Posted
15th May 2001
Genes + Money = Danger
The
revelations below highlights the need for increased scrutiny
of the NZ Dairy Board's intention to give Celera considerable
money for sequencing. This intention was announced by the Dairy
Board chief scientist (chemical engineer Kevin Marshall) at
the NZ Dairy Workers Union annual congress, Hastings 14 June
2000. He refused to give Bob Mann anything in writing, and has
just recently acted hard-done-by, posing as wounded when his
announcement is bounced back at him. He now denies any intention
to pay Celera lots of money, but refuses to reply to Mann's
detailed questions. The time is overdue for Dr Marshall to state
clearly how much money he intends to pay Celera, which is evidently
a dubious investment. More generally, it should be widely known
that Marshall had Dairy Board permission to pay out $30M/year
for five years of gene-tampering, within which his plan to pay
Celera was some unstated fraction. Any further digging will
of course risk investigation for un-NZ activities and subsequent
use of that information against the investigator. Something
I (Alan Marston - edit) have been subject to as recently as
this year when current politicians and police employees cast
aspertions in print and by phone conversation, attempting to
compromise me in the eyes of people cooperating over the anti-snooping
Swain Bill. And this despite never having been arrested let
alone convicted of any crime except free-thought. New millenium,
old rules.
From New Scientist magazine,
by Andy Coghlan
Celera,
the company which shared the glory for sequencing the human
genome in June 2000, now faces claims that its data may be riddled
with errors. As many as half the company's gene sequences for
the fruit fly may contain mistakes, says Samuel Karlin, a mathematician
at Stanford University in California. His work suggests there
might be many errors in other genomes that have been sequenced
using similar techniques, he says. But others have defended
the results. "I would take 50 per cent correct as a compliment,
not a criticism," says Gerry Rubin of the US's fly-sequencing
programme at the Howard Hughes Medical Institute in Berkeley.
An update next yearshould improve its accuracy to 75 per cent,
he says. Rubin was one of the coauthors when the head of Celera,
Craig Venter, published the full sequence of the fly genome
in Science in March 2000. The work was hailed as a vindication
of the "pure shotgun sequencing" technique the company used,
where copies of a creature's DNA are broken into little pieces
and sequenced. Computers then assemble the full sequence by
looking for overlapping fragments.
Gone missing
But when Karlin began to use Celera's fly genome, he spotted
lots of errors. "More than 60 per cent of their sequences were
in substantial disagreement [with known sequences], and this
got me a little bit angry," he says. So he did a fuller analysis
with his colleagues. They hunted through Celera's genome for
1049 fly genes whose sequence and function had already been
worked out and carefully checked in experiments. Although 26
per cent of the genes were exact matches, and a further 29 per
cent accurate to within 1 per cent, the remaining 45 per cent
contained a range of moderate to serious errors - or were missing
altogether. "We couldn't find a lot of the genes we were working
on ourselves," says Karlin. Other errors included the omission
of entire protein-coding segments of genes, or exons, while
other genes had been "read" from the wrong starting point. Karlin
claims there could be worse errors in both the public and private
versions of the human genome. "Everyone was rushing," he says.
But the public project relied on a slower, more accurate version
of shotgun sequencing - and Celera ended up including a substantial
amount of data from the public project in its version (New Scientist,
17 February, p 4).
Decades of work
Meanwhile,
Karlin warns researchers to take care if they're studying any
"new" genes revealed by Celera. "My advice is to do whatever
part you're working on again," he says. His analysis reveals
the perils of relying too much on computers, Karlin says. "People
are trying to get away without doing experiments." Celera plays
down the criticisms. "We never said that the fly genome was
totally and 100 per cent complete," says spokeswoman Heather
Kowalski. "Annotation and analyses of genomes can go on for
decades." Karlin's work appears in Nature (vol 411, p 259).
He initially sent his paper to Science but the journal didn't
publish it. "They sat on it for five months," he says. .
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