chloroplast and other genes (was Lucy in Newsweek)

B.J.Tindall bti at DSMZ.DE
Tue Apr 6 12:59:10 CDT 2004

Since I seem to have started this ball rolling, I will comment further.
There are a far greater number of prokaryote genomes available than for
eukaryotes, and they are generally much smaller. Our general overview now
is that even prokaryotes are far more complex (genetically) than was
imagined some years ago. What is happening now is that far more attention
is being turned to how the "coding data" (i.e. the genes) is being turned
into an organism. This is not just the conversion of a single gene into a
single protein, but other topics are surfacing, such as complex
interactions and gene expression. What appears to be happening is that the
genetic tools we have developed in the past 10 years now allow us a
different level of access to certain types of data, but certainly do not
automatically replace studying the organism at other levels. In fact gene
expression (as proteins or biochemical pathways) seems to becoming
increasingly important, which means that the inter-relationship between the
genes and the expressed phenotype is talking on a more important role. As
was pointed out in earlier e-mails it is not just a case of comparing
morphological characters with simple gene similarities, but understanding
the way the underlying genetic information gives rise to that morphology.
That is complex enough, to which we then add the other dimension of how
this has changed over geological time. In contrast to Rich's comments I am
not convinved that faster computers are the solution. We need to look at
things from a biological point of view, which often means parallel thinking
as well as linking the relevant data sets (genes, gene expression,
proteins, biochemical pathways, and morphology etc.).
Lots of things to do, but not enough time to do it all!!

InAt 23:03 5.4.2004 -1000, Richard Pyle wrote:
>>  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
>On the other hand, I've been accused of being overly optimistic before...
>Richard L. Pyle, PhD
>Ichthyology, Bishop Museum
>1525 Bernice St., Honolulu, HI 96817
>Ph: (808)848-4115, Fax: (808)847-8252
>email: deepreef at

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