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One of the real surprises to me in college was…bacteria.  Now I had encountered these characters before (I guess everybody has, since more of the cells in a human body are symbiotic bacteria living inside of us than are…well our own actual cells).  However, in college I learned the full history of life on Earth.  It is mostly a history of bacteria:  multicellular creatures only show up for the last 600 million years.  For over 3 billion years, the world belonged to the bacteria alone.  I also learned about extremophiles—bacteria that can live in boiling hot temperatures or in oxygen-free environments.  Some extremophiles can metabolize inorganic things like sulfur and arsenic.  They can live without the light of the sun in the fathomless depths of the ocean on poisonous elements. The oxygen we breath was created as a waste product by these first archaebacteria.  The planet’s atmosphere was once a reducing atmosphere, where paper would not burn (assuming you had any…billions of years before trees plants evolved, much less paper-makers).  Bacteria made it an oxygen world where things burn…including our metabolisms. They changed the world in a fundamental way that we industrial humans with our infernal carbons cannot match.

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The archaebacteria sound like aliens (indeed, there is a real possibility they actually originally were aliens), but they are also our great-great-great ever-so-great-to-the-100th power grandparents.  I don’t need to wonder whether evolution is real: I have seen it in a science lab when we put a pellet of penicillin on a petri dish and watched as the bacteria evolved resistance to it (not really a super-smart experiment in hindsight, but a super-compelling one). I wish I could impress upon you how astonishing bacteria are.  They are the true sacred seed of life–the undisputed masters of Earth.

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However, this is old news.  The new news is that there are so, so many more bacteria than we realized.  The earth beneath our feet is filled with bacteria…but the stone beneath that is filled with bacteria too.  And the weird hot putty beneath that stone (the gabbro) is also filled with bacteria.  There are bacteria in the depths of the world.  Living bacteria have been discovered in the gabbro 1400 meters beneath the basalt floor of the ocean.  There is a barely discovered world of secret life deep beneath our feet—a true underworld of secret unknown species of micro-organisms.  The size of this ecosystem is enormous.

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To quote a news article from..yesterday,  “The record depth at which life has been found in the continental subsurface is approximately 3 miles (5km) while the record in marine waters is 6.5 miles (10.5km) from the ocean surface.”

If these are the true boundaries of the underworld bacteria biome, it means that there is a region of secret life twice as large as all of the world’s oceans combined.  Based on past experience though, it is not unreasonable to doubt that deeper pockets of bacteria will be discovered as our drilling and bio-assaying become more sophisticated.

Most of the super deep bacteria spend enormously long periods in suspended animation.  Sometimes they enter a metabolic suspension so profound that they seem dead or inanimate (which is maybe how we missed them for so long).  At present, scientists and writers are calling them “zombie-bacteria” because of their half-alive status (which seems like an appropriate nomen based on their underworld habitat).

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I wish I could tell you more about this realm of life on Earth, but I can’t.  Not only am I not a bacteriologist or geologist, additionally we (meaning all of humankind) simply don’t know the answers yet.  More research is necessary.  Sadly, it is probably going to be slow to materialize.  Our leaders seem incapable of grasping that surface life needs to continue longer than a few decades (at least if they hope for meaningful long term economic growth).  I shudder to imagine them furrowing their brows at the concept of vast stone oceans of zombie one-celled organisms…and explaining to their constituents why we need to know more about such things.  But we DO need to know.  In the synthetic ecosystems of my youth, the lack of coherent sustainable bacterial communities was the root cause of disastrous failure.  I don’t think our new underworld friends are going to fail or die any time soon, no matter what we surface beings do, yet if we want to take life elsewhere than Earth we are going to need to understand them much better.  Perhaps life did not spring from some pool of irradiated scum or arrive on a comet from beyond the solar system.  Maybe it came from the hot depths.  Maybe we are all underworld beings.

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Have you seen photos of Venus?  When the planet is observed in visible light it looks like a big bland ecru ball (see above).  Put a whiteboard and some plastic rolling chairs on that puppy and you would have a corporate conference room in some awful suburban office-park.  Yet ultraviolet imaging of Venus paints a somewhat more interesting picture of swirling bands or darkness in the heady acid atmosphere of our sister planet.  But what does that mean?

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The dark bands turn out to be the result of sulfur compounds (carbonyl sulfide, hydrogen sulfide and sulfur dioxide) and other yet unknown chemical compounds in the upper atmosphere of Venus.  On Earth these sulfur compounds are hallmarks of life…or of volcanic activity.  Some scientists are provocatively asking whether extremophile bacteria could have a place in the temperate upper atmosphere of Earth’ closest planetary neighbor.  The bacteria could use the rich sulfur and carbon clouds as building blocks and the UV (and other EM radiation!) bombardment of the sun for energy.  Perhaps, they muse, these dark bands are something akin to algal blooms in Earth’s oceans.

More than a billion years ago, Venus enjoyed a period of prolonged earthlike climate with surface water and an atmosphere which was not so hellishly heavy and hot.  But something went hideously awry and runaway greenhouse effect created a terrible feedback loop which changed the planet’s surface into the monstrous place it is today.  Apparently the igneous/volcanic processes of Venus are rather different than those of Earth, so it was probably not all treeferns, friendly dinosaurs, and bikini-clad aliens even before the runaway greenhouse phase melted away the old surface of Venus, but perhaps bacteria (or analogous lifeforms) could have evolved and escaped the catastrophe by moving into the upper clouds (which, as previously noted here, have temperatures not unlike those of Earth’s surface).

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My guess is that Venus is lifeless as a jackhammer (though, like a jackhammer it can give the alarming appearance of life), yet even if this is the case, we should know more about all of this! What happened to Venus’ original surface? Was there ever life there?  What is going on with its volcanoes and internal geology?  What is the composition of the clouds of Venus? Is there anything there other than strange sufur compounds and esoteric hydrocarbons formed from the mixture of sulfur, carbon dioxide, and UV radiation?   Once again, our nearest neighbor is beckoning.  We need to move forward with sophisticated atmospheric probes (like VAMP) and NASA should collaborate with Russia on their next Venus mission (it looks like our governments are closer than ever anyway).  For some reason, popular imagination disdains Venus, yet the questions there seem salient, and the possibilities for a nearby Earth-sized world of unlimited energy and resources seem, well, unlimited.

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A well-worn platitude maintains that the media never reports good news. Sadly, that is true to a degree: good news tends to be incremental and somewhat abstract, whereas our primate brains are hardwired to pay closer attention to scary stuff. All of which is a roundabout way to say that today’s post features tremendously good news! (I guess I’ll leave stupid CNN to fool you into clicking on their overly frightening tomfoolery—and to thereby collect all of the internet’s advertising dollars).

Anyway…on to the good news: researchers at Northeastern University in Boston, Massachusetts have discovered the first major new class of antibiotics in three decades. Effective new medicines are always precious and amazing, but this discovery takes on particular significance due to the fact that rampant overuse of antibiotics has created a legitimately frightening worldwide health crisis. I blogged about this emergency earlier but the basic idea is that we have overprescribed antibiotics, and used them in our crammed factory farms to such an extent that bacteria are evolving wholesale resistance to them. Worst of all, marketers have added some of our most effective antibacterial compounds to ordinary cleaners as a sales gimmick-thereby undermining the utility of these life-saving chemicals.

Chemical Structure of Teixobactin molecule (via "Nature") it is incredible that this was dicovered this month and we already have this!

Chemical Structure of Teixobactin molecule (via “Nature”) it is incredible that we already have this diagram!

The new antibiotic has been christened as Teixobactin. It was discovered in a Gram-negative soil bacterium known as Eleftheria terrae. The bacteria does not grow easily (or at all) in laboratories so it was grown in situ in a new microscopically engineered bacterium culture device—the “ichip.” Teixobactin blocks a particular peptide (a protein-like molecule) which Gram positive bacteria such as Staphylococcus require for building cell walls. In preliminary trials, certain aggressive highly protean pathogens like Mycobacterium tuberculosis and Staphylococcus aureus were unable to develop resistance to Teixobactin.

The ichip in situ!

The ichip in situ!

Hopefully you will have noticed that the new antibiotics were not discovered by Merck or Lily or some other giant conglomerate but instead by a university. Further research reveals that Northeastern was heavily supported by the National Institute of Health and analogous German research agencies (and the University of Bonn). A privately held company founded by the professors who created the ichip will hold patents on any pharmaceutical compounds thereby discovered. It is an interesting amalgamation of public and private (and international) funding and study. It should be of particular interest to obnoxious talking heads and politicos who always advocate pure-market solutions.

Berry's Bobtail Squid (Euprymna berryi) photo by Rokus Groeneveld

I have written before about the beautiful cuttlefish (marine mollusks of the order Sepiida). Cuttlefish are closely related to another order of mollusks, the Sepiolida, or bobtail squid, which are perhaps even more endearing.  With huge expressive eyes, tiny little tentacles, and opalescent skin, bobtail squids look like they were designed by a Sanrio artist having a strange day.  Sepiolida cephalopods appear to be all head (they are also known as dumpling squid or stubby squid because of this shape)–and their large rounded navigation fins, which stick out like Dumbo’s ears only add to the impression.   Members of the Sepiolida do not have cuttlebones but they are far more similar to cuttlefish than to other squid—perhaps their taxonomical classification will change as they are better understood.

Southern Dumpling Squid (Euprymna tasmanica) photo by David Mitchell

There are approximately 70 known species of bobtail squid living in the shallow coastal waters from the Mediterranean, to the Indian Ocean, to the Pacific.  To quote the Tree of Life Website, “Members of the Sepiolida are short (mostly 2-8 cm), broad cephalopods with a rounded posterior mantle.” The animals are gifted hunters which eat shrimp, arthropods, and other small animals which they chomp apart with a horny beak at the center of their arms. During the day, bobtail squid bury themselves in the sand with only their eyes protruding and then they hunt at night.  Certain species of bobtail squid are known to be poisonous, like the lovely Striped Pyjama Squid (Sepioloidea lineolata).  This poison is not well understood and may be contained in the slime produced by the creatures.

Striped Pyjama Squid (Sepioloidea lineolata) photo by Tony Brown

Bobtail squid are bioluminescent and they use this ability to disguise their profile when viewed from below–a helpful sort of camouflage which serves them as predators and prevents them from becoming prey.  Young bobtail squid are not born with the bioluminescent bacteria but must capture them from the water column in order to start the symbiotic colony within their own bodies.  The symbiotic relation between the bobtail squid and the bacterial colony has been much studied in the laboratory.

Bobtail Squid (photo by Adam Minu)

It was thanks to such studies that scientists first began to understand the method through which bacteria communicate with each other.  Called “quorum sensing”, such communication takes place within a group of bacteria by means of signaling molecules.  The chemical conversations allow bacteria to respond quickly and in aggregate to changes in their environment (to such a degree that a bobtail squid can tell the bacteria within its own tissues how much to fluoresce and can thereby determine its own luminosity by communicating with millions of living entities inside itself).  I have written before about how critical bacteria are to the planet and the Earth’s ecosystem.  Studying the bobtail squid provided the first understanding of the way that bacteria communicate with each other, but we are now beginning to suspect that such communication might take place on a vast—perhaps even a global—scale.

Juvenile Common Botail Squid (Sepietta oweniana)

Bacteria from the surface of a human tongue

For once, Ferrebeekeeper has a very important point which I desperately want you to walk away with. If you don’t want to wade through my carefully crafted exposition (which builds gradually to this important public health message by first contemplating the nature of Earth’s dominant living things), click here and the WHO will provide this message with brevity and decisiveness.

Today I would like to write briefly about the true masters of planet earth, the bacteria and discuss some very important aspects of our relationship with them.     Bacteria are everywhere and inside everything.  Our bodies contain more bacterial cells than cells which are our own.  They live in kangaroos, grapes, arsenic springs, molten-hot sea vents, and inside the earth’s mantle. In the depths of time, they altered the planet’s oxygen-free atmosphere into one where oxygen is plentiful and they alone among organisms (other than chemists) can fix molecular nitrogen from the atmosphere into ammonia. There are estimated to be more than five nonillion (5×1030) bacteria on Earth–which together vastly outweigh the biomass of all other living things combined.  They were here first (by billions of years) and they will probably be here last, when the sun expands into a red giant and swallows the earth like a cocktail onion.

I should probably write more and think more about bacteria.  We all should. Not only is the planet is theirs, but they are more diverse than all other organisms.  They likely exist in parts of earth we have never even reached. They may even live in a shadow biosphere which is based on biochemical reactions we have never thought of as life-like.  Who knows?

The Diversity of Life: Bacteria (prokaryotes) are in blue.

Unfortunately, like most people, when I think of bacteria, it is usually as a disease.  Even though pathogens only make up the faintest fraction of the teaming bacterial world, bacterial illnesses are terrifying.  Tetanus, typhoid fever, diphtheria, syphilis, cholera, bubonic plague, staph, pneumonia, leprosy and tuberculosis are all bacteria, as are many other wicked diseases.  For most of human history we knew these bacteria only by the results of their work and we lacked any means of dealing with them other than our immune systems and crude poisons like iodine, bleach, and alcohol.

However all of this changed in the twentieth century with the miraculous accidental discovery of penicillin, a substance produced by a certain mold which killed or inhibited bacteria.  Humankind discovered that many fungi and actinomycetes contained similar compounds, the antibiotics, which have made human life incalculably better and saved lives beyond the telling.  Of course, as with all good things, we have also abused these miracle drugs to cure minor ailments, market unnecessary household cleaners, grow fatter livestock, and treat viruses (which antibiotics don’t even cure).  Overuse of antibiotics stresses the healthy bacteria which live inside our bodies perhaps contributing to a host of autoimmune and degenerative diseases.  Even worse, bacteria reproduce with inhuman speed and, when not killed outright, quickly mutate into antibiotic resistant strains.  These antibiotic resistant bacteria are becoming widespread.  Many people in hospitals are dying.  Drug-resistant pneumonia, tuberculosis, and staph infections are beginning to spread.

A Diagram of Bacterial Resistance to Antibiotics

All of this is leading up to a pointed conclusion. Today is world health day and the WHO (world Health Organization) has launched a campaign to combat antibiotic and antimicrobial resistance.  They wish to combat drug resistance by (1) curbing overuse of antimicrobial compounds, (2) making sure that people receive the correct prescription and finish the entire course, (3) stopping the sale of substandard products, (4) curtailing agricultural and industrial use of these compounds, (5) convincing laboratories and drug companies to reengage and reinvest (antibacterial or antimicrobial drugs are not as lucrative as heart medicines, erection pills, and weight-loss medicine).  Here is the World Health Organization statement again and here is a link to a thoughtful piece about the problem in the Economist.

Most scary things you read in the news are inflated bogeymen that people have hyped up so you will click on their websites and watch their daft advertisements.  The nuclear meltdown in Japan will not hurt you unless you live in the shadow of an affected plant. You will never be bitten by a shark.    Your plane is profoundly unlikely to crash and even less likely to be blown up by terrorists.  The world is safer (for you) than ever.

But now you could die of an antibiotic resistant disease you catch in the hospital during surgery, and the odds for such an end will go up unless we all become more conscientious. Drug resistant superbugs could harm or kill your loved ones if we don’t act to fix these problems. So listen to the WHO, help out the many friendly bacteria (which help us all sorts of ways), and don’t abuse antibiotics or antimicrobial compounds.  Also, if you happen to be a powerful capitalist, some sort of executive, or a legislator, please try to work with the WHO to provide more rational incentives and rules for the sale, use, and creation of these compounds.

Thanks! Happy World Health Day and bonne santé to you all.

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