Saturday, January 25, 2014

Bacteria, Diffusion, and Kombucha...

Note: This program first aired January 25, 2014.

One thing you should know about me, if you ever happen to be in my kitchen, is that I love fermented foods. I love making them and I love eating them. My refrigerator is packed with jars of kim chee, pickled cucumbers and turnip, fermented salsa verde and hot sauce. I use naturally occurring bacteria to do my culinary bidding. The bacteria make the food more digestible and tasty and preserve it long into the winter. The bacteria in all of my ferments are, if everything goes well, invisible. I see and taste their effects and by products, but never the bacteria themselves. In the past year I’ve embarked on another fermentation adventure; I’ve started making kombucha. Kombucha a fermented beverage made from sweet tea. Its very different from the other ferments I make in that the bacterial culture is present in a very visual way. Kombucha is fermented using a symbiotic culture of bacteria and yeast (called a SCOBY), and it makes a bit thick rubbery mat that floats on top of the tea in your fermentation container. The sight of it doesn’t bother me at all, but some other people in my family can’t stand the sight of it, and will never drink kombucha because it comes from such a weird looking gelatinous mass.

The culture forms a large mass because one of the bacteria involved makes cellulose, otherwise it is likely that we might not see much evidence of these bacteria and yeasts, which is how some of us like it. If individual bacteria could get big enough for us to see, they might look just like the SCOBY, gelatinous, slimy, and nondescript, putty colored. But individual bacteria can’t get that big, and there is a good and simple physical reason why. It has to do with the ratio between surface area and volume, and the process of simple diffusion.

Diffusion is the phenomenon of particles moving from an area of high concentration to an area of low concentration. It is, for individual bacteria, a passive process, it requires no additional energy to make it occur. Following the laws of the universe, as long as nothing impedes it, diffusion will happen all on its own. We talk about it in terms of bacteria because it is how bacteria get their nutrition and get rid of their waste. Nutrients diffuse across the cell membrane into the bacteria, because they are more concentrated outside than they are inside the cell. Waste products move in the opposite direction for the same reason. The rate at which things diffuse is determined by several factors, including the concentration gradient and the mixing rate. The biggest factor though is surface area. The more surface area, the more surface there is for nutrients to pass through. That is a good thing. BUT, the more surface area, the more volume. In fact, the volume increases much faster than the surface area does. At a certain point, there isn’t enough surface area to have enough diffusion to support all the biological activity that is needed to make that much volume survive. Nutrients can’t diffuse in fast enough throughout the bacterial cell. Waste can’t get out fast enough. This is why individual bacterial cells are limited in size. Simple diffusion can not support the metabolic needs of the cell once it gets too large.

These are organisms that have been engineered by evolution to make natural processes further their very existences. Life is the antithesis of entropy, the physical process of increasing chaos that occurs in the absence of the input of energy. Life is matter organized and perpetuated, but in the case of these very small organisms, they are using a bit of physics to further their biological prerogative. Relying entirely on diffusion has created physical limits that the bacteria must live within, but for them the trade off has been worth it. They have been alive on Earth longer than anything else by billions of years, and there are more of them than anything else living.

In thinking about this, I’ve realized this is the same way I’ve come to feel about winter, or summer, or rain. I can fight the cold, or the heat, or the damp, or I can accept it, and even incorporate it into the yearly cycle of my life. Yes, the cold of winter creates a limitation in my life, my ability to lounge about in a sun dress and flip flops, but these natural phenomena serve the natural parts of me in some way. The cold slows me down and draws me in, the heat opens and relaxes me, the damp hydrates me, all things I need at one time or another. It’s a lesson from the invisibles of this world, let nature work for you. And take full advantage of the potential of anything that is going to happen anyway. Things are complicated enough as it is.


The issues of diffusion and bacteria are very nicely summarized at this referenced blog:

Animal Winter Adaptations

Note: This program first aired January 18, 2014.

December was brutal this year, with sub zero temperatures, deep snow and ice storms. But now, merely a few weeks later, it feels like early spring. On my walks around various neighborhoods its not just my eyes and my skin that are fooled by the warm moist air. My nose has sensed a creature roused by the spring like conditions the past few days; my nose has been smelling skunks.

Skunks are in the family Mustilidae, or the weasel family. They are unusual for weasels in that their strategy for dealing with winter is to store food as body fat and while away winter in a semi dormant state, usually in a communal den that allows them to share body heat with other skunks. It is not uncommon for them to rouse periodically and even emerge from their dens if the weather is nice, that can explain the skunkiness of a warm winter day. They don’t have to come out and eat, if they are able to store enough fall food as body fat, there is no real reason for them to forage mid winter. They may just want some fresh air.

That body fat issue actually describes a line of demarcation in mammals’ winter coping strategies. The accumulation of body fat and the subsequent living off of it all winter long is but one winter strategy that Maine mammals can utilize. Carrying around a lot of body fat is a burden, animals that partake in this strategy generally don’t put on the weight until the fall, triggered by some kind of environmental cue (most likely shortening day length) that synches their circannual rhythm and initiates some kind of horomonal or physiologic change that increases body fat storage. Its worth noting that fat storage is the strategy of another group of animals that uses this to deal with winter in an entirely different way. Animals that migrate away from Maine in the fall spend all summer eating and fattening up to fuel their fall escape. It is common for them to travel hundreds of miles or more, and not eat during the journey instead burning the fuel accumulated over the summer.

Animals that live off fat for the winter are just caching food in a different form. Instead of stashing it in their burrows, they are stashing it on their bodies. It gives them the most flexibility in terms of whether or not they need to wake up and eat. Contrast the semi dormant fatty skunk or bear or the fully hibernating ground hog with the chipmunk. Chipmunks are often held up as “true hibernators”, but really that term doesn’t mean any one thing exactly. Chipmunks are different from skunks, bears and ground hogs in that chipmunks don’t lay on heavy stores of body fat. They build huge underground burrows and store as much food as they possibly can in them. If you watch squirrels and chipmunks at your bird feeder, you will notice a difference in their behavior. Red and gray squirrels will eat each seed one by one on the spot, as they find it. Chipmunks collect seeds, filling their cheek pouches and returning to their burrows to lay the seeds up for winter. They will spend all summer doing this. Then in the winter, they enter a torpid state, cued by cold temperatures. Torpidity means they have a lowered body temperature and much reduced metabolic function. They wake up periodically to eat. The more food they have stored, the more time they can stay awake, and the advantage of being awake is that they are less vulnerable to predators like weasels when they are awake. A torpid chipmunk can rewarm and arouse fairly quickly, in an hour or less, but that is still to long to ward off a predator’s attack. Awake or asleep, they will spend most or all of their time in a subterranean burrow, waiting out winter.

The last major category of mammal strategy is a bit counter intuitive. The animals that are the most active in winter, usually have little to no body fat. They may grow an extra thick insulating layer of fur, but body fat is a burden that would simply slow them down. Physiologically, fat is food stored on the body for a time when food resources are scarce. Animals that remain active all winter are animals who’s food sources are abundant in winter, so they have no need to store body fat. Red and Gray squirrels, weasels, and snow show hares all fall into this category. If you spend any time in the woods after a snowfall, you will quickly understand that these are the vast majority of the tracks you see, because these animals must constantly be searching for the food that will feed their internal fires.

And how about us? How do we deal with winter? We are tropical animals, evolved at low latitude with the sun high in the sky. But we are also animals who biologically made their last big leap in evolution during a period of glaciation, so lets not rest too heavily on that tropical animal gambit. It is true though that we do have temperature thresholds, above and below which we do not function effectively, we have to create a microclimate around us if the external environment does not match up with our operating parameters. This is especially true in the winter. Physiologically we are all active mammals in the winter, none of us enters torpor or hibernation, we maintain our body temperature, we eat, drink and eliminate. Yet, I see reflections of each of the animals’ winter strategies in the ways we live this time of year. Some of us spend a lot of time in our burrows, eating through our summer stores, others of us flit around on the landscape seemingly impervious to the temperature, and eating as much as we can. Two ends of the spectrum of the body’s reaction to winter, where do you fit in?


I’ve been reading Bernd Heinrich’s Winter World. Most of the material for this week’s show originates there.

What is Fire?

Note: This program first aired Saturday January 11, 2014.

If you are one of the 12 to 14 % of Mainers like me, who use wood as our primary or only heating source, you, like me, have been spending a great deal of time lately, attending to your wood stove. The recent ice storm and subsequent power outages, as well as the recent arctic cold have gotten me thinking about fire and our reliance on it. When the high for the day doesn’t get above zero, you know very concretely just how much you depend on that iron box of glowing embers in the middle of your house.

The reaction that causes fire is a combustion reaction, the rapid oxidation of a fuel (rapid being the key word here, oxidation can also happen slowly, like rust). In this case the fuel is wood; chemically wood is a carbohydrate, made of carbon and hydrogen and oxygen, and contains lots of other elements that aren’t part of the combustion reaction. When combustion happens, the bonds between the carbon and the hydrogen atoms break apart due to the input of heat, breaking bonds always takes or absorbs energy. In the course of the reaction, those atoms rearrange themselves into different compositions, and to do so they need to form new bonds. The formation of a bond, any bond, releases energy. Fire is hot, or exothermic, because the new bonds that form in the products release more energy than it took to break the old bonds in the reactants. The bonds in the reactants are in the wood. The bonds that form in the products are those in carbon dioxide, water, and other byproducts of fire. The difference in the bond energies of the players involved gives us a reaction with a temperature we can feel. This time of year, we only want exothermic reactions.

This is all well and good, but when I sit in front of the woodstove and watch the fire, I want to know, what is fire? What are flames? What is smoke? When you first light your fire, you need a spark, some initial heat to get the reaction going. What that initial heat is doing is vaporizing the wood. When wood is heated to approximately 300 F, volitaile organic gasses or VOCs are evolved, or released. Pure carbon, carbon dioxide and carbon monoxide can also be released at this time. Initially, these gasses and particles aren’t burning. They are what we call smoke. Smoke is primarily unburned VOCs and carbon particles. And the VOCs? Chemically, if you do the math and balance your equation, what you end up with as the formula for the VOCs is formeldahyde. Smoke, it turns out, is nasty stuff, and that nastiness is why the people who design, build and sell woodstoves put so much energy into clean burning technology. The next thing that should happen in your fire building progression is flame. Flame is the smoke, the VOC’s catching on fire, combusting. That is a good thing, it means the formeldahyde goes away, and leaves us in the best scenario, with carbon dioxide and water. When burning wood, complete combustion is not totally realistic, so unburned carbon, carbon monoxide, and even a few unburned VOCs can persist. It really depends on how much oxygen can reach the fire, and how hot the fire can burn. The hotter the fire, the more fully evolved the gasses, the easier they burn.

Additionally, when the VOCs are evaporated out of the wood, pure carbon, and ash are left behind. Once all the VOCs are gone, all you have left is char or charcoal. These are the glowing embers left behind when the fire burns down. They are still burning, but it is the pure carbon that is burning, so there is no gas left to evolve and make a flame.

Lastly, when the fire is out, all that are left are bits of unburned charcoal, and ash. Ash is everything in the wood that can’t burn, all the mineral components of the tree. There is still potential heat in the charcoal, but the ash is at the end of its role as part of wood, completely liberated from the biological structure through chemical emancipation. When you empty the ashes from your stove, you are closing the last of the great winter circles. The carbon, hydrogen and water have gone up the chimney. The minerals, the bones if you will, of the tree, you empty into a metal bucket and spread on the garden, the driveway, the icy path. You didn’t know you were running a tree crematorium did you? So scatter those ashes with respect and dignity, and gratitude for the trees of the future, the trees yet to come you are fertilizing.


Nice level headed info from the “How Stuff Works” website:

Wow, there are a lot of great videos on science on Youtube. Here’s one:

An amusing blog by Cecil Adams, a person who attempts to answer any and all questions:

Bangor Daily article citing census data on number of homes in Maine with wood as primary heat: (newer? numbers cited in a Portland Press Herald opinion piece put the number at 14%)