Rick Shory

Offering a little something you might not otherwise have

veg frame showing visualized lines


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One-square-meter vegetation sampling frame, ultralight

This is an update of instructions originally published March 2001.

First, let’s look at what this is for, so the steps will make sense.

A standard protocol in some vegetation surveys is “percent cover” in a one-meter area. You are supposed to visually estimate the percent of plant species or other things. This vegetation frame we are going to build is to help with that.

veg frame showing visualized lines

What this veg frame is for

The four sides (or “legs”) of the frame are marked in 1/10 meter (10 cm) increments. This makes it easy for you to mentally grid up the ground inside the one meter square. These are the pink dashed lines in the picture above. Each small square is 1% of the full meter square.

In this example you might estimate the tree trunk as about 25% (purple solid line), or a little less. The exact way you do this would depend on your study protocol, but this post is about the equipment.

You have to carry the frame around in the field, so it is as light weight as possible. Each leg is shock-corded in pieces, like the tent poles of a dome tent. This lets you fold the frame up small for easy packing. Also, as shown here, if there is some obstruction, you can just fold part of a leg out of the way.

In a day’s work, you typically take the frame apart and put it back together a lot. So the leg ends stick together with Velcro. You can just fish the legs through the brush, touch the ends together, and they stick. One end of each leg is visually distinct from the other, so you can see at a glance which ends will connect. You don’t have to fuss with trying them all different ways.


The core of the design is the fiberglass tent pole sections. You can buy them from:

Tentpole Technologies (“TT”)

Explain that you want sections that will be one meter long, and will fold up in thirds. If TT can look up previous orders from me (rickshory.com) you can order the same thing.

If you’re really pinched for cash, ask if they will sell you the raw materials, the fiberglass pole sections and the shock cord. You can save some money by putting in the labor to assemble them yourself.

One tent pole section, showing black and white ends

One “leg”

TT typically makes the poles with one white end, and the rest black. This is all to the good. It makes the two ends visually distinct. If you are assembling them yourself, take note of how they will finally fold up, so as to be most compact.

In order to apply the colored bands, mark the poles at 10 cm intervals. It is rather tedious to make the marks one at a time, each successively 10 cm from the last. Below is an easier technique.

Lay out a strip of tape, such as blue painter’s tape (as shown below), or masking tape. Use tape at least two inches wide, or improvise from narrower strips laid parallel. Two inches will give you enough width to arrange all four poles side by side.

jig, made of a board, to align poles for marking

Jig for marking poles

If you plan to do this a again, you can make a jig by applying the tape to a 4-foot-long board, as shown. Then you can put this arrangement away between uses. If you are only going to do this once, you can put the tape directly on a table and discard the tape when done.

lines on tape, 10 cm apart

Marks on tape

Now, you only need a short ruler to lay out marks on the tape at 10 cm intervals. (The tape saves marking up your table.)

the ends of the 4 poles, visually aligned on the tape

Pole ends aligned

When you line up your poles, the ends may not align exactly. However, having the whole meter length at once lets you get them as even as possible. The ends may go part of a centimeter beyond the furthest marks, but this is OK. It’s well within tolerance.

sharpie pen, marking all 4 poles at once

Mark all 4 poles at once

Now, you can mark all four poles at once. Where marks fall on the white and silver sections, you only need a tiny dot to find the location later.

glint mark on black part of pole

Only a glint shows on black

However, on the black sections, the mark will only appear as a faint glint of a slightly different color quality (this is ink from a black Sharpie pen). Although you may have to hunt a bit for these marks, this will still be quicker than, say, sticking temporary bits of tape to mark the places.

Below is an example of a pole after the color bands are on.

example pole showing color bands

Color banded pole

I use two easily distinguishable colors, the “main” color (red here) and a “tip” color (violet in this example). The widths of the bands help visualize percent cover, but the colors themselves help keep you from losing the poles in the woods.

The main color is most important because there’s more of it. I use a color that will stand out in the environment. In leafy green vegetation, a hot color like red, orange, or yellow would be good. However, in a red desert, I might use violet for the main color instead. You may not realized how easy it is to lose equipment like this until you are actually out in the field.

rolls of vinyl electrical tape

Vinyl electrical tape

The material to make the color bands is vinyl electrical tape. Various colors are available at most hardware stores. Bright fluorescent “DayGlo®” tape would be better, but I have never found it in a field-durable form. There is a product called “gaffer’s tape” in fluorescent colors, but this is much like masking tape, and would not last long in field work.

I put the tip colors on first, to avoid mixups. You want the two ends of each pole readily distinguishable from each other, but all four poles the same. It’s easy to get confused if you start applying the color bands at random.

In all the banding, wrap the tape onto the pole tightly enough that it stretches. There are a few details that will increase field durability.

tape at the start of a wrap is angled

Tape tip angled

At the start and end of each wrap, you overlap the tape somewhat. If you start with the tape tip torn at an angle (as shown), the overlap will not bulge out so much, and will abrade less. (This example wrap will go up to the next mark on the silver section, above and to the right.)

tape being torn to terminate a section of wrap

Tear tape at the end of a wrap

At the end of the wrap, if you tear the tape at an angle, this end also will be more neat.

tape tearing at an angle, ready for the next wrap

Tape breaks at an angle

The tape will then naturally break leaving an angled tear, ready to start the next wrap.

For pole junctions that will not need to pull apart, you can just continue the tape up or down from fiberglass pole sections to aluminum ferrule. However, at junctions that do need to pull apart, make two tape wraps, one on each side of the junction.

pole junction pulled apart, showing separate tape wraps on each side

Don’t tape across pull-apart junctions


If you want to add a label, now is the time, before putting on the Velcro ends. In this example, I show my web domain. You may want to put a barcode for inventory, or some contact information so lost equipment can be returned if found.

example of a label on a pole

Example label

You want your label to still be readable, even after years out in the weather. Otherwise, it’s not worth taking the trouble. In field conditions, a label just stuck on would soon be damaged or gone, from moisture, abrasion and dirt.

labels packing slip

Weatherproof labels

A paper label would quickly degrade. I use these weatherproof labels, item number OL1825LP, from onlinelabels.com. Note that these are very small labels. You do not have much room on a slim tent pole.

tubing being cut

Shrink tubing

Even these tough labels would break down or wear off if left exposed. I cover the labels with transparent “heat shrink tubing”, often used in electronics to insulate wires. The size is 0.375″ (9.53mm) diameter. It is available from DigiKey, part number A038C-4-ND. A piece 2.4″ long is good for covering each label.

tube sleeved over label

Tubing in place

Apply a label and slide the shrink tubing over it.

tubing above a candle flame, shrinking into place

Heat shrinking

Heat the tubing to shrink it in place. Using a candle, as shown here, you can “roll” the pole as you gradually feed it past the flame. Start from the larger aluminum ferrule end to avoid trapping any air bubbles. If you take care to keep the tubing above the tip of the flame, you will not have any black soot.


I use two different colors of sticky-back Velcro, to accentuate visual contrast.

roll each of black and white Velcro

Sticky back Velcro

The hook Velcro of one color goes on one end of each pole, and the pile Velcro of the other color goes on the other end. It does’t matter which goes on the “tip” end, as long as you are consistent for all four legs. That way, you know at a glace “opposite” ends will always stick together.

Velcro strip being cut to 5.5 inches

Length of Velcro

If you cut one length of Velcro 5.5 inches long, this will supply all four pieces you need for the legs.

Velcro strip 5.5 inches long being cut in 4

Divide into 4.

You can fold this and cut it in half, then cut each of those in half again.

cable ties being made into open loops

Prep cable ties

The Velcro backing is pretty sticky. However, in the dirt and wet of field work, it would come loose. Hold it on with small 4-inch cable ties. It is convenient to prepare these by partially inserting the tail, to make small loops. Then, they will be ready to use when you stick on the Velcro.

Velcro section being wrapped around pole end

Stick Velcro on

Wrap the Velcro sections around the ends of the poles. The Velcro will overlap slightly. Note that the exact point of one-meter length on the pole is about a centimeter in from the end. This lines up with the center of the width of the Velcro.

cable tie pulled tight around Velcro, tail of tie being cut off with wire cutters

Finish

Slip on a cable tie, pull it tight, and cut off the tail.


bundle held by fingertips to show how light weight

Finished bundle

The finished set is convenient to be bundled up with a rubber band.

pole end with rubber band around

Band stowage

While you’re using the frame, you can put the rubber band around a leg end. There, it will be handy when you pack up.

bundle on scale, showing weight 9.6 ounces

Bundle is light in weight

The entire set weighs only about 275 grams, less than 10 ounces.


I developed this while working on federally funded research grants, so the design is in the public domain. You can build a set for about $35 in parts.

People also request to buy the complete sets from me. These have been people in agencies, who can’t justify the setup overhead. For materials and labor, I charge $192 per set, plus $21 shipping. Free shipping on two or more sets.

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Geotrivia

Victoria, British Columbia, Canada, is arguably an attempted clone of jolly old England. How does it compare in latitude with, say, London?

London (51.510939, -0.126423) is more than 200 miles (320 km) further north than Victoria (48.429074, -123.365744). Victoria is a little south of the latitude of Paris.

So, what does England line up with in the contiguous United State?

Nothing. The southernmost point of England, in the Isles of Scilly (49.863444, -6.400884), is about the same latitude as Campbell River, British Columbia (50.024343, -125.282589), or Garibaldi Provincial Park (49.914004, -122.751321). Further east, it lines up with Winnipeg, Manitoba (49.876143, -97.142472). This is more than 150 miles (240 km) north of even the odd jut the US border makes north at Lake of the Woods (49.384471, -95.153387).

The northernmost point of England, on the border with Scotland (55.810209, -2.036247), is 80 miles (128 km) north of the southernmost point of the Alaska panhandle (54.662193, -132.684565), so this is the only overlap between England and the USA, far southeast Alaska. Unless you count the Aleutian Islands (southernmost point: 51.215139, -179.130465), which actually dip a little further south than the M25 ring road around London (51.258421, -0.083643).

Which is further north? Medford, Oregon, far south in the state, near the California border? Or Medford, Massachusetts, in the vicinity of Boston, in chilly New England?

The two towns are at practically the same latitude. The center of Medford, Oregon (42.339493, -122.860266) is only about 6 miles (10 km) south of the center of Medford, Massachusetts (42.424104, -71.107897), so close their outskirts would overlap.

Which is further north? Portland, Oregon, with its mild, almost Mediterranean climate? Or Portland, Maine, on the icy rockbound shore?

Portland, Oregon (45.524255, -122.650313), is about 125 miles (200 km) further north than Portland, Maine (43.659443, -70.267838), which lines up on the Oregon coast with mild, green, foggy Reedsport (43.703852, -124.103028).

What does Maine line up with on the West Coast? Surely, feels like it must be Alaska!

No, the furthest north point of Maine (47.459851, -69.224461), lines up with the Southcenter freeway interchange of I-5 and I-405 (47.462883, -122.265114), in the southern part of the greater Seattle metropolitan area.

Why are west coasts so much milder than east coasts?

This is oversimplified, but: Equatorial winds push warmed ocean water from the east, which sets the major ocean basins into great gyres, clockwise in the northern hemisphere, counterclockwise in the southern. Winds in the mid-latitudes are from the west, so as they pass over the warmed water brought poleward by the gyres, the air picks up heat and carries it to the first continent it meets. Since the winds at these latitudes are generally from the west, the warmed air will come on to western shores. There are complexities beyond that, but that’s basically it.


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Gibbs economics

I was asked to review the book “Solar Hydrogen Generation: Transition Metal Oxides in Water Photoelectrolysis” in regards to alternative energy production. I loved the geeky chapters because I’m a sucker for any sort of super technical chemistry gossip. But I want to offer my perspective on the gap between such information vs. practical systems. Most people realize there are “complications”, but I would like to share my ideas on how to think of these complications in a systematic way.

I will use an economics analogy to explain a thermodynamic term called “Gibbs energy” (in older publications “Gibbs free energy”). Gibbs energy is the deal-breaker (or -maker) in a physical system, to tell whether it will “go”. It’s like a bookkeeping analysis to see if a business model is viable.

This is of course way oversimplified, but: You have raw profit, and you have organization costs. If you have enough profit, you can gloss over management. If you have a slim profit margin, your system may still work if carefully managed. There are even cases where an otherwise unprofitable system will work if you “add” enough of the right kind of organization.

Gibbs energy has two terms, which I’ll simplify to “energy” and “entropy”. Energy is the basic “bang” of the system, sometimes obvious sometimes not. Entropy is the “organization” of the system. More organized means lower entropy. In the technical thermodynamics of the Gibbs equation, the energy and entropy terms are of opposite sign. This means, conceptually, “buying” organization using energy, or vice versa.

For a simple system, like an electrochemical cell, the terms are fairly straightforward to quantify. However, any system of real relevance, such as biological life or renewable energy, is much more complex, partly because it is less definite just where the boundaries of the system are. Though harder to quantify, it can be easier to conceptualize.

For example, a pure substance is more “organized” than a mixture, thus lower entropy. Picture a gold ingot sitting beside a heap of mine tailings. The gold is more “organized” than the original state, the mountain of ore. You can see that you have to “pay” energy, effort, management to get the gold. Incidentally, the whole scene, gold plus waste rock, is now less organized, higher entropy; but that’s another story.

Back to the case of the semiconductor hydrogen reactions. At the scale of the titanium dioxide (or whatever) particles, the system “goes”. Ultraviolet light hits the slurry and activates it, splitting water into hydrogen and oxygen. (This is not technically correct. It’s actually “electrons” and “holes”, and the chemical reactions may bypass hydrogen and oxygen. But it will serve for analogy.) So far, the practical use of such systems is to get rid of some undesirable organic pollutant. The oxygen produced “burns up” the pollutant, and a little hydrogen may bubble out.

But say you want to adapt these reactions to actually get a flow of hydrogen. Now you are faced with providing a feedstock of the organic material, as well as getting rid of the “burnt” carbon dioxide. Alternatively, you could let the slurry bubble out a mixture of hydrogen and oxygen — extremely explosive. Either way, your management costs have shot up. The larger system has to be much more “organized”. Is there still enough overall energy, enough “profit”?

Say you could magically get clean hydrogen. Hydrogen is a gas, and gases are inherently high entropy, relative to liquids and solids. The atoms are flying around more freely. To bring it to a more organized, manageable state, you can see you would have to expend effort. You could compress it into high-pressure tanks. You could liquefy it at extremely low temperature. This management “costs” energy, and cuts your overall profit.

Maybe you could chemically combine hydrogen with carbon to make a fuel that would be liquid at room temperature. That’s what gasoline is, and is why such fuels are so popular. But there is yet no practical way to do that. It would take extremely organized chemical reactions. Again, the management costs.

The closest that exists so far is the work of George Olah, which has come to fruition here. At first glance, this seems like the answer. You take carbon dioxide and water and you end up with the liquid fuel methanol. Methanol is a fair substitute for gasoline, not quite as high energy density because it contains some oxygen (it’s already part “burnt”). Poisonous, to be sure, if we drink it, and will readily kill anything it’s spilled on in any quantity. In this regard, similar to gasoline. But methanol is more readily biodegraded, once dilute enough.

But peek behind the curtain, using Gibbs energy, and you see how the Iceland plant is “cheating”. The energy is geothermal, essentially free. The carbon dioxide feedstock is volcanic gases, already concentrated; that is, lower entropy. To collect the same carbon dioxide out of the atmosphere would take enormous “organization” costs of energy. Maybe someday it’ll be feasible, but not now.

I want to make a nod to the supposedly “poor” efficiency of biological life, as photosynthesis. The number is usually quoted as a sad one or two percent, compared to our even crude solar cells at 10%. But look at the outputs.

Solar cells make electricity, which must be used at the same moment it is produced. By some reckoning, it has infinite entropy. The “management” term is our huge electrical infrastructure, with all its controls, including any storage. Yes, we have made it work, but it works best for steady inputs like hydropower or fuels we can burn at will. For “higher entropy” inputs that fluctuate, like solar and wind, we have to provide ever more organization.

As an aside, I saw a blurb about future cities harvesting their own energy, the skyscrapers coated in “quantum dots”. I love it! Those would presumably be molecule-sized solar cells, each feeding into the grid. What a wonderful futuristic image, compared to the clunky ones we have now: Blocky three-by-six foot panels, weighing some forty pounds, holding arrays of hand-sized solar cells. Most people don’t realize that if even one cell in the array gets shaded, the efficiency of the whole thing plummets. (This is why solar installations look so stark. There can be no shading anywhere.) This problem could be solved, but again at an “organization” cost of more complex electronics. The management of a cityscape of quantum dots would be, well, futuristic.

But, organization is clearly the way to go. Looking again at photosynthesis, the final output is a chemically stable solid, say wood or grain. It just sits there until you’re ready to use it. This is accomplished by the extreme organization of biological life. Life just “does” it for you.

Unlike transition metal oxide systems that need scarce, high-energy ultraviolet photons, plants can get by on abundant, low-energy red photons. Plants deal with the high entropy (extreme dilution) of their feedstocks without you even noticing. They scrape together enough carbon out of the fraction-of-a-percent carbon dioxide in ambient air. From this smidgen, they build huge forest trees, continents of waving grass, fields of corn. They quietly eke out their soil mineral feedstocks in a similar way. They don’t have to go halfway around the globe for strategic metals.

Each chlorophyll molecule is essentially your quantum dot. The highly organized biochemical machinery is in place to bring that energy out into a stable carbon-based compound, such as glucose, even at the cellular level. This is done with no extreme pH sulfuric acid or potassium hydroxide electrolytes, no nightmarishly high temperatures. This energy stock can be stored locally in the cell as starch, or transported. No batteries. No spinning flywheels. No explosive pressures or high voltages. When the energy stock is to be transported, the transport system is part of the package too, in the form of the plant’s vascular system, which runs on water.

We haven’t even talked about repair, recycling and replacement of defunct equipment. For built technology, these issues are routinely swept under the rug when looking at product lifecycles. Heavy metals from electronics leach into groundwater. Plastics spiral into the oceans. Even innocuous materials have be dumped and buried in landfills.

For biological life, the recycling was all worked out millions of years ago. Dead plants just rot. Before they die and rot, they live with dust, dirt, grime, muck, random weather conditions, scarcity, breakage, etc. All the things anybody who has ever tended machinery knows can be a full time job.

Again, for real-world systems, the “management” (entropy) costs are easier to conceptualize than to quantify. But when you look at all the entropy terms that living things routinely play ball with, a one or two percent overall “efficiency” is phenomenal. Biological life is the benchmark to beat.

close up of Greenlogger, in case


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Greenlogger

From the early 20teens, till now, I have been working on a project I call “Greenlogger”.

It started from work I did with Dr. Heidi Steltzer at Colorado State University. She had the idea to log “greenness”, over the growing season, from a natural ecosystem such as a patch of prairie or tundra.

This is important in climate research. If you set up a number of such monitors, you can do experiments to simulate climate change. For example, in dry prairie, you can artificially water some sites and exclude rainfall from others. In tundra, you can melt the snow away early from some areas, using black ground cloth. You can hold the summer temperature a few degrees warmer by placing small tentlike structures. Also, long term records across many years will be able to show actual climate change.

tentlike structures on tundra

Structures used to warm tundra sites, for climate change experiments

You monitor “greenness” spectrally, that is by looking at what light is reflected from plants and whatever else is covering the ground. You want this to be automatic, that is by electronic instrumentation. For climate change research, you want remote undisturbed sites, typically miles out on the high plains, in alpine meadows, or north of the Arctic circle. Visiting such places is expensive. You can’t afford to pay for people to go there, day after day, for manual observation. The other advantage of instruments is that they have no bias or opinion, and they don’t get bored.

Spectral data is available from satellites, but only to a certain resolution, typically with pixels 30 meters on a side. If your experimental sites are only the size of a card table, the satellites will see nothing. Some day drones may be feasible, but they presently lack the reliability and repeatability, not to mention the flying range. There are various legal and jurisdiction issues with drones too.

So, Dr. Steltzer had got her research proposal funded to use individual ground-based monitors, one at each site. I came onboard to make this happen.

I inherited a good part of the design.

You might think the spectral way to monitor greenness would be to take pictures, and analyze them for the color green. This is fraught with all sorts of complications, such as dark shadows in the frame, changing light conditions, and the fact that plants are such different colors green. To keep consistent with decades of scientific work, such as from satellite imagery, the greenness factor we used was “Normalized Difference Vegetation Index”, abbreviated “NDVI”.

Here’s an oversimplified version, but it will explain the equipment design. Plants absorb visible light to use for photosynthesis, but they reflect infrared because it is no use to them. So, basically, the higher the infrared reflectance relative to visible, the more “greenness” down there. At large scale, you can make greenness maps of whole continents from satellite imagery. At small scale, there are instruments to clip onto individual leaves. We were working at an intermediate scale, looking at reflectance from a living ecosystem, such as meadow or tundra, in chunks about one meter size.

The design for the monitoring devices had developed from two directions. One, obviously, was to detect the infrared and visible spectral bands. The other was weatherproofing. Satellites are far above the atmosphere, and you can take the clip-on devices home. However, ground based instruments that will run unattended must handle all the vicissitudes the environment can throw at them. The evident choice, at least for off-the-shelf, was weather station parts.

To make all this happen, I had to use quite a bit of patching and overdesign. Some of the spectral detectors were photodiodes. These had amplifier circuits. Which needed batteries. Which required cases for those batteries. The batteries had to be kind of big, to assure they would run the whole time. And so the cases were big. And needed supports. Kind of big supports. By the time I came along, the design had solidified into the “mantis”.

site showing manits, with person for scale

“Mantis” greenness monitor, deployed in Wyoming

Can you see the resemblance? The frame of steel bars looks rather like a giant insect. The head is looking out, pensive and intent. The body is slung behind.

It wasn’t long before the mantis began to evolve. I had to adapt it for a project in Alaska. There would be more extensive data collection, so there would be additional sensors. These would require a more complex weather station box. That meant “bigger”. Each mantis would have its own solar panel. Even as a mock-up, the insect is metamorphosing, sprouting new appendages.

mantis mock-up, frame and instrument boxes

Mock-up of mantis, adapted for tundra project

The sensor cables had to be protected from gnawing varmints out on the tundra, so they all were sheathed in metal conduit. The Alaska design looked less like an insect than an octopus.

tundra version of mantis, top view

“Octopus” mantis

As in all science, you need lots of “replicates”. You can’t just have one experiment and one control, because any two sites will naturally be different. For the Alaska project we needed about two dozen of these mantises.

I had to finalize the design, and scale up for the total number of parts. I cleaned out three local Home Depot stores, to procure some parts! I had to figure things out, down to the last nut and bolt, and get it all shipped to Alaska. There would be no neighborhood hardware stores out on the North Slope tundra.

Things went well. At the research station, we spent some days in the lab trailers assembling all the mantises.

people assembling mantis parts

Mantis assembly

When they were ready, we took them out to the tundra and got them going.

person carrying completed mantis on his back

Mantis on the way to tundra site

In all, I worked on this project for three years, setting up the mantises each spring, and bringing them in at the end of summer. Each one weighed thirty-five pounds. Each one had to be taken a quarter mile out via a boardwalk, so as to keep the tundra pristine. Sometimes people helped me with them. Sometimes, in the spring, we could use snowmobiles. But still, there was a lot of lugging. I couldn’t help thinking about what all the thirty-five pounds was doing. I knew the design.

The heavy steel frames were to support the boxes, which were to anchor the sheathing, which was to protect the cables, which were to reach the sensors. But the active guts down in the sensors was — tiny. At the other end, the frame needed extra iron to support a sizable solar panel, and a big battery, to power the weather station, which had to run all the time because it was general purpose. But the actual data chip down in the recorder was — tiny.

man carrying mantis on back across tundra, Brooks Range in the background

Packing thirty-five pounds of iron

What if I could put a tiny sensor right with a tiny data chip? Suddenly, all the boxes, sheathing and cables disappear.

The spectral readings are only in the daytime, none at night. So that’s the only time you need solar power. Could the instrument “sleep” at night, and get by with a tiny solar panel, and a tiny battery, just enough to wake it up each morning?

A good bit of the mantis design was how to get the data out. A weather station case needs robust hinges and a latch, to stay weatherproof. You open it, and plug in a cable. The other end goes to your laptop, which you have to lug out to the site. You have to make sure your laptop stays charged, and try to keep it from getting rained on too much. You have to be sure to bring the right connector cable! Also, while you have the weather station case open, it can catch rain, hail, and snow. So you put in desiccant packs to dry it out. And indicator cards to monitor that the desiccant is still working. And more desiccant packs when the first ones quit.

What if you never had to open the instrument case? What if the system transmitted it’s data wirelessly, such as by Bluetooth? No need to bring a USB cable, or worry if you brought the one with the right style end.  What if, instead of a laptop, you could pull the data in on your smartphone, which you could just keep tucked inside your jacket pocket?

I started working on this. I had not done much electronics since grad school, so I had to get back up to speed. I could not use the popular Maker platforms, like Arduino and Raspberry Pi, because they need too much power. My thing had to run on the trickle of energy available from a few solar cells. I could not depend on a wall plug nearby.

So, I had to get down to the raw microcontroller level. A microcontroller is like a one-chip computer. (The word is abbreviated “uC”, as the lowercase “u” is easier to type than the Greek letter “mu” (“µ”), for “micro”.) Many uCs have low-power “sleep” modes, but you need to program them on a chip level for this.

I found that uCs had advanced quite a lot since I’d used them in my Masters project. Overall, much easier to program. Interfaces had been standardized, so it took fewer pins to connect to other chips. I knew I needed at least light sensors, and a micro-SD card for data storage.

I got used to surface-mount components. Before this, I had always worked with through-hole parts. Through-hole electronic parts have wire leads that you put through holes on the circuit board. Then, you melt solder into the hole. This both makes the electrical connection and holds the wire in place. With surface-mount, however, the component has only metal patches for leads, or short pins. These connect to flat metal pads on the circuit board. The solder acts as both an electrical bridge, and “glue” to hold the part on the board.

through hole and surface mount light emitting diodes

Through-hole compared to surface-mount (SM) LEDs. The SM LEDs are the three pale patches in the carrier strip.

With no wire leads, surface mount parts can be much smaller. At first it was mind-bending to work with an electronic chip no bigger than a grain of aquarium gravel. Steady hand, and don’t sneeze. Pretty soon, though, I was thinking, “This one sure is wasting a lot of board space. Can’t I find a smaller version?”

greenlogger prototypes in glass jars

Prototypes in Mason jars

Some of my first prototypes were in Mason jars. I learned that you can mollify the TSA by simply putting a nice note, with your phone number, in your checked baggage. Say something like, “This is a vegetation data recorder, for environmental research.” No need to say, “Not a bomb!”

Once in a real case, I hoped it looked less like a bomb.

greenlogger prototype boards in clear plastic case

Prototype in weatherproof case

I called my device “Greenlogger”. I was doing this on my own, not part of any job. Of course I thought about eventually making some money off it, but I wanted it reliable first. So, instead of trying to sell them at this point, I offered to loan them out for testing.

There is no substitute for real-world testing. I did not know if it would work to run the instrument in a totally sealed case. Maybe the electronics would get too hot, or there would be some other problem. But I decided to try. I rigged up some basic stands from PCV pipe.

greenlogger mounted on stand made of PVC pipe

Simple stand

In field tests, the instruments worked, but I learned other things too! At one site, where researchers set Greenloggers out on Colorado’s Mt. Evans, at 14,130 ft elevation, animals tore the heads off. What else would leave teeth marks? So I had to re-design the mounts.

In a few years, my Greenloggers were standing in the field next to mantises. The solar power was keeping them charged, so they could run indefinitely.

field site in Wyoming sagebrush, both mantises and greenloggers

Greenloggers with mantises

The scheme I came up with to get the data by Bluetooth was tap-to-wake. Most of the time, the Bluetooth is shut off, to save power. When you want to communicate, you rouse the logger with a sharp tap. My design contains an “accelerometer”, which measures all forces of acceleration. A tap is a rapid acceleration, and so it’s the signal to wake up and connect.

Overall, things were working pretty well. The light sensors were getting readings that spanned about 6 orders of magnitude, from moonlight to full noon sun. I put a temperature sensor on the circuit board. This would not tell much about the environment during the day, when the case bakes in the sun. However, it might give a clue if something failed. If an instrument died, and the temperature record leading up to that was climbing and climbing; well we need to figure out how to keep things cool. At night, though, the instrument temperature would drop to ambient, and the record would correspond to local weather.

Greenloggers mounted above head-high vegetation, on long-legs PVC stands

Long-legs Greenlogger stands

It’s important for an instrument to know what time it is. Each mantis was, essentially, a semi-mobile weather station. Weather stations need to timestamp their data. If, say, the temperature is recorded, but not when it was that temperature, well, that’s not much use.

Commercial weather station instruments incorporate a real-time clock (RTC). This is like an embedded wristwatch. Modern electronics can keep pretty accurate time, to about a minute per month. For the mantis weather stations, the RTC would be set during the initialization process, while connected to a laptop. After that, it’s understood that a free-running RTC can “drift”, that is, run a little fast or slow.  To keep it accurate, you need to periodically correct any drift, and that means a field visit.

I built an RTC chip into the Greenlogger. You can set the RTC by Bluetooth, so you do not need to open the instrument case. My prototypes kept pretty good electronic time, but of course there was the inevitable drift. This was not going to be good enough for months, or years, of unattended operation.

Early on, I considered a doing it like radio clocks, which set themselves by the US standard time signal transmitted from Colorado, or perhaps use one of the European services. But my instruments might be deployed in far remote locations, out of range. I needed it to work anywhere in the world. I thought GPS would be the way, but it took a while to figure out.

GPS works by triangulating on three satellites. The GPS receiver knows the distance to the satellites by very accurate time signals, so timing in inherent in the technology. GPS output contains this time signal, along with the location.

A big part of the solution was simply the physical technology. A “GPS receiver” basically consists of a chip and an antenna. The antenna has to be good enough to pick up the faint signals from distant satellites. The chip (or chip set) handles all the complex math of extracting those satellite signals into simple usable data. Both the antenna and the chip posed serious conundrums in terms of size, cost, and power management in my design.

The good news is that GPS is becoming so universal that the technology is advancing rapidly, and things are being mass produced. I could get the chips for under $10, in quantity. The antenna, however was another matter.

Discreet antennas are expensive, and take special connectors so as not to degrade the signal. Also, they are quite “big” as electronics goes. An integrated circuit chip can be shrunk to the size of a rice grain, because it does everything by microscopic transistors. However, an antenna has to be a certain minimum size to match the wavelengths it deals with. The GPS in your smartphone actually uses part of the internal metal casing for its antenna, but this is serious woo woo design, like doing acupuncture on a cricket.

Fortunately, modules were becoming available that integrated the GPS chip right with an antenna, as well as all the onboard electronics. I designed in one of these modules, but then the company went out of business. This was right when I was putting some of my prototypes out for long term testing. So they had a “hole” in the board where the GPS was supposed to be.

Other products came available, but they were bigger, and harder to interface. “Big” may not seem like much of a complaint when the thing is half the size of your thumb, but board real estate is precious. I had finalized my design to fit in a certain small plastic case. If I had to rework that, it would be a big step backwards.

GPS is a classic example of “asynchronous”. For an electronic system to read, say, a memory chip, or a sensor, it just, well, reads it. This happens in a nanosecond, or at worst a few milliseconds. On the other hand, a GPS subsystem doesn’t just “have” the data you want. It has to go get it from the satellites. This can take a few minutes, or at worst half an hour! For my Greenlogger, this ought to be OK, because it just needs to correct for RTC drift maybe a couple times a month. But how to run that?

I had found a new GPS module that would work, but controlling it was looking complicated. My main uC would be pretty busy: First, it would try to wake up the GPS. Then, check if the GPS actually did wake up. Next, see if the GPS is transmitting anything. If so, see if what the GPS is transmitting makes any sense. If it does, winnow through the firehose-spray of information the GPS is emitting, to see if we have got a time fix yet. If good, snip out this tidbit, and set the system time. Keep track of how long all this is taking. It could be, we are stashed in a metal file cabinet somewhere, and the GPS is never going to get a reading. If it takes too long, forget it. Gracefully shut down the GPS, whether we got a fix of not. Make sure the GPS is correctly shut down, so it isn’t leaking precious system power. If we never got a fix, peek out every now and again to see whether the project scientist has finally put this device outdoors under the open sky, where we can breathe!

This would have taken about a quarter of the total computing power of the main uC, juggled in along with all the normal data logging. It would have taken a bunch of board space, and a rat’s nest of signal traces. I started toying with the idea to put all this on a separate board, with it’s own auxiliary microcontroller. The GPS module itself was already on a separate board, in order to fit everything inside the instrument case.

This turned out to be the solution. There is kind of a joke in microcontroller design, about sleep modes. Modern uCs feature a wonderful array of sleep modes. The uC can shut down functions to save power. But if a uC goes too deep asleep, so it isn’t doing anything any more, how can it ever wake up again? Kind of like the joke about write-only memory. But in this odd case, it was just what I wanted.

The main uC chip sends one time-request pulse to the GPS uC, and then forgets about it. The GPS uC takes it from there. It handles all the waking up of the GPS module, babysitting it while it watches the sky for satellites, and patiently listens to it babble about what it’s seeing. If the GPS module takes too long, its uC puts it back to bed. But if all goes well, the GPS uC finally gets a valid time from the GPS, and sends it as a set-time signal back to the main system. This is the same signal you can enter, say from your smartphone, to manually set the time. The main system has only the relatively simple housekeeping, to keep track of how many days since it last got a time update, and periodically ask for a new one. Meanwhile, every time the GPS uC runs, it finishes by swallowing a whole bottle of sleeping pills. So it then uses no more system power. This is OK, because each time the main system wants a time signal, it brute-force resets the GPS uC, to raise it from the dead.

After a number of design iterations, I finally had it so the Greenlogger could set its own time anywhere in the world. The GPS module added a somewhat uncomfortable $30 to the parts cost, but, well, how much would it be send a technician to, say, Greenland once a month for the sole purpose of updating the instrument’s clock?

Greenlogger, on camouflage colored stand, to blend in with sagebrush terrain

Camo Greenlogger

In spring of 2014, I had the opportunity to set out three Greenloggers for long-term testing, at remote sites in western Wyoming. In autumn of 2016, I went back to look for them. One had been stolen, but the other two had kept on running through two winters, recording temperatures down to -24 degrees Centigrade.

In the winter weather, one of the instruments held a record of temperature staying at exactly freezing for about three days, with muffled light levels, indicting it was buried in snow. Then, as its battery ran low, it went into hibernation and stopped recording. It remained running in ultra-low power mode. About ten days later, when it got more solar power, it woke up and started recording again.

Overall, I was satisfied how robust they were, but this was in the gap when I did not have GPS working. After two and half years, both devices had serious clock drifts, of 4 and 5 months! So now, with GPS installed for automatic time setting, I have prototypes out for winter testing in Greenland and Alaska.

I thought these loggers could be repurposed. For example, they already serve as solar site evaluators. They record just how much sunshine reaches a spot, day after day, through all weather.

They also serve as trackers. One prototype I loaned, was shipped back to me, broken. From the log, I could see what had happened. I had packed it up to ship at 6:30 PM on June 25, 2017. After that, it recorded darkness. About 5 PM on July 11, it started detecting light again. It got a GPS fix, and corrected its clock by 31 seconds. It also recorded that it was now in Alaska, on a tongue of land in a small lake in the middle of Yukon Delta National Wildlife Refuge.

Research collaboration plans change. A few days later, it recorded that it was at the airport in Durango, Colorado, evidently en route on a transfer to Greenland. On July 20, it recorded a location on Cape Cod, Massachusetts. That evening, it was dropped hard enough to reset. It lost its location, though the clock kept running. The same thing happened a couple more times over the next few days. On July 22, it was recording temperatures below freezing. Freezing in late July? Greenland! The light level traces showed the never-quite-dark summer cycle of the midnight sun.

Then, on July 24, the record abruptly stopped. I received the device back August 9, shipped from an address in Maine. The battery clip was broken off the circuit board, evidently from impact. Repaired, in Portland, Oregon, it recorded the solar eclipse of August 21, 2017.

Every electronic system needs a Reset button. To avoid having to open the instrument case, I had equipped the circuit with a magnetic reed switch. This works similar to how a strong magnet picks up a chain of paper clips. The magnetism travels through the iron, and makes normally un-magnetic pieces stick together. In the Greenlogger, you can bring a strong magnet close to a certain corner, and two tiny contacts, normally separate, will touch. Thus you can “press” the reset button from outside the case.

It turns out other things can make the contacts touch, such as a hard slam. I thought about leaving this in the design, to determine if the scientists were playing softball with my instruments. But, no; if I want that I should program the accelerometer. Instead, I plan to replace the reed switch with a magnetoresistive sensor, which responds only to magnetism, not physical shock.

close up of Greenlogger, in case

Latest design

I know of one more issue I need to fix. I call it the climb-out-of-reset hang. The commercial weather station boxes we used have this same problem. It is classic in energy harvesting designs.

If ever the battery discharges too low, so the system completely stops, the instrument can never start up again, even with sunshine blazing on the solar panel. It seems there would be plenty of power available, but this is what goes wrong:

Say the battery drains down, and the system totally dies. When there is solar power again, the battery starts to recharge. There is an exact point of voltage when the system electronics are just barely able to start. They start, and try to run through their initialization routines. However, this small sip of power is enough to drop the battery back down below the critical threshold, and the system dies again. The battery recharges. The system starts — and the cycle repeats, forever.

If you connect the system to a well charged battery, the voltage droops a little during initialization. But right after a successful startup, the system can go into battery management mode, and keep itself on a strict energy diet. However, on a slowly-charging battery, what the system really needs to do is hold off on powering up, at all, until the charge is well above the start threshold. But the system had no way to know how to do this — because it’s still dead.

Since the system cannot rely on the intelligence of the uC, it needs some sort of hardwired holdoff circuit right up next to the battery. This is tricky because these “dumb” electronics have to work, and make critical decisions, based on fractions of a volt. Not much electronics works reliably on fractions of a volt!

Everything else in this project was impossible, but now it’s working. It’s going to be really cool when the holdoff circuit is too!


Documents for using Greenloggers: https://github.com/rickshory/Greenlogger-Docs

The code that runs the Greenlogger microcontrollers:

Main board uC code: https://github.com/rickshory/AVRGreenlogger

GPS board uC code: https://github.com/rickshory/GPS_time_841

The printed circuit boards: https://github.com/rickshory/Greenlogger-PCBs

The mantis was developed under government research funding, and so is in the public domain. I wrote sections of the documentation, which includes instructions for data processing. We developed two tools for processing data from the mantises, Greenloggers, and other recorders such as iButtons.

The documentation: https://github.com/rickshory/mantis-docs

The two data tools:

One using, Microsoft Access: https://github.com/rickshory/mantis-Access

A cross-platform one using Python: https://github.com/rickshory/NDVI-modules

 


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Proteins wrecked by microwave ovens?

I was out hiking with Dr. Jeff, another chemistry nerd. He has long been in touch with, and sympathetic to, the health and woo woo scene. He mentioned that people back in the 1980s were concerned that microwave ovens were racemizing the amino acids in protein.

I was astounded. Perhaps most amazing was the fact that none of the people I knew who were opposed to microwave cooking had ever mentioned this before. It seemed like it could be a very legitimate health concern. However it also seemed like it would be fairly straightforward to get a definitive answer, one way or the other. Either this is a big problem, and there’s a huge cover-up going on. Or else it’s not a problem; but if not, why not?

Amino acids (all except glycine) exist in two forms, left- and right-handed. This is analogous to how a glove can be either for your left hand or your right hand. Unlike gloves, which usually work in pairs, biological life can normally use only one of the types, say left-handed. The requisition is for shipments of only left-hand gloves.

Left- and right-hand gloves are mirror images of each other. You can toss a left-hand glove around any way you want, and it doesn’t change into a right-hand glove. Well, unless you turn it inside out.

At this point, the analogy breaks down. An inside-out glove is not “really” the other-handed glove. The stitches show, and the lining is different. But on a molecular level, if you flip an amino acid “inside out” it actually becomes the other form. Clean, with no seams.

I am not going to go into this too much, but the “handed-ness” is from the four bonds of a carbon atom being tetrahedral. You can look this up if you want, but basically, if you take a tetrahedron, and mark each of the four points a different color, you can do this in two different possible ways, and the two ways are mirror images of each other, left- and right-handed.

Atoms are not really hard little balls, as they are modeled. Everything is always swinging, jostling, twisting. The parts attached to the four tetrahedral points are getting shoved around. If things get knocked, just right, and with enough force, one point could get pushed between two of the other points, momentarily crowded in an uncomfortable way. Then the bonds would pop back into a tetrahedron — but now in the other mirror-image shape.

As soon as Dr. Jeff mentioned it, I could immediately see that microwaves might be just the right energy level to do this. They are not strong enough to break bonds, but presumably could rearrange bonds. Parts of molecules easily resonate at these low energies, with bonds stretching, swinging, scissoring. Was it dire? Or no issue?

Say you had a washer-dryer or something that had the strange power that when you ran gloves through it, it could knock them inside-out. This analogy is a bit forced, but is to explain the chemical term “racemize”. Say, you put in a batch of left-handed gloves. They would start getting turned into right-handed gloves. The process is random, so soon some of the right-handers start getting turned back into left-handers. Eventually, you end up with a fifty-fifty mix. In chemical terms, this would be a “racemic mixture”, and the molecules would be said to have been “racemized”. In biological terms, living things only want the left-handers. Are the right-handed ones inert waste? Or poisonous? Or will they have some weird effect nobody bargained on?

Armed with these search terms, I started investigating. It turns out quite a bit is known about amino acid (“AA”) racemization. In the rough-and-tumble of molecular existence, it has been going on ever since there were AAs. Some AAs are more susceptible than others. And there are factors of the molecular environment. For example, a particular AA built into a protein may be like a glove clenched around something, and therefore quite difficult to turn inside out. Or presumably, it could be otherwise, and easily flipped. Still, all else being equal, at higher temperatures it goes faster. Heat equals molecular jostling, and stronger jostling means higher probability of a strong enough knock to cause the flip.

Ok, we can start to relax. Since racemization is constantly going on, life has had to deal with it from the get-go. The wrong-handed AAs are not poisonous. Life either spits them out, or possibly has ways to pop them back into the correct form. That would be the topic for another investigation.

But, are microwaves speeding up the process, and “wasting” the food value of proteins? Interestingly, the only search hit that included “microwaves” was a process for intentionally racemizing AAs, bragging that it was as good as ordinary heat. It makes sense. Heat is just molecular motion. Microwaves jostle the molecules, and so add heat.

Since racemization is a random process, the longer time it goes on, the further it progresses. So I am probably getting more AA racemization in my slow-cooker crock pot, than in the fast zap of the microwave.

One of the most interesting links that turned up was using AA racemization to estimate the age of whales. The lens of a whale’s eye is largely protein. It gets laid down, layer by layer as the whale grows, from the outside, like rings of a tree. The inside, the “heartwood”, has been there for a long time. AA racemization has been going on, in its random way. Whales live in the sea, where the water is of relatively constant temperature, so the faster-at-higher-temperature racemization rate is not such a factor. I’ll let you look it up, if you want to know how old the whales really are.

Myself, I’ve moved on to worrying about other food problems than AA racemization.


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Video plant ID with your smartphone

Since what-you-see-is-what-you-get through a smartphone camera, you get the view through any lens you put over it.

However it’s hard to keep everything steady while taking pictures.

You can hold your botanical hand lens in place with a rubber band or two, like this.

lenshack

Here’s an example of the results.

magpic

Of course, you can also shoot video. If it’s a video call, like Skype, you can ask the person at the other end of the line about the plant as you pan and zoom around it.

A simple example like this, (Oxalis corniculata L.) you would naturally identify yourself, without any help. However, suppose it were something outside your experience, such as:

LOPE_closeup

Here’s the real value of video plant ID. You can draw on expertise anywhere in the world you have connectivity.


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Poplars north of the Brooks

Title: Populus North of the Brooks Range: Temporary Adventives, or Yet Another Sign of Global Warming?

Abstract:

Populus L. is rare north of the Brooks Range in Alaska. Populus balsamifera L. (balsam poplar) is noted from a few refugia and Populus tremuloides Michx. (quaking aspen) is not reported at all. The current observations, however, find them both to be fairly common in disturbed areas such as roadsides and old gravel diggings. This may represent northward spread of these species due to climate change, or merely temporary survival after accidental introduction. These first observations are presented as a baseline, to allow determining this in future years.

Introduction:

The word “tundra” means “treeless”, and that is the character of Alaska’s North Slope, from the Brooks Range to the Arctic Ocean. In this open country, trees stand out. People have noted the few stands of Populus balsamifera L. (balsam poplar). One grove is at Ivishak Hot Spring, where geothermal warmth creates a microclimate equivalent to much further south. Scattered populations of P. balsamifera are known from along major rivers, where flowing water evidently contributes to warming the soil. One locally known site is a very steep south-facing slope in a sheltered hollow.

The limiting factor is evidently permafrost depth. Tundra soils are typically frozen most of the year, with only the surface thawing in summer. The permanently frozen subsoil, which extends to great depth, prevents penetration by tree roots. The common factor in all previously observed P. balsamifera stands appears to be that the soil thaws to greater depth than typical for the North Slope tundra.

Populus tremuloides Michx. (quaking aspen) is the tree with the greatest range in North America, being found in all of the 50 United States. Yet the range maps in both Flora of Alaska and of NRCS indicate it is not present north of the Brooks Range at all.

This observer, therefore, thought it was remarkable when he began finding both of these species near Tookik Field Station (TFS). Toolik is the site of many ecological surveys, with exhaustive documentation of all natural phenomena. Yet Toolik botanists were evidently unaware these two species existed in the vicinity.

Methods:

These observations were undertaken during a brief stint at TFS, 26 August to 7 September 2011.

The overall plan was to record parameters on each individual of Populus seen. The goal was to choose parameters that will readily show changes in health, biomass and/or abundance in future years. The parameters chosen were GPS location, height, age, and number of clonal stems. In addition, digital photographs were taken, though these may be of limited usefulness as hard data.

GPS locations were recorded using a hand-held Garmin GPSmap 60CSx. Positional accuracy was typically good to 2 to 3 meters. Locations were recorded as waypoints. Individuals of Populus were scattered, so there was seldom any ambiguity as to which waypoint corresponded to which individual. The datum was WGS 84. Waypoint coordinates included both decimal degrees and UTM. Waypoint timestamps were automatically recorded in Pacific Daylight Time (default time zone for the device).

Where coordinates are given in this document with no other explanation (for example: 68.03210853, -149.67015512) the first number is latitude and the second is longitude, both in decimal degrees. Positive latitude means north of the equator and negative longitude means west of Greenwich meridian. The datum is WGS 84.

Heights of individuals were measured using a folding 2-meter tape, and are given in centimeters, to the nearest centimeter. The number recorded is the maximum height of any stem from terminal bud tip, measured straight down to solid ground surface. Seldom was there sufficient slope that the “tallest” stem by these criteria was in question. Much of the local tundra is spongy, so “solid ground surface” could be indefinite; but all Populus were on sites having a hard substrate covered by no more than a litter of fallen leaves.

Determining individuals

Both observed species of Populus have a marked tendency to send up adventitious stems from their spreading roots, and thus to become clonal colonies. In only one case was there any possible ambiguity as to which aggregation of stem represented a clone. In this case, two clumps were near each other, not much more distant than the size of the clumps. In all other cases, clumps were widely separated.

At the observation time, deciduous tundra species were in the process of normal autumn senescence, their leaves turning yellow and gold. The different Populus clumps varied in shade of leaf color and timing of leaf fall, providing another means of distinguishing the various clones from each other, and from Salix (willows).

In the data record, each Populus clone is considered one individual. In the single ambiguous case, the two clumps are recorded as separate individuals.

Individuals are coded using the standardized NRCS species codes, followed by an underscore and a three-digit numerical identifier. The numbers are the order in which the individuals were found, 001 being the first. The NRCS code for P. balsamifera is POBA2, so the code for the first individual found of that species is POBA2_001. The species code for P. tremuloides is POTR5, so the first found individual of that species is POTR5_001.

In recording stems per clump, stems were counted as distinct if they had at least 1 cm of space between them at ground surface. This arbitrary criterion might possibly yield some confounding counts in future years, if stem bases widen to have less than this distance between. In most cases, however, stems were either well distinct, or closely aggregated. Clones that produced aggregated sprouts appeared to be rapidly proliferating. If such clones remain as healthy in future years, the stem count will increase to indicate this, even if there is some uncertainty in the number or stems.

Some stems were very short, but they were counted if they had even one recognizable leaf or bud.

Distinguishing species

P. tremuloides is easily recognized. The leaves have a distinctive shape range, from cordate to broadly lanceolate, often wider than long. The laterally flattened petiole, which causes the leaf to “quake”, is also diagnostic.

P. balsamifera would not be confused with P. tremuloides but possibly with some of the shrubby Salix (willows). All had yellow leaves (at the observation time), and some Salix leaves were similar in shape to P. balsamifera. However P. balsamifera stems have a distinctive upright growth habit with a central leader, while all local Salix are spreading. After eye training to develop a search image, P. balsamifera was easy to spot. An unambiguous diagnostic was the axillary buds. In P. balsamifera these have a large, pointed, enwrapping scale with a shorter truncate scale distal to (“in front of”) the large scale. Salix have a single sack-like bud scale.

Populus Axillary Bud

Axillary bud of P. balsamifera, showing bud scale structure common to all species in the genus Populus. This unambiguously distinguishes them from Salix (willows).

All putative Populus individuals were checked for these diagnostic characteristics.

Age estimates

Age of Populus individuals was estimated by counting bud scale scar rings. This is a non-destructive technique useful for estimating growth years of woody species where the plant can be observed all the way to the top.

Bud scales are modified leaves. When they fall off after bud break, scars remain on the stem similar to those left by the bases of petioles of regular leaves. Since the bud scales are in close proximity to each other, their scars form a visually identifiable “ring” around the twig where the terminal bud was that winter.

As the stem elongates out of the bud during the season’s growth, the first leaves are close to the bud scale ring, and close to each other. As growth continues, the leaf bases become spaced further apart, up to a typical maximum.

As stem growth slows in anticipation of dormancy the leaf positions again become closer together. When the terminal bud forms, the bud scales have no stem extension between them, and so their bases form another ring.

Bud Scale Scar Ring

Ring of bud scale scars on P. balsamifera stem, indicating sections that developed during two succeeding growing seasons. A few bud scales persist.

It is thus possible to read back along a stem and count the previous seasons of growth. The pattern of leaf/scale scars becoming more distant from each other and then close together again defines a year of growth. It is usually possible to read back at least 5 years at high confidence, often more.

Deciduous trees can perform two or more cycles of bud break and growth in a single year. This is rare, and usually due to extremely favorable growing conditions, unlikely in the arctic.

This scar ring count can only yield a minimum age, for various reasons:

As woody stems become older, the bark thickens, stretches, and cracks. This finally obscures the leaf/scale scars.

Many deciduous trees have the ability to persist as stunted seedlings for years, then grow rapidly when conditions improve. Coupled with bark roughening at the stem base, this could hide many years of a tree’s age.

If a stem is broken off, growth resumes from a lateral bud. All the growth information above the break is lost, though the remaining stub above the activated lateral bud indicates at least one year’s growth, and the change in branch angle is evident. The Populus stems observed had many partially missing tops like this, probably due to winter storm damage.

Similarly, aboveground stems may be completely removed by browsing, disease, or winter kill. If the roots re-sprout, as Populus easily do, scar rings can only count the years since this occurred. In a few cases the remains of dead stems indicated the clone was older than the oldest living stem observed. Usually, though, the group appeared too young for this to be so.

Search protocol

A “GPS track” was recorded while searching for individuals. This is a semi-standard technique used in rare plant surveys. The GPS receiver is set to internally record a position periodically by time interval, by distance interval, or by an “auto” algorithm combining both time and distance. The “auto” setting was used.

This track provides a series of locations that define a search path. Since recording is automatic, it does not distract from the search. Each track location is timestamped. This allows geo-referencing of the digital photographs by matching the photo file creation timestamp to the nearest track point timestamp. Timestamping also verifies observation date and time.

The track can later be displayed on a map to show the path searched. It can reasonably be assumed that any individuals of interest within a certain proximity to the search path would have been seen, the proximity depending on terrain. In the open North Slope tundra, this proximity would be at least ten meters either side of the search path. By this means confirmation of absence can be established for an area.

(This post is under construction.)