All posts by James Jukosky

The Lives (and Deaths) of Poplars (Branch I)


Several expletives escape my mouth as the monstrous gray poplar I’m cutting tilts in the wrong direction and pinches the bar of my chainsaw.  I tug hard on the saw and push on the poplar, but I don’t have the leverage to move the tons of leaning tree.  Finally, after several sweaty hours using winches, ropes, and a handsaw, I manage to topple the tree in the opposite direction I initially wanted to fell it in.  It creaks and groans and crashes down hard, right onto the sheep fence!  It takes another two hours to saw it up into firewood for sugaring, throw the limbs into a burn pile, and bend the fence back into shape as best as I can.  Poplar is a very soft wood and easy to cut, it burns quickly which is great for boiling sap but not so great for burning in a woodstove to heat your home.  Many people think of them as “junk” trees.  My relatives that are New Hampshire natives call them “popple”, but they are also called white poplar, quaking aspen, and their scientific name is Populous tremuloides.


I’ve been clearing some of our land where a large poplar stand has grown for the past 60 or so years.  It is in the middle of an open field on the edge of an old barn foundation and some of these trees are large, much bigger than I can put my arms around.  They are also on the edge of our driveway and the limbs come crashing across it during some of our more intense New England storms.  This causes some moments of panic when we are trying to get to work.  So, my wife and I determined that we need to reclaim this section of field.  I’ve read short facts and snippets about the biology of poplars.  For example, white poplar mainly reproduce through root sprouts and this stand that I am cutting down are probably all genetically identical clones. Most of the trees in one stand are also all male or all female as well.

To get a better grasp on this particular group of trees I gathered some data on the poplar stand by counting growth rings of ten random trees and measuring the diameter at breast height of 10 random trees. Most of the poplar in the stand are bigger and I only found new saplings at the very edges of the stand out in the field. The sparse number of smaller trees in the undergrowth were mostly small maples and ash. The trees that I counted rings on ranged from 12 to 45 years old and were an average age of 29 years old. The diameters at breast height ranged from 6.4 to 19.4 inches (16.2 to 49.3 centimeters). I could tell that these poplars were fast growers, some of the growth rings measured 1/4 to 1/2 inch think. So, they were packing on quite a bit of girth in these years. It seemed to me that most of these thicker growth rings were when the trees were in their teens about 15-19 years old. This suggests to me that these were really good growth years or that these trees reach a critical mass with the number of branches and leaves at this age and are able to really take off and grow quickly.

While chopping these trees into movable bits, I’m intrigued by their shape and structure and I want to know more.  IMG_1311Why do these trees grow so fast?  Why do the grow where they grow?  Can you figure out which tree is the original clone?  Why do these trees seem to die when they get to a certain size?  How old are the trees in my stand (I answered this one)?  As I work clearing this spot, I will continue to do some research to learn more about the lives and deaths of white poplars.




A Home For A Bumblebee Queen

Eastern Bumble Bee (Bombus impatiens) By Bob Peterson from North Palm Beach, Florida, Planet Earth! [CC BY-SA 2.0 (], via Wikimedia Commons
Eastern Bumble Bee (Bombus impatiens)
By Bob Peterson from North Palm Beach, Florida, Planet Earth! [CC BY-SA 2.0 (], via Wikimedia Commons

Today was a gorgeous post-summer solstice June evening with warm sun and a beautiful breeze. I was walking around my honeybee hives when I heard a deeper, louder buzz in the brush toward the back of the hives. In the grass was a queen Common Eastern Bumblebee (Bombus impatiens). She was flying between patches of dirt and not visiting any flowers for pollen and nectar, but crawling through cut grass, dirt mounds, and small plants. I called my eight-year-old son over to come watch and we followed this bumblebee as she made short buzzing flights and inspected the ground at each new spot. I’m pretty sure that she was looking for a home to start her colony in. This particular species (Bombus impatiens) likes to nest underground, so she was probably looking for an empty mouse hole to live in.

Bumblebee queens hibernate during the winter and emerge in the spring and early summer. Newly emerged queens establish a site for a new colony and begin to forage for pollen and nectar from flowers. Pollen is their main protein source and nectar is how they get most of their carbohydrates. After establishing a nest site, bumblebee queens will lay eggs in a small ball of pollen (she mated in the previous fall). These eggs will hatch into larvae which grow, spin a cocoon, and metamorphose into bumblebee workers. As they mature, the female workers will take over the foraging duties and the queen stays in the nest to lay eggs. Later in the summer drones (males) and new queens are produced and these leave the colony to mate. After mating, the new queens bury themselves in soil or other plant material and hibernate through the winter. The old queen and colony workers eventually die as fall turns to winter and there are few flowering plants to forage on. In the following spring, mated queens emerge from hibernation to form new colonies and the cycle begins anew.

My son and I watched this queen bee look for a new home for about 20 minutes until she buzzed off quickly in a direction that we could not see or follow. At that point it was dusk, so, I’m not sure that she successfully found permanent lodgings today. Perhaps we will be able to find a bumblebee colony in our fields this summer and observe it for some time.

Colla, S.R., L. Richardson, and P. Williams. (2011). Bumblebees of the Eastern United States. FS-972. USDA Forest Service and the Pollinator Partnership.

Goulson, D. (2010). Bumblebees, behaviour, ecology, and conservation. Oxford: Oxford University Press.

4 Great Resources for Teaching Evolution

Evolutionary theory is the core of biology and encompasses a broad range of concepts.  Luckily, for teachers like me there are some well-developed educational resources.  I teach an introductory 2 credit college-level evolution class and would like to present some web resources that have fabulous activities for all educational levels.

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The Understanding Evolution site is a collaborative project of the University of California Museum of Paleontology and the National Center for Science Education it has a large number of teaching materials for evolutionary concepts at all levels K-12 and including college.  One of my favorite things about this site are the conceptual frameworks and teaching goals that are in the teaching lounge for each grade level category Also, the teaching goals are directly linked with ideas for lessons and articles for further reading.

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The Howard Hughes Medical Institute’s educational site Biointeractive is a treasure trove of lessons, articles, lectures by well-known scientists, animations, and documentaries.  Some resources that I particularly enjoy using in and out (for homework) of my evolution class are the short film “The Origin of Species: The Making of a Theory”, all three episodes of the documentary “Your Inner Fish” with Neil Shubin, and the lizard evolution virtual lab. The short film “The Making of the Fittest: Natural Selection and Adaptation” and the accompanying problem set and spreadsheet “Allele and Phenotype Frequencies in Rock Pocket Mouse Populations” are particularly engaging for students.  This film and problem set describes the work of Michael Nachman who has identified a gene that is important in rock pocket mice adaptation to predation pressures in different colored landscapes.  The data that students analyze is real data from the study.

National Center for Case Study Teaching in Science (NCCSTS)

The case study method of teaching applied to college science teaching, from The National Center for Case Study Teaching in Science

The National Center for Case Study Teaching in Science has over 63 case studies related to evolution.  Some of these are clicker cases, directed problem solving, role-playing, or debate oriented, however they all have a story to engage your students with.  Sometimes it is hard to teach science without just lecturing the content and these case studies certainly help.  Cases that I use in my evolution class are “An Antipodal Mystery” about the difficulty scientists had in classifying the platypus when it was first discovered and “What is a Species?: Speciation and the Maggot Fly” a clicker case study on mechanisms of speciation and different species concepts.   The case studies are free but there is a $25/year access fee for the answer keys.

Last but not least is this short TEDED animation by Paul Anderson and Alan Foreman.  In just over 5 minutes they do a pretty good job of describing the major microevolutionary mechanisms.

I hope you find these resources useful for your teaching and learning.  If you have any additional resources that are great for teaching evolution please let me know in the comments below.

How does your pee come out?

Pixa_egiten_0001This week’s big question comes from my son who is in second grade (kids always have the best science questions).  He was wondering, “How does your pee come out?”  So, let’s take a little journey through the urinary system.

We can begin in the kidney where blood is filtered and urine is formed.  In humans, the kidneys are a pair of bean shaped organs located in the abdomen near the bottom of the rib cage.  Inside of each of your kidneys you have millions of microscopic tubes called nephrons.  At the beginning of each nephron is a tiny tuft of tangled blood vessels called the glomerulus (pronounced glow-mare-you-lus).  Blood is literally pushed through several membranes and then into the nephrons.  During this filtration process, stuff like red blood cells and white blood cells, and proteins are too big to pass through the filter.  However, a great deal of fluid (blood plasma) and almost all of the dissolved stuff such as salts and sugars also pass into the tiny tube of your nephron.  You can think of the nephrons as pee processing pipes.  Any water, salts, sugars, or other molecules that we need are reabsorbed into the blood vessels surrounding the nephron as the blood filtrate flows down the winding tubules.  Any extra fluids or waste products are not reabsorbed or are secreted from cells lining the tubules, they keep flowing down the nephron and end up as urine.

A nephron
A nephron

Urine leaves the kidneys through a series of tubes.  First it is dumped from the millions of nephron tubules into the collecting duct.  The collecting ducts empty into a space called the calyx (pronounced ka-licks).  The calyces (plural for calyx) join together like tributaries and merge into a wide river in the renal pelvis and this is where the river of pee leaves the kidneys.  Urine is transported down from the kidneys to your bladder by muscular tubes called the ureters (yur-re-ters).  Gravity helps pee drain down into your bladder, but it can still move down the ureter if you are standing on your head or lying down and sleeping.  The walls of the ureter actually contract in coordinated waves called peristalsis, propelling urine to the bladder.

Urinary System

Your bladder is a stretchy storage sac for pee.  How stretchy?  Well, a bladder that is fairly full can hold about 500 ml (1 pint), but it can still stretch to nearly twice that volume (think about the size of a 1 liter water bottle).  Near the bottom of your bladder is a tube to the outside of your body called the urethra (yur-ee-thra).  In males the urethra passes through the penis and in women it opens to the outside just above the vagina.  You have two circular valves or sphincters that normally keep the urethra pinched off when urine is not passing through.  The internal urethral sphincter is closer to the bladder and is controlled by reflexes in your spine and other parts of your nervous system that you cannot consciously control.  The external urethra sphincter is under conscious control, so you can “tell” it to open and close as needed.

When your bladder fills, it stretches and nerves fire in response to this stretch and activate a spinal reflex.  Usually, you feel the need to pee before urine volume is greater than 400 ml (a little less than 1 pint).  The spinal reflex causes a layer of smooth muscle in your bladder, called the detrusor, to contract and the internal urethral sphincter to open.  Babies pee whenever their bladders are somewhat filled and this reflex is activated because they haven’t developed conscious control over urination yet.  However, most people after infancy have conscious control over the external urethral sphincter and can choose to keep it closed until it is convenient to urinate.  So, to recap the whole peeing process, urine is made in the kidneys, travels down the ureter to the bladder, the bladder fills and stretches, the smooth muscle of the bladder contracts, the urethral sphincters open, and urine travels down the ureter outside your body, preferably into a toilet or perhaps the base of a tree (if you are outside).


Marieb, E. N., & Hoehn, K. (2015). Human Anatomy & Physiology (10th edition). Boston: Pearson.

The Science of Caffeine, Ignobels, and Your Own Personal Microbe Cloud

I haven’t written much recently as the beginning of the semester is always a crazy time.  However, I thought I would share a few of my favorite science related media.

The first is the “Science of Caffeine”, a short video produced by the American Chemical Society on how we metabolize caffeine and how it elicits its effects.  I could use a cup of coffee right now!

The second is a short NPR audio news clip describing how scientists have found that everyone has their own personal microbe cloud spewing forth into the space around them.

Wherever You Go, Your Personal Cloud Of Microbes Follows

Remember Pig-Pen? The little kid from Charles Schulz’s Peanuts cartoons who walked around in a cloud of dirt? Well, the human body does spew a cloud, but instead of dirt it contains millions of microorganisms. “It turns out that that kid is all of us,” says James Meadow, a microbial ecologist who led research about the microbes shadowing us during postdoctoral work at the University of Oregon.

The last one for today is a BBC article on the 2015 Ignobels.  The Ignobels are awards for improbable scientific research.  My favorite 2015 Ig award is that a physics team from Georgia Tech found that there is a “Universal Urination Duration.” Basically, all animals large and small urinate in an average of 21 seconds (plus or minus 13 seconds).

‘Universal urination duration’ wins Ig Nobel prize – BBC News

From the section Science & Environment A study showing that nearly all mammals take the same amount of time to urinate has been awarded one of the 2015 Ig Nobel prizes at Harvard University. These spoof Nobels for “improbable research” are in their 25th year.

Sad Animal Facts

This is one of the funniest biology related sites that I’ve come across on the internet.  It features interesting animal facts accompanied by a cartoon.  Check it out and have a laugh.

Sad Animal Facts

Nature creates them and Brooke Barker draws them.

Here’s a few to get you started:

I’ve got some bad news about walruses.

I’ve got some bad news about ferrets.

I’ve got some bad news about dwarf lemurs.

Harvesting Blood is Hard on Horseshoe Crabs

Credit: Laurel Wilkerson / USFWS
Credit: Laurel Wilkerson / USFWS

The first time I saw a horseshoe crab (Limulus polyphemus) up close was while swimming on the sandy beaches where Bass Creek empties into Buzzards Bay on West Island in Massachusetts. I pulled it off the sandy bottom and marveled at its smooth shell, spiny tail, and the many spider-like legs on the crab’s underside.

Angel Schatz
Angel Schatz

Though these creatures have been in existence on earth for 350 million years (the earliest human fossils appear about 200,000 years ago) they still look like something out of a science fiction alien movie. Despite their apparent ability to survive for millions of years on Earth, there is evidence that New England populations of horseshoe crabs are declining and that some of this decline is linked to the harvest of horseshoe crab blood for biomedical testing materials. This blood harvest is not all that fatal to the crabs, so their decrease in numbers may not be due to just mortality alone. A recent study by scientists at the University of New Hampshire and Plymouth State University suggests that the harvest of blood during spawning season may be influencing the horseshoe crab’s behavior and ability to reproduce.

Humans have harvested horseshoe crabs for hundreds of years for various purposes. Until the 1970s they were commonly harvested to be ground up as fertilizer and they are still a common bait source for the conch and eel fisheries. The Atlantic States Marine Fisheries commission reports that horseshoe crab populations in New England have been declining since 2004 despite the fact that bait harvests in the area have been cut in half. However, during this same time period, the harvest of horseshoe crab blood for biomedical use has increased by 76%. It is estimated that about 200,000 crabs were collected in the 1990s to harvest blood while more than 610,000 were collected in 2012.  The downward trend in horseshoe crab populations is even more apparent in Pleasant Bay, Massachusetts where the crabs have been harvested for biomedical use for 30 years and a moratorium on collection of horseshoe crabs for bait purposes has been in place since 2006.

If you have ever had surgery, received vaccines or other injections, had a joint replaced, or received any kind of implantable biomedical device, you were probably protected by horseshoe crab blood. The substance that is harvested from the blue blood of horseshoe crabs is called Limulus Amebocyte Lysate (LAL) and it is used for the detection of bacterial endotoxin, a complex molecule found in the cell walls of gram-negative bacteria. LAL is essentially a series of proteins that cause coagulation in the presence of gram-negative bacteria. In horseshoe crabs this clot traps bacteria while antimicrobial agents in the clot neutralize the invader. A variety of sensitive biomedical assays have been developed around this horseshoe crab blood product. Scientists are working on alternatives to LAL in biomedical testing and some are currently available such as the Pyrogene assay by Lonza that uses a recombinant form of horseshoe crab factor c to detect endotoxin. This recombinant protein is produced in the lab and not harvested from horseshoe crab blood. However, the LAL test remains the most widely used and it is extremely effective as it is capable of detecting picograms to nanograms of bacterial endotoxin (one millionth of a billionth of a gram of endotoxin).  Thus horseshoe crab blood is very valuable and LAL can cost $15,000 per liter (1 liter = ~1 quart).

When horseshoe crabs are harvested for LAL only a small percentage of them actually die. Crabs are harvested by trawling nets or by hand capture from beaches and shallow water and 50% of the LAL harvest occurs during the spring spawning season when the crabs return from deeper water to reproduce on sandy beaches. Crabs are transported to labs for blood harvest usually in open-air containers and not in seawater aquariums. At the lab, about 1/3 of each crab’s blood is drained and the crab is returned to the point of capture. The whole process usually takes 24-72 hours. The mortality rates are 8-15% in male and 10-29% in female horseshoe crabs.

Despite the fact that mortality is pretty low during the LAL harvest, fewer females are showing up to spawn in areas where crabs are harvested for biomedical purposes. Perhaps the stress of the bleeding procedure is affecting the horseshoe crabs’ behavior and physiology during their breeding season. To make a crude analogy, suppose you were in your bedroom about to have sex and somebody grabbed you, threw you in a truck for a half a day, stuck a needle in you and drew off about 1.5 liters of your blood. After waiting around for another 6 hours or so they threw you in the truck again and dropped you off in your bedroom or at least someplace close to your house. Chances are you might have lost your mojo and be a little disoriented for a while. If you were a horseshoe crab you might have even lost out on the once a year spawning opportunity.

Rebecca Anderson, Win Watson, and Chris Chabot, researchers at the University of New Hampshire and Plymouth State University, recently tested the idea that the biomedical bleeding process affects the behavior and physiology of female horseshoe crabs and published their findings in The Biological Bulletin. They fitted crabs with accelerometers to monitor their activity and measured hemocyanin concentrations both before and after the bleeding procedure. Hemocyanin is a molecule that carries oxygen in horseshoe crab blood it contains copper and accounts for the bright blue hue of their blood. It is similar to hemoglobin, which carries oxygen bound to iron in human blood and accounts for its red color. Their study saw similar mortality (18%) as has been seen before in studies of the horseshoe crab bleeding procedures. They also saw significant reductions in the amount of circulating hemocyanin in crabs six weeks after the bleeding procedure. Bled crabs were slow and sluggish and overall activity was reduced for several weeks. Human activity has a circadian rhythm that is governed by light-dark cycles, we are more active during the day than we are at night. Horseshoe crabs follow a circatidal behavioral rhythm. Their activity levels follow the patterns of tides coming in and out. This study showed that circatidal activity patterns were not as strongly shown for several weeks after bleeding.  In summary, the bleeding procedure befuddled female crabs enough that it could affect their ability to reproduce during the several week long spawning period in the spring.

Why should we care about dwindling numbers of horseshoe crabs on Atlantic shores? Declining numbers of crabs carry serious changes for the ecosystems they inhabit. Horseshoe crab burrowing moves sediments around in marine and estuary environments, so their activity can influence nutrients in the water. They are also an important source of food for shorebirds, fish, and crustaceans. The eggs of Limulus are an important source of nutrients and energy for migrating shorebirds.

Horseshoe Crabs and Red Knots; Credit: Gregory Breese/USFWS
Horseshoe Crabs and Red Knots; Credit: Gregory Breese/USFWS

Red knots (Calidris canutus rufa) stop on beaches in Delaware Bay during their spring migration from South America to their breeding grounds in the Arctic. While at these beaches they refuel by consuming eggs of breeding horseshoe crabs. Several studies link the severe decline of red knot populations to declines in horseshoe crab populations due to overharvesting. So, dwindling numbers of these crabs may cause ecosystem and population changes that could alter other marine and estuarine species.

The development of alternatives to LAL for biomedical testing may mean that someday we will not have to harvest horseshoe crabs for their blood and that their populations might rebound naturally. However, until those tests become economically viable and widely used our impact on the horseshoe crabs, which are a vital resource for humans and other animals, will need to be carefully monitored. In their study, Anderson, Watson, and Chabot indicate that, “to maintain the integrity of the stock needed to supply the industry, adaptive or flexible management strategies may need to be considered.” The Atlantic States Marine Fisheries Commission has developed a set of “best management practices” that suggest reduced out-of-water transport and holding times and cooler, less stressful temperatures for crabs during the bleeding procedure. Anderson, Watson, and Chabot’s study focused on current “industry standard” bleeding procedures and in a recent interview Chabot indicated that he is very interested in studying the “best management practices” and whether or not they will make a difference in how the crabs behave after bleeding.

Where did 4 legged animals come from?

I just wanted to post this well-done HHMI biointeractive video on the origin of tetrapods (animals with four limbs).  Neil Shubin is in it and it is a classroom length version of book and the PBS documentary “Your Inner Fish”