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'[OT]: Was: Space trave Now: "Gene" Splicing'
2002\08\20@095846 by Jim

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 "Some people seem not to have grasped the significance
  of moving genetic code between species, something
  that could never happen in nature."

Please correct me if I am wrong, but I am of
the impression that genetic science has discovered
that a wide range of species possess similar,
verily, common genes - although not all traits,
characteristics, or facets of these genes manifest
themselves in the formation of each creature or
plant in each of the creatures/organisms in those
so-called varied or different "species" (obviously).

What has been discovered is that a wide range of
what we call "life" possesses remarkable similarity
at the *genetic* level. Various 'things' are turned
on or enabled to be developed depending on the
"species" (remember, the concept of different "species"
predates genetic-level science - I liken it to early
claims that the world is *flat* before disproval
occurred and the true nature of the earth was
discovered).

We aren't all as different as we *think* we area,
therefore, I am going to extrapolate that inter-species
gene splicing doesn't carry the risks that some leap
to conclude.

RF Jim



{Original Message removed}

2002\08\20@114117 by Russell McMahon

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>   "Some people seem not to have grasped the significance
>    of moving genetic code between species, something
>    that could never happen in nature."
>
> Please correct me if I am wrong,

You are entirely correct as fas as you have gone but, as they say, the devil
is in the details. And it may be a VERY large devil :-)

I am not a biotech professional but I have been reading extensively in this
area. I have several contacts in the industry - one has been involved in GMO
production and another in vetting GMO applications. I am certainly not an
expert in this area (yet :-) ) but feel I know a reasonable amount. My
"study" has been directed specifically towards GM and the areas of likely
concern. There are no doubt some biotech professionals here who can fill in
the gaps.

> but I am of
> the impression that genetic science has discovered
> that a wide range of species possess similar,
> verily, common genes -

There is much genetic commonality both between creatures which are
apparently close by inspection and also a degree of commonality between
species which are apparently very far apart. For example, horses and
lettuces share some common genetic material. Primates and homo sapiens have
a lot of genetic material in common. AFAIR the figure is about 6% difference
in the non-garbage DNA. This may sound close but it can represent a vast
difference in end product. Note that there is vast amounts of APPARENTLY
unused materail in DNA. When scientists compare eg apes and mankind they
have tended to exclude this material in making comparisons. An examination
of the garbage DNA (which makes up typically around 90% of the total) shows
that it has charcteristics which are possessed by certain types of data. It
appears that there is more to it than meets the eye but as yet it is keeping
most of its secrets. This should not surprise us. The difference in the
garbage DNA between species may be a very significant factor in their real
differences. In some gene sequencing techniques it is found that some genes
are lost if the "garbage" is stripped during sequencing.

Note that we don't need to know HOW the arrangements that we see arose in
order to start to explore them. It MIGHT be wise to try to find out how but
that can be annother issue. But might not be. Key contenders (and how key
will depend on your world view) are evolution via natural selection from
scratch, Divine creation (source = "being" from outside system), and
"Panspermia" - seeded from somewhere else whether purposefully and with
alien involvement or by serendipitous act (source = being inside system).
Rejection out of hand of all but  one's favoured alternative may cost you
dearly in one way or another.

> although not all traits,
> characteristics, or facets of these genes manifest
> themselves in the formation of each creature or
> plant in each of the creatures/organisms in those
> so-called varied or different "species" (obviously).

This is true but it is far more complex than this. The complexity of the
system is beyond our present imagining. We are learning to crawl as it were,
but know how to make the machinery run by pulling levers and pressing
buttons, so we do. This is not too bad a metaphor. What we have discovered
is vastly complex interacting machinery. Real genuine machines. The very
simplest fully working self reproducing system (a cell) is complex beyond
belief. A common metaphor is that a cell contains as much complexity as a
large city. I don't find that useful enough and want to seek to find a
better image.

An apparently minor change can have results out of all proportion. Consider
a gene to be a sub-program.The subprogram typically results in the creation
of a machine - a protein, via some intermediate machines. Originally it was
thought that genes produced a single protein each but each gene can in fact
make a number of programs and thjerefore proteins. As stored in DNA the gene
contains extra "pieces" of code which are not part of the finished
sub-program. When the subprogram is copied out of the DNA (onto MRNA) to be
taken to the protein making machine the unwanted pieces of code are cut out
and the wanted fragments rejoin. Lo and behold - they can rejoin in
different ways. Each way of rejoining creates a different protein when they
are read. Imagine trying to write programs like that - chop out 6 segments
of unwanted code, join the pieces in various ways and get N useful working
programs with substantially different results. To make different proteins
that all work and are useful is a miracle. A protein is a series of
molecules which fold in an extremely  complex manner.  Designing such a
folding pattern to do something useful would be a major achievement, Making
a program that writes N such sequences when chopped up anmd recombined in
different ways beggars the imagination. (If it doesn't you need to try to
imagine harder :-) ).

But it gets worse (or better).  The relative location of genes to each other
and the proximity of other "things" up and downstream in the DNA alter how
the gene works. The presence of various "chemicals" in the nucleus of the
cell (where the DNA is stored) or in the outer courtyards (where the Ribosme
protein making machinery waits to read the mRNA and create proteins) will
alter / turn on / turn off what DNA is read. The "chemicals" can be
environmental or can have been produced (and typically are) by the prior
processes which have occurred. Talk about program complexity! The amount of
interleaving, overlapping and interaction is beyond reasonable belief. We
know vast amounts about how it all works - but I'd bet that if we sat a
how-it-works-101 exam set by the creator/alien/blind-watchmaker we'd not yet
rate more than a few % on the test.

Stick any new gene into DNA and you can have a fair bet about what it will
do. But certainty is absolutely unassured. The very best techniques
available allow you to insert genes quite accurately into the target genome.
But not always. It is not currently possible to always be CERTAIN where an
inserted gene will end up. In practice, insertions go to unexpected
locations, multiple copies occur and strange results can happen at any time.
Even if we get what we want where we want it and it does what we expected
there is absolutely no guarantee that something unexpected wil not make
things change. The "machinery" can be affected by new chemicals, heat or
cold, failure to get enough water or light, or too much and much much more.
When we play we can NEVER (so far) be certain of what the results will be.
The further we get away from what nature "allows" the more probable it is
that the results will not be typical of what we have experienced previously.

A single human Interlukin 4 expressing gene was inserted in mousepox. MP is
a mild mouse disease. IL4 is a commion human body product useful in allergy
and infection applications. Added to mousepox it produced a highly lethal
mouse disease that killed all exposed mice in short order. The result was
entirely unexpected by the reserachers.

> What has been discovered is that a wide range of
> what we call "life" possesses remarkable similarity
> at the *genetic* level. Various 'things' are turned
> on or enabled to be developed depending on the
> "species"

Yes - whether by evolution or the use of a common toolkit.

> (remember, the concept of different "species"
> predates genetic-level science
> - I liken it to early
> claims that the world is *flat* before disproval
> occurred and the true nature of the earth was
> discovered).

Species is a very specific concept. It means that naturally fertilisation is
not observed to occur. You can in fact breed inter-group sterility between
creatures of the same species by artificial crossing. There are some gulls
which vary little by little around the world until having gone right round
you find they cannot breed with each other. The compatability has been
"selected out".

Species are nature's way of saying no :-)

Regardless of WHY it is this way, nature has a set of barriers which are not
crossed by normal means. It seems highly likely that the more dangerous
paths which lead to major catastrophe have been blocked in nature. All 3
models (evolution, God, Alien) would lead us to expect this would probably
be so. Where we do find interspecies crossover we usually find  disaster.
AIDS, BSE/CJD, Rabies, and others. A few cross species infecters convey
benefit. Cowpox (actually ratpox transferred via cows!) conveys immunity to
smallpox! Which might lead one to worry about the risk to humans from
mosuepox with interleukin 4 expression added.

> We aren't all as different as we *think* we area,
> therefore, I am going to extrapolate that inter-species
> gene splicing doesn't carry the risks that some leap
> to conclude.

The quantitative differences are relatively known. The human genome has been
entirely sequenced. What they mean is very largely unknown. We are 95% or 5%
like chimpanees (depending on garbage inclusion or not). Horses contain
lettuce genes. Those who seek to explain such things "to the masses" make
vaaaaaast leaps of faith which alas they often seek to hide with
blandishments. I am just completing "Climbing Mt Improbable" by Dawkins. A
more dishonest book with the facade of open revelation is harder to imagine.

We don't know anything! Almost.
We can push the buttons and watch the flashing lights.
We can make it perform many of its tricks. We often enough have no idea of
what other tricks it MIGHT do. We can be certain that we are increasing the
probability of doing new and novel things when we do things that nature has
"decided" not to let itself do. We don't know if the new and novel things
will be dangerous BUT we have had a crystal clear demonstration that a very
simple change can be. We know that we can make dangerous new designer
tailored diseases. Stumbling upon utter disaster is clearly a possibility.
Our present approach is an extremely good way to maximise our chances of
doing so.

If we fall off the edge of the world it will not be because we didn't know
that it might vcry possibly be possible !


                   Russell McMahon

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2002\08\20@115743 by Cole Christopher J

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> An apparently minor change can have results out of all
> proportion. Consider
> a gene to be a sub-program.The subprogram typically results
> in the creation
> of a machine - a protein, via some intermediate machines.

The example which springs to mind is that of Sickle Cell Anaemia - caused by the substitution of *a single base pair* somewhere in a gene to do with haemoglobin production.

From 'being normal' to having a life threatening disease thanks to one base in 3 billion being 'wrong'. Ouch.

Chris.

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2002\08\20@122728 by Brendan Moran

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> Rejection out of hand of all but  one's favoured alternative may cost you
> dearly in one way or another.

Thanks Russell, I think I have a tag line :)

--Brendan

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2002\08\20@211447 by Russell McMahon

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Ken (not on list)

> I am continually amazed by what I percieve as a widespread belief that
> natural always equates to good and artificial often equates to bad.

       > rest of post at end

Agree. But not sure whether that is agreeing or disagreeing with something I
said :-)

I am trying to be, while not in the middle, at least be wandering the battle
ground and not far out on one side. I am PRO GE in the general sense but
also pro common sense.

I am well aware (as you might expect) of the bad things that are
specifically human infecting. What I have been commenting on is the ability
or normality of "greeblies" to infect cross species or bring in new genetic
material via pathways previously unused, at least recently. Nature appears
to have erected largish barriers on almost all such pathways.  We are in the
process of leaping high over the barriers and depositing genetic material in
locations that nature has chosen not to allow its own processes to get at.
It is hard to see how undesirable and unpredictable results would not be
expected.

The lessons "learned" by long term infectors are matched by the lessons
"learned" by our bodies against them. Usually. Arms Races, when found, tend
to be relatively balanced, else the race would be over. Hopefully it's not
our race.

Smallpox lost by being too dangerous. Or so we hope - it may yet be back.

Interestingly - AIDS is PROBABLY natural (some suggest a germ warfare lab)
but probably resulted from massive human contact with green monkey viscera.
Ebola appears not to have had the interfering human hand involved, yet.
(Some suggest it as a prime germ warfare candisdate but I suspect that it is
a little too hair-triggered for that). BSE probably rose from feeding
Scrapie infected sheep central nervous system (CNS) material to cows. New
variant human CJD "probably" arose from feeding cow CNS material to people.
BUT cross species prion diseases appear to have occurred from cows in 1947
in USA when many mink farms were wiped out about a year after receiving feed
from a  central feed plant that rendered "downer" cows. (Note that this
seems to be another prion disease in cows and NOT BSE/CJD). So it appears
that we may have had about 30 years warning of cross species prion disease
transfer caused by rendering animals and using them as feed. Cross species
prion transfer in the wild was already known. If we ever get (or cause to
arise) a prion disease that attacks non CNS area in its final form (ie in
body tissues etc) we are in deep trouble. Prion infectiousness is high,
small physical infector size (<virus and << cell) makes containment
"interesting" and destruction by normal means just doesn't work. The only
known cure for a person with CJD is to incinerate them at 1000 C . Not that
such little things are liable to stop us though ...



       Russell


> Nature (i.e. natural processes) has long proven that it is very good at
> producing "bad" things and the likelihood is that it will continue to do
so.
> Obvious examples include the pathogens of old (B plague, poxes (various),
> influenza, polio, diptheria), and (probably) more recent ones (AIDS,
Ebola,
> CJD and other prion nasties, etc.)  Then there are diseases of direct
> genetic or cellular origin where patahogens are (probably) not involved.
> There are probably other categories too which I can't think of right now
> (some might even want to add obesity and diabetes to the list).
>
> All of these are undeniably natural.
>
> If nature is so good at coming up with these "baddies", then given that it
> is generally agreed that it does so very slowly through whatever
mechanisms,
> is it not reasonable to assume that humankind will do much better (in
terms
> of baddies created per unit time) by actively exploiting essentially the
> same mechanisms on a large scale ?
>
> In a nutshell  - if nature can produce such baddies are we perhaps
deluding
{Quote hidden}

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2002\08\21@010511 by Jim

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Russel, here is what I was referring to earlier about
a compound (PBB) inadvertantly being added to cattle
feed - which then made it into the food chain.

I think we have far more to fear from conventional human
mistakes, than GeneEng'd food sources, but, that is no
reason to halt scientific study in that area.

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

http://www.dscr.dla.mil/htis/novdec01.htm

Researchers in the US have found that exposure to Polybrominated Biphenyls
(PBBs) may cause an increased risk of cancer to the digestive and lymph
systems.

The study looked at the incidence of cancer in individuals exposed to PBBs
after a 1973 food contamination incident in the state of Michigan, in which
1 ton of PBB fire retardant was added to cattle feed by mistake, thus
contaminating the animal and human food chain.

Approximately nine million people were affected. Some 25 years later, in a
study published in 1998, researchers found that humans in the group with the
highest exposure to the contamination were 23 times more likely to develop
digestive cancers, including stomach, pancreas and liver cancers.
Preliminary results also found a 49-fold increase in lymph cancers.

- - - - - - - - - - - - - - - - - - - - - - - - - -

http://www.valuelogicmaths.com/vlfood_sec07.htm


b) Poisoning

Bulk production by industrial farming scales up the risk of food poisoning,
and introduces new risks. In 1973 a Michigan factory which produced both
fire-retardant (poison) and animal feed, got the two mixed. The poison was
sent out to hundreds of farms and used unsuspectingly. When cattle started
dying the cause was not traced for some time: animals slaughtered were
converted into feed which affected healthy animals: meanwhile infected meat,
eggs, and milk were sold, and thousands of chickens which had inexplicably
stopped laying were sold to an international soup company. The poison (for
which there was no known antidote) was chemically akin to one which causes
cancer and genetic defects (Observer 5 Dec 1976).

- - - - - - - - - - - - - - - - - - - - - - - - - - - -

Chemical of the Month Carcinogen Profile: Polybrominated Biphenyls (PBBs)

http://www.prop65news.com/pubs/p65news/issues/9409/940909.html

A PBB-containing commercial product, FireMaster FF-1, was mistaken as the
feed supplement magnesium oxide. Initially, health problems in dairy cattle
indicated a poisoning, but several months passed before PBBs were identified
as the problem. Following the establishment of a Michigan Department of
Agriculture (MDA) farm animal testing and quarantining program, over 30,000
cattle, 2,000 swine, 400 sheep and 2,000,000 chickens exceeding PBB
tolerances were destroyed (MDA meat fat 0.02 ppm, FDA milk 1 ppm, FDA 0.1
ppm eggs). During the nine months between the initial accident, detection,
PBB identification, animal testing, and quarantines, PBB contaminated food
products were consumed by producers and consumers. Epidemiological studies
targeting the exposed population continue in order to evaluate long- term
risks.

- - - - - - - - - - - - - - - - - - - - - - - - - -

RF Jim

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