Azza and Mimi

I have been really surprised at how often Azza and Mimi play together now. And they don't mess around--furniture is usually rearranged in the process. They rarely make any sound, except for grunting or panting. Okay, that sounds really off-color...you need to get your mind out of the gutter! Even Mimi body-slamming the couch will shift it a centimeter or two.

Two female terriers just don't play together. Most of the time, they can't even occupy the same room at the same time. 

Azza isn't a terrier. But she is young and full of energy. Mimi is a terrier. She wants to be in charge pretty much all the time. And yet, when they play, she is perfectly willing to "pretend" to take a bone from Azza (getting the bone isn't the point of the game). Azza's most often employed wrestling tactic is to simply sprawl on top of Mimi, which only lasts for a second or two until Mimi squirms her way out from under and shoots across the room to another piece of furniture with Azza hot on her tail.

I've tried to video their hijinks but they get suspicious when I stop typing or clicking the mouse and they stop playing to see what I am up to--walk? treats? game of tug or fetch?

Anyway, here are some fun pics of them playing.

 

T3i initially gave this toy a rating of 2 out of 10. But after it lost both upper limbs and head, I tied a knot in its neck and it remains a favorite. Revised T3i rating: 8.

I have no idea what they are doing. I think they both have an antler chew. But really, there's no telling.

Cow Salting and Hay Fluffing

I mentioned a couple of posts ago that I am doing some grunt work for a nutritional study of dairy cows. It's not like I have tons of free time at the moment. However, helping out with the study now means that I will be able to assist with the calving in a few weeks. Currently, my official duties are morning hay fluffing and occasional evening cow salting.

In a post I made years ago, I talked about the term "chute fluffer" which was common in dog agility circles at the time. Since the term "fluffer" has an off-color origin in the porn industry, it may have fallen out of use by the agility folks by now (most likely as a result of prudish hand-wringing and cries of "think of the children" but that's a rant for another day). 

But my regular morning job with the cows is perfectly described by the title "hay fluffer." 

The cows are being housed in a new barn on campus for the duration of the study. This is the first time the barn has been used since the construction was completed, and like most things, there are a few maiden voyage bugs that need to be sorted out. 

All of the alfalfa hay that will be used in the study was stacked into an enormous wall of bales under the barn roof. I can understand why they want this stuff to be kept dry...but the wall of bales was placed so close to the pens that it creates all sorts of problems: can't easily get the carts carrying weighed allotments of hay to each pen, barely any room to use brooms and forks and shovels, and most importantly, there is no room at all for feeding troughs or bins. 

I know nothing at all about cow husbandry but the lack of feeding bins was pretty obvious to me the very first time I went to the barn. 

As a result, the evening alfalfa hay and the morning grass hay are tossed onto the concrete floor in front of each pen. The cows tear into the alfalfa in particular with gusto. It's quite something to watch and to hear. They can't stuff it into their mouths fast enough. It smells sweet to me so perhaps it tastes sweet to them. The aisle isn't that wide but it is wide enough that the cows eventually toss and spread their feed out so much that they can no longer reach it. 

Cows love alfalfa hay.

Enter the hay fluffer. Every morning at 10am I have to go to the barn and fork and sweep the hay back up to the pens (in the aisle that isn't wide enough to use either tool very effectively). This is a job that would be completely unnecessary if some thoughtful planning had gone into the placement of the wall of bales, leaving room for feeding bins. But I'm not in charge, I'm just free grad student labor.

I'm also the substitute cow salter for 6 or 8 evenings a month. Some of the cows are eating special alfalfa and get normal salt, but some of the cows are eating regular alfalfa so they get special salt. We need each treatment group to consume a certain amount of each type of salt. The salt is loose and medium to fine grained, sort of like table salt, only it's pink because it is actually a salt+mineral mix. So the cow salter comes along behind the evening feeder and sprinkles measured allotments of each type of salt on top of the alfalfa piled in front of each pen.  

Besides positioning myself to help with calving, one of the other benefits I've reaped is a brand new pair of boots:

I went with the steel-toed version because, well, toes are pretty useful for walking and things like that. Steel toes are probably overkill but one thing I learned from a couple of my petroleum industry jobs is that attention to safety is not time or money wasted. And boy oh boy, they are toasty warm in that damp, drafty barn! Yes, they are expensive but the remarkable attention to detail would surprise you.

Two Photos

I found this photo when I was cleaning up the memory in my camera. It makes me sad to see it but the dogs had such a fun time that afternoon. This is how I want to remember Harry.

Happy times. Dhahran, January 2013.

This is also a photo of happy times, or at least sleepy times. I study at a table near the back door and it can be a bit cold there. The dogs refuse to stay in beds close to the gas stove; that was Harry's spot. So I moved the beds next to the table.

December 2014. HellBeast is tucked behind Azza.

Feathered Black Boxes and Licking Rocks

I can't recall if I've posted my musings on this particular topic before, and I'm too lazy to go back and check. Apologies if this is duplicate rambling.

In my last post, I wrote about helping with day zero blood draws on dairy cows in a nutritional study. I just got an email from Jean asking if I could drop by the barn every morning and push hay back into the feeders. It seems the cows push it out overnight. And she asked if I could sub in now and then for her grad student who oversees the evening feedings. Fairly menial tasks, sure. But it positions me well for the calving to come! I of course told her I'd be happy to take care of those tasks.

Visiting the cows every day is a great opportunity to learn more. In fact, over the summer, I made sure that every day I spent time in every pen with the chickens in my feeding trials. The chickens were feathered black boxes, the interesting chemistry churning away inside them. At the time, I observed subtle changes in feeding and excretion patterns that I only later understood when I was in the lab analyzing the tissues.

Which brings me to the point of this post. Animal science is a lot like geology. Let me list some of the reasons.

Black boxes. Rocks and animals don't speak. You must learn to use all of your senses: what you see, hear, feel, smell, taste, all can be important. What? You've never licked a rock?

Data. In the world of geology, you never have enough data, you never have it in the right location, and the data that you do get is in half a dozen different formats with extraordinarily variable scales (nanometers to thousands of kilometers, nanoseconds to billions of years). Except for the parts about kilometers and billions of years, animal science seems to put you in exactly the same position. 

Remote sensing. I'm using this term quite loosely. Besides what you observe, a geologist has to collect other data using tools and machines and computers. You may not have to design and build these things but you need to know how they work in order to use them appropriately. You can't transport yourself down to the bottom of a 20,000-foot deep well to see what is going on in the reservoir; even if you could, you'd need special glasses because what is going on is on a microscopic scale anyway. It's the same for animals. We can take xrays and ultrasounds and run blood tests but they are similarly small windows that are still at a remove from the whole organism.

Integration. As geologists, we make measurements in the field or collect samples or interpret data, and none of it makes any sense until we start building maps and other integrative displays, adding bit by bit until patterns emerge. Animals are the same. We can observe and record our observations but true understanding doesn't come until we start putting all the bits together. Interpretation requires rigor and method, integration requires creativity.

It was a risk but I included a very brief summary of this idea in the personal statement I had to write for the vet school applications. I am of course not saying that if you are a scientist of flavor x, you can willy-nilly start doing science of flavor y. I am drawing parallels between two specific types of science because I thought that the similarities were unexpected and interesting. I suspect that as I learn more about animal science, I'll find many differences that are just as unexpected.

Opportunity

A couple of Saturday mornings back, I willingly spent several hours getting soaked by rain, cow slobber, cow shit, mud, and blood (bovine and some of my own). It was tremendous fun!

This wonderful opportunity came up when I found out that one of my committee members was starting a nutritional study on dairy cows, currently pregnant, and their calves, arriving in late January-early February. This will be a follow-up to a study she did last year. The paper on the first study was published a couple of months ago and we discussed it in our nutrition journal seminar. Upon my inquiry, I was told that no vet school students or students from the Animal Sciences department had participated in the first study. I was astounded. The study is certainly scientifically interesting. But it also represents a great opportunity to get large animal exposure--and it only requires a student to show up. Maybe vet school students don't need that kind of experience but undergrads who aspire to go to vet school sure do need it. I couldn't understand why they weren't elbowing each other aside to volunteer.

My vet school applications have long been completed but I figured that any chance to get some large animal exposure would not be a waste of time.

So I emailed Jean and offered my services. She was happy to have me come along. That Saturday was day zero of the study. We were going to get about 25 ml of blood from each cow. The blood would be analyzed to establish chemical baselines before the cows started eating the various dietary treatments. There are about 50 cows in the study so extra hands for this particular activity were going to be very valuable.

I met her on campus at 7am that morning. It was raining but not that cold. Three undergrads joined us, all sophomores (and all young women) in the pre-vet honors program. Besides taking a few special honors courses, they each have to complete a research project. I think at least two of them showed up with the idea that this project might be their honors research project. I began to have a few doubts about my fellow volunteers when one of them walked up wearing a pink hat knitted to look like an animal's face and ears, a pink rain coat, and pink rubber boots.  

We loaded up the equipment, piled into various cars, and headed out to the OSU dairy farm north of town. Four guys, students at OSU who work at the farm for money, wrangled the cows from pasture to barn to pen to chute. Two more men, one of them a vet at the OSU vet school, helped restrain the cows' heads. Jean kept track of the paperwork. 

It was up to me and the three girls to collect the blood samples. I was getting more and more excited--I had no idea that we'd get so involved.

Let me describe the chute. It was entirely contained in the barn, starting from a largish pen at one end to a narrow chute snaking around the wall that ended in what is called a compression chute. This is a special chamber with sides that can be ratcheted in and a two-piece collared door at the front. It is opened up to let out a cow, and the next cow, seeing open pastures in front of her (the barn had no wall on that side), would run forward. The wranglers pulled the sides in and slammed the collar together at precisely the right moment to capture the cow with her head sticking out. As you might imagine, this mightily pissed quite a few of them off. They were so close, just this close, to freedom. They bellowed and tossed their heads, spraying us with slobber and shit. Only the first cow didn't have poop on her head and neck so there was lots of poop spraying too.

A rope knotted in a sort of bridle was passed over their noses and foreheads then cinched down to a metal bar on the side of the compression chamber. This pulled their heads to one side. The vet then grabbed their nostrils and pulled their heads to the side even further, stabilizing himself and the cow's head against the side of the chute. Why all this drama? We were going to get the blood from their jugular veins so needed full access to the right side of their necks. We also needed them to be relatively still. 

Each volunteer was told to do 5 cows each then we would start the rotation over again. It was a complicated business. It wasn't until my 7th cow that I finally got the hang of jamming my hand in to the side of the cow's neck to make the jugular pop out. You really have to jam it in there. There's the complication of using a little cup with a double-ended needle on it; the collection tubes are pushed into the cup, filled, pulled out, next one pushed in, all while the needle remains in the cow's vein. Three tubes per cow. I managed to stick myself with a needle that had some anticoagulant on it and my thumb didn't stop bleeding for the rest of the morning. It was a very tiny prick and you could hardly see it with all of the mud and shit anyway. 

You jam your left hand into the vein low on the cow's neck, feel for the vein location with your right hand then, still with your right hand, jab the needle in and lock the first tube into the cup. This one-handed maneuver was tricky but I'm a quick study. I missed the vein only one time (have to start over with a new tube and sometimes a new needle if that happens) and managed to keep going even when a few of my cows started tossing around (hard to believe they could do so with all the restraints but some of them find a way). 

At this point I should mention that the front opening of the compression chute was positioned just inside the drip line of the barn room. We were bent over, sometimes kneeling in the muck, faces inches from the cow's neck, rain dripping down the back of our necks from the roof. 

Only one of the three undergraduates kept going. The other two were incredibly tentative, unwilling to jab the needle in and then they were so nervous that they missed the vein. Every. Single. Time. (In an adult, pregnant, pissed off dairy cow, it's about the diameter of a garden hose; not only can you feel it but you can see it.) One girl never completed the procedure on a single cow. As a matter of surprise to no one, pink girl was one of those two. They held the cup like a pencil, like they were going to write on the cow's neck. They weren't strong enough or not willing to jam their hands into the cow's neck hard enough to make the vein pop out. They were reluctant to stand in the rain, hesitant to kneel in the mud. They were scared when we got a particularly lively one, often dropping the entire assembly instead of bracing against the cow to keep the needle in and blood flowing. Jean and the other OSU vet were giving them step-by-step guidance, and the other girl and I made sure that replacement vials and needles were in their hands before they asked for them. They weren't left to flail on their own for very long (initial flailing is necessary of course), yet even with all that support, they still gave up.

Well, more cows for me and the other girl, I told myself. Turns out she had been raised on a farm and had done blood draws a couple of times on her family's cows.

I was on quite an adrenaline high from the morning. I managed to jump right in and find my stride. It gave me a lot of confidence to successfully repeat the procedure on so many cows. I know that in vet school, when asked to do a blood draw on a horse, cow, goat, or sheep, I will be able to do it. I will know what to do. 

I hardly even noticed the rain even though I was soaked. But, as we let the last cow out of the chute to trot off into the field, we all noticed that the rain stopped, the sun peeked out, and an enormous rainbow formed not 200 yards from us.

When reflecting on the morning on the drive home, I found myself a bit disappointed in the two girls who gave up. They claim they want to be vets, so you might reasonably assume that they know they will have to work with large animals at least in vet school if not afterwards. They showed up at 7am on a rainy Saturday morning so they either figured out or were told that this would be a good opportunity for them. Yet they were not able to follow through. 

Yes, I know, they are young. That was pretty obvious. But opportunities like this one don't drop out of the sky every day. It bothers me that they didn't seem to realize what a significant responsibility Jean was offering them. These kinds of activities build an "animal experience" resume.

Of course, I told Jean that I'd help with the calving in January-February. Freezing weather, nights spent in cold, drafty barns--it's going to be great!

Telling Tales

Upon receipt of the bit of writing below, my French professor wrote in the margin (in French) "You could write French stories." I'm preening, that's for sure--that's quite a complement from Madame M. who is extraordinarily exacting about our grammar. The assignment: write a story about two animals using the three main past tenses (I ate, I was eating/did eat, and I had eaten [before something else happened]). Obviously we have the same three tenses in English but we don't make quite the same big deal about them as the French do.

I chose to retell the fable of the frog and the scorpion (it's antecedent could be this Aesop's fable). You probably know it. Sometimes the frog is a fox or another animal. The frog carries the scorpion on its back across a river, and halfway across, the scorpion stings it. As they are both drowning, the frog asks the scorpion why he did that, and the scorpion replies "I had no choice, it's in my nature." Grim, yes, but I thought it was an appropriate tale since in the novel by Sartre that we are reading for class, everything that happens is predestined.

To puff it up to a length somewhere between 250 and 300 words, I had to embellish the story with background details that aren't usually in the fable. But that's the very nature of storytelling, isn't it? 

L'histoire de la grenouille et le scorpion

Il était une fois un scorpion qui vivait dans un tas de feuilles séchées qui étaient tombées des arbres à l’automne dernier. Près de les des arbres il y avait une grande rivière. Elle s’étendait si loin que le scorpion ne pouvait pas voir l’autre rive. Au bord de la rivière dans les joncs où l’eau était plus tranquille vivait une grenouille verte.

Un jour, le scorpion est allé à la rivière. Il a découvert la grenouille qui était en train d’attraper des mouches et de s’admirer dans l’eau. Le scorpion s’est présenté avec beaucoup de politesse. La grenouille a retourné la salutation.

Il a dit à la grenouille qu’il voulait lui demander de l’aider. Il avait besoin de traverser la rivière parce que le jour précédent il avait reçu une lettre de son frère qui vivait sur l’autre rive. Il était très important pour lui de traverser la rivière pour voir sa famille.

La grenouille réfléchissait à sa proposition. Pour traverser la rivière, le scorpion devait être sur son dos. Elle lui a dit que s’il la piquait, elle mourrait. Et le scorpion, il noierait.

Le scorpion a protesté. Il ne pourrait jamais faire mal à son amie ! Il a insisté. Il a supplié. Il a même pleuré quelques larmes.

Avec un soupir, la grenouille a accepté. Le scorpion est monté sur son dos et la grenouille a commencé à nager.

Au milieu de la rivière, le scorpion l’a piquée. Comme ils se noyaient, la grenouille lui a demandé pourquoi il avait fait cette chose-là. Le scorpion lui a répondu qu'il n'avait pas de choix, c’était dans sa nature.

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. 

What I Learned Today: Four Ways to Make Chicken Meat Taste Fishy

I'm stealing this idea for a blog post theme from a friend. I think it will make a good umbrella under which I can occasionally post about odd and intriguing things that I learn about.

Today I want to write a bit about four different mechanisms for making poultry meat smell fishy. This is certainly not a desired experimental outcome--chicken tenders that smell like fish? That's gross. But this very outcome has been reported by some researchers conducting broiler and layer feeding trials. How this can happen was a matter of some debate during my thesis committee meeting last week. It wasn't heated in the sense of being antagonistic but it certainly was intense. Since it seemed to be a topic of interest, I thought it would be time well spent to read some papers and try to figure out why this happens. What I found out is kind of interesting so I thought I'd write about it here too.

We first have to start with the larger issue: why do fish smell fishy. Living fish and fresh fish don't smell fishy. The fishy odor develops in marine products after they have been harvested. The smell is mainly caused by the formation of a molecule called a trimethylamine (although several dozen other kinds of molecules are also involved in creating the fishy odor).

See, animals that live in the ocean have a bit of a problem. They live in a saline solution but their cells also contain saline solutions. The concentration of sodium and potassium ions inside and outside of cells is delicately balanced. If those ions are out of balance, cells can't make energy and things generally go downhill from there. A very large number of biochemical processes depend on this balance being kept just so. So back to fish. They have developed some special biochemical mechanisms to keep the sodium and potassium ion concentrations in the correct balance. One of these depends on a molecule called trimethyl oxide. When a fish is killed, these molecules are slowly and inexorably converted to the insanely stinky trimethylamines.

You might take fish oil supplements. I don't take them myself but I give them to the dogs. I learned that the fish oil in those capsules has been subjected to an amazingly complicated purification process which includes a deodorization step to remove the trimethylamines.

So the first way we can make poultry meat smell fishy is to feed chickens diets that contain fish meal or fish oil that has not been purified to levels acceptable for human-grade consumption. Chickens consume the trimethylamines and their eggs and meat will smell fishy.

It also turns out that some chickens and some people have a genetic mutation in their DNA so that they don't make working copies of a particular enzyme that breaks down trimethylamine. We need this enzyme because our gut bacteria naturally make trimethylamines as part of their life cycles. If we don't have the mutation, no problem. The enzyme breaks down the molecules in our gut. But if you or a chicken has this mutation, then you can still smell fishy even if you never consume any fish product of any kind because the trimethylamine that is made by your gut bacteria is never broken down. So the second way for (some) poultry meat to smell fishy is to have strains of chickens with the mutated gene. People with the mutated gene have a disease called trimethylaminuria and they smell fishy too.

However, our gut bacteria have plenty of tricks up their tiny sleeves. They can make trimethlyamines out of choline. Choline is an essential nutrient which means that we must consume it in our diets; it is essential for chickens too. Diets deficient in choline can cause disease. However, if we feed chickens diets that contain large amounts of choline, we overwhelm the ability of their systems to break down all the resulting trimethylamines...and their meat and eggs can smell fishy. This third mechanism is not well quantified (how much choline is "too much", does it depend on age or type of chicken, does it depend on other dietary elements) but we know it happens.

And finally, the fourth mechanism for making poultry meat smell fishy has nothing at all to do with fish or bacteria. When you are trying to create a consumer product that is "enriched in omega-3 fatty acids" you are trying to increase the concentration of long-chain polyunsaturated omega-3 fatty acids in the parts of the chicken that we eat. I know, that's a mouthful. We generally abbreviate that mess to LC n-3 PUFA. Long-chain means the carbon backbone of the fat molecule contains between 18 and 22 carbons linked together. Polyunsaturated means that some of the carbons are linked with special molecular bonds called double bonds. You should already know that diets high in saturated fatty acids, fats with no double bonds at all, are strongly correlated to increased risk of heart attack and stroke; to be healthy we are supposed to consume fewer saturated fats and more unsaturated fats. Some of the omega-3 fatty acids can have up to six double bonds. We are trying to put more of these kinds of fatty acids into chicken meat and eggs. But there is a problem.

When a fatty acid has lots of double bonds, it is more susceptible to peroxidation than the unhealthy fatty acid that lacks all those double bonds. Peroxidation refers to a specific process by which a chain reaction breaks the unsaturated fats apart at their double bonds. Not only does lipid peroxidation form free radicals (very, very bad things to have floating around your cells) but the fatty acid fragments are converted into other molecules such as aldehydes and ketones. And most of these are quite stinky. 

When this happens, the meat tissues can change color, will taste bad (rancid), and will develop an off-flavor that is often described as "fishy" even though it isn't caused by the same molecules as fishy odors in fish. This is not an immediate process in general. Normal, every-day chicken meat will undergo peroxidation given enough time but it will happen sooner in "enriched" chicken meat.

So that's the fourth mechanism to make poultry meat taste fishy: enrich that meat with long-chain polyunsaturated fats and fail to protect the fats from peroxidation by lax handling, storage, and/or lack of antioxidants in the meat or diet.

It turns out this animal nutrition business is rather complicated. And there is no way to avoid the related issue of human nutrition and health--we and chickens are what we eat.

Back to School, the Continuing Saga

You'd think that since I'm only taking two courses this term, I would have lots of free time. French is not that difficult but I spend a lot of time outside of class working on the many assignments. It seems like a major one is due every other day. No, my mistake, it seems that way because it is that way. 

My other class is biostatistics. That very word may cause some of you to get glassy-eyed, but not only am I enjoying the material, I'm learning new skills that I am applying to my own research. The class has a heavy focus on applied analyses with just enough theory to confuse and confound. Most of the examples are based on human health studies but nutrition is nutrition. Substitute "broiler birds" for "males aged 20 to 49 years of age who don't smoke" and you've got a winner!

At the end of each week, I return to the statistical analyses of my experiments and understand them just a little bit better. The math is easy, trivially so. But the intellectual leaps we need to make every week--ah, well, it takes quite a few re-readings of the lecture notes and text and homework problems to get those down. 

Progress on the thesis must continue too. I at last feel like I have a handle on that. Even though the feeding trials are long over, it's only been in the past three or four weeks that I could clearly articulate my hypothesis and describe the two experiments in less than a billion stumbling words. I've always found it ironic that being succinct requires far more time and effort than being verbose.

I'll get the chance to practice my succinctness next week when I give a short departmental seminar, about half an hour, to introduce my project and dangle a couple of preliminary results. Two days after that will be my first committee meeting. I hope that the next time I see the committee gathered is the last time they need to gather, at my thesis defense in June. 

I've got a title for my project now too: Enzyme supplementation of poultry diets as a tool to enhance n-3 fatty acids in human diets. Sexy, isn't it?

Missing Harry

I've been asked by several friends how the other dogs are reacting to Harry's absence. Even though we live with our animal companions, it can be hard to tell how they are reacting to something. Or to put it another way, it is far too easy to anthropomorphize and ascribe to them human emotions when they may actually be feeling something quite different. And it can be easy to miss subtle changes in their behavior and demeanor.

When Harry was here, he had his choice of two beds positioned in front of the gas stove for his daytime napping. It had been more than couple of years since he was able to jump on the furniture due to the arthritis in his shoulder and his increasing frailty. The beds were well padded with extra blankets. He freely rotated between the two and Azza often stretched out next to him in the evenings.

During the day, Azza is crated. I have crated her since she was a puppy. The crate is a happy place for her. A few months ago, I made the mistake of leaving her out with Mimi for about an hour when I ran an errand one afternoon. I came home to find chunks of the windowsill missing. No, when there is no human about, Azza goes in that crate.

While Harry chose his spot in front of the fire, Mimi's regular daytime napping spot was on a dog bed on the couch next to the gas stove. She prefers to be on furniture whenever possible, mainly because I've always allowed it. She could see Harry on the floor at the foot of the couch, she could see Azza in her crate, and she could see out the front windows. It was an excellent vantage point.

After Harry died, I noticed that Azza was not spending any time in the dog beds by the fire even though the weather was getting cooler in the evenings. Was it the beds themselves? As an experiment, I removed both of the beds that had been there for the last few weeks that Harry was with us and I set up another bed next to the kitchen table where I spend most of my time studying. 

Azza

Azza immediately claimed that space, literally diving into the bed and curling up with a big sigh. Mimi has long been using a crate located on the other side of the table to keep an eye on me.

Mimi

That wasn't a subtle change--it was pretty obvious. Azza doesn't want to hang out anymore in the spot where Harry spent most of his rest time. She is still perfectly happy using the dog beds but not in that spot. 

The really interesting change is where Mimi now naps during the day: on top of Azza's crate! Once I figured this out, I put a bed up there. It is toasty warm from her body heat every day when I get back from campus. She can still sort of see out the front windows but I think it is an inferior perch for monitoring the street outside. But I don't think she chose the new spot for that reason. I think that she moved because she felt alone on the couch on the other side of the room. Azza may not be her first choice of companion, but she's now the only choice.

You can read what you want into these things. I can't tell you what they are thinking or feeling, I can only tell you what the dogs have done since we said goodbye to our old man.

This Time of Year

Fall is my favorite season. When I lived in places where there wasn't really a fall season, I always felt a bit cheated. 

Up here in the Pacific Northwest, fall is lovely. There are lots of diverse types of trees and shrubs with leaves that change colors. It's not quite as majestic as the oft-touted New England fall but I think the contrast of changing leaves interspersed with the numerous evergreens is more interesting.

I find the small but accumulating changes that I make in the house interesting too. For example, there's the gradual switch from regular sheets and a light cotton cover (I have to be covered with something, even in the summer) to flannel sheets and a thin fleece blanket to the full treatment of flannel sheets and down duvet. The arrival of winter will be marked with the addition of a heavy blanket on top of that--but we aren't quite there yet. The cozy bedding makes burrowing back in bed with the dogs for just 10 more minutes irresistible, after they've been fed and pottied, of course (Mimi's bladder waits for no one and no thing).

Shorts suddenly become just a bit too breezy except for a few hours in the early afternoon. Short sleeves are still necessary (campus buildings are horribly overheated) but now I need a light sweater or jacket when I go out (really, just the rain jacket: it's been raining buckets up here for some days now). The bulky winter fleeces and wools remain stored away for now.

I vacuumed the dust out of the gas stove and re-lit the pilot light. As a result, another small change is the sound of the blower coming on at four in the morning as the stove fires up to take the chill out of the main room before I get up.

My interest in using the oven to cook food has revived. Apple crumble. Roasted veggies--this has to be the best way to cook carrots. Roasted pork chop with potatoes and garlic and fresh rosemary from my plants out front. I've got an enormous pot of pinto beans bubbling away as I write this. While I do suck it up and cook beans in the summer too, the chilly, damp mornings of fall seems to be a better time for it. 

The dogs and cat are making small adjustments in their routines mainly by choosing different napping spots. Even Azza doesn't want to linger outside now: a perfunctory perimeter check, a task that she has taken over from Harry, and she is ready to come back in. But that wetness makes their morning walks quite a bit more interesting--damp air and moisture on leaves hold on to odors longer than dry air. Because of my schedule, I can usually manage to find an hour when it isn't raining, or at least not raining very much, to get them out every day.

Fall tells us summer is over and winter is coming. Up here it is a relatively long season in its own right with its own pleasures and rhythms. I am lucky that I can be in the moment and enjoy them.

Creative Inspiration: Poultry Nutrition and Sartre

I’ve been expending quite a bit of creative energy lately on French class. We have substantial writing exercises due every week. For example, for four of those assignments this term, we have to watch a movie or a news show, anything we choose as long as it is in French then write something about it. Yesterday I watched a rather touching short film on YouTube (okay, I had to watch it three times, but at least it was short) then pounded out an essay in a couple of hours. If I were to write in English for a couple of hours, I could easily break the 1000-word mark. In French, I end up with about 350 words. Still, I now have several verb tenses and a handful of conjunctions at my disposal so it isn’t 350 words of “Sally sees Spot.” 

For my first “écoute” I watched a half-hour show about raspberries and strawberries. I can’t bring myself to listen to half an hour of news from Syria in French; it’s bad enough to get it daily in English. The fruit show was quite amusing. It is part of a semi-regular series on TV5 Monde. The famous chef narrator highlights gastronomic specialties from different regions of France. Besides interviewing a raspberry farmer and a strawberry farmer located in this particular region, he interviewed the director of a cooperative that packages up all the “fruits rouges” from the area and ships them all over the place. The chef also spent far too much time interviewing a woman who makes perfume, somewhat pointlessly I thought since she admitted that it’s very hard to make perfumes using fruits like strawberries as raw materials since they don’t have much oil in them. They nattered on, and on and on, about how the scents of the “fruits rouges” could “evoke memories of childhood” with their “clear, ringing notes.” I was howling with laughter. The French can Frenchify anything, bless their hearts. I expected one of them to drop the Proust bomb at any moment but they never did. 

We are also reading a book this term, Les jeux sont faits by Jean-Paul Sartre. Yeah, that Jean-Paul Sartre. The title has an idiomatic translation. It means, the die are cast. Sartre originally wrote it as a screenplay, and it was in fact made into a movie in 1947. Each chapter is a short, self-contained scene. The sentences are fairly short and contain lots of interesting action verbs that describe what every character is doing at every point. “He shrugged his shoulders, picked up the pen, and signed the register.” “He turned away from her, headed across the room, opened the door, and exited the room.” It definitely reads better in the French. I pulled out over 300 new vocabulary words in the first 40 pages, most of them verbs. While the story is meant to illustrate some points of Sartre’s philosophy (death is absurd, one’s fate is predetermined but one must always struggle to overcome that, etc.), we don’t talk about that in class. We focus mainly on the grammar and the general story itself. I quickly developed a system: I do the first reading with only a pencil to underline things I can’t figure out from context, I do the second reading with a dictionary, sometimes two dictionaries, often looking up dozens of words per page and making extensive margin notes (yes, I write in books, I believe that the concept of the book is sacred but any individual book is not particularly so) then I set the book aside for at least a night (to take advantage of latent learning) before I do the third reading where I try my best to read it at a natural pace with understanding. I might even read sections out loud for the third reading. That’s a tremendous amount of effort but it ensures that I not only understand what’s going on in the book but I understand the grammar. 

All that thinking and listening and reading and writing and talking in another language keeps my brain warmed up for working on my thesis. For example, in the first half of October, I read 52 papers on poultry feeding trials in which they fed the birds some form of omega-3 fatty acids. Not a typo: 52 papers. As a result, I can clearly articulate what prior work has been done, what the knowledge gaps are, and what my own feeding trials accomplish with respect to the gaps. I meet with my thesis committee for the first time in a couple of weeks and I have to make a brief presentation to them. I needed to get all that sorted out.

Poultry nutrition and Sartre make for odd bedfellows but the combination seems to be working well.

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.

An Elaboration

So, let's say you are a creative and passionate person, maybe a poet or a musician, who is "inept at science". You have two young children. You read on the internet that vaccines cause autism. Since you are inept at science, you read this and you believe it. You don't investigate this claim any further because science is hard and you don't understand it. You believe this claim, however, because it meshes with your social views that large pharmaceutical companies are evil. You believe it because you think that taking drugs is putting poisons into your body, or at least, the drugs that you don't like because alcohol and caffeine are not drugs, right? You believe it because you saw something about this on TV but you can't really recall the details. You believe it because your sister-in-law, whom you really like, sent you the links. So you don't get your kids vaccinated. Measles is a disease that is entirely preventable when vaccines are administered. I could spin some tale about your child making another one sick, or you having to declare bankruptcy when your child has to be hospitalized for a preventable disease, but I won't do that. Instead, I'll just say this: it doesn't matter whether you are passionate and creative or not, in the flat, globalized world we live in today, unless you live naked under a freeway overpass and live on tubers and fungus that grow in your own shit, every single day you are responsible for making decisions that can affect others' lives. And even if you do live under that overpass, your shit is probably polluting some water source.

I would argue that making those decisions using critical thinking criteria is your duty as a citizen of the 21st century.

Let's consider another example. I'm sure that Texas Republican congressman Steve Stockman is really passionate about continuing to get re-elected. He may even be creative, possibly emulating Bush II by painting or practicing the difficult prose format of the short story in his spare time. Stockman also sits on the House Committee on Science, Space, and Technology. On September 17, 2014, in reference to his difficulty in understanding how sea level will rise due to melting ice sheets, he stated that "if your ice cube melts in your glass, it doesn't overflow." I'll leave it to the reader to learn why that statement is problematic.

One might think that Stockman has an even greater duty as an elected representative to consider the problems he is confronted with in his elected role in the most rigorous and thorough manner, even if it means he has to deal with some hard math or science ideas in the process. But in truth, is his burden as a citizen in our modern world any more or less than yours or mine?

How about another example? Here in Oregon in November, we will be asked to vote on a proposition that could require all foods containing GMO to be labeled. There is plenty of shouting going on from both sides which obscures the real issues. The ballot, if passed, would require that foods, raw or processed, that contain components that were produced by genetic engineering be labeled as such. It exempts plant hybridization from its definition of genetic engineering, which is nothing more than special pleading. And for that reason, I will be voting against this ballot measure. 

Our lab techniques are not doing anything that people and microbes haven't been doing for many thousands of years in the case of the former and millions of years in the case of the latter. Yes, today we are doing it faster. But there is nothing new going on here. The ballot initiative is selectively anti-science and purposefully playing on emotions rather than encouraging critical thinking about the issue (because after all, the big agriconglomerates follow closely behind big pharma in the evil-doing department).

Oregon contains lots of creative and passionate people. Should we forbid those folks to vote on this ballot initiative in November if they are "inept at science"? Well, no, that isn't how democracy works. But I would certainly argue that everyone who chooses to cast a vote has a responsibility to try and understand the issues they are voting on. Maybe that means they need to learn about food labeling. Maybe they need to learn what a GMO is. It's a deceptively simple proposition with a complex set of related but obscure issues attached to it. 

It takes effort to sort out these issues, to find sources that provide background for them, and effort to not apply confirmation bias to everything we might read or hear about the issues. All that effort, well, that takes work. Are creative and passionate people not able to expend that effort? Are they too busying being creative? That's of course just as ridiculous as claiming that scientists are too busy being rational to be creative. Posing this as a dichotomy reinforces stereotypes. Emotion is easy, it's hard-wired into us. Critical thinking requires effort and a lot more time. But they are not either/or states of being. You don't suddenly wake up unable to write poetry or music after you learn how to think critically.

My post of yesterday had this point: we need to do a better job at teaching our young people relevant science and critical thinking skills, emphasis on relevant and critical. No, they don't need to become scientists. But they need to learn how to deal with the problems our world faces today. It doesn't matter what they grow up to be--poets or politicians or physicists.

Scientific Thinking

I was having coffee on campus with my friend Rachel this morning, and as it does every week, our conversation spiraled wildly out from our own research woes and successes (she's a biochemist) to the general state of the world.

One thing we share in common is an appreciation for science--we take pleasure in viewing the world through that lens. Perhaps it goes even deeper than that: we find it difficult to view the world any other way. But what glory there is to be found in knowing why, or if not knowing why, trying to find out (see: spiders can learn).

Today, we wandered into the topic of anti-vaxxers and anti-GMO-ers. She railed a bit on bubble-headed celebrities misleading the herd but I thought that there was more to it than that. It doesn't take much time on the internet to discern wide and relatively deep anti-science sentiments in the US and Europe. These views usually cross class, race, education, and even political boundaries. 

Vaccinations have been tested over and over using the most rigorous standards for clinical trials (randomized, double blind, etc.). They save lives. To argue any other position with respect to vaccinations is to engage in anti-scientific thinking. 

Same with GMOs. As Rachel aptly pointed out, there is no difference, none whatsoever, in the DNA of a tomato, an E. coli bacteria, or you, except in the particular sequence of the molecules in the DNA. The building-block molecules are all the same. We have been selecting horses, dogs, corn, thousands of organisms, for centuries, in some cases hundreds of thousands of years, to change those organisms to suit our fancies or our needs. Techniques to create a RoundUp-resistant wheat strain are based on the exact same theories that humans in the middle of the Eurasian continent used to select wild grasses that had heavier seed heads lo these many centuries ago. We've managed to speed the process up quite a bit, of course, and we use fancy machines and such. But the theory underlying the work is the same. And I would not for a moment defend some of the practices of the large agriconglomerates. But GMOs are not evil in and of themselves. 

No, the fundamental problem is that the average person does not understand science. She doesn't understand physics or chemistry. And she definitely has no solid grasp on genetics, the water cycle, or immunology. 

So we decided the solution was to stop teaching physics and inorganic chemistry. Oh, you want to learn about that? Then go to grad school. Instead, we think that kids in elementary school should be reproducing Mendel's pea experiments, that kids in middle school should be learning about global climate, that kids in high school should be learning about disease, epidemics, and epidemiological experimental design (Ebola, anyone?). You still think chemistry is important? Teach that through food science. Fermentation should cover most of what you need.

We need citizens who are prepared for the reality of our world. Who cares that a ball rolls faster down a steeper incline? Why in the world do you need to know about metal catalysts? Wouldn't it benefit our society now and in the future to have not just scientific specialists but all citizens thinking about how to address the problems we have now, not the problems science was dealing with 300 years ago?

We need citizens who can think rationally and critically. You read the headline "Breastfed kids perform better in school." You shouldn't view that as a refutation or acknowledgement of your particular social perspective. You should ask yourself, how were the participants in that study selected? Are they representative of a larger, general population? Were other factors taken into account? Could such a study be randomized and blinded, the gold standards for these kinds of experiments?

Too bad Rachel and I aren't in charge.

Murphy Strikes!

My master's project is setting some land speed records. Feeding trials, lab analyses, statistical analyses of the lab data, collecting and reading papers, writing the thesis, writing papers for publication, preparing a talk or two, and taking classes--all of it getting squeezed into slightly more than one year. 

Since early July, I've been toiling daily in my advisor's lab. I'm sick of the place, that's for sure. About the only positive thing I can say is there are windows. The lab is in the basement of a 60-plus-year-old building. Lining the ceiling of the basement hallways are the steam pipes used to heat the building. They contain steam year-round even if they aren't sending heat to the rooms in the upper floors. As a result, walking to the lab is like taking a trip into the underworld: dark, musty, and stinking hot.

The only AC source in the lab is a puny window unit at one end. At the height of summer, even with the window unit going full bore, it was usually no cooler than 85 F in there for hours on end. The ceiling of the lab, like the rest of the basement, is festooned with pipes.  The cabinetry was new when the building was built. It has a quaint charm, to be sure. I'd take air-conditioned over quaint any day, however.

I had previously agreed with my advisor that I would try to finish all the lab work before classes started, which they will do on Monday. It was an ambitious plan but she has learned that she can push and I will deliver. So I was counting down the days of this last week.

I planned everything out so that I only had some fairly simple tasks to do this week. I wanted to take a short break before the term began since I have been working non-stop all summer. I was planning to run the last GC samples on Wednesday night, get the printouts on Thursday morning, interpret them, and email the data to my advisor that day. Then take a couple of days off. But I'm sure you can see where this is going. Murphy, who deserves his own special room in hell, struck with a vengeance on Tuesday. 

The GC, or gas chromatograph, is a box-like machine that heats up liquid samples at one end of a glass tube, heats them enough to turn them into a gas, and detects the molecules that float out the other end. The tube contains materials that cause the molecules to come out in molecular weight order: little ones first, then bigger ones. And the detector also measures how much of each molecule it senses so you can determine both which molecules are in your sample and the relative percentage of each molecule type. We are using it to determine which fatty acids are in the chicken tissues--did we successfully enrich the breast and thigh tissue with long-chain omega-3 fatty acids. It takes about 11 hours to run 16 samples. I have 32 samples per tissue so I set up 16 samples to run at 8am, return to the lab in the evening, and set up and run the second half. I'm sure you are thinking, why not run them all at once? That would make sense, wouldn't it?

It would make sense except that it's so hot in the lab that the hexane that we use as a solvent volatilizes in the sample vials as they sit in the tray waiting their turn. The increased vapor pressure in the tiny vials (they hold about 1.5 mL) pops their tops off and entire samples evaporate into the room before the GC gets around to them. Yes, in case you were wondering, I learned this the hard way. (If I were to write a "pro tip" addition to my advisor's procedure protocols, it would run into the dozens of pages.) I pointed a box fan at the GC and turned the AC vents in its direction but that didn't help.

I was already resigned to this every-12-hour arrangement. Although it's a pain and increases the overall time that I spend running the samples, that in fact isn't the problem. The problem is that the GC oven is cooled with various gases (helium, compressed air, etc.) and, sometime Tuesday night during my run, the compressed air tank ran dry. The GC is smart enough to shut itself down when it can't cool the oven. But I still have almost 50 samples to run! Here's where Murphy really got me: the gas tank supply company only delivers to campus twice a week.

Fortunately, one of those delivery days is Friday. I plan to camp out in the lab in the morning and wait for the gas tank guy to show up. I'll be running samples most of the weekend but I think, just maybe, if Murphy has already done his worst, that I will just finish before classes start.