Rick Shory

Offering a little something you might not otherwise have

veg frame showing visualized lines


Leave a comment

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.

Advertisements


Leave a comment

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.


Leave a comment

Germinating ginkgo seeds

I had never grown ginkgo (Ginkgo biloba) seeds before, so when I noticed them under a tree in late November, I collected some to investigate.

I had a ziplock bag with me, and filled it up with the “fruits”. Botanically, these are not fruits at all, but that’s another story.  It’s well known that these smell bad, at least when freshly fallen. The odor is described as rancid butter, or dog shit. However the autumn weather had been torrential rain, and the scent was all leached away.

gb010_bagged

It was about a month before I got around to the seeds. Meanwhile, I left the bag outdoor so the “fruits” would stay moist in the wet autumn weather. On December 31, 2015, I started my experiments.

gb020_berries

The “berries” were single or in pairs, on stalks.

gb030_nuts

When I peeled off the fleshy covering, inside were the seeds.

gb040_visegrips

I gently cracked them open.

gb050_kernels

Inside were the kernels.

I knew that, botanically, ginkgo seeds are not like angiosperm seeds, where the embryo plant grows to a certain stage, and then various inhibitions come into play to keep it dormant. The ginkgo life cycle is more like a fern.

The brown dots on fern leaves shed microscopic dust-like spores. These drift on the wind. If a spore lands in the right conditions of moist soil, it grows into a prothallus. Prothallii are quite common, once you learn to spot them. Here is a picture of some that appeared in one of my potted plants.

gb060_prothallus

The dark green membranous thing in the lower right is the prothallus. It looks like a bit of seaweed washed up, that hasn’t dried out yet. It grew from a drifting spore, by the grace of drip irrigation watering that kept the soil continuously moist. The prothallii of most kinds of ferns can only develop in continually moist sites (this is where to look for them), though some cliff ferns have prothallii that can survive drying out.

With good luck, the prothallus grows to full size, which is only about a quarter inch across. When mature, it develops male and female gametes on its underside. When there is enough water, the male ones swim to the female ones, presumably sometimes to a different prothallus for genetic mixing. The fertilized zygote develops into a lump of cells, nourished at first by the prothallus. When this embryo plant gets big enough, it puts its first root down, its first leaf up, and grows into what most people recognize as a fern. The lighter green leaves towards the top of the photo are such a baby fern. It is growing out of a different prothallus than the lower right one, but it is behind the leaves and hard to see.

Other spore plants, like horsetails, also produce these gametophytes. “Gameto-phyte”, because it forms the gametes. The horsetail gametophytes I have seen are also green, but fleshier. Still other spore plants, like club mosses, supposedly produce lumpy gametophytes underground, but I have never seen them. The general plan is, the spore grows into a gametophyte, which only does two things: Produces gametes, and then nurtures the main plant till it gets on its own.

It doesn’t seem fair. The fern gametophyte has to eke out a living as a miserable prothallus, harvesting enough sunlight to grow and start the next generation, while desperately living on the edge of death by desiccation. But the main fern plant is big and robust, with roots and tall fronds, and all. Why couldn’t it help out the next generation of gametophytes with some of its bounty?

This is evidently what ginkgoes have done. Instead of casting spores to the wind, the ginkgo holds them on little stalks. As a spore develops into a gametophyte, the tree feeds and shelters it. Instead of having to live free or die, the ginkgo gametophyte has a pampered life. How the gametes get to it from a different gametophyte is another story, but the hint is: Pollen.

So, I looked at these ginkgo kernels, and I thought: When I want to grow ferns, I get the spores, and set up moist mellow conditions, and by and by they to grow into prothallii. Then I just wait. In their own sweet time, they get around to the gamete thing, and then start with the lump of cells. Once the first fern leaf appears, I’m home free.

So, here with this ginkgo seed, it’s all been done for me. No fragile prothallus to fuss over. This gametophyte doesn’t have to be green because it doesn’t need photosynthesis. It was well provisioned by the tree. So, instead of thin and membranous, it’s fleshy and packed with stored food.

gb070_slice

I sliced some of the ginkgo kernels open, and there were the developing plant embryos. This was exactly analogous to the lump-of-cells stage of a fern plant on its prothallus.

gb080_quarterlength

The ginkgo plantlets were different sizes. Some were about half the length of the seed, but some were as short as a quarter the seed length.

gb090_blank

Some gametophytes had no baby plant at all. I guess sometimes the male ginkgo is shooting blanks.

So, I thought, maybe it’s the same as growing ferns. You just set them up and let them take their own sweet time. They don’t need light in this case, but they probably want to be moist.

I divided my ginkgo seeds into three groups. I put them in ziplock sandwich bags with damp sawdust. Probably sand would have worked as well, or moist leaves, or even torn-up wet strips of paper.

gb100_40degbag

One bag I kept about 40 degrees. This was outdoors in an unheated garage. It might have occasionally got frosty, and sometimes as warm as 50 degrees.

gb110_60degbag

One bag I kept about 60 degrees. This was indoors, on the floor of the basement.

gb120_80degbag

One bag I kept about 80 degrees. This was in a plant growing room with warm lights.

On February 3, 2016, I checked on them. This was after about a month, 34 days. All three had been going for the same length of time.

gb130_40degseeds

I picked three seeds at random out of the 40 degree bag. The embryos had grown some, but not much. They averaged about half the length of the seed.

gb140_60degseeds

I picked three seeds at random from the 60 degree bag. Here, the embryos were definitely bigger, about three fourths the length of the seed. If you can see, in the middle one, the root is starting to push out of the gametophyte.

gb150_80degnuts

When I came to the 80 degree bag, I did not pull them at random. I grabbed the first three that were obviously clambering to get out.

gb160_80degseeds

It looks like ginkgoes have something like hypogeal germination. That is, the seed does not get pulled up above ground. The embryo elongates to push the leaf bud outside the seed, along with the root, and then a shoot grows up from that. The upper ends of the “cotyledons”, or whatever they are, stay inside the seed, to continue feeding from the gametophyte.

So, it appears to me that ginkgoes do not have true seed dormancy, as angiosperms do. To avoid coming up too early, in the midst of winter, the ginkgo embryo simply develops very slowly, as long as things stay cold. Instead of counting chill hours, they just pace themselves. When spring comes, they speed up. The warmer it gets, the faster they grow.

If you want to grow ginkgo seeds, just keep them warm, and they’ll sprout. They absolutely do not need to be frozen. Deep freezing would probably kill them. Drying out would probably kill them too. After all, they are just gametophytes.


2 Comments >

Botanical term: “Imbibe”. Most seeds can remain dry-dormant for long periods of time. When they take in moisture to capacity, they are said to “imbibe” it, or to “become imbibed”. Some seeds, like the beans used for food, noticeably swell. Others, like tree seeds such as apples and maples, do not look much different. In these cases, the main change is internal texture. The plant embryo, which was hard and brittle when dry, becomes leathery or soft.

The state of “being imbibed” with moisture is distinct from simply “wetted”. Seeds with an impervious coat may not become imbibed, even when soaked in water. On the other hand, many seeds will become fully imbibed when placed in soil that seems scarcely moist to the touch.


Leave a comment

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.


Leave a comment

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.


Leave a comment

Transplant fairy ring

I wondered if you could transplant fairy ring mushrooms, Marasmius oreades. I found you can.

There was a fairy ring in my front parking strip. I dug out a chunk of it with a trowel.

piece of sod with mushrooms

Explant

In the back yard, I made a hole the size of that chunk. I put the chunk of sod, with mushrooms, in it.

piece of sod with mushroom, in new location

Implant

A year later, there was a new fairy ring of mushrooms where I had put the sod. The ring increases about two feet in diameter each year.

new fairy ring of mushrooms

New ring

I did this because I like these mushrooms, more than I care about a perfect lawn.

Years ago, I was told the four characteristics to distinguish Marasmius oreades.

  1. The stipe is tough and wiry (for eating, I only use the caps).
  2. The stipe has some stray flocks of mycelium at the base. These look like white cottony fibers.
  3. The gills are of different lengths. Some span the whole distance from the edge to the stipe, but some only go partways in from the edge to the stipe. These partial ones fill in the spaces between the whole ones.
  4. The gills do not actually attach to the stipe. They inner edge of the gill may be in physical contact with the stipe, but is not truly connected to it.

The guy who explained this to me said the dangerous mushroom most likely to be mistaken would be the sweat-producing clytocybe (Clitocybe rivulosa, Clitocybe dealbata). He said you must check each individual mushroom to make sure. The most definite difference is that the clytocybe gills connect to the stipe, or even run down it a little.