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.