Making New Friends


Traveling on the Slime Highway

The question is, why are politicians so eager to be president?
What is it about the job that makes it worth revealing, on national television,
that you have the ethical standards of a slime-coated piece of industrial waste?

- Dave Barry


by James A Shapiro

One dictionary's definition:

"Widely distributed group of microscopic, one-celled vegetable organisms..."

As a matter of fact, the nearly universal image of a bacterium is that of a simple, single-cell organism.  But:

That view is now being challenged.  Investigators are finding that in many ways an individual bacterium is more analogous to a component cell of a multicellular organism than it is to a free-Iiving, autonomous organism.  Bacteria form complex communities, hunt prey in groups and secrete chemical trails for the directed movement of thousands of individuals.

J A Shapiro, author of the preceding quote, attributes the simplistic picture of bacteria to medical bacteriology, in which disease-causing bacteria are classically identified by isolating single cells, growing cultures from them, and then showing that they cause the disease in question.  In the microscopic real world, bacteria virtually always live in colonies, which possess collective properties quite different and much more impressive than those of the single-cell-in-a-dish!  That old human urge for reductionism has led us astray again.

Shapiro seeks to remove the blinders of reductionism in an article in the June, 1988, issue of Scientific American:

Bacteria as Multicellular Organisms

We have room here to mention only the Myxobacteria, many of which never exist as single cells in nature.  Even those that do are "social" in the sense that, when two cells meet, they align themselves side by side and go through ritual motions that seem foreign to such "simple" organisms!  (Where is this "dance" encoded in the single cells?  Do they have "memories?")

Movements within colonies of Myxobacteria are highly coordinated.  Trails of extracellular slime are secreted and serve as highways for the directed movement of thousands of cells, rhythmic waves pulse through the entire population, streams of bacteria move to and from the center and edges of a spreading colony, and bacteria aggregate at specific places within the colony to construct cysts or, in some species, to form elaborate fruiting bodies.

The Myxobacteria also collectively form baglike traps to engulf and digest prey.  It is apparent now that as simple as a single bacterium may seem, bacterial colonies are pretty complex.

from Scientific American 258:82 June 1988


Slime "Has a Mind of Its Own"

Paris - Squidgy slime mould with just a single cell to its name has the intelligence to find the shortest way around a maze, Japanese researchers' say.

Scientists from the Bio-Mimetic Control Research centre in Nagoya took a piece of Physarum polycephalum, an amoeba-like organism, and placed it in a 30 sq cm maze consisting of a path of smooth gel on which it could travel, and "walls" of dry plastic film which it shunned.  The slime then spread its network of tube-like legs, called pseudopodia, to fill up all the available space in the maze.

Enticing pieces of food were then placed at separate exit points of the maze.  There were four possible routes between the two points.  Sensing the food, the slime withdrew from the dead ends of the maze then stretched its body along the shortest route between the two piles of nutrients, effectively "solving" the puzzle.

The researchers say they were astonished by this feat, which they ascribe to the slime's drive to survive.  "To maximise its foraging efficiency, and therefore its chances of survival, the [slime] changes its shape in the maze to form one thick tube covering the shortest distance between the food sources.  This remarkable process of cellular computation implies that cellular materials can show a primitive intelligence."

The study is published in this week's British science journal Nature. - AFP

Source: The Dominion Thursday 28 September 2000

Even single-cell animals such as the slipper-shaped paramecium have primitive sensory and learning capabilities.
With practice, paramecia can learn to back more quickly out of narrow glass tubes.


See also:

bulletFractal Evolution (further on in this section) - By the 1980s, a home computer could handle arithmetic precisely enough to make colourful pictures of the Mandelbrot set, and hobbyists quickly found that exploring these pictures at ever-greater magnification gave a vivid sense of expanding scale.  If the set were thought of as a planet-sized object, a personal computer could show the whole object, or features the size of cities, or of buildings, or of rooms, or books, or letters, or bacteria, or atoms.  The people who looked at such pictures saw that all the scales had similar patterns, yet every scale was different.  And all these microscopic landscapes were generated by the same few lines of computer code.  Why not presume that human consciousness is an evolved expression of cellular consciousness?

According to David Attenborough, bacteria can be found living more than two miles below the surface of the earth (where they may reproduce as infrequently as every 500 years).  In fact, the biomass of bacteria exceeds the mass of all other animals and plants on earth combined.  Further, 90% of the living protoplasm in our own bodies is actually bacteria.

Old Salts

The New Mexican desert grows creepier and creepier.  Ever since a spaceship supposedly crashed outside the town of Roswell in 1947, this arid landscape has been the rumoured home of all kinds of alien life.  How fitting, then, that evidence unearthed not far from Roswell suggests that life could indeed have come to earth from outer space.  The biologists who performed the research even have living examples of this evidence growing on their laboratory benches right now.  There is no need to panic, however: the creatures in question are harmless bacteria that were found preserved in a crystal of rock salt.  But according to their discoverers, these very same bugs last wriggled a quarter of a billion years ago.

Back then, in the Permian era, a vast inland sea covered much of west Texas and south-eastern New Mexico.  As the outlet linking this sea to the ocean became blocked, the sea began to evaporate slowly, leaving behind the mineral and saline deposits of the so-called Salado Formation.  Russell Vreeland and William Rosenzweig, biologists at West Chester University in Pennsylvania, together with their colleague Dennis Powers, a geologist, started analysing Salado salt crystals in the hopes of finding some biological record of this bygone time.  As they report this week in Nature, they found what could be the world's oldest surviving life forms.

Trapped inside the crystals of rock salt were tiny drops or "inclusions" of brine, capable of serving as perfect biological time capsules from the Permian era-provided they had not been contaminated since.  The researchers' most pressing concern, therefore, was to establish that the crystal samples, and their precious cargo, had remained intact since their formation.  By using stringent sterilisation procedures, the researchers satisfied themselves that modem bacteria had (literally) only a billion-to-one chance of slipping into their ancient samples.  Then, after carefully drilling a hole into the crystals' walls and removing the few microlitres of fluid from each inclusion, the researchers began testing their samples for life.

Of the 66 inclusions examined, three showed evidence of viable bacteria.  So far, the biologists have characterised just one of these strains.  It is a spore-forming bacterium, dubbed 2-9-3, which came from a crystal that was retrieved from the wall of an underground shaft in New Mexico.  Through DNA sequence comparisons, Dr Vreeland established that 2-9-3 was 99% identical to a modern species called Bacillus marismortui, which has recently been shown to inhabit the brackish waters of the Dead Sea.  Both 2-9-3 and its modern cousin appear to have adapted for survival in their respective salty homes.

But 2-9-3 is able to tolerate salinity only to a certain extent.  When its surroundings grow too salty, it forms spores and waits until conditions improve.  Indeed, this seems to be the key to its longevity.  Dr Vreeland speculates that, as the Permian sea dried out, 2-9-3 retreated into its spore, where it survived comfortably, encrusted in salt, until aroused from its suspended animation 250m years later.  (The previous record for longevity was held by another bacterium, which was revived after 25m years, after being extracted from an extinct bee trapped in amber.)

All of which gives rise to another, more fascinating, speculation: could such long-lived spores have been the vessels that spread life through the universe?  This theory, known as "panspermia" (literally, "seeds everywhere"), turns on the existence of organisms tenacious enough to be able to survive long and difficult journeys across the vast distances of interstellar space.  The work of Dr Vreeland's group provides the most convincing evidence to date that such creatures do indeed exist.  Crossing the galaxy in their crystal ships, these spores could then flourish on any planet where they found a hospitable environment.  An intriguing suggestion - especially since that very scenario could have brought life to earth, aeons ago.

Source: The Economist 21 October 2000

Science Is Too Quick to Monkey with Life

by Lawrence Hall

In Naples, Italy recently, two scientists announced that they had revived extraterrestrial bacteria found inside 4.5 billion-year-old meteorites at a museum there.  Bruno D'Argenio, a geologist with the Italian Research Council, and Giuseppe Geraci, a molecular biologist at Naples University, announced their findings to officials at the nation's space agency.

The dormant bacteria - called "cryms," or crystal microbes - came back to life after they were sterilised at 950oC and put in alcohol.  "When in contact with a physiological solution, they became visible and began to move" and gather in clusters, D'Argenio said.

The scientists examined and identified microorganisms identical to the cryms discovered in the meteorite at the Naples museum in 50 samples of billion-year-old terrestrial rocks from five continents.  The cryms were then cloned and their DNA analysed.  "Their genetic code is unlike any known on earth," says Giovanni Bignami, scientific director of the Italian space agency.  "Life would have formed as an initial seed in the proto-planetary nebula from which all the planets originated.  This microorganism can be found in planetary bodies and in the meteors fallen to earth."

Yes, the science is intensely interesting, but one must wonder whether researchers have thought through the consequences of reviving such life.

Source: The Star-Ledger (New Jersey) Wednesday 16 May 2001 (the Italian scientists' results have not been independently verified that I could find).

For a more light-hearted look at bacteria, from the "Futures" column of Nature, see also:

bulletTuberculosis Bacteria Join the UN (further on in this section) - What no one anticipated was that the enhanced bacteria... 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?"

The Line of Least Resistance

Understanding the biochemistry of bacteria will lead to more relaxed bacteria - and healthier humans

Geneticists have long promised that their science will bring a revolution to medicine.  Yet like all revolutions, this one has had its victims.  It has been built on the corpses of legions of bacteria that have perished in the course of decades of research.  Now other bacteria may reap the benefits of this sacrifice.  Using information gleaned from studies of bacterial biology, researchers are designing medicines that will cure people, while also giving bacteria a bit of a rest.

That may sound odd: surely the point of medicine is to kill bacteria, not to cultivate them?  But trying to exterminate bacteria has had nasty consequences.  An antibiotic kills the weakest specimens in a population.  Those that are resistant to the drug survive and resume breeding.  Over time, the resistant strains outnumber the susceptible ones - and the antibiotic becomes useless.

Worries about antibiotic resistance now loom large.  Last year, America's Food and Drug Administration approved Zyvox, a drug that introduced a new class of antibiotics to patients for the first time in 25 years.  But in April John Quinn, of the University of Illinois at Chicago, and his colleagues reported in the Lancet that some people had developed infections resistant to the new drug after using it for only three weeks.

In March, America's Center for Disease Control published a new set of guidelines for controlling and reducing the dosage of antibiotics in patients.  Agricultural use is a problem, too.  According to the Union of Concerned Scientists, based in Cambridge, Massachusetts, around 70% of the antibiotics made in America go directly to farm animals, because dosed beasts grow larger.  The hordes of antibacterial soaps and detergents in the shops also increase the pressure on wild bacteria to evolve resistance.

This state of affairs has a familiar ring to economists, who know it as the "tragedy of the commons".  In the short term, each group - of doctors, farmers or vigilant housekeepers - overuses a common resource, to the detriment of all in the long term.  The solution could lie in exploiting another idea beloved of economists, game theory, and tailoring it to the constraints imposed by natural selection.  The idea is to slow the arms race between antibiotics and bacterial evolution, either by interfering with bacterial mechanisms of resistance or by suppressing them entirely.

Acting Defensive

When a bacterium detects a dangerous chemical, it mounts a host of responses.  One of the most important is to chew up the toxin with custom-made resistance enzymes.  The natural precision of these enzymes has been a boon to medicine makers over the decades: chemists have been able to generate new varieties of antibiotic by tweaking the design of existing compounds just enough to fool the enzymes.  If the resistance enzyme cannot recognise and destroy the new variety, the drug can do its work unhindered.

Natural selection, however, soon catches up.  This has prompted researchers to look for ways to interfere with the actions of the bacterial enzymes themselves.  Gerard Wright and his colleagues at McMaster University in Ontario, Canada, found that some resistance enzymes bear a resemblance to a family of molecules known as the protein kinases.  Because protein kinases seem to be involved in a variety of disorders, pharmaceutical and biotechnology companies have been looking into their structures for years.  The resemblance between the two groups of compounds means that inhibitors of protein kinases also inhibit bacterial resistance enzymes.  Dr Wright is now trying to find a way to reverse bacterial resistance by modifying one of these protein-kinase inhibitors.

Bacteria also safeguard themselves from toxins by turning on an "efflux" system, a form of cellular garbage-disposal that ejects any offending substance without further ado.  The efflux mechanism is a molecule bound to a bacterium's outer membrane.  It locks on to the offending toxin and ejects it through the membrane.  Some species of bacteria have several types of efflux system.  Microcide, a firm based in Mountain View, California, has found a compound that attacks three of these systems in Pseudomonas aeruginosa.  As hoped, this compound augmented the potency of antibiotics in mice infected with this pathogen.

Eventually, bacteria would evolve around such gimmicks, just as they evolved around antibiotics.  The only way to stop this evolution is to neutralise the threat they pose without killing them too quickly in the process.  That would slow down the arms race between the bacteria and the drug makers, and Michael Alekshun and Stuart Levy of Paratek Pharmaceuticals in Boston, Massachusetts, think they have found a way to do it.  They have identified a regulon (a collection of genes whose expression is regulated by a single protein) in the genome of Escherichia coli.  This regulon controls the bacteria's defences against antibiotics.

When E coli senses a dangerous chemical, a protein called MarA activates this reguIon, which is known as Mar because its activation confers "multiple antibiotic resistance".  Mar starts up the cell's efflux system, and also stops the cell from allowing any more threatening molecules in by halting the production of porin, a membrane protein that acts as a channel into the cell.  Once the threat subsides, the MarR (for "Mar repressor") protein turns off the Mar regulon, and the cell returns to its normal state.

To disguise an antibiotic attack from a bacterium, all that is needed is an increased concentration of MarR and a lowered concentration of MarA.  This month, at a meeting of the American Society of Microbiology in Orlando, Florida, Dr Alekshun and Dr Levy will unveil the crystal structure of the MarR protein, a discovery that makes it easier to find molecules that will interact with it.  They have started the hunt for molecules that will alter its function, and are also analysing a set of substances that inactivate MarA.

Initially, the researchers saw controlling the Mar regulon as a means to increase or restore the potency of existing antibiotics.  That would be good, but would almost certainly result in the evolution of resistance in due course.  Further experiments, though, produced an unexpected result.  E coli without Mar A do not form communities.

Usually, as bacteria float past a congenial surface, they adhere to it and form a mass of accumulated layers called a "biofilm".  In time, they produce a sturdy sugary coat that guards the biofilm's tenants from antibiotics.  Infections are often the result of biofilms forming on soft tissues.  But in the Petri dish, bacteria without MarA did not form biofilms.  Dr Alekshun and Dr Levy believe that the Mar regulon must also control some important process related to biofilm formation.

If the phenomenon occurs in bodies, as well as glassware, then inactivating MarA would stop infections forming.  Bacteria could not gain a foothold, and the host's immune system could simply flush them out of the body.  Antibiotics could then be used more sparingly.  By the same token, bacteria could stop racing to improve as well: because a Mar-based drug would render bacteria harmless but would not kill them, it would not impose a strong selection pressure.  Just as game theory suggests, a compromise that reduces the damage done by both sides can work to their mutual benefit.  Sometimes mercy is more than its own reward - even when it is shown to germs.

Source: The Economist 5 May 2001

For more on bacteria, see also:

bulletMom Was Wrong (the next page in this section) - Some experts believe bacteria formed at least 3 billion years ago, when Earth itself was fairly young.  By 1.5 billion years ago, they were all over the place.  Without them, there would not have been enough oxygen in the atmosphere for higher life forms to survive...  (The last article contains more information on the benefits and drawback of slime.)
bulletTalking Bacteria - "This idea has taken hold that these bacteria want to communicate with each other.  It may be just too good to be true..."

For articles on bacteria, centrioles, chairs, nebulae, asteroids, robots, memory, chirality, pain, fractals, DNA, geology, strange facts, extra dimensions, spare parts, discoveries, ageing and more click the "Up" button below to take you to the Table of Contents for this Science section.

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