Native Plants, Habitat Restoration, and Other Science Snippets from Athens, Georgia

Friday: 18 February 2011

Yesterday  -  @ 07:31:56
Part 1. Waking Up.

The last five consecutive days have had us in the 60s with pleasant clear weather. We've had only six additional days above 60 degF since December 1, for a total of eleven. That actually beats last winter, when we had only eight days above 60 during the same period. But in the winter of 2007-2008 we'd had 28 days with temperatures above 60, and 29 such days in the same period 2008-2009. So no question about it - it's been a cold winter!

It's been just over five years since I'd seen my first armadillo on our property, Nov 23 2005. They had just reached our area. Since then I've only seen them occasionally at night, but their holes and grubbings are to be found everywhere. I suspect they've had a very significant influence on the ecology of the litter and soil beneath.

On yesterday's walk, I surprised this armadillo and he took off in a wide circle around me and up the hill. I was surprised at how fast they can move. He paused just briefly for a last look before zipping down his hole.

I'd spotted a butterfly a couple of days ago, but hadn't been able to see it clearly enough to identify it. Whatever that one was, this one seems to be a Question Mark, Polygonia interrogationis (thanks, Dale). It was taking a little rest break on a projecting buttress root overlooking Goulding Creek. I'd documented them previously Mar 4 2008 and Nov 19 2007, so quite a broad range of activity.

Part 2. Overdone Chicken.

The walk was interrupted, about half a mile from the house, by a page for a chicken house structure fire. The page was initially made to our sister FD on our southern border, but these sorts of calls tend to spread, so I made my way home just in time to get the call for a tanker from Wolfskin. Fire Chief Ed had been on a bike ride and stopped by the station on his way home to open up and get out the trucks, and the tanker was ready for me to take when I got there.

The route to the farms on Union Point Road, Hway 77, is over Hutchins-Wolfskin Road, a dirt road only partly gravelled, but it had at least not rained for a week or so. The road was fairly good, but it's also extremely long. I checked in as I turned in the drive to the farm, and just missed the cancel. So I got to stay there for a couple of hours as the only responder from Wolfskin. Chicken houses burn fast, and the main action is to keep the fire from spreading.

Part 3. Shades of Pleasantville.

About 9pm there was a page to that same FD on our southern border, for a location right on the border. Cat stuck up a tree.

But for a few hundred yards, that page might have been to us, and a life-long dream would have been fulfilled. As it was, a SECOND page had to be made to the lucky department - we would have responded instantly, and we have ladders too.

We followed the progress over the next hour, and indeed there were inquiries from 911/Central to query whether cat had been rescued. Eventually it was. I'm so jealous.

Sunday: 13 February 2011

Not the Way  -  @ 07:08:08
Here's what an exponentially growing sourdough culture looks like.

I stirred the culture down, mid exponential phase (left), got up a few hours later, and it was just about to come out of the jar. I don't know *what* would have happened if I hadn't gotten up early!

Besides the amusement factor, I had a reason for doing this. I mentioned, the other day, that the routine for making bread does not involve exponentially growing cultures (though you do try to inoculate your bread dough with as active a culture as you can). In normal bread making, you have a large number of yeast and bacteria organisms to which you add only three or four volumes of food. You typically have your bread in the oven within a few hours, not enough time for the population to reproduce more than once or twice, if at all. You're just taking advantage of what the beasts do with the food during the next few hours, and what they do is produce some flavors and lots of carbon dioxide. You are relying on the current generation of hopefully numerous and happy bugs, not ten or twenty generations down the line.

But I was curious to see if I could get a measurable exponentially growing culture, so I prepped a cup or so of fresh dough (no organisms), a bit wetter than what you'd be working with when actually making bread, and inoculated it with about a teaspoon of a starter culture. This is like adding 50 volumes of food to the culture, rather than three.

I measured the activity of the culture by measuring the height of the mixture in the jar. The plots below show relative heights on the y-axis. Don't worry too much about the height of the green curves - that has more to do with my increasing impatience to stir things down and get them started again, and sometimes a rush to get to bed.

For about eight hours, nothing much happened, as you can see with the leftmost green rise curve. Then the culture started perking up, and began to rise. Once a rise had gone just past doubling, I stirred it back down and the results are seen in the second green curve from the left, at the beginning of Day 2. The remaining green curves are just repeats of this process. (The absence of a green curve on Day 2 8 hours was because of the near overflow in the photos above.)

Why so many green curves? I had to do stirdowns periodically - ideally I'd just keep measuring the rise in culture, but I don't have a jar three feet high. You can imagine all the other complications of something like that.

The slopes of these curves reflect the rates of growth during the rise period, between stirdowns. It's rather hard to see the change in the slopes in that figure, so here's what a plot of these growth rates look like, versus time.

The growth starts out slow for the first 24 hours or so, and then picks up until it peaks between 40 and 50 hours, and then begins to drop back down. Presumably the yeast and bacteria have peaked in numbers, and are now rapidly using the remaining food available. At peak, the doubling time is just a little more than two hours. By 60 hours, what would have been a promising bread dough is now a starter culture of its own, wanting to be fed.

The consistenty and color of the exponential dough was up to the last quite different from a starter culture too. Whereas a starter is a buff or tan color, with a very sticky consistency, the exponentially growing dough was white, very elastic, and did not stick particularly. By the 60 hour time point, it had changed, literally overnight, to resemble the color and stickiness of the usual starter.

Now these are not direct measurements of yeast and bacterial reproduction. They're measurements of how fast the culture rises in the jar, so they reflect the amount of carbon dioxide being produced (plus a few other things that make this only the crudest of growth rate measurements). But it should be roughly indicative of the numbers of active cells, assuming they're metabolizing at about the same rate throughout.

It should be noted that there are several controls I should have been doing along the way. But I've already accumulated a half dozen mason jars of various sorts of cultures around the house and in the fridge, and we don't want to test the patience of the other residents of the house too much.

An occasional sacrifice of one of those jars for a production like Friday night helps for a few days, anyway. The fruits of our labors, and much better than a previous effort last week.

Later, I'll summarize what I think we've learned in terms of using sourdough starter as a source of yeast and bacteria for cooking purposes, but here's one thing:

We don't like to keep bread dough out at room temperature for 24-48 hours, waiting for it to rise. Besides the length of time, there's no telling what's also growing in it. That's two reasons for not going the exponential growth route. Instead we inoculate our six cups of flour with two cups of active starter, rather than a tablespoon, to hasten things along. We maintain our starter the way we do so other things don't grow in it.

How does this relate to commercial dried activated yeast in a packet? I suspect that if you were able to separate the sourdough yeast out from rest of the starter, you'd find that the dried, purified sourdough yeast would amount pretty closely to the teaspoon or so of what you get in that packet.

Thursday: 10 February 2011

Third Snowfall of the Winter  -  @ 06:46:49
Of local interest, 2.4" new snowfall accumulated last night after midnight, before ending around 6am. This amounted to 0.25" liquid melt, although 0.37" melted snow and some initial rain and freezing rain was collected in the rain gauge. Doubtless some snow melted.

We probably had an atypically high amount of snow here in Wolfskin. Or maybe Athens, reporting an inch or less, was atypically low. Now that CoCoRaHS reports are trickling in, it looks like outside of Athens at least doubled that. Nonetheless it will be gone by the end of the day, unlike the last delivery that lasted a week.

Also unlike the snow in those previous events, this one stuck to the trees.

With this event adding to the Dec 26 and Jan 9 snowfalls, our winter total is (so far) 10.6" of snow. That elevates us to second place in the records since 1920. First place is 12.0", in the winter of 1935-36. Pretty cool!

Monday: 7 February 2011

Louis Louis  -  @ 07:34:01
It may be a little pretentious, but I'm going to present this in the form of a scientific research paper, with a little more rambling chattiness than you'd generally see. I will play fast and loose with the references, with a few links in the text and notes of interest at the bottom - not the way scientific papers are usually done!


Wild sourdough starter cultures quickly lose the ability to evolve carbon dioxide gas after a feeding with a wheat flour and water addition. With the time frame of several days this is not due to the loss of vitality of the yeast and bacterial components of the starter community, but rather due to the exhaustion of easily metabolized organic nutrients.


Anyone who uses sourdough starter knows that you have only a limited period of time when the resulting bread dough is capable of maximum rising. After that period, you don't get much in the way of a rise. I set out to investigate the length of activity under conditions of feeding of the starter. Note that these are not the conditions of actually making the bread later, but I think we can do some extrapolations.

An established sourdough culture is a complex community of a number of species of fungi and bacteria. The fungus is probably the wild yeast Candida milleri, and the bacteria probably a number of species of lactic acid bacteria Lactobacillus. The community is an ecological symbiotic mutualism, with the yeast and the bacteria cross-feeding each other co-dependently, and the bacteria maintaining through the release of the waste product lactic acid a highly acidic medium that inhibits the growth of unwanted bacteria and fungi.

Both the yeast and at least a portion of the bacterial species release the gas carbon dioxide as they feed, and the release of the gas causes tiny bubbles to form in the medium. It's this accumulation of gas that causes the pudding (as it is for the starter) to rise to some point where it can no longer support itself (about 50% of the initial height, in my case). That rising, of course, is what bread makers want, since it produces a light bread instead of a dense tough cracker. In this experiment, the rising reflects metabolic activity and is conveniently measurable with a ruler.

Materials and Methods

An established, 2-month-old spontaneous culture of about 2.5 cups wheat sourdough starter in a quart mason jar was used for this experiment. After 24 hours without feeding, the starter was fed 1/4 cup wheat bread flour and 1/8 cup water, amounting to about 10% fresh food, by volume. This was stirred down, and then the height of the starter was measured over the next 4 hours as it rose. The culture again was stirred down, and the height again measured as the starter rose. This process was repeated as the starter aged up to 56 hours after the initial feeding. Temperature was maintained around 65 degF.


The figure below shows the height of the starter above the initial 8 cm level at various times after the stir down. Each curve represents the behavior of the culture as it rose following a stir down at the indicated time after the initial feeding. The maximum level of rise could not be sustained much beyond 50%, about 4 cm above the initial level, and measurements were not taken beyond the time to achieve this degree of rise.

Figure 1. Measurements of height of the starter at various times after stir down.

Figure 2. The rate of rise at various times after feeding.

The slopes of the apparently linear curves (i.e., the rate of rise) were calculated in units of cm/day for each of the above curves, and then plotted as a function of the time after the initial feeding.


Figure 1 above shows consistently that the longer the time after feeding, the slower the culture is to rise after being stirred back down. Figure 2 recasts the slopes of the multiple curves into a single curve showing the effective metabolic rate of the culture as it ages after a feeding. By four hours, the rate of rising is down 10%, and by eight hours after feeding the rate of rising is only 50% of what it was initially. By 25 hours after feeding, the activity is less than 20% of that of the first four hours after feeding.

One thing that is somewhat surprising is that there is continued activity, even if at a lower level, even 56 hours after feeding. This may reflect an ongoing food availability beyond what is introduced upon initial feeding. Bread flour contains not just 70% starch and 12% protein, but also sugars and much smaller starch fragments resulting from the milling process. These provide a more rapidly utilizable source of energy in the early times after feeding. In addition, bread flour contains alpha and beta amylase enzymes that were once a part of the wheat seed, and these enzymes help to break down the starch into simple sugars after they've been hydrated upon addition of the flour to the culture.

After a time, the culture may then become limited in growth to whatever simple sugars can be produced from the much longer starch molecules available. Such simple sugars would only result from the metabolic activity of the yeast and the bacteria themselves, for as long as the longer starch molecules remain as a resource. The 20% activity at 25 hours continues to drop, but may be sustained at 5-10% for some time, a result that is suggested by the shape of the curve in Figure 2 at long times after feeding.

Regardless, for cooking purposes, that 5-10% residual production of carbon dioxide by a starter (or dough) many hours after feeding is probably not very useful. A bread maker would probably call this a "dead" culture.

We are not observing exponential growth here. Exponential growth is seen when a small number of organisms are used to inoculate a much, much larger amount of food - scraping off a minute colony of bacterial cells into a half-cup flask of sterile nutrient broth will show exponential growth with appropriate conditions. The organisms double in number again and again.

We're doing the reverse here: we're taking a large number of hungry organisms, and adding just a little food in the form of flour, and then watching the result. So we don't see exponential production of carbon dioxide in Figure 1, rather, the rate of rise for each set of measurements is approximately, and startlingly linear, to a point. Over this time frame and under these conditions we're probably not getting much actual reproduction - i.e., growth - at least of the yeasts.

There are limits to the use of the rising of the culture as a way of showing metabolic activity. First, the starter itself will rise only so high in the jar, and then it seems that further production of carbon dioxide cannot support the weight of the starter medium. That represents the limit of how long we can monitor activity. Second, as the rate of carbon dioxide decreases at longer times after feeding, it's likely that entrained bubbles don't form as rapidly as the carbon dioxide diffuses out of the starter. And third, the consistency and composition of the starter itself will change as time goes on after feeding, becoming more or less stiff and responding differently to accumulating carbon dioxide. Still, I'm pleasantly surprised at how clean the results were.

What does this mean as far as making bread is concerned? This experiment used the conditions of the starter culture, which are not those of the final stages of making bread. For our starter experiment, we added a small amount of food relative to the volume of hungry organisms (about 1:10). When you're making bread you're adding three or four volumes of food to a volume of hungry organisms (about 30:10). There's a lot more food available, and therefore a lot more oomph in terms of rising. Even during the dough making process, though, we're probably not seeing exponential growth, especially in the short time frame involved.

My little experiment was probably done under hypoxic conditions, i.e., little oxygen. Each time I stirred the risen culture down, I probably did introduce a little oxygen into the starter, but I didn't take pains to do so, although I did try to do it the same way each time. Carbon dioxide is heavier than air and probably keeps the yeast in fermentation mode, which produces less rise. The yeast and bacteria don't care - both are able to deal with the lack of oxygen. The yeast will switch to a less productive metabolism, fermentation, in the absence of oxygen, though. Add oxygen, as Louis Pasteur did, and you'll get a lot more oomph, as food is more efficiently broken down to lots more carbon dioxide.

And that's part of what you do when you knead dough - you're introducing a lot of oxygen into the mass. You're incubating the mass of bread dough with a much larger surface area exposed to the air (and oxygen), and so rising bread dough is likely to be in an aerobic state for a good length of time. This means the yeast, at least, is using up its food much more rapidly (Lactobacillus doesn't use oxygen at all, even when it's present).

The differences in my experimental setup and the reality of making bread dough will tend to cancel out, and these times can probably be used for baking purposes as well. The ultimate result is the same - the dough will run out of steam, and probably within 4-8 hours after it's all mixed together. Enough for two rises, max. Don't expect your dough to keep on rising indefinitely.

Random Notes (not normally in a scientific paper):

I mentioned cross-feeding and co-dependency in the establishing of a mutualism in the starter culture. The wild yeasts are unable to metabolize the sugar maltose, which is a product of the breakdown of starch. The lactobacilli can utilize this sugar, and so the yeast are by accident cross-feeding the bacteria. The yeast don't mind the acidic environment that the lactobacilli create through their waste products, and so the culture is kept clean of other organisms.

Domestic activated bakers' yeast CAN use maltose, so lactobacilli will not be able to establish a mutualism with them - that key element of co-dependence is lacking. This doesn't mean you can't add activated yeast to the bread dough to give it extra oomph. You just can't use activated yeast to start a long term culture. The prediction is that the acidic environment would not be established and the culture would quickly become overgrown with awful nasty shit.

Starter cultures before making bread are usually hours or days past being fed, but they're still good. To get them motivated, goose the organisms prior to making bread: a "proofing" is normally done for a period of several hours in a 1:1 culture:flour/water mix before mixing in the remainder of the flour, water, etc., to make the dough.

The wild yeasts that are used to start a sourdough culture probably come in from the bread flour, and not the air. Occasionally an effort to start a culture would appear to fail - the flour and water mix would start bubbling and then would subside, even when fed. One possible explanation, via Peter Reinhart is that a competitor bacterium (becoming more common on wheat used to make flour) has temporarily gained a foothold and is interfering with yeast growth. The new culture may recover, but if acidity is not established it may be overrun with undesirable fungi and bacteria. Peter Reinhart's solution is to add some pineapple juice at the beginning, for early acidification of the culture that will prevent the growth of the competitor, but allow the lactobacilli and yeasts to establish themselves.

Bread makers put their rising dough in warmth, to rise, and that kind of warmth may be a little too warm for sourdough. It seems that the wild yeast prefer cooler temperatures, closer to the 65 degF I was using here, actually, and no warmer than around 80 degF. They'll stop metabolizing at higher temperatures. The lactobacilli are fine with warmer temperatures. So a warmer temperature rise work, since a portion of the lactobacilli will produce carbon dioxide, and you'll get a more sour dough, but the rise may actually be slower since the temperatures are too high for the yeast . A cooler rise will be less sour, but perhaps not so slow as you might think, since the yeast demographic is more active.

I can see that I'm going to have to make some changes in my starter growth conditions in the summers here, where we may be 10-20 degF above the yeast optimum for significant periods of time.

I enjoyed reading through Wild Yeast Blog's five myths about sourdough starters. This includes mention of the famous San Francisco sourdough starter, also addressed in this short Discover article.

The old Usenet newsgroup (remember Usenet?) keeps its sourdough FAQ here. Lots of interesting stuff.

Since pizza is such a fine topic, you'll find a lot of discussion of the perfect pizza and how to achieve it at Jeff Varasanos' site. Sourdough is discussed there too.

Saturday: 5 February 2011

No  -  @ 10:39:49
"Yeast is a microscopic plant of fungous growth, and is the lowest form of vegetable life. It consists of spores, or germs, found floating in air, and belongs to a family of which there are many species."

So much Wrong, so much Wrong.

Found copied and pasted into too many websites to even begin to try to find the murky origin. Sounds like it came from my 1930 vintage botany book ("bacteria are tiny colorless plants that do not do photosynthesis"). But as Glenn commented, if it's on the web it's gotta be true.

Heaven help us all. ; - ) 

Thursday: 3 February 2011

The Month of January  -  @ 15:35:31
It's The Month of January, Number 60 in a series, which means I began this five years ago. The word for January is "winter." I'll say more about this, but it's *winter*, and it gets cold in winter. The weird thing for the eastern half of the country isn't that it's cold, for this month it was not particularly so on average - it's been *wet*, and that is the answer to the silly rabbits clutching the pearls over all the snow. And why has there been so much water in the atmosphere?

Here are the usual temperature anomalies products, at the National Weather Service Climate Prediction Center.

Again, the western US experience differs: it experienced somewhat warmer than average mean temperatures in many places, but not nearly so much as in December. Again, the eastern US experienced its own reversal, with colder, but not all that much colder, temperatures in much of the east. And again, this was not nearly as extreme as in December, when many places felt temperatures 8-10 degF colder than normal on average.

What's interesting about these panels is that the daytime highs were much more anomalously low than the nighttime minimums, in the east, and similarly in the west. Things just didn't warm up much during the day in the east, and cooling down wasn't commensurate at night. Presence of clouds (water vapor), at least in the east, would be a reasonable hypothesis here.

We find the National Weather Service Climate Prediction Center's precipitation plots here, and this time the plot may be accurate. What's interesting here is that although there was so much snow in January, especially in the east, the total precipitation was actually considerably lower than normal most places. Doubtless you'd find a lot of eastern incredulity in those extensive brown patches that got so much snow in January. And yet our measurements of liquid water confirm this. It just doesn't take that much water to make a whole lot of snow - it just has to be in the atmosphere.

For Athens:

For Athens, our December temperatures had averaged 7-8 degF lower than normal reflected in both daytime highs and nighttime lows, the latter breaking records on two occasions. January was cooler, but not nearly so extreme, and that's consistent with the temperature anomalies above. The big news was our snowfall, of course - 5.4" here in Wolfskin and we didn't get as much as some local areas. Along with the snowfall in late December, we've had 9.2" this winter, we're in fourth place for highest recorded winter snowfall. The *current* winners: 1935-36, 12.0"; 1982-83, 10.6:; and 1939-40, 9.8".

Here is my plot of low temperatures, this time, for the month of January in Athens. As usual, the black dots are for the years 1990-2009 (black dots), 2011 (green line), and 2010 (red line).

To me it's remarkable how seldom all the weather pornographers have noted that much the same sort of winter we had last winter has repeated itself this winter, at least in much of the east. More snowfall, somewhat lower to much lower temperatures. This is all due to the Arctic Oscillation, which carries its own grim message. The parallels to last January can be seen this Januarry too. Certainly cooler than normal, and for a lot of the month except at the beginning and for a short period at the end.

January was still not abnormally cooler - only by 1-2 degF over the month. While we had only one day warmer than one standard deviation above the mean, I'm very surprised to see that we had only 4 nights cooler than one standard deviation below the mean. It seems that while things were cooler overall, they were so continuously, with no real extremes or much in the way of breaks of warmer weather. We didn't break any record lows and didn't even come close. It was just continuously cooler.

The figure below shows the Athens precipitation data which are official for our area. As usual the green line shows our actual rainfall, the red shows the average accumulation expected. The black dots are rainfall over the last 20 years, the vast river of peach shows the standard deviation.

In January, we started out with a surplus after a big rain the first of the year, but in the end Athens received 3.32" precipitation, lower than normal rainfall. Same true for Wolfskin, which finished out the month at 3.69" liquid equivalent, and for January 4.69" is normal. A third of that liquid came as snowfall at the end of the first week of the month, which persisted until the end of the second week as a mix of ice and snow.

Checking back at this neat prognosticator, our local area is predicted to have colder and wetter than normal temperatures and precipitation for the next couple of weeks and then to go to the more typical warmer and drier La Niña influence in the southeast. But that's been the case all winter, and the prognostications readily admit that for the long term they're making longer range (one to three month) forecasts based on the La Niña weather pattern currently in progress. That's proven to be wrong all winter, but what can you do with an unleashed, largely unpredictable Arctic Oscillation?

ENSO stuff:

Without fanfare, La Niña has been declared sometime in the last month. Of course now that it's real, we know it to have begun back in July 2010.
La Niña is expected to continue into Spring 2011, at least. What was up with January was the same thing that was up with December, which over at least the southeast portion of the continent was decidely non-La Niña in its temperatures, if not precipitation.

As was true last winter, especially in January and February, we were under the influence of a deeply negative Arctic Oscillation. This pattern of sea pressure, as well as its close relative the North Atlantic Oscillation, is like a dam between the arctic and lower latitudes. At high positive values of the index, the dam is strong, preventing the incursion of cold air. At negative values, the dam breaks, cold air flows southward, the eastern US and Europe typically get much colder than usual temperatures, and the arctic loses much of its cocoon of cold.

Interestingly, the AO operated similarly last winter (I mentioned this March 1) when we were under the influence of El Niño, and again in January when we are under the influence of La Niña. It seems that in the winter, the AO trumps the influence of the ENSO, regardless of which phase it's in.

Unlike the ENSO, whose phases persist over many months, sometimes more than a year, the AO and NAO fluctuate over periods of days and weeks. The AO is difficult to predict, but tentatively it's expected that the negative index will not hold for the rest of the winter. If it becomes positive then we'd expect a more normal, warmer winter influenced more by La Niña.

NOAA's Monthly State of the Climate product for November is now up - January has appeared, and so has the State of the Climate for 2010. Detailed explanations for weather events occurring during November(or whatever month is current) can be found for the several sections of the US under the National Overview. There are many interesting weather- and climate-related items to be found here.

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