Sunday, December 30, 2012

Of Mice and Oogonial Stem Cells

Note: This program first aired on Deecmber 29, 2012.

I was asked by a listener recently, if female chickens are born with all of the eggs they will lay over the course of their lives, like human females are. This made me wonder if all females have this characteristic, if that is a distinguishing feature of being female—that the cells that become the gametes form in the embryo, and are not replenished as the individual matures. Conventional wisdom states that we females have a set amount of eggs (more than likely more than we will release in the reproductively active period of our lives), we do not make more as we go along. This is in contrast to males, who are able to continually replenish their supply of gametes.

We need to pause for a moment and return to high school biology, and revisit the concepts of meiosis and mitosis. Our cells have two sets of DNA in them, one from our mother and one from our father. That DNA is in the form of chromosomes. Mitosis is simple cell division, we get two cells when we started with one. The chromosomes in the cell all line up, split in half, and each half then replicates itself in the new cell; each new cell ends up with two sets of chromosomes, just like the parent cell had. Meiosis is cell division that results in the formation of gametes. What makes gametes special is that they have only one set of DNA in them, a mash up of DNA from the mother and the father. In meiosis, the chromosome pairs line up, swap DNA and then get separated from each other into two separate cells. Then the chromosomes themselves split in half, and the halves end up in two more cells, yielding a total of four cells from the original one, each with a single set of genetic information. That is what makes gametes gametes, they have only one set of DNA and they need to join with another gamete cell to get a full set of genetic information, enough to make a new individual. The traditional thinking has been that , at least in mammals, meiosis occurs in the ovaries of the embryo. As a female’s reproductive organs are forming, meiosis is going on, and all the eggs the female is going to have are formed then.

Before we get to the chicken issue, I have to break it to you that the conventional wisdom here has been shown to be wrong. As early as 2004, researchers discovered that in mice, the females seemed to be able to maintain a supply of healthy living eggs, even when fed toxins that would kill their follicles. This meant that the mice could generate new eggs, a discovery that flies in the face of the conventional understanding that mammals are born with the only eggs they will ever have. Since then researchers have identified the stem cells in human ovaries, called oogonial stem cells, that do the same thing for us. These oogonial stem cells are able to undergo meiosis at any point and produce new oocytes or eggs. What isn’t clear is if these oogonial stem cells are just a back up system, or if they share responsibility for egg production with the original meiotic cells in the ovary.

So, on to chickens. It turns out this is a very difficult question to answer definitively. Most of the literature refers to the “all the eggs you’ll ever make” phenomena as occurring in either mammals, or “higher animals ” (which by the way are apparently all vertebrates except fish). There is, thus far, no evidence of oogonial stem cells in chickens, but that doesn’t mean they aren’t there, it just means no one has looked, which is a different thing altogether. Likewise, this conventional wisdom principle has likely been laid like a blanket on top of our knowledge of all “higher animals”, meaning, it is unlikely that scientists have studied the embryos of every species close enough to declare that all higher animal females are always born with all their eggs. To be fair, closely related things usually behave in closely related ways, so this blanket technique may not be as imprecise as I am making it sound. We do know that certain worms continually make new oocytes, so it is not unheard of in that natural world, but chickens are closer to the higher animals than to round worms.

The final word? I suspect that chickens, like humans, make most of their eggs during the development of the embryo, and may, like humans, potentially retain the ability to generate new eggs as needed. This question illustrates nicely, the limits of our knowledge, and way we construct what we know, or think we know about the natural world. Thanks Greg, and keep your questions coming.


From Science Daily, a digest of the original study from Massachusetts General Hospital and the University of Edinburgh, demonstrating that female mice can grow new eggs:

National Geographic’s take on the same study:

Need a review of mitosis and meiosis? Check out this nice slide show from the good folks at PBS:

A bit here on the traditional take on female oocyte development:

Whoa. Here’s a scientific article about what can regulate meiosis in chickens!!

The truth? Its complicated…

Winter Solstice

Note: This program first aired on December 22, 2012.

6:12  am, Friday December 21, 2012. That’s the local time of the occurrence of the winter solstice. Yes, we tend to think of the solstice as a day, but astronomically, it is a moment in time. At that moment, the planes of the earth’s orbit and axis are perpendicular to one another, with one pole pointed towards the sun and one pointed away from the sun as much as possible. On the winter solstice, here in the northern hemisphere, this day will have the longest night of darkness and the shortest day of light of any in our 365 day trip around the sun, simply due to the angle of the axis of earth’s rotation. The sun’s arc in the sky will be at its lowest, and the location of its rise and set will be the furthest south along the horizon. Once we have passed this point in our orbit, the days gradually begin to lengthen (you and the plants won’t notice until at least February), the sun’s rise and set will edge further north along the horizon, and the sun will creep higher in the sky each day, all as we move along the ellipsis and the axis of earth’s rotation slowly moves parallel with the plane of the orbit (this occurs at the equinoxes).

We call the winter solstice the start of the winter season, but plants and animals (and us) have been responding to the drop in temperatures and the decreasing amounts of sunlight for some time now. Starting with the shortening days of late summer and fall, plants begin their period of outward dormancy. Leaves senesce (or die back or fall off) and the living tissue of the plant becomes limited to the roots and perhaps the above ground stalk. This limits the damage the cold and lack of water can do to the plant. Most seeds are fully developed by this time and should be being dispersed throughout the environment. Animals have three ways to deal with the rigors of winter; they can leave or migrate, hibernate or “tough it out”. Again, as early as late August, observant bird watchers can see birds flocking and preparing to leave our area for warmer, lower latitude environments.   When it gets truly cold as winter really begins, many animals enter a state of torpor, with marked drops in metabolic activity. This decreases their physiologic needs, allowing them to wait out the challenging conditions of winter. Hibernation is the most commonly used term for this, but the phenomenon actually encompasses a spectrum of dormant like behaviors. Of course many animals just tough it out, relying on their stores of body fat and whatever food they can find in the winter, to remain fully active..

Humans have been observing the cycles of the natural world for as long as we have been on this planet. And as the natural order draws in and appears to pause at the cold and dark time of the year, humans have created rituals of observance that inscribe these natural patterns on human culture as well. Black Friday not withstanding, many of our holiday traditions throughout the year are based on early pagan celebrations tied directly to the solar cycles of solstice and equinox. Traditions include contemplative rituals that reflect the quiet and dark of the year, and rituals that celebrate the return of the light. So as we enter these last few days of the frantic modern holiday season, take a moment to reflect on where this frenzy of visiting and parties, family time and gift giving came from—our ancestors, who had all the time in the world to watch the path of the sun and the arc of the moon, and who knew this earth with an intimacy we can’t even fathom today. It is my belief that this level of deep deep knowledge is healing, restorative, and as the events of the last week have shown us, we are deeply in need of this. This holiday and solstice season, honor those that have come before us and pause and pay attention, noticing where the sun comes up and where it drops below the horizon. Do this every day and by February, you will be ready as that extra light creeps into your life. Happy Solstice everyone.


Straight from the horse’s mouth:

Ask an Astronomer--

Cute teacher website from the state of Michigan:

There is so much great new age info out there on the pagan rituals as they relate to modern holidays and solar cycles. Google it and you’ll find lots of wild and wacky and very interesting reading.

This is the best show I’ve ever heard on the symbolism of solstice and our winter holidays: (spoiler alert: Santa is a Shaman…)

Islands in the Intertidal

Note: This program first aired December 15, 2012.

If the intertidal zone can be considered one of the most rigorous habitats on the planet, due to its consistent inconsistency, part time ocean, part time land, then tide pools are the oasises in the intertidal zone’s deserts.  A tide pools is like an island. An island is a little piece of land, terrestrial environment, surrounded by water, a physiologically hostile environment (at least to the land based organism on the island). A tide pool is the same thing in reverse—an oasis of habitat stranded in a larger hostile environment.

As a general concept, tide pools allow organisms to live further away from the contiguous coastal ocean than they “normally” would; further away meaning higher up the intertidal zone. The pools provide a little piece of sea like habitat in the middle of a dry beachfront or rocky shore. Of course, all tide pools are not created the same, and it would be a misconception to think that they perfectly recreate the conditions found subtidally. No, tide pools, though they do offer marine organisms a more desirable situation than simply being stranded on a rock in the sun at low tide, do present their own set of physiologic challenges and inconsistencies to the plants and animals that call them home.

The further away a tide pool is from the low tide line, the less like the ocean it tends to be. And the smaller or lower volume a tide pool is, the more easily its environmental parameters can stray from those found in the mother ocean as well. The shape of the tide pool matters too—a big wide but shallow tide pool may have a high volume of water but that water will have a wide surface area in contact with both the atmosphere and the underlying substrate, both vectors for change of the physical parameters of the pool. Finally, the tidal cycle itself varies. Sometimes of the month the tide is low during the hottest sunniest part of the day, at other parts of the monthly tidal cycle, the intertidal zone is covered during this time. The organisms that live in this environment must be endlessly and admirably flexible, dealing with dramatically different parameters on a daily basis.

All of this is to illustrate the main point, that though tidepools are typically characterized by their height in the intertidal zone, no two tidepools are the same, and the high and low characterizations I’m about to talk about need to be taken with a grain of sea salt.

The higher the tide pool is in the intertidal zone, the further it is from the contiguous coastal ocean and the longer the organisms that live in it are castaways “on the island”. The temperature of these pools can vary greatly, as air temperatures vary much more than ocean temperatures due to the differences in the physical properties of air and water. In winter these pools get colder than the ocean, in summer they get much warmer. The salinity can vary much more than the ocean as well; when it rains or snows, the salinity in a high tidepool can drop dramatically as the sea water is diluted by fresh water precipitation. When the sun is intense and the water is easily heated, salinities can increase as evaporation takes place. Even the pH of a high tidepool varies. At  night the pool can experience low pHs (acid conditions) because the organisms in the pool are respiring and producing carbon dioxide, which when dissolved in water, creates carbonic acid. During the day, the photosynthetic organisms in the tide pool will photosynthesize and take up carbon dioxide, which causes the pH to increase and the water to become less acidic. High tide pools tend to have lower biological diversity because of the wide range in physical parameters.

Tide pools that are closer to the ocean, have less variation in all those parameters, because they are replenished by the contiguous coastal ocean sooner and more often than the higher tidepools. As a result, the lower tidepools exhibit higher biodiversity and host communities that look more like neighboring subtidal zones. The closer the island is to shore, the more like shore it will look.

Thursday, December 6, 2012

Tide Pool Fanatic

Note: This program first aired December 1, 2012.

Looking through an old resume recently, I noticed that I listed “tidepool fanatic” on my list of other skills and interests. Seriously, and it got me the job too. And I am not the only one; there are millions of us*, you can find us pawing through seaweed, looking under rocks, and staring into tide pools every time we go to the edge of the sea. The organisms we find in the intertidal zone are our windows to the mysteries of life under the ocean surface. Twice daily the veil is pulled back and the tribe of the curious gathers to explore the unknown.

The intertidal zone is the area at the edge of the ocean that is regularly covered and uncovered as the tide rises and falls each day. Places like Maine, with high tidal ranges have a large and diverse intertidal zone. Places like Florida, with very small tidal ranges have minimal intertidal diversity. The intertidal zone is populated with marine organisms, meaning organisms adapted to live in the salty aquatic environment we call the ocean. These are some of the toughest organisms in the world, and this is why: imagine yourself as a land based, air breathing being, having to survive, day after day, totally submerged in sea water half of the time. This would certainly challenge your physiology, to put in nicely. This is the kind of challenge (albeit in the opposite direction) that organisms in the intertidal zone face twice daily, every day. As organisms dependent on the ocean’s water, they are stranded out of it for some, if not most of their lives.

Consider the benefits of the ocean, if you are a marine organism that is. Being submerged in water means that you can breathe; water brings with it food for many organisms, water provides a medium for motility (and breeding and hunting), water provides environmental stability in terms of temperature, salinity and pH, in short, the intertidal zone comes alive at high tide. Consider the difficulties of living in the terrestrial environment, if you are a marine organism. You can’t breathe air (with a few exceptions), the temperature and salinity can fluctuate dramatically with season and weather events, you can’t eat, and you could easily dry out. If you are algae, you just have to lay there as you fell. Its rather undignified when you think about it. Clearly, these organisms would be much better off if the tide just came in and stayed in.

Or so we think. The reality is that the organisms we see in the intertidal zone live in this marginal environment because they get outcompeted (which is just the scientific word for bullied) in the sub tidal environment. The intertidal organisms do better in that incredibly stressful intertidal zone, because they evolved physiologic and structural adaptations that protect them from drying out, suffocating, cooking and freezing. Subtidal organisms just can’t do that. Take them out of water and they die.

I have huge respect for the resilience of the intertidal organisms. They eke out a living in a consistently inconsistent habitat, organisms of the ocean that can exist on land, at least temporarily. This sounds pretty significant, but how different is it from our own situation? We humans are predominantly visual animals, yet, we evolved in and exist in an environment that grows dark for half of the time we are in it, effectively negating our primary sense. So perhaps the achievement of the intertidal organisms isn’t as amazing I led you to believe. I don’t care, you’ll still be able to find me staring into the nearest tide pool, imagining the scene when the tide comes in and all of the organisms live the fullest expressions of their lives. Perhaps that is why so many of us love the edge of the sea. Its rhythms of activity and rest, and abundance and famine so readily mirror our own.

*Full disclosure: this is a complete guess.


Oh there are so many books on the intertidal environment! Though it is old, I still love the Sierra Club Naturalist’s Guide to the North Atlantic Coast (Cape Cod to Newfoundland) by Michael and Deborah Berrill.

Don't Call It a Comeback: Wild Turkeys in New England

Note: This program first aired on November 24, 2012.

Come November, many minds in America start daydreaming about the bird that could have been our national symbol, the Turkey. Amazingly, that bird you buy in the grocery store or order from your local farm is the same species as those wonderful prehistoric baby dinosaurs you see in flocks along the roadside or in the fields as you drive to work.

Wild turkeys are found throughout the lower 48 states and into parts of Mexico. The species is actually comprised of 6 sub species, separated by geography. All of the sub species are derived from the southern Mexican wild turkey (Meleagris gallopavo gallopavo). This is the species that the Aztecs of Mesomerica and the Anasazi of the desert southwest were known to have domesticated, one of the few “New World” organisms that lent itself to agriculture. Interestingly, this Aztec domesticated turkey was then brought to Europe by Spanish conquistodors and gained popularity there.  It was further selectively bred in Europe and then came back to the new world with the colonists, who had no idea that there was already a wild turkey waiting for them here in colonial North America.  The sub species we see here in Maine is the Eastern Wild Turkey; Meleagris gallopavo silvestris), and as a sub species it is able to interbreed with the domesticated turkey.

Wild Turkeys were once abundant throughout New England, but the spread of agriculture during the colonial period up through its peak in the 1800’s, combined with unrestricted hunting nearly exterminated the species in our area. Most New England states went from being almost entirely forested at the time of European colonization to being 60 to 90 % cleared for cropland and pasture. This clearing of the land strongly decreased diversity across the landscape and obliterated wild turkey habitat. Turkeys need mixed woodland with nut bearing trees like oaks and beeches as a food source. They roost high in trees at night to avoid nocturnal predators. Young turkeys need dense shrubbery for cover and lots of insects to feed on to fuel their rapid growth. A patch work of diverse northern hardword forest is ideal for them, and that is what has been regenerating in much of New England since agricultural clearing peaked in the 19th century.

The turkeys we see around today are a result of reintroduction programs throughout the northeast.  Maine’s reintroduction program started in 1977 and 78, with 41 turkeys from a wild population in Vermont, followed by 70 more Connecticut turkeys in 1987. From those 111 birds come the 50 to 60,000 we have in the state today. That is a phenomenal recovery, and speaks clearly to the importance of habitat restoration in the field of conservation biology. When released from the pressure of unregulated hunting and total habitat destruction, wild turkeys are able to thrive, achieving population numbers and ranges that are likely higher and wider than the precolonial population. So if you are partaking in the traditional turkey feast some time this holiday season, take a moment to reflect on the marvelous resilience of the bird you are eating.


Maine Inland Fisheries and Wildlife info:

Vermont also has some nice things to say about wild turkeys:

The Lewiston Sun Journal article on wild turkeys in Maine:

Yep, he really did say that: Ben Franklin, though he never made a public fuss about it, did think the turkey to be a more respectable bird than the eagle.

Nice article in Wired magazine, regarding new research on the domestication of turkeys in North and Meso America

Jared Diamond Guns, Germs and Steel—learn all about the few species that native North Americans were able to domesticate (and why that bad luck doomed them).

Tuesday, November 20, 2012

Microbiome Part 9: The Finale--Bacteria and Mood

Note: This program first aired on November 17, 2012.

This week, we wrap up our exploration of bacteria and the microbiome with a final look at the world within us; the cutting edge of human microbiome research. What scientists are discovering is the fact that the bacteria in your gut can influence your mental state. So not only do they digest your food, synthesize your vitamins, regulate your immune system and keep their pathogenic brethren in line, they also strongly influence how calm, anxious, bold or depressed you might happen to be.

Several recent studies on mice have demonstrated this effect quite clearly. In one study, the behavior of “normal” mice was compared to mice who were fed a diet that included a probiotic supplement. The probiotic mice proved to be less anxious and more confident in behavioral tests, and had lower levels of the stress hormone cortisol in the their urine.  In another study, two different strains of mice were compared, one bred to be passive and timid and the other bold and courageous. When bacteria from one mouse strain were transplanted into the other mouse strain, the “transplantee’s” behavior changed to match the behavior of the donor mouse strain. In other words, putting bacteria from a passive mouse into a bold mouse can make a bold mouse passive. Putting bacteria from a confident mouse into a timid mouse can make a timid mouse confident. This shows that the personality traits we have come to think of as having a genetic basis (the scientists who bred those strains of mice certainly thought that), are in fact quite plastic and seem to depend on composition of the gut microbiome rather than genetic code.

In a rather circular piece of logic, it also seems that the mind can influence the population and diversity of the gut flora as well. In times of stress, gut flora becomes less diverse and robust, creating openings for more serious dysbiosis and disease—think of it as an extreme case of butterflies in the stomach. So the bacteria influence the mind, and the mind influences the bacteria, and around and around the maypole they go.

So how does this work? The literature refers to the rather heady “brain gut enteric microbiota axis”, but the actual mechanisms of communication are not completely well known as of yet. A few things are quite clear. The gut houses a huge amount of nervous system tissue, so much so that it is commonly referred to as our “second brain”. This second brain is connected to our first brain by the vagus nerve, a large bidirectional nerve pathway that originates in our brain stem and invenerates almost all of our viserca*. Most of the neurons in the vagus nerve are sensory, they collect information about the state  of the viserca and send it back to the brain. The remaining neurons carry info from the brain back to the viserca. In the first mouse experiment I discussed, the one with the probiotic-ed mice, when researchers severed the vagus nerve in those probiotic supplemented mice, the treatment effect vanished. So the probiotics may still have been in the gut, but the anxiety reducing effect of them could no longer be communicated to the brain. This tells us that at least in that experiement, the vagus nerve played a huge role in communicating whatever the probiotic bacteria were doing.

It has also been noted that the nervous system tissue in the gut produces many significant neurochemicals, including all the big ones like serotonin, dopamine, GABA, norepinephrine, and acetylcholine. It turns out, the gut bacteria make these chemicals too, many of which down regulate the excitability factor in the brain leading to enhanced calm. What isn’t clear is if it is really the bacteria that are responsible for the neurochemicals that we always ascribed to the nervous system tissue in the gut. And the actual means of communication between the gut and brain has not been fully parsed out. The vagus nerve is clearly part of it, but these neurochemicals must play a role as well.  And all of this has huge implications for medicine and treatment of everything from mental illness to autoimmune diseases.

The day is coming when your personal ecosystem will be easily assessed, imbalances identified and addressed, and health restored, all on the basis of your individual mix of microbial flora. I personally am incredibly excited about this, and look forward to the day when we in western medicine, work with our microbiomes, instead of exclusively against them, acknowledging our place in the much bigger we are just a part of. The tide is turning.

*Everything except our spleen, for some reason…


Gut bacteria and mood—the mouse study

Gut bacteria in infancy determine happiness (via serotonin levels)

Gut bacteria and anxiety and depression

A great overview from the American Psychological Association and Dr. Siri Carpenter, Sept. 2012

The show that started all this wondering for me, RadioLab. Take a listen here:

Emmanuel Denou, Wendy Jackson, Jun Lu, Patricia Blennerhassett, Kathy McCoy, Elena F. Verdu, Stephen M. Collins, Premysl Bercik. The Intestinal Microbiota Determines Mouse Behavior and Brain BDNF Levels. Gastroenterology, Vol. 140, Issue 5, Supplement 1, Page S-57

Microbiome Part 8: Human Symbionts

Note: This program first aired on November 7, 2012.

Most of us can accept and understand, perhaps subconsciously, that our guts are full of bacteria, and that those bacteria help digest our food.  We’ve talked about this in recent weeks and it is a concept most of us are comfortable with: If there are bacteria on our bodies, your gut, that wild independent ecosystem within you, is exactly where you would expect them to be.

The problem is, our gut isn’t the only place bacteria live on our bodies, and digesting food isn’t the only thing they do for us. Human beings have literally been described as mammal/bacterial symbionts,  organisms completely and utterly at the mercy of the symbiotic relationship they have evolved with microscopic partners over millions of years, organisms that are actually collections of trillions of organisms—one big one and billions of little ones. One source even calls it “the human super organism”. Now to be fair, I am sure this symbiosis is not limited humans, though I am not familiar with studies of the microbiome of the domestic house cat, or the elephant, or of dolphins ( as a side note: It is very likely that this research has been done, or at least proposed). I think that when we look closely, we realize that our definition of life as we know it has to change. We find that without exception what we used to call an individual organism is in fact an accumulation of organisms working in concert. Its true: no man is an island. And nature isn’t red in tooth and claw, its symbiotic.

So when you look at the human organism, you find bacteria not only in the gut, but everywhere else on the body as well. And just like in the gut, these bacteria in all the other places in our body are doing a job for us. An excellent example is on our skin. We are covered head to toe with bacteria, and amazingly it is not a homogeneous community. I remember being amazed by some of the first research that came out on the human microbiome; it outlined the discovery that the bacteria on your right hand are a completely different community than the bacteria on your left hand. Each area of the body is a distinct ecological niche for our bacterial partners.

The bacteria on our skin play a similar role to the bacteria in our gut, in that they help prime the immune system, keeping it at the ready without stimulating full blown activation. More interestingly they seem to regulate their own community with the checks and balances we see in any ecological system. For example Staphylococcus epidermis is a very common skin bacteria (hence the epidermis name), and while generally innocuous, can result in some nasty infections, especially in the immunosuppressed or otherwise ill. There is evidence though, that it also secretes antibiotic compounds (endogenous antimicrobial peptides to be exact); these compounds are the bacteria’s own chemical warfare against competing bacteria. Many other sampled skin bacteria do the same. Their infighting is our benefit, by releasing all these anti biotic compounds on our skin, they keep each other in check, never allowing one type to grow to the point of becoming pathogenic. That is why you should go easy on the hand sanitizer and antibacterial soap. These products can disrupt the balance of bacteria on the skin, and lead to more pathogenic bacteria in the long run.

So our coconspirators in this thing we call the human superorganism not only keep our immune system tuned and ready for action, they also police themselves, to our benefit. When their balance gets disrupted, by antibiotics, ultra clean living or some other environmental insult, or when you get dealt a weak hand (coming out the sun roof instead of the “normal way” is a fast and sure way to start out life with a microbiome deficit) your microbiome is less able to manage itself, leading to dysbiosis and a whole host of illnesses. So don’t micromanage your microbiome. Let them do their work and attend to their own bacterial business.  In most instances, you’ll be better off for it.


Check out the good work by the folks at the Human Food Project:

The title of Michael Specter’s article in the Oct 22, 2012 New Yorker says it all: “Germs are Us”—if you haven’t read it, run out and get it. It will make you want the Heliobacter pylori bacteria in your stomach!

Lynn Margulis was really on to something when she wrote Symbiotic Planet (1998 Basic Books ISBN 0465072712)

“The skin’s secret surveillance system” Nature July 26, 2120

Great article from Germany’s Spiegel “Western Lifestyle Disturbing Key Bacterial Balance” 9/21/2012

On the skin biome—“Skin microbiota: a source of disease or defense?” From the British Journal of Dermatology, March 2008

Wednesday, November 7, 2012

Microbiome Part 7: Human Bacterial Partnerships

Note: This program first aired on October 27, 2012.

It should be clear to you, if you’ve been following this show for the past several weeks, that bacteria influence every aspect of life on Earth. Omnipresent, that is how you should think of bacteria. From the endosymbiosis theory of the origins of chloroplasts for photosynthesis, and mitochondria for energy metabolism to the nitrogen fixing role of symbiotic microbes in plant roots, bacteria are intimately involved in all biological processes. They even single handedly support the non photosynthetic ecosystems of the deep ocean hydrothermal vent communities, supporting life without light, something we used to think of as impossible.

I want to turn our gaze inward now, to the cutting edge of medicine and microbiology, to the human microbiome. Our bodies are a vast universe and play host to thousands of different kinds of life forms. There are estimated to be more bacterial cells on and in our bodies than there are human cells, by at least an order of magnitude. It turns out, we’re actually more than the sum of our parts.  We function more like a forest ecosystem or a coral reef than the individuals we once thought we were.

All of these microbes evolved right along with us, over the millions of years of hominid evolution. Our microbiome has been even been described as an additional organ, one we all have that most of us have no awareness of whatsoever. These bacteria we host fill many ecological roles in our bodies, and in return get a stable and generous living environment. They do so much for us in fact, that without them we could scarcely live. Remember when I talked about bacteria as external digesters? Most of them (and certainly all the ones we are talking about now) are heterotrophic and must ingest nutrients from outside their bodies. The two to five pounds of them living in our guts at any given time are doing just that; digesting all that food we swallow. We physically break the food down into smaller pieces, and we even synthesize some enzymes that chemically break down the food molecules into smaller more absorbable bits. What we can’t or don’t digest (primarily certain complex carbohydrates and fibers) we give to our gut flora, that two to five pounds of bacteria we carry around in our intestines. As decomposers, they are able to at least partially break down the less digestible components of the food we eat, and we can benefit from this. That digested food can be absorbed by our cells. Some of the byproducts of this bacterial digestion are the short chain fatty acids that are so critical to many metabolic pathways, and are thought to play a an anti inflammatory role in the body as well. The microbes also synthesize certain essential vitamins and cofactors that are not otherwise found in the food we eat.

From a nutritional standpoint, our gut flora close a loop that we are not capable of closing on our own, we’ve never had to evolve complete chemical digestion because we’ve been co-evolving with our symbiotic microflora for millions of years. In the coming weeks we will look beyond the simple digestive symbiosis, and explore the various other ways the human microbiome affects and improves our quality of life. 


The New York Times did several articles on the human microbiome this summer, in conjunction with the release of the NIH Human Microbiome project report.

Kolata, Gina “In Good Health? Thank your 100 Trillion Bacteria” New York Times, June 13, 2012

Zimmer, Carl “Tending the Body’s Microbial Garden” New York Times, June 18, 2012

Also, from 2010: Zimmer, Carl (he’s a leading American science writer, who’s latest book is on microbes) “How Microbes Defend and Define Us” New York Times, July 12, 2010

Direct from the source: The National Institute of Health’s Human Microbiome webstite:,

“The structure, function and diversity of healthy human microbiome”—one of the seminal articles from the Human Microbiome Project

Small intestinal bacterial overgrowth happens when large bowel bacteria get into the small bowel (think Girls gone wild meets Mardi Gras), and raise havoc. We tend to think of the gut flora as being in the colon, but there are bacteria in the small bowel too, just less of them and of a different type


Sunday, October 21, 2012

Microbiome Part 6: Carbon Cycle

Note: This program first aired on Saturday October 20, 2012.

We are carbon based life forms, ask anyone at NASA*, Earth is covered with the stuff. Plants use carbon to hydrogen bonds to store the energy of the sun, that is the essence of photosynthesis. They also use the carbon they take out of the atmosphere (or fix) to build the structure of their bodies. We eat the plants (or the things that eat the plants, or even the things that eat the things that eat the plants), getting not only energy from those carbon to hydrogen bonds, but also the building blocks of our bodies as well. If that were the end of the story, life on Earth would have ended a long time ago, because we would have run out of our main source material, carbon.

Like all elements, carbon isn’t satisfied to simply stay put. It moves around the Earth and in and out of various forms over the course of time. The regularity of the journey of carbon is well documented, and referred to as the “carbon cycle”.  There are several sinks or reservoirs of  carbon; some are short term and others are long term. The long term sinks are thinks like the fossilized carbon that make up underground beds of fossil fuels we so love to burn, or limestone, a sedimentary rock formed at the bottom of the ocean from the chemical union of carbon dioxide gas and various minerals** present in sea water. Once carbon makes it to one of these reseviors, its stuck there for a while, baring some physical process that brings it to the surface of the earth for weathering. The parts of the carbon cycle we are more interested in today are the “fast” components; the movement of carbon dioxide out of the atmosphere, into plants (via photosynthesis), and then back out again (via respiration both by the plant and the things that eat the plant, but probably more importantly respiration by the microbes that decompose all that plant and animal matter, liberating and recycling the carbon and many other nutrients, making them available for use once more).

If you play out the thought experiment “what if all the bacteria disappeared tomorrow?”, the result might look something like this: piles and piles of dead plants and animals, just stacking up, and the amount of carbon available steadily dropping. What would essentially be happening is that carbon would be moving out of the atmosphere into biological material, via photosynthesis and the food chain. The carbon would be building up in a biological “carbon sink or resevior” in the form of organic biomass. If nothing ever decomposed, that carbon doesn’t get to move out of the sink its stuck in and the sink would get fuller and fuller as time went on.

The soil is the largest land based carbon sink in the carbon cycle (the oceans hold over an order of magnitude more, much of which gets locked eventually into abiotic limestone). Soil is comprised of both mineral elements and organic elements. Its those organic elements (dead plants and animals) that comprise the carbon sink part of the soil. One concern with the increase in average global temperature that is accompanying climate change is the idea that as temperature increases, bacterial decay of organic material in the soil will also increase, freeing up much of the carbon stored in the soil, liberating it back to the atmosphere. So would it make sense to try to get rid of all those soil bacteria and prevent them from doing their ecological job? Besides being impossible, I think this would be foolhardy. In the words of John Muir, the visionary nature man himself: “When we try to pick out anything by itself, we find it hitched to everything else in the Universe”.

The decomposition part of the carbon cycle isn’t something we like to think about, we think of decomposition as a bad think in the back of the refrigerator. Think too long about bacterial decay and you eventually come around to the question of what happens to your own body when you are done with it. So I can’t blame people from shying away from this aspect of the carbon cycle. I can only hope that by focusing on the grand cycles of the building blocks of life, we can learn to see death, and its accompanying decay, as liberation. Bacteria are literally the doulas and midwives of this cycle, ushering carbon, our most essential substance, from one phase of existence to the next. So the next time you dig in the garden, dump the compost or simply walk in the woods and smell that wonderful leaf decay smell, pause and reflect on, and revel in, the moment for what it is, a snap shot of grand loop that is much bigger than you.

Post Script:
*And just WHY are we strictly carbon based? Because carbon is unique among elements in that it has four spots each atom that can form bonds, and it can bond in a wide variety of shapes. Similar atoms (same column of the periodic table), like Silicon, also have four bonding spots, but tend to form crystal lattices, instead of the wide variety of that carbon can attain. It’s also apparently the fourth most abundant element around, meaning, there’s lots of it out there.

** Mostly calcium and magnesium.


Kenneth Todar “Online Text book of Bacteriology”

Totally worth looking at: from the American Society for Microbiology

From one of my favorite websites, NASA’s Earth Observatory

From the American Museum of Natural History

Ah the Union of Concerned Scientists…
Thanks for all your level headed thinking.

Microbiome Part 5: Decomposers

Note: This program first aired on Saturday October 13, 2012.

No one really knows how many bacteria are on the Earth. People have come up with models and sampling protocols to try to determine how many individual bacterial cells are on Earth (five million trillion trillion), how many species are in any given proverbial teaspoon of soil (five thousand or more), and how many different species exist globally (a few thousand to a billion). Many scientists believe that the bacterial biomass on the planet far exceeds the biomass of all other living things. Needless to say, there is little consensus and much research needs to be and is being done.

Taxonomically, bacteria make up the roots of the tree of life. They had the planet to themselves for nearly 2 billion years, and then single celled eukaryotes and multicellular eukaryotes (us included) came along and stole the spotlight. We’ve talked before about the photosynthetic role of bacteria, but they have another equally or even more important ecological role on the planet. Bacteria, along with fungi are the great decomposers of our world.

Decomposition doesn’t sound like a very fun job, and to our sensibilities, it often doesn’t smell very good. It is incredibly important however, to the cycling of nutrients and raw materials of life. There are two major biochemical reactions that drive life as we know it (with of course, a few exceptions). The first is photosynthesis; plants use the energy of the sun to take simple molecules and turn them into more complex molecules. In doing so, they store some of the sun’s energy in the bonds that hold those complex molecules together. Simple to complex. The second major biochemical reaction is respiration. All organisms respire, meaning, they take large complex molecules and break them down into smaller simpler molecules, in the process gaining the energy that was stored in the bonds of those large molecules. This is what we do when we eat. This is why plants photosynthesize—they don’t do it for us, they do it to make food for themselves (we just happen to get it before they do in some instances).

Organisms that eat are also know as heterotrophic, hetero meaning different, trophic meaning eating, so heterotrophs eat food that is different from themselves (by comparison, photosynthesizers are autotrophic—they self feed). Heterotrophs have essentially two options for eating; they can ingest food and digest the complex molecules internally, or they can keep the food outside of them selves and digest it externally, absorbing the molecules only once they have been at least partially broken down. We are of the former type, we ingest our food, secrete acid and enzymes, and with the help of some bacteria, liberate nutrients and energy from that food. We don’t however, get all of the nutrients or energy from our food, not close. The classical ecological number is 10 percent, as in only 10% of the energy from one trophic level gets passed on to the next one, the other 90% is lost as waste (in the form of heat and feces). The reality is that this number varies quite a bit with different feeding levels, but the take home message here is that most of what we eat doesn’t actually get into us. My personal theory about why this is has to do with the difficulty of digestion. Our body has to work quite hard to chemically break down those big food molecules. If we work too at it, we might just start to digest our own bodily tissue—that is one of the roles of mucus in the digestive track, to protect ourselves from our own digestive enzymes.

Bacteria are of the latter type. They are external digesters, excreting digestive enzymes to break down food molecules (both large and those that are partially digested and excreted as feces) and then absorbing the smaller molecules that result. Again, I am not a microbiologist, but my personal theory on this is that bacteria, being prokaryotic, lack a nuclear membrane and have their DNA loose inside their cells. I expect that it is to their advantage to not in any way jeopardize their genetic material by having digestive enzymes also floating around inside their cells, hence, external digestion. Fungi, the other group of great decomposers also digest externally and this pattern leads me to believe that breaking down these larger molecules into smaller inorganic nutrients may be a rather harsh process, which is why both decomposers do it this way.

We’ll continue this discussion about the ecological role of bacteria next week as we look in more detail at the specific nutrients that bacteria are so vital in keeping in play in the biosphere.


From the master himself: Stephen Jay Gould, "Planet of the Bacteria," Washington Post Horizon, 1996, 119 (344): H1

The factoid about the microbial biomass making up the largest single carbon sink came from this author, but to be honest, I read it on Wikipedia…I’m not proud. Fenchel, Tom (1998). Bacterial biogeochemistry : the ecophysiology of mineral cycling (2nd ed. ed.). San Diego: Academic Press.

Just for fun:

“First-Ever Scientific Estimate Of Total Bacteria On Earth Shows Far Greater Numbers Than Ever Known Before” Science Daily, 1998

Microbiome Part 4: Photosynthesis

Note: This program first aired on Saturday October 6, 2012.

If all the bacteria on Earth were suddenly to vanish, would you care? They are too small to be seen (unless of course, you’ve left something alone in the back of the refrigerator for way way too long), so would you even know it? In fact, some of you, without thinking it through fully, might think it would be a good thing if all the bacteria on earth were to vanish. But, I can say unequivocably that that would be an unmitigated disaster. They have an important job to do here on Earth, many jobs in fact. If all the bacteria on Earth were suddenly to vanish there are many ways we would miss them.

It is often said that bacteria are responsible for much of the oxygen we breathe. This may come as a surprise but many bacteria are indeed photosynthetic. The only source of the free oxygen gas we breathe is photosynthesis, it always has been. Before there was photosynthesis, there was essentially no free oxygen in the atmosphere, and all life (entirely prokaryotic) was anaerobic. The photosynthetic bacteria are the cyanobacteria (popularly known as blue green algae), the green and purple sulfur bacteria, and the purple non-sulfur bacteria.  In terms of oxygen production, the cyanobacteria are the heavy hitters here. The sulfur bacteria by the way, photosynthesize using  the energy of light from the sun to change CO2 into sugar the same way plants do, except that they use hydrogen sulfide instead of water in the chemical reaction. This sounds crazy until you look at the periodic table and see that oxygen and sulfur are in the same column (and thus behave the same way, so the difference between H2O and H2S actually isn’t that great).

We can attribute essentially all of the oxygen we breathe to bacteria if we recognize that the chloroplasts in plant cells—the grass on your lawn, the leaves on the trees around your house, the algae in the ocean—were originally bacteria. This is the theory of endosymbiosis. The original plant was probably a hungry single celled protist that engulfed a cyanobacteria, but then failed to digest it. The bacteria realized it had a good gig there inside the protist, surrounded by a soup of half digested food and all. The protist had a good deal going as well, now housing its own sugar making factory, which is all that chloroplasts do inside a any cell, they absorb light and use that energy to rearrange some commonly found chemicals and store the energy of the sun in the chemical bonds in the sugar they make. The oxygen we breathe is a byproduct, really a waste product, of that process (note, those sulfur bacteria that don’t use water?  They don’t make oxygen either, their waste product is, unsurprisingly, sulfur).

So, directly (through photosynthesizing mats of cyanobacteria), and indirectly (by being responsible for the existence of chloroplasts in plant cells), bacteria save the day and make life  as we know it possible.  And the best part is, that isn’t even half of all the good stuff they do here on Earth, but we’ll have to save that for next time.

The University of California Museum of Paleontology has a huge and amazing website devoted to education about evolution and the tree of life, as well as the geologic past:

See for yourself, Oxygen and Sulfur ARE in the same column!

“From Endotymbiosis to Synthetic Photosynthetic Life”, Andreas Weber and Katherine Osteryoung (full text available)

Thursday, October 4, 2012

Microbiome Part 3: Antibiotic Resistance

 Note: This program first aired September 22, 2012.

The germ theory of disease, that certain diseases are caused by microscopic organisms, is well established in traditional western medicine today. Thinkers and healers flirted with the idea for centuries, but it took until the 1800’s in Europe for the idea to gain any traction, and after much controversy and resistance,  and to actually change behavior in many hospitals. Behavior like washing your hands after you finish an autopsy, before you go on to examine your next patient (who might be a woman about to give birth). We’ve come so far with the idea that now seconds after a doctor touches you, they rush to the sink to wash their hands, not wanting to risk their own safety with any of the germs (ie bacteria) that might be on your skin.

By the start of the early 20th century, many scientists and researchers had noticed that certain molds inhibited bacterial growth. This observation and the subsequent experimentation it spurred on led to the development of penicillin and the vast array of modern antibiotics we now have available, ushering in the age of modern medicine and the end of many now easily cured diseases. If you have been paying attention in the last decade or so, you will have heard about the growing problem of some of these wonderfully useful drugs not working anymore. Many of the harmful bacteria that are targeted by these drugs are becoming increasingly resistant to their effects.

Antibiotic resistance is a multifaceted problem. The first is a problem of evolution. Quite simply, there is genetic variation for any given trait in any given population. The variation arises from random mutation, and the ones that end up being helpful to an individual’s survival and reproduction get passed on. Ones that have a negative effect don’t get passed on as much, or at all. That’s evolution in a nutshell: differential reproduction. So in a population of bacteria, there may be a version of a gene that gives that particular bacterium resistance to an antibiotic (more on this in a moment). When we douse the bacteria with something that will kill them, the only ones that live and survive and reproduce are the ones who have that have the resistance gene. So, on an evolutionary level, antibiotics select for resistance genes.

Now let me tell you a story about a cave in New Mexico. It is one of the deepest and most isolated caves in the world. Virtually no one has been down there. Yet, when researchers took samples of bacteria, they found that nearly every strain of bacteria was resistant to at least one type of antibiotic currently in use. As a whole, the cave bacteria were resistant to nearly every antibiotic currently in use. The reason for this is fascinating. Essentially, antibiotics are weapons, and though we discovered them, we didn’t invent them, bacteria did. Bacteria evolved antibiotics to kill other bacteria, and gain competitive advantage in their environments. If humans were to use a chemical weapon, they have to protect themselves with a gas mask. The antibiotic resistance genes are the “gas mask” of a bacteria—the genes protect the bacteria from its own chemical weapon, so it can use it on other types of bacteria. The bacteria in the New Mexican cave demonstrate this—they don’t have antibiotic resistance genes because of us, they have them because of each other.

So the genes for resistance to pretty much all antibiotics occur naturally in normal populations of bacteria.  We know how mechanisms of evolution then select for these resistant genes when we apply antibiotics to a population of bacteria. And we know from our discussion of lateral gene transfer, how readily bacteria will swap genes between species.  Putting these three things together leads to the perfect storm of rampant antibiotic resistance we see in our hospitals today.

The hard part is that we can’t do anything about the first factor (the naturally occurring resistance genes) or the last factor (lateral gene transfer is a process that is 3.5 billion years old and going strong).The only one we have any control over is the evolutionary one, and the only way we have influence there is to refrain from participating, in other words, not using the antibiotics, or at least, not using them unless we really really need them.

So bacteria may be at times our foes. In coming weeks, we will look at the other side of the coin, and examine how they are our friends as well. In fact they are such good friends to us,  that we couldn’t live without them.


From “Contagion” The Harvard University Open Collection on Diseases and Epidemics:

Dr. Hani (2010). History of Antibiotics. Retrieved 19 Sep. 2012 from Experiment Resources:

Science Daily “Key to New Antibiotics Could Be Deep Within Isolated Cave”

Genereux, Diane P. and Carl T. Bergstrom “Evolution in Action: Understanding Antibiotic Resistance” Chapter 13 Evolutionary Science and Society

Microbiome Part 2: Lateral Gene Transfer (aka Bump and Grind)

Note this program first aired September 15, 2012.

Bacteria are thought to be the original gangsters, the form in which life sprung forth from the primordial soup. And that was nearly 3.5 billion years ago. One line of questioning in the current fervor of microbial research is then “what is the evolutionary history of the prokaryotic clades?”—those groups of microorganisms with no membrane to keep their DNA nice and tidy, who may or may not be closely related to each other. And when we say evolutionary history, we mean how did the prokaryotic diversity we see today arise, who evolved from whom and which groups are more closely related, meaning, which groups evolved from a common ancestor relatively recently.

It turns out, this question is much easier to ask than it is to answer. And the reason for this is that we have to compare the genes of these various organisms in order to determine how related they are. The more genes they share, the more closely related we can assume them to be. It actually is quite complicated trying to decide which genes to compare. Some have said, why not compare them all? Well in some cases that is exactly what is going on. Researchers are comparing entire geneomes  from various prokaryotes. The trick is to get them all lined up correctly, so you are comparing the similar areas of each genome. And this only really works for organisms that have relatively few genes. Even the super computers get overwhelmed relatively quickly with large amounts of genetic data. Other researcher pick out specific types of genes, and compare just those. These minutia lead to terrific and heated debates about the relationships of various groups of organisms we can’t even see!

The real reason though, that reconstructing the evolutionary history of bacteria is so difficult is that they don’t behave the same way we do with respect to our genetic legacy. Pretty much all of us Eukaryotes reproduce sexually. We find a mate, combine our genetic material, and produce offspring that carries a mix of our DNA, some from one parent, and some from the other. That is the only way our genes move from individual to individual, through direct heredity. Tracing and comparing genes gives us a picture of lineage.

The problem is that prokaryotes don’t behave that way, when it comes to their DNA. Instead of finding that special someone to settle down with and start a family, they are all about one night stands. And infact, not only one night stands, but trans specific hook ups. Prokaryotes are willing and able to swap chunks of DNA with any other prokaryotic cell they encounter, regardless of whether or not it is the same species as them. This promiscuity is quite frankly, a little shocking.  This bump and grind life style is known as lateral gene transfer, and is the reason it is so hard to reconstruct the evolution of bacteria and archea. They don’t follow the lineage based model of our own genetic methodology. They swap genes all over the place, all the time, so the presence of a gene in a particular bacteria may not be telling you anything about that cell’s parent, it may just indicate that that cell happened to bump into some other prokaryotic species and they did a quick genetic switcheroo when no one was looking. Theoretically this MO, and not sexual recombination, accounts for diversification in early prokaryote evolution.

So what this means is that our models for piecing together the puzzle of the early evolution of prokaryotes doesn’t work. The chaos that is lateral gene transfer makes this virtually impossible at least for now. It also has some incredibly important implications for human health, all of which we will be talking about on future episodes of the World Around Us.

Timeline of early life on Earth from the New Scientist:

More than you ever wanted to know about comparing bacterial DNA:
“Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution” Se-Ran Juna, Gregory E. Simsa, Guohong A. Wua, and Sung-Hou Kim,

The pros and cons: “The advantages and disadvantages of horizontal gene transfer and the emergence of the first species” Aaron A Vogan and Paul G Higgs*

Tuesday, September 4, 2012

Microbiome Part 1

Note: This program first aired on September 1, 2012.

The microbiome is a hot topic in science media and research circles right now. Google the term microbiome and you get thousands of relevant hits. It is a new field because the techniques that enable us to identify microbes are relatively new, like cheap and fast genetic sequencing. Previously, many microbes were unable to be cultured in the lab, making them impossible to identify let alone study. This is a field that is changing at an incredible rate. We are going to spend some time with the microbiome so today I want to cover the basics.

Biome is another word for ecosystem, the totality of an abiotic environment and its living components, classically in a distinct climatic region. Biome usually refers to the big picture; desert and rainforest are textbook examples of biomes. The term microbiome refers to the biome or ecosystem of microorganisms, wherever they are found. The human microbiome has been in the news quite a bit lately, this refers to the human body as a biome for microbes. Various Earth microbiome projects seek to identify the microbial communities involved in the traditionally recognized climatic biomes (the deserts, the rainforests). What we are learning from all this is that microorganisms are everywhere, and are intimately involved with every important cycle and function in our bodies and on Earth. It is not an overstatement to say they are a really big deal.

So what are microorganisms? The term encompasses bacteria, yeasts and other fungi, viruses, and microscopic plants and animals—really the only qualification is to be microscopic. When we talk about microorganisms, we generally think of bacteria as the dominant player, but keep in mind all those other organisms as well. They will come back into our discussion later.

If you think back to your high school biology course, you may remember a little bit about bacteria.  They are single celled organisms that lack a nuclear membrane. Knowing this may help you pass your SATs, but what does it really mean? To start, the world is divided into two kinds of organisms, prokaryotes and eukaryotes. Prokaryotes are organisms without any kind of membrane bound organelles, the most important of which they don’t have is a nucleus.  Its as if in our bodies, our organs weren’t distinctly delineated, and everything, including our brain, just sloshed around loose inside us. They are almost always single celled, with a chemically complex cell wall, and a loose tangle of DNA somewhere inside them, as well as smaller loose bits of circular DNA. Eukaryotes are the opposite; they are often large, and usually multicellular. They have many bound organelles in their cells, to perform all kinds of metabolic functions, and they have a true nucleus that houses their linear DNA. Just for the record, we are eukaryotes.

Prokaryotes can be further divided into two groups, and amazingly, they seem to be more distantly related to each other as we are from either of them. The two groups are so different they each qualify as a separate Domain of life, domain being the step above Kingdom in classical taxonomy. When we lump everything that is alive together, Domain is the first level at which things are sorted. Two of those domains are microscopic prokaryotes, the Eubacteria and the Archea. Archea are often called “extremophiles”, they are the organisms that live in hydrothermal vents, hot springs, hypersaline solutions and other extremely hostile environments. The Eubacteria are generally what we are referring to when we talk about “germs” or bacteria, and as far as we know currently, are key players in the microbiomes of both our bodies and our environments. In the interest of completeness, the third Domain of life is the Eukaryota (the one that contains us and pretty much all the life we can see with our own eyes).

We’ll be talking more about bacteria and other members of the microbiome in the coming weeks as we explore the world that is not only all around us, but inside us as well.


The New York Times did several articles this summer about the human microbiome and new research coming out regarding it. This is one:

The L.A. Times did s similar series:

Interesting personal site from a fellow science nerd:

The National Institute of Health’s Human Microbiome project:

The Earth Microbiome project:

The University of California Museum of Paleontology maintains a fantastic website with excellent information about a range of topics and links to other good external sites:

The Tree of Life Web Project  is a terrific and growing web resources for learning about phylogenetic relationships between groups of organisms. Highly recommended:

Monday, August 20, 2012

Gender part eight: Anthropogenic Chemicals and Human Sexuality

Note: This show first aired on August 18, 2012.

Here on the show, we’ve spent the last several weeks talking about gender. As humans, our tendency is to think of gender as a hard and fixed quality with few exceptions. That is because we are mammals, and mammals have the hardest and most fixed sexual differentiation system on the planet. I hope that I’ve been able to convince you that in most other groups of organisms, gender is a variable and plastic endeavor; that is the norm, we are the outliers (our transgendered brethren not withstanding).

We humans may be in for a nasty surprise in the coming decades. It turns out that our genders are getting a tiny bit more plastic as a result of well, plastic, and a multitude of other substances that we have created in the lab in the past 50 years or so. It turns out that many of these chemicals (you know all the names: phthalates, bisphenol A, PCB’s, atrazine, flame retardants, DDT etc) are what we call endocrine disruptors. They have estrogen like molecular structures, and thus bind with estrogen receptors on our cells and turn on estrogen sensitive genes. The few that aren’t direct estrogen mimics still have a net estrogen like effect on the body. We talked about hormones and their effect on the sexual development of the human body in our discussion of why men have nipples; it will be useful to revisit it here.

So, the human form has a default mode, and that is essentially female. In the absence of other directions, our genetics describe a female body whose development is governed primarily by estrogen. Males develop because genes on the Y chromosome tell certain cells to make androgens like testosterone. You can have a Y chromosome, but if there is damage on it, and it doesn’t do its job, you won’t develop as fully male, or have a host of other reproductive problems. In humans, as in most organisms, expressed gender is a result of the balance between estrogens and androgens, regardless of the genetic make up of the individual. Which brings us to our endocrine disruptors.

Lets start with a chemical so common scientists refer to it as “ubiquitous” in terms of human exposure, phthalates. There are two main catagories (and many many individual chemicals), high density and low density phthalates. High density phthalates  are used as plasticizers in plastics and polyvinylchloride (PVC). They make plastics softer. Chemicals in this class were banned for use in children’s toys nationwide in 2008. Low density phthalates are used in cosmetics and other smelly things, they make fragrances last longer (this is why the first hint that a woman is pregnant is that she starts purchasing fragrance free personal care products!—more on why in a moment). They are quite volatile and readily leach out of what they are in, so, phthalates are everywhere.

Phthalates function as an antiandrogen endocrine disruptor, by at least in part, inhibiting the synthesis of testosterone. No testosterone? No male development. What we actually see is a group of alterations to male sexual organs that has a name; “phthalate syndrome”; it includes reduced penis size and impaired testicular descent among other things. Studies have also concluded that phthalates interfere with male brain development, and result in “reduced masculine play in boys”. Many other anthropogenic endocrine disruptors work in similar ways, disrupting the testosterone pathways in the developing male. Its important to note that for many of these effects, the window for problems to occur is very early in embryonic development when those bipotential gonads are first differentiating, and requires very low exposure levels. Hence those pregnant ladies and their fragrance free lotions.

Endocrine disruptors affect females as well, to be sure, but they generally do not masculate them, in a mirror image of the male effect. Early onset of puberty and multiple reproductive abnormalities are among the more common effects noted for females.

So its not just feminized frogs and hermaphroditic polar bears anymore. The bird of our toxic legacy has come home to roost. Because many of the chemicals are relatively new (as in the past 30 to 40 years), and their impact is often in utero,  but we don’t become reproductively active for a couple of decades after that on average, the negative effects on our reproduction can be delayed and difficult to connect back to our inutero exposure to an endocrine disruptor. So what does this mean for gender in humans? We might not be able to fill our biological roles quite as well as we once did, which, at the risk of sounding melodramatic, may have significant long term impacts on the future of the human species on this planet.

Swan, S. H. et al, “Prenatal phthalate exposure and reduced masculine play in boys”
Swan, Shana S. “Environmental phthalate exposure in relation to reproductive outcomes and other health endpoints in humans”
McLachlan, John et al “Endocrine disruptors and female reproductive health”

Info about the national phthalate ban

Nicolopoulou-Stamati, P. and M. A. Pitsos “The impact of endocrine disrupters on the female reproductive system”

Post Script: So, how do I avoid phthalates anyway? First, the good news is that phthalates have a very short residence time in the body, as short as a day or two. So if you are successful in lowering your exposure, your body burden will decrease rapidly.  Due to the ubiquitous nature of phthalate use in consumer products, it is difficult, (but not impossible) to lower your phthalate exposure. Below are a few links with some good ways to start you on your way.

Saturday, August 11, 2012

Gender part seven: What they got wrong in Finding Nemo

Note: This program first aired on August 11, 2012.

Once upon a time there was an entertainment company, and they set out to make a film for children that was accurate about life in the ocean, but entertaining at the same time. They chose a clown fish for their main character, and featured several other real fish and animal species as supporting characters. They went scuba diving on real reefs, to see how real fish move, in an attempt to get their animation as accurate as possible. The film went on to be one of the top grossing kids movies of all time, and win four Academy Awards. You can guess by now I am talking about Disney’s Finding Nemo.

They got a lot right in finding Nemo, but there’s one thing they got wrong, really wrong. Here’s the thing about clownfish. Most of us know that they live in a symbiotic relationship with a host anemone, a creature that would sting and possibly kill most reef animals. What most of us don’t know is that clown fish live in  strict social groups, of usually 5-6 animals. At the top of the hierarchy is the breeding female. She is the largest of the group, and calls the shots.  The next in command is the breeding male. After that, the three to four smaller, non breeding, male fish.  This is how it works, the female is in charge, but if anything happens to her, everyone below her gets a promotion and bumps up in the hierarchy. The male becomes the female, and the biggest of the asexual fish becomes the male. So, when Nemo’s mom got eaten by that barracuda at the beginning of the movie, Nemo’s dad should have switched it up and become Nemo’s new mom, because clownfish are sequential hermaphrodites.

In clownfish, it appears that stress hormones control this process. Clownfish are born male, but switch to female when they fully mature. In a social group the breeding female keeps all the other fish in her group stressed by harassing them and limiting their access to recourses. This keeps them from developing fully and with their resources going towards stress hormones instead of growth, they remain male. If something happens to the female, the stress pressure is temporarily released, and everyone in the group has a bit of respite. They actually grow, and the largest male, the one that was the breeder actually gets to mature into a female, at which point, he starts harassing all the other fish again, and the cycle starts over. This is the sex change suppression model, the normal course of development is impeded by strict social control. Its important to note here that the normal course of development is a switch from male to female, the system in question just controls when that happens. The other main model of sequential hermaphrodism in fishes at least, is the sex induction model. This requires an awareness on the part of the individual fish of sex ratios or size ratios in a large group. When the ratio becomes too skewed, a sex change is initiated to rectify the situation. For you salt water aquarists, Sea Goldies and various species of wrasse are subject to this kind of sex change. 

Sequential hermaphrodism is common in many gastropods as well as a few flat worms, the random crustacean and even an echinoderm. None of these species are as cute, and screen friendly as Nemo though. Though I understand why Disney ducked this issue when it made the film, I think the world would be a more interesting and open minded place if parents had to explain sequential hermaphrodism to their children, and kids grew up understanding that when it comes to gender (and most everything else for that matter) the world doesn’t necessarily work the same way we humans do.


Interested in the challenges of animating a fish?

Personal communication, Dr. Ann Cleveland, Maine Maritime Academy, Castine Maine (once again, having a clownfish researcher for a boss has its perks!)

Interesting perspective on just how unique the clownfish transformation is:

 Abstract only online: Environmental Biology of Fishes
Volume 29, Number 2 (1990), 81-93, DOI: 10.1007/BF00005025 outlines the models of different mechanisms for sex change in fishes