A consensus is emerging among scientists and engineers that
the only feasible alternative to the fossil-fuel, metal-bashing type
of.industrial economy of today is a hydrogen economy. When fossil fuels
start to become very expensive in the next two or three decades at the
latest then hydrogen fuel can be the only one that can produce
electricity and also be the basis of the chemical feedstocks that
are badly needed for plastics, pharmaceuticals and similar carbon-based
products.
Nuclear power will not be the basis of a hydrogen economy because it can
only produce expensive electricity. It would be possible to produce
hydrogen (by electrolysing water) but only very expensively. Nuclear
power will undoubtedly continue for specialised purposes, such as making
nuclear weapons or preparing radioactive chemicals for medical or other
scientific uses, but not as a basic energy technology that underpins a
country's overall economy.
Silicon- or germanium-based solar cells have also been proposed but these
can't be the basis of a hydrogen economy either because the production of
the basic capital equipment of this technology would require the most
massive use of intensive high-energy production methods -- something that
is going to become prohibitively expensive as fossil fuels decline. Like
nuclear power, solar cells will also be valuable in the future but only
for specialised uses.
The only method that will produce hydrogen cheaply and in large enough
quantities to sustain a world-wide population on a continuing basis will
be by the use of bacteria, powered by sunlight. However, those who talk
about a hydrogen economy most enthusiastically -- usually politicians and
CEOs of the automobile industry (wearing hypocritical hats as
eco-warriors) -- are not aware that a hydrogen economy is probably going
to produce a society with a totally different infrastructure from
today's.
The article below describes some of the work that has now started on what
has been a largely unknown area of science -- bacteria. A minority of
bacteria are below the earth's surface but most are on or near the
surface and directly powered by sunlight. It has been realised only very
recently that bacteria comprise as much as half of the earth's biomass
and that the total amount of solar power that they consume every day is
thousands of times greater than the power that mankind produces and
consumes today.
Thus there could be no shortage of power and chemical feedstock for
mankind's use in the future if we were able to tap into the world of
bacteria. The following article from the New York Times contains
some intriguing intimations of this approach -- particularly that of Carl
Venter's work. The latter is to find the precise genetic sequences that
will produce hydrogen. These sequences are likely to be found in only a
very small number of bacteria, and occupying only a very small niche in
the total world ecology. However, once these are discovered, it will also
be necessary to know what their environments are in detail, so that the
bacteria concerned can be scaled-up to fairly large-scale manufacturing
dimensions.
However, the production processes of hydrogen from solar power will have
quite different characteristics from the type of highly-centralised
petrochemical refineries that are the basis of today's economy. Hydrogen
will be able to be produced almost anywhere on the habitable surface of
the earth -- and even on the surface of sea in some places if desired. If
sufficient water can be supplied -- the only major chemical feedstock
that will be required -- even deserts and mountain terrains could be
used. This will mean that, to a very considerable degree, the equilibrium
of mankind's economic infrastructure and built environment will be
shifted towards something more resembling agriculture in which hamlets
and small villages will start to become self-sustaining again.
Over the longer term, the genetic knowledge gained from the development
of a hydrogen economy will lead to even more innovative technologies.
Multi-cellular 'factories' with custom-made DNA will be able to produce
organic materials that are at least the equivalent in performance of many
that are produced today based on metals and crude plastics which require
high-energy methods that have been enabled by the use of petrochemicals
from fossil fuels. For example spider silk is far stronger than steel
wire of the same dimensions and there is no reason why artificial spiders
and the like should not be able to produce a vast range of construction
materials. Over the longer term future, there is no reason why DNA
processes cannot produce carbon-based analogues which are fully
equivalent to present-day consumer goods -- and, indeed, bearing in mind
the fantastic complexity of living beings, such goods could be far more
sophisticated than present-day products.
If our present fossil-fuel based technology were to continue decade after
decade as it has done for the past two or three centuries, then there can
be little doubt that the accompanying trends towards large cities and
metropolises, even megapolises, would only intensify and make our lives
even more alienated and deficient in community responsibility and social
satisfactions. But the fact that the new successor technologies can be
widely dispersed will inevitably change our infrastructure towards
something rather more similar to agriculture. Even more so, when
considering the sheer variety of factory systems that will be necessary
in order to produce a sufficient variety of consumer goods, the scenario
will have a variety and complexity rather more akin to the ecology of
hunter-gatherer times -- that is, with far, far smaller populations than
at present.
"Ridiculous", some will say. But many populations in Europe are
already procreating at much less than replacement rate and are on the
verge of falling steeply anyway within the next decade or two. Even the
growth of the large populations of the undeveloped world is now slowing
down, except in some Islamic countries where women are denied
opportunities for education and contraceptive choice. When and if any of
the undeveloped countries reach the standard of living -- and the
life-style -- of the developed world, then it is almost certainly the
case that their populations will decline steeply, too. So the prospect
already looks highly achievable.
The problem really is: Will there be sufficient groups of talented
scientists who will be able to solve the highly complex problems that
will be involved in determining at least the first of the necessary DNA
sequences that will rescue us as fossil fuels become exhausted and very
highly-priced in the coming decades? The prospects are not necessarily
favourable. There are few countries today in which the culture values
intellectual excellence even more than consumerist prosperity and which
significant numbers of highly talented people will be allowed to carry
out research into genetics without too much regulatory interference. I
can only think of three possible candidates at present -- America, China
and Israel.
Keith Hudson
<<<<
A NEW KIND OF GENOMICS, WITH AN EYE ON ECOSYSTEMS
Andrew Pollack
Determining the complete DNA sequence of a single species has become
almost commonplace. It has been done for humans, mice, rice plants and a
host of microbes, among others. Now some scientists are moving to a more
audacious challenge, sequencing "metagenomes," the DNA of
entire ecosystems.
The new efforts seek to read all the DNA in the bacterial communities
found in a patch of soil or seawater or even the lining of the human gut.
Deciphering the genetic blueprint of all of the microbial species may
help tell scientists which species are present and how they work
together. Thousands of previously unknown micro-organisms may be
unearthed, as well as new drugs, chemicals and ways of harnessing
bacteria to fight pollution.
"We think this is a window on biology that is really unprecedented
in its implications," said Dr. Jo Handelsman, a professor of plant
pathology at the University of Wisconsin, who coined the term
metagenomics to refer to the new field. Others call it community
genomics, environmental genomics, or microbial population
genomics.
By whatever name, the task will not be easy. There can be thousands of
different microbial species in a spoonful of soil. "A milliliter of
seawater, in a genetic sense, has more complexity than the human
genome," said Dr. Edward F. DeLong, a senior scientist at the
Monterey Bay Aquarium Research Institute in California.
Besides soil and seawater, scientists are trying to read all the DNA of a
bacterial community that contributes to acidic runoff from a former
California mine, and of another community of seabed-dwelling microbes
that can be used to produce electricity. Other projects are looking at
microbial communities in the guts of termites and gypsy moths, since
microbes play a role in the way these pests wreak their damage.
Among those entering the field is Dr. J. Craig Venter, the maverick
scientist whose biotech company, Celera Genomics, defied skeptics and
determined the human genetic sequence in a scant three years. Dr. Venter,
who now runs nonprofit research institutes in Rockville, Md., is trying
to determine the genomes of all of the microbes in the Sargasso Sea, an
area of the Atlantic Ocean near Bermuda known for its floating seaweed.
That area of the ocean is considered relatively devoid of life.
Nevertheless, Dr. Venter said, "Just from the Sargasso Sea alone,
we've discovered more new genes than in the human genome."
The project is being done by Dr. Venter's Institute for Biological Energy
Alternatives, which seeks to harness microbes to make clean-burning
hydrogen fuel and reduce global warning. Another of his research centers,
the Institute for Genomic Research, is trying to sequence the genomes of
all the organisms in the human intestinal tract. The information could
lead to new ways to diagnose and treat diseases.
Until now, scientists have started with a known species, be it humans or
anthrax bacteria, and sequenced the genome to learn more about it. But
metagenomics works in reverse. It starts with the DNA of unknown
organisms and then tries to figure out what the organisms are.
More than 99 percent of bacteria cannot be grown in laboratory cultures,
so scientists know almost nothing about them. But it is possible to
extract DNA from a sample of soil or seawater without knowing the
identities of the creatures that are the DNA sources. "We don't know
what the species even look like," Dr. Venter said. "All we know
of them is their genetic code."
This DNA will consist of fragments from all the species present. The
challenge is to sort out which fragments come from the same organism and
then to arrange them in the correct order to determine the complete
sequence of each species. Such genetic blueprints could then provide
clues about what species are present and what their roles are.
The payoff could be vast. Bacteria constitute more than half the living
matter on earth and play essential roles in numerous environmental
cycles. They turn nitrogen in the air into a form usable by plants,
produce about half the oxygen on the planet, break down minerals and
clean up pollution.
"Microbes are kind of the master chemists of our planet," said
Dr. DeLong of the Monterey Aquarium. Bacteria are also the source of most
antibiotics and of some other drugs and industrial enzymes and of the
genes that confer pest and herbicide resistance to genetically modified
crops.
There have already been some discoveries from sampling environmental DNA.
Dr. DeLong, sampling microscopic plankton from the surface of the Pacific
Ocean, discovered certain bacteria that could convert sunlight into
energy, a role normally played by plants.
"It's a whole new class of light-driven energy generation that
exists in a category of microbes that's really abundant," he said.
"It remained invisible until we applied these genomics
techniques."
Diversa, a company in San Diego, bases its business on extracting DNA
from creatures that can survive in extreme environments, like super-hot
deep-sea vents and the highly alkaline soda lakes of Kenya. It then
searches the DNA for genes that provide the code for novel enzymes. One
enzyme, found from sampling DNA in the soil of the tropics, is expected
to cut in half the cost of a critical step in manufacturing the
cholesterol-lowering drug Lipitor.
Community genomics got its start in the 1980s, when scientists began
sampling microbial DNA from the environment and studying a single gene
that coded for part of the ribosome, the cell's protein-making
machinery.
Virtually every creature on earth is thought to have this gene, though it
has changed through evolution. So looking at it could tell scientists how
many different types of microbes were present and into what broad
categories they fell. But it did not tell them more about the way the
bacteria functioned.
In the 1990s, scientists began to analyze larger fragments of DNA,
looking for genes of interest. This was how Dr. DeLong found the
photosynthetic bacteria and Diversa the enzyme to be used in making
Lipitor.
Now, to get even more information, scientists are trying to determine the
complete genome sequences of all the bacterial denizens of a community.
The technique they use is called shotgun sequencing, which was used by
Celera in sequencing the human genome. Because gene-sequencing machines
can handle only small stretches of DNA, the DNA to be sequenced is broken
into random fragments. After the sequence of each fragment is determined,
powerful computers assemble the pieces in the correct order by looking at
overlapping sequences.
It is like shredding multiple copies of a book into tiny pieces and then
trying to figure out the text.
But while this has been done for individual species, doing it for
hundreds or thousands is expected to be much harder, like shredding and
reconstructing multiple copies of multiple books. Dr. Venter says
computer simulations indicate that it should be possible, at least for
the Sargasso Sea.
Many scientists still doubt that. But success is already being seen on
more narrow communities. Dr. Jill Banfield, professor of earth and
planetary science at the University of California at Berkeley, is
studying the microbes found 400 feet underground at Iron Mountain, an
abandoned mine in Northern California. The microbes contribute to the
highly acidic runoff that has made the mine a major hazardous waste site
under the federal Superfund program.
Dr. Banfield, who is working with the Department of Energy's Joint Genome
Institute in nearby Walnut Creek, says there are probably just seven
different species in the sample, either bacteria or archaea, another type
of microbe that tends to inhabit extreme environments. The full genomes
of the two organisms have already been determined. "As far as I
know, it's the first time a genome has been recovered from a truly
environmental sample," she said.
There are some obstacles to overcome before even trying to put the DNA
fragments together into the correct order. Extracting DNA fragments from
the environment can be difficult, particularly from soil, which contains
acids that break down the genetic material. And one or two species may
dominate in an environment, outnumbering other species by as much as
100,000 to 1. So the DNA fragments will be mainly from the dominant
species.
"When somebody says they are going to sequence all the bacteria in a
soil sample, well, that's rubbish," said Dr. Julian Davies, an
emeritus professor of microbiology and immunology at the University of
British Columbia.
Dr. Davies started a company to find new antibiotics by extracting genes
from soil bacteria that could not be cultured in the laboratory. But
antibiotic production is often governed by many genes, not just one, and
it was impossible to extract DNA fragments large enough to contain all
the necessary genes, he said.
Still, sampling techniques are improving. Diversa has a method, based on
the relative density of DNA's chemical units, to prevent rarer species in
a sample from being overlooked.
There is still debate about how valuable it will be to reconstruct the
genomes of all members of a community. That alone will not necessarily
tell which genes are active or how the bacteria interact with one
another. "What you get is a catalog," Dr. Davies said.
"You get unnamed organisms. The question is how can you tell what
they do."
But Dr. Steven R. Gill, a microbiologist at the Institute for Genomic
Research, countered that if a creature's genetic blueprint was known,
"we can go back and reconstruct its metabolism."
Besides providing clues about the roles organisms play, such information
may pinpoint nutrients they need, allowing previously unculturable
organisms to be grown in the laboratory. And once all the genes in an
organism or community are known, it will be possible to make gene chips
to study which genes are turned on or off as environmental conditions
change.
Some scientists think ecosystem genome sequencing may eventually be used
to monitor the health of environments or to predict environmental
impacts. That could apply not only to the external environment but also
to the ones inside people.
Dr. David A. Relman, an associate professor of medicine and microbiology
at Stanford who is collaborating on the project to read the DNA of the
bacteria in the human digestive tract, said changes in those bacterial
communities contributed to diseases like colitis.
It may be possible to find patterns in the bacterial population that will
predict when someone is about to get sick. The human gut metagenome
project "will be the first step in identifying these patterns,"
Dr. Relman said
New York Times --21 October 2003
>>>>
Keith Hudson, Bath, England,
<www.evolutionary-economics.org>,
<www.handlo.com>,
<www.property-portraits.co.uk>
