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[Tvoivozhd <tvoivozd AT infionline.net>]

So much for the really stupid argument that "throwing money at a problem 
doesn't solve it." Throwing money at a problem is precisely how problems 
are solved, including yeast research, which has been generously funded.

It worked fine for the Manhattan Project, worked fine for defeating 
Hitler and Yamamoto.  "Throwing money" at a problem is the only way to 
solve it, as the GI Bill solved the problem of a feared replication of 
the Hoover days march on Washington by veterans demanding the "huge" 
$500 bonus promised them for misery and death in the trenches of 
Europe.  Throwing money via the G.I. Bill also made the U.S. supreme in 
academic and industrial research for twenty years---proving the value of 
throwing money at education.







Yeast: toasting the end

Yeast research as we know it will end with the solving of the organism 
on April 1, 2007, give or take 8.37 days. So said Mark Johnston, 
president of the Genetics Society of America, presenting on the future 
of the model organism at the biannual Yeast Genetics and Molecular 
Biology meeting this past month in Seattle. In combing through the Yeast 
Proteome Database, he found that so-called known yeast genes have 
followed a remarkably linear upward trajectory, reaching 4,679 as of the 
end of July of this year. A continuation of that trend, says Johnston, 
of Washington University in St. Louis, will mean that the organism's 
6,000 genes will be known by April Fool's Day 2007.

The prediction has inherent flaws and implied cheek. Budding grad 
students need not fear; even a 'known' gene can still be pretty 
mysterious. The University of Toronto's Tim Hughes put things into 
perspective; he says that Mark Robinson, a data analyst in his lab, 
spent a few weeks querying Medline to find what many might have 
suspected, that two-thirds of the genes may indeed be known. He 
confirmed this by abstract searches that included each of the 6,000 
yeast-gene names (and their aliases) in conjunction with the word 
"cerevisiae" or "yeast." But, 50% of the papers were on a mere 10% of 
the genes.

The disparity mirrors a divide in the yeast community. A few researchers 
take genomic approaches to find out a little about many genes at once, 
while more scientists focus their work on a particular gene or pathway. 
Global information feeds the more directed researchers, whose questions, 
hypotheses, and innovations feed back into the high-throughput technology.

The loop is best demonstrated in the wealth of resources available to 
so-called yeast people, far more than those enjoyed by the Drosophila, 
C. elegans, or mouse communities. From mass spectra, to two-hybrid 
interactions, to protein and sequence microarray analyses, and even 
images of organismal morphology, yeast people are swathed in 
information. Add to that the physical resources: chips, reagents, 
plasmids, and mutant strains, including the resource to end all 
resources: a set of strains carrying deletions for practically every 
nonessential gene.

But the glut of resources may serve as a harbinger of the end. Dan 
Gottschling, at the Fred Hutchinson Cancer Research Center in Seattle, 
says that discussions with grad students at the meeting worried him. 
Many were afraid that the interesting questions in yeast were drying up, 
making it a less attractive model for study.

And for senior researchers working on more directed studies, the 
available resources breed a sense of entitlement. A session on yeast 
resources, opened to audience participation, drew many requests for 
better controls or data sets tailored to specific needs. Some provided 
stinging gripes about false-positive results, and requests for new 
resources ranged from a collection of temperature-sensitive alleles for 
all essential genes, to a request for monoclonal antibodies raised for 
every yeast protein.

An almost palpable tension is surfacing. "It's definitely a tension we 
feel at [the Saccharomyces Genome Database] because we want to cater to 
both groups," says Eurie Hong, lead scientific curator at the database, 
which stores and freely distributes yeast genome data. Gottschling says 
it's a friction with somewhat deeper roots. "It speaks to the sociology 
around the whole system, the dynamic of someone who has spent their 
whole life working on the details and the new guy working on the 
technology to free us from those chains."

But at meetings like this the groups break bread, drink beer, and extol 
the virtues of APYG (the awesome power of yeast genetics). In truth, the 
demands and requests are so great because projects seemingly 
unapproachable in other organisms are quite easy in the tiny eukaryote. 
"It's not impossible to make these things in the mouse; it just costs 
100 times as much," Hughes says.

And while Johnston admitted that his prediction about "solving" the 
organism tastes best with salt, he implored researchers to strive to 
understand in a meaningful way how each yeast gene and each network of 
genes fits together to create the whole. Such a systems-level 
understanding has been within reach for other communities, but for 
reasons that may have included a lack of funding or interest, the task 
was dropped. "Don't abandon it like the E. coli guys," Johnston urged.