On Wed, 22 Oct 2003, Keith Hudson <[EMAIL PROTECTED]> wrote:
>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.
[...]
>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.
When you suggested this last winter, I pointed out the work being
done with direct catalysis using TiO2 and sunlight:
On Tue, 17 Dec 2002, pete wrote:
>
> Date: Tue, 17 Dec 2002 18:08:07 -0800 (PST)
> From: pete <[EMAIL PROTECTED]>
> To: [EMAIL PROTECTED]
> Subject: FWk: Cracking water with sunlight
>
[...]
> Here's where I saw it, this is from a usenet post from
> sci.space.tech:
>
> ****
>
> It has been known for some time that titanium oxide (TiO2) can
> catalyze the electrolysis of water, if a photon is provided. The
> limiting factor here is that the photon needed to be in the near-UV.
> However, just a few weeks ago, it was reported that doping TiO2 with
> carbon induces it to absorb photons from the visible range (Khan,
> Al-Shahry, and Ingler, Science Vol. 297, pp. 2243). On this improved
> catalyst, the visible-range photons will also catalyze water
> electrolysis. Efficiency has been increased eight-fold over pure
> TiO2.
>
> The point? You can now make H2 with water, the titanium-carbon
> catalyst, and sunlight. The process isn't efficient enough to be
> considered commercially competitive, but the break-even point is less
> than a factor of two from present efficiencies.
>
> --
> John J. Ladasky Jr., Ph.D.
> Department of Biology
> Johns Hopkins University
> Baltimore MD 21218
> USA
>
> ****
>
> I'm not sure why it's not considered commercially competitive if
> it requires no energy input cost. Perhaps an issue of rates.
>
> Anyway, I looked at the Science article, it appears the process also
> requires a bias voltage of 0.3V and generates a "photocurrent" of
> the order of 100 mA, though if I'm understanding correctly that
> isn't a power draw from the mains. Also, the authors demonstrate
> that the catalyst is not degraded in the process, over months
> of testing, so that's not an issue either.
>
> I will quote from the accompanying gloss from the Science editors:
>
> ****
>
> CHEMISTRY:
> Catalyst Boosts Hopes for Hydrogen Bonanza
>
> Robert F. Service
>
> Green-energy aficionados have long dreamed of using the sun's rays to
> split water molecules to release hydrogen gas, which produces only water
> when it burns. Now on page 2243, chemists report that adding carbon to
> the well-known water-splitting catalyst titanium dioxide increased the
> catalyst's ability to convert the energy in sunlight more than eightfold,
> to 8.5%, just below the U.S. Department of Energy's 10% benchmark for a
> commercially viable catalyst.
>
> ****
>
> What the numbers mean, from the article, is the percentage of incident
> (photo) energy employed in the conversion process. It seems to me
> if it's sunlight, who cares if it's less efficient, just make your
> farm larger.
The centrepiece of this technology is the TiO2 electrode. Well, it
turns out that TiO2 electrodes have also been the object of some
other rather earth-shattering research over the last decade, which
has culminated in the technology described in the October Scientific
American, in the "Innovation" section (probably also on their web
site). It has been discovered that in a solution with a TiO2 electrode,
application of voltage causes the migration of the oxygen molecules out
of the matrix into solution, leaving the metal atoms to collapse back
into a pure metal crystal! For those who don't immediately understand
the implications of this, consider that titanium is, at about one
half a percent, the seventh most common metal on the surface of the
earth, after iron, aluminum, sodium, magnesium, potassium, and calcium.
It is equally ubiquitous as these, though extremely rare in non-oxidized
form. It is present in almost all rock, generally in the form of
TiO2. As a metal, it is about as strong as steel, slightly heavier
than aluminum, more resistant to corrosion than either (via a
micro-thin oxide layer).
The announcement in SA says that pilot projects generating Ti in
kilogram quantities per day are already in operation, and industrial
multi-ton per day facilities are only a couple of years away,
At this point, titanium might easily become as cheap as aluminum.
Imagine the effect on the economy of lightweight rustproof cars!
However, for the present discussion, my attention is drawn to
the sudden interest which will be drawn to the production of
TiO2 electrodes, and the possibilities this holds out for the
rapid acceleration of developments in TiO2 technology for the
production of hydrogen. Titanium chemistry may be the "next big
thing", technologically. And titanium catalyzed hydrogen production
may give bacterial processes a good run for the money.
-Pete Vincent
>
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>
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