Me, Microbes, and I

 

It has been said that “No man is an island.” While you may quibble that it should be “No one is an island,” we know what it means: We human beings depend on one another. We depend on each other, and we also depend on ecosystems to provide us with water and clean air—among other things. Yet there are other important ecosystems within us and on us.

You are no island: no, you are more of a continent complete with colonists, invaders, battles for resources, and turf wars. And there are a lot more of “them” than there are of “you,” about one hundred trillion of them. As one article in the Economist put the idea, “…humans are not single organisms, but superorganisms made up of lots of smaller organisms working together.”

Microbes can be used in soil cleanup
Microbes (Photo credit: Wikipedia)

We have known for a long time that our guts harbor “good” bacteria (yogurt companies advertise about probiotics) and health officials caution against unnecessarily taking antibiotics which could harm good bacteria. These bacteria, it turns out, have evolved along with us (Homo sapiens) and are part of our being. And, in turn, our bacteria evolve within us, having numerous generations during a person’s lifespan, and adapting to changing conditions.

What is now coming out of research is how essential those bacteria are to our physical and mental health. For instance, on our skin, “Staphylococcus epidermidis fends off skin infection and enhances immunity,” the Economist article says. Maybe that antibacterial soap isn’t your best choice for healthy skin.

Researchers call the symbiotic relationship that microbes have with particular animals or plants a microbiome. The sheer magnitude and diversity of your microbiome is staggering. “The typical human is home to a vast array of microbes,” evolutionary biologist Olivia Judson wrote in the New York Times. “If you were to count them, you’d find that microbial cells outnumber your own by a factor of 10. On a cell-by-cell basis, then, you are only 10 percent human. For the rest, you are microbial.” A human being has 23,000 different genes. Our microbiome has almost 150 times that number, about three million genes.

In their proper places, microbiomes are truly symbiotic, a collaboration of human and micro-critter. We provide hospitable living conditions, and the microbes help break down foods for digestion, synthesize vitamins, and help our immune system. Inoculation with microbiota begins when we travel through the birth canal. Among other things, our new gut bacteria will “affect the wiring of nerves in the stress system, influencing how the body reacts to stress for the rest of its life,” writes Tom Siegfried in Science News. Our mothers’ influence, then, goes even further than we knew.

When they are not in their proper place or when unwanted bacteria come in, the results can be distressing, painful, or even deadly for the host. Researchers have linked off-kilter microbiomes to obesity, diabetes, heart disease, autism, and some autoimmune diseases.

Rejiggering some microbiomes apparently cures some diseases. “The past few years have shown that having good relations with the 100 trillion bacteria which inhabit the gut is essential to human health,” reports an Economist article. “If relations break down, hostile bacteria may invade and previously friendly ones may turn hostile. When things do go wrong, though, doses of corrective bacteria can make a difference.”

The method of delivery for healthy bacteria to the intestine is rather yucky. Yes, eating yogurt with probiotics can help people with irritable bowel syndrome, but pretty much everything else requires a fecal transplant—a “trans-poo-sion,” if you will. Gastroenterologist Thomas Borody says, “By implanting another person’s stool, that other person may contain bacteria which manufacture antibiotics. And this is the key: bacteria make molecules that kill other bacteria. In fact, most antibiotics come from bacteria.” Fecal transplants can change the gut’s microbiome, and this changes our health.

Scientists have just begun to understand our microbiome’s interaction with us. For one thing, there is much to learn simply due to the number of these critters. “The adult human intestine contains trillions of bacteria, representing hundreds of species and thousands of subspecies,” one scientific abstract says. We are also at the beginning of this scientific process; a time that is analogous to when people knew willow tree bark relieved headaches but had not yet identified acetylsalicylic acid (the active ingredient in aspirin) as the reason.

Our microbiomes and earth’s biomes (plants and animals found in particular habitats) have evolved and continue to evolve as conditions change. Understanding their complexities will help improve our lives. And, as always, more research is needed.

Updated: Now with 100% more Steve Martin.

You know, medicine is not an exact science, but we are learning all the time. Why, just fifty years ago, they thought a disease like your daughter’s was caused by demonic possession or witchcraft. But nowadays we know that Isabelle is suffering from an imbalance of bodily humors, perhaps caused by a toad or a small dwarf living in her stomach.

 

 

References/Further Reading

Dubner, S. (2011, March 4). Freakonomics. Retrieved June 6, 2013, from The Power of Poop: http://www.freakonomics.com/2011/03/04/freakonomics-radio-the-power-of-poop/

Flam, F. (2012, June 9). Philly.com. Retrieved June 7, 2013, from We and Our Microbes are in This Together: http://www.philly.com/philly/blogs/evolution/We-and-Our-Microbes-are-In-This-Together.html

Jane A. Foster, K.-A. M. (2013, May). Gut–brain axis: how the microbiome influences anxiety and depression . Retrieved June 4, 2013, from ScienceDirect: http://www.sciencedirect.com/science/article/pii/S0166223613000088

Gavura, Scott. I’ve been prescribed an antibiotic. Should I take a probiotic? http://www.sciencebasedmedicine.org/ive-been-prescribed-an-antibiotic-should-i-take-a-probiotic/

Judson, O. (2009, July 21). Microbes ‘R’ Us. Retrieved June 7, 2013, from New York Times: http://opinionator.blogs.nytimes.com/2009/07/21/microbes-r-us/

Perelman School of Medicine at the University of Pennsylvania. (2012, March 15). Genetic Variation in Human Gut Viruses Could be Raw Material for Inner Evolution, Perelman School of Medicine Study Finds. Retrieved June 13, 2013, from Penn Medicine: http://www.uphs.upenn.edu/news/News_Releases/2012/03/bushman/

Perry, W. (2012, July 6). Protective Skin Microbes Help Fight Off Disease,. Retrieved June 5, 2013, from LiveScience: http://www.livescience.com/21871-skin-microbes-immune-response.html

PsMag. Our Destiny Lies Not in Our Stars, But in Our Bacteria. http://www.psmag.com/environment/our-destiny-lies-not-in-our-stars-but-in-our-bacteria-62968

Siegfried, T. (2013, May 28). Microbes at home in your gut may also be influencing your brain. Retrieved June 4, 2013, from Science News: http://www.sciencenews.org/view/generic/id/350674/description/Microbes_at_home_in_your_gut_may_also_be_influencing_your_brain

The Economist. (2013, February 21). Evolution: History Repeating. Retrieved June 7, 2013, from The Economist: http://www.economist.com/blogs/babbage/2013/02/evolution

The Economist. (2013, April 11). Microbes and men: Consumer microbiomics . Retrieved June 6, 2013, from The Economist: http://www.economist.com/blogs/babbage/2013/04/microbes-and-men

The Economist. (2012, August 18). The human microbiome: Me, myself, us. Retrieved June 4, 2013, from The Economist: http://www.economist.com/node/21560523

The Economist. (2012, November 3). Treating disease with microbes: Bugs in the system. Retrieved June 4, 2013, from The Economist: http://www.economist.com/news/science-and-technology/21565586-bacterial-medicine-starting-emerge-bugs-system

Virginia Tech. (2013, February 8). Villain stomach bug may have a sweet side. Retrieved June 6, 2013, from EurekaAlert!: http://www.eurekalert.org/pub_releases/2013-02/vt-vsb020813.php

Xu J, M. M. (2007, July 5). Evolution of symbiotic bacteria in the distal human intestine. Retrieved June 6, 2013, from PubMed.gov: http://www.ncbi.nlm.nih.gov/pubmed/17579514

Zimmer, C. (2006, January 3). From Bacteria to Us: What Went Right When Humans Started to Evolve? Retrieved June 4, 2013, from New York Times: http://www.nytimes.com/2006/01/03/science/03zimm.html?_r=0

Zimmer, C. (2013, May 22). Meet Your New Symbionts: Trillions of Viruses . Retrieved June 4, 2013, from National Geographic: http://phenomena.nationalgeographic.com/2013/05/20/meet-your-new-symbionts-several-trillion-viruses/

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Is Optimism Rational?

Matt Ridley’s book, The Rational Optimist: How Prosperity Evolves, continues to be my favorite book. It is not simply my favorite non-fiction book; it is my favorite book: challenging, witty, and chock-a-block full of facts. If you are pessimistic about our world’s future (as I was), you owe it to yourself (and your children) to read Ridley’s book–this is doubly true if you are a teacher. I like it so much I own it as an audiobook, an e-book, and a hardback book, and I refer to them quite often. On his website Ridley has this about the book: “In this original, optimistic book, Matt Ridley puts forward his surprisingly simple answer to how humans progress, arguing that we progress when we trade and we only really trade productively when we trust each other. The Rational Optimist will do for economics what Genome did for genomics and will show that the answer to our problems, imagined or real, is to keep on doing what we’ve been doing for 10,000 years — to keep on changing.”

In this video Ridley makes his case:

PS, I should mention also Frank Robinson’s website, The Rational Optimist. His book is The Case for Rational Optimism, which, he writes, “examines the facts, and finds that in reality, humans are fundamentally cooperative, the world is becoming increasingly peaceful, and the causes for it are growing ever stronger.”

Beer and Civilization—Who Knew?

This will be in tomorrow’s today’s Record-Bee in the Green Chain column. It is also cross-posted on my Batch-22 blog.

 

I hope you had a happy Earth Day. It happened, thanks to beer.

Fermentation First

Evidence mounts almost daily that beer started humans on the path to civilization even before the invention of agriculture some twelve thousand years ago. A recent paper in Evolutionary Anthropology says that, based on tests of artifacts, cereal grains were collected (sometimes from areas as far as sixty miles away) “for the purposes of brewing beer” to be used in feasts, which then “led to domestication…” That is, brewing led to the collecting of seeds for cultivation. And, feasts in prehistoric times were given for much the same reasons as they are today: to mark religious events or to impress others and also to make social, political, and commercial connections.

Edited copy of Image:The Brewer designed and e...
Edited copy of Image:The Brewer designed and engraved in the Sixteenth. Century by J Amman.png (Photo credit: Wikipedia)

In “Uncorking the Past: The Quest for Wine, Beer, and Other Alcoholic Beverages,” Dr. Pat McGovern says, “Wherever we look…we see that the principal way to communicate with the gods or the ancestors involves an alcoholic beverage…” As examples, he mentions “the wine of the Eucharist” and “the beer presented to the Sumerian goddess Ninkasi…”

Fermenting Agriculture

Eventually, people decided planting and tending was easier than going long distances to get the needed grain. Agriculture raised the density of the desired plants in an area and the people as well. Farmers stayed in one place for a while and had an affinity for places that had settlements since they could sell or trade their surplus grain there. In the settlements, people specialized at particular jobs and purchased or traded for goods and services they wanted. (See: “How Ancient Trade Changed the World“)

Grain (and beer) had the advantage of being storable: it would last for relatively long periods, and as a result, could be transported. That meant farmers could bring their grain to market and make a profit, and others could profit from shipping it abroad. In many ways, globalization occurred during the Bronze Age and probably earlier in Neolithic times.

Bar Tabs, Invoices, And The Tax Man

Because people were now living in greater concentrations, the amount of stuff around became more than what one person might be able to remember—it had to be written down. Pictures of goods soon became stylized symbols, which could be made faster and got the point across. Sumerians (in what is present-day Iraq) started making notations for bookkeeping about 5,000 years ago. “The first examples of writing,” Heather Whipps says in an article on LiveScience.com, “were pictograms used by temple officials to keep track of the inflows and outflows of the city’s grain and animal stores which, in the bigger Sumerian urban centers such as Ur, were big enough to make counting by memory unreliable.”

Then, just as in today, taxes on alcohol provided revenue to the ruler, so reports had to be submitted. One of our oldest examples of writing is a receipt for beer. In 2050 BCE, a scribe named Ur-Amma accepted about four and a half quarts of the “best beer” from a brewer named Alulu.

The Rest, As They Say, Is History

The advent of farming was both helpful and harmful depending on where you looked. Farming massively disrupts the landscape (often through deforestation) to grow food or fiber. Yet, compared to a nomadic or hunter-gatherer lifestyle, farming used much less land, freeing the rest to revert to a more natural state. “The remarkable thing about farming, when it was invented 10,000 years ago,” says science writer Matt Ridley, “was how much smaller its footprint was.” According to Ridley, the first farmers needed about one percent as much land as the hunter-gatherers needed.

Civilization Is An Enormous Improvement On The Lack Thereof. – P. J. O’Rourke

So, to recap, civilization came about because of agriculture, and agriculture happened because humans chased a beer buzz. As poet John Ciardi said, “Fermentation and civilization are inseparable.”

Civilization, and its improving living standards, means we have time to do something besides just toiling to stay alive. Civilization, and its specialization of labor, allows us the time to set aside a day to remember the world on which we depend: Earth Day.

Cheers! Prost! Salud!

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Weekend Postcard: Economics at Work

“Give me that which I want, and you shall have this which you want…”

Adam Smith

This picture is of sheep grazing (and resting) at a local winery‘s vineyard, Vigilance Winery and Vineyard (which, by the way, has a great sunrise picture).

This shows economics at work. The rancher obviously thought it worthwhile to transport the sheep (someone let me know if these are actually goats. UPDATE: Those are definitely sheep. Goats, apparently, will eat anything that doesn’t move and a few things that do. We suspect that having the vines demolished is not in the owner’s financial interest.) to the vineyard to graze down the cover crop, and the vineyard owner thought it worth the compaction cost to save on fuel and labor by not having to mow.

Sheep in the vineyard of the Vigilance winery.
Sheep in the vineyard of the Vigilance winery.
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Managing That Wild Natural Look

English: This picture if of a Golden Trout fro...
A  golden trout from French Creek in the French Canyon. Located within the John Muir Wilderness in California. (Photo credit: Wikipedia)

In 1978, I was just beginning my career with the California Department of Forestry and Fire Protection (Cal Fire). I worked in the southern Sierra Nevada range as the Assistant Forest Manager at Mountain Home State Forest. The federally managed 1.2 million acre Sequoia National Forest surrounded the 4800-acre state forest. On most of the state forest’s eastern boundary Mountain Home abutted the newly designated Golden Trout Wilderness.

Our neighbor, the United States Forest Service, was struggling to transform the Golden Trout Wilderness Area from primitive to pristine.

The Wilderness Act of 1964 required that the GTWA would be “an area where the earth and its community of life are untrammelled by man.” Well, many thought that man had pretty well trammeled the area. Quite a few high country lakes and streams had been “coffee can stocked” with rainbow, brook, and brown trout. The native golden trout had crossed with many of the rainbow (golden trout is a sub-species of rainbow) to produce a hybrid trout that looked just like a golden until you drilled down to the chromosomal level.

The question was, then, how to make the wilderness into wilderness, to resemble a time before man changed it. Drumroll please…

The answer was to destroy the fish population, using the poisonous insecticide rotenone, to “save” it.

The strategy was and is to “chemically treat the headwaters of drainages with rotenone above fish barriers to remove non-native trout species that compete or hybridize with native trout,” a U.S. Fish and Wildlife Service brochure [PDF here] notes, “After that, native trout are reintroduced to the reclaimed habitats.” Many of the high country lakes were left sterile since the agency experts decided that was their natural state before European or Indian contact.

Some of the Forest Service’s people thought that was a crazy idea, saying, “If it looks like a golden trout, why not call it a golden trout?” After all, golden trout (Oncorhynchus mykiss aguabonita) is a sub-species of rainbow trout (O. mykiss).

But, why destroy a vibrant fish population? In her book, Rambunctious Garden, Emma Marris explains, “For many conservationists, restoration to a pre-human or a pre-European baseline is seen as healing a wounded or sick nature. For others, it is an ethical duty. We broke it; therefore we must fix it.” The pre-human or pre-European state thus becomes “the one correct state.”

The irony, of course, is that pristine areas are illusions; people have to work hard to make them to look how people think “pristine” ought to look. Peter Kareiva, the chief scientist of the Nature Conservancy, along with his two co-authors, argues that the great lengths we go to “removing unwanted species while supporting more desirable species,” such as drilling wells to provide wildlife with water and manipulating the land through “fire management that mixes control with prescribed burns,” we “create parks that are no less human constructions than Disneyland.”

So, oddly, the more natural we want a place to look, the more human management it needs.

 

Further Reading:

 

What happens when we can find traces of everything everywhere?

It is easy to get worked up about toxic substances (especially, it seems, synthetic ones) being in our bodies, yet as Brian Dunning at Skeptoid notes, it is natural to have toxic substances there. He points out that plutonium is “one of the most dangerous substances known.”  But because we live on a planet with plutonium that occurs naturally, “…every person and animal that ever lived has an average of about 20,000,000 plutonium atoms in their bone marrow, simply because we live on this planet.”

So, if you knew that a synthetic chemical from a product (or products) was in your body, is that something that your government or the company should have warned you about? Andrew Maynard (@2020science on Twitter) talks about “The ethics of being able to measure everything – an ethical perspective on the measurement conundrum.”

http://youtu.be/SfmX1hPUnyQ

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Taking the Romance out of Environmentalism

Cover of "The Skeptical Environmentalist:...
Cover via Amazon

My latest Green Chain column for the Record-Bee.

Just after 7 p.m. on Sept 5, 2001, Mark Lynas, a writer and a member of the Green Party in Britain stepped into the Borders Bookshop in Oxford and “pied” former Greenpeace member Bjorn Lomborg with a sponge cake topped with whipped cream.

Lomborg was at the bookstore to talk about his just completed book, The Skeptical Environmentalist. The general thrust of the book was that environmental problems are highly correlated with poverty, thus making people wealthier and healthier would mean fewer environmental problems. This finding did not sit well in the green community.

“Pies for lies,” said Lynas as Lomborg wiped whipped cream out of his eyes.

Last month, Mark Lynas, the righteous green, did something extraordinary. He apologized for being wrong about genetically modified (GM) crops.

He did not apologize half-heartedly as you or I did when our mothers made us say we were sorry to our sisters for putting their Barbie dolls in the toilet. No, he meant what he said and he said it quite publicly in a speech to the Oxford Farming Conference:

“I want to start with some apologies. For the record, here and upfront, I apologise for having spent several years ripping up GM crops. I am also sorry that I helped to start the anti-GM movement back in the mid 1990s, and that I thereby assisted in demonising an important technological option which can be used to benefit the environment.

“As an environmentalist, and someone who believes that everyone in this world has a right to a healthy and nutritious diet of their choosing, I could not have chosen a more counter-productive path. I now regret it completely.”

So, he and his cohort—and there is no use sugar-coating this—spread lies. “This was also explicitly an anti-science movement,” he said. “We employed a lot of imagery about scientists in their labs cackling demonically as they tinkered with the very building blocks of life. Hence the Frankenstein food tag…”

He admitted assuming using GM “would increase the use of chemicals.” What he found instead was that “pest-resistant cotton and maize needed less insecticide.”

He believed “[T]hat GM benefited only the big companies.” He discovered “billions of dollars of benefits were accruing to farmers” because of what they did not need to use.

He had heard GM seed contained “Terminator Technology” to keep farmers from saving seed for the next crop. He discovered that hybrid crops “did that long ago, and that Terminator never happened.”

He had assumed that poor farmers did not want GM. What he found were farmers breaking local laws to get GM seed “because farmers were so eager to use them.”

He had “assumed that GM was dangerous.” When he looked into it, “It turned out that it was safer and more precise than conventional breeding…”

The path Mark Lynas took to embrace GM (and nuclear power) is similar to the one Bjorn Lomborg took.

Lomborg, an associate professor of statistics at the University of Aarhus in Denmark, turned against the shibboleths of the green movement as the result of a project he began with his students to disprove Julian Simon. Simon, an economist, argued that the environment was on the whole getting better. Knowing that simply could not be true, Lomborg and his students gathered data. The more sources and statistics Lomborg and his students combed through, the more they found themselves agreeing with Simon’s heresy, and less with green dogma. The book, The Skeptical Environmentalist, was the result; it had 2,900 references to allow others to check the work.

These heretics, and others such as Patrick Moore and Stewart Brand, looked at their beliefs, weighed those against the facts and changed their minds. Such thinking marked the philosophical movement of the 18th century, which we now call the Enlightenment. It emphasized using reason to scrutinize previously accepted doctrines and traditions.

Others, the Romanticists, responded to the Enlightenment’s reason by emphasizing emotion over rational science and rejecting its search to understand the workings of nature. Romanticism placed the individual’s perceptions at the center of the universe and Nature was, according to one textbook, “a revelation of Truth, the ‘living garment of God’…” Little wonder that primitivism, worship of nature, and mysticism were hallmarks of Romanticism.

Who knows, with these defections we may be seeing a new Enlightenment.

 

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