Living with Microbial Life

Carl Sagan in the Encyclopedia Britannica: "A localized region which increases in order (decreases in entropy) through cycles driven by an energy flow would be considered alive."

There are a lot of microorganisms in this world where we sometimes only think of as a habitat for ourselves and life that we can see, either directly and unaided with our eyes or with a microscope or electronmicroscopy. But in fact, we are only a very small part of it. Life is huge and it includes bacteria, fungi, protozoa and viruses, although viruses are technically not alive they attain a life with an assist from living cells when the virus invades the cell nucleus and hijacks a cell's machinery to replicate itself. All of these life forms are commonly referred to as microbes, but colloquially a "microbe" only refers to bacteria.

These small molecular organisms are much better at surviving than humans. They can adapt faster. It takes a human about 20-24 years to generate a new generation. Bacteria can do it in 15-20 minutes and a viruses which is activated; ergo, inside the nucleus of a eukaryote cell, can mutate even faster. Natural selection operates much more efficiently; that is, they crank out considerably more variety in their communities in this microbial world.

Madeline Drexler in Secret Agents (2002) wrote: "A billion bacteria inhabiting a thimble can be vbirtually wiped out on Monday and be back in full force by Tuesday."

Bacteria, also known as "prokaryotes" are about 1,000 times larger than viruses and alive. They don't have a nucleus, like eukarotes. They're primitive and have a tangled neglace of DNA, circular and attached to their membrame and sometimes also have smaller rings of DNA known as plasmids.

Antibiotic Resistance

"Antibiotic resistance is the ability of a bacterium or other microorganism to survive and reproduce in the presence of antibiotic doses that were previously thought effective against them. Examples of microbe resistance to antibiotics dot the countryside, plaguing humankind. For instance, in February 1994 dozens of students at La Quinta High School in southern California were exposed to the pathogenic (disease-causing) agent, Mycobacterium tuberculosis,and eleven were diagnosed with active tuberculosis. Many strains of this bacterium are multi-drug resistant (MDR). As for the sexually transmitted pathogen Neisseria gonorrhea,which causes gonorrhea, the antibiotics penicillin and tetracycline that were used against it in the 1980s can no longer be the first lines of defense, again because of antibiotic resistance. If only 2 percent of a N. gonorrheapopulation is antibiotic resistant, a community-wide infection of this persistent strain can occur." (Paul K. Small, Genetics - January 1, 2003)

"The phenomenon of antibiotic resistance in some cases is innate to the microbe. For instance, penicillin directly interferes with the synthesis of bacterial cell walls. Therefore, it is useless against many other microbes such as fungi, viruses, wall-less bacteria like Mycoplasma(which causes "walking pneumonia"), and even many Gram negative bacteria (*) whose outer membrane prevents penicillin from penetrating them. Other bacteria change their "genetic programs," which allows them to circumvent the antibiotic effect. These changes in the genetic programs can be in the form of chromosomal mutations, acquisition of R (resistance) plasmids, or through transposition of " pathogenicityislands."" (ibid)

Resistance and Public Health

"The effects of antibiotic resistance are reflected in the agriculture, food, medical, and pharmaceutical industries. Livestock are fed about half of the antibiotics manufactured in the United States as a preventative measure, rather than in the treatment of specific diseases. Such usage has resulted in hamburger meat that contains drug-resistant and difficult-to-treat Salmonella Newport,which has led to seventeen cases of gastroenteritis including one death. Some MDR-tuberculoid strains arise because patients are reluctant to follow the six-months or more of treatment needed to effectively cure tuberculosis. If the drug regimen is not followed, less sensitive bacteria have the chance to multiply and gradually emerge into resistant strains. In other cases the "shotgun" method of indiscriminately prescribing/taking several antibiotics runs the risk of creating "super MDR-germs." Moreover, millions of antibiotic prescriptions are written by physicians each year for viral infections, against which antibiotics are useless. The patient insists on a prescription, and many doctors willingly go along with the request." (ibid)

"Because global travel is common, the potential of creating pandemicsis looming. In many Third World countries, diluted antibiotics are sold on the black market. The dosage taken is often too low to be effective, or the patient takes the drug for a very short time. All these behaviors contribute to the development of resistant strains of infectious organisms. If humans are to gain the upper hand against MDR bacteria, it is the responsibility of these industries and the public to educate themselves and to engage in careful practices and therapy." (ibid)

To put this all more in perspective, as stated by epidemiologist David Morens, "When an enterovirus like polio goes through the human gastrointestinal tract in three days, its genome mutates about two percent. That level of mutation -- two percent of the genomed -- has taken the human species eight million years to accomplish."

If we are going to win the war with bugs I'd say the bugs have a decided advantage over us.

Is a virus alive? (**) A virus is an example of simplicy. HIV virus only has 9 genes. Practically all viruses, with some exceptions, are very, very small. The word virus is from Latin meaning "posionous substance" and in a pure sense it is nothing more than nucleic acid. It is DNA or RNA surrounded by an envelope (Bacterium also has an envelope and eukaryote cells do not). The shell is made of protein and sometimes also lipids, which is not unlike that of bacteria. The biologist, Peter Medawar calls them "a piece of bad news wrapped in protein."

They're tiny. Millions of them can fit on the period at the end of this sentence. You can only see them with an electron microsope. They have several shapes, from rod like to fanciful forms with multiple heads and tails. And outside a LIVING cell, they are dormant, which I guess means they are not quite dead but not alive (g). Not alive and incapable of synthesis, that is, until they commandeer the raw materials from a living cell.

A virus cannot be cultured; they can only be propagated with live cells OR fertilized eggs, tissue cultures or bacteria. Viruses make us sick by killing the host cells or changing the way a cell functions. A response by a human host is a fever which is good. This heat inactivates many viruses. It is one of our natural ways of fighting a virus. If you get the flu, a fever is one of your defenses against the virus. We also secret a chemical which is called interferon which blocks a virus replication and our immune system makes antibodies which tagets the virus. Science has also provided antivirals and vaccines which help to retard or prevent influenza and other viruses.

But, as George Bush would say, "It is a very hard job." And about that he would be right. But of course he wasn't talking about viruses, was he? (g)

For two billion years bacteria ruled the earth. Just bacteria. Eukarotes, which made possible advanced life on the planet has within it's eukaryotic cells mitochondria. The origin of complexity is believed to have originated with mitochondria, an ancient bacterium and complex multicellular life is inseparable from mitochondria. Without it, we would not be here. (We get it from our mothers)

Life on earth would like not have evolved beyond bacteria if it had not been for mitochondria, the energy source for complexity. Mitochrondrial uses oxygen to burn up food. A billion mitrochrondria could fit in a grain of sand.

Science's Unchartered Waters

One great unchartered territory for science (there are so many) is the mind. What is intelligence?

I was listening to a lecture from the Museum of Science in Boston about gut Bacteria and it really is amazing how much we are learning and how much we don't yet know about what seems simple, but isn't, the bacteria which shares this super-organism we call our body - with us. I don't know who rules, them or us?

Bacteria are intelligent in colonies. Not individually, but together, like spores they learn and make intentional decisions. They are not the automata we once thought they were. But we have not yet caught up with the knowledge base on how bacteria really make a living and how they make decisions.

All of us are built from large carbon based molecules - macromolecules. And if not, we would not be from this planet. We all share a lot of the same equipment and we are all the product of evolution.

The cunundrum for science is in spite of all our high tech and all the images we have of the brain - as much as we understand molecular interactions (which we did not understand even one tenth as much a few years ago) we still don't know how learning is accomplished beyond the firing of neurons and how axons and dendrites react to electrical stimulation. Oh, we have an idea what happens, why - we're not yet sure.

Maybe we're looking in all the wrong places? Maybe we need to be looking at those bacteria we share our bodies with - which make up a lot more of the genes in our bodies than we do and have 90% more cells than the 10% belonging to us. So who rules, bacteria or us? There are 100 trillion bacterial cells with bacterial DNA in our body to 10 trillion cells with our DNA in our bodies.

The gene is the basic building block for life ON THIS PLANET. We have no idea what it would be elsewhere. Maybe it won't be carbon based. We don't know.

Why do ants in ant colonies individually serve the greater good of the entire colony? There is some kind of intelligence going on there - and in bee hives and in any almagamation of animals there is a `collective' intelligence. Some animals are incredibly, shall we say, simple. Yet together that simple-mindness adds up to incredible intelligence.

So do microbes think? We don't think they do, not the way we do anyway - not that we really know. After all, we have a pretty good idea about the mind that is not a "blank slate" as was the view not too long ago and the immune system has a very sophisticated memory system, although science does not yet know how it works. So why not microbes?

Bacteria has the advantage in Darwinian terms or evolutionary terms of altering very fast. Generational times are like every 15-20 minutes for bacteria. Measure that against 25 years in generational time for humans. It takes us 100 years to grind through 4 generations. Bacteria can go through 50 generations in a day.

Little Lucy had a pea sized brain. We have about 1400 cc of brain but Neanderthals had bigger brains than Homo sapiens and we survived, they didn't. Some say we may have eaten them. Others say we hybridized with them. I prefer that conclusion myself but we really don't know. We use to think the size of the brain determines intelligence - but we're not sure.

So when RNA is transcribing DNA due to environmental causes, i.e., ultraviolet rays, toxics, and other unhealthy things genes mutate and the beneficial mutations are exploited by their reproductive advantage over time to become the dominant gene. Just how intelligent is that? Pretty intelligent actually though not that anyone consciously thought about this gene or that one. Natural selection does the thinking for us but would you call that intelligence? It depends on how you define intelligence and how much it really does.

Bacterial colonies confront an environmental toxin and random mutant bactera are selected because the generational time is very fast that are capable of neutralizing the toxin's lethal effect. We all need to be thankful to the bacterial that lives in our guts for all the good work they do - that is in addition to extraction of nutrients we might have missed otherwise which these bacteria carry to our livers where metabolism takes place and vitamins are integrated into our cells where they do some good things.

You need to think twice when the doctors suggests streptomycin because those antibiotics may kill infection but streptomycin also binds to ribosomes and wrecks the fidelity of protein translation, killing bacterial cells indiscriminately - even good bacteria.

Of course if there is the possibility of improving one's survival with tuberculosis by using streptomycin you might want to consider using the antibiotic - unless you are confronted with resistant strains of Mycobacterium tuberculosis in which case it wouldn't do you any good and might adversely affect your already ailing health.

Mutations are NOT so plentiful and beneficial mutations are rare. Most mutations are inconsequential. They don't matter and they aren't selected. Another words, as Frank Vertosick in The Genius Within: Discovering the Intelligence of Every Living Thing (Harcourt Brace, writes, "random mutation alone seems inadquate for the task at hand. It seems like, if Vertosick's thesis is correct, that some intelligence is necessary for antibiotic resistance so maybe evolution is getting a little help from intelligent bacteria colonies? He goes on to say, "Like professional gamblers at a Vegas blackjack table, bacteria know the game is random, but they also know a few tricks that can tilt the odds heavily in their favor."

How about abiotic stress sensing and GABA (gamma-aminobutyric acid) response in plants? Is the metabolic response the defense a plant develops which improves breeding strategies (or transgenics) a form of intelligence?

Nature of the Human-Animal

Much of scientific thought today is you don't come out of the womb with a "blank slate" but for at least a century that doctrine has prevailed in the social sciences and humanities. Everything we are or become is not a just a result of socialization. It isn't that easy or simple, even though most customs and social relationships have been explained in that context. A lot of what we took for granted (because it was the prevailing meme) has been wrong if we are to believe what has been proposed as the new behavior sciences vis-a-vis sociobiology.

Neither are humans animals in their natural state noble savages as wrongly described by John Dryden's The Conquest of Granada (1670) and incorrectly attributed to Jean-Jacques Rousseau (1712-1778). "I am as free as Nature first made man, Ere the base laws of servitude began, When wild in woods the noble savage ran."

Mother Nature is a Cruel Bitch

The indigenous Americans were not so noble as they have been portrayed. There were often as savage as humanity has always been. Rousseau had in mind Hobbes (1588-1679) when he said "So many authors have hastily concluded that man is naturally cruel..." Yes, I believe with Hobbes, who is not the darling of the Left, that we human-animals are cruel. As cruel as mother nature is also cruel. (mother nature is a cruel bitch) The left rejected Hobbes and his view that man's nature is brutish.

"Contrary to predictions made by opponents in the 1970s and 1980s, sociobiology was not a nefarious plot to give scientific credence to a right-wing policy agenda...." -- from "What is Darwin's Truth?" (Darwin's Truth, Jefferson's Vision, The American Prospect - July 1, 1999 by Melvin Konner)

Conspiracies have always been grist around many nefarious plots used to give credence to views - like the "goodness of man" etc.

There are no perfect theories. That's why they are theories though the evidence is overwhelming for many theories, i.e. evolution for example. It is Darwinism which succesfully organizes behavior and social organization. The most successful theory ever, "descent with modification", has been the engine behind cultural memes and biology and may also be the key behind the growth and expansion of the universe.

Hank Roth

Useful Bibliography

• Garrett, Laurie. The Coming Plague.New York: Farrar, Strauss, Giroux, 1996.
• Ingraham, John, and Caroline Ingraham. Introduction to Microbiology,2nd ed. Pacific Grove, CA: Brooks/Cole, 2000.
• Nester, Eugene W., et al. Microbiology: A Human Perspective,3rd ed. Boston: McGraw Hill, 2001.
• Schaechter, Moselio, et al. Mechanisms of Microbial Disease,3rd ed. Baltimore: Williams and Wilkins, 1998.

Notes

1. (*) "When the popular press writes about the emergence of "superbugs," bacteria that resist all of the weapons in the antibiotic arsenal, public enemy number one is always methicillin-resistant Staphylococcus aureus (MRSA)...The gram-positive bug lends itself to sensational headlines given the thousands of cases of infection reported each year, including those of otherwise healthy young people. But industry observers say a bigger problem of antibiotic resistance lies in gram-negative organisms, which tend to strike the very old, the very young, and the very sick." (Lisa Jarvis, Imminent Threat, April 14, 2008 - Volume 86, Number 15 - pp. 21-24 - Chemical & Engineering News)


2. (**) Computer Viruses are Alive? - "COMPUTER viruses should be treated as a life form, Stephen Hawking, the British physicist and leading theorist on the origins of the Universe, has told an audience of computer enthusiasts in the United States...In a speech on the nature of life, Professor Hawking said computer viruses fit standard definitions of living systems, even though they have no metabolism of their own. The computer virus exploits the metabolism of the host computer it infects, and becomes a parasite. This parasitic existence is a key characteristic of biological viruses, as is the ability to replicate only inside the cells of a living host...Dr Richard Dawkins, professor of evolutionary zoology at Oxford University and author of the The Selfish Gene, said yesterday that although Professor Hawking's claim was interesting, even biological viruses are on the borderline between living and non-living things." (Susan Watts, The Independent, August 4, 1994)