106** Sun  4 May 97~ Charleston SC  DoE Biomarkers
	cf Uranium; checkpoints

Define mandate: how genomics will affect our lives, with
special emphasis on

o (Exogenous)  Toxicology 
	assay exposures
	define mechanisms
		targetted on DNA: mutagenesis
		targetted on gene expression
	predict outcomes
		optimize comparative studies

o (Endogenous) Polymorphisms
	personal identity
	forensics
		who's who, who dun' it today
		who was who, in history and evolution
	disease susceptibility
		prognosis, prophylaxis, mechanism
	medications;  environmental toxins and features

Set aside for now vast areas like signal transduction, intermediate
regulatory pathways; higher orders of organization in cell biology;

post-transcriptional, post-translation modification of gene products

===

Recall, 35 years ago:
  at a Ciba Symposium in London, on the Biological Future of Man

"
.fi
     Now we can define man -- genotypically at least he is six feet
of a particular molecular sequence of C H O N P atoms, the length
of DNA tightly coiled in the nucleus of his provenient egg and in
the nucleus of every adult cell."

.fi
I had thought then this was a bold manifesto of biological
materialism, a reductionist perspective that deserved some tempering
respect for other parallel "definitions of man".  Knowing nothing
then of how one would go about extracting the actual sequence of
nucleotides, it would never have occurred to me that the actual
pursuit of of chopping up those 2 meters would be thought a worthwhile
scientific pursuit.  I will confess I have had some caveats about the
transformation of biological research into that engineering project;
but these are greatly mitigated by the emergence of functional
genomics: the association of sequences with their role in biological
mechanism.  And there is no one who can doubt the power of these
methods today.

In fact, much of that 1962 symposium was a debate with HJ Muller and
Julian Huxley, that we should be placing the brunt of our effort in
the use of genetic understanding not in eugenics but - to coin a
phrase as I did - in euphenics.  That is in enhancing life's chances
for those born with a given genetic load, by intervening in the
development of the phenotype.  For the next several decades, if not
indefinitely,  I believe that remains the consensual wisdom.  There
are very few problems amenable to us at the level of germline
modification that would not be dealt with far better by prenatal
diagnosis and selective promotion of healthier fetuses.  And this
approach is free from the looming hazard of congenital monstrosities
likely to ensue from misplaced insertions of remedial genes, hard
to avert for sure.  At this moment, many new reproductive technologies
are being practised, like ICSI, with a minimum prior validation from
animal studies.  Fortunately most of the anomalies will be drastic
ones and not survive pregnancy.  Few data are published.

It goes without saying that remedial medicine does not further the
raw aims of natural selection: one can say that a sign of civilization is
the overriding of brute biology by law and custom.  Just as we now
enjoy life expectacies twice those of our primitive ancestors',
more closely coupled to the reproductive period.  All of these generate
new problems, and opportunities.  We can well say we have already
drastically revised the human species, strictly in terms of life
span, not to mention the breakdown of geographic isolation, and
the overall separation of sexual from reproductive functions. 
With all that is said about the impact of "the new biology" on human
affairs, nothing compares with the extension of life span, and
the voluntarization of death with many accompanying burdens.

These thoughts are brought closer to the fore by Dolly ---
work that cries out for confirmation.  Many will see as Wilmut's
most important scientific contribution that he has found a way that
somatic cells can be desynchronized, perhaps be relieved of their
parental imprinting, so they can function in ovo.

When we speculate about the application of cloning to humans, we
have to recall above all how precarious the procedure is, how many
failures for every "success", and the overhanging likelihood of
congenital malformation.  Those who seek a kind of "immortality" by
cloning will be sorely disappointed:  at most they are setting up a
royal inter-generational conflict.  It often takes a geneticist to
point out that, as important as are the genes, they are not our
total destiny: education, life experience, human interactions; as
well as many contingencies of trauma, infection, infatuation, and
intoxication mold us equally.  I am no advocate of cloning; but I
have little sympathy for the idea that a twin is robbed of his or
her individuality.  How we exercise our free will (albeit molded by
our worldly experience) with whatever heritage we enjoy is the measure
of our personal integrity and responsibility.

===
Hardly my place to touch on every element of this week's themes
-- beyond my time and even my capacity.   A few notes

o Toxicology  (exogenous)

Paradigm of toxicology will be the perturbation of gene expression
e.g. with libraries or chips of gene probes.

Has to be used with common sense: may not be too revealing about
death by fire, or by membrane destruction or by indiscriminate
DNA-crosslinking.  There will be provocative effects by chronic sublethal
doses; but as in the pyromaniac example they may not be entirely
revealing about the toxic levels.

But nothing will be more illuminating than the use of these methods
in comparing the responses of different tissues, or of different
species, say to chemotherapeutics or environmental toxins.  Only
within recent weeks have we had a glimmer, e.g. of the tissue
specificity of cis-platin for testicular cancer.

We obviously face an enormous impasse in the definitions of toxicity
presented to us by TOSCA, with a tacit need to assess the chronic
toxicity of 10's of 1000s of compounds, when present methods will
entail something between and $1 and $10 MM each.  Besides the costs,
we have to face a myopia that may be almost inevitable, as we
focus on the obvious.  I have found it almost beyond belief that
 could find no serious studies of mutagenesis on the part of uranium
or uranyl salts.  It is so identified with radioactivity, that
it is preempted by radon and gamma rays; nevertheless it is a
DNA reactant used in photofootprinting analysis.  Most of our
epidemiological extrapolations on the health burden from radon
come from studies of uranium miners; and the role of uranium as
a primary or a co-factor is ignored.  An enormous bill from
enforcement of radon standards is at stake.  Perhaps there is
mitigating information from direct studies of uranium carcinogesis
(not known to me at this instant) that should be put in the balance.

One has to observe the anomaly of the Department of Energy
progressively downsizing its programs in basic radiobiology research
-- once, I have to say, the pride of the nation with leaders like
Alexander Hollaender -- just when it is facing enormous national
bills for remediation of its polluted production facilities.

We once thought it would be easy to assay and understand the mechanisms
of mutagenesis.

Now:  general understanding that in any given generation the burden
of somatic mutagenesis, namely cancer, greatly exceeds that of new
currently expressed germinal mutations.  In fact, the experts I poll
have given me no compellingly proven case of environmentally induced
(chemical or radiation) mutagenesis in human germ cells.
Mostly this obscuration -- for we do not doubt it is there --arises from our
existing mutational (and segregational) load -- a legacy of the
accumulation of historic mutational events of the last 10 to 100
generations.  As the generations go by, the incremental genetic load
from environmental (radiation and chemical) pollution will aggregate
as well.  But a few generations is a long time in which to await
new biotechnical innovations; so rightly it is this decade's cancer
deaths and the like that preoccupy us.

Caveat:  many mutations, and especially those associated with genetic
defect, are not simple base substitutions, but more complex
insertions, about whose instigation by chemical and biological
intruders we know nothing.  There are examples in other animals of
virus-related insertional elements.  And we know of X-ray activation
of  endogenous leukemia viruses in mice, allowing for quite indirect
pathways of X-ray and perhaps chemical carcino- and mutagenesis.

Modern outlook:  Mutations  are rarely if ever primary outcomes of
chemical alteration of DNA.  Even a simple deamination of cytosine
to uracil leaves an anomolous mismatched base pair.  Almost all
DNA alterations are subject to repair:  this is a double edged sword.
In somatic cells of metazoa better that damaged DNA result in a mortal
cell than a neoplastic one.  In some circumstances, DNA repair
can result in more surviving mutants or cancers.  Recently, we
have come to understand the role of checkpoint management by e.g.
P53 in overseeing such decisions.  We have very little information
on the physiological regulation of the DNA-repair system, other
than its provocation by DNA damage.  Mutation rates are assessed
as if they are constants of nature, rather than endpoints of complex
developmental and physiological processes.  Even less studied are
the repair systems in situ in fetal tissue, and in various life
stages.  If half the tested chemicals are today assessed as known
mutagens; the other will probably prove to be co-mutagens or anti-
mutagens in some context.  We need to get away from simplistic labels.

We are  under enormous, sometimes valid pressure to limit the use
of animals in toxicological assays: most of the public does
distinguish between rodents and more pettable felines and canines.
Probably all of us have some qualms about what we inflict on higher
primates, and will want to be sure that some superordinate purpose
is at stake.  It is hard to think of anything dumber than using
animals for LD-50's, when they would have so much more to teach as as
complex integrated mechanisms.

o Polymorphisms (endogenous)
	personal identity:
A good heading to bring up the question, is the chromosomal genome,
more precisely the DNA sequence therein, the entire story of
hereditary determination?

We can think of a range of supplementary mechanisms - they have a long
history of defenders, sometimes among the advocates of "the
cytoplasm".  Before the triumph of DNA-reductionism during, say, the
1960's, it was sometimes proposed that genes [DNA] might well account
for intra-specific variation.  But species identity was embodied in
the cytoplasm, a "plasmon".  Absent interspecific crosses that was and is a hard
proposition to attack.  We can of course now carve out the
mitochondria, chloroplasts, and their recently found relatives -- apicomplexan
plastids in malaria.  These can be thought of (and mustnot be
forgotten) as accessory chromosomes, albeit with distinctive modes
of transmission -- and occasional traffic to, perhaps from, the
nucleus.  There are hints of other, small DNA plasmids, certainly
in the wake of gene amplification -- none have yet been identified
in germinal transmission (and as mentioned we know very little of
other viruses penetrating and being transmitted by human germ cells.)
This happens often with arthropods -- there is some chance that
Orientala tsutsugumushi, scrub typhus, is a hereditary symbiont
in ticks (influencing their sex ratio) that only accidently gets into
human life histories (usually to our grief).

When we go beyond DNA particles, we enter the murky fields of
epigenesis, but this term may I admonish you, has no explanatory
content for molecular mechanism.  Most genetic phenomena are nucleic;
some may be epinucleic (viz. attached methyl groups or acetylated
histones); some may be extranucleic.  Some epigenetic phenomena
are nucleic -- like the diversification of immunocytes by
intracellular recombination and mutagensis.  Surely some are connected
with methylation, epinucleic; some may be extranucleic -- sustained
cycles of autoregulated transcription factors.  Gene imprinting
and the silencing of one of the two X's may be connected with all
of the foregoing: the most exciting news lately is the cis-action
of the Xist RNA gene product.  This must also be autoregulating
with positive feedback for the same chromosome, negative in trans.
We have a lot to
learn, especially how these states are sustained from one cell
generation to another.

A most interesting question is whether a disembodied genome, given
some undistinguished soil, could generate and self-assemble all the
organelles that the genome encodes.  The mailboxes have somehow
to be in place to read the zipcodes of signal peptides, for the
assembly of the mailboxes and the traffic lights.  Imaginably,
egg only out of egg; perhaps try sooner with yeast.  All this might
well fail, speaking for a continuity of cytoplasm, and yet have no
bearing whatever on hereditary difference.  That will depend on
whether there are alternative viable states, cytoplasms that will
give different outcomes with the same implanted genome.  There is
some old literature on developmental anomalies with reciprocal hybrids
in frog species, and a spot of newer with mammals, that may shed some
light on this question -- which is also closely tied in with the
conditioning of somatic cell nuclei for initiation of embryonic
development in the cloning paradigm.  These cybridizations will
be great fun, but the first that has to be put in order is the
role of the known entities like the mitochondria.

	forensics
Need for quality control.  Common sense about statistics. Close
relatives known and unknown more consequential than arguments about
millions vs billions.  And handling of evidence.

	disease susceptibility
		prognosis, prophylaxis, mechanism
Greatest insights, e.g. AIDS and CRC-5
Bad luck:  malaria & Hb-S.  Despite paramount example of molecular
medicine.  Duffy better luck,


	medications; environmental toxins and features
Pharma industry can no longer ignore pharmacogenetics.  Importance
of handy diagnoses as costs  <= drugs.

EPA and OSHA is a bit further along in beginning to incorporate worries
about the most susceptible individuals as considerations in
risk assessment and risk management.  We have a minimum demand
for the relevant knowledge.  At the extreme we may face the dilemma
of how far we go in making the world safe for every genotype, and
fend off the impulse to mold the genotype as a less costly strategy.
The latter is, of course, part and parcel of the evolutionary
process for 4x10^9 years,  but not always to the satisfaction of the
individuals who have been sacrificed on the way.  Social protection of
the individual from the vagaries of natural selection is what we call
civilization.

There will be a lot of discussion about ethical dilemmas deriving
from genomic science.   There are particular worries about
No-discrimination!!  I subscribe to the common ethos when it comes to
health insurance -- in most advanced countries, we have gone a long
way towards a commitment to socializing the burdens of ill health
arising from bad luck, genetic or environmental.  We don't even look
too closely at self-inflicted illness that might be remediated by
self-care  -- partly because the evidence is still coming in on
many aspects of interaction of lifestyle and genotype.  When we
learn more about how to anticipate our personal idiosyncrasies,
there will be more tension between a social motif for lowering
health-care cost burdens, and our ornery individualism of
rejecting everyone else's advice.  But the tensions over health
insurance will be small compared to life insurance.  If the individual
is entitled to know his own hand, and keep it to himself; and then
raise the ante ad lib, this turns life insurance from a game of
craps to a game of poker.  I doubt if life insurance, except for
routinely capped, group policies, will survive those stresses.  Or,
there will be an offshore industry that will offer policies to
individuals who are willing to submit their genetic health
certificates to join a common pool of those who are risk-adjusted
accordingly.

But I suggest we have not yet reached the most telling ethical
consequence of our work: that is simply success in our endeavour,
providing the public what they demand by way of health improvement
and life extension.   That has already happened throughout the 20th
Century, with a near-doubling of life expectancy, and we are just
beginning to see the fallout in issues of generational
responsibility; prolonged intervals of debility, and the
voluntarization of the act of departing the stage.  To the extent
that we can foresee the actual consequences of our research, which
is hardly ever, I hope there is a consensus to concentrate on those
ameliorations that will enhance the quality of life for all those
extra years that medical science has already visited on us.




But Problems of life insurance: poker vs craps