Thursday, December 26, 2013

Animal Earth

For the past several weeks, I've been deeply engaged in reading Animal Earth, a fine book by Ross Piper. Very highly recommend; Piper writes lucidly and with a sense of humor, and the photographic illustrations are, to understate the case, superior.

The book brings home the extraordinary diversity of life at the microscopic level, calling attention to overlooked yet essential animal phyla such as Loricifera, ancient lineages of animals which the general public completely overlooks and is probably even entirely unaware of. Yet we share our planet with tens of thousands of such species, which easily outnumber us both in numerical terms and that of sheer biomass.

No one—even specialized biologists—knows much about these creatures, yet they form the essential underpinnings of life on the planet. Marine plankton—the larval stages of a staggering variety of arthropods, as well as other animals—are one of the planet's great microbiological reservoirs, creating the invisible understory of all—yes, all— marine life. Yet damage to plankton populations is difficult, if not impossible, to gauge, and methods for assessing the overall health of plankton populations present challenges of scale and complexity it is nearly impossible to evaluate, let alone overcome.

Large scale activities that result in gross, easily visible habitat destruction and the extermination of larger animal species generate the overwhelming majority of concerns about ecosystem damage. These are often the result of mechanical processes such as strip mining, deforestation, and overfishing. Yet the chemical pollution of biological microsystems may well turn out to be the greatest long-term threat to ecosystem health. Physical damage can, after all, be overcome; but if the foundational microbiology of a system is disrupted, any short-term recovery may turn out to be impossible.

The fossil record, especially the Burgess shale and other benthic (sea-floor) lagerst├Ątten, demonstrate just how long many of these species have been with us; 500 million years and more. Their durability testifies not only to their resilience, but also how essential to ecosystems they are. No organism can persist in a habitat or body shape for that long unless it is performing essential roles for which it is, for all intents and purposes, perfectly adapted. Many of the smallest life forms we encounter in the world of microbiology fall into this category. These small life forms are the ones most likely to be compromised or destroyed by trace chemicals in their environment; amounts that seem insignificant to larger creatures represent massive doses on a microbial scale.

It's unlikely that the world will see a rush to the serious study of such tiny creatures any time soon; and while we continue to ignore them, the destruction of their populations seems assured.

The situation presents powerful arguments in favor of the most conservative approach possible to the introduction of new chemicals intended for widespread use and distribution, and stricter controls on the emission and control of all chemical waste processes of any kind, not only industrial, but also household wastes.

Wednesday, December 11, 2013

A sense of touch

This article on the ability of bacteria to detect form through a sense of touch is very interesting.

As with other cases across the biological spectrum, we're continually astonished when "lower" organisms display the ability to do things we thought were unique to higher ones... especially humans. Yet in this case, we can safely say that all of the macroscopic sensory abilities and behaviors we see have their roots, as well as their parallels, in the microbial kingdoms. Macroscopic behavior is a reflection of microscopic behavior; big things reflect little things.

This fractal arrangement is consistent throughout nature, so much so that it gets glossed over. But even the smallest creatures are not, in the end, so much unlike us. The same, or at least similar, sensory tools are needed to orient, to taste, to "see," on every level.

Microbes, which perhaps seem to be alien creatures, as small as they are, thus share an oft-unrecognized kinship with us. Not only do they colonize us, parasitize us, and coexist with us; each microbe is a legitimate, unseen life carried forth and lived out according to imperatives that, to it, are just as compelling as our own. There is a sensory and molecular awareness within these creatures; and it's to be appreciated, not dismissed.


Tuesday, December 3, 2013

Nanoplastic and Other Micropollutants

In the world of the unseen, the law of unintended consequences dominates.

Our pervasive use of plastics... which don't biodegrade well, if at all... has inundated the environment with plastic waste. It's unsightly... and when we see it we're sometimes dismayed, even though by now the sight of it is so common that we've developed a sort of visual immunity, whereby we edit it out of our vision. This enables the vast majority of people to walk right past most plastic waste without picking it up. 

It's always someone else's responsibility.

What most of us don't understand in the least is that plastic, like all other materials in the environment, is subject to mechanical forces that steadily erode it. Abrasion takes place as plastic is transported by wind or water; it rubs against branches, grinds against sand and stones, and creates smaller and smaller particles... which, as it happens, aren't really much more biodegradable than the larger pieces the plastic first came from.

The net effect, over the past city or more years, has been the creation of a steadily increasing sand-like substrate of plastic nano particles, tiny little bits of plastic that are so small as to be nearly invisible to the naked eye.

No big deal, you might think; but it IS a big deal, as scientists at Plymouth University reveal in the link. Plastics assist in the transfer of toxic chemicals into small marine organisms who ingest them; and these small, uninteresting organisms form some of the foundational elements in the food chain on shorelines—and, of course, in many other cases.

Not only are plastic nano particles present on shorelines, they are becoming increasingly abundant in suspension in water, where they affect aquatic food chains all over the world. Imagine living in a world where you began to have to inadvertently eat pieces of plastic with your spaghetti, your hamburgers, your bagel; these tiny organisms are already in that world. they can't escape the consequences of our polluting activity and they aren't able, as we are, to discriminate between plastic particles and food particles. It's absolutely certain that because of this, nanoplastic pollution is already wreaking havoc on food chains and biodiversity in the microsphere; and it's all taking place out of sight. the long term effects are likely to be severe, but the phenomenon is drastically understudied and the public is (as usual) not just uninformed, but completely ignorant—and, let's admit it, probably won't care anyway, at least not until it impacts their lifestyle.

Treating issues of this kind with a shrug of the shoulders and a "who cares" is not good enough. Much stronger environmental controls need to be placed on the production and use of plastics, which will take a major rethinking on the part of both producers and consumers.

Monday, December 2, 2013

Microbes and population balances

Readers will perhaps recall that in the last post, I explained that the application of fertilizers and mechanized agriculture have vastly expanded human populations... well, I didn't say that specifically, but we all know it's true. The sheer number of human beings on the planet has exploded; and the balances and population levels of countless different organisms have consequentially suffered or benefited.

One of the well-known situations in ecological analysis of the biosphere is that species maintain balances relative to one another — that is to say, they are not exactly "balanced," but the density of various  species is directly related. If one species becomes more dense, another one become will be less so, and so on.  There are winners and losers not only in the primary species, but in all of their accessory companions.

Dependencies change. One of the recent cover articles in Scientific American (see King of Beasts, in the November 2013 issue) explains that it's quite likely that the rise of human predators on the great plains of Africa led to a notable reduction in the diversity of carnivores who competed with them.

What I suspect is true — although I don't have any proof for it — is that the expansion of human population has had, and is having, similar impacts on the microbial world. That is to say, microbes exist in specific balances with one another and with the macroscopic species that they interact with. Drastic changes in the macro environment that affect microbes will ultimately have effects similar to the ones hypothesized by Lars Werdelin.

For example, wherever there are a lot more human beings, there's a proliferation of the specific bacterial species associated with human activity. This is self-evident. A second self-evident consequence is that these bacteria compete with other bacteria; and since, even on the bacterial scale, resources are limited, if bacteria and other microbes associated with human activity get a leg up because of all the humans they have to interact with and colonize, they are able to reproduce and spread at the expense of other bacterial species that would find other, different conditions more favorable.

This may not seem like it means a lot; but it what it means is that environmental holocausts, in which huge populations of important species are eventually lost (again, see Werdelin's article), can take place on the microbial as well as the macroscopic scale. The microsphere functions in essentially the same way the macrosphere does; and our manipulation of the environment may have the result of completely overwhelming important microbiological communities we haven't studied or looked at. This can lead to a wide range of malaises that affect the health of species such as, for example, bees.

 Let's think about that one for a minute. It's well-known that bee populations have been collapsing all over the world. Everyone assumes that this must be because of either a pesticide, a group of pesticides, a pathogen (infectious disease, whether viral or bacterial) or a new kind of parasite — although they haven't been able to identify any special new parasites, just lots of the old ones in weak hives. But what if it has something to do not with what the bees have — that is, pesticide or disease affecting them — but with something they don't have? What if we have inadvertently wiped out bacterial species that they need for their survival, which now can't populate their bodies and their hives properly? This "subtractive effect" — whereby a missing microbe is what causes weakness in a population — is much more difficult to measure, but it almost certainly exists.

 I haven't seen much discussion of this particular issue in scientific journals, but it strikes me that biologists ought to take a closer look at it.

Sunday, December 1, 2013


Agriculture has many unintended consequences. It has impacted the global carbon footprint for thousands of years; scientists at Lamont-Doherty (which is in my immediate neighborhood) discovered some ten years ago that evidence suggests this effect began as much as 5,000 years ago, as soon as mankind began clear-cutting large tracts of land for cultivation in Asia Minor. Interestingly, studies of arctic ice cores suggest that the carbon emissions produced by agriculture underwent significant dips during successive episodes of bubonic plague in Europe and the Middle East—plagues which substantially reduced populations and took large areas of agricultural land out of production, returning it (however temporarily) to forest.

One of the most dangerous and pernicious effects of agriculture, however, has relatively little to do with its very serious impact on atmospheric carbon levels; and that is the application of fertilizers.

Fertilizers, which dramatically increase the available amount of nitrogen and phosphorus in soil, work hand-in-hand with fossil fuel (mechanized) agricultural production methods to magically boost soil productivity. As we have explained in earlier posts, this boost in soil productivity comes directly at the long-term expense of microbial populations; and the detrimental effects of that soil quality depreciation have only recently begun to be understood, because most of the negative effects are both long-term, and invisible. 

Today, when we see vast desert areas that used to be rich, fertile agricultural land (much of Asia Minor, for example, falls into that category) we assume it's because of climate change; but the first and foremost cause of the decline of the land into unusable desert began with the destruction of its microbial communities, a long-term degradation that was unseen and beyond the ability of the cultures causing it to understand or measure. We are now at a point where some few scientists do understand this problem; yet it is receiving little or no attention in the press, because it lacks glamor, and is difficult to solve. Nonetheless, it represents one of the greatest long term threats to human populations. Continued destruction of the microsphere (my own newly coined term for the microbial communities we rely on for survival) will eventually do society as we now know it in if it isn't halted.

This recent article about the effects of fertilizer runoff on coral reefs underscores the unseen effect of agriculture on ecosystems. Although the scientists involved had their attention drawn to the situation because of the damage being done to coral reefs—which are glamorous, touristy, and thus deemed worthy of consideration by the public—what the article does not make clear is that the damage extends to a wide range of other creatures which cannot be so easily seen. The damage cited here is, after all, damage specifically inflicted on very tiny creatures—coral polyps. The only reason we notice it is because these nearly microscopic creatures secrete exotic skeletal structures—corals—which we find aesthetically appealing. There are a host of other microscopic creatures around them, both in their immediate vicinity and all the way down to the reefs through the waterways that carry the pollutants—which are also affected. 

The damage to the coral reefs, which is grave, is thus only the last damaging effect we can see; the end result, so to speak, of a pollution event that has damaged ecological infrastructure all the way down the line from the place where it was originally applied to the soil. The soils have been negatively affected; the streams that carry the runoff from the agricultural areas are affected; the rivers the streams feed into are affected; and the estuaries the rivers run into are affected.

After running this damaging course which leads all the way to the sea, the runoff finally wipes out corals, and suddenly we are alarmed and take notice. It's kind of like having a cancer that has spread through the entire body but only gets noticed once it has erupted on the skin. There is widespread, systemic damage; but our assessment of that damage is crudely limited to the areas where it's most visible.

The coral reefs are indeed telling us we're in trouble; but what they are telling us is that the trouble is everywhere. Not just on the coral reefs.

Intelligent, long-term solutions to the problem of agricultural runoff are thus vital to the future of both agriculture and the ecosystems that support it. Mankind's future well being depends on understanding this properly.

Monday, November 18, 2013

How old is life, really?

I've mentioned the theory of panspermia in earlier posts; briefly put, the theory that life is ubiquitous and that it evolved somewhere other than earth.

A significant component of the evidence offered to support this theory is that life seems to have appeared so early on in earth's history that a molecular structure such as DNA—which is a highly evolved and optimized molecule that must have undergone millions of years of evolution to attain its present level of sophistication and efficiency—couldn't have had time to arise and refine its abilities.

Earth, after all, is presumed to have been a hot, molten ball of fiery magma for much of its earliest history, with properties that preclude the existence of life in any form, even that of extremophiles. The earlier that evidence of organized life turns up, the more likely it is that panspermia was the source of that life.

Now a new discovery has pushed the origins of life back even earlier than expected. This is pretty cool stuff, making it more and more likely that the fundamental building blocks of earth's life originally arose on another planet... more than likely, even another solar system. Life may be a heritage that dates back to the first billion years or so of the universe, when galaxies were still forming... in which case life is approaching 13 billion years old, or something like that. Given the propensity for carbon to be the arbiter of all organic chemistry, that life may well have been DNA based... at which point we would have to say (I think you can see this one coming) that life is built into the very DNA of the universe.


Of course, all kidding aside, this would be miraculous news indeed. If DNA based life is indeed an integral and inseparable part of the universe's character and nature, it carries what are perhaps nearly metaphysical implications.

Sunday, November 17, 2013


Speaking of the persistence of life, etc., etc, How cool are these? 


the blog author has a new book out. recommended.

Saturday, November 16, 2013


For many years now, I've been watching the enormous flocks of redwing blackbirds that gather in the Piermont marsh. If one is there at daybreak, one frequently gets to see them take off — almost at exactly the same time, relative to sunrise, every morning.

 I would guess there are probably between 5,000 and 10,000 blackbirds in the marsh.  One of our favorite activities on summer evenings is to sit up on our deck in the Sparkill Gap (the first break in the basalt dike of the Palisades north of Manhattan on the west side of the Hudson River) and watch the birds come back to the marsh; never in the huge flocks that they leave it in, but always in tight clusters of 10 or 20, sometimes 30 birds. On rare occasions a larger flock comes back; but never the masses that leave together in the morning.

One of the phenomena that isn't recorded in the video above is a strange and striking moment that takes place just before the flock takes off in the morning. When one walks along the marsh in the darkness, say, about 5:00 AM, the birds are dead silent; I can verify this, because I've done it many times. But as soon as the first light starts to show in the sky, some few birds begin clattering — at first softly, but then in increasing numbers. As the light intensifies, the clattering gets louder and louder, until — after perhaps 20 minutes or more of anticipation — it reaches a crescendo. At this point, it often sounds like a huge, rushing waterfall in the immediate vicinity. If you come upon it and don't know what it is, you will certainly think it is the sound of a large river rushing over stones.

At this point, an extraordinary event takes place. All of the birds instantly stop making all the noise, at the same time. There is no tapering off; it's as though someone turned off a light switch, and the power went out.

Moments after that, they take off.

Listening to this phenomenon, I've wondered exactly what it is that triggers the behavior. Whatever it is, all the birds instantly sense it at exactly the same time, as though they were psychic; but of course, birds make relatively imperfect mediums. There must be a natural cue.

 I think what it is is the total volume or decibel level. There's a point, a threshold, that's reached; and when this threshold is reached, it triggers the flight behavior.

I've never heard of anyone studying this before, although it's possible someone has. In any event, it's one of those miracles one has to be there to fully appreciate.

This morning, my wife and I were there just to take off, once again. We watched impressive masses of birds wheel and dive over the marsh, circling while more and more birds peeled up out of the phragmites into the dervish black cloud above it. They behave as though they were a single organism; and this kind of behavior, where large groups of organisms take collective critical behavioral cues from a threshold of chemical signaling, is well known in the microbial world. The chemical signaling is one thing; but this audio signaling is another story, a signaling of vibrations.

One wonders whether there are bacteria who do something like this as well.

Thursday, November 14, 2013

Microbes are forever

I've been making the point for some time about how incredibly durable microbial life is, but perhaps this particular article makes the point better than I can myself.

The characteristics of these microbes suggest that life is not only durable, it's incredibly durable. The assumption that life arose on Earth, which is practically an obsession with some biologists, is most likely a deeply flawed one. We can see from the temperatures and pressures that bacteria survive at that many different planets other than Earth, and sometimes quite unlike it, harbor the conditions in which life could arise. Life may not be special at all; life is, more probably, a default condition, something that arises almost anywhere it can. We can assume, instead of presuming life's rarity, that life is everywhere, that it is common, and that it spreads in the same way that... well, that bacteria do.

As I've pointed out before, and as Simon Conway Morris indicates in his fine book Life's Solutions, the DNA molecule is an incredibly sophisticated piece of machinery that, to all appearances, has survived millions and probably even billions of years of evolutionary pressure to arrive in the condition that it operates in in ordinary life forms. Because it has been on the planet since the inception of life as we know it — this is nearly certain — we have to stretch the imagination past the breaking point in order to  hypothesize circumstances in which a long enough timeline existed on earth for this molecule to reach its current fine-tuned state of evolutionary sophistication. My own gut feeling, on the whole, is that life arose on another planet, and another solar system, perhaps billions upon billions of years ago, and that it may have evolved many, many times over the course of the evolution of the universe.

Because carbon has unique properties, the argument most biochemists would make is that all life forms will be carbon-based, and that almost all of them will share molecular structures quite similar to the one we see in DNA. Biochemistry, you see, is subject to tight constraints given the laws of physics and chemistry; only so many things can happen, not everything. Once you stray from the tried and true, known proven principles of known biochemistry, you have to jump through incredible hoops in order to create a condition where life employs different molecules in order to work. As Morris points out in his book, the organic chemistry of life in Betelgeuse is going to look like biochemistry on earth.

 Not only that, most of the life forms will look like the ones we have here, especially on planets similar to Earth in terms of temperature and chemical structure. What we see around us is what works; leaves look like leaves because that's what works. Fish look like fish because that's what works. Tens of thousands of Hollywood alien movies notwithstanding, alien life is going to look pretty much like life looks here. That's because evolution continually produces the same solutions to problems within the same narrow range of chemistry and physics. If life evolves again somewhere else, its chemical structure will probably look like ours; and the physical organisms it produces will probably look like us as well.

Above all, what we need to do is cultivate a respect for the durability of these organisms around us, which we seem more interested, generally speaking, in exterminating than finding ways to live with. Our habit of attempting to exterminate bacteria instead of understanding them has led to a deepening set of problems that are going to be difficult to untangle; and we will address that in future posts.

Wednesday, November 13, 2013

Tuesday, November 12, 2013

Thermal ranges and microbiota

Temperature has been much in the news over the past few years. It's becoming apparent that no matter how much clamor the deeply misinformed far-right climate change deniers raise about it in the United States, the story is here to stay.  

We live within an extraordinarily tiny range of temperatures; a slice, so to speak, from the spectrum, as though we were a pair of eyes only able to see orange. Living organisms around us, in the meantime, have found ways to colonize a much wider (although still relatively tiny) range of temperatures; microbes (and, let's be fair, some larger organisms) are able to fully function from temperatures near freezing all the way up—in the case of microbes—to temperatures in excess of the boiling point of water. These creatures are called thermophilic organisms; and their presence in underground high-temperature waters, such as those found deep in South African diamond mines and at the mouths of undersea thermal vents, suggests that thermophilic microbe may well have been among the first life that evolved on earth, perhaps even the very first life.

Our presumptions about the temperature ranges and conditions life can function in have been progressively challenged over the past fifty years; microbes, it seems, can probably even survive the condition of interstellar space without losing the ability the thrive and reproduce if they make it to a new solar system. While the idea of intergalactic travel seems, today, impossibly remote, it seems to be reasonably certain that among the trillions of galaxies, ours cannot be the only one that supports life.

Life on the smallest scales displays a resiliency absent in larger forms. The conditions it needs to support it are, for one, far more focused. Nutrients can be derived from far more basic building blocks—even molecular ones— with far less obstacles to finding and assimilating them. The difficulty of procuring food, it might be said, is roughly inverse in proportion to size. Small creatures need little food; large ones need lots of it. Microbes, in this sense, have the decided edge in the competition for energy resources. They can live in marginal circumstances, subsisting on marginal resources; larger creatures need far more tailored environments, built on far more complex food pyramids. So microbes have the advantage not only in terms of temperature, but also scale.

We humans see ourselves as flexible in terms of temperature and scale; imagine ourselves as supremely adaptable to a wide range of environments. Yet microbes outperform us handily in this area, and they do so without any of the specialized equipment we require when operating outside our comfort zone. Speaking as regards to suitable habitat, we're actually confined to an incredibly narrow range of circumstances; even a tiny step outside them causes us to resort to protective clothing and vehicles. 

We think we rule the earth; but in reality the bacteria do. They live and reproduce in massive numbers in places we will never go; places deep in the earth, where life has found what are, to us, completely alien paths to survival. They share the same DNA, but their destinies diverged from ours billions of years ago.

Even then, some of them have developed novel approaches to DNA and reproduction itself; which shows you just how incredibly creative archaic microbes can be.

Sunday, November 10, 2013

Soil denial

Cultivated boxwoods at Villa Lante, near Viterbo, Italy

Just after I wrote the recent posts on soils, the following article about soil degradation was posted on science news. I think it makes all the points I've been trying to make about soil quite effectively. The most important point, perhaps, is the widespread ignorance regarding this subject. Human beings are positively cavalier about their treatment of soil; and the soils we use for agriculture are only a fraction of the problem. All of the soils in suburban environments are being subjected to the same—or worse—indignities that agricultural soils are, and there are few to no controls being exercised.

No one educates children or the public on these matters, so we live in a culture of soil ignorance—in which no one really knows what soils do or why we need to preserve them—and soil denial, in which people think you can do anything you want to soils without creating long-term problems. Imagine a world, two hundred years from now, where trees won't grow properly anywhere in settled areas; where flowering plants struggle to survive and the green landscape we enjoy today is a thing of the past.

We can manage fertilizers; but bacteria are a far subtler proposition. Bacteria are best left to manage themselves; we need to become aware of them and help preserve and create environments that foster their growth and well being, not exterminate them wholesale.

Friday, November 8, 2013


The effects of micro-chemistry on our day to day lives is profound.

Scientists have just begun to debate the effects of endocrine disruptors in earnest; and there's plenty of cause for alarm. We're flooding the environment with chemicals of this kind; and one thing we can be sure of is that we share the biochemistry that triggers the problems across a tremendous range of species and creatures. That is to say, if an endocrine disruptor affects us, it almost certainly affects other animals... and may well also affect microbes.

BPA and other xenoestrogens wreak havoc on ecosystems; but the subtlest effects may well be at the microscopic level where—let's face it— the chemical interactions all take place. "Trace" amounts of an estrogen mimic may not seem to have much effect on a human being, but what they may do to much smaller organisms is not only impossible to see, it's very difficult to evaluate. The incentives to study impact on microbiological communities is low; researchers find it difficult to attract funding to study things no one can see; and the public certainly isn't interested. Even worse, the systems being affected are extremely complex, and it's difficult to know just where to begin. So there's been a dearth of insights into the effects of endocrine disruptors; and at the same time, industries dedicated to the manufacture and sale of the chemistry are fighting to keep their products on the market.

What's sobering is to consider that we live in a veritable sea of these chemicals. The tissue of every person you know is saturated with foreign substances, many potentially toxic; and our children are growing up in a pool of this stuff. Most of it is entirely unregulated; industry seems to have the ability to put anything it wants to out in the market without regard for long-term consequences.

It's clear that worldwide governments ought to exercise much tighter controls on the introduction of novel and unknown chemistry into the manufacturing environment and the food chain.

 This is an essential principle to remember. Almost anything that ends up being produced for the manufacturing environment ultimately ends up somewhere in the food chain. If we aren't eating it; smaller organisms are eating it; and everywhere, when it comes to chemistry, it's affecting the microbes around us. Manufacturing with the use of  sophisticated chemistry is creating trillions of tiny little Frankensteins around us, unseen parts of chemical experimentation. With the literally trillions of experiments of this kind of better taking place with the introduction of foreign chemistry into ecosystems, it's only a matter of time before one of the Frankensteins turns out to be a true monster, as opposed to a caricature of one.

 It may seem like paranoia to filter your water and eat organic food; but, especially for families with younger children, this may be the first and potentially only line of defense against exposure to disruptive chemistry that will affect childhood development in negative ways.

Wednesday, November 6, 2013

Bat holocaust

Bats are dying.

We used to have a large population of bats in the Northeast; but they're all dying off.  In earlier years, we would sit on my deck and watch dozens of bats come out at dusk to catch insects over the Sparkill pond; now, if we see one or two bats, it's a big deal.

What's killing them is a fungus that causes their noses to turn white. It may look cute, when you see it in the above photograph; but it spells nearly certain death for the bats.

The fungus causing this is unpleasantly resilient; and the story is, unfortunately, a perfect subject for this blog, since it involves a hitherto unknown microorganism which emerged from nowhere to destroy an entire population of creatures which are, in their own small right, essential for the ecosystem we inhabit.

It would be one thing if something of this kind took place once in a while; but it is happening everywhere, all the time. This snapshot is a microcosm of the phenomenon taking place all over the world, as organisms are introduced to microbiota they never involved with and were rarely, if ever, exposed to. The blending of invasive species on the macrobiotic scale is what concerns us; yet it is the microbiological blending of species that is wreaking havoc in the natural world.

Another example of this is that the moose population in Northern America is dying off. Human beings love to refer to macro events as causing such problems; but it's likely we are going to trace it to a microbe of some kind or another. Perhaps more alarmingly, outbreaks of novel  and extremely deadly diseases like MERS-CoV— which, in a topical consistency, often turn out to have their origins in bat populations — are also turning up.

Taken individually, the cases seem unique, and we don't think much about them; but taken together, the indications are that we are seeing massive migrations of microbes out of old areas and into new ones. We only notice the immediate effects, which are unique; microbes and viruses that cause instantly visible results of one kind or another are going to be the rarity. What is taking place over the long-term is much more disturbing, because the subtle changes being worked on the ecosystems around us will be long-lasting, and, from the point of view of human lifespans, for all intents and purposes, permanent. Eventually, one of these changes will result in a major problem for human population somewhere; and by the time that's recognized, it will be too late to do anything about it.

 I'm sure readers are wondering what, if anything, can be done about this. The difficulty, perhaps, is that little can be done. We can, however, reduce the overall impact we are having a microbe populations by trying to limit the amount of alien chemistry we dump into the environment. Healthy local microbial populations are generally better able to resist the invasion of foreign ones. This principle is consistent across the spectrum of size and biology. It is, almost certainly, the overall weakening of local microbe populations that is rendering them so vulnerable to the invasion of new ones.

Monday, November 4, 2013

What soils used to be like

Open air market, Campo dei Fiore, Rome

Ancient soils used to be much richer... and better... than they are today.

It's not just because soils were deeper and thicker... which was most certainly the case. It had a lot to do with the microbe populations. When we examine the scant remnants of our soil heritage, we discover that they had a diversity we can only dream of in most places today.

I make this point because we're generally unaware of what we're losing. The damage we're doing to the microbe infrastructure of the planet is appalling, and no one ever talks about it. What we're headed for, however, is a steady degradation of quality in the critical underpinnings of the soils we depend on for agriculture.

Science... and governments... ought to be devoting major resources to studying this problem, but very little is being done. It comes down, once again, to the problem that people won't spend time or money on trying to understand the unseen aspects of our environment—even though they turn out to be some of the most important parts of what is taking place around us. A collapse of our microbial infrastructure—both that of the soils and that of the oceans, where plankton are the ground floor of the entire food chain—would spell absolute disaster. We don't know enough about it to know how to fix it if it breaks; and evidence suggests that collapses of this kind may have taken place for natural reasons in the past, with what amounted to catastrophic results for the macrobiotic species.

A long term study needs to be undertaken to analyze the wild relatives of our most important crops and the symbiotic bacteria and fungi they grow in conjunction with. It may well be that we can vitally enhance crop health, productivity and viability by better understanding the microbial relationships that support them.

Soil conservation is no casual thing. Yes, it's true we recognize the need to preserve soils now—and it's come to us very late in the game. Even in the US, where we have deep insight into this question (prompted, in part, by the self-inflicted disaster of the dust bowl) we have a spotty record right up to the present moment. Farmers may have learned to preserve soils, but real estate developers certainly haven't; and countless thousands, probably millions, of acres of some of the best farmlands in the United States have, over the last five decades, been completely destroyed in order to make room for shopping malls and suburban developments.

It takes thousands of years to build a good soil column. It takes a few days for a bulldozer to destroy it. The action is criminal; yet we call it progress. And in foreign countries the pressures of development are ruining soils much, much faster than they are in the United States.

Saturday, November 2, 2013

Oil and microbes

I thought it might be wise to explain to readers in some more detail the difference between the Exxon Valdez oil spill and the BP Deepwater Horizon blowout.  The subject is interesting mostly because invisible microbes played a huge and under appreciated role in the BP spill; But there are a few political lessons to be learned along the way.

The above pictures are pictures from the Exxon Valdez spill.

The reason you didn't see pictures like the above ones when the Deepwater Horizon well blew out is because there weren't any. Very little, if any, of the oil actually reached the shore in any quantity; and relatively few marine creatures were killed.  Although a great deal of hyperbole was used to describe the disastrous effects to marine life, media struggled to find any actual examples of dead animals. 

To contrast, estimates are that as many as 250,000 seabirds alone were killed by the Exxon Valdez spill.

 The Exxon Valdez spill took place near the shore, in an area densely populated by animal life. It is, in addition, an environment that is cold,  and oil congeals, with relatively few microbes that can eat it. Metabolisms consequently run much slower; and because of the nature of the area, it has not evolved a microbial infrastructure designed for the consumption of oil. The results were not only disastrous but long-lasting.

Microbes in the much warmer waters of the Gulf of Mexico have been evolving for tens of millions of years in concert with the natural oil seeps in the floor of the Gulf,  which deposit as much as 1 million barrels of oil per year into its marine waters. Tens of millions of years is an awful long time for bacteria; it involves trillions upon trillions of generations. Oil, dispersed in warmer marine waters, is an excellent energy source if you learn how to use it; and if there is anything we know, it's that bacteria will find a way to exploit just about any energy resource they come across. Consequently, the waters of the Gulf are rich in bacteria that can feed off dispersed oil. 

A small cadre of marine biologists is aware of this fact; but the vast majority of people aren't. Had the oil in the Gulf been left to its own, some would've washed up on shore — and, certainly, there would have been some problems. The vast majority of it, however, never showed up anywhere; efforts to collect it were in vain, and only a tiny amount of it was burned off. 

Probably more than 95% of the oil was dispersed into the water column in extremely dilute form, where bacteria consumed it. These bacteria rendered it essentially harmless to the environment. Less than a year later, marine biologists and environmentalists alike were scratching their heads trying to figure out where all the oil went. It wasn't long before people realized that bacteria had probably eaten it. Dire predictions to damage to the fisheries turned out to be wrong; in fact, fisheries did much better the year after the spill, because fishermen stopped fishing for a significant period of time while the well was blowing out. Ironically, the resultant drop in pressure on fish populations allowed fish stocks to increase, not decrease. (Remember, it's perfectly okay for fishermen to kill all the fish they want; but not oil companies.)

Human beings, of course, always follow the ancient adage: when in trouble, fear, or doubt, run in circles, scream and shout. So during the spill, the media raised a daily hue and cry about how incredibly disastrous and awful it was; government agencies, in conjunction with BP and other third-party contractors, raced around spraying extremely toxic chemical dispersants all over the place, trying to break up the oil. The dispersants, it turns out, were actually far more toxic than the oil itself, and it seems that they did a lot more damage than the oil did, since the oil was something that occurs naturally in the environment in the first place, and the dispersant is not. There aren't any bacteria that eat dispersants.

 The reaction to the spill, in other words, was pathologically stupid. It did, however, generate an enormous amount of sensationalism and gave people the appearance that something meaningful was being done, when in fact nothing of the kind was taking place at all. The whole cleanup operation was very much like the security lines we stand on in airports today, where TSA employees triumphantly confiscate tubes of toothpaste to prove to us that we are being kept safe from terrorists.

Failure to properly understand environmental issues, and overreaction to such problems, is a common issue in America. This is because the media colors the picture so intensely. The public values the opinion of the news media more than the opinion of scientists by a very wide margin; so when scientists try to direct public response to disasters, they are promptly overwhelmed. Politicians, who feed on the news media with a great deal more zeal than any bacteria feed on oil in the Gulf of Mexico, jumped on the situation to exploit it to the maximum extent possible. The response did more damage than the spill itself; yet, two years later, we continue to live in a world where the mythology of the oil spill dominates the picture. It has morphed into a giant feeding trough for the state and federal government to dip their probosces into.  (See also here and here.) The evidence of actual damage is minimal; the demands for reparation are in the tens of billions of dollars. Businesses 50 or more miles from the coast that incurred no conceivable damage from the spill are collecting money from BP.  BP's lawyers are fighting this nonsense; but the shameless shakedown continues. 

I cannot stress enough, conducting matters in this way will dangerously devalue and stain the credibility of future, more legitimate environmental damages claims. Excessive corporate punishment is just as bad as insufficient corporate punishment; perhaps even worse, because it gives corporations a finger to point.

 In the meantime, no one says a single word about all of the nitrogen pollution flowing down the Mississippi River from agribusinesses, who are, let us remember, heavily subsidized by the federal government — 

unlike BP.

 What's really interesting to me is that bacteria have evolved to be so efficient at eating oil. They took what may have been as much as 5 million barrels of oil and sucked most of it up without leaving a drop. This is a truly amazing feat; and it makes us wonder exactly how many other things bacteria are consuming that we don't really think about or even know about. 

The bacterial process drives a great deal more of the recycling on the planet than any other known process; yet we've done little research into understanding how bacteria achieve these feats, or ways in which they might be used to help us in sustainable and natural ways.

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.