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SCIENCE-FOR-THE-PEOPLE  June 2004

SCIENCE-FOR-THE-PEOPLE June 2004

Subject:

MannGram®: Scientists find new type of gene in junk DNA

From:

Robt Mann <[log in to unmask]>

Reply-To:

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

Date:

Fri, 4 Jun 2004 15:19:07 +1200

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (189 lines)

        MannGram®: Scientists find new type of gene in junk DNA
                                June 2004

        The daily email bull of a main GM-promotor organisation (funded by
the NZ govt as its main science advisor) just featured this gasser:

---

*******Items Web-mounted on Thursday, 3 June 2004**********
<http://www.rsnz.org/news/date/2004/6/3>

Scientists find new type of gene in junk DNA
   In the yeast genome


---

        It's not widely known that there are currently several defns of
'gene'. (This is one reason why statements of the 'number of genes in a
human genome' differ.) A given stretch of DNA may count or not count as a
gene, according to which defn is applied. This fact alone should give
pause to any outside the technical field as they consider claims of
predictable properties in GMOs. For the purposes of inserting transgenes
and especially for the purposes of predicting deviant metabolism that may
be caused by the violent insertion of cassettes of transgenes to force
illegitimate recombination, what constitutes a gene is a key issue.
         The fact that the GM crops now released are all based on
illegitimate recombination classifies them as - in the technical language
of geneticists - GM-bastards. It astonishes me that the movement for
control of GM, tho' relatively aware that what we are in is a PR-war, fails
to use this technical term. I can assure you gene-jockeys hate it,
complaining it's - you guessed it - emotive.

        I have felt for a few y now that, if we are going to try to rank
problems of GM, the most important problem is not this or that transgene -
tho' some of them are particularly worrying - but the genomic
discombooberation entailed in the methods used for inserting the
transgenes, no matter which they are. Several classic CumminsGram®s, and
the odd MannGram, have made this point. Biolistics most of all, and
synthetic modified T-plasmid insertions to a less extreme but still drastic
degree, would be expected to, and are now known to, disrupt the target
genome in numerous harmful ways. Most of the target cells are killed; of
the survivors, most are obvious monsters. In the selected tiny minority
not obviously duds, a variety of delayed harm has come to light - e.g
lower yield & weaker stems in some GM-crops, deviant metabolism (in Showa
Denko bacilli), incr fungus susceptibility, etc etc. The identified types
of damage are mostly, if not entirely, not what anyone could have predicted
from any foreseeable properties of the CaMV promoter etc. It is the brutal
fact of illegitimate recombination creating GM-bastards that is 'the'
problem, no?
        Could the questions implied by this line of reasoning be examined
scientifically, e.g by inserting constructs containing minimum numbers of
foreign genes - just copies of genes already in the target cells, with
the minimum foreign genes needed to achieve detectable expression -
compared with constructs carrying more foreign genes? What should be
monitored in the GM-bastards & their progeny, in expts along these lines to
illuminate this issue?

        BTW this forcing of illegitimate recombination is indeed, if ever
there was one, a rape of Nature. Why has this not been latched onto, nay
harped on, by the feminazis (& their wimps) who control much of the
communication in the media, courts, bureaucracies & legislatures all so
failing to control GM? I have tried to interest some hevi-doodi Quaker
activists in making more of the ghastly penetrativity entailed in current
GM, but they've not done so AFAIK; perhaps this is because the person
pointing out this tactic for them is a notorious critic of their ideology.
My own personal opinion is that these crude insertion methods must cause
insertional mutations and (insofar as such metaphors are ever valid) should
indeed by seen as rape, overwhelming natural barriers to insist on alien
insertions. I just don't want it claimed that this somehow casts
aspersions on men past or present, or on any political issues alluded to by
wimminsLib.

        The RSNZ teaser reminds us that the gene-jiggerer trade has
perverted science worse than ever in history. The 'lego' model of biology
required for the current mutational methods producing GM-bastards (e.g
RoundupReady® soybeans and any progeny or sideswiping infections) is known
to be junk science. But its main commercial practitioners are still
getting away with the assumption that lack of knowledge of the functions of
the vast majority of our DNA, or of yeast's DNA, justifies calling it junk.
Even the circumlocution of J Celera Venter 'of more forensic than
physiological significance' will not put on a scientific basis the
insertions, usually into sites of unknown function, of synthetic DNA
'cassettes' designed on proven falsehoods ('the Big Four Rule OK' and other
oversimplifications; and a choice of defn of 'gene' that may be
inappropriate). If a stretch of DNA contains no sequence recognisable as a
gene by any of the several current defns, that may mean only that
inappropriate defns have been used; indeed the RSNZ hack implies by his
phrase ' new type of gene' that some further defn may have originated this
PR.

        The tiny glimpse of understanding of a few % of the genome upon
which current gene-tampering is based, and the yet smaller understanding of
the 'non-coding' majority, should lead us to expect with Lewontin an
endless series of nasty surprises in the unforeseeable behaviour of
GM-bastards.

        I copy for convenience a recent media item indicating some
awakening to the issue of 'junk' DNA.


> 'Junk' DNA reveals vital role
> Inscrutable genetic sequences seem indispensable.
> Nature Science Update, 7 May 2004
> http://www.nature.com/nsu/040503/040503-9.html
> HELEN PEARSON
>
> If you thought we had explored all the important parts of our genome,
>think again. Scientists are puzzling over a collection of mystery DNA
>segments that seem to be essential to the survival of virtually all
>vertebrates. But their function is completely unknown.
>
> The segments, dubbed 'ultraconserved elements', lie in the large parts of
>the genome that do not code for any protein. Their presence adds to
>growing evidence that the importance of these areas, often dismissed as
>junk DNA, could be much more fundamental than anyone suspected.
>
> David Haussler of the University of California, Santa Cruz, and his team
>scanned the genome sequences of man, mouse and rat1. They found more than
>480 ultraconserved regions that are completely identical across the three
>species. That is a surprising similarity: gene sequences in mouse and man
>for example are on average only 85% similar. "It absolutely knocked me off
>my chair," says Haussler.
>
> The regions largely match up with chicken, dog and fish sequences too,
>but are absent from sea squirt and fruitflies. The fact that the sections
>have changed so little in the 400 million years of evolution since fish
>and humans shared a common ancestor implies that they are essential to the
>descendants of these organisms. But researchers are scratching their heads
>over what the sequences actually do.
>
> The most likely scenario is that they control the activity of
>indispensable genes. Nearly a quarter of the sequences overlap with genes
>and may be converted into RNA, the intermediate molecule that codes for
>protein. The sequences may help slice and splice RNA into different
>forms, Haussler suggests.
>
> Another set may control embryo growth, which follows a remarkably similar
>course in animals ranging from fish to humans. One previously identified
>ultraconserved element, for example, is known to direct a gene involved in
>the growth of the brain and limbs.
>
> To solve the conundrum, experts predict a flurry of studies into the
>enigmatic DNA chunks. "People will be intrigued by this [finding]," says
>Kelly Frazer who studies genomics at Perlegen Sciences in Mountain View,
>California. "It is the kind of stuff
> that blows people away."
>

> Hard to believe
>
> Geneticists have known for some years that there are critical sections of
>DNA aside from the much-acclaimed genes. A fair fraction of the mouse and
>human genomes, aside from protein-coding sequences, show strong
>similarities.
>
> But ultraconserved segments are particularly unusual because they are
>100% identical in man and mouse. Until now, some thought they were human
>DNA that had contaminated mouse samples. "People had a hard time believing
>it," Frazer says.
>
> The presence of exact copies in different animals suggests that even tiny
>changes in the sequence of these segments destroy whatever they do, and
>have been weeded out during evolution. Non-essential regions of DNA, by
>contrast, tend to accumulate mutations so that the sequences vary in
>different organisms.
>
> Figuring out what the mystery segments do will be difficult.
>
> There are few similarities between one region and another, so these
>cannot be used to provide clues to their function. One laborious technique
>will be to genetically engineer mice that lack one segment and see how
>that affects their growth and
> behaviour.
>
> Once the function of ultraconserved elements is resolved, researchers
>will still have to tackle other vast tracts of the genome that are similar
>in different organisms, says geneticist Kerstin Lindblad-Toh of the Broad
>Institute in Cambridge,
> Massachusetts. "This is the tip of the iceberg," she says.
>
> References
>
> 1. Bejerano, G. et al. Science, published online,
>doi:10.1126/science.1098119, (2004).
>
>
R

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