Month: February 2014

Our Mutual Friend

What species has been domesticated for thousands of years, lives in our homes, helps to feed us, comes in different strains (‘pedigrees’), was one of the first to have its genome sequenced, and has limited alcohol tolerance—like us? I’m not thinking about one of our furry friends, but we would soon miss it.

I was musing about yeast while the breadmaker pounded dough to a low drumbeat in the kitchen. We don’t normally regard yeast as a companion species, but it has been with us longer than dogs or cats. It has had a much greater impact on human culture than either of them, and all because of the peculiar way it generates energy for life—by fermentation.

This is one of the first processes we learnt about in biochemistry class, and one of the simplest. Yeast cells possess an enzyme (zymase) that converts 1 molecule of glucose into 2 molecules of ethyl alcohol and 2 of carbon dioxide. Alcohol and gas are just waste products to these cells, but gifts of the gods to us. We have been harnessing fermentation to make bread and drinks for thousands of years before we figured out how it worked. The transformation of a heavy lump of dough into a light loaf of bread or a cloudy ‘must’ of grape juice into wine seemed miraculous to our ancestors.

And wine that makes glad the heart of man…and bread that strengthens man’s heart (Psalm 104)

The man or woman who first discovered fermentation has gone unrecorded, although archeological relics suggest it was in Egypt and the Middle East thousands of years ago, perhaps in Neolithic times. Like a number of great discoveries, the breakthrough probably came not to someone searching for a better bread or drink, but to a quick-witted person whose curiosity was aroused by changes in a lump of uncooked dough and a jug of fruit juice left out in the warm. Instead of discarding them, as most of would, he or she watched the natural experiment develop and tested the product. It was good. They had no notion about the underlying biochemistry, and it took a long time to realize that the process that raised dough and fermented juice were the same.

France’s greatest 19th Century scientists were engrossed with the process because the wine industry struggled for vintages of consistent quality and that didn’t spoil. Their names come straight out of textbooks—Lavoisier, Gay-Lussac, Cagniard de la Tour, and above all Louis Pasteur.

It is hard to put ourselves in the mind of people who until fairly recent had no clue that fevers, ‘fluxes,’ and biological decay are caused by microscopic organisms. Yeast, bacteria, and sperm (‘animalcules’) first came into view under the simple microscopes invented by the draper of Delft, Antoni van Leeuwenhoek. That was two centuries before Louis, the genius who unveiled the world of tiny things and announced a ground-breaking germ theory of disease.

He had an uphill struggle. Many fellow scientists were unconvinced that fermentation is caused by living cells, and they don’t need oxygen to ‘breathe.’ It was thought to be a purely chemical process, and the debate grew bitter with Justus von Liebig, a German chemist who can be claimed to be the Father of Marmite (concentrated yeast, see Post March 23, 2013). When knowledge is familiar and deeply-rooted it’s hard to understand there was ever a contrary view. It seems obvious that yeast is a living thing. Poured into a lukewarm sugar solution you can see them generating gas bubbles from ‘breathing.” Bake them in bread and they die. Transfer a few into a vat of nutritious fruit juice and the broth soon ‘boils’ (Latin fervere, hence fermentation).

The domestic and industrial applications of these energetic little friends are endless. As a dietary supplement yeast is unrivaled as a source of B complex vitamins. Yeast fermentation is used to make other liquors: kumis from milk/ kombucha from tea/ kvass from rye/ soy sauce, tauco and doenjang from soybeans/ root beer from sassafras (until it was declared carcinogenic and replaced). It didn’t matter if the alcohol content was low so long as there were bubbles. Fermentation of cereals looms large for manufacturing biofuel so our automobiles can run on 10% alcohol. Yeasts are used as low cost bioremediators to mop up pollutants like, including copper, zinc, nickel, and arsenic in groundwater and ponds. They even render safe the explosive TNT!

But our friends, domesticated baker’s and brewer’s yeast, have shadier relatives that also like to find a sweet place to call home. Yeasts spread by air or contact can spoil foods and on our bodies they have a particular fondness for orifices. If our immune systems did not protect us from pathogenic species we would soon succumb to them, and patients with weakened immunity need treatment with fungicides to protect them.

But when home bread makers get together the talk is positive, and only about the staff of

Home made bread
Half eaten, and it’s still warm!

life, exchanging formulas, and recommended suppliers of flour and yeast. Not all are loafers like me, happy to let a bread making machine do the hard work. Some of them love the exercise of beating dough, and a few use such violence that I wonder what is in their minds.

When two cycles of kneading and resting in the machine are complete I haul the dough out. I love how a sloppy mess of ingredients changes into an elastic, living ‘organism’ at blood temperature. I punch it down for a final rise (‘proofing’) in a baking tin before sliding it in a hot oven.

Bread making brings out the experimenter. My current favorite recipe for making a 2 pound loaf is:Bread recipe

It takes barely 15 minutes hands-on to make a loaf, but an eternity to cool enough for cutting the first slice.

Home made wine
Vintage label from our wine cellar

Alas, home wine making from berries (even grapes!) takes so much longer. I don’t have the patience. It was disheartening to open a vintage that was tenderly stored for a couple of years only to find it was contaminated with something that made it sour. Louis might have chuckled that I should have washed my feet before trampling fruit.

But if a recipe goes wrong I blame myself, not the yeast. Humans have shared life with yeast cells for thousands of years in a cooperative relationship that ecologists might call mutualism. We give them sugars to grow and they give us alcohol and bubbles in return. We are mutual friends.

Next Post: Dog Smart

The Wolf Sharing my Fire

Lilah by firesideThere is something incongruous about the notion that the golden warming herself by our fire is still mostly wolf. It doesn’t fit her doggy nature. But how much shaggy wolf is still inside her remains a moot point.

They are members of the same species, share a common ancestor and have nearly identical DNA. However there have been ~20,000 years of domestication in the making of modern Max and Molly, which offered plenty of generations for molding their behavior and appearance. It really does matter how much wolf still hangs on in dogs because it affects attitudes and how we train them.

We all know what wolves are like, or thought we did, and will never forget the Grimm story of Little Red Riding Hood.

Little Red Riding Hood by Grimm

It is paradoxical that the closest relative of our best friend is one of the most reviled

Little Red Riding Hood
“All the better to see you with” Walter Crane (1845-1915)

creatures, an arch-enemy of farmers and shepherds, and the fount of so many myths and scary stories about blood-thirsty wolves and chimeric werewolves.

Even biologists held hard views about wolf society until recently. The pack was regarded as a hierarchy topped by an alpha male and an alpha female which claimed first rights to a carcass and kept discipline in the lower ranks. Peace was preserved by a mien expressing threats of aggression towards subordinates who responded with submissive gestures. This fierce portrait reminds me of feudal societies in which royals and nobles used to rule vassals by accepting homage in exchange for privilege. So inured are we to old assumptions about these animals that attitudes can resist the challenge of research throwing fresh light on their behavior.

The TV celebrity Cesar Millan evidently bases his dog training program on an outdated picture of wolves (The Dog Whisperer/ Leader of the Pack). If it seems unfair to use him as an example I’m sure he knows that being picked on is the price of winning public attention. He certainly deserves admiration for a talent in handling difficult animals and his endeavors to save and rehabilitate abandoned dogs. But he makes no apology for the conflict between his philosophy and science: “Once your dogs see you as their pack leader, the dog on dog aggression will stop as they stop fighting for dominance because you will be their calm-assertive pack leader.” He believes we must become accepted as leaders of our pets’ “pack.” Since dogs strive for dominance, we must firmly lay down rules and boundaries for them, otherwise we lose control. This disciplinary style has sometimes gotten him into hot water with humane societies, despite so obviously being an animal lover. Nevertheless there is surely a risk that this thinking can be used to justify the harsh and cruel treatment that dogs have suffered down the ages. The victims may not even understand why they are being punished.

Another TV presenter Victoria Stillwell (It’s Me or the Dog) trains dogs in almost the opposite way, as her website name implies, Positively. Her policy is to shower them with love and treats to reward good behavior, which we might call positive reinforcement. According to Victoria most trouble with dogs is their owners’ (our) fault, so we need at least as much education as they do. Sometimes a cameraman on her show catches the expression of a dog looking on “sympathetically” at its owner being grilled by the bossy Englishwoman.

Of the two views, Millan’s is harder to reconcile with the new understanding of wolf society. Extrapolation wolf→dog is becoming blurry.

Gray wolf
Gray wolf. Courtesy US Fish & Wildlife Service

Until recently wildlife researchers had to fall back on zoos for studying these animals. But in captivity packs are loose associations of individuals that seldom share a family history and live in confined spaces. It is not surprising in an artificial environment that animals are anxious and find ways to adapt behavior to avoid injury from those famous fangs. But we have probably misread some of their gestures, like the lowered head which was interpreted as submission to a supposedly superior wolf. This posture is actually an excellent position for grabbing the “boss” by its throat, but perhaps it had a friendly meaning and was cementing a social bond. We can’t be sure.

The new picture of wolf society has emerged from studies under natural conditions by tracking wolves wearing radio-collars and with GPS technology. Blood samples revealed genetic relationships within packs (L. David Mech & Luigi Boitani, Wolves: Behavior, Ecology and Conservation, Univ. Chicago Press). Contrary to impressions of a band of bushwhackers banded together under feudal leaders, a pack turns out to be just a family party. Its members are usually close relatives, and often former cubs that never split away from their parents. Sometimes an animal adopts the solo life, but they benefit from sticking together when there is big game to be had, like moose and bison.

We expect more cooperation than competition within families. Members are more loyal and less aggressive to each other, and the greater harmony boosts success in hunting and breeding and avoids danger and injury. Consequently more genes are contributed to the next generation to shape evolution of the species, as predicted by kin selection theory. Besides, no dominance hierarchies have been found in wolf packs apart from the relationship between Dad, Mom, and their offspring. Nor should we expect to find them in dogs. When they go wild, they never become wolf-like in behavior or jostle to create a hierarchy, although they can form a fractious group. There appears therefore to be no teeth to Cesar Millan’s belief that successful dog training requires us to fill in for the tough alpha wolf depicted in old stories.

If we think we know dogs I suspect that familiarity often blinds us to the marvel and mystery of our furry companions. While their wolf cousins are afraid of us and terrified of fire, dogs are comfortable with both. Sociobiology theory rules out altruism in animals and caring for the welfare of others unless they are genetically related, but there are remarkable examples of untrained dogs that have saved lives at their own risk (see Hero dog drags another dog to safety).

John Bradshaw, a British biologist, explains Dog World by taking us back to the origin of the canine family about five million years ago (Dog Sense, Basic Books). The Swiss Army knife is his metaphor for the genome of “proto-dogs.” Flexibility enabled their descendants to spread across six continents and evolve into many species of jackals, foxes, coyotes, and wolves. Perhaps it was this adaptability, he argues, that made domestication from wolves possible, and the emergence of an animal with greater loyalty and willingness to please us than any other.

I was musing about dogs while Lilah was dozing at my feet and sharing heat from logs on the fire. She opened an eye to check I was still there. It wasn’t an anxious look waiting for instructions from her alpha male: she was only looking at her “dad.”

Next Post: Our Mutual Friend

Groundhog Day

My groundhog day will arrive when the raider of our strawberry patch sits in the cross-hairs of my sights. Last year the little ‘hog’ grazed it to the ground, leaves and all.

A neighbor over the fence told me he often sees our groundhog padding across his yard towards our back forty. I imagined the critter was a little larger than a guinea-pig with a snub nose, but my friend stretched out his arms.

“Whoa, that’s a giant!” I guessed it was a fisherman’s tale, but apparently not. After a

snow tracks
Groundhog, rabbit and deer tracks in the snow

heavy snowfall Tuesday night I found his broad tracks mingling with those from rabbits and deer. Evidently, our raider was on the rampage again, even while his northern relatives are still curled up in hibernation to give gardeners and farmers a break—all the critters except one.

There is a groundhog that has made the little Pennsylvania town of Punxsutawney famous. To other nations, it is a mystery why a country with a long history of hunting and extirpating animals devotes a whole day to Groundhog, which falls after Martin Luther King Day and before Presidents’ Day. It could only happen in a nation of animal lovers.

Phil boasts more titles than any European royalty, but his celebrity status rests on a reputation for being the only true weather forecasting groundhog. On Groundhog Day, he emerges from his burrow to be presented on stage at Gobbler’s Knob in front of his

followers and TV cameras. There he informs his Inner Circle of grim-faced men in black frock coats and top hats about the weather for the next six weeks. If Phil sees his shadow winter weather will continue; if he doesn’t see it we can expect an early spring. It’s a question that everyone is interested in after bitter weather from the polar vortex.

The tradition was brought to the USA by immigrant farmers from Germany where badgers were the seers. According to an old proverb: The badger peeps out of his hole on Candlemas Day and, if he finds snow, walks abroad; but if he sees the sun shining he draws back into his hole.

Predicting the last day of frost and higher ground temperatures has always been important for spring planting, and farmers often looked to nature for wisdom—when animals came out of hibernation or the thickness of their fur coats or the crop of winter nuts and berries. You can see why people thought these were signs, but not how they work. But perhaps when anticyclones are ‘parked’ for days or even weeks over the continent in winter, which creates calm, clear and cold weather, people associated the sunshine and shadows cast by them with continuing cold. At least that’s my theory for Punxsutawney Phil.

CandlemasGroundhog Day coincides with Candlemas mid-way between the winter solstice and spring equinox. The day was probably marked in pagan calendars, later becoming a Christian Feast Day when candles were blessed in churches like a festival of lights and when it was time to predict the change of season.

If Candlemas Day be fair and bright

Winter will have another fight.

If Candlemas Day brings cloud and rain,

Winter won’t come again.

Phil’s reputation suffers when his predictions turn out wrong, but how can one groundhog predict the weather across all the climatic zones of a continent? Minneapolis and Miami are totally different. I decided to check his record over the past five years at the closest major weather station to his burrow—Pittsburgh PA. As a Pittsburgh Steelers fan I think he’d approve my choice.

The average temperatures for February and March in 2009-11 and 2013 were all rather cold, although he only saw his shadow in two of the four years. And after he saw it again in 2012 the following two months were 10°F warmer than normal. Looking further back, he seems to have been right 50% of the time, which is what you’d expect for a binary choice by a statistically astute groundhog.Groundhog forecast

Like traditional weathermen and almanacs, Phil’s reputation is based on a long history of record-keeping. He announced his first forecast in the long winter of 1887-88, and is undisputed as the oldest groundhog in the world. Most of his kind survive no longer than 6-8 years in the wild (hopefully less in my yard), but his longevity is owing to a secret elixir that he sips at his summer picnic to keep him young. When you notice his coat color has changed from grey and grisly to brown and sleek you know that he has been rejuvenated again, which is more times than Doctor Who of the British TV sci-fi series.

Shortly after dawn this morning, Phil’s big day arrived. He faced followers who had temporarily forgotten about the Superbowl. Soon enough we were told that he had seen his shadow, so there are six more weeks of winter ahead. Quite how he managed to see his shadow on a rainy morning with cloud cover down to 400 feet mystifies me. Oh well, it’s just a bit of fun!

Next Post: Lovely Lilah

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