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SCIENCE-FOR-THE-PEOPLE  August 2010

SCIENCE-FOR-THE-PEOPLE August 2010

Subject:

LUNCHTIME WITH Mr BIG

From:

Robert Mann <[log in to unmask]>

Reply-To:

Science for the People Discussion List <[log in to unmask]>

Date:

Sat, 14 Aug 2010 13:03:47 +1200

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (237 lines)

			LUNCHTIME  WITH  Mr  BIG

R Mann
Auckland Jan 2001


	The big lecture theatre in the medical school was almost full 
by noon on Jan 26 when J Craig Venter, president of Celera Genomics, 
was to speak at 12.30.   A communist was giving out leaflets in the 
main foyer quoting Prof Steve Jones on the failure of gene therapy 
and saying the human genome project is mostly a waste of money. 
Extra 'security' was on.
	I found myself sitting with a yacht broker who was here in NZ 
to help Venter buy a luxury yacht.  This engaging man was fulsome in 
praise of the NZ luxury yacht industry.  I felt ashamed that we 
aren't doing anything more useful with those skills, but I kept my 
peace.  Instead I advised him "sign him up quick on the way to the 
airport before the bubble bursts".
	The yacht dealer arrived with a charming woman, who had 
attended one of Venter's big announcements of "completion" and now 
gave the general impression of a devotee.   She spoke with warm vague 
evangelical enthusiasm of the many medical benefits to come from DNA 
sequencing of humans and animals.  I asked her *what* benefits she 
expected; as she recited again the vaguest fantasies, with no attempt 
to identify any reality, I felt I was observing a devotee  -  she 
held this faith with a blatant disregard for fact & reason that 
reminded me of totalitarian sects.
	The reserved seats at the front were occupied at 12.25 by a 
phalanx of personages including the chief executive (vice-chancellor) 
Dr Hood who is also a director of numerous corporations.  The 
chairman, Dr Peter Gluckman dean of the med school, then introduced 
Venter with fawning adulation  -  "one of the most distinguished 
scientists and entrepreneurs".

	J Craig began by simply saying he had followed for 5-6y 
'basic science ideas'.  Early in his career he had sequenced an 
adrenalin-recognition protein, which took a decade by the then best 
methods.  (He also passed what was to me a welcome quip that 
biochemistry had at that time been fixated on a fad attributing 
almost everything to cyclic-AMP.  Now, if only he could see the 
current fad, rather than exacerbating it   . . . )
	Venter operates, in an area about the size of a football 
field, 300 x U$300,000 sequencing machines run by 9 staff.  A further 
50 staff are employed in making each day 300,000 plasmid clones which 
are then sequenced.  These 'shotgun' sequences are far bigger than 
used in other approaches, necessitating huge computing to assemble 
them into the whole from one chromosome or one microbe, etc. 
Venter's main impact on sequencing has been by computing.  He claimed 
he's doing one or two terraflops in 1500 "high-end" CPUs, with more 
than 100 terabytes of storage, collaborating with the hitherto kings 
of supercomputing, the modellers of nuclear explosions at Sandia. 
Thus, he said, the biggest computing effort is devoted entirely to 
what he is pleased to call "biology".
	Some couple dozen genomes have been caricatured into the 
4-letter alphabet by this method at Celera and the similar TIGR.  The 
first was _Haemophilus influenzae_ which took a year or two but today 
would take a day or two.  The 5-chromosome plant genome of a 
mustard-family plant, _Arabidopsis_,  120M base-pairs, about 4% the 
size of the human genome, is to be the basis of crop-GM; a sequence 
for it was announced Dec 2000.
	The number of genes in the human genome has been whittled 
back to 26k and falling (mainly by revising the definition of a CpG 
island).  I guess this may be intended to help relieve the log-jam at 
the Patent Offices  -  but patents were not mentioned.
	The human genome has been classified 1.1% exons, 24% introns, 
and great grey lengths of non-coding DNA for which the term 'junk' 
was not used but which Venter stated to have "more forensic than 
biological function".

	J Craig's PR site www.celera.com features many claims of 
imminent medical product e.g.
>
>A Fatal Flaw in the Hearts of Children
>	Scientists identify a gene involved in the sudden cardiac 
>deaths of healthy children.

My favourite gleaning in a quick scan of Celera's website was
>  Leverage the same infrastructure and workforce that sequenced and 
>annotated the Human Genome!


	The popularity of these sequencing fads is, just lately, 
overwhelming.  Venter says he has spent U$250M without making any 
sales.  Having got Blair & Clinton to hype his arbitrary 'draft' 
human DNA sequence, he now says Feb 15 is to be the real completion. 
He still calls this future advanced draft "essentially complete"; 
nobody asked him what that key adjective 'essentially' means.
	So far from claiming imminent benefit from any of this DNA 
sequencing, he now mocks genetic determinism.  The different genomes 
contributed by his "number of" volunteers allow us to "tell the males 
from the females", but "there will not be a genetic determination of 
African-American".  He announced, as if it were a great & recent 
discovery, that bowel cancer is caused by not only defective genes 
but also toxins from food, so that not only genetics but also 
environment contribute to the disease.  He mentioned biology with 
apparent respect, and used the term 'holistic' at least twice.  I 
wondered whether U of Ak honchos who had been purging biologists in 
favour of gene-tamperers felt any twinge at this stage.

	"Your stock rose from about $3 to $300, and now it's about 
$30.  How do you explain that?"  asked Dianne Yates MP (without 
identifying herself at all).  "Ah yes  -  there's always one in the 
audience  -  a stockholder!" replied Venter.  He ascribed the big 
rise to the hope of a new future; blamed Clinton for crashing the 
stock market; and added a few glib econobabblings which I couldn't 
understand let alone recall.

	Dr Jorg Kistler, who recently earned a personal chair at 
Auckland in electron microscopy, asked  how realistic are hopes of 
gene therapy.  In a similar vein, but humorously, a local votary of 
the gene-tampering fad, director of biological sciences A R Bellamy, 
excelled himself by asking "what do you advise Dianne Yates to do 
about her insurance?".  The responses were a series of ill-connected 
sound-bites reminiscent of the style of our babbling minigorilla now 
'heading' the WTO.  Venter downplayed the utility of DNA sequencing 
for predicting medical risks.  A dozen 'disease genes' have been 
announced in the past couple months, he said with implied 
disapproval.  Mutations in the CF gene cause not only cystic fibrosis 
but also 9 other diseases; and more importantly, many changes in that 
gene cause no ailment at all, he said.  Indeed, "variation does not 
come at a deterministic level."  We can crudely find predilections 
for some ailments, but at best estimate only a probability (said in 
such a way as to imply this is not enough for insurance companies). 
Some of the predictions are unjustified, so laws are being 
misconceived on no better than novel prejudices.  If we can't tell a 
black from a white by their DNA, the insurance companies are likely 
to be disappointed by attempts to foretell illnesses.  Comparing 
individuals by 'vertical SNP analyses' i.e. single-base mutations has 
yield no clear conclusions.  For risk readings, we'll have to move on 
to 'proteomics', he averred.
	For this *really* up-to-the minute commerce, sequencing 
proteins, he showed a large box with few readouts, a prototype 
sequencer.  A laser source feeds a time-of-flight mass spectrometer 
to sequence proteins even in mixtures.  (This claim is incompatible 
with his desire to ignore post-translation mods such as 
glycosylation, which certainly would be identified in such a 
sequencer  -  if it works at all.)
	 The ultimate response to the misguided hopes for medical 
predictions from DNA sequencing would be to sequence everybody's 
genome; so many differences would be discovered that nobody would be 
able to get life insurance cover.  I thought this was a serious 
contender for the title 'ultimate cynical nerdism'; although Venter 
insists Celera is a non-profit organisation, he made some smug vague 
complaint about high personal income taxes, and would not appear to 
be the sort of person who much needs life insurance.

	In his regular glib flippant way, Venter seemed to affirm 
atheism.  A dating system for evolution over hundreds of millions of 
years is based on sets of at least 3 gene repeats, he seemed to 
suggest.  These data imply, he expounded, that it has taken 10^8 - 
10^9y to create the human, rather than "somebody saying one day, 
'let's do it' ".  In this flippancy J Celera was impliedly denying 
not only the 6-day creation but also the Creator; but he said nothing 
definite on these matters, so I hold out some hope that I 
misunderstood his vague theological quips.

	Gluckman was good enough to let me ask an early question:
		"The leader of the Arabidopsis genome project which 
you mentioned  -  a graduate of this university  [my first grad 
student, but I didn't mention that]  -  passed thru here a couple 
years ago and gave a talk.  He said 'odd' bases do not occur in the 
copies which are sequenced.  But we have known for 4 decades that 
'odd' bases exist in DNA.  Apart from the role of methylC in CpG 
islands silencing transgenes & so forth, he said 'we don't have a 
handle on them'.  So his sequences are not accurate but are 
simplified on the slogan 'The Big Four Rule OK'.  What is the role of 
odd bases in your work?"
			Although so important as to show pictures of 
himself speaking at the podium with the crest 'The President of the 
United States', with Clinton looking up at him, Venter resorted to a 
personal wisecrack, quipping to Gluckman  "is this your local version 
of a minority?".  This childish behaviour may be a sign that he is 
not as confident as he seems in his ideas such as the slogan 'The Big 
Four Rule OK'.
	He proceeded to admit his output is indeed only in the 
4-letter alphabet T, A, G & C.  This simplification he claimed to be 
minor, an attitude he mainly justified by pointing to the similar or 
worse backwardness in identifying 'odd' groups tacked on to some 
proteins.  "It's the same with proteomics  -  the glycosyl residues 
and so on can be pinned down later.  It'll take a century to get all 
these embellishments."
	Carrying on from this reply remarkable in part at least for 
its candour, he uttered what I thought was one of his more quotable 
conclusions:  "There's no single hi-thruput method to solve all 
biological problems."
	The final questioner, quite possibly a devotee like my 
neighbour, cooed in Noo Eege style "how will folks be led to accept 
instead of fearing?".  Venter replied "it *is* fearsome  -  given 
genetic determinism", and warned that spurious detection of a fault 
in the CF gene in a foetal sample might provoke an unwarranted 
abortion.

	Gluckman asked for confirmation that the way to get ahead 
with the "Knowledge Economy" is for universities to transfer 
technology to biotech corporations.  Venter responded with some 
econobabble which I took to be affirmation of this strategy.  What is 
actually being done is that Bellamy is purging biologists to make 
room for gene-tamperers who are expected to bring in money from 
venture capitalists; this gives a somewhat different impression from 
Gluckman's sketch of the process.
	Gluckman appeared to be proximally concerned to use the 
occasion to persuade Hood & others that the University of Auckland 
should do as Venter said Australian universities had wisely done  - 
pay to get connected to his database.  How easy this might be for 
students to use Venter perhaps hinted at in his advocating that 
advanced computer skills should be central in the med school. 
Gluckman said a formal announcement should be out soon after 
negotiations on Feb 26.
	 What good might come of all this was left completely 
unclear, to me at least.  But the loud lengthy applause as the 
session ended left no doubt that the generally young audience agreed 
with Gluckman: J Craig is one of the great scientists and great 
entrepreneurs.

	Dianne Yates MP departed in the company of the devotee I had 
met earlier.  I accosted Yates with a brief attempt to disillusion 
her  -  should that be a step still open.  She identified her problem 
as inability to assess "the discrepancies"  -  I took her to mean the 
differences between Celera's sequences and those of the public team 
as he had called it.  I replied that almost everyone is similarly 
handicapped.  She moved on across the carpark, listening to the 
devotee.

	As J. Craig swept celerically out the med school front door I 
cheerfully called out exhorting him to keep after those 'odd' bases. 
He smiled  -  but then he had done that most of the time.   I would 
be very surprised if he had learned anything from this event, so 
great is his cockiness.
	And yet the fact remains that he had not even claimed, let 
alone proven, any benefit from his sequencing.

	Truly, we live in the age of bullshit.  The biggest con, 
degrading science to junk and technology to disreputable dangerous 
furphies, is gene-tampering.

R

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