Thursday, June 5, 2014

Why genetics and dog training?

I won’t lie to you. When I first started thinking about teaching genetics courses for the Association of Professional Dog Trainers, I was mostly excited about the second class, which covers behavioral genetics of dogs. The first class was just something we had to do in order to get everyone up to speed on the basics of genetics, to have the information they needed to understand the second course.

But, of course, basic genetics is relevant to every day life with dogs and is interesting on its own. I don’t blog about genetics much, because I’m shoulders deep in highly technical stuff in my PhD program which is hard to communicate to people who aren’t equally immersed in the field. But when I stop to think, it’s not hard to come up with questions about dogs that you can’t answer without basic genetics.

  • In the past decade, new advances in technology have enabled the discoveries of more and more genes in both humans and dogs. These discoveries get reported in the popular press, such as the gene for small size in dogs (discovered in 2007). What exactly is a gene? What does it do? What does it mean to have different “versions” of a gene? It’s hard to understand these news tidbits if you don’t really get some of these basic concepts.
  • When you breed a lab and a poodle, you get a labradoodle with very predictable appearance. But if you breed two labradoodles, you can't predict what the puppies will look like. Some will look more like labs, others more like poodles. They're all the same genes, so why is one generation so different from another?
  • Why is blue merle color associated with deafness in dogs, so that if you breed two blue merles to each other, you're almost certainly going to have some deaf puppies? 
It’s easy to get caught up in the details of a field and forget that that’s not all there is. I’m trying to remember to get my nose out of the books (or PDFs of articles) once in a while and look around me.

(Genetics is beautiful and fascinating and I’m extremely lucky to have the chance to talk about it, through the lens of a shared love of dogs, in my upcoming classes with the APDT.)

Saturday, May 24, 2014

Fish personalities?!

My mobile buzzed: I had a text message from my husband. I’m bored. Call me. He was driving to New England and stuck in traffic.

I called. He asked how my day had been. How was that boring meeting? It was great, I said. I got to talk to a fellow grad student about a project of his during the coffee break. We were talking about a new way of studying fox personalities, using a method he had applied in his study of fish personalities.

ARKive photo - Male three-spined stickleback attacking pregnant female Husband: Wait. What personalities?

Me: Fish.

Husband: Did you say fish?

Me (wondering if the connection is bad): Fish.

Husband: The things with scales that swim?

Me: Fish! Yes!

Husband: ...have personalities?

Oh. Right. Sometimes I forget that my world is not other peoples’ world.

Me: Yes! Some are shy and some are bold.

Husband: Oh right. Continue.

I mean, what’s personality, really?  We make it sound like a big deal when we say that fish have them. My boss doesn’t even like me to say that our foxes have them when I am writing grant applications.

When you break it down to these small traits, like shyness and boldness, it makes more sense, though, right? Some fish are shy: when you put food in their tank, they hide a little bit longer before they will come out to eat. Some are bold: not only do they explore more and hide less, they are more likely to attack other fish who try to take their fishy belongings. If you haven’t observed these differences, I assume it's because you haven’t kept fish.

Different personalities are better (“more adaptive,” if we’re speaking Science instead of English) in different environments. An environment with lots of predators? Better to be shy, more cautious, and check out the surroundings before going for some food that's floating out there in the open. An environment with fewer predators, but lots of other fish of the same species as you? You had better go get that food fast before someone else does, rather than waiting to see if the coast is clear.

So it makes sense for a species to have a reservoir of personality types. This way, when an environment changes (there’s a new predator, or increased population density), that variation is there to be drawn upon. Lots more birds around to eat the fish all of a sudden? The fish with shyer personalities will do better, the ones with bolder personalities will do worse, and the population will gradually come to have more shy fish in it, so that the population as a whole can survive the change in environment.

For sure, human personality is a lot more complex than fish personality. But that is exactly why my friend’s lab studies fish: better to try to understand a simple system first before tackling the more complex one. A lesson I don’t seem to have learned, jumping right in with my questions about dog personality. Oh well.

[If you’re a dog trainer or just interested in dog genetics, you can learn about the genetics of dog behavior with me this summer in an online course with the APDT!]

Sunday, May 4, 2014

On nature and nurture and their interactions to make a personality

My mom called me yesterday because she had experienced some Science and was excited about it. She was watching a TV episode about aggression and how it appears in nearly every species. She called me to say that she thought my lab should look for the gene for aggression. “It should be easy,” she said, “because it should be the same gene in every animal.”

Aggressive silver fox

Yeah, you’d think that there would be single genes controlling bits of our personalities (human and dog — I think dogs are much more interesting, but in this case it’s much the same problem). Only ten or twenty years ago we thought we were in the endgame to find these genes: once the human genome was sequenced, we expected to be able to do a series of big studies to find these answers. Take a few hundred humans and sort them into “violent“ and “not violent.” Then look at markers in their genomes and use computers to find associations: all the violent people should share one marker, which will tell you where the gene for violence is. Done.

But we did those studies and we found, again and again, that these sorts of personality traits don’t give up their answers this way. In fact, in the case of zero personality traits have we found one (or even two or three) genes that control that trait. Sometimes we find genes that we think control a solid chunk of a trait, only to find that it was a statistical error — if you ask enough questions, you’ll find an interesting set of data just by chance. But if you ask the same question of another set of data (in other words, do another study), you’ll see that the first one was wrong. And this is what we have seen, for trait after trait.

Now, occasionally we’ll find a personality trait for which a little bit of it can be explained by one gene. When I say a little bit, I mean that if there is a normal amount of variety in this trait — say, in how violent a person is, ranging all the way from a pacifist to a psychopath — then the genes we find will explain about 0.1 percent of that variety. The rest is — what? Chance? Environment?

It’s a bunch of things, probably. For one thing, it’s surprisingly hard to define a personality trait. What’s violence? In dogs, we diagnose different kinds of aggression: territorial aggression, owner-directed aggression, dog-dog aggression, fear aggression. Are these all the same thing? Probably not. So instead of looking for one trait, “aggression,” should we look for four traits? Maybe. But do we actually know that those are the right four? Maybe there are six. Maybe there are ten. Maybe there are a hundred. We need to understand the traits we study better, and ask more detailed questions about them.

For another thing, yes, environment is important! Genes are important, but they are nowhere near the whole story. And environment is complicated. Certainly the difference between a pet store puppyhood and early life with a responsible breeder is huge. But can you lump early life experience into two bins, “good” versus “bad”? There are all kinds of variables. In the pet store, what kind of crate was the puppy kept in, how much interaction did it get, how young was it when it arrived? At the breeder’s, were there other adult dogs besides the mother to interact with, were there any small children, were there any bad interactions with other dogs or people? And a hundred, a thousand more questions.

I read recently about a pair of conjoined twins with very different personalities. These two had the same genes, because they came from the same embryo originally. And they had the same environment, because due to being conjoined they had to spend their lives in each other’s company. So how could their personalities differ? The article theorized that they reacted to each other, with one taking a bold, outgoing role and the other becoming shy and retiring in compensation.

And finally, the most interesting idea, in my opinion as a genomics researcher: what if we aren’t going to find the answer by looking at the sequences of DNA that make up genes? What if we are going to find the answer by looking at how the genes are regulated? If it isn’t that my dog is more fearful because some gene is a little broken, but she is more fearful because some gene is getting turned on much more or much less often than it should? It’s hard to investigate gene regulation when you have questions about the brain, because to do it you kind of have to get inside the brain, and it’s hard to do that without killing the person you’re studying. But I think looking at regulation is where things are going to have to go, and researchers are working on finding non-lethal ways of doing it.

So, nature and nurture: both important. Personality: super, super complicated. But also wicked interesting.

[If you’re a dog trainer or just interested in dog genetics, you can learn about the genetics of dog behavior with me this summer in an online course with the APDT!]

Thursday, April 24, 2014

I'm not dead

Dear everybody: I'm not dead, I'm just spending all my writing energy writing other things than blog posts. I keep asking my brain for an inspiration for a blog post and it keeps telling me "but you just wrote that long story for that magazine!" Ah well. I will keep asking.

Monday, March 17, 2014

Learn about the genetics of dog behavior with me

As promised, my big announcement: I will be teaching two online courses for the Association of Professional Dog Trainers this summer.

DNA, courtesy of Wikipedia

 The courses are open to APDT members and non-members, so anyone can take them. I'm working hard to make them fun, and I would love to see some blog readers or Twitter followers in the class!

The first class is just a basic grounding in genetics, nothing really special about dogs (although I use dogs for many of the examples). So if you have a solid or even just passable genetics background, you don't need to take that. If you're not sure you could explain what a gene is or what a chromosome is, though, you would probably be a bit overwhelmed in the second course without having taken the first one.

The APDT is an organization that I've respected for quite a while, so I'm thrilled to be working with them. If these classes are well-received, they will repeat periodically, so if you can't take one or both this summer, you should get another chance later.

Saturday, March 15, 2014

The state of the Zombieverse: spring 2014

No matter how many times I resolve that I will post at least once a week, life always seems to get in the way. So I figured I’d make lemonade from the lemons and tell you guys about what I’ve been up to. I know a lot of you enjoyed the posts about life as a shelter medicine intern, but I’ve been suspicious that life in the lab would be less interesting. (“Today I found the perfect set of pipetters! It was awesome!”) Still, it seems possible that there are people out there who wonder what first year PhD students spend their time doing, so here it is.
Me escaping from lab for Scio!

I went to ScienceOnline Together 2014, which was a great deal of fun. The head of my lab smiled tolerantly and let me go — she doesn’t do much layperson-level science communication herself, but she knows I love that stuff and figures there’s probably a good reason for me to get better at it. I went to a discussion about engaging undergraduates in science (run by two undergraduates), where I learned that Facebook is the Thing right now but Twitter might be catching up; a brainstorming session about providing explanations of various scientific concepts to people at a variety of levels, elementary school through expert; and an intergalactic gala, where I met Malcolm Reynolds, the Doctor, and an inflatable Dalek, and ate carbonated ice cream which was made before my eyes.

Back home but still on the science communication track, I have been kicking around ideas with another science blogger here about improving science communication education at UIUC. Let me tell you a story about how much the world needs help training aspiring scientists about science communication! I was in class with some undergrads, and they were talking about our recent midterm. One said: “I didn’t really understand that question where we were supposed to explain the findings as if to a scientist, and then as if to a non-scientist. What did that mean?” The other replied: “I don’t know, so I just wrote the same thing twice.” Ouch.

So yeah, I had some midterms. The one mentioned above was for an excellent class on genes and behavior. I really dig the structure of this class: every week we read some articles, then discuss them on the message board. We come to class already understanding the articles fairly well, and we discuss them more in person, both in small groups and as a full class with the professor. It’s a great design, though it does suffer around midterm time when the students are too tired to muster the energy to do paper analysis. Still, it is always better to read articles than a text book!

I also had a project for a statistics class. Statistics can be mind-bogglingly boring, but it is really essential to understand it if you want to be able to analyze your data well. In my experience doing my Master’s work, asking a statistician for help will lead to some terrifyingly complicated analyses that you will only understand during the moments that he is explaining them, and will immediately become completely opaque when you are trying to explain them to your advisor the next day. Anyways, this stats class was designed for grad students, not undergrads, and this project was to do some analysis of our own data. I am a first year student, so what do I not have yet? Data. I have a bunch of RNA which had been sitting in the sequencing machine for weeks. My hope was that sequencing would finish up in time for me to analyze that data for the class. Nope. So, with the teacher’s permission, I made up the data. It was kind of fun. Not enough significant results? Let me just change those numbers... This is apparently not something we are supposed to do in real life, unfortunately.

Did you hear me mention RNA in the sequencer? Yes, I am also doing research! Last semester was a lot of time at the bench, doing ridiculously finicky extraction work to get RNA out of tissue samples. RNA, you will remember from high school biology or some such, is a single-stranded copy of DNA. The cell makes these single stranded copies for use in making proteins, so RNA is part of the whole translation mechanism whereby DNA turns into an organism. Because RNA is single stranded, it isn’t as stable as DNA (which is double stranded), so handling RNA is a really annoying process involving gloves and this magic spray bottle which kills the evil RNA-eating demons which apparently live in the air, your hands, on counters, and on the mobile phones that undergraduates like to leave in your work area.

But once you get the RNA extracted into teeeeny little vials, you can send it off to be sequenced. What I will get back (what I got back a few days ago, but which involves a lot of processing before I can extract useful information from it) is information about which genes are expressed at different levels in particular tissues. I am using tissues from foxes selected for tameness versus foxes selected for aggression. (Remember, I work on the tame fox project.) Why is that interesting? Well, it seems likely that a lot of the differences that we see in tame foxes aren’t due to changes in their actual genes, but changes in how those genes are regulated. So maybe tame foxes express more of a particular gene rather than a different form of that gene. If I know which genes are expressed at higher or lower levels in tame foxes, I can start to guess at the functions of those genes, in foxes and, eventually, in dogs and humans.

What else? Helping the head of my lab teach her class in domestic animal behavior. I have been working behind the scenes to find good papers for students to read and writing questions to assess the students’ understanding of those papers. It’s the perfect job for me. I get to read a lot of papers about domestic animal behavior, and I get paid to do it.

Finally, I’ve been working on another project which is days (DAYS, I tell you) away from being ready to be announced here. I think it’s safe to say I find it more exciting than you will, but I still think you should check this blog daily in breathless anticipation!

Saturday, February 22, 2014

The spectrum of hoarding

There was almost no furniture in the entire house. This was unusual for hoarder houses, which are usually packed full of stuff or just of trash. But she was a somewhat unusual hoarder, with only 26 cats and one dog. We stood in the living room and talked to her about her animals. We could see into the kitchen, which was swarming with cats, on the counters, poking out of empty cabinets, sleeping in the sink. The woman we were talking to told us how she loved them but how her son had called us in because he was concerned about them and about her.

While we talked, her dog urinated in the middle of the empty floor in front of us. She didn't notice. The room contained a couch and an entertainment center and absolutely nothing else: the entertainment center had a few knicknacks but was mostly empty. On it sat the box of flea preventative that our team had given her months ago. It was unopened.

And everywhere was the smell of urine. I could barely stand to be in the room, but I could do so without a mask, which made it one of the cleaner hoarder homes. All I could think of was getting outside and getting a breath of air that was not thick with ammonia, so thick that my eyes watered and I could not fill my lungs. But this woman lived here. She could no longer smell it. She no longer noticed or cared when her dog urinated in the middle of the floor. And I remembered another time I had smelled this smell: at a cat shelter in another part of the country.

That was in rural New England. The two women running the place called it a shelter, but I knew it was really a hoarding house. They did not know how many cats they had. They would find cats unexpectedly dead, because no one had noticed for days or weeks when they were sick. And everywhere the smell. Not as bad as in the hoarder house in the big city, but bad enough to scare away adopters. Yes, they opened their doors to adopters. They advertised their cats for adoption. But adopters who brought these cats home risked bringing a sick animal into their lives, or contracting ringworm from their new pet, a story I heard unfold at least once from this shelter. The women running the shelter grilled every potential adopter and turned many away for not being good enough for their cats. And they continued taking in more cats — if they turned them away, they said, what would happen to them? But could another fate have been worse than dying trapped in that place, where adopters did not want to come, and were turned away when they did? Was this place a shelter or a hoarding house or some weird combination of the two?

But the combination isn’t weird. It happens all the time. I saw it again at a shelter in the deep South. This shelter proclaimed that they would kill no animals, and they did not, even the dogs who had been there for seven or eight years, that had gone insane and were unadoptable. These dogs were loving with the shelter staff, but when I came within a dozen yards of their enclosures they would erupt in terrifying, violent barking. I had no doubt that if I entered their enclosures I would be badly bitten. One dog was not aggressive, but hardly seemed to see the rest of the world any longer: he spun in circles around his enclosure, up on the roof of his dog house, down on the ground again, paws hitting exactly the same point every time. Over and over and over.

And the dogs who were not yet insane were not moving out fast enough. I could see their fates. This shelter was so overwhelmed with the number of dogs they were managing that they did not have the energy to keep these dogs mentally healthy, or to do the extra legwork it takes to adopt out a large dog in an area like the South which is so overpopulated with them. These dogs needed transfers to different shelters, they needed adoption events, they needed foster care to get a break from the shelter. They got none of those things. And as soon as a cage opened, it was filled with a new dog. This shelter actually transferred dogs in from outside their community. If they had not done so, they told us, what would have happened to those dogs? Where else could they have gone?

When I started to look, I started to see it everywhere. How many shelters provided enough space for their cats? Even the shelters that have big condo-style cages for cats in their adoption areas, with enough space to move around and a separate area for the litter box, even these shelters still have cats in tiny three by three foot cages in the back, in the sick rooms, in the intake and holding rooms: not enough room for a cat to stretch out, not enough room to get away from the litter box to eat. Even these shelters tell me of course they can’t use that antibiotic, because it must be given twice a day, and they don’t have time to visit so many sick animals twice a day, so they must use the one that doesn’t work as well but can be given less often. Even these shelters say, Of course we would love to have dog play groups, but we don’t have enough trained staff to manage them.

So what is sheltering and what is hoarding? A good shelter provides a needed service: a brief place for an animal to stop on its road to a new home, some medical care, some help finding that home. Keeping that stay brief is the hard part. It is, in fact, a very hard part, balancing keeping the animal healthy (it’s hard and potentially unethical to adopt out a sick pet), finding the right adopter (for that pit bull type dog that looks like row upon row of others in your shelter, for that orange cat that doesn’t come to the front of his cage to meet adopters), keeping them mentally healthy while you’re at it (play groups, training, just plain time out of the cage and time with humans).

And keeping large animals like dogs takes space. In fact, keeping a small animal like a cat takes space, much more space than we as a sheltering community realized until recently. Sheltering can so easily start to slip down the spectrum. It is a spectrum! Many shelters, real shelters, shelters that have legal non-profit status with the government, shelters that don’t smell like urine and have lots of volunteers and get grants and have spay-neuter services, yes these shelters too can fail to provide minimally acceptable care for their animals. Simply because they have too many.

What’s the answer? In one sense, it is simple. Call in someone from the outside, who can see your facility with unbiased eyes. Someone who doesn’t have to answer all the calls for pets that need homes. Someone who can look at the pets that you have and tell you how you are keeping them. This person must know how to assess humane capacity, so it can’t be just any animal lover. They should be able to look at your facility, know how much space is appropriate for animals of different sizes, and calculate how much space you have for each animal. Then they must look at your staffing, and calculate how much staff time you have for each animal. Not just to feed and clean them, but to spend time with them. To notice when they are sick: to look at them every day, carefully, and think about what they need and how to get it to them. To not be running ragged putting out fires, but to be able to plan adoption events, and to notice that dog that’s been here for months and needs special work to get out.

When this person tells you how many animals you can care for humanely, not just how many you can fit in your facility, you will be shocked. You will deny it. You will say that’s half what you can handle. You will point to your records: you’ve had many more than that for years! But they will insist: yes, you’ve had more. But you haven’t had them humanely. You have had a toe on the road to the hoarder end of the spectrum.

So in another sense, it is not at all simple. Because embracing humane capacity means accepting that you have not done as well in the past for your animals as you could. It means not beating yourself up over this, not feeling guilty, not indulging in denial. It means moving forward: it means promising yourself and the animals in your care that you will do better in the future.

And even harder, it means saying no. No to the animals that need a place. No to the people who just can’t find a home for their pit bull type dog but have to move, and the new place does not take animals. No to the mom whose dog bit her child but is such a loving dog with adults. No to the stray cat who is so sweet. Surely you can find homes for these animals? If you don’t, who will?

But that is the central point: you can’t do it humanely, but you try anyway, you will add to the problem. Sheltering is where it is because shelters try to do too much, and if a shelter’s doors are open, animals will pass through them. Shelters which have put waiting lists into place have found that many people do manage to find homes for their animals, if they have to keep trying. Some don’t, and they wait until a place opens. Will these people abandon their animals on the street? Will they take them to a quiet spot and shoot them between the eyes? Very, very rarely does this happen: when it does, it is big news. But you know what? Doing that is illegal. And that is where we need to prevent it: with laws, and enforcement of them. Not by saying, Okay, I will take over your responsibility for you.

That is what we as a society must embrace: responsibility. Not taking in animals that we can’t care for appropriately. And not accepting someone else’s responsibility. Being strong, and doing only what we can, and no more. Because by doing more, we actually do less.