"Weird" Science #4: Microbes and Soil

This post originally appeared on my personal blog. Ported to Forbidden Questions on 11/21/2011.

(If you've been following my "'Weird' Science" series, I hope you'll forgive me as I slip in at least one intervening post in the series before I get to the one I suggested would be next.)

As I began digging into Lynn Margulis' Kingdoms & Domains, I was struck by the diversity of microbial life she describes. And I was struck by the thought that microbes are not only invisible to the naked eye, but they are, as it were, largely invisible to our minds. We don't think about them.

Not only do we not think about bacteria and protozoa; we tend to ignore fungi, algae, worms and beetles, too.

As E. O. Wilson says in the Foreword to Margulis' book:

About 1.8 million species [of living organisms] . . . have been discovered and described [as of 2009]. that includes perhaps three-fourths of the extant hundred thousand or so vertebrates, and, at a guess, ninety percent of the quarter million species of flowering plants thought to exist. But the sixty thousand known fungi are fewer than five percent of the estimated total, and the fewer than twenty thousand named nematode worms, the most abundant animals on Earth, are probably an even smaller fraction of the whole. Moreover, all this ignorance shrinks in the dismaying presence of the "dark matter" of the eukaryotic universe--or if you prefer, the Subkingdoms (Domains) of Archaea and Eubacteria. The exploration of what could turn out to be tens of millions or even hundreds of millions of well-differentiated strains of these subvisible organisms has scarcely begun.

--Kingdoms & Domains, p. lxi

What Wilson says is one way to look at or think about the diversity of life of which we are unaware.

I would like to suggest a few other ways, too . . . for your thoughtful consideration.

1. Dr. Bonnie Bassler of Princeton University describes an amazing bacterial "social life." Yes, they actually communicate . . . in rather intricate ways. --That's the primary thrust of the following video. But she says something else, about a minute into the video, that ought to catch your attention, I think. Paraphrased: The human body has about a trillion cells in it. And those trillion cells host--either in you or on you--about 10 trillion bacteria. You have about 30,000 genes in you; the bacteria you host have about 100 times the amount of genetic material or information. "So," says Bassler, "when I look at you, I think of you as 1 or 10 percent human and either 90 or 99 percent bacterial."
   
   
    
2. Based on a study of the bacteria on 51 different people's hands, researchers found that the average person had more than 150 different species of bacteria living on his or her hands. But get this. The researchers summarize their findings in this way: "[W]e identified a total of 4,742 unique phylotypes [species of bacteria] across all of the hands examined. Although there was a core set of bacterial taxa commonly found on the palm surface, we observed pronounced intra- and interpersonal variation in bacterial community composition: hands from the same individual [i.e., the left and right hands--JAH] shared only 17% of their phylotypes, with different individuals sharing only 13%." [Emphasis added.]
    
3. "Good soil is absolutely teeming with life. . . . A mere teaspoon of good garden soil, as measured by microbial geneticists, contains a billion invisible bacteria, several yards of equally invisible fungal hyphae, several thousand protozoa, and a few dozen nematodes."
   -- Teaming with Microbes, p. 19.
    
4. "Remember that teaspoon of good garden soil? Perhaps 20,000 to 30,000 different species make up its billion bacteria--a healthy population in numbers and diversity."
   --Ibid., p. 24.
    
5. "[A]n acre of good garden soil teems with life, containing several pounds (about 1 kilogram) of small mammals; 133 pounds of protozoa; 900 pounds each of earthworms, arthropods, and algae; 2000 pounds of bacteria; and 2400 pounds of fungi."
   --Ibid., p. 28.
    
6. Allan Savory presents a fairly standard food-web energy pyramid in his Holistic Management book (mentioned in my Monday post, "Weird" Science #2: Soil, Part 1):
   
   
   
   
   I think this is pretty common knowledge: Animals are unable to convert solar energy into forms useful for metabolism. Therefore, in order to survive, they (we!) depend upon plants and algae to convert the energy from sunlight into organic matter--carbohydrates, fats, proteins and innumerable vitamins and phytonutrients--that we are then able to ingest and metabolize for our life needs.
   
   However, Savory pushes this energy pyramid idea forward several more steps . . . in ways I had never imagined . . . primarily due to my blindness to the world of microbes and soil:
   
   

   The energy pyramid also extends below ground where the energy flow greatly affects . . . a biologically active soil community that [also] requires solar energy to be conveyed underground mainly by plant roots or surface-feeding worms, termites, dung beetles, and others.

   --Holistic Management, pp. 151-152.

From here, things get really strange.

I first heard about what I am about to share in a series of lectures from Acres USA. But now I am reading all about these things, in detail, in Lowenfels and Lewis's truly wonderful Teaming with Microbes.

In the same way we humans have domesticated and now farm plants and animals for our benefit, so (say leading soils researchers) plants have established interdependent, symbiotic relationships with most of the protozoa, earthworms, arthropods, algae, bacteria, and fungi that surround their roots. The plants send food (about half of all the carbohydrates and other nutrients they produce) down to their roots . . . and then, through their roots, they exude these nutrients (in a liquid called exudate), into the soil. This exudate, in turn, feeds the bacteria and other organisms that live in the rhizosphere (the area of the roots).

Meanwhile--hang onto your hat!--the microbes in the soil protect the plants' roots. Literally. And, in many ways, they also feed the plant.

As Lowenfels and Lewis explain things: "In return for exudates, [mycorrhizal] fungi provide water, phosphorus, and other necessary plant nutrients" (p. 25). Similarly, some plants prefer nitrogen in the form of ammonium (NH₄) while others prefer it in the form of nitrate (NO₃). Well guess what? The types of nitrogenous compounds available to plants are largely controlled by the microbes in the soil: "In fungally dominated soils, much of the nitrogen remains in ammonium form." In bacterially dominated soils, certain bacteria will convert the ammonium into nitrate. . . .
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I'm going to quit here.

. . . Oh!

No I'm not.

I wanted to show you two photographs. So let me do that and then I'll quit.

These two photos are from Teaming with Microbes, pp. 12 and 13.

I said above, "[T]he microbes in the soil protect the plants' roots. Literally."

Lowenfels and Lewis discuss many ways they do this besides what I am about to show you. But these two photos did for me what the authors say they did for them. They woke them up--and they snapped me to attention--and they caused me to think: What is going on that I am unaware of down there under the soil?

The authors explain: "[O]ne autumn, . . . a gardening friend e-mailed two stunning electron microscope pictures. The first showed in exquisite detail a nematode trapped by a single looped fungal strand, or hypha. . . ."

Continuing with the story as the authors tell it:

Wow! This was quite a picture--a fungus taking out a nematode! We had never heard of, much less seen such a thing, and it started us wondering: how did the fungus kill its prey? What attracted the blind nematode to the rings of the fungus in the first place? How did the rings work?

The second image showed what appeared to be a similar nematode, only this one was unimpeded by fungal hyphae and had entered the tomato root. . . .

The authors ask about this photo: "Why wasn't this nematode attacked, and where were the fungal hyphae that killed off the first nematode?"

--Stay tuned for the answer in "'Weird' Science #5"!

"Weird" science #1: Louis Pasteur

This post originally appeared on my personal blog. Ported to Forbidden Questions on 11/21/2011.

This is one of those posts I have been tied up in knots over because I have simply not had enough time to study it out to the final degree I want to. But I think I have gone far enough to share it with you so, if you are intrigued, you can study it far enough to feel comfortable yourself either to affirm or deny its veracity.

If you think I may be following a primrose path to error, please feel free to correct me!

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I had always been led to believe that Louis Pasteur was a great person, worthy of great honors. After all, it is he who developed the germ theory that led to most of the tremendous advances in late 19th and early 20th century medicine and, of course, to the process that bears his name: pasteurization, "a process of gently heating foodstuffs like milks to kill these organisms without changing the flavor or nutritional value." I have even found him held out by many conservative Christians as a model of religious rectitude.

This is what I have been taught.

Except now I am finding that nearly everything I was taught about Pasteur's science and discoveries, not to mention the value of pasteurization, may be wrong.

More specifically, I'm learning, there is quite a number of historians who claim,

• Pasteur didn't "discover" what is credited to his name. All of those "discoveries" were known before he came along. --It appears the case for this is quite strong. (See Chapter 1 of The Dream and Lie of Louis Pasteur for one source.)
   
  • Question, however: Could it be said that Pasteur "discovered" the germ theory in the same way that it can be said legitimately that Columbus "discovered" America (even though we have definitive evidence Columbus was not the first European to make it to the Americas and back)? No, Columbus was not first in the sense of absolutely no one having done it before. But, yes, he was first in the sense that it was only after Columbus went and returned that "America" came to be generally recognized for what it was. I.e., he was first in somewhat the same sense that George Washington was "first in war, first in peace, and first in the hearts of his countrymen." . . .
    
    My point: Is it possible that, while, as R. B. Pearson notes, it was proposed by many people even centuries before Pasteur that diseases are transferred by microscopic "seminaria contagionum" (Geronimo Fracastorio (1483-1553)) or "animalcula" (described in 1683 by Antonius van Leeuwenhoek) or "germs" (proposed in 1762 by M. A. Plenciz), the world really needed a Pasteur to popularize the concept and make it stick?
     
• I lack the capacity to judge one way or another on this matter, but several credible sources suggest that bacteria are not so much the causes of disease as they are the consequences. Microorganisms are, as it were, the "cleanup crew." When a macroorganism is weak, the microorganisms will come in to put it out of its misery and/or digest (and, thus, remove) the diseased parts. They say that the germ theory of disease--the theory that germs cause disease--is ill-conceived.

It was/is this latter point, really, that has put much of my blog writing on hold over the last few weeks. I have had this post semi-written (up to the words "ill-conceived") for the last month. But/and I have not been able to get far enough into the underlying literature to feel satisfied about the truth or error of the claim.

So let me share some of the sources I have perused:

The Dream and Lie of Louis Pasteur. --That, actually, was my first introduction to this set of weird ideas. It focuses primarily upon Bechamp and Pasteur. I received the link from a friend who has bought into the theory that "the [physical] terrain [of the host body] is everything; the germ is nothing."

The Lost History of Medicine. A development of the terrain/germ dichotomy with lots of links.

. . . I would like to develop this more, but I think the development will come in subsequent posts. (Be glad! 1--I'm getting this stuff published. And, 2--maybe my posts will be shorter than they used to be when I would get into this kind of stuff!)

For those who think I have jumped off the deep end, that I would even "listen" to this kind of stuff, let me acknowledge that I am finding myself extremely skeptical about the claims. But I am intrigued that, even if (as I expect), the authors of these articles--and the books and articles that they reference--are mistaken in some fundamental ways, they are probably more right than conventional medical advocates are willing to acknowledge. Put another way: Conventional medicine has some insights (but claims far more knowledge and competency than it has a right to claim), and these possible "quacks" are onto some keen insights that most of us ought to know about and utilize to our benefit. At the same time, I expect, they also claim far too much for their theories than they have a right to claim. --Just for example, "The terrain is everything," I imagine, is way overblown. So, too, I'm sure, is "the germ is nothing." But it would be extremely valuable to notice the terrain, and pay attention to the terrain, and to work on the terrain--something that conventional medicine, by and large, refuses to do; and something that the U.S. government, through its subsidies, actively undermines (a subject we will return to in subsequent posts).

So. Onward!

I hope you'll join me as we see where this leads. . . .