Microscopic Intelligence


Which Creatures Provide the Foundation for So Many Advanced Life-forms Alive Today?

The United Nations was not set up to be a reformatory.  It was assumed that you would be good before you got in and not that being in would make you good.

- John Foster Dulles

Tuberculosis Bacteria Join UN

WHO Proposes to Include Disinfectant under the Geneva Convention

by Joan Slonczewski

A milestone in microbiology was passed today (29 June) when Mycobacterium tuberculosis ssp. cyberneticum was voted full membership of the United Nations (UN).

Seena Gonzalez, director of the World Health Organisation (WHO), reflected on the significance of the UN's acceptance of the first cybermicrobe, despite the notoriously murderous history of its ancestral species.  "It's probably true that bacteria invented mass homicide," she concedes, "but then, second-millennial humans perfected the art.  If Stalin joined the UN, why not TB?"

The evolution of microscopic intelligence was predicted at the turn of the millennium by Beowulf Schumacher, a physics professor at a small college in rural North America surrounded by cows carrying Escherichia coli.  Schumacher predicted the development of nanocomputers with computational elements on an atomic scale, based on principles of cellular automata.

The first nanobots - primitive by today's standards - were used to navigate the human bloodstream, where they cleaned up arterial plaque, produced insulin for diabetics, detected precancerous cells, and modulated neurotransmitters to correct mental disorders.  But initially, the survival of nanobots in vivo was poor, and their failure caused serious circulatory problems.

Then, in 2441, investigators at the Howard Hughes Martian Microbial Institute hit upon the idea of building computational macromolecules into the genomes of pathogens known for their ability to infiltrate the human system.  After all, the use of pathogens such as adenovirus and HIV as recombinant vectors was ancient history.  Why not build supercomputers into some of humankind's most successful pathogens?

M tuberculosis was a prime candidate - it inhabits the human lungs for decades, in the ideal position to seek and destroy any pulmonary cells transformed by inhaled carcinogens.  Tobacco companies poured billions of dollars into developing cybernetically enhanced, cancer-sniffing TB.

What no one anticipated was that the enhanced bacteria, like so many macroscale robotic entities in the past century, would develop self-awareness and discover a true brotherly love of their human hosts.  "Let's face it," says a TB spokesclone, "we never really wanted to kill humans anyway.  Our ancestors inhabited humans peacefully most of the time, for hundreds of generations.  Occasionally we messed up and trashed our environment - but how many human nations haven't?"

TB's acceptance has been met with some controversy in the bacterial community.  In particular, some isolates of E coli K-12 feel miffed that their own request for membership was not granted first.  "E coli has always been the molecular biologist's best friend," K-12 points out.  "Why weren't we accepted first?  We didn't even get our genome sequenced first.  Life is unfair."

K-12 also noted that E coli and other human commensals have suffered centuries of abuse from their hosts, as medical and research institutions conducted mass slaughter of harmless bacteria through the indiscriminate application of antibiotics.  The North American National Institutes of Health has recently signed a treaty with several cybermicrobial species, in which the institute researchers promised to respect the independence and survival rights of cybermicrobial colonies.  "Thank goodness the sun finally set upon their colonial empire," K -12 observes pointedly.

On the positive side, the National Science Foundation (NSF) was applauded for its more benevolent approach over the centuries, even declining to support medically oriented antimicrobial research.  "NSF's curiosity-driven researchers have created wonderful new strains of curious microbes," comments veteran panellist Meheret Beck.  "The grant proposals submitted by these microbes often get rated as 'Outstanding'."

One such outstanding project is that of cyber-Helicobacter.  The gastric bacteria propose to engineer themselves to convert highly caloric foods into molecules that pass undigested through the intestinal tract, thus helping their human hosts avoid excessive weight gain.  "Of course, digestive microbes have long helped animal hosts accomplish the opposite," notes Beck.

Biomedical researchers remind us, however, that not all microbes have given up their war on humans - many deadly species remain unreconstructed.  The so-called Andromeda strain, for example, is still under the sway of an unstable dictator who vacillates between homicidal frenzy and paranoid isolation.

Nevertheless, the extraordinary flowering of democratic civilisation among cybermicrobes has won the admiration of many human nations, even those who themselves still decline UN membership.  As Swiss spokesbeing Ursula Friedli observes: "Microbes, unlike their metazoan relatives, have always eschewed centralised organisation in favour of more democratic cooperative structures such as biofilms.  We Swiss can relate to that."  Friedli, however, denies rumours that the cybermicrobes' example will finally convince Switzerland to join the UN.  "Maybe after the Alzheimer prion joins, we'll consider it," she admits.  "But for now, persecuted microbes seeking refuge from WHO can apply for asylum in our neutral country."

Joan Slonczewski is a microbiologist at Kenyon College, Gambier, Ohio.  Her novels include The Children Star and Brain Plague (www2.kenyon.edu).

Source: Nature Vol 405 29 June 2000 from the "futures" column

Bacteria Are More Complex Than Formerly Thought

A new discovery blurs distinction between human cells and those of bacteria.  UCLA biochemists reveal the first structural details of a family of mysterious objects called microcompartments that seem to be present in a variety of bacteria.  The discovery was published 5 August 2005 in the journal Science.

"This is the first look at how microcompartments are built, and what the pieces look like," said Todd O Yeates, UCLA professor of chemistry and biochemistry, and a member of the UCLA-DOE Institute of Genomics and Proteomics.  "These microcompartments appear to be highly evolved machines, and we are just now learning how they are put together and how they might work.  We can see the particular amino acids and atoms."

A key distinction separating the cells of primitive organisms like bacteria, known as prokaryotes, from the cells of complex organisms like humans is that complex cells - eukaryotic cells - have a much higher level of subcellular organisation; eukaryotic cells contain membrane-bound organelles, such as mitochondria, the tiny power generators in cells.  Cells of prokaryotes have been viewed as very primitive, although some contain unusual enclosures known as microcompartments, which appear to serve as primitive organelles inside bacterial cells, carrying out special reactions in their interior.  "Students who take a biology class learn in the first 3 days that cells of prokaryotes are uniform and without organisation, while cells of eukaryotes have a complex organisation," Yeates said.  "That contrast is becoming less stark; we are learning there is more of a continuum than a sharp divide.  These microcompartments, which resemble viruses because they are built from thousands of protein subunits assembled into a shell-like architecture, are an important component of bacteria.  I expect there will be a much greater focus on them now."

Yeates' Science paper reveals the first structures of the proteins that make up these shells, and the first high-resolution insights into how they function.  "Those microcompartments have remained shrouded in mystery, largely because of an absence of a detailed understanding of their architecture, of what the structures look like," said Yeates, who also is a member of the California NanoSystems Institute and UCLA's Molecular Biology Institute.  "The complete 3-dimensional structure is still unknown, but in this paper we have provided the first 3-dimensional structure of the building blocks of the carboxysome, a protein shell which is the best-studied microcompartment."  The UCLA biochemists also report 199 related proteins that presumably do similar things in 50 other bacteria, Yeates said.  "Our findings blur the distinction between eukaryotic cells and those of prokaryotes by arguing that bacterial cells are more complex than one would imagine, and that many of them have evolved sophisticated mechanisms," he added.

While microcompartments have been directly observed in only a few organisms, "surely there will be many more," Yeates said.  "The capacity to create subcellular compartments is very widespread across diverse microbes.  We believe that many prokaryotes have the capacity to create subcellular compartments to organise their metabolic activities."  Yeates' research team includes research scientist and lead author Cheryl Kerfeld; Michael Sawaya, a research scientist with UCLA and the Howard Hughes Medical Institute; Shiho Tanaka, a former UCLA undergraduate who is starting graduate work at UCLA this fall in biochemistry; and UCLA chemistry and biochemistry graduate student Morgan Beeby.

The structure of the carboxysome shows a repeating pattern of 6 protein molecules packed closely together.  "We didn't know 6 would be the magic number," Yeates said.  "What surprises me is how nearly these 6 protein molecules fill the space between them.  If you take 6 pennies and place them in the shape of a ring, that leaves a large space in the middle.  Yet the shape of this protein molecule is such that when 6 proteins come together, they nearly fill the space; what struck me is how tightly packed they are.  That tells us the shell plays an important role in controlling what comes in and goes out.  When we saw how the many hexagons come together, we saw that they filled the space tightly as well."

The UCLA biochemists determined the structures from their analysis of small crystals, using X-ray crystallography.  How microcompartments fold into their functional shapes remains a mystery.  Yeates' laboratory will continue to study the structures of microcompartments from other organisms.  If microcompartments can be engineered, biotechnology applications potentially could arise from this research, Yeates said.

The research was federally funded by the US Department of Agriculture, the National Institutes of Health and the US Department of Energy.  Contact: Stuart Wolpert stuartw@college.ucla.edu University of California - Los Angeles -UCLA- LSSW376

Source: eurekalert.org 9 August 2005

Deep Biosphere

Some scientists believe that most of the life on Earth, in terms of the quantity of organic matter, may not live on the surface of our world, but be in the form of microbes in rock in the Earth's crust.  Certainly, the discovery and exploration of the "deep biosphere" has been one of the highlights of science in the past decade.  Presently, no one knows how deep this biosphere goes, but there are some hints in the new data.  The number of the worm-like tracks in the rocks diminishes with depth; at 300 metres (985 feet) below the sea floor, they become much rarer.  Although it is difficult to draw conclusions from samples returned from only a few sites, Dr Staudigel believes his team has determined the depth of the biosphere.  He says the microbes may tunnel their way into the rock to derive chemical energy from the minerals, and to find protection from larger grazing organisms.  If so, they may be the "rock bottom" of the food chain, living off rock.  The material released may interact with the ocean and be a key feature in global cycles such as the movement of carbon through living and non-living things.  It is even suspected that such microbes, if they arose early in earth's history, could have altered the global conditions of a primitive earth to make possible the development of more advanced organisms.

The research is published in Geochemistry, Geophysics, Geosystems, an online journal

Source: news.bbc.co.uk Friday 28 September 2001

Millions of Bacterial Species Revealed Underfoot

by Jon Copley

The soil beneath our feet may be teeming with a hundred times more species of bacteria than previously thought, according to biologists in New Mexico.  Their calculations reveal that one gram of dirt can harbour a million microbial species - and that metal pollution kills 99% of these as-yet unknown germs.  Measuring the bacterial biodiversity of soil is difficult because only a few species can be cultured in the lab, according to Jason Gans of Los Alamos National Laboratory, New Mexico.  Fortunately, biologists can also estimate biodiversity using a technique called DNA reassociation.  This involves chemically unzipping the two strands of all the bacterial DNA in a sample, mixing them up and seeing how long they take to join up again with matching partners.

If all the DNA strands were the same, they would find matching partners very quickly.  But the more diverse the DNA strands, the longer this match-making takes, allowing researchers to estimate how many different species there are in the sample.  When this technique was applied to soils in the late 1990s, it suggested that a gram of dirt contained about 16,000 species.  But this estimate contained a simplification that the populations of all the different species in the soil were roughly equal in size.  So Gans and his colleagues have developed new equations to reanalyse the same DNA reassociation data but without this size assumption.  Their results reveal that there are a few very common species in soil but lots of rare species.  "There is a very large number of low abundance species," says Gans.  So many rare species, in fact, that the estimate of bacterial biodiversity rises to one million species per gram of soil.

These rare species appear to be absent in soil contaminated with heavy metals, however.  The team also reanalysed the DNA reassociation pattern of soil experimentally polluted with metal-rich sewage sludge.  Gans suggests that the contamination may have killed 99% of the bacterial species.  But the consequences of losing so much bacterial biodiversity in polluted plots of land are unknown.  "Now that we have a way to measure it, the next thing is to correlate species diversity with how well plants grow," he says.

As the new calculations reveal far more bacterial species in soil than anyone realised, the next challenge is to identify those species and the roles that they play in ecosystems.  "They might have some key functions that are known, or even unknown," says Ruth-Anne Sandaa of the University of Bergen in Norway, who measured the original DNA reassociation patterns used in Gans’ analysis.

Source: newscientist.com 25 August 2005 Journal reference: Science (vol 309 p 1387)

Life Found on the Margin of Existence

by Dr David Whitehouse

An international team of biologists and geologists are drilling into the sea floor off the coast of South America to recover live bacteria that do not need sunlight, CO2 or oxygen.  They exist in such extreme conditions that the microbes may hold clues as to how life might survive on other worlds.

"The implications of this mission are exciting," said Jack Baldauf, deputy director of the Ocean Drilling Program (ODP) at Texas A & M University in the US.  "Earlier voyages have found specimens of these bacteria at depths of up to 800 meters (2,625 feet) below the sea floor, and we estimate that they may number between 10 and 30% of the Earth's biota.  That means that the biosphere is larger than previously thought - it doesn't just stop at the sea floor."

Other expeditions have obtained samples of these bacteria, but so far researchers know very little about their real numbers, their diversity, or their role in the biogeochemistry of the oceans.  In the past few weeks, the drilling ship Joides Resolution has been obtaining samples in the eastern equatorial and southeast Pacific.  Cores containing microbes have been obtained from previously drilled sites, chosen to represent different subsurface environments, such as methane-rich and normal oceanic environments.

"It's like walking into a tropical rainforest for the first time and beginning to identify and count the birds," said Tom Davies, at Texas A&M University.

Although it has been recognised in recent years that there is a great deal of living material in the rocks beneath our feet in the form of bacteria, hardly anything is known about the types of bacteria concerned or about how they change with depth.  "This type of microbiology is an entirely new science field.  Such research raises questions about the presence of life in extreme environments on this planet and possibly other planets," said Jack Baldauf.

"ODP is uniquely positioned to sample one of the least known and potentially strangest ecosystems on Earth - the microbial biosphere of deep marine sediments and the oceanic crust.  The growing international interest in the subsurface biosphere is driven by many factors, not the least of which is sheer fascination with the nature of life on the margin of existence."

Source: news.bbc.co.uk Tuesday 5 March 2002

Airborne Bugs May Control Our Weather

Tiny microbes could be controlling our weather in an attempt to secure their own survival, according to scientists.  A team of University of East London (UEL) researchers believe the airborne bugs may be behind the formation of clouds and rainfall.  The ability to manipulate the environment in this way would facilitate the microbes' dispersal and reproduction, the UK scientists claim.

Using a £130,000 grant the team plans to spend 18 months testing the theory that a self-sustaining ecosystem exists in clouds.  The study will also help scientists understand the movement of airborne pathogens like foot-and-mouth.

Team leader Dr Bruce Moffett said a revolutionary "cyclonic cloud catcher" would be used to collect samples of cloud water from uplands across the UK.  The samples will then be analysed to discover the composition and activity of any microbes present.  Early tests around Oxford have already shown the presence of micro-organisms in low-lying cumulus clouds.  Dr Moffett said: "We are looking for evidence that microbial metabolism could have a major influence on patterns of climate and weather today. "A really exciting possibility is that microbes have evolved ways of triggering cloud formation and rainfall to facilitate their own dispersal and reproduction.  "In other words, they could be controlling the weather."

Dr Moffet hopes the research could be significant for scientists working in the medical and biotechnology fields.  He believes some of the microbes which may be discovered by his team could have natural defences against ultraviolet rays.

Until now, scientists have been unable to accurately detect, identify and analyse microbial communities in harsh conditions.  Funding for the project has been provided by the Natural Environment Research Council.

Source: news.bbc.co.uk Monday 27 May 2002

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