Rick Shory

Offering a little something you might not otherwise have

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Summer in Ketchikan

I don’t think I could ever explain my life in Portland to the people I get to know on field projects. It would be as hard to explain my field life to Portland. But I’ll try.

I’m in Alaska two months, working for the Forest Service. I’m doing plant surveys, which uses my botany skills. I’m based in Ketchikan, though most of my work is much more remote. I’m out all week where there is not even phone service.

The land around here look like Oregon at 4000 feet elevation. Imagine being on a mountain lake in the Cascades, the hills all around in green forest. The alpine starts a mere thousand some feet higher. From my bunkhouse room in Ketchikan, I look up at a little peak called Deer Mountain, an afternoon hike. The pale green alpine meadows stretch above the dark green forest. There is still one patch of winter snow high up on that mountainside, though that white dot shrinks week by week.

Now imagine your mountain lake stretches for miles, zigzagging through every valley, till it cuts up all the land into a series of islands, inlets and fjords. Make your lake salt water, and there you have this part of Alaska. There are few roads; the sea channels are too wide for bridges. So it’s mostly getting about by boat. Or seaplane.

We boat out to the work area Mondays. When I was coming up here, friends said, “Oh, you’ve got to do the Misty Fjords tour!” Well, I get the tour of misty fjords a couple times a week, and paid to do it. Misty means it rains a lot, and even when it doesn’t rain it’s wet. So a lot of work in rain gear.

The remote quarters is a barge. This sounds grim, but isn’t. The “barge” is a very nice two-story house, floating on the water. On the water makes a lot of sense. No mice, no bears trying to get in the windows. And a tugboat takes it to town for winter maintenance.

I work alongside people surveying for wildlife, forestry, and fish in the streams. Along side, to get out to the sites, on overgrown logging roads. Then, they are going up the creeks in hip waders, or scrambling the ridges giving bird calls. I’m pretty much alone in the forest.

My procedure is to go through the forest looking for any rare plants. By now, I know all the normal Alaska plants, so anything unusual would stand out. Sometimes, an atypical formation of leaf catches my eye. But then it turns out to be only a common plant, chomped by deer so it looked odd. Or something like that.

Entering the forest is like crossing the veil into another world. At first, I would look at it from the road, an impenetrable wall of brush and boulders. I could not see a person could actually get into that. But now, I scramble in. In twenty yards, I’m in a dim grotto beneath tall trees. Moving through this is not so much walking, more like the sport of parkour. Southeast Alaska forests are an obstacle course of head-high huckleberry brush, gigantic fallen logs, root wads, ferns, skunk cabbage, devils’ club, and rock formations. Fortunately, it is mostly layered in thick green moss, like foam rubber. So, when you stumble, you bounce.

This whole land was covered in glacier not too long ago. I get the impression, the ice, one day, just melted, leaving a wild terrain of jagged peaks, jumbled boulders, cliff-sided ravines, and random hollows. Then it rained. Soon, everything was covered in thick green moss and trees. Water filled the hollows to make lakes and swamps, then found its way, as best it could, into streams and creeks. The drainage patterns seem to defy gravity.

There are lots of bears. I have not seen a bear, except occasional ones as we drive around a corner. The bear looks at our oncoming rig, turns, and lopes off into the brush. I have not seen a bear when I am on the ground. But I know they’re there. Scrambling through the forest, I see lots of bear “sign”, some of it still steaming, with flies buzzing around.

I am not much afraid of bears. I have worked in the woods for years, and every bear I’ve ever come across was running away from me as fast as it could go. Bears have learned that things smaller than themselves can still be dangerous, such as porcupines. Bears that encounter humans associate us with things mostly bad. Bears have an even better sense of smell than dogs, a range measured in miles. I imagine them complaining how we stink up the forest with our boot rubber.

I am not much worried about an encounter with a bear, though maybe I should be. I do carry pepper spray. A better precaution is just letting the bear know I’m there. I try to make lots of noise, so there are no unpleasant surprises. It’s likely that when I arrive, often a bear will move discreetly one hill over, and I will never even.

The euphemism, “wearing bear repellent” means not taking showers, and thereby letting yourself smell very much like a man. I personally think that’s a very good idea. The more the bear can smell me, and knows exactly what I am, the less likely I am to ever see that bear.

Back at the barge in the evening, we cook dinner. Some people fish off the deck. There’s games and videos for relaxation, till bedtime. The long Alaska daylight comes back about 3 AM, so you can wake to a bright sky, but still have hours to snooze till time to get up.

Everybody I work with is great. Maybe it’s something about government service weeds out any jerks. I guess you have to be dedicated, to put up with all the bureaucracy. There are some beautiful men, but I think no more than Oregon. After a while, it all feels like brothers and sisters.

When we boat back to town on Friday, the white towers in the distance make it look like Ketchikan is a space-age city of the future. But what you see is not the town at all, but the cruise ships. They are huge, taller than any of the downtown buildings. Locals diss the ships, but to me it’s all new and intriguing.

As we motor by, I study the cruise ships. They are so big, it takes a long time to pass one and I have plenty of time to look. They are stacked deck on deck, with a row of orange lifeboats clustered on each side, like barnacles above tideline. Each of those lifeboats is larger than the boat we’re in. On the top deck there are may be giant-screen TVs, or even whole water parks.

These tourist ships move during the night from one tiny Alaskan town to another. During the day, they’re docked, and the passengers stream ashore. A big part of the economy is tourism. Locals gripe that only in the evening, after the boats leave, you get your town back. But me, from bustling Portland, I don’t know the difference.

Ketchikan does Fourth-of-July. There is a parade, which I got the best part of by walking along side the lined-up floats. It was not hard to find. Ketchikan, like most southeast Alaska towns, consists of mostly one single street, wedged between the mountains and the water. The Forest Service quarters is on that street, so I stepped out the door, and there was the parade lineup.

I wonder who first thought up the theme of ten-years-after? It’s great, I’m sure, for all small town parades. Being as this is 2019, there was the float for “Class of 2009”. Decade after decade, they counted down. I picked the one closest to my graduation, “Class of 1969”. I figure the floats are populated by honorary X-9’s, in addition to those on the exact year. Even better, as you get along in life, you may be forgiven if you can’t even remember your exact year.

Of all the groups, the Native Americans are, of course the most interesting. Though, to me, the most cryptic. About when I got to the front of the lineup, the parade started, and I got to see it all over again in motion. The native people came along, chanting something utterly crosswise to the rest of the ambience. A song of religion? Of community? Of anger? And what did the blood-red face paint mean?

Portland parades are thronged. You get where you are going to watch it, and you stay there, unless you are willing to virtually swim through people. There’s something to be said for low-key small town festivities. At no time was there any difficulty strolling along the sidewalk, even with the whole town on the street.

Finally, the last float went by, and the smells of cotton candy and Filipino barbeque gave back to the clear salt scent of the sea.

That night, I climbed the 3rd Avenue hill and watched the fireworks out over the channel. Small craft spangled the water like fireflies. One of the tour ships had positioned itself offshore for a better view.

The official fireworks were not the only display. The public had been warned that the forest was very dry — incredibly, it had scarcely rained in a week. But some people couldn’t resist. As I headed back down the hill, fireworks erupted from right on the roadside. Some people, parked in the narrow verge on clifftop, were shooting off fountains and florals to rival anything in the official display. I mentally wagged a finger at those yahoos. At the same time I warmed to their generosity. I mean, those things cost money! I passed by, in a lull between guys lighting off a volley, then running for cover. In the fading glow, high-fives and fist bumps.

I walked on, figuring discretion is the better part. Well down the hill, I looked back. The multicolor fountains of incandescence were replaced by a calmer light display. The flashing red and blue of a cop car.


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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.

close up of Greenlogger, in case

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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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Poplars north of the Brooks

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


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.


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.


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.)

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Twilight Hike

It’s funny how I have got used to how outrageous it is here.

The snow is melting fast. It’s a couple of feet deep and real mushy when it’s warmed by the sun. It’s troublesome to walk on. We posthole, even in snowshoes. This weekend, I want to take a hike up in the hills. I think, when will the snow be the most firm? During the coldest part of the day. When is the coldest part of the day? At night. But there is no night.

A few minutes after midnight Saturday, the sun finally dips below the horizon. No, that would be Sunday by now, not Saturday. About 1 AM I set out. Bright sunset light fills the air. The entire north horizon glows, all salmon and orange, halfway up the sky. I hike out across the lake, which is still frozen solid. It’s covered a foot or more deep in icy, crunchy white snow.

I set out from the sauna landing. I head towards the cove on the furthest distant lobe of the shore. Crunch, crunch, crunch, one step in front of another. Finally, about half an hour later, I get there. The edge of the lake is subtle. The old snowdrifts slope gradually up to land. The shelving rock and willow thickets dream in the frozen twilight.

I explore around the hills in that ethereal light. I have a project. I have heard the furthest-north patch of balsam poplar is over here somewhere. I am looking for it. There are thousands of square miles of poplar in Alaska, but none here north of the Brooks Range, except these few. Tundra means no trees. It feels like high alpine meadows above timberline, except the mountains are far away.

The land rolls off to infinity in all directions. At a glance, it looks like prairie. Dark blocky shapes in the distance suggest ranch outbuildings or road cuts. But it is all to fool the eye.  Human vision looks for things like that, but there is no trace of man’s affairs in that direction for literally hundreds of miles, to the Chuckchi Sea.

I explore on. The sky overhead is never any darker than blue. The sun under the north horizon is so close that high clouds glow. The temperature is in the 20s, but so dry it doesn’t feel cold. Hours after sunset, it has never gotten dark.

About 2 AM I find the poplars. They are a miniature forest, none taller than me. They spread across a steep south-facing knoll, above a hollow of snow that, come summertime, will be a small lake. It is evidently the warmest spot in the whole area, a little pocket of further south. Years ago, maybe centuries, a lucky seed rode a storm over the Brooks Range.

Mission accomplished, I am not yet ready to turn home. I decide to see if I can find a way up a nearby small peak, Jade Mountain. Jade is a popular day hike, though the route, in summer, is proscribed. Most of the way crosses tussock-tundra, which is spongy and humpy; hard going for us humans with our flat feet. Toolik folks have found the easy route. It strings together patches of rock and gravel. But that way goes along top of a cliff, and up and down three gullies. Plus it’s on the other side from where I am now.

I am on a gradual north slope. It’s an easy grade up from a broad col. Maybe next summer I’ll come back and look at with no snow.  Probably, it will turn out to be the worst tussock-tundra ever. But here now, at the end of the winter, it’s just crunch, crunch, crunch, one step ahead of the other. Some of the easiest walking of the whole trip.

I make it to the top just as the sun is peeking over the horizon, 3:20 AM.


Moon over the Brooks Range

The moon over the Brooks Range, to the south

On the way down I think, this is opposite. Usually, the sunny side makes for the softest snow. But here I am, treading straight into the sunrise. But this early sun is far, far north. It won’t be high enough to warm things today till it has swung halfway around the sky.

I can see Toolik in the distance, a huddle of lab trailers in the white tundra. The tallest tent, the cold storage facility, glints in the dawn sun.  It looks like a plastic cathedral above an impressionist village. I head home in as much a bee-line as possible.

In places, snow has buried thickets. The black, furry twigs of Richardson’s willow evidently absorb heat, even under the surface, and rot out the drifts. More than once, in places like that, I collapse through a few feet. Not dangerous, just surprising. Soon, I detour when I see willow twigs bristled the drifts.

Other areas, even on the flats, the daytime warmth has undermined the snow, under a harder crust. The surface whumps down when I step there, sometimes in slabs as broad as a house. In avalanche country, collapsing snow slabs would be a serious warning sign, but here on the flats there is nowhere an avalanche could run.

Hiking back across the lake, I learn to step the snowshoes down heel-first. That makes the slabs fracture forwards. Toe-first will crack the snow straight down in front, which catches the snowshoe prow on the next step out.

About 5 AM I come near shore. It is full morning daylight, in bright clear sun. Over the white tundra, small birds are singing cheerily.  Some of them are robins, the same robins you might hear chirping over an Iowa farm field.

The snowy surface of the lake slopes up to the gravel pad Toolik is situated on. Uh-oh, a couple of people have pitched their tents right there. The crunch, crunch, crunch of my snowshoes cracks the morning silence. Oh, well, I think, just keep a steady pace, and get the torture over as soon as possible. Maybe they’ll forgive me, and then they will be able to get back to sleep. I climb up past the tents, making far too much noise.

I step through the banks of snow plowed up from the pad, and am suddenly back in the everyday world of Toolik, right by lab trailer 2. I slip off my snowshoes and stash them back I our project truck. I walk across the frozen gravel to the dining hall and erase my name from the trip sign-out board. Then I go to my weather port, climb into my sleeping bag, and sleep till about 9 AM.

I hiked all night, and it was never dark. Within a couple more weeks, the sun will not go down at all.

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Richardson Highway, Alaska

I sent a message to a guy today, something like:

  I’m going to be through [your town] tomorrow.  I’d like to stop and say hi.  If that’s OK here’s my phone number so you can call me so I know how to reach you.

  Now I am tortured by remorse.  I feel like this was a totally inappropriate thing for me to do.  He and I have had a couple of exchanges.  Friendly enough, but he has put out only road directions and travel advice.  He has shown not one spark of interest in meeting me.

I keep telling myself, I left him an easy out.  All he has to do is not answer.  But this violates one of my strong working principles, of letting myself know what I know.  I knew he was not interested, and I was trying to pretend otherwise.

On the other hand, if I had not sent that message, I would be tortured by remorse.  I would be calling myself a coward for not even having the guts to send a simple message asking a guy if he wants to meet me.

I would be reminding myself I am trying to break out of the middle-child paradigm.  The middle child grows up with no expectations.  Unlike the oldest, the middle child never got the attention of being the only one. Unlike the youngest, the middle child never got to be the baby.  He just got lost in the shuffle.  He lived on hand-me-downs, and learned to make his own fun.  And now he doesn’t know how to ask for anything, at least not in any way that’s going to get it for him.

Ain’t no way to win!

Rainbow, among high trees

A splash of rainbow. View from the highway. A rainstorm, as autumn comes on.

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Turnagain Arm, Alaska

Six times, from the air, I have studied the lay of the waters around Anchorage.  Once on landing and once on take off, each of the three times I’ve been through Anchorage International Airport.  Knik Arm and Turnagain Arm are the two waterways that bracket the city.  From the above, they looked like forbidding masses of swirling grey water.

Finally, I am exploring Anchorage and environs from the ground.  The Chugach Mountains provide a spectacularly beautiful setting, and I have a sparkling day of warm September weather.  I am gratified to report that, from sea level, Turnagain Arm is a swirling mass of forbidding grey water.

At a glance, it doesn’t look all that different from one of the friendly channels of Puget Sound.  Comparable width, comparable length.  Of course there would be things to know, in Puget Sound, about currents and tides.  The thing to know about currents and tides in Turnagain Arm is — fuggedaboudit.

What on earth is going on out there?  I see rollers cresting and breaking, way out in the middle of the channel.  The tidal current seems to be always rushing in, or rushing out.  Or perhaps both at the same time.

In Puget Sound, the water would be alive with work boats and pleasure boats.  Here there are none.  No docks or harbors either.  The tidal bore, which can roar in at a height of up to six feet, is a tourist attraction.

In Puget Sound, there might be clam diggers out at low tide, or at least people strolling, enjoying the beach.  Not here.  There are signs all over saying do not go out onto the mud flats.  Quicksand.  Thirty foot tides.  Die.

Perhaps recklessly, I brave the shore.  I do stay on the solid sediments, in easy reach of the breakwater boulders.  I perceive this beach is nothing to mess with.  I go back and sit on the boulders. By and by, the rising tide comes chuckling in over the rippled mud, at the pace of a brisk walk.

From Western Washington, I am used to the waters being something you do things with.  You have a relationship with it.  You go on it, and sometimes in it, and over it, and you put things in it and get other things out of it.

I guess, here, all you do is look at it.