The Magnum Opus from the Mama Bear:

Bacteria are us
by Lynn Margulis

What is my dangerous idea? Although arcane, evidence for this dangerous concept is overwhelming; I have collected clues from many sources. Reminiscent of Oscar Wilde’s claim that “even true things can be proved” I predict that the scientific gatekeepers in academia eventually will be forced to permit this dangerous idea to become widely accepted. What is it?

Our sensibilities, our perceptions that register through our sense organ cells evolved directly from our bacterial ancestors. Signals in the environment: light impinging on the eye’s retina, taste on the buds of the tongue, odor through the nose, sound in the ear are translated to nervous impulses by extensions of sensory cells called cilia. We, like all other mammals, including our apish brothers, have taste-bud cilia, inner ear cilia, nasal passage cilia that detect odors. We distinguish savory from sweet, birdsong from whalesong, drumbeats from thunder. With our eyes closed, we detect the light of the rising sun and and feel the vibrations of the drums. These abilities to sense our surroundings, a heritage that preceded the evolution of all primates, indeed, all animals, by use of specialized cilia at the tips of sensory cells, and the existence of the cilia in the tails of sperm, come from one kind of our bacterial ancestors. Which? Those of our bacterial ancestors that became cilia. We owe our sensitivity to a loving touch, the scent of lavender , the taste of a salted nut or vinaigrette, a police-cruiser siren, or glimpse of brilliant starlight to our sensory cells. We owe the chemical attraction of the sperm as its tail impels it to swim toward the egg, even the moss plant sperm, to its cilia. The dangerous idea is that the cilia evolved from hyperactive bacteria. Bacterial ancestors swam toward food and away from noxious gases, they moved up to the well-lit waters at the surface of the pond. They were startled when, in a crowd, some relative bumped them. These bacterial ancestors that never slept, avoided water too hot or too salty. They still do.

Why is the concept that our sensitivities evolved directly from swimming bacterial ancestors of the sensory cilia so dangerous?

Several reasons: we would be forced to admit that bacteria are conscious, that they are sensitive to stimuli in their environment and behave accordingly. We would have to accept that bacteria, touted to be our enemies, are not merely neutral or friendly but that they are us. They are direct ancestors of our most sensitive body parts. Our culture’s terminology about bacteria is that of warfare: they are germs to be destroyed and forever vanquished, bacterial enemies make toxins that poison us. We load our soaps with antibacterials that kill on contact, stomach ulcers are now agreed to be caused by bacterial infection. Even if some admit the existence of “good” bacteria in soil or probiotic food like yogurt few of us tolerate the dangerous notion that human sperm tails and sensitive cells of nasal passages lined with waving cilia, are former bacteria. If this dangerous idea becomes widespread it follows that we humans must agree that even before our evolution as animals we have hated and tried to kill our own ancestors. Again, we have seen the enemy, indeed, and, as usual, it is us. Social interactions of sensitive bacteria, then, not God, made us who were are today.

Great 3 Quarks article, Germs are Us—an exposition on the same theme:
http://3quarksdaily.blogs.com/3quarksdaily/2006/03/germs_are_us.html

Social Fiction’s amazingly good rantessay of Bacteriopoetics:
http://www.socialfiction.org/?n=1439

Bacteria are cults of interpretation not endless reprints of a few domesticated strands as if they were best-selling paperbacks. In the wild only a fraction of bacterial species can be cultured and the smallest working unit is the individual only in artificial situations of abundance…

The savage simplicity of the bacteria is not a sign of its stupidity but a token of its long term commitment to survival. When looking at the tree of life in terms of creative ability it is clear that it is not the bacteria that are primitive; it are the branches ‘above’ them that are caged in an ancient, conservative, over-elaborate and fragile textual heritage. The lichen, that many-coloured plant-like coat of nothingness, that centrifugal furry Mandelbrot cloak spreading-out in search for a minimal splash of sunlight across otherwise lifeless mineral surfaces underscores the point that the vortex may be the ideal but that the bacterial condition is above strict obedience to even its own principles.

Social Fiction’s Bacteriopoetics archive:
http://www.socialfiction.org/?tag=bacteriopoetics

“SEED Magazine on Bacteria” highlights:
http://www.socialfiction.org/?n=363

The Psychic Life of Micro-organisms:
http://www.archive.org/details/psychiclifeofmic00binerich

From the 09 Edge Question, What Would Change Everything?
http://www.edge.org/q2009/q09_8.html#davies

PAUL DAVIES
Physicist, Arizona State University; Director, Beyond; Author, The Cosmic Jackpot

SHADOW BIOSPHERE

A hundred and fifty years ago, Charles Darwin gave us a convincing theory of how life has evolved, over billions of years, from primitive microbes, to the richness and diversity of the biosphere we see today. But he pointedly left out of account how life got started in the first place. “One might as well speculate about the origin of matter,” he quipped in a letter to a friend. How, where and when life began remain some of the greatest unsolved problems of science. Even if we make life in the laboratory in the near future, it still won’t tell us how Mother Nature did it without expensive equipment, trained biochemists and - the crucial point — a pre-conception of the goal to be achieved. However, we might be able to discover the answer to a more general question: did life originate once, or often?

The subject of astrobiology is predicated on the hope and expectation that life emerges readily in earthlike conditions, and is therefore likely to be widespread in the universe. The assumption that, given half a chance, life will out, is sometime called biological determinism. Unfortunately, nothing in the known laws of physics and chemistry single out the state of matter we call “living” as in any way favored. There is no known law that fast-tracks matter to life. If we do find life on another planet and we can be sure it has started there from scratch, completely independently of life on Earth, biological determinism will be vindicated. With NASA scaling back its activities, however, the search for extraterrestrial life has all but stalled.

Meanwhile, there is an easy way to test biological determinism right here and now. No planet is more earthlike than Earth itself, so biological determinism predicts that life should have started many times on our home planet. That raises the fascinating question of whether there might be more than one form of life inhabiting the terrestrial biosphere. Biologists are convinced that all known species belong to the same tree of life, and share a common origin. But almost all life on Earth is microbial, and only a tiny fraction of microbes have been characterized, let alone sequenced and positioned on the universal tree. You can’t tell by looking what makes a microbe tick; you have to study its innards. Microbiologists do that using techniques carefully customized to life as we know it. Their methods wouldn’t work for an alternative form of life. If you go looking for known life, you are unlikely to find unknown life.

I believe there is a strong likelihood that Earth possesses a shadow biosphere of alternative microbial life representing the evolutionary products of a second genesis. Maybe also a third, fourth… I also think we might very well discover this shadow biosphere soon. It could be ecologically separate, confined to niches beyond the reach of known life by virtue of extreme heat, cold, acidity or other variables. Or it could interpenetrate the known biosphere in both physical and parameter space. There could be, in effect, alien microbes right under our noses (or even in our noses). Chances are, we would not yet be aware of the fact, especially if the weird shadow life is present at relatively low abundance. But a targeted search for weird microbes, and the weird viruses that prey on them, could find shadow life any day soon.

Why would it change everything? Apart from the sweeping technological applications that having a second form of life would bring, the discovery of a shadow biosphere would prove biological determinism, and confirm that life is indeed widespread in the universe. To expect that life would start twice on Earth, but never on another planet like Earth, is too improbable. And to know that the universe is teeming with life would make it far more likely that there is also intelligent life elsewhere in the universe. We might then have greater confidence that the answer to the biggest of the big questions of existence — Are we alone in the universe? — is very probably, no.

http://www.worldchanging.com/archives/002999.html

By Jamais Cascio

Geobacter is quite the interesting genus of bacteria. As extremophiles, they can live quite happily under conditions too toxic for most creatures big or small. Moreover, many Geobacter microbes are able to convert those toxins into materials far less dangerous—a process referred to as “bioremediation”—sometimes generating electricity in the process.

But in trying to better understand how Geobacter is able to do all of this, researchers at the University of Massachusetts at Amherst—including the original discoverer of the Geobacter line—stumbled across another remarkable characteristic of these creatures: nanowires. Geobacter is criss-crossed with tiny (3-5 nanometer wide) protein wires able to conduct electrons out of the cell.

The remarkable and unexpected discovery of microbial structures comprising microbial nanowires that may enable a microbial community in a contaminated waste site to form mini-power grids could provide new approaches to using microbes to assist in the remediation of DOE waste sites; to support the operation of mini-environmental sensors, and to nano-manufacture in novel biological ways. This discovery also illustrates the continuing relevance of the physical sciences to today’s biological investigations.” [...]

Ultrafine wires, often referred to as nanowires, are required for further miniaturization of electronic devices. Manufacturing nanowires from more traditional materials such as metals, silica, or carbon is difficult and expensive. However, it is easy to grow billions of Geobacter cells in the laboratory and harvest the microbial nanowires that they produce. Furthermore, by altering the DNA sequence of the genes that encode for microbial nanowires, it may be possible to produce nanowires with different properties and functions.

Another interesting implication of this research is that it suggests a mechanism for microbes to share energy in a mini-power grid. The nanowire pili of individual Geobacter often intertwine, suggesting a strategy by which Geobacter might share electricity.

The article appears in the current Nature, and is available for download (PDF) from the Geobacter Project website.

http://www.geobacter.org/publications/Nature_2005_Jun.pdf

The future will be built with the guts of creatures far too small to see.

Running meditation on the theme of “Nature as Interface”—I’m going to be using Tumblr more often in the future:

http://brainsturbator.tumblr.com/post/68974700/nature-as-interface

Also good brainfood—browse through the PhysOrg “microbes” archive:

http://www.physorg.com/tags/microbes/

Figured I might as well add this here, too:

“The problem with bio-art is that it’s often made of living tissue — and sometimes living tissue gets out of control.

That’s what happened late last week at a New York MoMA exhibit called “Design and the Elastic Mind,” where a tiny living jacket made out of stem cells had to be put to death for growing too fast and trying to burst out of its container. 

The art piece was called “Victimless Leather,” and according to The Art Newspaper: 

The artists, Oron Catts and Ionat Zurr, say the work which was fed nutrients by tube, expanded too quickly and clogged its own incubation system just five weeks after the show opened . . .

Paola Antonelli, head of MoMA’s architecture and design department and curator of the show, says she had to make the decision to turn off the life-support system for the work, basically “killing” it. 

Ms Antonelli says the jacket “started growing, growing, growing until it became too big. And [the artists] were back in Australia, so I had to make the decision to kill it. And you know what? I felt I could not make that decision. I’ve always been pro-choice and all of a sudden I’m here not sleeping at night about killing a coat…That thing was never alive before it was grown.”

Of slightly related note, which I though might interest you in connection with the other links I’d posted on Tim’s site:

What BitTorrent can teach you about highway traffic control

Their Autonet plan would center around ad hoc networks of vehicles and roadside monitoring posts supported by 802.11 technology (the prototype uses 11b). The vehicles would essentially be the “clients” in such a system and feature graphical user interfaces to pass along information to drivers.

Left-brain dominance is based on the conscious repression of the anerobic bacteria in the body—so by opening up the pineal gland there is a new super awareness of bacteria which normally would go unnoticed.  If I eat “normal” food I have to eat about a BULB of garlic a day to counteract the anerobic bacteria which is transduced into my brain via the vagus nerve—along with the serotonin.  For left-brain dominance the huge amounts of serotonin of the lower body are not able to bypass the blood-brain barrier.  The cilia noted by Lynn Margulis are none other than the spirochetes—the spiral vortex which is the same as the Tai-Chi complementary opposite harmonics.  PRIONS (spirochetes) are the interface for nanosilica particles to create the post-apocalyptic matrix mind control for nanobiomotors to take over Earth - - sure it’s a “second” genesis but one that relies on the mass sacrifice of humans through holographic microchipping using nanotechnology.  I’ve talked to biology professor Phil Regal who got the U.N. to stop the release of a G.E. bacteria back in the 1980s—he argued that it could have destroyed the life in the oceans.  Yet now ocean life is being destroyed by global warming, toxic waste, g.e.os, nitrate pollution, etc.  So will chaotic networks of bacteria nanowires save the planet?  Again through the mass sacrifice of humans scientists will find a way to make it happen.

http://brainsturbator.tumblr.com/post/70543361/dream-job-working-for-mitchell-joachim

“Eric is a student still entering his final year of architecture at Rensselaer Polytechnic Institute in Troy, NY. Currently, he is researching and developing a proposal for the fabrication and genetic manipulation of a flesh based architecture - combining inVitro processes and tissue engineering with Cad/Cam prototyping. He is excited in utilizing this research as a tool to generate not only discourse but to aid in its realization.”

Positioned at the confluence of art and science, we are a tightly knit group of designers, artists and scientists who seek to develop new forms of biological products and designs using biotechnology. The skills and ideas each of us bring to this project will, we predict, synergize to produce radical new designs.

The time has finally arrived when the costs of biotechnology have diminished to make it financially practical for these tools to be applied by small groups of skilled and motivated individuals. In
essence, our endeavor harkens back to an earlier era of small craft workshops, albeit utilizing state-of-the-art techniques and resources.

Ever since the advent of novel forms of genetically engineered micro-organisms containing human and other genes, originally utilized as “protein-factories” if you will, coupled with the established
technologies of tissue culturing, we seek to develop not just new organisms, but synthetic ecosystems as well.

Until just recently, the application of these revolutionary biological technologies have been used almost exclusively by big-pharma and other large scale for-profit consortiums. It is seen in pharmaceutical companies carrying out massively parallel robotically guided screens for small drug molecules to the equally massive shot-gun screening of the human genome at the dawn of the new century.

This is contrasted with the relatively much smaller scale of cutting edge development carried out by academia, whose fruits of scientific labor are all too often co-opted by corporations.

We aim to change this condition.

Co-Founders: Oliver Medvedik, Ph.D. and Mitchell Joachim, Ph.D.
Bioworks Institute

Our microbes, ourselves:
http://www.physorg.com/news151608095.html

In terms of diversity and sheer numbers, the microbes occupying the human gut easily dwarf the billions of people inhabiting the Earth. Numbering in the tens of trillions and representing many thousands of distinct genetic families, this microbiome, as it’s called, helps the body perform a variety of regulatory and digestive functions, many still poorly understood.

How this microbial mélange may be linked to body weight changes associated with morbid obesity is a relevant and important clinical question that has received recent attention. Now, a new study suggests that the composition of microbes within the gut may hold a key to one cause of obesity—and the prospect of future treatment.

In the January 19 early online edition of the Proceedings of the National Academy of Science, researchers at Arizona State University’s Biodesign Institute in collaboration with colleagues at the Mayo Clinic, Arizona, and the University of Arizona, reveal a tantalizing link between differing microbial populations in the human gut and body weight among three distinct groups: normal weight individuals, those who have undergone gastric bypass surgery, and patients suffering the condition of morbid obesity—a serious, often life-threatening condition associated with diabetes, cardiovascular disease, cancer and psychosocial disorders. Obesity affects around 4 million Americans and, each year, some 300,000 die from obesity-related illness.

A collaboration aimed at uncovering the links between the microbial composition of the human gut and morbid obesity began when Dr. John DiBaise, a gastroenterologist at the Mayo Clinic, Arizona, became interested in both the underlying mechanisms of obesity and plausible alternatives to gastric bypass surgery—still the only reliable long-term treatment for the extremely overweight.

DiBaise turned to Bruce Rittmann, Ph.D., an environmental engineer and a member of National Academy of Engineering, whose Center for Environmental Biotechnology uses its expertise to examine microbial populations important for cleaning up pollutants and generating renewable bioenergy. Rittmann invited Rosa Krajmalnik-Brown, assistant professor of civil and environmental engineering, to collaborate and apply her microbial ecology expertise to this project. The three researchers were able to leverage seed funding from the Mayo Clinic and ASU so that they could combine their respective talents. DiBaise recruited 9 middle-aged volunteers in three groups—normal weight, morbidly obese and following gastric bypass surgery—to participate in the study.

The research team’s central hypothesis is that differing microbial populations in the gut allow the body to harvest more energy, making people more susceptible to developing obesity. These small differences can, over time, profoundly affect an individual’s weight. Supporting this view is the study’s confirmation that the microbial composition among obese patients appears significantly altered compared with both normal weight individuals and those who have undergone gastric bypass surgery.

A microbial managerie

To tease out the microbial human gut composition, Husen Zhang, a postdoctoral scholar working with Rittmann and Krajmalnik-Brown, used an advanced DNA sequencing technology and sophisticated ecological tools. The team examined 184,094 gene sequences of microbial 16S rRNA, a molecular structure which provides a characteristic fingerprint for microbial identification. The analysis was conducted with the assistance of University of Arizona’s Rod Wing at the Bio5 Institute, using a novel sequencing technique known as 454-pyrosequencing, which allows a significantly larger number and greater diversity of gut microbia to be identified.

The group’s latest findings represent the first investigation of gut microbiota from post-gastric-bypass patients to date.

By examining a specific region of the 16S rRNA gene known as V6—PCR amplified from the stool samples of the 9 test subjects—the researchers were able to classify a zoo of microorganisms, which fell into 6 broad categories, with two bacterial phyla, the bacteroidetes and firmicutes, predominanting.

The resulting composition of gut microbiota in the three gastric bypass patients differed substantially and in potentially important ways from obese and normal weight individuals. This means the drastic anatomical changes created by gastric bypass surgery appear to have profound effects on the microorganisms that inhabit the intestine. This change may be part of the reason that gastric-bypass surgery is the most effective means to treat obesity today.

The team’s study is the first molecular survey of gut microbial diversity following surgical weight loss, and has helped solidify the link between methane producing microbes and obesity. Specifically, the microbial populations extracted from obese individuals were high in a particular microbial subgroup, hydrogen-producing bacteria known as prevotellaceae. Further, such hydrogen producers appear to coexist with hydrogen-consuming methanogens, found in abundance in obese patients, but absent in both normal weight and gastric bypass samples. Unlike the hydrogen producers, however, these methane-liberating hydrogen consumers are not bacteria. They belong instead to the third great microbial domain—the Archaea, (with Eukarya and Bacteria making up the other two).

Energy managers

During the course of digestion, calories are extracted from food and stored in fat tissue for later use—a process delicately regulated by the multitude of microbial custodians. The intermediary products of the digestive process include hydrogen, carbon dioxide and several short chain fatty acids (SCFAs).

Results suggest a cooperative co-existence in obese individuals between hydrogen-producers and hydrogen consuming methanogens. Rittmann explains how this mutually reinforcing relationship, known as syntrophy, may contribute to obesity:

“Organisms producing hydrogen and acetate create a situation like cars flooding onto the highway. The methanogens, which remove the hydrogen, are like the offramps, allowing the hydrogen cars to get off. That allows more acetate cars to get on, because some hydrogen cars are coming off the highway.”

The methanogen offramps, by removing hydrogen, accelerate the efficient fermentation of otherwise indigestible plant polysaccharides and carbohydrates. The effect is to boost production of SCFAs, particularly acetate, which will be taken up by the intestinal epithelium and converted to fat. The result over time may be increasing weight, eventually leading to obesity.

While weight regulation involves a complex interplay of genetic predisposition, exercise, eating habits, and other factors, manipulation of the gut’s microflora, particularly the methanogenic Archaea, may provide additional avenues for the treatment of morbid obesity.

The researchers stress that the study is preliminary, but were encouraged by the findings from their small sample. Future investigation is needed to establish the differences in composition of gut microbiota across different age groups and under varying weight-loss regimens involving diet and exercise. Nevertheless, the study’s findings point to new avenues for modifying the body’s energy harvesting efficiency—perhaps by manipulation of the Bacteria-Archaea nexus.

Source: Arizona State University

Great new keyword—phycology, which even google insists must be a typo for “psychology,” which is proof that Bernays PR works. 
http://en.wikipedia.org/wiki/History_of_phycology

Plant-Bacteria Interaction: Applications for Agriculture—limited preview but still a goldmine, unfortunately the hard copy is $190
http://books.google.com/books?id=YUQA9VqDYTsC&dq=best+vibration+frequency+for+plant+growth&source=gbs_summary_s&cad=0

Algae Base: working towards a global list
http://www.algaebase.org/

“Teaching Material for Phycology”
http://www.phycology.net/Content/PNetGroupContent.cfm?MID=142