chloroplast and other genes (was Lucy in Newsweek)

[Richard Pyle]

>  My impression is that some 10 years ago we were given the impression
> that
> > once complete genomes were available we would have all the answers.
> --------------------------------------------------------------------------
>
> The interesting feature of all this is, that if and when we
> arrive at a nice final picture of the genome, we will be
> committed to the results of something like a parsimony analysis
> for a final, definitive phylogeny. Yet, we'll still know - or
> SHOULD know - that undetected homoplasy may have us barking up
> the wrong tree!

Maybe.  But maybe by then we will have attained a level of "intellectual
fortitude" (as I've been referring to it) that the algorithms can identify
patterns of homoplasy and other phenomena that confound the issue in the
context of our current teeny-tiny fraction-of-the-genome sequences and our
rudimentary (at best) understanding of the complete scope of information
contained within the genome.

Related to this, Pierre Deleporte wrote:

> Viewed this way, rushing for extensive complete genomes sequencing (or
> exhaustive morpho-anatomical descriptions either) could effectively appear
> like putting the cart before the horse. Sequencing some complete genomes
> seems interesting only in that it provides a larger spectrum of potential
> evidence in which to search after some unsuspected kinds of optimally
> informative data.
>
> Indiscriminate analyis of all we can scratch is likely an infantile
> sickness of phylogeny inference. People who try to freeze the practice of
> analysing all available data indiscriminately as being "the panacea" tend
> to obscure the need for improved understanding of evolutionary processes,
> hence improving relevant knowledge and making optimal use of it, which is
> the correct acception of the "total evidence" principle.

My speculation about the future isn't so much a "same as now, but better"
scenario; but rather a complete paradigm shift in our understanding of, and
our ability to extract information from, the genome.  As I said previously,
I think our ability to generate complete genomes will arrive sooner than our
ability to understand the information they contain. I see the "paradigm
shift" as analogous to the transition from vacuum tubes to solid state
transistors. Imagine how big the room would be if you tried to build a
computer with as many vacuum tubes as there are transistors on a modern
Pentium 4 processor.  This is sort of like trying to imagine what it would
be like to have complete genomes for dozens or hundreds of individuals of
millions of species (i.e., hundreds of millions to billions of complete
genomes), and a computer algorithm that can sort through it all in a
reasonable time period.  Sound crazy?  We will endure twenty iterations of
Moore's law over the next three decades. That potentially means computers
with 2^20 (~10^6) more transistors than today's fastest processors.  Much,
much more powerful computers will be at our fingertips if quantum computing
technology is established by then.

But more importantly, we will (eventually) have a much, much improved
understanding of how to interpret the information contained within the
Genome.

On the other hand, I've been accused of being overly optimistic before...

Aloha,
Rich

======================================================
Richard L. Pyle, PhD
Ichthyology, Bishop Museum
1525 Bernice St., Honolulu, HI 96817
Ph: (808)848-4115, Fax: (808)847-8252
email: deepreef at bishopmuseum.org
http://www.bishopmuseum.org/bishop/HBS/pylerichard.html