Never A Dull Moment

The samples and cases submitted to the veterinary diagnostic lab are inherently unpredictable. No appointments need to be made, although we do ask that clients call the lab before bringing in a large animal for necropsy. With a few exceptions, we accept submissions directly from owners and commercial entities. The result is that there is nothing like a normal day to day routine at the lab. My section, Pathology, which includes necropsy and histopathology, is particularly prone to unexpected surprises. 

Surprise! There's a dead goat in the cooler on the dock, on top of two neonatal calves, all dropped off over the weekend. And the goat has no paperwork with it....

Surprise! There's a dead chicken in that box on the counter, shipped without any ice packs, literally creating a stink in the Receiving.

Surprise! It's 2pm, and Tyson just arrived with 36 live broiler breeder hens from three different farms, and didn't call ahead!

Pathology has no routine or predictability at all. We have to be ready to accommodate whatever comes in. In just the past week, I've had to deal with several cases that nicely illustrate how unpredictable my job is.

We have an incinerator to dispose of the tissue waste we generate. The incinerator occupies a fair bit of my management time each week. It is touchy (won't start if it is raining, or right after it has rained, for example). It is also a dangerous piece of equipment. We burn around 4,000 lb of animal remains a month, and use a forklift to hoist bags weighing as much as 1300 lb into it. But remember that unpredictability factor? In December, we burned just over 9000 lb due an unusually high number of horses submitted for necropsy. I was scrambling to keep the propane tank filled during the last two weeks of the year. 

The incinerator lid is raised by cranking up two bottle jacks, one on each end. The jacks and the lid roll back as a unit on a track, exposing the interior of the incinerator. A week ago Friday, one of the jacks failed. It had been leaking hydraulic fluid, and I knew it was on its last legs. So when the techs came back and reported they couldn't get the lid opened, I drove to the incinerator (it's in a secure fenced maintenance yard across from the lab), measured the existing jacks (their labels had been scraped off by the incinerator manufacturer so they could be painted black), and drove to AutoZone to get two more. On Tuesday, one of my techs and I ripped out the old jacks and rammed in the two new ones. Good thing I'm handy with tools.

On top of that, I was scrambling to get more propane. Our walk in cooler was full because we didn't burn on the Friday as we often do to clean it out for the next week because of the jack issue. I usually call or text the propane delivery driver directly but he wasn't answering on Monday. It's pretty useless to call the company directly. But our director still has the business card of a "customer experience" rep at the propane company who helped him set up the tank back in 2018. One call to that guy and we had a full tank of propane (1000 gallons) the very next day. 

A young boa was submitted for necropsy that week. Against the usual backdrop of dogs, cats, cows, and chickens, I quite enjoy these unusual species. Even if I am not on necropsy duty that day, I always take these cases when they come in. They are challenging to handle, and their anatomy and pathologies are always interesting.

On Wednesday morning, I get this picture via text from a veterinarian friend.

That is a very sick calf with green snot coming out of his nose and eyes. Poor little guy. I actually received three photos of the calf, along with this text: "what tests?"

I had to laugh. This particular vet is young, but very good. He works really hard to help his large animal clients. And obviously, we have a lot of mutual trust and respect since he knows he only has to text me to get an immediate response. 

I first replied "gross" then I suggested some testing options and the samples needed, and let him know what I thought should be prioritized in case the client couldn't afford or didn't want to run everything I recommended. 

I had another vet call me on Thursday morning to tell me about a horse she had seen that had large bleeding ulcers in its mouth. Uh oh, a short list of differentials, at least one of which was reportable, came to mind. I've worked with this vet before so we chatted for a while about the case. I told her, I've got to escalate this so hang tight and I will get back to you. I texted the state vet. He happened to be in his office, and came right down to mine. He said, get her to email everything including pictures. She did, and I forwarded all of it to him and to the USDA APHIS vet in charge. They eventually decided it was not a disease issue that needed their involvement, and passed the entire mess back to me and the vet who called me. 

I get calls like this from vets and animal owners/producers daily. Since taking this job, I've worked very hard to make the lab a resource for reliable information and assistance. The result is that I spend many hours each week helping other vets and animal producers and owners, calling, texting, emailing, gathering information. By now, most of the practicing vets in the state have worked with me, and they just call me directly. It also helps that I have a solid relationship with my state and federal colleagues. 

Finally, it was Friday, and I was taking a breather in my office thinking the crazy week was almost over when the state vet pops in. We have a situation, he says. New developments, he added. I thought he was still talking about the horse with the oral ulcers. He said, oh no, something entirely new.

Turns out a brown bat had gotten into the atrium of the building and people were running around in panic while others were trying to catch it. The atrium of the building divides the building into two halves, the lab side and the Department of Agriculture admin side. All of us on the lab side have been vaccinated for rabies as a requirement of our job. Nobody on the admin side has received this vaccine. 

I told the state vet, I'm on it. He and I rushed towards the atrium, only to be met by two admin folks coming towards us with a very small bat trapped in a very large net someone had rounded up from Forestry. Neither of them had gloves. Oy.

I asked repeatedly, any human contact? Any spittle, blood? Any scratches or bites? Negative, negative.

Since the bat was secure for the moment, I had them follow me back to our necropsy area. We ran into the lab director on the way, and I told him, just keep moving, don't look, everything is under control. I put on gloves, grabbed a plastic sample transport container out of necropsy, and maneuvered the bat (stunned into immobility or injured) into the container. I closed the lid, and sent them on their way. 

As a general rule, we don't accept live animals for necropsy. As a result, we don't keep euthanasia drugs at the lab. That's partly because we don't want to euthanize animals here, and partly because we don't want the hassle of maintaining DEA licenses and keeping inventory and so on. However, we do accept live poultry. We use CO2 gas to euthanize them. While this is not recommended for euthanasia of mammals, it was my only option and was how I euthanized the bat. Within an hour of the state vet showing up in my office, the bat had been euthanized, packaged with completed paperwork, and was on its way to the Department of Health for rabies testing. 

Admittedly the bat was kind of unusual, but most of the rest was just a normal week for the lab. Never a dull moment.

Fun With Fungi

Rain. So much rain. Fungi with amazing colors and textures are popping up all over my property. Here's a sampling. 

Well Hello, Little Frie....Oh Fucking Fuck

As I was walking to my car yesterday morning to leave for work, I noticed ...something... in my far peripheral vision.

 

 

Yeah. I had passed within a couple of feet from her.

She was a real beauty, as you can see. But I'm afraid I'm not willing to share my property with poisonous snakes, so I had to dispatch her.

I calmly put my bags in the car, and opened the garage door. I went in and put on my knee-high work boots, grabbed a shovel and a hatchet, and did the deed.

I briefly considered taking her body to work to take a look at (I have the PPE, the tools, and a way to properly dispose of her). But then decided that was probably taking things just a wee bit too far.

Argh! Bedbugs!

I am working my way through my second interaction with bedbugs. The first time I encountered these savage little blood-sucking bastards was way back in 1995 or so. There was no question then that I picked them up on a trip to Thailand. This time, they came back with me from a hotel in Fayetteville, where I stayed for two nights for an agility trial. The trial was in mid-March, so it took a while for them to make their way from the travel crate containing dog bedding in the garage upstairs to the bedroom.

Over a period of three nights, these disgusting pests ravaged my legs and arms. The pustules don't always appear right away so it took that long for the full horror to be exposed. Bedbugs often leave bites in short tracks. And the itch gets worse over several days. I had many dozens of bites on my legs, fewer on my arms. I will definitely have some scars from this.

The solution now is the same as it was in 1995. Wash everything that can be washed, and dry on high heat. Wash it all again just in case. Tear the bedroom apart, moving all the furniture away from the walls. Vacuum, vacuum, vacuum. Empty canister after every vacuuming, carry the trash bag to the can outside, and spray the canister with alcohol.

Then I applied diatomaceous earth. I piled that stuff up along the baseboards, rubbing it into the carpet. I rubbed it into both sides of my futon and all of the bed frame crevices. I let everything sit for a week, vacuumed it up, and repeated. Make sure you wear a mask when using diatomaceous earth (we should all have plenty of masks these days) since breathing those tiny silica particles is not good for you.

After two weeks, I decided to move back into my bedroom. Sadly, I may not be done, since I got a single bite on my knee two nights ago. I will have to move back downstairs tonight, and treat the bedroom again this weekend. But I'm just as persistent as bedbugs, and I will prevail.

Polishing That Resume

I was busy this week buffing up the resume credentials.

I am now certified to operate our forklift. I'm sure you are asking why I would ever need this skill. Well, we generate a fair bit of biological waste in the Necropsy unit, and we've got to dispose of it somehow. And "somehow" has to conform to an array of laws and regulations. We have a brand-new incinerator in a maintenance yard across the street from the lab, and we use the forklift to lift a specialized bag containing said biological waste out of a container and up into the incinerator. We typically burn between 1000 and 1500 lb of material at a time. That's not really a lot, since an average horse or cow weighs 1000 lb. Nobody at the lab was certified to run the forklift, so I arranged for the training and now 8 of us are certified. Plenty of hands to help whenever we need to burn a load of waste.

This week I also attended a day-long continuing education event on Arkansas aquaculture. I learned about the species that are cultivated in the state, and about important commercial fish diseases and parasites. After lunch, we had hands-on activities doing necropsies and looking over some lab testing procedures. I successfully pulled 3 mL of blood from my little catfish.
















The necropsy part was great. I knew absolutely nothing about fish anatomy before the class, and boy, are fish weird. There are only two chambers in their hearts, although they kind of cheat on the chamber count and add a third structure that acts as a pressure regulator out of the ventricle. They have two long kidneys tucked up near their spine like mammals. In some fish, the function of the cranial part of the kidney can be different than the posterior part. Their kidneys have an excretory function but freshwater fish lack the structures to create concentrated urine, for example. And of course they don't have lungs or a diaphragm. They have very simple guts, basically a stomach and intestine. I was surprised to learn that they do not have cloacas like birds but have two separate outlets, one for urogenital things and one for poop. Comparative anatomy for the win!

Just Look At This Dude!

Look at this bug trying to pass himself off as some dried up pine needles hanging off the wires. He's been there all day.

Lions and Tigers and...Snakes

Yesterday I did a necropsy on a 16-year old albino corn snake. In vet school, our lectures on snakes and reptiles and amphibians were cursory at best, and covered nothing at all on the anatomy of these animals. When I got the email that the snake was coming in, I hustled over to the bookcase and grabbed the first relevant textbook that I saw. It took me about an hour to read and take notes on the chapter on snake anatomy. There was a decent figure in there, so I photocopied it to take down to the necropsy floor. I skimmed other chapters to get an idea of what kinds of diseases were most common in snakes. I also specifically researched zoonoses. I already knew about Salmonella (any reptile can give you salmonellosis), but I also learned that snakes commonly have cryptosporidia in their gut and those little parasites don't care who or what you are, they will make you so fucking sick with the vomiting and shitting that you will wish you had salmonella instead. Right--everyone on the floor was going to wear full PPE (personal protective equipment) including face masks.

And of course, I also immediately sent up the bat signal to one of my classmates who keeps snakes as pets. He was super helpful, giving me tips on how to determine a body condition score for snakes (that's an important thing in vet med, we do it for all species but you look at different parts of the animal depending on the species, and we never talked about determining a BCS for reptiles during school). He also kindly shared other miscellaneous bits of knowledge that one can only acquire by actually keeping snakes around all the time. Not my cup of tea, snakes, but this is my job now.

Snakes appear to have gone out of their way to make their anatomy as weird and difficult as possible (no diaphragm, one lung, three-chambered heart, two aorta, no urinary bladder, tongue hidden away in a pouch in the mouth; I could go on). Thankfully, livers and kidneys are fairly recognizable organs in most species and serve as good landmarks. I did my best, and to be honest, I found some surprises in this snake that may actually provide a cause of death. That's a rare enough outcome for any necropsy in any species, but even better because this one was so unusual.

And today I did a necropsy on a bobcat. The bobcat came in last week but we had to submit brain tissue for rabies testing before we could proceed with the necropsy. It was negative.

So when I was in vet school, still in second or third year, a cougar came into necropsy. Everyone was super excited and it was the talk of school...until that darned thing tested positive for Yersinia pestis, otherwise known as The Plague. Yeah, THAT plague! That's a reportable disease and Homeland Security got involved because bioterrorism. All students in necropsy at the time had to take a course of antibiotics (no opt-out on that), and a mountain of paperwork was created. The pathologist in charge of the case still tells stories about it.

The director of the lab told me during my first week here that tularemia was pretty common in Arkansas. Tularemia? That is a horrible disease! It affects rabbits, but also quite often affects felids. Felids...like bobcats.

So I spent this morning researching gross lesions that I might expect to see for Francisella tularemia, Yersinia pestis, and what the hell, Bacillus anthracis too (anthrax). Going for the full apocalypse. All three are zoonotic (nasty deaths for humans) and reportable. I made notes on the tissues I needed to collect, what tests I needed to request, and where I might send all this shit because we don't test for any of those diseases at our own lab.

I emailed one of my mentors at Oregon State (had some questions about the snake) and told her I had read up on these three diseases before doing the bobcat necropsy. She replied, "I'm so proud that you are considering the absolute worse case scenario before going on the floor!" Snark? Humor? True compliment? All of the above! I'm nothing if not cynically thorough.

So the bobcat had a femur fracture and likely died of starvation/dehydration. No evidence of infectious disease. Even so, I was ready.

Woes of the New Homeowner 2

Well, one of the PODS arrived. Not entirely sure where the other one is (the one with all of the furniture). And yes, I'm quite annoyed. I posted a very unhappy one-star review on google. PODS quickly tried to get me to contact them but I'll let them stew for another day. The unpacking will help to refocus my ire.

And it seems like I am going to take a million photos like this:

Archie is a delicate flower and having reactions to his mosquito bites. The other dogs don't seem to be having the same problems although the mosquitoes are astonishingly numerous. I'm looking into having the yard and house regularly serviced for insects. I've never seen so many fucking insects in my life. Most are benign, I'm sure. I just don't want them anywhere around me or the dogs.

Vermin

I've got a vermin problem. More specifically, my neighbor and I have a rat problem. He has a very large pile of lumber stacked next to the fence and covered with a tarp. This is perfect rat habitat--nice and dry during the winter, cool during the heat of the summer, excellent protection from cats and dogs. That takes care of the rat housing problem. What about their nutritional needs? Not to worry. They have been dining out in my five-star compost pile for months. I've known they were there. The dogs definitely know the rats are there. I think they have almost caught one on more than one occasion.

Once the rats started stealing all of the vegetable matter from my compost, and eating the sprouted seeds from the containers of cat grass I was trying to grow for Beast, I decided they were getting too bold, probably too numerous, and that it was time to do something.

Since I have never actually seen them or their droppings, I only suspected they were rats. I spent nearly half an hour at the Bi-Mart reading labels of every single type of rat trap and poison and repellent product they had on display.

Poison really worries me because the rats are literally on the other side of the fence. Any poison I push or drop into their posh lumber condos could easily make its way back into my yard and pose a huge risk for the dogs. Even the new traps with the poison block contained within a plastic unit that the rodent has to enter seemed to be too risky.

So it had to be a trap. There are so many different ways to trap rats and mice. I eventually selected a TomCat snap trap, working from the theory that as messy as it might be, I'd rather dispose of dead bodies than try to re-home live rodents. I have boxes and boxes of exam gloves, plenty of plastic bags, and I go every day to a large veterinary teaching hospital where I can properly dispose of dead animals.

The first two nights, I baited the trap with cheese (smoked gouda, it's all I had) and pushed it next to the compost container. Nothing.

Then I realized, these rats don't know what cheese is. They have been living the ultimate vegan lifestyle for months. Last night, I baited the trap with a bit of eggplant rind that had a nice juicy hunk of eggplant attached. And I put the trap IN the compost pile.

I woke up to find this. The relatively small size (for a rat), the smooth, dark grey fur, and the hairless tail that is much longer than the body identify this as a black rat.

According to one of the local newspapers, the population centers of Oregon are seeing increasing problems with black rats. They are attracted to backyard chicken coops (they eat the chicken feed and can also kill chickens). My neighbor and I don't have chickens, but apparently we've provided an acceptable alternative. 

I may get a second trap. I've got plenty of bait and all summer to work on this project.

Azza, My Delicate Little Flower

At the end of the spring term, Azza and I were bouncing back and forth between her regular vet and the emergency vet clinic. It was an expensive round of visits. I've always been worried about how to handle Azza if she got sick. Well, I got a chance to find out.

She doesn't allow many people to touch her even when they are here in the house and she's seen them several times. There are some visitors that she quite likes but she is selective. Even though I muzzle her before we enter an exam room, it takes a vet with a calm and sure hand to even get close enough to listen to her heart and lungs, or dog forbid, touch her as part of a physical exam. Forget about that rectal temperature business. Not happening. So when she began to vomit blood and pass fresh blood and mucus instead of stool, my first thought was how to manage the inevitable vet clinic visits. It really helps that I have continued to introduce her to new things (agility trials, for example, which she only views from afar but that is quite enough for her) and to new people. During our various vet visits, it was of course necessary to draw blood for testing, and she would have to be touched by at least one other person besides me. I would muzzle her and hold her, instructing techs that they had one shot so bring all the tubes they think they might need. On one visit to the emergency clinic, the tech brought in five vacuum tubes of various sorts. I laughed and said, she'll be light headed after you pull that much blood out of her (not really, but it's a good vet med joke). 

Her symptoms were frustratingly non-specific: episodic inappetance, vomiting, and bloody stool every few months over a period of a couple of years that suddenly and dramatically increased in frequency and severity. I acted so quickly when things got bad that she wasn't even dehydrated yet. Coming up with a definitive diagnosis was difficult. Lots of things had to be considered and ruled out: pancreatitis (she did in fact have acute pancreatitis but it was secondary to the real problem), Addison's or hypoadrenocorticism, parasites, ingested toxins, even salmon poisoning (which isn't from the salmon but from the Neorickettsia bacteria that lives in flukes that infect the liver of the salmon), and so forth.

We eventually came up with a presumptive diagnosis: IBD, irritable bowel disease caused by food allergy and an out-of-control auto-immune response. It's presumptive because a definitive diagnosis would have required a biopsy of her colon. I did not want to subject her to that procedure. Somehow, even though her symptoms were pretty severe, we managed to give her temporary relief without ever hospitalizing her.

This IBD is particularly pernicious because her own immune system is attacking the digestive epithelial cells that line her gut. Fortunately, medical diets for our companion animals have become quite sophisticated, and it turns out that we were able to resolve her problems by switching her to a hydrolyzed protein diet. Although Hill's makes one called z/d, and the terriers are thriving on Hill's Ideal Balance kibble, I chose to feed Azza Royal Canin's Ultamino. Proteins in the hydrolyzed diets, usually chicken, are broken down from very long chains of amino acids into small groups of a few or even just singlet amino acids. That's what happens in your gut when you eat chicken: your pancreas releases proteases that break the chains into smaller and smaller pieces, eventually breaking them down into individual amino acids which pass into your gut epithelial cells. Azza's body doesn't have to do that now. Her gut doesn't even register these little bitty groups of amino acids as "chicken" so she can eat protein without triggering an auto-immune response. 

Her improvement upon switching to Ultamino was amazing. We had her on quite a few drugs to calm her gut down but those were all finishing up just as I started her on the new diet. She loves the taste of the kibble and eats it with gusto. Her symptoms resolved in just a few days. She's been through most of a 25-pound bag now and I was relieved that she was doing so well.

She was doing well until I gave her a new flea treatment last night. See, fleas are becoming resistant to fipronil, the active ingredient of Frontline. I've used Frontline for years but I knew that I was rolling the dice since fipronil-resistant fleas were becoming more widely reported in Oregon. And sure enough, those little fuckers showed up in my back yard. So after doing some research, I decided to switch the dogs to Nexgard. It uses a different chemical to kill the fleas (afoxolaner), and it is an oral medication (Frontline is a topical). 

I gave each dog a Nexgard chewable last night after dinner. Within one hour, Azza was scratching her belly, neck, and head incessantly, chewing on her skin on her legs, and had a head tilt and was shaking her head constantly. Her neck, chest, belly, and inside her ears were bright, inflamed red. I managed to get her to her regular vet this morning (saving the emergency clinic visit fee) just as her scratching began to break her skin. She got a diphenhydramine shot (you know it as Benadryl) plus some prednisone. Since she'd never had antihistamines before, I was curious to see how she would react. It will either makes dogs sleepy or it will make them hyper (same for people too). Turns out it makes her sleepy. I'm now giving her diphenhydramine orally every 8 hours. Combined with the prednisone, her symptoms have become greatly reduced. Not gone, she is still scratching and licking but it's not as frantic, and her skin is not so red (ah, the immune-suppressing magic of corticosteroids). Her head tilt and head shaking seems to be gone. If I can keep her quiet, she sleeps. 

So what caused this allergic reaction? It could have been the beef flavoring since we know she has problems with proteins, it could have been the coloring agents, it could have been the medication itself. All I know is that I am switching back to a topical flea treatment (I'm looking into Activyl, which has a completely different chemical that disrupts the life cycle of the fleas; fipronil and afoxolaner are flea neurotoxins). Nothing more by mouth for this delicate little flower!

Archie the Snake Killer

I have had resident northwestern garter snakes in my yard since I moved in. They live in the cool crawl space under my house, and I think that they dig into the dirt there to overwinter. I've seen them in all sizes so I know that they reproduce too. I am careful to avoid them when mowing--they like to bask in the sun in the mornings and don't always move out of the way without a nudge. Northwestern garter snakes aren't particularly large, they aren't aggressive or poisonous, and although sadly they eat up all the toads, they also eat slugs and other creatures that I would rather not have in my yard. I keep deep bark mulch around all my bushes and flowering plants and the snakes like to hang out in the loose mulch around the base of the larger ones. In short, they have fairly predictable behaviors and routines like any other animal.

Northwestern Garter Snake.

Because he is a fox terrier, Archie is extremely alert to movement. The snakes attract his attention immediately. He is also quite smart, and he has figured out their routines and behaviors just like I did.

Archie hunts those garter snakes. He lurks around the larger bushes or systematically searches through larger sunny patches. And when he finds one, he kills it by grabbing it behind the head and shaking the life out of it. He whips those poor snakes so fast that blood comes out of all of their orifices. He then guards the dead snake for a few minutes--I've seen him snap at Mimi to chase her away from his precious prize--but he eventually loses interest and heads off to look for more trouble elsewhere.

Here he is with snake blood on his shoulders and paws (he gets it on both sides and on his head but you only need one gory photo as evidence). He doesn't roll on the snakes. This blood is from the snake smacking into him as he whips it back and forth.

I keep part of the yard fenced off so the snakes have a safe space to cavort, but they insist on coming into the main yard where Archie inevitably finds them. While I am sad for the snakes, there is not much else that I can do to protect them. And Archie is acting like a fox terrier is supposed to act. Other than giving him a bath afterwards, I don't intervene. In fact, I'm rather impressed with his dedication to this activity.

Archie the Snake Killer. It would make a good tattoo!

A Rude Encounter With Nature

Archie did not have a good morning. It started out like most other mornings this summer. Part of our morning routine is a complete poop patrol of the backyard. This includes what I call the back forty, a small ell off the main backyard. The house is on a corner lot so this ell is paralleled by a sidewalk and a street, and separated from the main part of the yard by a short stretch of fence with a gate that I keep propped open. It's a bit neglected. The dogs like to play back there so I make sure that it is part of the regular poop patrol but I don't do much with the space itself--it's weedy and dry.

Anyway, I decided to mow all of the backyard this morning. Archie loves to help me mow, shadowing my every step. I started in the back forty. After some tight corners with the mower around the propane tank, I was just getting into the rhythm when I saw Archie explode into a frenzy of running, diving, rubbing his face on the ground. He was covered in bees! On his head, his side. I managed to call him to me (his recall is getting so much better!) and we ran around to the main part of the yard where I brushed the remaining insects off of him. He was frantically flipping and rubbing in the grass.

I've encountered these little fuckers before. Last summer, I had two different nests of them in flowerbeds in the front yard. They are social, live in nests in the ground that they dig, usually located around something like the stem of a large plant or a pole that extends into the ground. And they are extraordinarily aggressive if their nest is disturbed. They interpret disturbance fairly liberally so I keep an eye out for them. They cling to clothing, or fur, and sting multiple times. They will even sting through clothing. Bastards.

I've never gotten a good look at them except to figure out that they are around 10-12 mm long, fairly dark in color with clear wings, and they are not bumblebees. I have plenty of those in my yard, more than one species, and they are easy to identify. After doing some research, I think that these things are some sort of wasp, not bees. A lot of the evidence points to wasps: nesting activity so late in the summer, aggressive defense of the nest, etc.

I inspected Archie carefully for swelling or similar adverse histamine reactions. I put him in the house and kept an eye on him for about 15 minutes just to be sure. Then I went back to see if I could find the nest. Sure enough, they were coming and going from a small hole located next to the pipe containing the electrical supply for the propane tank meter. I must have bumped it with the mower and by sheer bad luck, they went for Archie instead of me.

I cobbled together some water hoses and sprayed the wasp nest with poison. My experience of last summer suggests I will have to do this a second time to completely eliminate the nest. Of course, before I resorted to poison last year, I tried benign solutions such as trying to drown them out. All that did was provide them with a regular source of water and make them more active and aggressive. At one point, I was having problems exiting my front door because one of the nests was under a rosebush about four feet away. So, poison. I'll also set out some hanging traps, which don't seem to attract bumblebees (although plenty of sweat bees make it into them).

Poor little Archie. Even when I finished mowing the main part of the backyard, Archie decided he wanted to stay in the house. That was not at all like my happy-go-lucky puppy. 

I generally take a live, let live attitude towards the insects in my yard. As long as doing so won't endanger me, I capture and transport spiders back outside. I don't break spider webs unless I absolutely need to. Instead of poisoning the horrifically slick moss coating my sidewalk and driveway last winter (all the poisons are terribly toxic for fish and amphibians), I sprinkled sodium bicarbonate over everything--it changes the pH and the moss dies. Works great and it's cheap! I plant flowers in the front yard that attract bumblebees and butterflies. But these little ground-nesting, stinging wasps--they have to go. I can't have myself, and now the dogs, attacked when we wander around in our yard.

An Early Arrival

Anna's hummingbirds remain in the Pacific Northwest during the winter so I've regularly cleaned and filled my feeder, even moving it to a more sheltered spot next to the house so that it was less likely to freeze. During December and January, I would take it in at night. The feeder is monitored twice daily by a male Anna's. Sometimes a female shows up, sometimes another male Anna's drops by, but mostly it's this one male.

The male Anna's knows both me and the dogs and will come into the feeder even if we are walking around in the yard. So it caught my notice a couple of weeks ago when a tiny, very skittish, orange-ish hummer starting showing up.

In the summer, I have up to five species of hummers show up. One of these is the rufous hummingbird. They are distinctive birds with their coppery backs, black wings, white neck ring, and iridescent red throats. I had both male and female rufous hummers visit my feeder last summer.

It's a male rufous, possibly a young one because he is extremely tiny. I have definitively identified him after numerous sightings, made rather difficult because he'd flit off if he even saw me through the kitchen window. I finally got a photo, not the best because it was taken from inside the house through dirty glass and a screen. I had to hide around the corner and slowly extend the camera out so that this little guy wouldn't zip away in fear.

He's here far too early in the season, I think. I hope he survives until the weather warms up. I've been thinking that I will set up a second feeder to increase his chances.

The Elusive Male Calliope Hummingbird, Plus A Beetle

To my great surprise, on June 28, I observed the elusive male Calliope hummingbird at my feeder. In addition to his small size, his throat markings are diagnostic. During his three visits to the feeder, I studied him carefully with the binoculars that I luckily had in hand already. The female Calliope came first at her usual time, and I had pulled the binoculars out to observe her. She flew off then suddenly the male appeared. If you don't bird-watch, you may not understand the pleasure one gets when observing an "uncommon" species in one's own backyard. 

When I was making the daily poop scoop tour of the backyard this morning, I encountered this creature:

It is a banded alder borer; scroll down in link to find the entry. This bug eats dead wood on a variety of different trees. Despite its rather ferocious appearance, it doesn't eat living wood or kill trees. So after snapping a few pics, I left it in peace.

Hummers!

I finally gave in and installed a hummingbird feeder in my backyard. I wasn't hesitating out of lack of interest--I've been bird-watching as a hobby for decades. I suppose it was the result of a sort of inertia, waiting until I knew what was going to happen with the vet school project.

Now that I've decided to stay here in Oregon (daily proving to be a good decision), I've also decided to stay put in the same house I've been renting for the past two years. The rent is rather high, the house is old, it has no AC, and the heating sources in the winter are expensive. These are compensated by two important things: I feel like the amount of space is just right, and the fenced part of the yard is enormous, a luxury in a rental house. Of course, the latter implies regular mowing duties, which in the Pacific NW begin in February, but the dogs just love all that space to run around and play.

Back to the point. I feel a bit more settled now. So I put up a hummingbird feeder.

In Texas, I had only one species of hummer visit my feeder: ruby-throated. The challenge there was to identify the number of mated pairs that visited. Here, I have FIVE species that frequent my feeder. Taking into consideration the males and females of each, you are potentially looking at ten variations on little, busy, buzzy, greenish birds to identify. 

To keep the feeder in shade as long as possible, I mounted it across the yard in a location that is visible from my kitchen window and back door. I keep a pair of binoculars and a bookmarked copy of Peterson's handy. 

So far I have definitively identified male and female black-chinned hummers, male and female Anna's hummers, male rufous hummers (they are the most shy of all the species), male Allen's hummers, female Allen's/rufous hummers (can't be distinguished in the field but I probably have both since I've seen males of both species), and most exciting of all, a female Calliope hummer. I've not seen her mate. Maybe he keeps watch while she feeds. She visits every day so I suspect he's around, just shy/vigilant. 

Calliopes are the smallest North American hummers and described as "uncommon". The first time I saw the female, I wasn't entirely sure of the identification. But after weeks of observation, there is no doubt that at least one Calliope female is visiting my feeder. She is significantly smaller than the other species, so small that her wingtips extend past her tail feathers when she is at rest, and she has to stretch from the perch to reach the feeder.

My little flock maintains regular feeding hours but there is never really a crowd and none of them seems to guard the feeder. I see birds land every few minutes throughout the day, with rush hours at dawn and dusk, but rarely see more than one at a time. Lots of people in this area put up feeders (for example, my next-door neighbor has one hanging outside his living room windows) so I think we can assume that resources aren't terribly limited for them. 

The species spatially segregate. The black-chinned hummers always approach from and leave in the same direction while the Anna's males arrive and depart from another direction. I can now usually tell which species is arriving simply from the direction of their approach!

Except for the rufous males, the birds have become quite bold, even cheeky. They check out the dogs all the time, and often perch in the forsythia inches above a dog stretched out in the grass napping in the sun. I did have to work a bit with Azza to convince her not to chase the hummers the same way she chases bees and moths and such. She's been very good and now barely lifts an eyebrow as they buzz right over her head.

Sorry, no pictures. No camera in my possession can take pictures of such small birds from such a distance. 

Super Powers and Poisonous Frogs

I think I've mentioned before that the students taking animal science classes are overwhelmingly female. There is nothing inherently wrong with that but it's always nice to have a balance. So I was quite pleased to find out at the beginning of the term that the grad students taking the biostatistics course come from departments all over campus. The class is comprised of about 30% men--still skewed but reasonable. Students in public health, social sciences, and some of the other physical sciences are required to take the class so it has a pretty large enrollment every fall term, around 70 or so total.

We meet twice a week for lecture and once a week for a lab which is taught by a TA (teaching assistant, a grad student hopefully familiar with the course content). In lab, we learn how to use a specialized computer program to calculate various statistics. The lab content generally runs a lecture or two ahead of the lecture content. But for most labs, the TA gives us a quick crash course to introduce just enough of the new concepts so we can run the program and do that week's lab assignment.

Totally by chance, in my lab section, there is only one guy. He's memorable by that fact alone but there is something else that really sets this guy apart. He has a super power the likes of which I've never seen before.

He sucks the intelligence out of your very marrow if you sit within six feet of him. Sit right next to him and you are doomed. 

He's also a whiner. This serves as a convenient warning flag rather like the brilliant coloration of poisonous rainforest frogs. 

He complains vocally, loudly, petulantly, about everything he doesn't understand, which is everything. If you aren't paying attention to the warning flag and you happen to sit near him, or even worse, choose to do so, you get what you deserve: all your intelligence will disappear in a matter of minutes.

Today he compared reading the textbook to reading a "user's manual for an electric toothbrush in Cantonese". His exact words. I suspect that he believes himself to be clever and amusing but I find him embarrassing. I want to tell him to grow up, shut up, and listen. But I'm afraid to get too close. 

Our Microbacterial Overlords?

A joke that I’ve heard more than once, and even made myself, is that humans are nothing more than warm sacs for our gut bacteria. There are several subtexts to this joke. The one I want to focus on is that while the human body contains at least 37,200,000,000,000 cells, or around 37 trillion cells (these guys did the most recent estimate*), the microorganisms living in and on us number ten times more (around 370 trillion cells); even so, microorganisms are small (sorry to be obvious) so they only account for about a kilo of our body mass. From the perspective of those bacteria, we are indeed a mobile unit providing them with food, shelter, and opportunities to propagate.

What is the function of all these microorganisms? I decided to look into some of the recent results of the Human Microbiome Project (HMP). The word microbiome refers to all the microorganisms that live in and on us (mostly bacteria, some fungi). Using computerized genetic sequencing techniques that we now perform quickly for large quantities of data, the HMP has given us an astonishing, if still incomplete, picture of our microbiome.

Some background. Our DNA, long protein molecules, are wrapped up into neat bundles we call chromosomes. DNA molecules contain codes for making more proteins. Proteins are like the worker bees of cells. They can be messengers, carrying chemical signals from one place to another. They can be receptors that receive those signals. They can be enzymes that help chemical reactions in the cell operate faster, or operate under energetically unfavorable conditions. They can be the molecules that are changed by the enzymes. This is far too short of a list but you get the idea.

There is extreme variation in the number of chromosomes between species and within species. In fact, the number of chromosomes isn’t much of an indicator of anything useful. What’s important is how many different proteins those DNA molecules code for. One of the surprises from the Human Genome Project was how few proteins our DNA codes for, around 20,000 proteins, about the same number as the fruit fly. (We are not special.)

The microbiome project looks for proteins that aren’t us. In fact, this is exactly the point of the microbiome itself: by acting as the host for the microorganisms, we get access to new proteins and new biochemical functions that come with them, without having to evolve the machinery, that is, the genes, to code for them. Many of these proteins are critical for our survival such as vitamins, enzymes that can utilize special nutrients, and proteins that operate within our immune system by turning it on in the first place and by causing diseases when things go awry. There are some researchers that have suggested that our microbiome may even influence our behavior; albeit fascinating, that is a topic for another day. One of the remarkable conclusions of the microbiome project, one among many, is that humans are a “supraorganism” that is a composite of both human and microbial biochemistry. So it seems that they are more our partners than our overlords (still, I think that is a debatable point). In fact, our health depends on the health of our microbiome to a fairly large extent.

There are still plenty of unresolved questions: does our microbiome vary as we age? (Probably but it still needs to be verified.) Does a healthy microbiome depend on specific species or on the general set of functions provided? Does our microbiome depend on where we live? Should we collect a lot of data from a small number of related humans located in one place or sample widely across the globe? Both designs will give interesting results but they will be answering different questions. There is plenty more to be learned from this multi-lab, multi-country research initiative.

An interesting side note: most of our microbiome is located in our gut, specifically our colons, although there are microorganisms on every single surface in and on us. So the HMP obtained some of their samples from human feces. I will never again complain about having to pick straw and cedar shavings out of chicken droppings in order to get a clean sample.

*While the current trend is towards increasing open access, which means the full publication is available online in a format such as PDF and you don’t need a subscription to get to it, many journals embargo articles for a year or two after publication. The abstract of the publication, a summary of the hypothesis and results that appears at the beginning of all scientific papers, is nearly always available without cost. There are very good reasons for embargoing papers which are beyond my scope here. Open access doesn’t necessarily mean better. It is caveat emptor in the world of open access, since any fool can create a masthead and self-publish these days, or charge other fools to publish their work, without going through that messy peer review process. In this case, the peer-reviewed article that I linked to is published in the Annals of Human Biology, which embargoes newly published articles. Nonetheless, even though you can’t read the full paper without a subscription to this journal, you can get the main points from the abstract.

Harry and the Coyotes

I lived in Salt Lake City for some years and, before I ruined my right knee, I used to go running in the foothills of the Wasatch Mountains in the early mornings. I had three smooth fox terriers then, Harry, Iz, and Dyna, and I would take them with me. Only deep snow or temperatures below 20F would stop us from going.

The dogs were young but relatively well trained and because the trails were in BLM-managed land, I let them run off lead. Despite the easy access of the trailhead at the top of a fairly tony neighborhood, the trails were not heavily used, at least in the mornings. There were vistas from some of the hilltops where you could see the city spread out at your feet.

One crisp fall morning, I managed to convince a friend of mine to accompany us. The trail began with a gentle curve around a hill, climbing slowly until it suddenly shot off in a straight line, mostly up, towards the hill tops. Once you rounded the first hill, you could no longer see the parking area at the trailhead.

We were around a mile and a half from the car when a pack of coyotes appeared on the trail, coming up from below us. They were somewhat spread out but were clearly operating as a unit. As usual, the dogs were ranging ahead. I managed to call Iz and Dyna to me and snapped their leads on, but the coyotes separated Harry from us and charged him.

He turned and ran, heading farther up the trail.

I threw the car keys and the leashes to my friend, told her to take the two dogs back to the car, and I took off after Harry and the coyotes. Her eyes were as wide as saucers but she turned around immediately.

The coyotes had a lead on me and it was a steep climb. By the time I crested the hill, I could see nothing, hear nothing. I began to call Harry’s name, but I was out of breath, freaking out, and what came out of me was panicked howling.

Suddenly, a man appeared, a bow hunter. He floated up from below me just like the coyotes had done. He told me he had been in the ravine below and had seen the coyote pack tracking us. He said he saw them separate Harry. He said, is that how you normally call your dog to you? I was sobbing and yelling, but I took a breath and said, no. He said, try to call to him in a normal voice.

Suddenly, in the thick scrub oak below us, we heard dogs fighting, one crying out in pain. The bow hunter shot off like he was one of the deer he was hunting, leaping down the hill before I could react. I followed as best as I could but I was dressed for trail running, not bushwhacking. I could hear the dog fight continue, but it was moving, changing location, heading down the gully. Then, suddenly, silence.

I caught up to the bow hunter. He said, we need to climb back up to get a better view. As we crested the top of the hill again, I looked back down the trail and saw my friend running up the trail towards us. She was yelling and waving her arms but she was too far away to make out what she was saying. I continued to call Harry.

The bow hunter and I waited on the hilltop while I periodically called Harry, pausing to listen in between. All we heard was the wind. I was mentally frozen, sure that the coyotes had killed my dog. The bow hunter kept telling me to trust my dog, trust my dog, be calm when you call him. Finally, my friend got close to us and I heard her yell, he’s at the car! He’s at the car!

When she reached us, and managed to gasp out, Harry was hiding under the car when she got there with the other dogs, I collapsed on the ground, sobbing. If you read historical fiction, you may have read something like “she fell onto the sofa insensible.” Well, I was insensible, literally without senses, for several minutes. My friend had tossed all the dogs in the car, not even stopping to check Harry for injuries, and turned around again. The bow hunter kept talking to us, made us drink some of his water, and jogged back with us to the car. I can’t remember what he said now. I only remember thinking, he’s in the car, Harry made it that far.

Once the coyotes separated him from us, Harry did run up the trail further, then down into the ravine. There was indeed a fight. He had a nasty bite on his right rear thigh, a puncture on the outside and more of a tear on the inside. Amazingly, that was his only injury. I think we can infer that Harry was more interested in getting away than making a point.

Somehow, he managed to keep running and make it to the car along a route he had never been before, and there he waited. Quite amazing, really. The event was physically and emotionally traumatic for him. The vet warned me that when dogs get into fights like that, it can take a couple of days for them to recover even though their obvious injuries are relatively minor (he didn’t even require stitches). Indeed, it took Harry four days before he moved off his warm fleece blanket nest at home for anything other than meals and potty breaks. The fleece blanket he was curled up in was a get-well present for Harry from my friend G and my running partner of that morning; they brought it over that day. I still have that blanket, or what’s left of it. It’s well loved, just like my tough little dog Harry.

Spiders in the Garden

Back in the spring, I planted four small spruce trees along the western fence line of my back yard. They aren't as tall as the fence and so do not provide me any shade yet. But they are growing. 

It turns out that spruce trees are excellent habitat for spiders. I've identified at least two kinds that took up residence in them over the summer. One kind builds funnel webs tucked in between branches. You can see them lurking at the center of the funnel if you sneak up quietly and make sure your shadow doesn't fall on the trees first. The other kind, a common garden spider, builds vertical webs between the trees and between the fence and the trees. The distances are around 3 to 4 feet, nothing particularly difficult for these spiders. The spiders started out quite small, maybe the diameter of a pencil eraser, but they appear to have had a successful summer of hunting and several of them have leg spans that are easily over an inch in diameter now.

I check on the spiders every morning when I let the dogs out for a last potty before I head off to the lab. Over the course of the summer, I've collected some interesting observations about these spiders and their webs.

First of all, when they were small, the spiders often centered their webs in the middle of the two objects. It is rare now to find a centered web. Nearly all the webs are offset closer to the trees. My cursory online research suggests that the spiders are simply adapting to the more likely position of prey, mainly flies, midges, mosquitoes, and the like.

But here's a really interesting thing. When the spiders started building their vertical webs back in the early summer, they would build them at a variety of heights. However, the dogs walk between the trees--the trees get watered and the grass grows green and lush there so it's a favorite pooping area, and the lane between the trees and the fence was part of Harry's daily perimeter check. And I mow the lawn of course. So the lower webs would get broken on a daily basis. 

It only took about 2 to 3 weeks but the spiders stopped building webs below Azza's head height.

That's right. I think the spiders learned that low webs were not productive so they all shifted their webs to about 3 feet up and higher. The dogs walk between the trees with impunity. I can easily push the mower between the trees and not touch a web.

In case you think that I am insane (I might be but this is not the best illustration of it), here's another example. I walk the dogs very early in the morning. Places along the sidewalk where bushes lean in close to mailbox clusters would seem to be reasonable locations for spider webs. But I never encounter webs in those locations, and I think it is because those spots are too highly trafficked--the spiders in those areas also learned that, although it might look like a nice easy distance, those are actually crummy locations for webs. I do find spider webs when I veer from the sidewalk however.

There is spotty research on this but it does appear that spiders will change the location, shape, and size of their webs in response to prey availability and type as well as competition with other spiders. One group of researchers did a cost-benefit analysis on spiders that move their webs. I turned up some amusing older references which state that spiders do nothing more than execute a fixed program, like a computer runs a program, when building their webs. Manifest destiny! But newer perspectives suggest that spiders exercise a degree of free will, that they can evaluate past experience and change their web parameters, when web building. That latter view is more consistent with what I observed, and that is a far cry from a computer running a fixed program!

I'd also like to briefly mention some super freaky little spiders that live in my front flower bed. I've only seen them there because in the front flower bed are two plants, mint and some other flowering thing, that produce white flowers. These spiders are tiny and pure white. They don't build webs; instead, they stalk their prey. And they mostly capture bees that visit the flowers. Truly diabolical.

Surrounded by Lavender

This weekend is the annual Lavender Festival in Oregon. Some of the farms are open year-round but on this weekend, all of them open their gates to the public. The festival website was fun to explore--it included useful map tools since the farms are scattered across the central part of the state. A friend and I did a little bit of planning and yesterday we visited three small farms that were relatively close to us.

This field was vibrating with thousands of bees.

I came home saturated with lavender. Depending on the farm, you might find essential lavender oil, lavender soap, lavender lotion, lavender-infused honey, mint tea with lavender buds, fruit and lavender jams, lavender chocolates, lavender lemonade (you can even get that in most coffee shops this time of year), lavender-infused herbs and salt, dried and fresh and potted and U-cut lavender, make-your-own lavender wreaths, lavender-themed artwork...and some of the larger farms had additional vendors, food, even music.


My friend and I had a good time looking over the lavender bounty. We hung around the distillation demonstrations--for the aromatherapy! I thought that the oil was in the leaves but it is in the buds. They have to be picked before they flower. When you distill, you start with an enormous pile of cut lavender, including stems, and a lot of water, and end up with a few liters of essential oil, a mash of plant material, and many gallons of lavender-infused water, a sort of weak tea. Some farms filter this water and sell it as a body mist; I thought that recycling was pretty clever.

I bought three plants--two are an unusual white-flowering variety developed at one of the farms. Even though HellBeast consumes everything organic that I leave out in the house (and some inorganic things, like flip flops), I also bought a bunch of cut lavender. HB seems to have met his match--he gave it a very thorough examination but the taste test did him in and he won't go near it now!

We sampled homemade lavender chocolates. The cilantro-lavender was a surprise but the white chocolate infused with lemon-geranium-lavender was outstanding.

This farm had landscaped gardens, fountains, and gazebos of various sorts in and around their lavender fields.

For my dinner that evening, I combined lavender honey, soy sauce, white wine, and crushed mint leaves that I cut right outside my front door and used this to pan-glaze a pork chop. I tossed a yam and green onions in the pan to soak up the extra juice. Mmm! You could really taste the lavender. It was fabulous.