Thursday, October 31, 2013

The BP oil spill and US agriculture

 It's Halloween, so of course we must have an environmental horror story; and if you stretch your imagination a little, perhaps you can envision a pumpkin in the orange flames.

Big, spectacular environmental disasters loom large in the public mind. Tiny, incremental ones that do far more damage don't get any press.

The BP Deepwater Horizon oil blowout is a classic example of this. It was spectacular. It spilled a lot of oil (although, scientifically speaking, an amount that may be equalled by the amount of oil that naturally seeps from cracks in the bottom of the Gulf every year.) People were killed. All because of BP's insatiable lust for oil and profit.

 Well, let me rephrase that. All because of our own insatiable lust for oil, which we burn and use constantly, and then attack and blame the oil companies for. It has become the fashion to point accusing fingers at the evil oil companies as the cause of all energy woes, as though we weren't the ones driving cars around every day to the supermarket and so on. Contradictions of this kind tend to drive me nuts; I am surrounded by thousands of individuals who complain about every kind of energy extraction, as  though they weren't using any energy themselves and weren't, in fact, indulgently using every little bit of energy they wanted to every day, in one of the most energy wasteful countries in the world..

In any event, as the prominent and expert marine biologist Carl Safina rightly pointed out in his detailed and carefully reasoned book on the blowout, A Sea in Flames, the blowout was not anywhere near as serious in the long run as the media would have anyone believe; and BP's response was not only entirely proper— it marks, to date, the world's most serious, extensive, and effective response to such an environmental disaster, aggressively eclipsing the response of Exxon to the Exxon Valdez oil spill, which occurred in a far more environmentally sensitive location—subject to far less long-term recovery—and killed far more animals.

Finally, let's remember, for a moment, that Exxon fought the settlement for years in court, instead of stepping up to the plate and doing what was right the way BP did.

 What's the difference between the two spills? Because of its natural oil seeps, the Gulf of Mexico's microbiotic infrastructure is well able to absorb and digest oil. Oil is, for the right kinds of bacteria, a rich source of food; and microbial blooms digested most of the oil that spilled from the Deepwater Horizon before it ever reached shore or impacted animal life. The media, in fact, had a difficult time finding any areas that were seriously impacted, so they kept playing the same footage over and over again in an effort to feed the sensationalism of the moment.  In Alaska, however, the waters are cold, microbial action is minimal, and the evolutionary infrastructure to feed on the oil isn't there. The two bodies of water are worlds apart in terms of their ability to absorb and digest oil spills.

When I explained this to my friends as the oil spill was taking place, and told them it would not turn out to be anywhere near as bad as the media was claiming it was, they were incredulous; but it turned out I was right all along. Go read Safina's book if you don't believe me.

All of this preamble, of course, to the fact that the real problem in the Gulf of Mexico is what is called the dead zone. This hypoxic (oxygen starved) area is caused by agricultural runoff from the Mississippi River, which contributes about 70% of the nitrogen overload which is destroying the biology of the Gulf of Mexico. ( the balance is being contributed by sewage discharge.) It's the largest dead zone anywhere in the United States, But it gets little or no media attention.

Some people have, laughably, suggested that these giant pools of poisonous runoff which exterminate all life where they gather are not having a negative effect on the biology of the area. Na├»ve contentions and complacency thus serve to keep the issue out of the public eye; but if we were really going to take issue with industries that pollute the Gulf of Mexico, the US agricultural industry would have to top the list by a wide margin. Millions of tons of runoff are polluting the Gulf every year — this is not a one-off, where an oil well blew out. If we want to go by the current estimate on runoff, and remind ourselves that mega-agriculture has been in place since the 1970s, we can count approximately 40+ years of nitrogen and potassium runoff into the Gulf from US agribusinesses, adding up to probably 40 or 50 million tons of pollutants dumped into the Gulf over that period.

 Sensationalism of the kind that surrounded the BP oil spill distracts the public from the serious long-term issues being created by the "quiet" industries that subversively dump their chemistry into our waterways out of the public eye. These are pieces of territory that ought to be scrutinized far more carefully, and loudly, by the media—yet everyone shrugs their shoulders and acts as though nothing need be done.

Something, however, does need to be done, and what that something is is a serious scrutiny of US agribusiness — and worldwide agribusiness — and the environmental impact that their runoff has on the microbial infrastructure of waterways all over the world. I can assure you, if a successful lawsuit prosecuted US agribusinesses on the scale that BP has so far been prosecuted, they would stand on their heads to clean up their act and find ways to reduce and otherwise minimize the impact their runoff is having on our waterways.

Politics and ignorance have prevented anyone from taking this step, but it definitely ought to be done. There is absolutely no reason that agribusinesses and fertilizer producers should be given free reign to pollute while the oil industry is held accountable for every gallon of oil that gets dumped into a creek, lake, river, or ocean basin.

Yes, oil spills are bad; but the sensationalist nature of press coverage on them takes our attention off the much more serious issues being caused by long-term pollution from other sources.

Tuesday, October 29, 2013

Water use and the textile business

I mentioned in my last post that the textile industry uses huge amounts of water. Because a large section of this blog is devoted to waterway pollution, I thought I'd explain that a little more detail, even though it's not directly linked to the microbe question.

What you see in the photograph is a digital textile printer that is being assembled right at this very moment. It represents a revolution that most people will never see or understand — but it is a very important one.

I can't tell you exactly where this printer is being installed, because it's privileged information, but I can tell you that it is in a foreign country — most textile business in the world is outside the US these days — and that the machine is costing its owner  $4 - 5 million in investment. Many of these new digital machines are now going into production.  Unlike everything that has ever been done in textile printing over the last several thousand years, these machines operate exactly like the computer printer you have at home. They just do it on fabric. This particular machine is one of the most advanced machines in the world, capable of printing king-sized sheet widths and operating at speeds of up to 75 m/m (that, FYI, is almost twice as fast as many of the high-tech rotary printing machines in the world today.)

 The machines can achieve resolution of imagery on fabric that rivals what you see printed on sheets of paper on a good laser printer. That is, the results are nothing short of incredible.

 So why is this a revolution? Besides, of course, the fact that the printing is of much higher quality than almost anything that has ever been achieved before on fabric.

Textile printing and finishing uses an enormous amount of water. Screens need to be loaded with ink before they are used, and washed clean between each printing run so that new ink colors can be introduced. The use of the water itself is  already a huge burden on the environment, because  the water has to be clean and, generally speaking, pH neutral (in other words, treated in order to be free of impurities) in order to be used. It is, in other words, probably at about the grade of drinking water, if not better. Water chemistry, after all, is pretty critical to fabric treatment and dyeing. If the water is off, technical processes can't be completed properly.

After the water is used, it needs to go through extensive water treatment to remove the chemicals that are introduced by the inks. 20 and 30 years ago, when I started my career, one routinely used to see the majority of this water runoff being discharged untreated into creeks and streams in Taiwan, Thailand, China, and other countries. The effects on the waterways were disastrous, to say the least; and the short-term gain that these countries realized by keeping prices low while ignoring environmental problems has been dramatically offset by long-term ecological disasters that the governments are now recognizing. Consequently, water treatment has become one of the major priorities and requirements for textile businesses in almost every nation.

Textiles has always been water intensive; but one of the counterintuitive developments in the textile business over the last 20 years has been the development of huge, staggeringly expensive textile industries in countries such as Pakistan, which is already water challenge. The contradictions in situations like this are glaring, and US consumers are generally unaware of the fact that the garments and sheets they are wearing and using are being produced at the expense of water resources everywhere.

The good news is that the digital textile printer is going to eliminate the need for many screens and constant interchanges. The technicians of the factory words being installed told me they estimate it will reduce water usage associated with a printing end of the business by about 80%. This is an enormous advance. Finishing processes, of course, will still need a lot of water — fabrics need to be  bleached before they are printed, and steamed afterwords. But because the bleaching process involves a more limited range of chemistry than the pigment and ink process, water treatment efforts can be more focused and effective, since the plants can narrow the range of their treatment to the finishing chemistry.

Printing machines of this kind will come to dominate the textile industry within the next 20 years, revolutionizing the way in which textiles are produced. There will be a great many other implications for consumers following this revolution, but I won't go into it here. I just wanted to let readers know that there are people out there that are thinking about ways to change our macroscopic impact on water resources, and that some of them are being successful.

Sunday, October 27, 2013

Gunk, Germs and Eel

One of the original events that triggered this blog was concerned about fertilizer runoff in my immediate neighborhood. Here's another article raising concerns about fertilizer runoff and its effect on our waterways and other bodies of water.

The article raises an interesting point. There are some types of bacteria and other microbes that have distinct evolutionary advantages over their brethren. When conditions remain the way they are, we may not see them much; but once they gain the upper hand, it's extremely difficult to get rid of them.

This isn't, of course, true of just microbes alone. Invasive species in general are all about getting the upper hand. We have grass carp from China in the Sparkill pond across the street from me; these fish are practically impossible to remove from a body of water once they become established. They are the dominant piscine form in the pond now. We do see occasional indigenous largemouth bass, bluegills, perch, and the odd eel here and there, but what there definitely are are thousands of grass carp.

 The difficulty with bacterial invasions are that bacteria have such enormously flexible responses to environments. Unlike larger creatures, they have a very fluid ability to get into every tiny crack and crevice of an environment. Eliminating them is a nightmarish prospect.

Our wanton spreading of fertilizer in massive quantities all over every nation has resulted in aggressive over-fertilization of waterways, but most especially bodies of water which are stagnant — that is, that have little or no exit flow to clear them of these nutrients. What happens is that the nutrients build up over time, creating a richer and richer environment for the explosive growth of species that never would have been able to gain a foothold without the presence of the fertilizers.

The resultant algal blooms are sometimes toxic; and when they are, it's disastrous, because they can poison an entire waterway and render it unfit for almost any other life form. But even when they aren't toxic, they deoxygenate the waterways where they bloom, rendering them — once again — unfit for other creatures.

The effects of actions like this are cumulative in the case of stagnant water ways. The fertilizers that get dumped into streams and rivers that drain into relatively stable ponds and lakes stay there. The costs of removing them are impossibly high, except on a micromanagement basis in the smallest bodies of water. We are thus creating a situation where we are slowly poisoning many of the waterways we rely on for both irrigation, drinking water, and recreation. The effects of this are cumulative — the waterways are acting as long-term "toilets" for our waste runoff.

 Some readers may be aware of the fact that I am in the textile business and travel to China a great deal. This job has given me the opportunity to see the dark side of water treatment issues, as well as the many mechanisms textile plants have to put in place to treat water. Textile printing and finishing, for those of you who don't know it, is an extremely water intensive business. Within the last decade, China has seen some spectacular and disastrous Lake blooms of algae — such as the one discussed in the article — in lakes such as Taihu lake near Wuxi, a major textile producing area. The government actually had to partially shut down textile production in the area in 2006 or 2007 to control the microbial problem.

Of course, the textile industry is only a tiny fraction of the problem with our waterways. Realistically speaking, the single greatest threats are twofold: first, nitrogen runoff from agricultural fertilizers, and second, micro-pollution by designer chemistry, that is, the drugs, pesticides, and other industrial chemicals which are routinely discharged and waterways without a great deal of thought for their long-term effects.

 Many people just shrug their shoulders and act like nothing can be done about this. What they don't understand that these long-term effects are very, very serious indeed, and likely to prove disastrous.

 In the next couple of posts, we'll speak about the textile industry and some positive developments there, and also compare the BP oil spill to the effect of US agricultural practices in the Midwest on the Gulf of Mexico.

Monday, October 14, 2013

microbes and energy

Here's a creative use of microbes.

The idea of using microbes for energy isn't completely new. There are efforts underway to breed bacteria that can produce the chemical precursors to gasoline and other fuels.

What's perhaps a bit more interesting is the possibility that toady's deposits of oil and natural gas were originally produced by bacteria.

Extremophiles that exploit extreme environments under the earth's crust where temperatures and pressures are high are only a tiny part of the story of underground bacteria. It turns out that there is a vast web of microbial life underground; some of them exploit food sources, such as radioactivity, which  are completely unconventional from our own point of view. Microbes go everywhere; the estimated total mass of bacteria on earth probably exceeds that of all other life forms. That is to say, they not only outnumber us; they weigh more.

All that biomass, as it reproduces and dies, creates huge reservoirs of organic waste under the surface of the planet, which creates a fertile zone for the growth of more, new bacteria that feed on that waste; and gases, secreted in microscopic but relentless amounts, are an ordinary, day to day by-product of bacterial action. Cow farts, rich in methane (and a possible major contributor to global warming gases) are just one odiferous example of this. So the bacteria under the surface of the planet are undoubtedly one of the generators of natural gas.

More intriguing, perhaps, is the possibility that oil deposits may be linked to bacterial action. There is simply so much oil in many deposits, and in so many different places, that the question of whether its presence can all really be ascribed to the burial and decomposition of ancient plant material has been raised. It may be that the oil we pump today is actually bacterial waste of one kind or another. If so, oil may be, to some extent, a renewable resource; although the time frame in which it's renewed is probably measured on the long time scale.

Life exists so far under the surface of our planet that it suggests it could easily exist under the surface of other planets whose surfaces appear, at first glance, the be hostile to life. Life may have originally evolved under the surface of the planet... ours or another's... conditions there may have been more favorable, earlier, than they were on the planet's surface, and more stable.

The ability of microbes to decay things certainly comes in handy. Creatures that eat dead life, both plants and animals, have specifically evolved to feed on those sources, and they are a vital part of the food chain. Without them, the nutrients that are locked up in the various complex chemical structures that bodies are composed of would remain unavailable for further use.

Sunday, October 13, 2013

Tough Nouggies

I'm sure, with all of this "alarming" news about microbes I post, people are asking themselves, "Gee whiz. How can it be that bad? Aren't bacteria and other microscopic life forms pretty tough?"

Well, you're right. they are very tough. Microbes are some of the most resilient and adaptive life forms on earth. So tough and adaptive, as it happens, that they can survive at extreme temperatures and pressures on both ends of the spectrum- from the freezing cold, pitch-black lakes and frozen deserts of Antarctica to the extremophiles that live at undersea volcanic vents.

They are, in other words, incredibly tough, so tough that the idea they could survive the conditions in outer space is entirely credible. This worries Mars lander scientists so much that they go to incredible lengths to sterilize the landers before launching them—and still, no matter how hard they try, scientists are afraid that our own bacteria will ultimately end up anywhere we send spacecraft, and possibly survive to contaminate it.

Despite this fact, the issue isn't so much that bacteria are or are not tough. The issue is whether or not the bacteria we need and depend on are tough enough to survive the insults we are delivering to them without a fundamental alteration of the biosphere conditions we need for our own survival.

The bacteria, in one form or another, will survive. That's sure enough. But with enough changes, the bacteria that support the macrobiotic life forms (including us) may no longer fulfill the functions they once did; or, they may cause subtle and deeply undesirable changes such as physiological and psychological diseases which don't appear, at first glance, to be associated with microbial disruption.

Our state of mind itself depends on microbes. This may seem like a ridiculous proposition at first glance, but before you render judgment, read this article about how mice behave when inoculated with alternative gut bacteria strains. It may be, in other words, that some of the psychological deficits we are seeing on the increase in modern societies are a direct result of gut bacteria disruptions.

Microbes don't have to die off to cause us problems; they just have to change. One small mutation in the makeup of a bacterial population can cause it to stop (or start) secreting a hormone that either can't do its job any more, or triggers problems no one could foresee. The migration of gut bacteria populations all over the globe has undoubtedly already had some effects of this kind. How do we know that the increase in random acts of terror violence isn't actually due to some bacteria that causes deep seated, conspiracy-prone paranoia? We don't, and it's chilling to think that the virulence and vehemency of this kind of behavior may be a communicable disease— that is, a microbial infection.

It's not a ridiculous suggestion. It may, in fact, be closer to the truth than anyone dares admit... it may be that a real zombie plague is already with us, and we just don't know it.

In some ways, the whole problem is that bacteria are tough. They take everything we can throw at them... mutate a little bit... and on they go. Changed, they no longer produce the predictable, more or less stable (actually, nothing is ever stable, but that's another subject) results we have come to expect from them. Run-of-the-mill friendly bacteria like E. coli become, by random accident, predatory killers; bacteria we can usually fight off like Staphylococcus aureus morph into nightmare bugs causing, among other things. toxic shock syndrome. All by accident, mind you; from the bacteria's point of view, they don't intend to poison us or kill us. It just works out that way.

Bacteria and other microorganisms are, basically, indestructible, at least in the big picture. We may think we rule the world; but in reality we live in a world ruled by them, where we are outnumbered trillions upon trillions to one. The fact that they are small is nearly immaterial; when it comes to niche, environment, hazards, and survivability, our size is a liability. Size matters; and nature has proven again and again that when push comes to shove, smaller creatures which reproduce faster have far better odds of survival than big ones who reproduce slowly.

So it's not the meek, strictly speaking, that will inherit the earth; it's the micro.

Respect is due.

Saturday, October 12, 2013

animal farm

Photo by the author

There's ointment on the flies.

Then again, there is antibiotic ointment... or a version thereof... slathered all over just about every large-scale farm animal in America.

In most of the developed world, the small family farm was wiped out several decades ago. With it went a whole way of life... ma, pa, apple pie... and healthy animals. The rich, diversified microbiota that had been naturally developing and passing down from farm animal to farm animal through thousands of generations of human farmers went, too, because the new model packs animals into mega-shelters with controlled climates and living quarters smaller, by equivalent, than a New York apartment closet space. The creatures are packed in beak to beak, cheek to cheek in a manner that would absolutely be considered abusive by any city ordinance of a citizen were found keeping pets in the same population density.  You've read the stories; the old lady who had fifty-three cats, and so on. 

While the old lady gets herself prosecuted, factory farms are allowed by law to pack animals together in much denser volumes; it's not only legal, it's encouraged. Farm factories, all private (and often taxpayer-subsidized!) operations don't allow the public in to see their operations any more; the conditions are too horrifying, and too many scandals have erupted when the ugly truth of these places gets broadcast.

Leaving aside the morals of the situation, which are deeply troublesome, let's consider the health implications. These animals are under severe stress, living in conditions that have nothing to do with their natural habitat; they are artificially bred and systematically deprived of ordinary exposure to disease pathogens, serially crippling their immune systems. They are fed diets (often corn-based) to fatten them that have nothing to do with the natural food balances that both their gut biota and digestive systems originally evolved to cope with.

They can get sick. Very sick.

The answer is to feed them enormous amounts of antibiotics. It's estimated that 84%!! of the antibiotics used in the United States each year are fed to farm animals. Yokel-based reasoning about this horror story completely ignores the basic problem: this level of antibiotic use is breeding drug-resistant microbes at an ever-accelerating pace. Other countries have banned or drastically reduced the use of antibiotics in farm feed, but the United States has yet to take any serious action in this critical area. make no mistake about it, the epidemic of antibiotic use is killing people; there's no doubt that exposure to residual antibiotics in meat products is rendering the infections in human beings less sensitive to antibiotics; the flood of antibiotics used in American foods is generating a massive evolutionary surge in bacteria which is rendering them nearly immune to the drugs we count on to save us.

This isn't a disaster waiting to happen. It's a disaster that is already happening; but because the disaster is largely unseen, it is discounted.

We must be aware of one more very disturbing but rarely noted fact.

The changes these antibiotics are causing in the visible section of the population—that is, the known microbes, the farm animals, and human beings they interact with— represent a tiny fraction of the total population of bacteria being affected by these drugs. Drugs, you see, don't just disappear after they are administered to animals; they're secreted, that is, excreted in urine or solid excrement.

The antibiotic drugs are, in other words, not gone once they're taken:  they're flooding out by the millions of tons per year all over globe into every conceivable ecosystem we can imagine. These drugs have been detected in almost every body of water tested for them.

And no one knows what they are doing there; except that they are certainly doing something. It is an uncontrolled evolutionary experiment on a massive scale; a modern version of the Island of Doctor Moreau.

Recommended reading: Animal Factory by David Kirby. This book will certainly open your eyes.

PS— in today's news... drug resistant bacteria are now impacting professional sports... now there's and event that might finally get Americans to wake up and pay attention!

Friday, October 11, 2013


One of the consequences of understanding disease as being caused by germs is a widespread perception that all germs are bad.

This finds its ultimate expression, perhaps, in certain varieties of obsessive-compulsive disorder, but the idea that "all germs are bad" is a now generalized one. It has recently expanded to include the idea that "all fungi and molds are bad;" basically, if you can't see it, it is bad and therefore, in one way or another, dangerous.

While germ paranoia of the hand-wringing variety may be amusing when regarded from a clinical distance, it becomes a truly dangerous thing in the minds of the ignorant. People are trained to believe not only that all germs are bad, but that if they are sick in any way they ought to at once take drugs designed to kill germs (antibiotics.)

Drug companies have found it most expedient to encourage such ideas in the interests of boosting sales; and, recently, personal care product companies who manufacture soaps decided that it would be a teriffic idea to market antibacterial soap—even though soap is, by its very nature, already antibacterial. Triclosan, the common antibiotic ingredient touted (and used) as an additive to soaps, toothpastes, and other products, has been put, so it seems, in every soap dispenser in America.

Lo and behold. Bacteria are developing resistance to triclosan.

In the same way, doctors began, back in the late 1980's, to prescribe antibiotics to children every time they had an ear infection—in spite of the fact that statistics showed that antibiotics didn't really help ear infections clear up that much faster. Well, mothers wanted the doctors to do something against all those bad germs... what were they paying them for, anyway? It turned out to be more expedient to write the child a prescription than to have to listen to the mother complain. And the next thing you know, bacteria that cause ear infections were not only on the rise... they were drug-resistant.

The phenomenon of MDR (Multi Drug Resistant) bacteria is so well known by now that it's hit the mainstream. Everyone has read at least one horror story about a patient who got this, that or the other bug which just couldn't be killed. What isn't well known is that our over-use of antibiotics—which has drawn little or no real legislative attention from the health authorities in any nation—is causing these problems on a greater and greater scale. The "superbugs" that cause these disease problems are not, furthermore, living in isolation. They have spread otu into the egenral population and are passing their resistance genes on to foreign strains of bacteria—other bacteria which, in many cases, we don't even know about.

This deeply disturbing trend, another issue that has been underreported in the media and under-studied in labs, comes about because of the ability of bacteria to share genetic material between species via plasmids, gene packages that can engage in what amounts to interspecies sex. This proclivity was greeted with astonishment and delight when biologists first discovered it in the 1950's—it seemed miraculous—but as drug resistance spreads deeper and deeper into bacterial populations, it's looking decidedly more hellish than heavenly. The problems we've created by dosing our children with antibiotics for ear infections have moved well past their original targets.

The issue is even more widespread, because humans are not, actually, the prime users of antibiotics in society today. That dubious privilege belongs to farm animals... of which more in the next post.

Thursday, October 10, 2013

Adjusting the Earth

Today we're going to examine a subject a little more down to earth.

We truly don't appreciate just how much creatures adjust the environment around them to suit the microbes they need.

Trees are an excellent example of this. All plants, for that matter. Every plant has a community of fungi and microbes it needs around its roots in order to help take up the nutrients it requires for survival and growth.

Disruptions to this community can spell the death of the plant; and in plant monocultures, such as those propagated by modern agriculture—where we actually encourage a complete lack of species diversity— we are creating a situation wide-open to problems.

But let's get back to the trees, which are the subject of today's post. Every tree has a very specific microbial need around its roots; and the nutrients that the tree's leaves deliver when they fall are exactly the right blend of chemicals and are at exactly the right acidity for that particular tree.  (This may seem like a minor matter, but small changes in pH can lead to large changes in microbiology.) This means that the leaves, when they fall, are creating the best possible conditions to nurture their tree's future growth. They're also finely tuned to create conditions that do not favor the growth of hostile species; so trees and other plants condition the soils around them to lower the chances of competition. This is equally true in forests, prairies, and even marshlands. 

You might think that if you take those leaves away and put other leaves from a different tree (or some other composting material)  in their place, it will have the same effect, but that's not exactly the case. When you take the leaves away from the tree, over the long term, you're depriving it of the specific micro-environment it needs, a finely tuned set of relationships which evolved over millions of years, and substituting another, much less beneficial one.

It may not seem this way when you rake leaves up and move them, but the habit of moving litter away from its natural environment is contributing to long-term degradation of soil microbial communities all over the world, wherever it's practiced. While it doesn't kill plant and tree populations right away, it places them under constant low grade, long-term stress, and it steadily degrades the soils in which the trees are growing. 

Soils build far more slowly than we deplete them; and the majority of human activity is soil-destroying and soil-depleting activity. Real estate development creates so much soil disruption in a single year worldwide that nature would require thousands of years to create new soils to repair the damage. We can get away with such nonsense for only just so long before it catches up with us. Many of the areas being developed are the ones with the best soils; which means that agriculture is gradually being pushed out to the margins of habitable landscapes, where it is more tenuous and requires a much greater investment in energy, time, and resources to cultivate. These marginal landscapes are, furthermore, microbially impoverished, compounding the problem.

While one can counteract the various soil deficits we create by artificially boosting plant yields using fertilizers, this practice is something like using cocaine to stimulate yourself and stay awake. It works really well, but for only just so long; eventually, a dependency arises, and the results are, in the long-term, disastrous. The tremendous proliferation of corporations who sell chemical products -fertilizers, herbicides and insecticides- to dump on lawns by the millions of tons per year are not helping any; the general public, poorly educated on soil conservation at best, is aggressively marketed with disinformation which tells them to amend their homeowner soils using clumsy, unsustainable, but—for the corporations—very "profitable" methods.

Like the overuse of antibiotics, which is breeding whole new generations of disease-causing but drug-resistant bacteria, the widespread effects of poor agricultural practices are causing long-term, hidden changes to the way that the microbes around us are supporting what grows in our soil. We can't see it, so we don't worry about it; but we should.

The artificially created environments in which most cultivated and suburban plants are growing is inherently unsustainable without the support of artificial means; and it's likely that it will take centuries for the long-term implications of the impoverishment of our microbial environment to become apparent. It's quite possible that in many places, we will discover soils have been rendered essentially sterile because of the lack of the correct long term microbalance.

Even worse, because we have so few people interested in studying this right now, we are unlikely to identify and analyze the microbial communities around plants to any degree of the depth necessary in order to know how to preserve them.

By the time the things we need to know are evident, they may well be gone.

Wednesday, October 9, 2013

Trees die slowly

There's nothing random about microbes. Each one has, like larger organisms, a specific niche and set of tools to exploit it.

That extends past life into death. When creatures die each one has their own specialized set of organisms designed to feed on its remains. That's true of plants as well as animals.

Let's take the above photograph of leaves as an example. The microbes digesting the two species are feeding on different chemistries; each leaf has its own peculiar mix of nutrients, proteins, and insecticides (natural pesticides) in the form of aromatics. Hence the different patterns of decay on the leaves: the microbes involved may well be different (though perhaps related) strains, even though the leaves fell in close proximity to one another. Each leaf has a particular set of microbes that breaks it down most efficiently; and here, efficiency is everything. The faster a leaf is broken down, the sooner its nutrients become available to the plants that are still growing in the immediate vicinity; and this applies especially to the tree the leaves fell from. So there is an evolutionary dialogue taking place between the tree, its fallen leaves, and its microbes. Microbes that digest its leaves better thrive; leaves with a chemical balance (acidity and nutrient mix) suited to the microbes feed them better; and the faster the leaf nutrients are freed up and leach into the soil (creating new soil in the process) the faster the tree can use them.

There's a principle to be learned here. Efficiency, in an ecosystem, is everything. Ecosystems rely on processing nutrients both before and after the death of organisms in order to thrive. Species that process nutrients faster, in symbiosis with their microbial partners, add efficiency to the system and enhance the ability of those organisms to thrive, reproduce, and hold their own against other species.

When efficiencies are lost— or new efficiencies arise, for example, the arrival of a new flood of nutrients better suited to the efficient growth of alternate species—the dominant species in any ecosystem, microscopic or macroscopic, begin to change.  This is because ecosystems are dynamic entities that respond to changes in efficiency by favoring the organisms, or mix of organisms, best able to use them efficiently. If kudzu, for example, uses an available niche more efficiently than native plants, it grows faster.

This holds true of microbes and fungi as well as larger animals. What it means that an alteration of microbial communities leads to new arrangements in the soil, water, and even air. Residents of North Carolina found this out to their increasing dismay in the 1990's when pfisteria, a dinoflagellate protist you really don't want in your waterways, underwent explosive growth in the tidal areas of North Carolina because of a flood of nutrients entering the watershed from the explosive growth of huge, factory-type hog farming upstream. The microorganisms cause debilitating disease and massive fish kills.

Let's be clear: from the point of view of the microbes, this is not a bad thing. The overall efficiencies of the tidal ecosystems in the Albermarle, Croatan, and other NC sounds haven't deteriorated as a result of this pollution. Odds are the systems are still equally efficient; but they are no longer the same systems.

And this is the lesson: changes in microbial populations can lead to fundamental long term changes in ecosystem efficiency, resulting in drastic changes to the animal and plant communities that depend on them. This phenomenon is still poorly understood, but if the fish kills in North Carolina (and, unfortunately, many other parts of the world)  have taught us one thing, it's that these changes are often unfavorable for man.

Spectacular fish kills are more obvious than slower, long term changes in soil-based microbial populations, but the changes we can't see up front are far more insidious and will, in the long run, be much more difficult to manage. Trees under stress caused by microbial changes may die much more slowly; and the causes may not be identified until well after it's too late.

Tuesday, October 8, 2013

Environment and Community

 Sandpiper, foraging for larval mole crabs and other zooplankton
Kitty Hawk, North Carolina
 photograph by the author

We are used to the idea of mankind altering his environment to make it more suitable for him. We not only build houses; we landscape areas, dig ditches, build highways, and so on. But it may come as a surprise to readers to hear that microorganisms routinely alter their own environment to make it suitable for themselves. The creatures that depend on them — ourselves, for example — also alter their own environments, believe it or not, to make them more suitable for the microorganisms that they need.

We're going to take one of the most striking examples of that today, although there will be more to look at later on. We've already explained that human beings require a healthy, and wide variety, of microorganisms in their gut in order to digest foods properly. Without them, we die.

Where do we get those microorganisms? Well, of course, we swallow some from our environment. But more importantly, we inherit some of them — quite literally inherit them, since we acquire them from our mother during the process of natural birth.

As peculiar as it may seem, the birth canal — the vagina — is a rich environment for bacterial growth, and in the days just before birth, it turns out, this environment is heavily populated with bacteria from the mother's own gut bacteria community. She has, in other words, a range of all the microbes that the child will need for its digestive system waiting for it in her birth canal. When the child finally leaves the sterile environment of the amniotic fluid — when the water breaks and birth begins — the infant moves through the vagina, opening and closing its mouth, and inevitably swallows billions — perhaps even trillions — of the bacteria that it will need to populate its gut with. So the first organisms it needs other than its mother are, logically enough, bacteria. And the very first act of its life, before it even leaves the birth canal, is to set up housekeeping with them.

Obviously, children that are born by cesarean section don't get this benefit. The rising tide of children born in this matter in modern Western societies is leading to a large number of children who don't start life out with the correct gut bacteria populations. This has long-term implications, since the developmental well-being of the child depends in large part on making sure it has the right gut bacteria from the moment it begins to ingest foods. Otherwise, it's digestive processes don't work properly, and, in addition, the immune system doesn't develop properly. This can lead to all kinds of overreactive immune system situations in later life, and may well lead to diseases such as autism, diabetes, and other maladies such as bipolar disorder and other psychological deficits.

Oddly enough, this could all be corrected by taking children born by cesarean, swabbing the mother's vagina, and making sure that some of that liquid was put in the child's mouth. But no one seems to think of things this obvious.

It gets a little more complicated than that. Breast milk, it turns out, has essential proteins in it which, although they don't do much for the child — it can't digest them — are in fact perfect for the gut bacteria developing the child's intestines. And it furthermore carries an additional wide population of bacteria that are absolutely necessary for the well-being of the child. Follow the links for some fascinating insights into this.

The point is that there is nothing passive about the way that bacteria are delivered to an infant so that it's gut bacteria populations develop properly. Nature is arranging things specifically so that the bacteria are not only present, but have exactly the right environment to support the growth of the organism. So you human beings don't just have bacteria; nature makes certain that they have bacteria, and it makes certain they have the right bacteria. It creates conditions ideal for those bacteria, delivers them, and then nurtures them. This is an example of bioengineering that goes to the root of what community means. Nature, and life, is a community, not a collection of individuals who act independently of one another. The perception of independent action is largely illusory, yet we endorse it as one of the foundations of our social contract.

Nature teaches us otherwise.

 Of course, human beings are far from the only organisms that do this. Think about this: every single organism with a gut has bacteria in it, and every single one of them undoubtedly has similar mechanisms to ensure that it has the right bacteria in it. The entire animal world is engaged in this activity — unseen, and underappreciated. Unfortunately, the action of chemicals in the environment and the accelerating spread of foreign bacteria into new environments is guaranteeing greater and greater disruption of this system, which leads to all kinds of diseases. Because we don't understand how the  system is constructed, many of these diseases don't, at least at first, appear to be linked to the microbial population, but most of them are, in one way or another. The situation becomes more serious every decade, with disturbing diseases such as psychological and immune system disorders becoming more and more prevalent.

We keep looking for the causes of these diseases in our genes; but it may well be that the causes of them lie in our microbial populations, a place we have only just recently started to look at more seriously.

 These arrangements do not stop with animals, which we will discuss in the next post.

Monday, October 7, 2013

The microbial atmosphere

Empire State Building, New York, Sept. 2013
Photograph by the author

You can't see them, but you are currently surrounded by a sea of microbes. Not just trillions of them; googols of googols of them (googol being the number one followed by one hundred zeros.) There are so many bacteria and microbes on the surface of the planet, in fact, that they form what is more or less an atmosphere, a living medium through which all life "swims." This medium is breathed in constantly by all breathing creatures; it is swallowed. It lives on, in, and around every living creature. The presence of microbes is 100% constant from the day an animal is born until the day it dies.

If we were deprived of this microbial medium, we'd all die. Everything would die. These are the fundamental and essential conditions that life exists under and is supported by: a sea of life through which we constantly swim.

Any impoverishment of the environment can lead to issues. Killing off microbes protects us, to some extent, from disease; but the negative consequences can be disastrous. Polio, for example, was rarely a problem before the twentieth century. Poor water quality very nearly guaranteed that infants were exposed to it; for reasons yet to be fully understood, the virus has little effect on infants, so the virus-rich water supply conferred immunity on the majority of the population. It was only when water supplies were cleaned up that children began to reach young adulthood without immunity; the results were disastrous. Although cleaning up the water supply has bee a good thing in many ways, it is definitely possible to have too much of a good thing; and the steady pace of extermination of microbes in the child-rearing environment is leading both to a host of old diseases on the rise and new, emergent diseases.

The bottom line is that we need the microbial communities we inhabit. Cleaning them up too much, sterilizing the environment, turns out to directly affect the development and responses of our immune system, with sometimes disastrous results.

Although I'm sure it sounds like a reach, it's useful to think of the microbial environment we inhabit as an atmosphere. Like air, it invisibly surrounds us, and like air it's a medium that we absolutely require for daily life. We literally and figuratively breathe it in and out.

Interestingly, science has readily identified and embraced the chemical atmosphere of air and water as essential to the support of life, but the microbial atmosphere has been largely ignored, even though it comprises a living atmospheric medium for all larger life forms. Found in the air, soil, and water, one might argue that bacteria and fungi bridge the gap between the these chemical media and macrobiotic life forms. They are, seen from a slightly different but analogous perspective, a tissue that holds the macrobiota of the planet together by translating chemical constituents into usable forms.

So we live in an atmosphere of microbiota; and we depend on them so much that it becomes apparent symbiosis is, on the whole, a more prevalent lifestyle than competition.

This is so much the case that larger organisms don't juts host microbes; they go out of their way to create situations that favor the microbes they need for their own survival. More, quite literally, than meets the eye goes on in this regard; and we'll discuss that in the next post.

Sunday, October 6, 2013

Man and microbe

Here we are at the tangled, integrated end of a process that began about three billion years ago with bacteria and other microbes, evolved from them, and carried them along through billions of years of evolution... only to discover each one of us is the unwitting repository for trillions of microbes, without whom we could not survive.

To cast an even more interesting light on it, one of the possible—and credible—origin-of-life theories is that life came from outer space. Yes... life may be alien. The theory is more accepted than the idea that God created life out of thin air, at least in standard scientific circles.

One of the reasons this theory is considered credible is that DNA is an incredibly sophisticated, highly evolved and optimized molecule. It's so good at what it does that it just doesn't seem as though there was enough time after the molten fireball of earth cooled off enough to support life for it to have evolved to the state we find it in in the earliest fossil records... about 3.4 billion years ago.  The question of how life evolved at all in the hostile environment of early earth is still actively puzzling scientists.

The earliest fossils are recognizably similar to organisms still around today, which just about guarantees they shared a version of the same DNA we find in ourselves. DNA, it turns out, is so very, very good at what it does that many of the structures it uses to create specific proteins, molecules, and body structures are preserved as analogs to one another in creatures that diverged five hundred million years ago or more.

Bodies change... niches change... but although in some ways DNA changes a lot, in other ways, it's actually a very, very conservative molecule. It rarely, if ever, re-invents if what it already has can be reconfigured to work in a new way. Organisms (we can think of DNA, in a broad sense, as an evolving organism) this highly developed, consistent, and durable probably took hundreds of millions of years to reach that level of sophistication; and this is, to be sure, rather unlikely to have taken place at an accelerated pace under the hostile conditions provided on the early earth.

In a certain sense, man himself is a collection of microbes, since each cell—fully integrated and cooperative though they may be—functions as an individual organism. We're reminded of this in unpleasant ways when we get cancer—this, after all, is the ultimate example of just how independent and, in fact, malevolently autonomous cells can still be under the right circumstances. White blood cells (macrophages)  wander around acting on behalf of our defensive systems; cancerous cells act something like that, only when they crawl between tissues, they are looking for places to metastasize—settle down, set up house, and... eventually... kill us, if we're unlucky.

So we're communities of microbes, hosting larger communities of biota. It's estimated there may be as many as 100 trillion "foreign" microbes in the average human being. Multiply that by a planet of 6 billion people... we're up to six billion trillion microbes, and that's just the ones resident in us humans. In contrast, consider that there are probably about ten trillion of our own cells in a human body. The microbes we carry outnumber us by about 10 to 1... or 100 trillion to one, if you want to count our conscious self as one, and our microbes as being on the other side of that fence.

We live, furthermore, in a sea of microbes, one so dense as to give people with OCD the willies.

The point of this excursion is to explain that we depend on our microbial population for survival. We don't just have the microbes; we need them, and the vast majority of them have been evolving in conjunction with animals... first arthropods, then amphibians and fish, then reptiles, and mammals, until finally they ended up here with us. Each microbe we host is exquisitely tuned to living on or in our body.

It isn't just this way for humans. All of life on earth is ultimately arranged this way; everything depends on microbes to function.

We'll take that up in the next post.

Saturday, October 5, 2013

Why microbes?

In order to gain a deeper understanding of why microscopic lifeforms are so important to the existence of life in general, we need to begin with the fact that these were the very first life forms.

Not only did all other forms of life develop from them, because they formed the initial communities from which all further developments in life evolved, all these developments in life ultimately built their livelihood directly on the foundations laid by this community of organisms.

Growth depends on the acquisition of nutrients, and in any given environment—especially, perhaps, the most primitive ones on early earth— the total amount of nutrients is quite limited. It furthermore always costs something in terms of energy to acquire nutrients and concentrate them. This is what microscopic life — the first cells — did. In doing so, they created richer, far more concentrated repositories of nutrients.

It turns out that one of the best ways to acquire richer sources of nutrients is to exploit pre-concentrated ones that already exist—that is, steal them, which usually takes less energy than doing the work of concentrating them. And indeed, very early on, lifeforms began not only to compete with each other for the available raw nutrient resources; they learned how to take them from one another. In other cases, they learned to cooperate with one another and share resources; but in either strategy, it became expedient to lock the nutrient resources up in one way or another so that they couldn't be easily shared or stolen. The idea was to make the cost of acquiring these richer sources of nutrients – that is, the bacteria themselves – high enough that it wasn't worth it to others, unless they were willing to give something in return. That could include anything from a mutually beneficial exchange of valuable substances up to the taking of the other party's life in order to get what they had. Cooperation and competition.

Locking these nutrients up took two obvious directions. One of them was to develop body shapes and forms that had strong defensive capabilities. Groups of cells cooperating were better able to defend themselves than single cells; and so one of the first steps in life was the advent of cellular communities, which developed into what we now call organisms. The organism is the microbiological equivalent of individuals and societies banding together to form an army. Communities of cells were better able to defend their resources; they were also, it turns out, better able, in many instances, to acquire them. It wasn't long, in fact, before they began actively altering the environment around them to favor their survival. This took a number of forms—still with us today—which we'll talk about later.

The second line of defense for nutrient resources was to lock them up in chemical forms that couldn't be used by adversaries. One of the best examples of this chemical defense mechanism is cellulose, which is incredibly effective at taking nutrients and locking them up in an unavailable form. It works so well that almost every plant on earth now builds its life around the production of cellulose. This has forced the many larger organisms that want to feed on it—after all, it is incredibly abundant!— to develop mechanisms that can defeat the chemical "locks" on cellulose by digesting it.

The mechanisms that allow animals to digest cellulose are all primarily microbiological. Because it's difficult to attack cellulose in any other than a chemical way, digestive juices of various kinds must process it, all the way from the macrobiotic (gut) level to the microbiotic (fermentation) one.

Despite several billion years of evolution since the advent of the first single cell organisms, everything on the planet is still arranged in exactly this way. Cells lock nutrients up to make them unavailable; and animals and plants which choose to acquire them have to use chemical tools to unlock those nutrients. Even the largest creatures with the biggest teeth and the most powerful muscles can only do the initial job of acquiring the foods; microbiotic forces have to unlock them and make them available. And in the vast majority of cases, in fact, probably all cases, larger organisms have recruited their own colonies of microorganisms to help them do this. (The whole process of decay is deeply tied to this activity.)

This means that when you get a meal for yourself, the meal isn't just for you. It's for the microbes in you as well; you need to feed them, or they can't feed you. Eating the wrong things for them will ultimately lead to bad results for you as well, because it will favor the development of microorganisms that aren't beneficial to your digestive process.

Although forms and sizes have changed over billions of years, the fundamental underpinnings of the food chain have never changed. Given the strong persistence of DNA throughout life as we know it, it's very likely that not only DNA, but also the nutrient-storing molecular forms it encodes for, are much the same as they were billions of years ago. We know, for example, that there were plants of one kind or another using chlorophyll that long ago. They are still doing it today — and so we exist in an unbroken chain that relies on chlorophyll and its molecular productions for energy. Without it, sunlight couldn't be converted; and without the sugars that it converts molecules into, pretty much nothing on the surface of the planet could live. (There is, of course, another chapter to this story—creatures under the surface.)

In a certain sense, then, microbes are running the show; all of us are just vehicles for their action and dispersal. The more efficiently an organism interacts with the microbial community it supports, the more effectively it competes in the acquisition of nutrients. So the microbiological community actually fuels the process of evolution in ways that are still not well understood.

Because of our general ignorance in these matters—and the impression that we can do little or nothing to intelligently manage such things—we have, on the one hand, blithely ignored our relationship with microbes and, on the other, attempted to exterminate the ones that we know cause disease. Both approaches have turned out to have their drawbacks; the one, because we cause harm we don't know about, and the other, because our short-term management of infectious disease in both livestock and humans has led to unforeseen problems in microbe evolution.

Microbe evolution is taking place all around us, all the time, and at a much more rapid pace than our own. 

We'll take that up next. 

Friday, October 4, 2013

the long timescale — a schematic

 Although this post may not seem to relate directly to biology in the subject at hand, I want to say a bit more about this subject of the long timescale, and how our perception of ourselves affects the way we treat the landscape and the biology around us.

 Because the damage to man's perception of the long timescale took place primarily because of a science-related event we refer to as the Age of Enlightenment, the subject is an important one.

In  the interests of further clarifying the question of the cycle of myth, the human perception of time, and the man's knowing of the place he is at, I have created the above diagram, which can also be found and shared at the following link: the long time scale.

 This schematic uses simple visual devices to contrast the way that ancient societies thought about time and themselves, versus the way we do. Time, on both sides of its blue line, is framed by the unknowable — which we will call God or the Gods. This unknowable property was entirely tangible to ancient societies, because they saw how little they understood about the way the world worked.

The result of this was a proportional allocation of perception to temporal forces and their relative importance. Gods, which represented unknowable but immensely powerful qualities, loomed the largest in the landscape, although they lay outside of time itself.

Ancestors, who did have some knowledge — often, it was considered to be better than and more important than contemporary knowledge — were highly valued. This was because of the knowledge base that they imparted to their descendants.

Individuals saw themselves as small players in a vast universe, the fortunate inheritors of a large body of knowledge that had been passed down to them which they could make only incremental contributions to.

Their descendants were considered to have high value, because individuals understood through the instrument of myth and tradition that they were playing the role of ancestors to them, and that the degree to which they performed this function would have an immediate and important impact on the future of their own families, cultures, geography, and civilization itself.

A modern reallocation of perception began during the Age of Enlightenment, when human beings — consequent to a set of admittedly important scientific discoveries —began to devalue everything that reminded them of their ignorance. The dawn of new sciences and the scientific method itself, along with a rise in belief in the ultimate triumph of rationalism, caused men to believe that earlier societies were primitive, and to be held in contempt.

This devalues ancestors dramatically. It also devalues God or the gods, because the perception becomes that all mysteries can be penetrated— often, very soon.  It's not even uncommon for this idea to be accompanied by the delusion that everything is already known, a premise that fundamentalists of various stripes adopt with great fervor.

 In this "system of the moment," descendants became relatively worthless, because one doesn't really owe them anything, and they are unable to contribute to the power structures du jour, which are the only things that matter.

It must be noted, however, that in absolute terms, virtually nothing has changed between the first and the second case. 

Measured against the total sum of knowledge about the universe that can be acquired, man's position is exactly the same as it was in ancient times. All of the knowledge he has acquired (and, in some cases, lost) since ancient times amounts to a zero sum measured against the total sum of the unknown: a fraction so small that one would be typing zeros after the decimal place for millennia in order to define it.

Nonetheless, humans, in a stunning display of hubris, have assumed that their gains are very major ones against the sum total of the unknown, and have consequently discounted it in their psychological landscape.

 The fact that man's total base of knowledge remains, essentially, unchanged from ancient times when measured as a percentage of all the knowledge in the universe is completely forgotten. The individual has now become the one with the power, not the universe and the gods. Modern societies are continually reminded of the fact that this isn't the case at all when natural catastrophe strike them, but they don't see the psychological and perceptual discontinuity that is given birth to their astonishment. Because they have forgotten the cycles of myth, the long timescale, and the essential on knowability and mystery of the universe, they have fallen victim to delusions in which they believe they actually know a great deal, when, in fact, we are profoundly ignorant.

The modern misperception of the long timescale leads to drastic mismanagement of future events and circumstances, since the perception of "now" becomes primary, and everything is seen exclusively as an opportunity for exploitation and personal gain. Because one no longer plays a role in a vast cycle where one owes a debt both to one's ancestors and one's descendants, one perceives one's self as fully licensed to act in a selfish manner.

 As I pointed out in one of the earlier essays on this, the long timescale is actually a dialectic between the transcendent and the immanent. In the first case, the transcendent — the mystery, the unknowable ability, of the universe and of life itself — is the powerful, formative, and transformational force that dominates the transaction between the individual and Being. In this arrangement, the ego is subordinate, even if only by the strength of social form and tradition.

 In the second case, the immanent, the known, and the materially tangible, is the powerful, formative, and transformational force that influences and forms the transaction between individual and Being. This arrangement is a direct affirmation and validation of ego at the expense of mystery and unknowability. It is the dominant form our society has assumed in the present day.

 We have reversed the psychological arrangement that evolved in man from the earliest time in which he formed societies, and we have done so in a few brief centuries. This essentially destructive reversal, which focuses us almost exclusively on our own self-importance, is gradually being seen for the mistake that it was from the beginning. Unfortunately, it is unleashing equally reactionary and divisive forces which — like many over aggressive immune system reactions — may do more harm than the good they attempt to bring.

Understanding these forces from this macroscopic point of view may help us to find sympathy for others, and create a different form of harmony that can include both what we know, and what we don't.

May your soul be filled with light.

Thursday, October 3, 2013

A gut feeling

 Microbial communities are highly interactive, and extremely fluid, within the ranges they inhabit. They create whole complex ecosystems of their own, which are largely invisible and entirely incomprehensible to us at our current state of development in microbiology. Teasing apart some of the relationships between various microbial communities will have a major impact on understanding a wide range of human diseases, many of which are caused, directly or indirectly, by imbalances in gut bacteria. Diabetes, autism, cancer, obesity, and heart disease have all been implicated. This means that a wide range of the major killers in the disease community have important links to the way that our microbes are balanced, and their interaction with one another and our body.

Even more disturbingly, imbalances in gut bacteria can definitely lead to macroscopic psychological manifestations, as has been proven repeatedly in laboratory experiments with lower mammals. this means that microbes don't just affect the way your body functions; they affect the way you think. As bizarre as it may sound, microbes may make you smarter.

Or they may make you go out and buy a gun and shoot a bunch of people at a movie theater. We just don't know; and that's what ought to worry us more.

All of this is part of an emerging science of emergence — that is to say, a deepening of our understanding of the properties of emergence itself. Put very briefly, and in layman's terms, emergence is the property whereby an aggregate population of simple elements — whether it be molecules, bacteria, cells, or organisms such as bees or ants — that, by themselves, display consistent and easily predictable behaviors, reach a critical mass of synergistic interaction whereby they suddenly display completely unforeseeable new agencies and an entirely different level of organizational abilities.

Put simply, intelligence itself— and the property of consciousness — are emergent properties of matter. You cannot, for example, take a look at a DNA molecule and predict by looking at that molecular structure that it will create a creature that does what a human being does. But if you put enough DNA together, and it tells enough other material elements what to do, you do get that extraordinary and unusual creature. Much has been made of this by prominent scientists such as Robert Ulanowicz (A Third Window: Natural Life Beyond Newton and Darwin) Stuart Kauffman (Reinventing the Sacred) and Simon Conway Morris (Life's Solutions),  all of whom argue, for various — and very good — reasons, that biology as it manifests displays inexplicable phenomena which cannot be grasped by reductive scientific analysis alone.

 These books are far from simple — although well worth reading — but the point they make is that we live in extremely complex biological systems which display properties science cannot fully understand under any current, or future, set of circumstances. We may create some good approximations of some small fraction of the world we live in, but that fraction will always be necessarily small, because of the enormous complexity and the extraordinary behaviors of biosystems.

 These systems are so complicated that we are not going to fix them by tinkering with them; but we can most assuredly alter and even ruin them by dumping chemicals into them willy-nilly. Every massive, wholesale alteration of the environment — whether it is an environment outside of a man's body, or inside of it — causes the potential wholesale collapse of the inner or outer ecosystem. A huge assembly of maladies ranging from the inconvenient — for example, IBS, irritable bowel syndrome — to the catastrophic — such as Crohn's disease and stomach cancer — are directly attributable to microbial disruption in human digestive systems and other parts of the body. It turns out, for example, that atherosclerosis— the leading cause of heart attacks — is, without any doubt, directly linked to long-term inflammation in the linings of blood vessels, which has been directly associated with periodontitis, the bacteria that cause gum disease.

 We depend, in other words, on the microbial communities that support our bodily functions. In the same way, the outside ecosphere depends on microbial communities that support every single function we observe. Our health and well-being are vitally depended on these systems, but, unlike the macroscopic biological events we can have an effect on — for example, you can operate on a heart to fix a valve — we are very nearly unable, and probably always will be unable, to affect the long-term changes in these microbial systems, because they are vast, complex, and operate in porous environments with little or no control on the influence of outside events such as weather, temperature, influx of an excessive or foreign materials, community interactions, and so on.

You can slow down a heart or stop it beating to perform an operation on it, because it's large enough to see, you know where it is, and you know what needs to be done to it. That description can't possibly be applied to any microbial community we are currently aware of, and it probably never will be. Heart operations are scalable; microbial ecosystem management is not.

 Most of what we deal with in terms of internal and external ecosystems must, of necessity, apply itself to macro solutions. Micro solutions, while they can be engineered for specific instances such as cancers, become much more difficult to implement. It's been discovered, for example, that every single cancer is somewhat different in each individual. If you and I both have, for example, prostate cancer, although they share many of the same characteristics, what works to cure my prostate cancer won't necessarily work to cure yours. Microscopic ecosystem solutions are almost certainly going to turn out to have the same unique and individual characteristics, but they will be far more complex, thus far less susceptible to outside management. This is compounded by the fact that they are tiny, invisible, far more subject to contamination by foreign agencies, and inherently unpredictable because of the fluidity of their interactions.

This is why having negative effects on microbe populations, wherever they reside, has long-term implications that ought to be of far more concerned to human beings than they currently are. We are already engaged in the largest reengineering of the microbial communities on the planet in its history, because we are introducing foreign agents that have never before existed on the planet, in the form of tens of thousands of different chemical products that are contaminating our waters, our air, and our soil.

 This question needs to be re-examined over and over again in more detail, because it is not being discussed enough in environmental communities. The idea that we can tacitly accept the proliferation of chemical products without restraint needs to be retired.

Wednesday, October 2, 2013

Underpinnings, part two

 Human beings rarely stop to think about the fact that every single thing they look at which is alive and growing — animal or plant — is absolutely and utterly, completely and irrevocably, dependent on the microbial communities that support it.

 If all the microbes on the planet died, or even a significant fraction of them, nearly every life process we are aware of would be disrupted in one way or another. Plants would stop growing; animals would die. Animals have been extraordinarily dependent on microbial communities for survival ever since they developed guts; without the microbes in their guts, they wouldn't make it.

 In order to understand this, we have to understand that the gut — a tube in which food substances are broken down into constituent molecular components — has existed since the cambrian explosion, perhaps earlier. Ever since creatures began to eat surrounding organic material — including each other — there has been a need to break down the walls of cells in order to get at the nutrients inside them. In many cases, the walls of cells, which are microscopic, can't be so easily affected by the action of larger structures like teeth — which many creatures, let's remember, don't even have — and the chemistry of the foods inside the cells was bound up by molecular relationships that lock the energy into inaccessible structures — for example, and perhaps most typically, cellulose, the primary form of cell wall in green plants.

In order to avail themselves of these rich reservoirs of nutrient, animals needed microscopic organisms that could act on the structures to break them down. Bacteria, it turns out, are ideally suited for this, for a number of reasons. First of all, they are small enough to act on a microbiotic scale; big things may be able to eat little things, but other little things need to help digest them. Second, due to their short life cycles, they evolve very quickly, so they can quickly develop new responses to new foodstuffs as new evolutionary developments make them available to creatures foraging in new areas. Third, they are capable of one of the most extraordinary acts in the animal world, one that is functionally impossible at larger levels — that is, the inter-species exchange of genes through plasmids. This gives them a developmental edge that has vexed medical scientists for several generations now, since it allows them to rapidly develop resistance to antibiotics across a wide range of species.

But let's get back to what this meant to early life, because it's fun and exciting. A quick trip to the American Museum of Natural History –  or any museum, for that matter, that has a good collection of large  herbivorous dinosaurs such as apatosaurus— will treat the reader to the sight of creatures that evolved massive bodies with huge guts. These gigantic intestinal reservoirs developed with only one purpose in mind; they were massive housing units for gut bacteria, which fermented and dissolved the huge amounts of plant materials these dinosaurs ingested. Just looking at the skeletons and the shape and size of the guts verifies that by 150 million years ago, the digestion of food stuffs by gut bacteria had been taking place for additional hundreds of millions of years, and had reached what may well be a zenith. It is standard operating procedure in any creature with a gut. The gut is a portable toolkit for microbial digestion, exactly like a set of cookware people bring on camping trips.

Humans aren't any different in this regard. We have skeletal structures, much like the dinosaurs, that support an abdominal cavity that carries around a very neatly organized, species-specific package of bacteria that acts as a bioactive Swiss Army knife. Gut bacteria have been evolving for millennia and are supremely adapted for the diet and lifestyle of the creature that has them. Creatures exist in lockstep with their gut populations; and the gut population itself is a very complex structure that includes both microbiotic creatures such as yeasts, bacteria, and fungi, and macrobiotic creatures such as worms.

 These populations, moreover, have existed in such exquisite balance for so many hundreds of millions of years that changing any of it changes the fundamental nature of the organism itself, since all of its inner workings are highly dependent on the balance of these communities.

 Anyone who doubts this needs to spend a few hours browsing the articles I've collected at my gut bacteria page. You will come away with a completely new appreciation of what not only human beings, but all species, consist of — a commensal and symbiotic community of organisms that must have one another in order to survive.

 We may think we are different than the species of ants who have a parasitic fungus that alters their behavior, causing them to undertake activities that helps the fungus spread; but we are not. The bacteria in us have a direct effect on our psychology, remarkable though that might sound, and the laboratory evidence supporting this contention mounts with every passing day.

There will be more details about this to discuss as we move forward.

Tuesday, October 1, 2013


 Mushrooms and moss, Tallman State Park, New York
 photograph by the author

Everything that you can see is supported by things you can't.

When Antonie van Leeuwenhoek —  the world's first microbiologist — first peered through the lenses of his microscopes in Delft, he revolutionized the world in a way that his contemporary, Johannes Vermeer, also did — he saw things in a new way. What he saw, however, had much more profound and exciting implications than anything Vermeer was able to observe on the macroscopic scale.

In van Leeuwenhoek's time, it was fundamentally impossible to appreciate just what this extraordinary "new" world of microbes meant. Initial investigation was largely a matter of cataloging. It hasn't been, in fact, until the 21st century, with the advent of DNA analysis, that we begin to know microbiology at the extraordinary level of detail that it's necessary to have in order to understand what is going on. This linked article about the understanding of what gut bacteria are doing in termites is an example of exactly what I mean by this.

 The bottom line is that microbes appeared to be novelties, zoological specimens for aesthetic appreciation, for the first few centuries we knew about them. It was only when it became understood that they cause disease ( see the germ theory of disease), which took place only in the 19th century —! — that human beings outside the immediate scientific community of microbiologists (who up until then had been considered, no doubt, a small community of obsessive cranks engaged in pointedly pointless studies) began to take a much more active interest in these communities in order to understand just what they meant to us. We began to see that microbes have a huge impact on us.

Plague diseases like the bubonic plague and cholera are specifically caused by bacteria; not only do they wipe huge swathes of human population out, they have, as William Hardy McNeill pointed out in 1976, major impacts on world history. The strange and under-appreciated fact is that who we are — our societies, governments, cultures, and history — has been determined to a significant extent by the microbes we share the globe with. People don't think about this in their day-to-day life, but if a plague breaks out — it's all they think about.

 The underpinnings of human culture and society are determined to an even greater extent by microbes, whose action in society is not limited to disease alone. Fungi such as Amanita Muscaria and psilocybin have influenced religious practices for thousands of years; the Mediterranean practice of fermentation of milk into cheeses through the action of bacteria has had a major worldwide impact on food culture; and other forms of fermentation are equally important in other cultures. Perhaps the most important and pervasive type of fermentation is the production and distillation of alcohol; this process is dependent on yeast microorganisms.

What this means is that no matter what you do, and no matter where you are, on a daily basis, you are interacting with foods and beverages that depend on microbiotic communities for their very existence. Disruptions to the microbial communities which make these processes possible would spell, perhaps, the end of the processes themselves. It may seem alarmist to suggest that invasive bacteria could create situations where something this drastic takes place, but the possibility is certainly there.

More important, perhaps, than the fact that microbes and their activity pervade our food culture is the fact that they live on us; and they live not only on us, but in us. The sheer number of microbes living in any human body is staggering, numbering in the trillions. There are thousands, and probably tens of thousands, of different species of bacteria inhabiting every human body; from their point of view, we are their ecosystem, their habitat. Habitat and ecosystem, you see, are a matter of scale: from our point of view, we live in the jungle, or the desert; from a microbe's point of view, it lives in the gut, or on the skin. The analogies are apt; the gut is dark and moist, with a rich and diverse community of microbes, like a rain forest; the skin is relatively dry and has a much smaller population, like a desert.

 We'll talk about this more in the next post.