Friday, October 31, 2014

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 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.


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.

Sunday, October 26, 2014

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.

Friday, October 24, 2014

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.

Saturday, October 11, 2014

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.

Thursday, October 02, 2014

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.