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

Sunday: 30 August 2009

Two in One  -  @ 05:14:24

I've thought I was behind in my Microstegium pull, year seven, but scanning over blog entries from last year convinces me I'm at least where I should be.

This is a section of middle Sparkleberrysprings Creek, looking downstream for about twenty feet (yesterday was a cloudy day under the canopy). It was to be a before/after shot, but the before shot was apparently taken through a fogged lens. Though interesting, it wasn't that interesting.

As I rounded the bend in the background I was dismayed to see a massive infestation of what turned out to be about 700 plants of all sizes. What you see here is the after shot. The plants you see include Christmas ferns, southern ladyferns, rice cutgrass, and quite a few other species in lesser numbers.



I'm not sure how many plants were pulled along this particular section, last year, but yesterday it was 2047 plants, here, and above and below. Last year it was 7600 plants along the entire 1000-foot creek length, so there seems to have been a significant incursion, and probably from upstream of our property.

What has happened, I think, is that this section has become a Microstegium trap. Two years ago that was a relatively fast-running stream course over a rocky bed. Then a heavy storm washed debris down, which became trapped against the fallen tree you see in the background. Over the past year the sand and mud has accumulated to a depth of a foot or so.

And with it has accumulated the weed seeds that wash down from upstream of where the creek enters the property. I've hiked along that portion quite some distance up, and there are vast stands of Microstegium. In the two major March floods we've had, one in 2007, the other this year, I would guess that a flush of seeds made their way and were dropped along with the sand, silt, and debris. The infestations are fairly localized, and always on the inner curves of bends where deposition occurs to make broad banks.

In this case, though, the leaky dam across the stream was responsible. There's always the temptation to clear the stream of the treefall and debris, but I'd rather leave this alone. The buildup of sand and mud has allowed the growth of plants that wouldn't otherwise be there, and the leaky damming has given us the mixed gift of concentrating the Microstegium instead of dispersing it further downstream. Eventually that debris will give way on its own and the mud and sand will be washed away - in the meantime it creates an interesting microenvironment.

The idea of a Microstegium trap is interesting, and I'm wondering if it could be put to advantage at the upstream entry to the property. The idea would be to create a similar diversion onto an adjacent bank that might trap and divert onto a "killing field" whatever infusion of seeds future floods might bring. That would act as a sort of barrier for downstream, preventing a large proportion of seeds from making their way further.

Just above that point, I was delighted to find a crop of chanterelles. We seem to have two major species of chanterelles. There is the Common Chanterelle, Cantherellus cibarius, which is much larger, sort of a yellow or buff color, and a more typically irregular chanterelle shape. Although I haven't seen these in several years, prior to that there would be very populous, spectacular emergences. (Retrospect is often informative: that link is to almost exactly three years ago; it was the last time we had a major emergence; we haven't had one since. Before that it was an annual event.)

Then there is this species, probably C. cinnabarinus, Red or Cinnabar Chanterelle.



Red chanterelle has a more typical mushroom shape than the other species, but the ridges (rather than true gills) that extend down the stem, and fork at the edge of the cap, mark it as a typical chanterelle.

Just about all but possibly one species of Cantharellus are edible, and choice. All references caution against the poisonous "lookalike" Jack O'Lantern Mushroom, Omphalotus olearius. The differences, especially the false gills of the chanterelle, are fairly obvious though.



Saturday: 29 August 2009

Here Comes the Sun  -  @ 06:57:53
There's always a good reason to review the planetarially important El Niño/La Niña cycle, for we all forget how it works, but this is a particularly opportune time for two reasons: we are entering an El Niño phase, and a solar minimum is coming to and end. Over the next five years solar activity will increase to a peak sometime in 2013.

What is the variation in solar activity? The sun's variation in activity is only about 0.1% from its quietest to its most active. But a paper (Meehl et al., Science 325, 1114 (2009)) in the most recent edition of Science presents a model for explaining some of the more subtle effects of even these tiny changes in solar activity on the El Niño/La Niña cycle.

To give it away, solar activity at its maximum tends to enhance La Niña events, and probably to suppress El Niño events. Conversely you might imagine that an El Niño at solar minimum (such as we are in) has the potential (other things being equal) of being particularly strong. (Notice that this is *not* to say that solar activity *causes* the El Niño/La Niña cycle, but that it has an influence that might now be modeled.)

Let's start with a reminder of what the El Niño/La Niña cycle is, roughly, before we enter the northern hemisphere winter. In the figure below, we're looking at a cartoon of the equatorial Pacific Ocean basin, with west on the left and east on the right. I like my clouds and lightning!

There are other things that are going on. The trade winds (green in the figure below) are not the ultimate cause of this phenomenon, since surely there is something more that causes trade winds to vary in their strength and sometimes direction. However, in normal years the trade winds blow east to west, driving warm 1equatorial waters (orange) across the Pacific. They actually blow warm surface waters west to pile up in a phenomenon called the westward intensification, and that's what you see here.

One consequence of normally blowing trade winds is that cold bottom waters (dark blue) in the east are pulled up to the surface (upwelling), providing the nutrients and oxygen that support abundant fish populations along the west coast of South America.



You might consider a La Niña to be a sort of a super normal condition, where trade winds blow even more strongly (the insets here are of sea surface temperature anomalies, from NWS-CPC):



In an El Niño, such as we are entering, the trade winds slow, and may even reverse direction. The pile of warm water sloshes eastward across the Pacific, bring upwelling of cold waters to a halt and moving the location of precipitation eastward.



With all the attendant effects of an El Niño it's good to present from the NWS-CPC this figure.

The top panel let you know, if you live in North America, about what to expect this winter. The bottom panel might be interesting in terms of comparison with last winter and spring, and even into the early summer, when we were in a La Niña and its lingering aftereffect.

Looks like Bev need not go to Arizona for warmth, since that will be the case in Ontario. She'll enjoy a rainy winter in Bisbee, considerably different from last winter.


Now on to solar activity. Sunspots are a rough indicator of solar activity. It may be counterintuitive, but generally the more sunspots the greater the activity and output of radiation. We've been in a period of low activity, with very few sunspots - the fewest in a minimum, since 1913.

As usual Richard Kerr does a good job of explaining the significance of the Meehl, et al. paper linked to above. I don't get the impression that there wasn't a qualitative explanation for the influence of solar activity on the El Niño/La Niña cycle, but rather that it wasn't modeled adequately with current global climate models, so failed to explain the larger amplification of solar cycle effects that are actually observed. Consideration of the influence of the stratosphere seems to be the report's contribution.

Since we don't have our brains programmed with a GCM, let's look at what's happening qualitatively. It all has to do with evaporation at the equator and influence on the trade winds that result.

In increased solar activity, evaporation is enhanced at the equator. Rising hot moist air moves north and south, forming clouds and eventually precipitation, which drives the trade winds westward. However, quantitative is important too, and the simplistic "bottom up" explanation doesn't seem to add up in the current GCMs. The trick was to convince the GCMs to simulate this pattern and that seems to be what the authors have done.

They incorporated the 11-year solar cycle into the models by adding considerations of the stratosphere to the "top-down" approach. Top-down refers to the warming of the atmosphere, and here particularly, the stratosphere. Increased ultraviolet radiation during a solar maximum produces more ozone in the stratosphere, especially above the ITCZ. The thickened ozone itself then absorbs UV, converting it to heat (ozone, in this way, acts as a greenhouse gas). This inhibits cloud formation and precipitation until the moist air has travelled north and south, where it dumps unusually heavy rain, producing even stronger trade winds. When they included these considerations, the output of the models more closely reflected the amplification of the tiny variations in the solar cycle.

Here is a figure from their paper that shows the precipitation changes over the Pacific, both measured, during a solar maximum, and modeled (below).

One thing to notice is the vaguely La Niña-like precipitation pattern, with abundant rainfall in the west and more importantly, reproduction of rainfall north and south of the equator, with reduction at the equator itself. Again, it's not to say that solar activity causes the El Niño/La Niña cycle, but that it influences it. And the trend of influence is in the direction of La Niña-like conditions. It's probably of some interest to point out that such a trend would lead to increased North Atlantic hurricane activity during solar maxima.


Now, that's a pretty crude analysis, but then I only play a climatologist on the internet, and so fortunately there are those who can better interpret the results and significance of the modeling. The Richard Kerr summary suggests that not everyone is impressed. I suspect RealClimate will have something to say about this soon.

1When I say "equator," I mean the intertropical convergence zone, the ITCZ, the meteorological equator. It migrates northward and southward with the seasons, so only coincides with the geographical equator twice a year. It's this annual cycle, incidently, that leads to monsoon seasons.


Thursday: 27 August 2009

Short Shameful Confession  -  @ 10:11:04
Television in the 60s. Practically worthless. But while I may have abandoned it by the mid 70s, at 13 years old in 1967 I loved "Dark Shadows". So it is that in the last few months I've gotten hooked on the youtube, and have spent 389 minisodes x 10 min = 3890 minutes, or about 65 hours watching "minisodes" of it. I get home late at night, write up my online student evaluations, and then I treat myself to the couple or three minisodes that have been put up that day. Glenn and my sister Susan have no idea what to make of me, but I've no difficulty getting off my high horse and slumming with the lowest. And just before bedtime, this invariably gives me a much needed laugh.

If you were of a certain age in 1967, and around here I may be the only one of that certain age, "Dark Shadows" was an irresistable draw. Those somewhat older than me were protesting the Vietnam War and those younger probably missed it, but who cares?

For those who don't know, "Dark Shadows" was a gothic/supernatural soap opera that premiered in 1967 and lasted about four seasons, with about 1245 episodes, if I have the count right. Like all soap operas, it was perpetually guaranteed embarrassment, as you followed the antics of people who don't exist, doing silly things that really don't matter or make sense, and trying to convince us of portentious events that couldn't happen, but at the age of 13 I loved it.

So did everyone on the schoolbus ferrying us to Oakwood Elementary School in Oakwood, Georgia. In a way, this was somewhat important, since I had very few interests in common with these rural bumpkin children otherwise. We could all get into "Dark Shadows," though, for "Dark Shadows" was the first soap opera targetted to kids. Many were the hot debates on that schoolbus, driven by an undoubtedly alcoholic Mr Chambers, who segregated girls on one side, and boys on the other. It cleverly aired at 4:30pm, which was when we would get home if our inebriated and tyrannical bus driver chose to deliver us first down our side road rather than selecting to deliver others farther on before turning around and bringing us home. We gnashed our teeth every time he fiendishly sailed past our side road. And Mr Chambers, knowing how he'd dashed our hopes, would look at us in his rear view mirror and grin - a truly terrible sight since the only teeth he had remaining were of a color that natural teeth are not. Every day for years we were driven to and from school by a likely psychopathic hillbilly from what had yet to become "Deliverance", I kid you not, and none of our parents had any idea. Is there no wonder left in the world?

So when I discovered that "Sailor" was cropping the extraneous parts out and presenting 10 minute youtube "minisodes" of each 24 minute episode, I got hooked again. We had a little crisis a while back when "Sailor" got his account deleted for unrelated transgressions, and had to begin reposting all his editions, but we've weathered that so far. If only he can keep his nose clean, we'll eventually be able to waste a full uninterrupted week of time rewatching.

It's a hoot. Vampires, werewolves, leviathans, phoenixes, parallel universes, going back in time: a pantheon of spooky cliches. It was a constant escalation of silliness that was delivered faithfully in the most melodramatic tones by an array of actors who really were actually quite good, either before or after their tenure on the show, and even sometimes during it.

Most importantly, there was always the goof to watch out for: stagehands appearing briefly in the background, loud offstage noises probably caused by stagehands dropping large objects, characters calling each other by the wrong names, beautyspots migrating all over the faces like confused cockroachs, microphones appearing and disappearing like the ghosts that also periodically appeared. Lines were almost ritually mangled - the actors only had a couple of hours to learn them before they had to perform. It was filmed live, and so none of these goofs could be edited out. For the first couple hundred episodes it was filmed in black and white, and then the wonderful world of color appeared. Clothing was by Orbach, and if there's nothing funnier in the 21st century, it's looking at clothing and hairstyles of the 60s and 70s as interpreted by a fashion designer of the time. The music and dancing in the Blue Whale, where earlier events take place, is an occasion for even more mirth.

So to elaborate a bit, and just a bit for I wouldn't want to spoil it for you, the story is of the wealthy, ancient, and more than a little nutty Collins family, in the mythical tiny seaside town of Collinsport, Maine, where it never seems to snow or get cold, although there are horrendous and dramatic thunderstorms. The Collins family, in their 200-year-old mansion, is watched over with an iron rule by the mysterious Elizabeth Collins Stoddard (Joan Bennett), the matriarch who hasn't left her house in 18 years and is therefore a kind of a role model to me. Into the fray comes the orphan, the young and eternally perplexed Victoria Winters, hired as a governess for young David Collins. "Vicki," the perceptive among us intuitively understand, is likely the illegitimate daughter of Elizabeth Stoddard, only darkly hinted at as only it could have been at the time, and it all begins.

Initially the supernatural was downplayed - we have a few doors opening and closing mysteriously, a few wails and weeping that cannot be explained (and never are). But soon young David is out to kill his father, which he very nearly succeeds in doing. We have the kidnapping of Miss Winters by the old family retainer. All of this was rather mundane, and it was probably at that point that the producers decided that the writers had better get on the ball introducing those continually escalating supernatural events that would so appeal to 13-year-old kids.

And so if there's anything that could summarize the full 1245 episodes, it's Jonathan Frid, who around episode 240 makes his appearance. He played the part of the vampire Barnabas Collins, with the claim that he's a long lost cousin from England. The word "vampire" was never mentioned, at least early on. It was censored out - indeed, if nothing else "Dark Shadows" is a historical compendium of censorship practices of the time. It was he who permanently invigorated the show, ramped up the melodrama, and it ultimately revolved around him.

But any more would be telling. If you care to waste a huge amount of time, you can start here. Or you can enjoy ten minutes or so of a hootful of unintended laughter from the 60s.


Wednesday: 26 August 2009

By Way of Explanation  -  @ 06:37:01
Fall semester at University of Georgia started last Monday, the 17th, at least a week earlier than in most places. It's been a little busier than usual, to say the least. I either haven't had or haven't taken the opportunity to get out much. Hopefully things are stabilizing now, and more regular posts will resume.

Because the ultra-dense population of students came together a week or more earlier than most, I suspect we're going to be a bellwether for the spread of nuclei of swine flu in the 17 to 21 year-old range. (Clarke and Oglethorpe County schools started August 6, so they're an even earlier indicator.) Let's watch.

I'm still watching for the baby box turtles to emerge. The earliest target date was at 70 days and that was August 21. There's many a slip between the the cup and the lip (which may not be the most appetizing or appropriate cliche), so nothing at all may happen. Let's watch.

And finally, Ted Kennedy. There will be far more said about this complex person, but I can't shake the ultimate sentiment that he was a unique and honorable man who was endlessly diligent in his efforts to support the less fortunate. When it comes down to the shameful screaming and ranting of the opposing group, and the decades-long efforts by Kennedy to establish some form of health care for those who can't afford it, I have no difficulty picking my side of the fence.

Sunday: 23 August 2009

Autotomy and Little Green Bombs  -  @ 07:56:14
I ran across this word in the form "autotomized" the other day. It's one of those words that not many people may know but that describes something most everyone knows an example of. It's the shedding of body parts, usually as a defensive measure. Many lizards do it, a lot of arthropods are capable of it, and sea cucumbers throw up their internal organs when threatened, later regrowing them. It's an interesting process, since usually (honeybee stings are an exception) there are anatomical modifications that act to prevent trauma and circulatory fluid loss following the shedding, and to regrow the lost body parts.

We usually think of Annelida as being the phylum that contains earthworms and leeches, but the largest group among the annelids is marine polychaetes, or bristleworms. They're very diverse, occupying many ocean habitats, ranging from freeswimming to bottom dwelling. You'd recognize some of them: Christmas tree worms, tubeworms, sandworms, and clamworms (a few photos here), although you might not have thought of some of these as worms. Do a google images search on "polychaetes."

So that brings us to the recent discovery of seven new species of polychaetes. I found the report in the most recent issue of Science (Osborn et al., Science 325, 964 (2009); subscription wall). Here's an individual of one of the new species, Swima bombiviridis:



All of these species are very deep ocean dwellers. They were discovered by remote operated vehicle one to two miles deep. While most polychaetes are demersel (bottom dwellers), three of the new species are strong swimmers, found as far as 1200 feet above the ocean floor. This individual has elaborate bristles extending from the parapodia ("legs") that act as swimming paddles.

Five of the species have four pairs of fluid-filled organs, and here's where the word autotomy comes in.

When disturbed, the worms drop these "bombs," and the globules then produce brilliant green bioluminescence, presumably distracting attention from the real worm. Is that cool, or what?


Here is a diagram of a cross section of a typical polychaete, taken from this interesting discussion of polychaete anatomy. Unlike earthworms and leeches, polychaetes have a number of head appendages and tentacles, including structures called "branchiae." In the interests of making them especially creepy-looking, these provide the foundation for the elaborations that can give polychaetes a spectacular appearance. In the case of the bomb-carrying species, the bombs are modifications of, and therefore homologous to, the branchiae.




Saturday: 22 August 2009

Storm Report  -  @ 08:21:17

More for the locals here: We were bewildered by the continued predictions of 70% chance of thunderstorms, sometimes severe, when what we actually had were blue skies, fluffy white clouds, and a thoroughly pleasant Friday denying the prognostications. Radar throughout the day showed absolutely nothing happening in the northern half of Georgia.

It seems to have been a matter of timing amiss, because about midnight a very significant storm system moved through our area. For two hours there was heavy rain and a lot of lightning.

I'm reporting 1.06 inches of rain during that two-hour period. Looks like there were somewhat lesser amounts in surrounding parts of the county (so far).

For our neighbors, I was half asleep but still cognizant enough to count the seconds between the lightning flashes and thunder. I'd guess there were a dozen strikes within a mile or less, and at least two to our north by less than a second. That would place the strikes just over the knoll, and probably smack atop one or more of three households.

An impressive display, a bountiful rain, and worth waiting for!

Friday: 21 August 2009

Goodbye to the Margaritaville  -  @ 07:52:10
I don't know how Wolfskin fire chief Ed ran across this little neon amusement, but we hung it on the door to the Margaritaville bay a couple of years ago. Googling shows it may have a connection to Jimmy Buffett, complete with parrot, but we'd named our beloved pumper long before any such discovery. It's a fitting introduction to the end of a long relationship.



You can see why we call our 1984 pumper the Margaritaville. She's been featured many times, for instance, here, or here and certainly no one in any of our 13 fire departments mistakes her for some other pumper. I don't know exactly how long we've had her, but it's been a decade at least, and she's been a faithful and well-used engine.

But over the past couple of years she's become intermittently cranky. Or rather the reverse, since electrical problems that have plagued her for years have led to an increasing frequency of dead batteries and nonstarts.

It was painful to have to remove the decals that we took such pleasure in applying.



So it was that yesterday we said goodbye to our old Margaritaville. Ed, Josh, Brian, and I arrived at 3:30 to begin the stripping process, removing all our equipment. Here's her bay, on the other side of the neon folly, and there are 1200 feet of 1.5 and 3 inch hose lying on the floor of the bay (but you've seen that before, last June, from the other end.






Brian took out our radio, flashlight chargers, and other equipment, and we brought in all the couplings, adapters, SCBAs, and other implements of destruction, and accumulated them in a large pile in the station.



It only took us a couple of hours, and at 5:30 Ed and Brian drove her away into the west for the last time, leaking water in the manner to which we had become accustomed.



And here's her replacement, arriving at 7pm.


By that time the rest of the crew had arrived, and we worked until nearly 10pm putting all the hose back on, and getting a good start on organizing the placement of other equipment. Brian installed the radio and flashlight chargers, tested them out, and found them good. Glenn had stopped on his way over and picked up sustaining pizza. A merry time was had by all although some of us are going to feel a bit sore today after the monumental effort of taking heavy hose off and then replacing it. We don't do that every day.

The new pumper is actually a "new old" pumper. It's a 1987 Ford, with an FMC chassis, same as the late Margaritaville, but has been scrupulously cared for. If you didn't know the real age, you'd still be able to figure it out - the side panel controls give it all away.

But it has a 1000-gallon water tank, compared to Mville's 750 gallons, and a good strong pump. And it starts! It has automatic transmission, as opposed to manual, and doesn't tend to run oncoming vehicles off the road by wandering from side to side. I'd argue that Mville was more generous in storage space, and that she had more in the way of strategic outlet ports, but since some of those no longer worked it would be a weak argument.

On the other hand, it doesn't have a personality quite yet, although the brakes are extremely squeaky and may be the nucleus of some kind of notoriety. It's red, of course, and there are those who find this to be a major asset, but I'm going to miss the margarita green.

(There are quite a few folks who worked hard to make sure this happened, but in the interests of discretion we'll just note that we all know who they are.)

Sunday: 16 August 2009

Over the Hump  -  @ 07:22:45

I think we can declare that we're past the peak of summer heat, now. It doesn't mean that we won't have some hot days, of course, but we're now trending downward.

Since Jan 2008 I've taken five to ten temperature readings a day, and have accumulated them on this plot, which you can get in larger format by clicking on the image.



The smooth purple line is the "official" Athens daily average, and the dots represent the temperatures taken by me - red for 2008, and green for 2009, to date.

I've pointed to the highest summer temperatures both years (above) and the lowest summer temperatures (below). It's significant to note that this year we have not gone above 100 degF, but that last year we had three occasions at 100 degF or more. I wish I'd recorded temperatures during 2007, because that summer, all in August, we went over 100 degF 13 times. The best I can do is to link to this page, which memorializes four days of hell that peaked at 107 degF on August 10.

There are four other squiggly lines that clutter up the above figure - one pair for 2008 (red and blue) and one for pair for 2009 (purple and sky blue). The former of each pair is a 25-point running average and the latter is a 100-point running average.

The 25-point is noisier, and all you really have to do is spot the peaks and dips, of which there are numerous ones. These clue you in to extremes that last two or three days, at least.

The 100-point is smoother, and that's because it doesn't pay attention until there is at least a week of extreme, given my five-ten readings per day.

For 2009, for instance, the sky blue line gives us a couple of weeks of extended extreme temperatures during the latter half of June, and then shows cooler than normal temperatures for a good bit of July. We've had a peak of several days of warmer than usual temperatures this past week, and that's shown by the sharp purple spike at that time.

Running averages are great for pointing out short and long term trends, but it's really the individual data points that you have to go to see what the actual temperatures were at any time.

As for rainfall, this year continues to register a considerable deficit - not quite as bad as last year, and certainly not as severe as the year before. The milder 2009 temperatures have helped to ameliorate the effects of lower rainfall, but have also obscured that fact.


Saturday: 15 August 2009

Barcoding Life  -  @ 06:35:48

Two blurbs in the recent issues of Science would be certain to generate controversy, if generally known: DNA barcoding of living organisms. There's even a blog at Rockefeller University that keeps up with this stuff.

You probably know what DNA fingerprinting is - if not from a biology course in the last decade, then from TV crime shows or jury duty. Some tiny sample of blood, semen, or tissue from a crime scene or paternity case is analyzed according to the size of certain fragments of DNA. These fragments differ from person to person, so by comparing the patterns you can get some sort of probability of whodunit, whether it's the crime scene or the father of the child.

DNA barcoding is similar, but seeks to identify the species of an organism, much as you might do from a taxonomic key or field guide. It's more sophistocated in that it actually sequences a particular fragment of DNA, and then compares it to a library of known sequences to determine what species that organism is.

For many biologists and for a lot of commercial endeavors, the ability to identify an organism or a part of an organism (for instance, a bag of seeds) is a desirable thing. Imagine that bag of seeds - how many people in the world can look at a seed and tell what plant it came from? Damn few.

For quite a few other biologists, there's something distasteful about DNA barcoding. After you've spent years learning how to identify organisms, what could be crueler than a machine that can do it in seconds?

For many lay persons, DNA barcoding smacks of an arrogance and lack of reverence for life.

I reserve judgement, but especially for the latter group I'd say it's at least interesting enough to think about it.

Here's the essence: choose one or two sequences of DNA that vary very little or not at all within a species, and vary detectably between species. Then given a library of sequences tagged for known species, you can identify any organism listed in that library.

In animals, a candidate sequence has already been found for 58,000 species (behind a subscription wall), using the coxI, or COI, mitochondrial sequence. It gives a nearly 100% reliability in identifying a species from a tiny bit of tissue.

In plants (and fungi), not so good - but now, for plants, two chloroplast DNA sequences have been identified to serve as barcode identifiers: the matK and rbcL DNA sequences. Between the two of these, identification is 72% accurate, and knowledge of the physical location of origin brings the accuracy close to 100%.

Now why on earth would you want to do this?

Suppose you're charged with conducting a periodic census of plants (or animals) in a tropical rainforest. You have two choices: You can either carry along a hoary old taxonomist who has spent years in learning a highly skilled specialty (once you've found one so willing). He's prone to conniptions, his knees hurt, and he spents hours looking at a single plant trying to figure it out. Or you can snip a bit of tissue from a plant, pop it into a vial of preservative, and send it off with perhaps thousands of others for identification through a library of DNA barcodes.

Or maybe you're an agricultural inspector of imported seeds or other plant parts. There's probably no one in the world capable of identifying with certainty all of those samples and if there is, he or she is certainly too busy for you. But DNA barcodes can.

You can see the future. Right now samples would have to be shipped off to a lab with the appropriate sequencing facility. But in five or ten years? You'll have a device the size of a cell phone, maybe even a cell phone. Pop a bit of tissue into it, the sequencing is done right there, the collection of A, C, G, and T is uploaded via cell or satellite phone and the answer is downloaded in a few seconds. A high school student can do it.

There are some technical problems, and here's one that's interesting. For several reasons, the vast majority of DNA that is available in the nucleus is generally unsuitable. But the DNA that resides in the mitochondria (and in plants, the chloroplast) is very useful. And that's why those sources of DNA have been chosen.

But mitochondria and chloroplasts are inherited through the maternal line. (Remember "Mitochondrial Eve?" Sperm cells do not contribute these organelles to the zygote - only the egg cell does.) So if you're trying to identify a plant or animal that is a hybrid, you won't get a proper indication that it is a hybrid. Your identification will tell you who the mother parent was, but that's it - you won't even know it's a hybrid. And with plants that happens a *lot*.

Another problem - contaminating organisms. If you're trying to identify a plant that has cyanobacteria growing on it, you'll get a mixture of results from the DNA that comes from the plant, and the DNA that comes from the cyanobacteria - maybe more than one species. Hopeless.

Here's an additional thought that might help to resolve the controversy between DNA barcoding and those biologists who are systematists. It appears that some degree of friction has been generated by "barcodists" crowing that this technology will "replace" systematics. Nothing could be further (farther?) from the truth.

DNA barcoding is a phenetic strategy of identification. It's analogous to using a field guide for identifying wildflowers based on the color of the flower, except in this case the "field guide" is the library of sequences. It doesn't, and can't, purport to giving any information about evolutionary relatedness. DNA barcoding is simply a unique characteristic that will identify something, much as your social security number hopefully uniquely identifies you.

Systematists are more interested in the evolutionary relatedness between organisms. As opposed to phenetics, this is phylogeny, a higher order of perception and understanding. DNA barcoding for the helpful identification of organisms is certainly useful, and potentially speeds things up enormously, but it doesn't substitute for a phylogenetic analysis.

Finally, the controversy that might emerge from the lay person: the use of the word "barcoding" is probably unfortunate. It connotes images of invasion of privacy and tattooed arms. Hopefully the above essay alleviates that kind of concern to some extent.

Then there are the folks who aren't particularly happy, for whatever personal reasons, at the notion of identifying *anything*, and I simply can't address their concerns. I don't understand them at all beyond that the effort of categorization interferes with the pleasure of the moment, and I'd prefer not to engage. Wanting to know what something is, and how it differs from something else is too essential to my nature to entertain rejecting that desire.

Having eliminated those two concerns, I'm not sure if that leaves anyone. Does it? For additional discourse, the Wikipedia article is a nice one.

Friday: 14 August 2009

In Lieu of Anything Really Important  -  @ 10:14:14
Things that have accumulated, for who doesn't accumulate things?

1. Helpful Hints

a. Gently scritch or lightly pat a cat right at the base of the tail. (That's just anterior of the tail, on the back, not posterior. Yuck.)

With four of our cats this elicits a strange behavior of craning the neck and licking at the air. Squit and Leona are very susceptible to this. Harry Pewter croaks repeatedly at the same time. The other cats show very little reaction. It seems to be akin to the hind leg scratching behavior you get when scratching the chest of a dog. Warning: do this only with cats you know and who know you. Do it cautiously even then. Cats do not suffer fools gladly.

b. If you are of a certain age, you probably have to use reading glasses, which are constantly trying to escape. I'm extremely nearsighted and have worn corrective contacts since graduate school days, and glasses for years prior to that. I mean, I am *really* nearsighted - my eye doctor doesn't even bother with the enormous E on the top, because I won't be able to see it. My gratitude for corrected vision through marvelous technology knows no bounds.

Alas, though, if I'm wearing my contacts now, at the age of 53, my closeup vision has gradually become as horrendous as my distance vision without, which is a terrific insult, to be both nearsighted and farsighted at the same time. However, if I take the contacts out, I can see perfectly fine closeup, but am practically blind beyond a distance of ten feet.

What to do? If this describes you, and you wear contacts for near-sightedness, try wearing only one. It's a little odd at first, and you'll still have some lesser degree of distance vision. But at the same time you'll be able to do closeup work without the reading glasses and still be able to recognize a friend at ten feet. Not recommended for driving, though, nor for really good distance vision.

(Yes, I know, bifocals are supposed to be the way to go, but I'm still battling the idea of that.)

c. Our university is death on academic dishonesty. For instance, it does not allow you to submit work from a previous course as fulfillment for an assignment in the current one, unless the professor has made a very specific statement to the contrary.

So if you're taking plant taxonomy and you have to do a plant collection, do NOT include flowers and fruits of a plant that doesn't flower or fruit until two months later. You will be so busted - did you really think a botanist wouldn't notice? Failure on *two* counts - what the university calls "lying or deception," and what your professor will call "arrogant stupidity."

2. Pet Peeves: I'm not really a grammar nazi - goodness knows I make enough mistakes, although I try not to, which I think distinguishes me from those who don't give a crap. And yes, I know, I'm tilting at windmills here, and there are far too many windmills to expend much angst over. This almost certainly says more about me. Still, there are two things that will cause me to be so distracted in my reading that I will scarcely be able to read further (farther?) for the genuine discomfort that I get:

a. Data. Data are plural; datum is singular. "My data *are* very good." "This datum is questionable." NOT "This data shows we're right," but "these data look like shit." Yes I know that the rationalization is that somehow "data" has come to be perceived as a collective noun, but I disagree. After all, you might well say "a group of pedants is a terrible thing," but you'd never say "a data looks bad to me," now would you? So end of story. Suck it up.

b. In the same vein (but with a lesser peevishness), "none of these people *is* here," not "none of them *are* present," no matter how odd it sounds. None is singular. This one doesn't bother me much - it's more that when I see it done right I rejoice. Now *there's* a writer, I think.

c. Finally, "begging the question," which we've done before. My reaction here is more one of sorrow than pique. There is the subtle, proper, elegant meaning - a plea to answer a question using circular reasoning. And then there is the barbaric vulgar one - "this makes me want to ask the question: (whatever it is)". Do you want to be a vulgar barbarian? Of course not!

3. I'm even less of a spelling policeman (though the confusion between homonyms like "their" and "they're" and the like is so easily corrected that I have to wonder). Here are a couple that I'm continually heading toward the dictionary for:

a. Does anyone have a special way to remember those pesky words ending in "-ent" or "-ant, or "-ance" or "-ence."?" Resistant/resistance? Resistent/resistence? I know it's the former, but only because it looks right. Some pairs just don't look one way or the other to me. I spend more time at the dictionary (and yes, I have one at my right hand) than I do for anything else.

b. "Further," or "farther?" This is a tricky one, and more of a grammar thing. I usually use "farther" for physical distances, and seem to use it much more frequently than "further," which seems more conceptually oriented.




Thursday: 13 August 2009

Turtleology  -  @ 06:20:41
It was in mid-June that we observed a box turtle laying eggs, and it's now about a week from the earliest point that we'd expect to see those eggs hatch. What the rest of this post is about happened weeks ago, just days after that post, but I've been thinking about it.

I like turtles, and so it was with interest that I ran across a neat report in the 10 July issue of Science by H. Nagashima et al. on the evolutionary origins of turtles (Science 325, 193-196 (2009)). That report is behind a subscription wall, but it was nicely summarized by Ed Yong. I'm not going to repeat that excellent summary, but will try something a little different.

It's likely to seem to most that the basic question, which is not how the turtle got its shell, but how did the shoulder blade get underneath the ribs, is a little like how many angels can dance on the head of a pin. But to developmental biologists these are serious questions. And the shoulder blade thing is an anomaly that must be explained.

The turtle "shell" is actually two unconnected shells, the carapace covering the back, and the plastron on the bottom. There are lots of variations on this - from turtles with incomplete shells to box turtles with fancy bells and whistles like a hinged plastron. Turtles have been around for a coupla hundred million years, and the elaborations that form the protective shells probably have something to do with this.

Where the turtle's shell comes from has actually been known for a long time - here, for example, is a 1982 National Center for Science Education article that cites papers going back as far as the 1940s. The key, as in the recent Science paper, is in studying the development of the embryo.

Here's an interesting couple of factoids what will impress your friends:

The plastron of the turtle comes from the shoulder girdle and the collarbone. Everyone knows where their collarbone is - especially if you've broken one - and if you feel it in front of your shoulders and imagine it growing downward to your hips in a sheet, then you can imagine having a plastron. It would leave your arms and legs free. Indeed, it would protect your underside, and there would be no need for a complete ribcage. And that's all we'll say about the plastron, because the interesting dilemma is found in the formation of the carapace.

The carapace of a turtle is formed from the ribs, which in a turtle not only broaden to form the shell, but just as importantly *stop* growing laterally instead of bending around, down, and together. This forms the carapacial ridge of the turtle, the edge of its carapace where it meets but does not merge with the plastron.

To put it another way, reach back and feel your backbone, and then trace a rib laterally outward, then bending forward and laterally inward until it ends at the sternum, or breastbone. Taken together, your ribs have mostly merged in the front to form a nice little cage that protects some important accessories.

In a turtle, the ribs do not continue around the side of the body as they do in non-turtle vertebrates like us. They stop lengthening at the sides, and then broaden and fuse to form the shell.

Here's the angels dancing on the head of a pin part:

If you reach back and up, you'll feel one of your two shoulder blades, or scapulae. These are large bones that form the attachment point for a number of muscles. And where do you find your shoulder blade? It's on *top* of your ribcage.

And that's where you'd expect to find it in a turtle, this weird little thingy sticking out from the top of the shell, but obviously we don't see that. Instead the scapula is under the shell (ribs), and the real question becomes: how did the shoulder blade get *under* the shell? That's what the recent Science paper shows.

Here's a pretty picture that shows the dorsal (back) view of three widely diverged vertebrates: a mammal, a bird (descended from dinosaurs), and a turtle. These were the three vertebrates whose embryos Nagashima and colleagues studied. The scapula is in red, and it's pretty clear that in the turtle it's now inside the ribcage and not on top. You can also see that the rib development has been arrested axially, so that a ribcage will not fully form.



One obvious hypothesis had been that the mass of cells that would form the scapulae *migrate* from atop to underneath the region that will eventually become the ribs. In animals, migrations of cells happen all the time during embryo development. But it's not just the shoulder blades that we have to worry about, it's all those muscles and stuff that have to attach. They, too, would have to migrate in a coordinated fashion. It turns out that the process of doing all this is much simpler and elegant.

By sectioning and staining of embryos in various ways to delineate bone and muscle, Nagashima showed that everything is pretty normal up until the pharyngula stage of development. The pharyngula stage is a somewhat later embryo stage in vertebrate development, 3-4 weeks in humans. It follows the blastula, the gastrula, and the neurula stages. Many organs and tissues, including bones and muscle, are in their early stages of development, just masses of cells waiting to be positioned and to become what they will. So at that point, the bones themselves haven't formed, but the tiny masses of cells that will form them are in place.

Here's what's different: In turtles, the upper dorsal part of the body does a twist, and inverts those imaginal masses of cells with respect to the rest of the body. The origins of not only the scapula, but also all the muscles that will form attachments, are now *underneath* the cells that will form the ribs and eventually the carapace.

Here's the critical set of views that show the twisting of one portion of that part of the body (the ribs are marked "r", the scapula "sc", and the numbers refer to days after fertilization):



So effectively the part of the body that makes the ribs and shoulder blades and muscle attachments turns outside in, and "presto," you have the shoulder blade inside the ribs.

It also turns out that there is a now-extinct species of turtle from 220 million years ago (center, in the figure below) that is intermediate between non-turtle vertebrates (left), and present-day turtles (right). The extinct species, Odontochelys, had a plastron, but not a carapace. The lower two-thirds of the figure shows an idealized comparison of what we've been discussing all this time.



The upper portion shows the scapula, again in red, and also shows muscle attachments in blue, orange, and green. It may not be perfectly clear, but one point would have to be that in the modern turtles, the muscles are also transformed inside of the ribs, just like the scapula is. (h is the humerus, dc is the dermal carapace (yellow), and pl is the plastron (yellow).)

So there are two things that make the carapace work: the axial arrest of the ribs that keep them from growing all the way around, so that they form the edge of the carapace, and the twisting that puts the scapulae and their attendent muscles on the inside rather than the outside of the ribs.

One last factoid to impress your friends with: you probably noticed all those muscle attachments to the plastron and carapace. The turtle is not simply a body inside of a shell, like a hermit crab. The shell is an intrical part of the whole animal. You can't pull a turtle out of its shell, at least not without killing the animal.

Extra credit: what would you look like if you'd done that inversion at the pharyngula stage?



Wednesday: 12 August 2009

Last Night's Activities  -  @ 08:29:57

Our local readers will know that we had an interesting late evening, last night. A small storm started up just north of Winder, and quickly grew in intensity and size, moving east southeast at a rapid clip. By 10pm it was directly approaching us here, with lightning flashing several times a second since half an hour previous.



Interesting how so many lightning strikes (the variously sized squares indicating length of time since the strike) are trailing the actual storm. That actually happened, and it's fairly unusual.

The rainfall was sufficiently intense to invoke an intense precipitation report from me, and in the end we had 0.83 inches of rain over the space of an hour, most of it falling within 20 minutes. There was lively action from the front porch as I made my way indoors when lightning struck a tree a coupla hundred feet away. Glenn, sitting inside, claims he saw ball lightning at my feet.

Our fire chief, on his way back from a five day trip to Michigan, and driving in perfect time beneath the storm, encountered a downed tree on Old Edwards Road that connects him with home. Since it fell across the road, he couldn't get home. Ed called our fellow Brian of the chainsaw, who proceeded on his way, and then Ed went to get a firetruck for the warning lighting, since the tree fell in a dangerous part of the road (and drivers do like to travel fast along there). By 11:30pm it seems they'd cleaned up. It wasn't a pageout, since Ed took the initiative, but he did communicate with 911/Central and I declare it a bona fide incident for the purposes of NFIRS. So very good on both Ed and Brian - at the very least they saved a lot of folks from having to detour eight or ten miles to get home, and at best may have prevented a nasty accident.

Sounds like more of the same throughout today, at least, and no complaint here - we've had no rain since the first of August.

In addition to our 0.83 inches: for others in the area, via CoCoRaHS, around 1.5 inches in east Clarke County, up to an inch around Arnoldsville north of us, and then petering off to 0.22 and 0.13 inches in Crawford and eastward, as the storm proceeded southeast, delivering them only a glancing blow, it seems.


Tuesday: 11 August 2009

School Begins...What Now?  -  @ 07:44:47
No Perseids that I was able to detect. While the moon was bright at 4am, I was still able to see eta Cas, which is a magnitude 3.5 star, quite close to us as these things go. A bright meteor would have been many times brighter than this, so at least during the period I was watching, from this location, it was a dud year.

The school year started in Clarke and Oglethorpe counties August 6 - we heard the schoolbus up in the cul de sac at the usual old 7:10am time. My guess is that we're at the forefront of the start of K-12 fall school openings. The University of Georgia starts its fall semester classes on Monday, Aug 17, though the students are gathering even now. For us, with our earlier schedules inviting transmission of something like swine flu aka novel H1N1, the great experiment has begun.

That experiment will be of the potential for swine flu novel H1N1 transmission to begin making its foray into our local population. The Centers for Disease Control have at least two vaccination webpages here, and here, but the summary is that a vaccine will be available no sooner than a month or two from now.

Don't rely on me for updates or expert information - I'm only reasonably well read. The CDC is the place to go, and the Reveres at Effect Measure have had numerous timely and expert posts on the subject.

Having said that:

The usual groups (the very very young, and the older) are encouraged to get the seasonal vaccination, as usual. Essentially everyone, really, but especially those two groups. The seasonal vaccine will not protect you from novel H1N1.

In the case of H1N1 it's the younger folks age 6 months to 24 years who are the targets for earliest vaccination, as well as those of any age who are of higher risk of medical complications. Those older than 24 years are encouraged to wait, unless they are healthcare and emergency medical workers, or pregnant women. Pregnant women are especially encouraged to get the vaccine. Unless I missed it, nothing is mentioned of educators, a category I fit into.

Once inoculations have been done for those groups, age 25-64 are in order, unless they fit in the above special categories.

That odd schedule alone is of interest, and the reason isn't just because of the concentrated potential for infection - that's always the case, every year, when the school season starts. Unlike seasonal flu, novel H1N1, like the 1918 influenza, seems to be targeting the younger population for extreme reaction. One hypothesis (there are several) is that the older folks like me have received some immunity already through a previous encounter decades ago with a cousin strain (I did receive the 1976 swine flu vaccine, for instance, although its relationship to 2008-9 H1N1 is unclear to me).

In the meantime, reasonable hygienic precautions are in order, tailored to your own specific situation. In my case, I'm going to be around students who sometimes show an appalling lack of awareness, and it's uncomfortable to have to ask them to sneeze and cough in some other direction, and please don't borrow my pen. I do an occasional handwashing, and keep my hands away from my face. I wash my hands before I leave. Those are reasonable precautions, and I don't intend to get more extreme than that.

We're at the beginning of something that could fizzle out to nothing more than an ordinary flu season, but could also become quite different from anything any of us has experienced.



Monday: 10 August 2009

Meteors and Cougars  -  @ 06:30:55
First, the concentration of dust and small particles that constitute the remains of comet Swift-Tuttle is crossing Earth orbit today and tomorrow. That means the Perseid meteor shower will peak tonight Monday through tomorrow morning Tuesday.

Unfortunately the moon is 55% full - on the wane but not sufficiently waned. Full darkness comes on around 10pm but the moon rises 30 minutes later, all local times. So after about 11pm the moon's brilliance will diminish the visibility of fainter meteors. Still, keep watching toward the north and northeast and upward, and avoid looking at the bright moon so as to save your night vision.

Too bad for us - after a week of no rain and more or less clear skies we're expecting 50% cloud cover starting this afternoon.

Second thing, last November a sportsman from Newnan shot and killed a Florida panther from his deer stand in Troupe County, in southwest Georgia. There seems to be no question of confusion - by all accounts he knew what he was doing. He also reported the shooting to the Georgia Department of Natural Resources, which complicates somewhat any knee-jerk inclination to label him as a complete monster.

There are only about 100 or fewer Florida Panthers (Puma concolor coryi) left, and most of them live in central south Florida. They represent the last wild population in eastern North America. This male appears to have wandered from there - DNA analysis released last week (and reported locally) shows him to have been a part of the population. (Unclear on why a DNA analysis would have taken the better part of a year.) At first it was assumed that it was an escape, based on his robust health and lack of parasites, but that seems not to have been the case.

Although there are no known populations of Florida panther in Georgia, the state does protect the species.

The designation of the Florida panther as a subspecies is based on distinguishing physical characteristics. However, mitochondrial DNA analysis fails to identify any DNA differences between the Florida species and the species as represented by the more common western cougar.

I have certain difficulties with this: mitochondrial DNA is useful for some things but it represents only a tiny portion of the total genome. This seems to me to be an issue of lack of evidence not constituting evidence of lack.

Secondly, if the DNA analysis carried out on this individual was successful, as reported, in identifying it as a member of the Florida population, then that's an admission that DNA evidence *does* distinguish the subspecies from the species at large.

There is some effort to find a way to reintroduce the Florida panther to its formerly extensive southeastern range. In the early to mid 1990s experimental releases of animals, and subsequent tracking, was done to provide preliminary data on behavior. The behaviors were as expected, and on both sides of the issue. The cougars wandered, as you'd expect with a 200-400 sq mi range, and the humans, on the other hand, chased them off.

Though it seems not to have updated its website significantly in a long time, the Florida Panther Society has a neat record of the tracking of many of these individual animals.

If you do an internet search on sightings of cougars in Georgia, it would appear that there are tons of sightings - practically everyone must have one in their own backyard going by this yardstick. But as pointed out above, "The official response from both the Georgia Wildlife Resources Division and the S.C. Department of Natural Resources is that there has never been a documented wild cougar found in either state in modern times."

I'd hope they update their assertions in view of the one killed last November.


Sunday: 9 August 2009

Year Seven!  -  @ 05:28:17

♪♫

It's that most, wonderful time, of the year.

♫♫

This year is Year Seven.

If you've been following along for awhile you know that this has been an ongoing project - eradication of Microstegium vimineum from much of the property. Here you will find the tools and suggestions of the trade, and here is last year's report.

Notice that the old cracked white five gallon bucket has been replaced by a sleeker, black model!

This is a morning job which begins around 8AM when the temperatures are low, and ends well before they reach a typical 90F around noon. That means it's actually the most uncomfortable in terms of humidity, which is at its highest during the day, but at least it's not in the mid 90s. I won't do this every day, and usually wind up around the end of September.

Year Seven is supposed to be the magic year, when the seeds have largely lost viability. Of course there's a spread to that so I have no naive expectations, Already I can see that our relatively cool and at least somewhat wetter spring and summer have had a substantial effect on the germination and growth of the plants.


So yesterday I began, as I usually have, with the couple of acres around the house, within the perimeter of the electric fence. Last year I collected 600 plants from this area, which would just about halfway fill the five gallon bucket. Now you might think that the completely full bucket this year would be alarming in its implications, but I see two possible reasons for this.

The bucket actually measures biomass, not numbers, although I've always used it as an indicator for numbers. This year I think it is misleading because the plants are so freaking large. So that bucketful actually indicates fewer plants.

Also, the season was initially very conducive to the germination of what seeds remain, and that has not been true in the past. So I think this year may truly exhaust the remaining seed bank - i.e., whatever viable seeds have just been sitting around waiting for a good year have shot their wad.

I am aware, though, that I may have reached a point of diminishing returns. I'm pretty careful, but I can't claim to get every plant, and any that I miss may mature and begin the process all over in a small area. If that's true, then there will never be an end to this.
I forget that this is not a completely odious and boring task. For one thing, Gene thoroughly loves to participate and is insistent on following me every step of the way. Normally on a long walk I will take note of where he is and sneak out in some other direction (sometimes this does not work!), but for this project he's welcome to accompany me.

And it does allow me to closely examine the forest floor over an entire area, and not just along the linear path I may follow on a typical long walk. I find a whole different set of interesting things that way. Sometimes I meet the nicest turtles!

Here's something else that provides independent evidence for the seed germination hypothesis:



Poison ivy has appeared in much larger numbers than in the past, pretty clearly from seed that germinated this spring. While I won't bother it outside the house area, I'd just as soon not have it within that area. So I mixed up a liter of 0.5% glyphosate, sacrificed a spray bottle, and spritzed the plants selectively. I'll be following the one above for the next week or two.

Yes, I could just dig the plants up, but this year I don't have an old pair of gloves to later discard, and the stuff just ends up contaminating something I didn't notice. Forget that.



Saturday: 8 August 2009

Longevity for Some  -  @ 05:25:23
These light bulbs, which finally burned out, were put in place in 1991 and so have been used frequently ever since. There is little to identify them, other than that they are probably Type A15, and what writing can be made out says they're 130 volt 60 watt. Glenn believes they're probably Philips bulbs.



I'd say about half of the bulbs are still in operation, at this point.

When you do an online search for light bulbs, even when adding technical terms, *all* the hits you get are for sellers. And going onto these websites is a little like going into the bad parts of town - you take the computer equivalent of your life into your own hands. Muggings are common, only here your browser does strange things and may even crash. Odd popups that can't be closed drift across the screen, obscuring the information you want. There are bad places, where clicking on a link has no apparent effect, other than to set the browser to cycling, suspiciously.

When you get home, you feel dirty and need a good strong antivirus shower.

At any rate, I didn't find what I was looking for. Them's the breaks.




Wednesday: 5 August 2009

Spore Days  -  @ 02:59:34
One of the consequences of our extremely dry weather of the last three years has been that emergences of fungi have been infrequent. As a result, I don't get much in the way of material to work with and learn, so I'm fairly poor at keying major groups out.

Two different mushroom emergences from Monday, both in a moist area under the canopy (thus the poor lighting conditions), and emerging in patches within ten feet of a moderate sweetgum tree. Lots of leaf litter consisting mainly of sweetgum, tulip poplar, and oak. We may have to revisit these, as I am way uncertain about the first one and have little idea about the second.

There were four or five patches of these light yellow-brown mushrooms. It wasn't clear to me if they were emerging from the ground or from a wood source just beneath the surface. I'll take a stab at the ID in a minute, but my guess if applied in the animal world would be analogous to wondering whether the find is a spider or an insect.



Clearing away the leaves a bit showed the tangle of smooth stems, without an annulus, or ring.



And the caps are lightly scaled and not particularly tacky. I neglected to check to see whether the gills were free, or attached to the stem. That will have to wait until later today, two days after these photographs.



My best initial guess is that these are ringless honey mushroom, Armillaria tabescens. (The mushrooms in this group are sometimes found as genus Armillariella.) This would be closely related to honey mushroom, Armillaria mellea. A. tabescens is said to emerge in about a month, A. mellea could be emerging now, but the former has no annulus and the latter does.

Photographs show a good deal of variability among A. tabescens with some, like the above link, resembling these specimens more than others. I have found definite A. mellea under similar circumstances, though, and the clumping manner and tangle of stems is similar to what we see here.

(As an aside, that honey mushroom finding was my only additional culinary experiment beyond chanterelles and morels. Washing the large clump simply produced an everflowing stream of viscous slime which miraculously disappeared upon sauteeing. However I was sufficiently nauseated by that time that I don't think I ate very much of the result.

Another aside: Armillaria is parasitic, and the appearance of large numbers underneath or attached to a tree is probably a very bad sign.)

Just about buried in the leaf litter within a foot or two of one of the above patches were these little clublike outgrowths.



Very close by, and even more buried in the litter were what probably is the same thing but much larger (fist size), and seems to be four individuals clumped over each other.



These could be basidiomycetes of the puffball group. There are also some of the larger, formless ascomycetes that they vaguely resemble. There are a couple of things I can look at to try to distinguish between these, including the possibility that a couple of days later they may have acquired a more familiar form.

If we were to grope for an animal analogy, being uncertain at this level would be similar to wondering whether a critter was an earthworm or an arthropod! That sounds pretty bad, but the distinctions that anyone can see make an earthworm different from an arthropod can be obvious in fungi only at a level that may involve a microscope or chemical tests. Higher taxa of fungi are different from each other in real, fundamental ways, but they are subtle and hard to detect.



Tuesday: 4 August 2009

Crack in the Earth  -  @ 06:14:58

In the scheme of dramatic events, this doesn't rate very high, but it is a small tragedy in the making.



This moderately sized tree, unlike the one behind it, just didn't grow quite fast enough to compete with the erosion of the high bank along SBS Creek. It seems to be aware of its impending predicament, with clutching roots reaching out toward the crack in the bank developing at the center right.

This is one of the small meanders that we've talked about before, and the occasional heavy rain that produces flooding of the creek has cut away at the bank under this tree gradually. It's only a matter of time before the inevitable happens.

When it does, the tree will bring down with it a crown of poison ivy, since that's the vine you see growing up the trunk at far left. Though we haven't had a surplus of rain so far this year, it's been closer to average than it has been in quite some time, and I imagine there is quite a top heavy weight of water held within the cells and tissues of the tree and vine.


You don't see this happening too much farther upstream, where the creek flows with less volume, but down at this end the creek has eroded quite a lot of earth, and is four or five feet below the surrounding floodplain. This is an ongoing part of that kind of bed formation.

It's not clear that the tree will die from this, although its fortunes will certainly change. It will assume a more horizontal position as it falls across to the other side of the creek. The contact with the ground will not do the upper trunk any good, as fungus will be able to colonize it, and it won't be in a very good position to do photosynthesis and make a living. However I have seen certain fallen trees, such as elms, send shoots upward from the horizontal trunk, and these grow into a line of clones themselves.

Sunday: 2 August 2009

Update on the Toolbag  -  @ 04:48:16
You might recall that last November, a toolbag got loose during a spacewalk. Since that time, 256 days ago, the toolbag has whirled around the earth somewhere around 4000 times. As a result of continuous and increasing friction with the tenuous edges of the earth's atmosphere it has very gradually lost altitude.

It's now about to come down. In the next few days, it will suddenly encounter a much greater density of atmosphere, it will heat up, and then it will drop. If you were lucky, you might catch it flaming slowly across the sky, but to be that lucky you'd have to live in the southern hemisphere.

Here's why:
Here is the "ascending leg" of the toolbag's orbit, just as it passes over Sparkleberrysprings at about 10am this morning. As you can see, the nighttime overfly is in the southern hemisphere. For us, the passage overhead will be only during the day.

We might also have the opportunity to see it at dusk, but sadly, no. Here it's descending over us, and again you can see that its passage over the northern hemisphere is confined to the daytime hours.

For something considerable larger, we might see it in the daytime, but for the toolbag, probably not. We'd need nightime hours for that. If the decay were to occur even a couple of weeks from now, the seasonal progress of the earth's orbit around the sun would once again bring the toolbag to our nighttime skies. But it will decay long before that.

You might well ask, or maybe I just might tell you, that the toolbag has drawn far away from the space station in its 4000 orbits around the earth. The orbit has changed significantly since last November. Notice how much smaller its circle is than than of the space station. That's because it's lower in its orbit now. And it looks like its about a coupla thousand miles away at this point.

You might also ask why the space station doesn't follow the toolbag in its fiery descent, for surely it too must be dropping in altitude, and that's just so - it is. But periodically the space station is boosted to a higher altitude to prevent just this sort of thing from happening. Occasionally, it's the shuttle that supplies this boost, but most of the time the Russian Progress cargo ships has lifted the space station out of harm's way. In the last year, the European Space Agency's Automated Transfer Vehicle (ATV, Jules Verne) has provided the capability.

Finally you might ask how it is you'd be able to tell the difference between a decaying object like the toolbag, were you so lucky to see it reenter, and a meteor. Easy! A meteor is over in a flash, because it reenters at a velocity ten times greater than a piece of space junk. For the fortunate, the toolbag will flame leisurely across the sky - depending on how things go, it could be visible for many seconds, maybe even a minute until it burns up completely.

Saturday: 1 August 2009

The Month of July  -  @ 07:04:23
It's The Month of July, Number 42 in a series. After a hot June, July turned out to have a lower average mean temperature, which is odd, but not unprecedented. In most respects it's been extremely comfortable here. How about you?

From the National Weather Service Climate Prediction Center, this is a plot of high and low temperature anomalies for the US. That's the difference in the average temperature for this July above or below the average for July over many years, plotted in colors. The anomalies are in Fahrenheit.



Once again the northern tier of states from Montana to the Great Lakes were unusually cool for at least the fifth month in a row, this month by 3-6 degF below normal. The northeastern states were also 2-3 degF cooler than normal, for at least the second month. Otherwise there has been quite a switch, with temperatures in the west and south central US much above normal, and temperatures in the southeast a couple of degrees below normal.

The National Weather Service Climate Prediction Center has once again moved their precipitation page. It's quite a labyrinth there, at CPC, with pages disappearing and renamed, sometimes redirected and sometimes not. At any rate, I found the precipitation plots here, this time.



The Pacific states, and with some exceptions, most of the area west of the Rockies, had subnormal rainfall. Most of the southeast could only boast normal rainfall at best, with a swath of ugly brown showing below normal levels. On the other hand, the southern Gulf states west of Georgia received normal to above normal levels, except for southern Texas. The Great Lakes states were similarly dry in July.

For Athens:

Summer may have arrived in June, with its high temperatures, but things cooled off a lot in July.

Here is my plot of low temperatures for the month of July in Athens. (It seemed appropriate to present low temperatures this time.) As usual, the black dots are for the 18 years 1990-2007 (black dots), 2009 (green line), and 2008 (red line).



This time around, we had only 4 days of high temperatures that were at least one standard deviation higher than average. But we had 12 nights below the standard deviation for our usual lows, and we broke 120-year low records on July 19 and July 20.

For rainfall, the figure below shows the Athens data which are official for our area. As usual the green line shows that official rainfall, the red shows the average accumulation expected. The black dots are rainfall over the last 19 years, the vast river of peach shows the standard deviation. Official Athens rainfall quickly fell below even one standard deviation below the mean, and stayed that way throughout the month.

I've added a blue line this time around to show the rainfall here at SBS, just 10 miles to the east of the official Athens station. Still slightly below normal but way above the official monthly total.



I wrote, in June, about the totals for June rainfall: Athens officially got only 1.66 inches of rain, compared to 3.94 normal inches, well below 50%. Here we got 3.20 inches for June, still below average but not by that much.

A similar situation repeated in July, with official Athens rainfall only at 1.25 inches, while most of the surrounding 35 CoCoRaHS stations dispute this figure. Here we got 3.94 inches, still below the 4.31 inches officially considered to be normal, but more than three times the amount official for Athens. I won't go into that more, since I wrote about it here, other than to say that the official rainfall for the Athens area is extremely misleading, and for the second month in a row. It makes a huge difference when you're still at the cusp of a drought!

I'll continue to link to this neat prognosticator in which you can get variously timed precipitation and temperature outlooks. El Niño is going to be having an effect now, and you might want to check that out.

Geekstuff:
NOAA's weekly ENSO update indicates that we're now in an El Niño, and that it is expected to intensify well into winter 2009-10. Expect a southerly jet stream bringing storms to the south.

Relive your favorite weather events of the year 2009, courtesy of NOAA. NOAA has a neat State of the Climate product. By clicking on the year, such as 2009, you can get to monthly and even weekly reports and zero in on regional descriptions that are much nicer than my own.



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