Some “old” news from Science 312, 1965 (2006):

I ran across this neat little experiment that determined how ants navigate. M Wittlinger, et al., of University of Ulm in Zurich noted that ants, in this case the Saharan desert ant, forage outward from their nests in a random sort of meandering way, exploring for food. It was how the ants returned that interested the authors. They do not, apparently, laboriously and wastefully retrace their routes. They don’t particularly use visual cues either.

Apparently they combine an internal “odometer” with a “celestial compass” to define distance and direction travelled, and then make a beeline (or antline) directly home.

The “celestial compass” part of the system is known to be one method that not only ants, but also bees and other hymenopterans use to determine general direction. The ant uses direct sunlight to determine the direction of the sun during its outward journey, and polarized sunlight as well.

But the distance travelled, the second part of the calculation, has had several hypotheses put forward. There’s the “energy hypothesis”, in which some kind of internal sensor monitors how much energy the ant used to move outward from the nest. But this has at least one problem - ants often return carrying loads of various sizes and it would be complicated for any sensor to judge energy usage when the ant can essentially weigh more or less unpredictably upon return compared to the outward journey.

And then there’s the “odometer hypothesis”, in which ants keep track of the number of steps taken and calculate total distance by multiplying the length of stride. The authors tested this in a rather clever, if unkindly way.

They treated ants' legs in three ways: they left them as is (the control), they severed a portion of the leg to reduce the stride length, and they surgically attached stilts to the ends of legs to increase the stride length. After some training of the ants to find a feeder located about 10 meters from the nest, they watched how the ants returned to the nest.

The point at which the surgery was done was important to the experiment. In one case the surgery was done after the ants arrived at the feeder, and then they were challenged to return to the nest.

The ants with untreated legs returned confidently and in a straight line accurately to the nest, as expected. The ants with shortened legs returned in a straight line, but consistently undershot the location of the nest by about half the distance, presumably wandering about aimlessly after an unsuccessful targeting. And the ants that had stilts on their legs overshot the nest by half again the distance. Clearly not only the length of stride was important, but also in some way the number of strides.

But the clever thing about the experiment was repeating it with ants *before* they left the nest for the feeder. Ants foraging outward on stilts, stumps, and normal legs were able to return to the nest accurately, regardless of their treatment, establishing that the ants were correctly counting their steps regardless of stride length.

I can see another question coming up: ants foraging outward randomly will use many more steps than upon direct return - how do they resolve this difference? I’d suggest that it’s done the same way I do when I count my steps to determine distance, but may not be moving entirely in a straightline direction (as when I have to navigate around a tree or other obstacle). I just don’t count my steps unless I’m moving in a particular straightline direction, a criterion it would be easy for the ant to make, using its celestial compass.

It’s certainly remarkable how ants navigate, but just as remarkable is how cleverly they trained some scientists to determine this.

We’ve reached the last two weeks of lectures in the semester. In the general biology courses, they’re talking about populations and evolution (the latter, unfortunately, is receiving increasingly shorter attention these days, almost a “filler” in case there’s a day or two available). As usual, maybe 3/4 of UGA students aren’t able to tell you how many people there are in the world (6.7 billion), how many expected in 2050 (10-12 billion), or even how many in the US (300 million, and remarkable because it’s been in the news lately). About the same number don’t particularly care, except as factoids to be memorized for the final, or perhaps as brief soundbites to be considered in-between cell-phone calls.

But population growth, and the sophistocated mathematical models to describe it, are interesting. While these students don’t see the first equation, the graphs do tweak their interest, however briefly.

Here’s exponential growth, unhindered by environmental resistance factors, or limiting factors. The curve starts out slow and then picks up speed in an accelerating fashion. It’s the sort of curve that you might see for a short period of time for bacteria on a petri dish, or what we’re now seeing for human population growth, currently.

A word about human population growth. In the late 1700s, Thomas Malthus wrote a treatise on this subject, pointing out that populations grew geometrically (as you see above) and food supplies grew arithmetically, that is, linearly. There would come a time, he hypothesized, when the numbers of people would be greater than their food supply and then would come chaos, famine, and massive death from starvation. Malthus' treatise was one of the foundations for Charles Darwin’s chain of reasoning leading to natural selection as a force behind evolution of populations.

The usual cohort has gleefully seized upon Malthus and pointed out that over the two centuries since, none of his predictions has come to pass, and fallaciously conclude that therefore they will never come to pass. Malthus, of course, could not predict scientific innovations that could abruptly increase food sources - such things as the Industrial Revolution that supported the chemical synthesis of nitrogen fertilizers, the production of pesticides in the 1940s, and the Green Revolution that saw the emergence of more productive hybrid plants in the 1960s. Gene technology is predicted to be the next Revolution that will up the food supply.

It probably goes without saying that many environmental problems can be attributed to all of these innovations: nitrogen fertilizer runoff into rivers and the ocean, pesticide organic chemicals as pollutants that cause deformities and mutations in animals at the top of the food chain, and the periodic massive failures of crops (corn in the 1970s, for instance) when hybrid plants are found to harbor defects that permit massive disease to demolish crops. There’s considerable suspicion that there will be similar environmental repercussion from gene technology - and for the first time the consequences are at least under discussion.

Well, back to population growth. That exponential growth is limited by a lot of things - an increasing lack of food, water, space, air; an increase in disease and predators; these are limiting factors. In a very simplistic way, species respond differently to these limiting factors:


Species with individuals that are large, have few kids, take care of their kids, and have long life spans generally show K-selection, the upper left panel. They eventually level off to a carrying capacity, the number of individuals the environment can support. The population remains, stably, at a constant level.

The upper right panel shows R-selection. These are species, such as insects and many kinds of plants, that have individuals that are rather small, short-lived, produce tons of kids, and don’t take care of their kids. They overshoot the carrying capacity and because of any number of things, perhaps their rapid reproductive growth, strip their food supplies. The population crashes. Gradually it recovers and then the cycle is repeated.

From a human point of view the left panel seems rather benign (although out of keeping with what we expect of a constantly growing economy) and the right panel looks dangerous (but is the panel that our constantly growing economic expectations is encouraging).

Which panel suits humans best? Currently we’re still in an exponential phase, and we would simplistically expect that because of the formulaic descriptions of K- and R- selected species that humans would naturally be K-selected.

Not necessarily. Remember that humans have the ability to (intelligently or foolishly) alter their environment to maintain population growth. This enables them to enter into the regime of R-selected species, with a suddenly burgeoning population that strips the environment.

If you’ve dabbled in anthropology, geography, sociology - you’re probably familiar with this kind of graph - age structure. That link, by the way, is an interesting one in which you can select any country and discover its age structure. Check out India, and despair. China, for all its huge population, is interesting. Ethiopia, despite its famines, maintains a depressing amount of population growth. Contrast with, say, Germany.


An age structure graph shows the number of individuals in each age bracket. The top half of the figure (A) shows a large number of immature kids (blue) compared to middle age (green) and older people (red). Fast forward 25 years, when those blue kids become green fertile people, and you can see that this population is growing rapidly, and over the next 25 years there will suddenly be a *lot* more people, no matter what.

The bottom two panels show other forms the age structure graph can take - a stable population is more or less up and down (B), and a declining population is more like an upside-down pyramid (C). There are countries that represent all of these alternatives, but human growth globally currently resembles the top one - continued growth.

So now, are humans K-selected or R-selected?

The comments to the previous post went in directions that I hadn’t anticipated, as I honestly wasn’t requesting encouragement so much as tolerance, but there’s no doubt that I enjoyed the former! I’ve replied in comments to many of the responses and have some others I continue to want to think about for awhile. At any rate, thanks for that.

No, this is not an example of the kinds of new posts I’m thinking of - you may be relieved on that point. It’s more of a manifest of a few shackles I intend to remove from myself, and at the same time an indication of how I intend to limit most comments of this sort. Further, I don’t plan to specifically post in this manner at all, but rather to subsume into posts of more familiar flavor a little more spice.

With regard to politics rearing its occasional ugly head there’s four points I want to make that might better give an idea of how I want to limit myself in commentary of this sort, rather than going off into pointless, vague rants. Perhaps these points are something reasonable fresh and unhashed:

First, a generalization. I don’t think there has been politics as such, at least not effective politics in the sense of the art of finding a solution, for at least twelve years, and the steady decline has reached new lows in the last six. Opposing points of view have been beaten by new parliamentary rules and intimidation in a pattern that has become most alarming to me. There has been no politics, there has been merely imposed policy of the most reactionary and backward sort in just about every venue. I don’t think this is good.

Second: environmental rescue, and finding solutions to environmental problems, is all-important. I’ve sensed, and not just subjectively but as a result of a fair amount of gained knowledge, that there is a clock ticking. Of all our problems, I think most of them link back to environment, and changes to climate, and even further back to continued, stone-age policies that encourage rampant population and demand insanely accelerating economic growth. Nowhere is the danger of the aforementioned replacement by reactionary policy for finding solutions to these problems more evident than in the realm of finding solutions to environmental problems. The US can’t be expected to save the world single-handedly, but in a strategic way it’s not even trying. Given that it’s a quarter or more of the source of the problems, US policy has spent the last six years actively resisting the actions of the rest of the three-quarter to try to find solutions.

As a corollary, yes, there are a great many problems, made worse by a political party that has seized monopolistic control of policy. Some of these have been deliberately made worse in order to maintain control by the party in power. Social problems have become far more distracting as a result. Long-term economic stability is threatened. Policies with respect to immigration boggle my belief. The increasingly fractured and unravelling situation in far too many parts of the world that were bad enough six years ago are now simply out of control. I suggest that all of these have roots in the consequences of a degrading environment, and that that is a result of a set of policies that encourage and demand unending economic and population growth that must inevitably strip the world of resources. At the same time these policies have discouraged exploring and discovering valid alternatives to fossil fuel energy sources, for one example. I think we can lay much of this at the feet of corporate influence of legislation, and will take note of that as it is appropriate.

Third, I expect and demand that the Democrats now in control of Congress reverse these policies. To do so, they are going to have to forget tit for tat revenge (a prospect that disappoints me, frankly) and work with their political opponents in resurrecting politics as the art of finding solutions. They’re going to have do this because the person in charge of a veto will determine whether they’re successful, and this clock I’ve seen ticking for the last six years demands that we begin to get some successes in these areas, and soon.

Fourth and finally, I naively believe in individuals as a source for change. I think they’re responsible for thinking about and enacting those changes in a personal way. No one person can be expected to turn his or her world upside down, but small, gradual, simple changes in ways of living can amount to large differences if enough people make them. Simple decisions, in so simple a thing as, for example, planting an oak tree instead of a hedge of redtips. Determining to do all your shopping during the trip to or from work, instead of making one or, usually more, “special” trips specifically for that purpose. Cooking half the time instead of buying prepared foods. The list of small simple things goes on and on.

It’s not encouraging. In the three weeks since the midterm elections, I don’t believe I’ve heard the environment mentioned, seriously, at all. The replacement of James Inhofe, chair of the Senate committee that oversees environmental issues, the Environment and Public Works Committee, by Barbara Boxer, is the only optimistic sign to emerge so far. Inhofe has wrought incredible damage, and Boxer has her work cut out for her. From my feeling of environmental issues as a sine qua non, I’d view her responsibilities and success as among the most important to watch.

This kind of post is the kind that I hope I don’t make very often - it’s graceless and wonky and I don’t particularly like it. But in view of what I said yesterday, it’s probably appropriate as an indicator of where my criticisms are going to emerge, when they do, and hopefully in ways that blend a little more artfully when they do emerge.

When I started this blog, more than two years ago, I cheerfully allowed a few days, even a week, between posts, and then as I became more and more enthused I ramped it up to once a day, sometimes even more. Now, in the last couple of months I’ve found myself skipping a day or two, or more. I wouldn’t have even noticed a sea change in the attitude but for writing, and that makes all the emotional changes crystal clear. Am I depressed? Have I become burnt out? Not exactly, but I have allowed myself to become hemmed in, and a little fresh air seems like a likely cure.

Robin, at the Dharma Bums, has (for me, anyway), a relevant post today that in a nicely short piece addresses a good many points. In particular there’s this one, at least as interpreted by me: sometimes it’s hard to post a pretty picture and be enthusiastic about it.

And that, to some extent, has been what this blog has come down to - posting pretty pictures. I’ve hidden, somewhat, behind the excuse of innocuous documentation, but I’m feeling more and more that what I’m documenting isn’t going to be here in ten years. What’s the point, without pointing it out? There’s more to what I do than pretty picture blogging, of course, but increasingly it’s the exception rather than the rule. And so, increasingly, I’ve found myself less and less enthusiastic, in part because I’ve allowed the objections and expectations of others to become my byword - don’t challenge, and certainly don’t offend anyone.

No, I’m not going to become a scold. I’m not going to approach from the point of view of being in your face. No, I’m not going to get all political on you, but more about that later. No, the changes aren’t going to be huge - there are those who won’t even notice them. And no, I’m not going to stop writing and posting - I don’t like that bit of manipulation that I occasionally see from bloggers, who a few days later, sometimes not even sheepishly, are right back at it again. I think a constructive change is in the works. Can I do it cleverly? Gracefully? I hope so.

I’m not saying there’s anything wrong with pretty pictures, they’re not going to stop, but I will leave you with this: just how many pretty pictures will there be left to take next year? The year after? In 2050? If you aren’t thinking of that everytime you see a pretty picture, maybe you deserve me

The directions to Sparkleberry Springs are not really that complicated, but some folks can get confused. My sister once lost her way but fortunately she did get back. She was lucky! She had her son and his banjo along. Don’t be alarmed - we’ve never lost anyone permanently.

My parents ALWAYS find their way here. ("We had a nice trip, Wayne", they’ll say, admitting nothing untoward, unexpected, or amiss. “It sure is a pretty drive” they assert.) Well, they’re great travellers, and old hands on the road, and have encountered all manner of strange things: we all know that, and they’re also from Fairhope, so.

The route involves a few odd turns onto roads you can’t actually see until you’ve made the turn. There is the steep hill where you have to put the brakes on if you want to go up, and of course you must, so look sharp! I don’t know whether it’s the perspective or what, but the gravity seems strange there.

Don’t let it get to you about the short stretch of road that runs under the twin suns or half a dozen moons, depending on whether you’re travelling in the night or day. We’re not really sure where it is, but it is scenic! Enjoy!

We note for your convenience that it’s on this section that visitors sometimes lose a few hours without knowing it. Sometimes it happens and sometimes it doesn’t. Why, there are times when I come home from work and arrive in time to say hello to myself before I leave. We all laugh about it here, and enjoy sharing tidbits about the future. It’s a resident thing - don’t concern yourself, unless it’s for Glenn who would otherwise get a free evening, free of me, or even two of me if He decides not to go to work. And as for Him, well, after all, it’s not my problem, nor yours, it’s His - He has to go to work!

Still, it’s because of this that we do advise visitors to plan ahead and leave about six hours early, just in case, and then you will therefore arrive on time. It’s not a problem for us - we’re used to it, and don’t mind early arrivals in the event of no temporal complications. But it’s *so* disappointing for visitors when they discover that half a day has disappeared into the ylem.

I should advise you, with great reluctance since it IS more fun to be surprised, about that hundred-meter section eight kilometers in which there’s no air. Just roll up your windows, hold your breath, gun the engine, and don’t get your panties in a wad. Sorry if you’re in a JEEP, but I did give you fair warning.

Don’t worry about the odd native flora and fauna you might catch sight of. They’re not dangerous, exactly; just don’t get out of the car. And - need I say it? Please don’t feed the plants, no matter how prettily they beg. We’ve lost a few fingertips that way.

The commute might be startling to the occasional hysteric, but you get used to it. Imagine driving a firetruck down some of the really back roads, and count yourself lucky.

Things are actually fairly normal, once you get here, except for the skies, of course. FC once asked if the skies were really that blue here, and I said, yes, they are REALLY that blue.

And at night, away from the city, the stars are REALLY bright.


I see that House has rotated 90 degrees and faces northwest in this photo. This can be exasperating, sometimes, on days when you really want it to face east, or west.

I’m going to forego my usual rant about Black Friday, the Day of Intense Greed, to just point out that I won’t be shopping today. Not that an aversion to shopping is unusual for me, but I’ll give it at least this amount of larger emphasis than I usually would, and then I intend to celebrate my own Day After Thanksgiving, call it Followup Friday.

I think I must have somehow conscripted Thanksgiving Day for my own personal use as a day to reflect on my incredible luck in the circumstances that have surrounded me. How much others do this, I don’t know other than to note that a fairly decent number of individuals seem to do the same thing. Sure, it is for many a day of cooking special things, and of feasting, and family is often involved. And undoubtedly there are the dark sides of those much less fortunate, and the historical twin of ascetic, intolerant pilgrims, and of European invasion and conquest that are associated with Thanksgiving Day (although I find Columbus Day to be more appropriate for recognizing that).

But still the day for reflection stands out for me, not that it takes a special day for that. There are all too many days that I reflect on the things that make me happy and secure. I can’t help but recognize the incredibly small chance that I was born into this time and place, rather than the thousand-fold greater chance of existing elsewhere or elsewhen. How on earth, and even beyond earth, did that happen? And the next step is, if I wish to take it, toward the anxiety of realizing how ephemeral are all these things I’m grateful for.

Yet, as Dr. Pangloss naively noted, we live in the best of all possible worlds, and Buckaroo Banzai seems to have realized that wherever you go, there you are. And Candide offered us the advice of cultivating our own gardens, so perhaps I would have been grateful for the things that surround me regardless of when or where I was born.

At any rate, we certainly didn’t eschew a modicum of material things yesterday. Glenn did the heavy work with the turkey, and the twice-baked potatoes, the brocolli and the dressing, all things that seem to have become our tradition. My role as the artist of ancillary dishes would normally involve the stuffing of mushrooms and the production of a cheesecake, but the mushrooms weren’t available.

Fortunately Mark H at Biomes Blog offered a substitute tradition in the form of wontons, and there’s something else to be grateful for! I love wontons as dumplings, so I got out the pasta maker and produced the wraps and made an interesting filling. And I tested out Mark’s advice on browning them before adding broth, and they were superior treats indeed.

In keeping with my own personalization of the Thanksgiving Thursday, I sense that Followup Friday will continue these reflections. After all, there are plenty of leftovers.

The US Thanksgiving is hands down my favorite mainstream celebratory day. It doesn’t exist to honor any particular thing, it exists to take note of everything. It doesn’t matter who you are, your sex is unimportant, no one cares what your economic class or what your politics are, and it’s irrelevant what ethnic group you’re a part of. It’s all inclusive. And it’s just icing on the cake that it occurs during my favorite season of the year. What a great idea! And have a good one.

It’s probably appropriate that at midnight one of the most easily recognized constellations, Orion, is rising in the east to announce the day. Coming home late at night, I just happen to be travelling southeast and Orion comes up like a monster. I never tire of it. The bright red star at mid-upper left is Betelgeuse, which is hankering to become a supernova in a thousand years or so, or maybe tomorrow! The belt and sword are obvious in the middle:


The above is how you’d see it on a clear night. Here’s a map:


And here’s how you’ll never see it! Binoculars would image the dimmer stars but never give you the enormous expanse. Same view, but a 15 sec exposure.


Zooming in a bit toward Orion’s belt and sword. The sword, at lower right, is the famed “star nursery”:


And another map at this scale of magnification.


By this time, the seven Pleiades sisters are visible as a distinct cluster of a dozen or so stars, high in the sky. Again, on a very clear night, you might see them almost this distinctly.


A little closer:


And about as close as we can get. Notice the little 9.0 and 9.8 magnitude stars which are just about on the limits for this camera, but how about that!


And finally, the inevitable map:

The honeybee genome sequence has been completed and appears in Nature (Oct 26 2006). It is the fifth insect genome to be sequenced. From Science (Oct 27 2006, p578 ) we learn that it has 10,157 genes identified so far.

Although the genome itself is considered essentially complete, the gradual sequencing has been available as it has been done, and has generated a great many publications in the last few years.

Why would we care about the honeybee genome? Honeybees have complex social behaviors, for one thing, with a caste system that is reflected in the very different physiologies of its members: queens, workers, drones. The sequence reveals that a number of gene families have evolved in a very specialized way. Bees communicate by odors, for instance, and have 165 odorant receptor genes, double those of fruitflies and mosquitos (the genomes of both insects have been determined).

And honeybees make a special food additive that turns a female into a queen: royal jelly. Without this additive, females turn into sterile workers. The genes for making royal jelly (the MRJP, Major Royal Jelly Proteins, have been identified and are evolved from a pigmentation gene complex, yellow, which is found in other insects including fruitflies. In fruitflies, Yellow is involved not only in body pigmentation, but also in behavior, especially male sexual behavior. yellow genes are common in arthropods of all sorts, but the derived MRJP genes are rare. yellow genes are found in some bacteria, but have apparently been lost in most non-arthropod lines, such as nematodes and yeasts.

It’s hard to keep track of all the literally hundreds of organismal genomes now being sequenced. That’s why we have the NCBI: National Center for Biotechnology Information, which archives and organizes all the sequences to date.

Here’s the NCBI Organism Tree, with links to some of the more complex organisms that NCBI keeps track of. You can click on any of these and begin to explore. You can, for instance, put in the sequence of Your Favorite Gene, and the bank will search for similar sequence in any other organism, or all of the for that matter.

You’re probably aware that the human genome sequence has now been determined. Here’s the NCBI Human Chromosome View, and each chromosome is linked to a wealth of sequence data. For instance, here’s NCBI: the Human X Chromosome.

An alternative view of eukaryotic organisms being sequenced can be found in the NCBI Organism List. And with some trepidation, I think it’s appropriate to cite what seems to be a good Wikipedia entry: the List of Completed Eukaryotic Genomes (Wikipedia).

Here’s a neat timeline of “firsts” in sequencing:

1977: First sequencing of DNA
1978: First viral genome (Phage Phi-X174 (5386 bases, 11 genes)
1995: First bacterial genome (Haemophilus influenzae, 1.8 million bases, 1740 genes)
1996: First eukaryotic genome (Yeast, 20 million bases, 16 chromosomes)
1998: First multicellular genome (Roundworm, 80 million bases, 6 chromosomes)
2000: First plant genome (Arabidopsis, 120 million bases, 5 chromosomes)
2001: First drafts of human genome (3 billion bases, 23 chromosomes)
2006: First tree genome (Balsam poplar, 550 million bases, 19 chromosomes)

Going through the lists of organisms that have been sequenced so far, or are in the process, there are just way too many viruses to account for now. Similarly for the prokaryotes, there are literally hundreds of bacterial species undergoing sequencing, but here’s a selected few along with a brief mention of the rationale for determining their genomic sequence:

Prokaryotes: Archaea and Bacteria
Acidobacterium (bioremediation)
Agrobacterium tumefacients (plant pathogen)
Anabaena variabilis (energy production)
Anaeromyxobacter dehalogenens (bioremediation)
Bacillus anthracis (anthrax)
Bacillus thuringiensis (Bt toxin)
Borellia bugdorferi (lyme disease)
Escherichia coli (human gut)
Mycoplasma genitalium (parasitic)
Mycobacterium tuberculosis (tuberculosis)

The major groups of complex organisms, eukaryotes, include some familiar names (as well as some unfamiliar ones). Some are of interest because of their evolutionarily close relationship with us humans - mammals come under this category. Others have served as genetic models for many many years - fruitflies, roundworms, Arabidopsis, sea urchins, mouse, and yeast all fall into this group. And of course many plants are of interest because of their importance as a food source, and the need to understand their genetics and biochemistry.

Here’s a highly abbreviated list (especially for protozoans and fungi) of eukaryotic organisms that have either been completely sequenced (bold) or are in the process of being sequenced:Protozoans
Chlamydomonas rheinhardtii
Social Amoeba, Cellular Slime Mold (Dictyostelium discoideum)

Fungi Brewers' yeast (Saccharomyces cerevisiae)
Soil Fungus (Aspergillus nidulans)

Plants Thale Cress (Arabidopsis thaliana)
Maize (Zea mays)
Rice (Oryza sativa)
Potato (Solanum tuberosum)
Wheat (Triticum aestivum)
Tomato (Lycopersicon esculentum)
Oats (Avena sativa)
Soybean (Glycine max)
Barley (Hordeum vulgare)
Balsam Poplar (Populus trichocarpa)

Invertebrate AnimalsRoundworm (Caenorhabditis elegans)
Fruitfly (Drosophila melanogaster)
Silkworm Moth (Bombyx mori)
Mosquito (Anopheles gambiae)
Honeybee (Apis mellifera)
Sea Urchin (Strongylocentrotus purpuratus)

Non-mammal Vertebrate Animals Pufferfish (Fugo rubripes)
Zebrafish(Danio rerio)
Frog (Xenopus tropicalus)
Chicken (Gallus gallus)

Mammals Mouse (Mus musculus)
Rat (Rattus norvegicus)
Pig (Sus scropha)
Cow (Bos taurus)
Wolf (Canis lupus)
Dog (Canis familiaris)
Cat (Felis catus)
Chimp (Pan troglodytes)
Human (Homo sapiens)

I note that the Cat Genome is not yet finished, but I couldn’t resist promoting their logo:

You know how I feel about these ravening beasts, so this is blatant, shameless manipulation, pure and simple. Saturday morning I heard a gunshot that was suspiciously nearby, so got on the orange and went cautiously down toward Goulding Creek to investigate. No hunters, but these two showed up. Mom was probably teaching Bambi which particularly valuable plants to eat when they came up me unexpectedly.

Run away!

Well that was a bust. The Radiant did not Radiate. I think Robin probably saw more Leonids than I did! I did see a couple of nice ones but they were never in the field of view of the camera.

I started playing around with the camera around 10pm, with temps dropping into the low 30s (F) by 3am, when I decided to hang it up. Not all was a bust though, I did work with camera settings for sky photography, and was pleased with the results. That is *after* I realized after 2 hours and 50 photographs that I had set the camera to the highest f/stop rather than the lowest. Dumb, dumber, dumbest!

Eventually, once I realized this rather basic and significant mistake, I was generally using these settings for the photographs below, and I might modify them somewhat still.

Robin, these settings are probably not useful for something as bright as the moon! You’d get a huge white square with no definition. The tripod is a great idea. Cut down the exposure time, don’t worry overly about the f-stop settings or the ISO setting.
ISO: 800 (background noise was evident at 30s exposures, correctible by image processing.)

Exposure: uniformly 30s, with Noise Reduction “on”. I might try reducing this to 15s for “closeups”.

Aperture: eventually fully open. f/3.8.

Focus: infinity, of course.

Field of view: as large as possible, but I did a few “closeups” with the telephoto, and that’s where I might reduce the exposure time. The streaking of stars due to earth rotation is evident at 30s.

Lighting: I chose auto, but there might be a better setting. The options don’t include starfields: “cloudy”? “shade”? maybe “incandescent”! Certainly not “flash”! Don’t use flash!

Photo format: I used the usual setting, Fine/Jpg, but I think I’ll try Raw next time.

Image processing: DO NOT save star photos as jpgs. Maybe there’s a way to do it without losing color, but once I’d closed out the PaintShopPro program and restarted it all processed images had lost all the great colors. Save images as *png* files. I have a feeling I have more to learn about this, but I do know that jpgs compress files with loss of information everytime you save, and pngs do not. Png format is not something you’d want to save a complex photo with, but for simple line drawings and things like this, it’s perfect and makes tiny little files.

Here’s a SkyMapPro screen capture of the Eastern Skies about 3am. The white square is what the camera saw at full field of view, and the green square is a blowup of the region containing the Beehive Nebula, M44.


Let’s look at the white square, the full field of view that was photographed. Our hopes were dashed, of course, that there would be a meteor within.


Saturn is in Leo right now, but it’s the Beehive, M44, that I’m interested in, so let’s blow up the map of Cancer, which contains that open cluster:


I’ve labelled the brighter stars with Bayer numbers so that the photograph below corresponds. The Beehive, labelled M44 above and below, is not the brightest of objects. It is visible unaided but only as a fuzz. This is one that I could probably do better on - the streaking is clear here.


Let’s look toward the north, and again here’s a SkyMapPro capture that encompasses the entire view that you’d see from the horizon up, at 3am last night. The green square encompasses an interesting region that includes some of the richest starfields in the sky - Perseus and Cassiopeia:


Here’s the SkyMapPro image of the region in that green square, which corresponds to the photograph below this image:


Here’s the corresponding photograph. I labelled the brighter stars again, this time with proper names, above and below. The region labelled Double Cluster is two large open clusters that, like the Beehive, are rather faint but large and located between Perseus and Cassiopeia.


So I was pleased with the results. The blue and red colors come through well, but the yellows show up as white. All in all, this seems to image stars down to mag7, which is about 2 orders dimmer than what most people can visualize with their eyes, and equivalent to a very good set of binoculars. The binoculars won’t give you these colors, though, which are not enhanced here, they are what the camera has seen.

I was up around 3am, and braved the cold weather ten or fifteen minutes at a time to watch for meteors. There wasn’t a huge amount of excitement but I did see a few bright ones and a dozen fainter ones that appeared to emanate from Leo.

If you’re under clear dark skies, you might consider photography. That’s what I’ll be doing. Right now the skies are a deep deep blue, with no indication from this reliable forecaster that there will be passing clouds in the next 12-24 hours.

Direction, exposure time, field of view, stability, focus, and aperture!

Direction: Whereever you want, but you might as well point it to where the meteors are coming from, the radiant, to begin with. It’s smack in the head of Leo. There will be three stars, directly east, about halfway up the sky by 3am (and lower down, earlier). One will actually be yellowish Saturn and the other white Regulus; orange Algieba is dimmer, but they’re easy to spot.


But don’t get your pannies in a wad over it - just point the camera east and up.

Exposure time: Paramount is the need for a stable camera that can be set to expose for perhaps 30 seconds. 30 seconds is a good choice - long enough to potentially catch something that just happens by, and not so long that it heats up the CCD detector too much (your camera will limit you, don’t worry) and you get noise and the stars become streaks. If your skies aren’t dark, you may not be able to expose for that long without getting a white field.

Field of view: Make whatever adjustments are necessary for as wide a field of view as possible, whether it involves screwing the SLR down or changing lenses. The wider the field of view, the more likely you are to catch something.

Stability: It would be nice if you had a cable release but it’s not really necessary. Make sure the camera’s battery is well-charged, if it’s a digital. Mount it on a tripod if at all possible, or set it up in a stable position viewing the upper eastern skies.

Focus: Set the camera focus to infinity.

Aperture: If you have the option of manual settings, set the f-stop to the lowest setting (that is, the largest aperture).

Sensitivity: If you have the ability to set your camera’s ISO, set it somewhere between 500 and 800 to up the sensitivity, but not too much, or you’ll get noise, and doggone it, noise sometimes can look just like a meteor!

I plan to set mine up on a tripod next to me. I’ll aim it at the sky, and then just press the shutter every minute or so, guessing that I might get lucky. I’ll try it out for awhile in the late evening to make sure everything is ok, make whatever adjustments are required, and then be ready for the real show from 11:45pm to 2am, and after.

Be aware that most cameras use a lot of battery keeping the shutter open, and that your batteries will be drained faster than they would in conventional daylight shots.

I expect to throw away hundreds of images. That’s how you take meteor shots.

The good news is that the moon is close to new and the skies are dark!

The Leonid Meteors peak late Saturday night (Nov 18, 2345 EST) to early Sunday morning (Nov 19, 0130 EST), so we are told by NASA. It always exasperates me in a small way when someone says a meteor shower will peak Nov 17, because of course it’s the nature of night to straddle two dates. *Which* half of the nighttime that’s Nov 17? After all, they’re essentially 18 hours apart!

But NASA is explicit, which is good, since the Leonids is a shower that could have a definite peak within a few hours, and that peak has occasionally in the past been truly spectacular. The Wayback Machine reminds us that in 1966 some observers estimated 100,000 meteors per hour, during a short period.

The reason for this is that the fragments of dust and gravel left from the passage of Comet 55P/Tempel-Tuttle have been well mapped and form debris clouds dotting the region around Earth’s orbit. If we pass through one of these pools, we get showers. This site shows the mapping, and suggests that we won’t be passing through any of the clouds of larger, thicker concentrations, but could pass through thinner, smaller ones. The top figure is probably the most informative.

The estimated time of passage (first sentence of this post) is absolute, and must be converted to your local time. It’s good news for the Earthlings of Europe and Africa, for which Leo will be overhead at the time of passage, moderately good news, with luck, for Eastern North America, for which Leo will at least be above the horizon.

But no one should despair, even if you live in Western North America. Meteor showers still carry an element of unpredictability and so it’s also good to watch when the point in the sky from which the meteors come (the radiant) is above your horizon. For the Leonids, which appear to come out of the constellation Leo, this is anytime from your late evening to dawn, regardless of where you are. That’s because all over the world Leo rises about the same local time, sometime before midnight.

So look to the east starting in the late evening and then as the night progresses, start looking up more and more, until by dawn Leo is straight overhead.

Leonids come from the Comet 55P/Tempel-Tuttle, so named because two fellows, Tempel and Tuttle, discovered it independently in 1865-1866. Calculating backward, it became clear that this was the same as the brilliant comet of 1366, which came within 3 million kilometers of the Earth in that year. And now we know that this comet returns every 33 years and replenishes the debris fields. It last returned in 1998.

The Tuttle mentioned is also the Tuttle of the 1862 Swift-Tuttle Comet. That comet, which returns every 130 years, is responsible for the August Perseid Meteor Shower. It last returned in 1992.

And while you’re at it, keep an eye a bit farther south, toward the constellation Monoceros (just east of the easily recognized Orion). The Monocerotid Meteor Shower, much more spread out than the Leonids, is expected to peak early AM Nov 22 local time, but is active from Nov 15 to Nov 25.

When Glenn and I were doing sequencing of several cotton genes in the late 1980s the procedure was entirely manual. From extracting DNA, preparing a library of clones, identifying and growing up the clones, and extracting *their* DNA, to the point of actually being able to sequence them required long weeks of work.

Once everything was ready, we could run one sequencing operation a day, using these huge chest x-ray sized glass plates set less than half a millimeter apart. Tediously, we would pour a buffered acrylamide solution between the plates, which would then polymerize into a jello-like, extremely thin gel. Set the clunker without dropping it into a buffer, hook it up to a power supply, load the samples, and let the DNA move through the gel for six or eight hours. If everything went right. We’d then tease the plates apart and hope hope hope we didn’t tear the gel getting it onto filter paper and drying it. We’d go into the darkroom, place a chest x-ray film up against the dried gel, and let it expose overnight. Then we’d develop the film and sit down at the light table, marking off the lanes and bands and writing down the A, C, G, and T sequences.

After all the weeks of preparation, we could sequence *maybe* 1000 nucleotides in a day, if we were lucky. Here’s a photo that shows something like what we could acquire. These four lanes represent a single sequence of (let’s count)... 31 nucleotides. Each lane, about a centimeter across, represents one of the four letters of DNA, and you read it upwards, like a ladder. You can go to NCBI’s GenBank, and you can search, and you’ll find a few dozen examples of our work, such as this one, one of our favorite genes, but it’s an infinitesimal part of the hundred billion nucleotides of DNA that are a part of that enormous bank of sequences.

We’re not doing sequencing these days, but you’d have to have lived in a mall for the last few years not to know that sequencing whole genomes (a genome is *all* the DNA that exists in the nucleus of a cell of a human, or any other organism for that matter), as well as a horde of lesser applications, is one of the primary objectives in all sorts of fields of science and medicine. Within the human nucleus are six billion nucleotides of DNA, arranged in 46 separate chromosomes. If we could somehow tease out of a single cell all those strands, linked end to end, such a strand would stretch a couple of meters - six feet.

Being able to accomplish this is due to highly automated machine-based technology and several important advancements in technique, including polymerase chain reaction (PCR) methods, replacement of our primitive thin slab gels with capillary gel tubes thinner than a human hair, development of fluorescent markers to replace our radioactive nucleotides, and computerized scanning and analysis to replace our light tables and marker pens.

Today millions of nucleotides can be sequenced per day, and the entire preparation that took us weeks or months and that 15 years ago netted us a few thousand nucleotides of sequence can now be done overnight. Here’s a tiny section of a fluorescence-labelled sequencing operation. EACH lane represents a single sequence, with each color representing one of the four letters of DNA. This section represents (let’s count)... 170 nucleotides. In today’s sophistocated sequencers, each lane is the size of a hair, and is scanned optically by computer. But look! Even at the rate of several million nucleotides per day, it takes a thousand days simply to sequence one human genome’s worth of DNA.

Enter X-Prize, which as you may recall sponsored the prize for the first commercial space flight (flying a vehicle, SpaceShipOne, into space and returning it safely twice in ten days), is sponsoring a new prize: complete sequencing and accurate assembling of 100 human genomes-worth of DNA in ten days.

That’s equivalent to 60 billion nucleotides per day.

A blurb in Science last month (Science 314, 232 (2006)) estimates that it will take about five years of further developments before a winner will emerge. Coincidentally, that’s about the same length of time it took to accomplish the first complete sequencing of a single human genome.

What will be required that will take five years? Vastly increased parallel computer processing, for one thing. Right now at least one company is using 1000 computers to assemble a single human genome in one week. The current automated technology is pretty much as sophistocated as it can be, and new strategies will have to be developed.

Why do it in the first place? Imagine that you become ill, and your doctor diagnoses cancer. He takes a biopsy and sends the tissue off to a sequencing facility. The next day your complete genomic sequence is ready, and the results are emailed back along with the pinpointing of the mutations that caused the cancer in the first place. Your doctor is then able select a therapy that targets that specific mutation.

Or consider pinpointing the mutations in genes that cause difficult genetic diseases like Altzheimer’s. By sequencing dozens of members of a family, the mutations can be found that cause such a polygenic disease.

Targets for applying all this stuff aren’t limited to humans, of course, and the months and years of work that taxonomists require to examine just a few genes among many closely and distantly related species can be extended to entire genomes of billions of nucleotides.

Ethics and legal issues? You bet. The fun is just beginning.

One of the most prolific and wide-ranging science fiction writers, Jack Williamson died this week at the age of 98. This year has also seen the premature loss of another of my favorites, Octavia Butler, whom I wrote about earlier this year.

Jack Williamson’s writing spanned a remarkable three quarters of a century, and he invented many of the frequently-visited concepts of science fiction. He coined the word “terraforming”, in which an inhospitable planet is converted through geological and biological engineering into a more friendly place to humans. A multitude of science fiction stories have investigated this concept, perhaps most exhaustively in Kim Stanley Robinson’s Mars Trilogy ("Red Mars", “Green Mars”, and “Blue Mars”).

Somewhat unlike Octavia Butler’s writing, which had a definite genre flavor, Jack Williamson’s writing was far-ranging. One of my favorites is “Darker Than You Think”, which treated lycanthropy as something peculiar to a genetic subspecies of distinctly sinister humans.

At the other end of the spectrum, he took Isaac Asimov’s robot concepts to a new, darker level. In “The Humanoids”, and then later, “The Humanoid Touch”, he envisions robots as authoritarian nursemaids, compelled by their programming to protect humans to the ultimate degree. Humans are not permitted to engage in ANY dangerous activity by the very creepy self-reproducing robots they’ve created.

It’s just a coincidence that a couple of weeks ago, in one of my periodic revisits to books already read, that I took down and enjoyed again a couple of favorites by Jack Williamson.

Yesterday I was down to SBS Creek dodging bullets and collecting Lobelia puberula seeds, and ran across this odd little plant. In trying to pull of a leaf and maturing fruits for identification I uprooted the whole thing, so that’s why it’s in a pot.


I first thought Ranunculus, one of the nondescript little buttercups, and then maybe even Waldsteinia, one of the rare little deep forest strawberries I’ve mentioned before.

Glenn went through the keys for buttercup family Ranunculaceae and rejected that, and then began to look at Rosaceae, and then the fruits sparked his recollection that he’d taken a photo of this plant back in June:


Oh well, it’s not uncommon - it’s White Avens Geum canadense. We typically find it flowering and fruiting in the late spring or early summer, so this one was a little outside its reproductive range.

Look at the cluster of achenes though - the hooks are great!


The hooks are formed by the female style which hardens and curves back. The remains of the stigma (red arrow) drop off (blue arrow) when the achenes become mature, and the hook is ready to latch a ride on some passing animal.

The world’s smallest flowering plant, duckweed (Lemna): does it or does it not stick to your hands and arms?

Apparently so, at least for me.


I tried it two ways, vertical dipping and removal, and horizontal. The above is the result with vertical dipping.

That also brought up another question: how long can Lemna tolerate desiccation?

A nice clump of duckweed on the left. I decided to use pondwater for the experiment, but didn’t want “gemmae” in it. Filtering through the strainer didn’t work so well - there was a lot of junk that got through. But coffee filters worked fine!


I’ve inoculated the time zero (no drying) with a dozen or so fresh plants. There’s also a negative control, filtered water, no inoculation, and then inoculations of plants after 1, 3, 10, 30, and 100 hours of drying. (I tend to like base 3.)


So under the lights they go. Will they grow at all?

Today is Veterans Day. As The Reveres at Effect Measure point out, the current designation has replaced the original Armistace Day, and then Remembrance Day, and of course this isn’t the only time the Cold War has perverted our memories. Nonetheless, and while this may not be the most scientifically rigorous post, it seems to fit, to me.

I was thinking to post the last colors of autumn, but I might have done the same thing weeks ago and I’d have been wrong. Some years the color changes have happened all at once and finished with a thud. This year seems to have been the right combination of cold and warmth and dry and wet. Different species seem to have practically had their own week to themselves, taking over in orderly march from the previous one and giving way to the next in line, with really outstanding results.

Speaking of warmth, temperatures yesterday were ridiculously high, topping 80F, which if recorded as such will exceed the 1931 80F record. It did give me the opportunity to test out the misting fan though, which works admirably. Evaporative cooling, latent heat, physics in action!

I’ve been going out and sitting in the early morning after dawn or in the early evening just before dusk to see what I can see. Yesterday morning I sat on the northwest slope with the sun rising behind me, looking down the terraces toward the floodplain. This is where our neighbor spotted the bobcat moving through the area a few weeks ago.

The Brachyelytrum, featured green just a few weeks ago seem to have succombed to the nights of frost last week, and are now clumps of gold glowing in the morning sun that filters through the trees. The now empty peduncles are left pointing at the deep blue sky.


I shifted my position a couple hundred meters south late yesterday afternoon, just as the sun was setting behind the ridge southwest of the little creek. I sat until near dark, able to view up and down the facing slope and up and down the creek for some distance. White oaks and northern red oaks are now serenading us with their reds and browns.

Who'da thunk that wild azaleas, this one growing out of a crack on Troll Rock, would turn such a brilliant yellow-orange? This same one was featured last mid-April, wearing a different set of colors. And is that the fall northern red oak from many previous stories? Why yes it is. Couldn’t have seen that from my vantage point a month ago.

So far, nothing of the real goal, but last evening I did catch sight of a flying squirrel landing on a tree trunk, and seldom-seen chipmunks scampering down the creek. The Brachyelytrum has turned yellow along the banks about 4 meters down a steep slope from where I’m sitting.

About half our baker’s dozen of friends who rent a couple of houses at Jekyll Island iat the end of December are women. And we’re basically all in the same age cohort - late 40s to 50s. And so the women are either on the approach to or entering what Jessica Tandy explained to Kathy Bates as “the change” (and then cackled pleasantly as Bates wailed).

For the last couple of years, I’ve been learning quite a lot, as my female friends are quite enthusiastic about detailing all about menopause if simply asked, and I’m certainly interested in hearing about it. The heat flashes are quite intriguing to all of us (why do they happen?), but I’m here to report that no one yet has experienced formication.

So the other day I was talking to my sister, who is not quite there yet, and we were discussing this. She mentioned a colleague who will be in a meeting, suddenly turn beet red, and whip out one of these handy little fan-mister combos. That was the kernel of the idea for our Jekyll gifts, additions to the arsenal for their Menopause Relief Kits.

So Bev had it right - the gadget is for heat flashes, and while I’m guessing my friends already have their own relief approaches of choice, they can put these little fans aside until their own little motors burn out.

Pablo was right too, and so the guys are each getting one as well. Not for the slightly seriously touted “manopause”, but for balance, and because seven or eight months out of the year are still and humid.

The reference to Jared Diamond is of the remarkable switch from an estrus cycle, which the vast majority of mammals employ, to a menstrual one in a few species of great apes. It’s Diamond’s contention that this is one trait, among many, that has honed human social structure.

Males are decidedly dull, biologically, arguably switched-off versions of the default human body, which is female. With a relatively simple hormonal control system, they just can’t compete with the complex array of half a dozen hormones rising and falling, with all their physiological effect. True, it may be a pain in the neck for women, but it’s a lot more fun discussing *that* in biology courses while dispensing with males in a few minutes. Throw in the effects of constant physical stress on the female student-athletes that I work with and discussions can get pretty lively.

I admit to a mild passion for gadgets of curious function. This does not include such things as cell phones, but here’s one that fits:


I should give you some hints.

The latest conversation with my sister prompted my search for this.

Jared Diamond, in “The Third Chimpanzee” makes a fairly big deal that humans and a few great ape species are unique among mammals in a reproductive strategy that relates to my original interest in this gadget. No kidding.

It was such an intriguing notion that I found a good deal and bought 15 of them for December gifts at our annual week with friends at Jekyll Island, where yet another use may be found.

That was satisfying, for me at least. Congratulations to all who worked so hard in front and behind the scenes to help make it happen.

Now they’ve got it, what are they going to do with it?

Georgia turned slightly redder, unfortunately, but we’re hoping for indoor flush toilets next year.

SMALL UPDATE: There are two Democratic House incumbents, both here in Georgia, holding on to a slight lead at this point in their races. If they prevail, then no Democratic incumbent in any race for Governor, House, or Senate, will have lost in this election cycle, a historical first.

This plant, Euthamia graminifolia, Goldentop, first appeared last year in the side bog to the Hyla Pond. We were fearful that it would turn out to be horseweed, but last week it opened into profuse goldenrod-like flowers.


With one exception (Solidago altissima - Late Goldenrod, what we might call our House Goldenrod) our other goldenrods, (Solidago spp.), just completely pooped out this year, apparent victims of the drought, but for whatever reason this Goldentop did very well. And as you can see above the little bees and wasps are ecstatic over it. I see at least three species here.

I haven’t been able to discover what species this apparent wasp is, but it was found in abundance all over the Goldentop:


As a good many frustrated wildflower enthusiasts complain, there have been and will continue to be a good many name changes as DNA analysis continues. And as I’ve pointed out, this is a difficult but indeed necessary thing. Systematics has for decades revolved around the idea that grouping organisms must be done in a way that reflects evolutionary origin, there’s just no getting around it.

And the Asteraceae are a great way to illustrate the point. Here’s a figure from Urbatsch, et al., 2002, Louisiana State University. I’ve simplified it somewhat and connected the lines of the family tree to four genera that I’ve written about before: Solidago, the Goldenrods, Euthamia, the Goldentops, which used to be in the Solidago, and for illustrative purposes, Erigeron, the Daisy Fleabanes, and Symphyotrichum, which used to be placed in the Aster genus.

(If people scream about anything it’s likely to be the new placement of North American asters into tongue-tying names like Symphyotrichum, but again, there’s no getting around it. The North American asters have diverged enough from Old World asters, and from each other, that they just can’t be kept together anymore. Old World asters, Aster, have the priority and get to keep the simple name.)

Remember that these kinds of figures, cladograms, are basically just family trees. They show how taxonomic groups (in this case, genera within the Asteraceae family) nest together. The more related they are, the closer together they nest. (Sorry about the size of the figure - it’s really a very small .png file. )

One thing to notice here (RED ARROWS) is how far away Euthamia, the Goldentops, is from Solidago, the true Goldenrods. Remember that they used to both be grouped into Solidago. It’s pretty clear that they deserve to be separated according to DNA analysis.

What’s happened to Euthamia/Solidago will probably happen to the “Desert Goldenrods”, Xylothamia (GREEN ELLIPSES). It’s pretty clear that there are two groups that are no more related to each other than the Euthamia are to the Solidago.

And finally, just for fun, I’ve BOXED in GREEN the Erigeron and Symphyotrichum genera, just because I’ve talked about them before. Notice that the Aster genus is not even on this figure - this figure is not a complete description of the Asteraceae.

Well, that was interesting.

I very reluctantly elected not to take the camera, not knowing the various strategies, tactics, and situations involving this destructive Saturday, and I wish I had. It would have been doable. Many were the cell phones going off recording the events, and I don’t have one of those little devices from hell, either.

It was a full 12 hours though, much longer than I thought. Our little VFD sent 5 of us, certainly in the upper age cohort, 48 to mid-fifties, with one 69-year-old. Most of the couple dozen students were in their twenties, maybe a few thirty-year-olds. But they took good care of us, made us do everything, and spared us no disciplinary rod when we screwed up, which we did.

The two houses were frame ca 1950s shotgun houses on the edge of Thomson, and part of the training was to prepare them during the morning. Ventilating, packing the demo rooms with wood pallets, knocking down porches. I was relieved that we weren’t required to do any roof work.

You’ll recall that we have new PPE (protective clothing) and SCBA (breathing apparatus), and that itself took what we figured was 20 lb off the total carry weight of the old stuff, but with everything on still ran 25-30 lb. Just taking it on and off twenty times during the course of the day was valuable training - all that stuff really does need to be put on *perfectly* and many are the straps and knobs and zippers that have to be adjusted and turned. We ended up getting our tanks filled three times during the course of the day.

We had three major excursions into the buildings during set fires. We were divided into groups of four or five and stood as backup with another hose for the group going in before us. When it was our turn we all went in crawling on knees pulling the fire hose, and went to the fire. The head person knocked the fire down, we backed out on our knees, rotated the head person to the back, and then did it again until everyone had done it. Our knees are not thanking us this morning.

The first excursion was basically a (brief) classroom inside one of the rooms, where we kneeled and were told how things were going to be done. Then with 15 of us crowded into the room, breathing tank air, they lit the fire with a massive propane torch. I will have to say it was a new experience to watch the flames spreading rapidly throughout the room and advancing along the 7-foot ceiling. The instructor demonstrated correct use of the hose to knock the fire back, and then incorrect use, which produced a roomful of very hot steam and smoke, a whiteout. It was pretty amazing how hot things go even through the PPE.

The last two were the actual group sessions, and then it was time to let the house go completely. The second house followed early in the evening and was much more interesting with standup nozzles creating water curtains between the burning house and two nearby houses, and the power lines close by. The heat from that house at its peak was enough to drive us back 50 meters.

We were pretty lucky to have this particular training opportunity, which was arranged and organized very well indeed by the Thomson Fire Department, with observers and ICS staff from the Georgia Fire Academy, Georgia Forestry Commission and other various, sundry alphabetized agencies. Normal training at the Fire Academy involves a permanent “burn building” which just uses gas jets and stacked pallets in a burn-proof room, over and over.

There were two fire trucks stationed on the scene all day, with a bewildering array of hoses of all sizes we’d laid out in the morning, somehow. There was a rehab station at an ambulance staffed with EMTs. We had to have blood pressure and pulse rate taken before and after each excursion, and it was made clear that anyone who fell above a particular number would absolutely not participate. The rehab station was stocked with an apparently infinite supply of water and some gatorade-like substance. The attention to safety was amazing and was evident at each step, with the ICS support staff and instructors actually outnumbering the students. Peekholes with hoses had been carved out of the eaves of our training house, with ladders and hoses there to put out any fire that we were not able to handle. That’s attention to safety.

In an environmental sense it’s just not a good thing, although I imagine the likely alternatives of disposable would have been no better - landfill for the demolished house remains, for instance. We just got lucky.

And yes, I’m sore, and my knees hurt. But no burns! The other WVFD fellows are sore too, but we’re all intact. Ours has always been a good, congenial group - I’m fond of the other four anyway, though we’re quite different from each other. Normally I’m very chary of the bonding word, but there’s no doubt that it applies here.

I’m off this morning, a cold cold morning for us here, to Thomson GA, for a day-long structure fire training course. Five or six of us will load up our PPEs and SCBAs and sometime today will be crawling through a burning building. Apparently they’re really going to use a burning building this time.

Has your October been as nice as mine? I hope so!

Our first real, hard freeze last night. In the next few days things should begin to look quite different. Our fall colors have been slow to develop, but to my eye more intense as they do occur. We’re pretty much at the peak, I think, and it’s a very satisfying visual experience.

Here’s the monthly summary of the climate of the month of October, here in Athens and US-wide.

Like September, October was mostly dry for us in Athens, although we did have one 2.75 inch glut of rain in the last week that put us at the average for the month. Temperatures were very pleasant most of the month. Here’s a summary, for our area:

June was a study in contrasts for Athens; July was simply been hot and dry, in August we had couple inches of rain above the average for the month, and in September we were two inches below average. October ended up just right, but we had a number of fire hazard days before it did.

And now, the details:

From the National Weather Service Climate Prediction Center, this is a plot of mean temperature anomalies for the US. That’s the difference in the average temperature for this August above or below the average for September over many years, plotted in colors. The anomalies are in Fahrenheit.


October was cooler than average for much of the country, with 0-4 degF below average, especially in the US midsection and southwest. A few scattered areas were slightly above average.

The rainfall situation over the US continued to be variable for October. Again from the National Weather Service Climate Prediction Center, this is a plot of mean precipitation anomalies for the US:


The Pacific Northwest continued to receive less than average rainfall, as did Florida and the midwest. The Rocky Mountain states were above average in rainfall, as was much of the northeast and the coastal TX-LA belt.

For Athens:

After five months of drought, rains were for the first time above average during August but then fell below average in September with 2.11 inches. June, our only month that came close to normal, would have been very dry, but the drought was broken only by last-minute reprieve of several inches of rain. For Feb, Mar, Apr, May, June, July, and August our precipitation (generally 4.5" per month average) has been 3.6, 2.5, 2.4, 2.2, 4.2, 3.0, and then a bountiful 5.76 inches in August. October finished out the month, just barely reaching the average with 3.5 inches of rain.

Here is the plot for our monthly accumulation of rain here in Athens. The red line is the average over 80 years of Augusts, and the river of peach defines the standard deviation range. Blue areas mean above-average; mustard areas are below. October is one of those months that can be extremely variable, with maybe one year in four resulting in up to twice as much rain as average, but this year was not one of them. There’s a lot of mustard for most of October, and then a deluge which put us into the blue for awhile:


A similar plot for the year to date still shows a lot of mustard. We are way behind expected moisture for the year with only 32 inches in an area that expects on average about 41 inches of rain by this time. We are still 25% normal, and are in a season that is typically pretty dry anyway, at least until December:


Here is my plot of high temperatures for the month of October in Athens, clearly trending downward over the course of the month. As usual, the black dots are for the 15 years 1990-2004 (black dots), 2006 (green line), and 2005 (red line).


In the end we had 6 days, all in the first two week, above the 17-year average for that day. This is not particularly different from the average 5 days above average temperatures experienced during October. There were 8 days when the lows were at least one standard deviation below the average low, and that’s just a couple of days more than for the average number of below-normal nights over the last 15 years. October this year has quite a comfortable month, one of the reasons it’s my favorite month of the year.

Geekstuff:
NOAA’s weekly ENSO update tells us that El Nino conditions in the Equatorial Pacific continue to intensify, and will probably last well into 2007. How much of the above weather for the month is due to the current ENSO conditions isn’t clear, although it doesn’t look like we in the southeast US have benefitted much yet. There is always a delay between a clear onset and its effects, of course.

I promised a few photos of some of the grasses that are now in flower, fruit, or otherwise still keeping on. Here in Georgia at least these are either now ready to harvest, if you like them, or will be soon. They can all be found growing along roadsides, and are pretty easily identified.

I’ve mostly emphasized form over detail here, since that’s how I recognize them, and this is much how you see them without putting on your reading glasses. These are some of my favorites.

Beaked Panicum (Panicum anceps, eastern US to the northernmost tier of states) The first grass I identified, and it appears faithfully in the fall every year. It’s generally about a meter tall. Very adaptable to dry or moist, open to semi-shady. It produces copious seed of high quality and I can’t imagine that it wouldn’t be a first-rate food source. My “Forest Plants of the Southeast (and Their Wildlife Uses)”, by JH Miller and KV Miller, says that all panicums are very imortant wildlife food sources for small mammals, ground and songbirds, and gamebirds. The stiff panicles differentiate it easily from the drooping ones of the grass below. Last March I wrote about Harvesting Seeds, which might be of some value here, and there is a more detailed photograph of this hearty grass, as well as here, too.

Purpletop (Tridens flavus, eastern US) Another common grass, this one a little taller (1.5m) than the former, and more droopy. It’s ready to harvest right now, here. It’s a sparse inflorescence, with a pagoda-like appearance, but unlike the stiffer P. anceps, is wispy and waves in the wind. As its name suggests, the fruiting heads are purplish in color, not quite the white that you see here. Wild turkey and bobwhite quail will eat seed of this.

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Without a doubt, one of my favorites, Splitbeard (Andropogon ternarius, Eastern US, north to PA and southern Great Lakes). The glowing fruiting structures you see here are really and truly the way you see them in the late afternoon driving along a road. Some are forked, as below, and some are not so obvious. The fluff appears in nodes all the way down the grass, and it looks like luminescent pearls all along the browning stems. This grass is quite sociable, and a large patch of it is very dramatic in the fall.


What I call fairy wands, and others call Silver Plumegrass, this is Saccharum alopecuroides. Eastern US, north to Great Lakes.

The stalks bearing the 12 cm plumes are 2-3m tall, and are not quite ready yet. Just a little longer, although these are beginning to shed seed. The plumes persist through winter, gradually releasing seed:

Bushy Bluestem (Andropogon glomeratus, much of the US, except the northwest and upper midwest) There are a lot of Andropogons: Splitbeard above, the various bluestems: big, little, and turkeyfoot, but this one is a plush grass, very much broom-shaped, and is nowhere near ready to harvest. The flowers are just emerging now. When ready it will have fluffy white seed emerging like a brush from the brown tops, and constitutes quite a nice mass of soft brown warmth in a cold winter. Broomsedges and Bluestems remain upright and full all winter and make large dense clumps that are great for quail and other groundbird cover and nesting. We see this plant especially along the coast in southern Georgia, and it’s fairly adaptable, but particularly likes low, moist or wet, sunny conditions.

I’m working on a set of photos of late warm season sun-loving grasses in the area, but in the meantime, let’s talk about Halloween.

Halloween was basically non-existent for me; I had to work and missed the festivities such as I engage in. We seldom have trick-treaters out here in the stix, down here in the middle of the enchanted forest, but this year Glenn reports a visitation. Our neighbors brought their two little ones - Mr and Mrs and the 4- and 2-year old boys were each dressed as Harry Potter, which I thought was pretty clever.

Sometimes people ask if it’s not scary living out in the middle of the enchanted forest, but no, it’s not. Remember, it’s enchanted! Still, at one time I might have found it scary. I was after all the kid who always had to feed the dog outside and whose overactive imagination envisioned some alien or creature grabbing me from the eaves above the dogdish and hauling me up. I was also the early-20s grad student who carried a silver knife with me for at least a year as I would walk two miles from home to the chemistry building in the early A.M. hours, after having seen “An American Werewolf in London”.

This isn’t very scary, but the late afternoon stark shadows render an excellent stereo opportunity:

Click pic for crosseyed stereo images (recommended) or here for wide (opens in new page).
(Instructions for Viewing)



It’s the Rana pond basking in the late afternoon Halloween sunshine, and fairly encapsulates my feelings about the months of October and November being my favorite season. The sun is warm and possible, inconceivable just a scant few weeks ago. The air temperatures are warm to cool but always pleasant, and dry.

Actually there probably is something scary here, Ms Snapping Turtle. She’s been a fixture for the last couple of years and we assume she’s in one of these three larger ponds. She moves around, and occasionally - once this year - we catch her in the act. Needless to say, we don’t go wading around in the little ponds anymore.

The ponds of course are totally artificial, but nonetheless support a variety of insect and amphibian life.

And of course they are filled .

A view from a slightly different angle. At this time of year the benches are generally occupied by cats in the late afternoon. Is that Gene in the background there? Why yes, I believe it is.

Click pic for crosseyed stereo images (recommended) or here for wide (opens in new page).
(Instructions for Viewing)

Do you have shady areas where you can’t get grass to grow? Maybe you’re trying to plant the wrong kind of grasses.

This is the time of year for gathering seeds, and targetting “boring” grasses are no exception. I’ve been concentrating on the much more numerous sun-loving grasses - Purpletop (Tridens flava), Beaked Panicum (Panicum anceps), Purple Lovegrass (Eragrostis spectabilis), the various bluestems (Andropogon species), and two of my favorites, Splitbeard (Andropogon ternarius) and Silver Plumegrass (Saccharum alopecuroides), but I’m not here to talk about these at the moment.

Humans get the vast majority of food, directly or indirectly, from just a dozen or so highly domesticated grass species: maize, rice, barley, wheat, and so forth. Animals also get much of their food from grass species, directly or indirectly, and so grasses aren’t really all that boring. They form a mainstay that nourishes a great many birds and small mammals, and the raptorian and mammalian predators that are active during the winter.

This is the time of year for warm-season grasses to produce their seeds, but other seasons aren’t bereft. There are also cool-season grasses that produce their seeds in the spring and early summer: Six-weeks Fescue (Vulpia octoflora), for one local example, several native fescues, and many Carex sedges as well.

Sun-loving grasses aside, I’ve been increasingly captivated by shade-loving grasses, something we usually don’t think of. Grasses are supposed to be sun-loving, but this amazing family has proved to be adaptable to many different environments, and shady areas, either moist or dry, is one of them. I’m motivated not just by their presence in the shade, but by their contribution to erosion control, and competition with invasive aliens.

Here’s a shade-loving grass that I’ve written about glancingly before: Brachyelytrum erectum, or Bearded Shorthusk. It has earned the distinction here of naming an entire bottom area Brachyelytrum Barrens. It is truly shade- and moisture-loving, never venturing much into sunny and dry areas, and has become something of a heroic signature plant for me, competing with and with my help taking over large areas from the evil Microstegium.

Here’s a nice patch of Shorthusk enjoying a pleasant early autumn day, as is Gene, indulging as no cat can resist the availability of a nice log for claw-sharpening and stretching activities:


Shorthusk is a clumping grass, not particularly attractive in itself but forming large, open colonies of thigh-high expanses. It produces seed in August, and many are the times I’ve pulled these clutching, embedding seed out of my socks.

Another clumping grass that has become among my favorite shade-loving grasses is Chasmanthium sessiliflorum, Longleaf Woodoats. While it prefers shade, it will also grow along the borders of a sunny and shady area, and doesn’t mind a drier environment, such as here:


It produces a long inflorescence, and as the name “sessiliflorum” implies, the very attractive fruits form along the stem, attached directly without a pedicel:


You might be familiar with “Upland Oats”, a very common planting that resembles the forbidden “Sea Oats” (you aren’t supposed to remove those from sand dunes, or collect seeds, for obvious reasons). Upland Oats is Chasmanthium latifolium, a relative of Longleaf Woodoats, and we made the mistake of planting it a long time ago and have spent an inordinate amount of time trying to dig it out and get rid of it. Although Longleaf Woodoats doesn’t produce the attractive “oat-like” infructescences of Upland Oats, its shade-loving preference and presence in drier shadier areas makes it much more attractive to us.

Previous grass posts:

Grass Flowers
Grass Families and Evolution
Cool-season Grasses
Seed Pictures