Blog

Wednesday, June 23, 2010

Real-Time Observation Is Always More Efficient Than After-The-Fact Parsing

Non-random environments (systems):

- have evolved (from a more simple past)
- are (variously) optimized to input conditions and output demands
- are sequentially constructed in layers
- are re-constructed periodically
- are derived from the constraints of pre-existing environments

Understanding (extracting pattern rules and instances of these rules) is made more efficient through observations undertaken over the course of an environment's construction period. Extracting pattern after the fact requires the act of inferring construction sequence from existing artifact. The number of possible developmental paths (programed algorithms) that will result in a particular artifact are infinite. Parsing through this infinite set towards a statistically biased guess at the most likely progenitor is lossy at best and computationally prohibitive.

For instance, the best (shortest algorithmic complexity) candidate produced by post construction parsing may indeed be a more likely (least energy) progenitor, but this may not predict the actual causal chain that resulted in that environment. Projections based on a statistically optimal history will diverge from the futures actually produced by the environment.

The only time that a statistical (minimum algorithm) parsing of an environment is guaranteed to match reality is when that parsing includes the whole system (the entire Universe).

Observing the genesis of an environment minimizes the mandatory errors inherent in statistical after-the-fact (Solomonoff) algorithmic probability parsing of a pre-existing system.

Said more succinctly; If you want to grow an optimal system, use algorithmic probability and algorithmic complexity as metrics towards optimization, but if you want to describe a pre-existing system, it is best to build this description by observing it's genesis.

Randall Reetz

Wednesday, June 16, 2010

DNA replication…

Yes, this shit is so amazing that it makes a hardened evolution theorist like me cough up some creationist thoughts (don't worry, it will be a temporary affliction).

This animation shows the lagging strand replication process in greater detail. If you are wondering why the lagging strand should have to be built in reverse, it is because the other side of the helix is inverted which would have necessitated an exact molecular machine to have been evolved from scratch, but in reverse! This molecule, "polymerase", is composed of 8005 atoms. The ingenious workaround, to run the strand through the same molecule backwards, though mechanically awkward, is far more likely (less complicated) to have evolved than would have been a mirror image of the whole polymerase molecule (or its function). In fact, it is probable that such a molecule might not even be physically possible given the "handedness" (right/left) of the atoms molecules must be built of. Because of this, I consider the asymmetry of DNA replication machinery to be evidence of the least energy dictated meandering of the evolutionary process.

By pure chance, an particular arrangement of 8005 things would happen once every 8005 to the 8005th attempts (8005 factorial). Of course molecules don't assemble by pure chance. Even if you dumped the requisite atoms into a box and shook it up, the assembly wouldn't happen instantaneously, some atoms would form small groups, and those groups would clump together into larger groups, etc. The atoms of each element have unique properties that effect their aggregation.

But that isn't the full story either because the polymerase molecule is built atom by atom by DNA.

Look at this…

It is called a Snow Plant. Comes out of the ground like an alien right after the snow melts. This one was just meters up the hill from a trail head on the northeast shore of Lake Tahoe. They are parasites of fungus that grows on the root systems of pine trees. Unreal!  [about 8 inches tall and more brilliant than this picture could ever show]

Recent Posts