December 2018

When you learn the facts of the situation, it’s really quite humbling.  Microorganisms make up about 60% of the biomass on the Planet’s surface.  They thrive in an astonishing variety of environments.  They’ve been around for nearly 4 billion years of the Planet’s 4.5 billion year history.  Their biochemical processes are worthy of a PhD and their metabolic repertoires encompass substances across an enormous spectrum, including some that would kill us humans in short order.  Yet we consider ourselves the dominant lifeform on the Planet, clocking in with a Planetary biomass of 0.0001%.  Do anybody else’s eyebrows besides mine go up at the notion of our being the sliced bread of the Planet’s evolutionary trajectory?  It’s time to face some facts and get down off our high horse, I think.

Let me confess right off the bat that microbiology has never been for me a subject of intense study.  Only recently have I delved into the subject in any depth, led to it by a desire to learn more about antibiotic resistance.  When people start talking about “the end of modern medicine” it gets my attention.  After my research I can only confirm the truth of the notion that the more you learn, the more you realize how much you don’t know. It seems these days like you need PhDs in six or seven disciplines just to be a reasonably well-informed know-nothing — string theory, epigenetics, materials science, the list goes on and on.  It’s enough to take the curl out of your perm if you think about it too much.  Information overload doesn’t begin to describe it.

As I said, research into antibiotic resistance started my ball rolling.  There’s a good explanation of the issue from the World Health Organization here.  I first became aware of the phenomenon a few years ago when I was living in Saudi Arabia, where antibiotics are handed out like candies.  A couple weeks ago I had a wisdom tooth out and along with the gauze tucked into the new hole in my lineup of choppers came a one-week regime of Clindamycin (a lincomycin class antibiotic).  That pushed the old eyebrows up in surprise.  Antibiotics for a tooth extraction?  I’d never expect to be handed an antibiotic regime after an extraction in the USA unless an infection developed subsequent to the procedure.  Here in the Philippines it’s standard practice to hand out antibiotics as part of the post-procedural regime.  I found myself uneasy about taking the Clindamycin so I did some research online.  I came to the conclusion that the healing process would probably go along just fine as long as I maintained a more rigorous regime of oral hygiene using things like an iodine mouthwash available over the counter.  That’s what I did and things healed up a treat without the antibiotics.  One point for the home team.

I have good reason to appreciate the dangers of microbial resistance to antibiotics.  In 2012 while working in Saudi Arabia I took a short trip to Oman.  It was a nice trip, easy flights, a few days spent looking about Muscat, then back to the daily grind in Dhahran.  Shortly after my return I developed a fever and things went downhill fast.  I knew what I had wasn’t the flu.  After two days on the couch I could tell that if I didn’t go to the hospital I’d be in serious trouble.  A friend ferried me down to the emergency room where I was admitted on the spot and ended up in the hospital for seven days, all the while on an antibiotic IV drip.

When you read history you often come across people dying of “fever.”  Well, I know now what that phrase really means: some kind of bacterial or viral infection.  What I had was in fact a liver infection — ultrasound revealed pustules, little white bumps that had no business being there.  The pathogen was never identified.  I was released from the hospital after seven days and placed on a regime of oral antibiotics for a full three weeks until I finally got a clean bill of health from the ultrasound results.  Had it not been the year of our Lord 2013 and had there not been a hospital with antibiotics readily to hand, I would have died — from “fever,” since nobody could even name the pathogen.  There was only one recourse for treatment: antibiotics and plenty of them.  Thank God they did their job, otherwise I wouldn’t have lived to tell the tale.

Since then I’ve followed the news about antibiotic resistance.  There are some very good talks on the subject from the Royal Institution, which conducts one of my favorite science lecture series.  Dame Sally Davies, Chief Medical Officer of the UK, gave an excellent lecture in 2016 available for viewing on YouTube here.  An equally good lecture in the series by American biologist Jenny Rohn entitled “Bacteria and Antibiotics: Revenge of the Microbes” is viewable here.  Having been myself brought back from death’s door by antibiotics, news like this makes my hair stand on end.   If the phenomenon progresses as projected the situation is grim, indeed.  I take this business seriously enough to question my own use of antibiotics, which led me to contravene the dentist’s prescription and leave the Clindamycin untouched.  I’m glad I did.

In the process of researching resistance I came across a recent body of work on microbial biomes.  It was all news to me, but it makes perfect sense when you think about it.  As usual, when I get the scent of some new domain of information I want to explore, I keep my eyes peeled for recent books on the subject for the general public.  Kindle to the rescue.  I came up with two interesting books on recent advances in microbial biomes and microbial ecosystems.  The first one directly relates to the symbiosis between microbes and humans, I Contain Multitudes: The Microbes Within Us and a Grander View of Life by Ed Yong.  The second deals with origin-of-life research based on microorganisms, Arrival of the Fittest: Solving Evolution’s Greatest Puzzle by Andreas Wagner.  Both authors have presented at the Royal Institution on their respective books.  Ed Yong’s lecture is viewable here and Andreas Wagner’s here.

Ed Yong knows his stuff but he reminds me of a Springer spaniel my cousin had who was named Hildegard Hamhocker.  Her life was lived on high voltage — about 440 volts, I’d say.  When I came in the front door and called out my hello Hildegard would launch from wherever she was, come barrelling down the hallway and knock me flat on my backside unless I yelled before she reached striking range, “Hilda, SIT!!”  Ed Yong has a similar intensity.  After reading the first chapter I felt like saying, “Absolutely fascinating.  Now then, why don’t you take one of your tablets, dear, and just sit quietly for a bit, I’ll be back in a jif.”  He pounds so fiercely on the table trying to make his case that you feel his hand will surely go through it at any moment.  Ah, the enthusiasm of youth …

Wagner, on the other hand, is Austrian and would have fit well into the kaiserlich und königlich (K und K, meaning “imperial and royal”) scheme of things during Vienna’s late Imperial era, when people ate pastries with dollops of whipped cream in the Cafe Central and discussed Freud’s latest scandalous hypothesis.  There’s definitely something Belle Époque about him.  He’s all wry grins and ironic one-liners delivered with impeccable timing, but at the same time his sentences are  so densely packed with information they expand like balloons while you read along.  His focus is squarely on biochemistry, which reveals the magic at the very foundation of the microbial world.  The expertise of our microbial companions in the business of chemical synthesis and analysis is breathtaking.  When I reached the end of Wagner’s book I realized that my perception of the world had changed permanently.  I’ll never again be unmindful of the teeming life going on at the microbial level across the entire surface of the Planet, be it land or sea.  Silly me, previously inattentive to 60% of the biomass on the Planet.  Attention to lifeforms present in every terrestrial biome in such astronomically large numbers should by right be front and center at every point of awareness.  And so shall it be for me from this point forward.  Thank you, K und K Herr Professor Doktor Wagner, for catalyzing that valuable insight.

In Part 2 of this series I considered the cosmic level and the difficulties involved with finding an individual stance in relation to it.  It’s difficult to imagine oneself fully at one’s ease in the company of something that would reduce one to quark soup in a matter of nanoseconds.  With our microbial chums, however, the intimate relationship has been present from the beginning of evolution itself and our awareness of it is simply post factum (as it is with most things we find out, truth be told).  Microorganisms have been busily pursuing their affairs for billions of years.  The configuration of cells that makes up a human being is perhaps novel in some regards, but the cells themselves are ancients of days.  The evolutionary history of our species reaches back less than half a million years.  Cells have a biological history extending back perhaps to the late Hadean eon when the Planet was in a state we would find unrecognizable — rotating at twice its present speed with the Moon whipping around it every five days at only a third of its present distance with tides like massive tsunamis striking every few hours.  No place for a lady, obviously.

When you’re sorting out a perspective it’s good to line up some facts so you have things on the right footing.  Let’s put down in black and white enough facts about the microorganism situation to get a proper toehold on reality:

  • we have no idea how many species of microorganism exist in toto
  • we’ve found microorganisms in every terrestrial environment we can reach for direct sampling
  • microorganisms have successfully adapted to environments in which no member of the kingdom Animalia (to which humans belong) could survive
  • microorganisms conduct a complex repertoire of chemical reactions that do not occur elsewhere in Nature (as far as we know at present)
  • the life cycle of microorganisms is so fast compared to “higher” lifeforms that the speed of their evolutionary trajectory is vastly greater than that of the “higher” kingdoms, e.g. Animalia
  • the healthy human body operates with multiple ecosystems of microorganisms that perform chemical services without which the human body cannot remain healthy or, in some cases, survive at all
  • the adaptability and innovability of microorganisms far exceeds in degree and rapidity that of any organism in the kingdom Animalia
  • only in 1977 did the existence of a separate kingdom of unicellular life, named Archaea, become known to humans through the work of Carl Woese (info here and here); other unicellular kingdoms may exist still outside our present knowledge
  • only a complete sterilization of the Planet’s surface, including some portion of the upper crust, could completely wipe out all species of microorganism currently alive

The Deep Carbon Observatory just came out a few days ago with the headline “Life in Deep Earth Totals 15 to 23 Billion Tonnes of Carbon—Hundreds of Times More than Humans” (article here).  The Observatory estimates that 70% of the Planet’s bacteria live in this non-surface environment it styles as a “subterranean Galapagos.”  The findings — new information to the scientific community — are gobsmacking:

Among many key discoveries and insights:

  • The deep biosphere constitutes a world that can be viewed as a sort of “subterranean Galapagos” and includes members of all three domains of life: bacteria and archaea (microbes with no membrane-bound nucleus), and eukarya (microbes or multicellular organisms with cells that contain a nucleus as well as membrane-bound organelles)
  • Two types of microbes—bacteria and archaea—dominate Deep Earth. Among them are millions of distinct types, most yet to be discovered or characterized. This so-called microbial “dark matter” dramatically expands our perspective on the tree of life. Deep Life scientists say about 70% of Earth’s bacteria and archaea live in the subsurface
  • Deep microbes are often very different from their surface cousins, with life cycles on near-geologic timescales, dining in some cases on nothing more than energy from rocks
  • The genetic diversity of life below the surface is comparable to or exceeds that above the surface
  • While subsurface microbial communities differ greatly between environments, certain genera and higher taxonomic groups are ubiquitous—they appear planet-wide
  • Microbial community richness relates to the age of marine sediments where cells are found—suggesting that in older sediments, food energy has declined over time, reducing the microbial community
  • The absolute limits of life on Earth in terms of temperature, pressure, and energy availability have yet to be found. The records continually get broken. A frontrunner for Earth’s hottest organism in the natural world is Geogemma barossii, a single-celled organism thriving in hydrothermal vents on the seafloor. Its cells, tiny microscopic spheres, grow and replicate at 121 degrees Celsius (21 degrees hotter than the boiling point of water). Microbial life can survive up to 122°C, the record achieved in a lab culture (by comparison, the record-holding hottest place on Earth’s surface, in an uninhabited Iranian desert, is about 71°C—the temperature of well-done steak)
  • The record depth at which life has been found in the continental subsurface is approximately 5 km; the record in marine waters is 10.5 km from the ocean surface, a depth of extreme pressure; at 4000 meters depth, for example, the pressure is approximately 400 times greater than at sea level
  • Scientists have a better understanding of the impact on life in subsurface locations manipulated by humans (e.g., fracked shales, carbon capture and storage)

The moral of the story is clear: size matters and small is best.  Microorganisms are the old masters, we big things are the latecomers in their debt.

Here’s where the information provided by Mr. Yong comes into play.  Having established that in the Big Picture we humans are very small potatoes compared to our microbial companions, we can then understand what role microorganisms play in the human body.  The Wikipedia article on the human microbiota is here.  Wonderment ensues when the facts come into full awareness.  It does well to take this information in slowly, since it’s game-changing with regard to the perspective one has of what constitutes a human being.  An article published in 2010 from a group at the University of Colorado at Boulder (text here) sums up the current state of knowledge at that point thusly:

The human microbiota consists of the 10-100 trillion symbiotic microbial cells harbored by each person, primarily bacteria in the gut; the human microbiome consists of the genes these cells harbor. Microbiome projects worldwide have been launched with the goal of understanding the roles that these symbionts play and their impacts on human health. Just as the question, “what is it to be human?”, has troubled humans from the beginning of recorded history, the question, “what is the human microbiome?” has troubled researchers since the term was coined by Joshua Lederberg in 2001. Specifying the definition of the human microbiome has been complicated by confusion about terminology: for example, “microbiota” (the microbial taxa associated with humans) and “microbiome” (the catalog of these microbes and their genes) are often used interchangeably. In addition, the term “metagenomics” originally referred to shotgun characterization of total DNA, although now it is increasingly being applied to studies of marker genes such as the 16S rRNA gene. More fundamentally, however, new findings are leading us to question the concepts that are central to establishing the definition of the human microbiome, such as the stability of an individual’s microbiome, the definition of the OTUs (Operational Taxonomic Units) that make up the microbiota, and whether a person has one microbiome or many.

From research done since 2010 a clearer picture of the human microbiota has emerged.  The estimate of the relative preponderance of microbial cells in the human body currently stands a ratio of about 1.3 to one based on DNA identification.  That means we’re one-third more microbial than human as far as the DNA in our bodily biomass is concerned.  If that fact doesn’t cure you of being uppity because you’re a bipedal mammal, I don’t know what will.  See how far you’d get on those two legs if all the microorganisms associated with your biology suddenly went on strike.  That’s right: microorganisms are people, too, so let’s not get too carried away with ourselves.

Ed Yong’s pounding on the table is unnecessary because a simple look at the data establishes the facts incontrovertibly.  We’re as much a part of the microbial world as we are of the mammalian one, biologically speaking.  There’s the element of consciousness, true, but while we’re alive on the Planet it’s a very localized phenomena about which we know next to nothing.  So it’s extraneous (although hardly superfluous) to our topic of the moment.  Biologically speaking we’re a composite, a mammalian body with which several different microbial biomes are associated symbiotically.  That’s a physical fact.  What does that fact to do one’s awareness of oneself if one embraces it fully?

I can only speak for myself, of course, but I have an answer.  The facts of the situation dimensionalize one’s awareness of oneself as a human being.  The best analogy I find comes from the world of art and involves the development of linear perspective in the early 15th century in Florence.  When you look at works created using linear perspective — say, Masaccio’s painting of the Holy Trinity from 1424 in Santa Maria Novella (info here) — it’s clear that something momentous has happened in pictorial representation.  The sense of space as a volume in three dimensions has entered depiction done in two dimensions.   There’s a trick worth a doff of the hat.  Precisely that kind of dimensionalizing is what I mean to capture about the changes in perception full awareness of the microcosm makes in my own consciousness.  I have now an awareness of the life of the microorganisms both outside and inside me, which adds another dimension to my conceptual apparatus.  In Planetary biology the macro is a by-product of the micro, just as in physics the quantum level is what later gives you galaxies.  In biology, you don’t get mammals unless you have microorganisms because they provide the structural underpinning for the macro level of multicellular life.

That teeming microbial life is invisible from the standpoint of my own conscious awareness, just as the molecular level of reality escapes my perceptual range.  Since incorporating some of the facts of the matter into my awareness, however, I find them surfacing as part of my thought repertoire as I go about my daily business.  I remember that micro-level of life and think about it much more often, in the same way that awareness of quantum or astronomical phenomena come into my head.  Fluellen in “Henry V” by Shakespeare hits the nail on the head in a metaphorical way:

Fluellen. I think it is in Macedon where Alexander is porn. I 
tell you, captain, if you look in the maps of the 
‘orld, I warrant you sall find, in the comparisons 
between Macedon and Monmouth, that the situations, 
look you, is both alike. There is a river in 
Macedon; and there is also moreover a river at 
Monmouth: it is called Wye at Monmouth; but it is 
out of my prains what is the name of the other 
river; but ’tis all one, ’tis alike as my fingers is 
to my fingers, and there is salmons in both. 

I warrant you shall find in the comparisons between the unicellular and multicellular levels that the situations, look you, is both alike.  Subatomic dynamics operational — check.   Periodic table in effect — check.  DNA encoding in place — check.  Proteins, lipids, etc. at the ready — check.  The difference is largely about how you group the bits together.  We’re the products of highly developed specialization.  But then so is Pyrolobus fumarii (info here), an Archaea that lives in hydrothermic vents in the deep ocean.  It can survive quite comfortably at temperatures as high as 122°C (251.6°F).  None of us big things could pull off that feat with equal nonchalance.

The main point of this tripartite post has been to document a shift away from a narrowly human perspective to one that includes more of the reality in which we humans are embedded.  As you can see, that expansion occurs on multiple levels simultaneously.  From the personal point of view perspective becomes kaleidoscopic, following the focus of consciousness as it moves between the levels of Reality according to thought and perception.

On a walk, for example, feeling the sun on my face might bring thoughts of Akhenaten and his lovely hymn to the sun (text here) together with thoughts of what actually produces the light that reaches me across the distance of space, which is nuclear fusion in the core of a star.  That conceptual conjunction leads me to ponder the difference between the mythic and the scientific and how we in the 21st century have done away with the mythic altogether.  Science guys are our equivalent of high priests now.  Seems a pity, somehow …

As I continue my walk I see lovely trees and think about what I learned from research done years ago on the symbiotic relationship between trees and mycorrhizal fungi.  Being now in a very different part of the world, I wonder what pairings go on here — very different species-wise I suspect, but probably only the names have changed since the symbiotic relationships doubtless serve the same purposes.  Then I go past a construction site where a large pile of excavated dirt sits.  Nothing remarkable in that, except that I know I only see part of it.  I wonder as I pass how many microorganisms are in it and to what families they belong.  Not likely to find anything from the Archaea there, the environment isn’t extreme enough, I think to myself, then into my mind comes an image of deep sea volcanic vents where such astonishing creatures find their equivalent of the French Riviera.

As I continue walking I register a moment of astonishment at the variety of life on the Planet, which offers a thrill of the first order as well as grist for the Science Guys’ mills for many years to come.  Here my mind boggles as I consider that all the heavier elements in all the things around me as well as in my own body come from the deaths of who knows how many stars over the course of the Universe’s long history.  Our own sun could never give us all the materials we use for life, it’s too small and can’t cook that rich a broth.  Our lovely Planet and all the life on it are possible because of events that happened who knows how far away or how long ago in parts of the Universe of which we may know nothing.  When the mind meets such scales of magnitude it can only stretch and wonder, it’s impossible to throw the lasso of conceptual thought around the full reality involved.  It’s too vast to be roped into a tidy comprehension.

That shifting of perspective is now native to me.  I’m delighted to see it develop along its own path as my days move forward — its development enriches my awareness and my experience alike.  The solely human perspective seems to me now almost alien — so limited, so confining, so wildly out of step with the reality both of the world and of the Universe we inhabit.  I know I’ll never know, can never know the full reality of the physicality of which I’m a part.  Such knowledge is beyond the grasp even of the Science Guys.  But it doesn’t really matter, I’m on the right track and my thoughts are pointed in the right direction.  I’m expanding just like spacetime is expanding, not contracting into my own humanness and forgetting that it’s only a small tile in the mosaic of Beingness.

The title of Ed Yong’s book, I Contain Multitudes, seems to me to fall short of the mark.  As my experience of the many levels of Reality moves forward it becomes ever clearer that the title of my own book should be I Am Multitudes.  My perspective has expanded to include all those things that form my own context as a physical being — from the microorganisms of the Planet to the fabric of spacetime itself.

What a great party to be at.  I propose a toast, ladies and gentlemen: to our fabulous Universe.  Hip, hip, hooray!

party cones clipart