Thursday, December 17, 2015

Let chickens be chickens

A week or so ago I encountered a letter to the editor in our local newspaper that made me peevish. Its author opined that chickens have better welfare when they are kept in rather than out of cages, because when not caged they are liable to get parasites and cannibalize each other.

I responded. But the letter to the editor format restricted me to 250 words, and I had more to say. Luckily, I have you guys to rant to! So here is my original piece in full.

Dan Miner's letter, published Dec. 5, sets up a straw-man argument about the welfare of chickens kept in versus out of cages. I'm responding from my experiences as a veterinarian with a special interest in animal welfare.

Are chickens in cages free from walking in their own feces? Yes – because they're standing on wire, which is unhealthy for their feet. Are chickens out of cages walking in their own feces? Only if you keep them crowded too close together. If you keep them with enough space that their surroundings don't fill with poop, then no, they won't be walking in poop.

Are chickens in cages able to engage in cannabalism? No – but they're denied healthy social interactions as well. Chickens don't actually want to kill and eat other chickens. They just do it if they're highly stressed. Keep them in a healthy environment where they have some space and the ability to engage in species-appropriate activities, like perching and scratching for bugs, and they'd much rather do those things instead.

Does the cage system protect chickens from parasites? Sure – and keeping a human in a glass bubble keeps them physically free of parasites, too, but would anyone with a normal immune system be willing to live like that just to avoid normal diseases? Healthy, unstressed chickens have robust immune systems that can handle normal diseases. But a stresssed, crowded animal isn't a healthy animal. When bird flu swept through commercial chicken farms this summer, resulting in massive numbers of deaths, which populations stayed healthiest? The outdoor birds, who were unstressed because they had the ability to engage in species-appropriate behaviors, and therefore had robust immune systems. The stressed-out, crowded indoor birds had weak immune systems with no ability to fight off the virus, and were so packed together that when it got into those populations, it swept straight through.

Chickens are only healthier in cages compared to out of cages if the out-of-cage environment is a crowded, stressful one. Many of those environments are, of course. I encourage those who care about chicken welfare to purchase eggs from chickens who are “pastured” or kept “on grass.” Mr. Miner is correct that “cage free” doesn't mean good welfare. He just doesn't realize that there's a better way to raise these animals – with enough space to move around and the opportunity to scratch around and hunt for bugs. Those are happy chickens.

Monday, December 14, 2015

Science with a sense of humor

I’m writing a peer-reviewed article right now. I can almost guarantee it’s something pretty much none of you will be interested in (it is not about dogs or foxes, but about genomics technology), but when it’s out I’ll do my best to blog about it in a way that makes it seem exciting. We’re at the review stage: reviewers give us a bunch of comments, we make the changes to the article, then we write a letter back to the reviewers. The letter is supposed to say things like “Thank you so much for your insightful comments. We made all the changes you suggested!”

One reviewer comment pointed out that at one point in the article, I had referred to humans as a model species. Now, model species are normally species that we use as models for humans. The best examples are laboratory rodents: we study rats in the hopes that what is true for rats is true for humans. The rats are a model species.

The reviewer commented “Are humans really a model species?” At which point my boss basically put her head in her hands and was embarrassed that we hadn’t noticed this stupid gaffe we’d made.

In my first draft of the reply letter to the reviewers, I replied to the question about whether humans are a model species: “They are to this veterinarian!” I, of course, love to read human research in the hope that what is true for humans is true for dogs. (But I made the change in the manuscript.)

I pointed this out to my boss and said, “Did you like my veterinarian joke?”

She: “Yes.”

Me: “Is it OK to have jokes in letters to reviewers?”

She: “No.”


Thursday, December 10, 2015

Dog genome ruminations

The other day I was re-reading the original dog genome paper, as you do. This is the paper published in 2005 to accompany the release of the first full dog genome sequence (of a boxer named Tasha) and accompanying annotation (a mapbook of what genes are located where in the very long sequence of bases that is the genome).

You might think that a genome paper wouldn’t be very interesting, because basically the point of it is to say “here is this genome. We published it. It was a lot of work, and it’s done, and now you can use it.” But most groups try to have something interesting to say in their descriptions of a new genome, and this one actually had a lot of interesting stuff about dog genomics in it.

Don’t just take my word for it. It’s open access, so you can read it for yourself.

Lindblad-Toh, Kerstin, et al. “Genome sequence, comparative analysis and haplotype structure of the domestic dog.” Nature 438.7069 (2005): 803-819.

The dog was one of the earlier mammals to be sequenced, so a lot of this paper consists of comparisons between dog and the other sequences we had at the time, human and mouse. We already knew that humans and mice were more closely related than humans and dogs in one sense: they share a most recent common ancestor. This means that as you follow the branches (and tangles) of the tree of life, first you get a branch that divides the most recent common ancestors of human, mouse, dog, and relatives from species like opossum and chicken; then you get a branch that divides the most recent common ancestors of human and mouse and relatives from dog and relatives; and only then do you get a branch that divides the most recent common ancestors of human and mouse. It looks like this:

Tirindelli, Roberto, et al. "From pheromones to behavior." Physiological reviews 89.3 (2009): 921-956. Fig 5
So we’d expect that human and mouse would share more genomic sequence than dog and human, right? Each of those branches in the tree of life represent a point at which one species becomes two, with resulting divergence in genomic sequence. So if the species divergence between humans and mice happened more recently than the species divergence between humans and dogs, then the genomes of humans and mice should look more similar than the genomes of humans and dogs. But it turns out, as this dog genome introductory paper reports, that dog and human share more genomic sequence, more base pairs, than human and mouse do. So how can that be, if humans and mice are closer together on the branches of the tree?

There are several forces contributing to this result, but the one that made me smile was the different rates at which each species reproduces. In the time since humans, mice, and dogs branched off from their shared common ancestor (before humans and mice branched off from their shared common ancestor), mice have had many more generations than humans and dogs. They reproduce so quickly compared to us and dogs that they have more chances to change their genetics from generation to generation. And as a result, while the number of divisions (places where the tree branches) are greater between human and dog than human and mouse, the number of generations of mice between today’s mouse and that last common ancestor of mice and humans and dogs is greater in mice than in dogs or humans. As the paper’s authors put it:

The lineage-specific divergence rates (human < dog < mouse) are probably explained by differences in metabolic rates or generation times, but the relative contributions of these factors remain unclear.

The other way of looking at it is saying that species age at different rates. So while behaviorally modern humans appeared around 50,000 years ago, and dogs appeared arguably 10,000-32,000 years ago, nevertheless the human population is about 4,000 generations old while the dog population is around 9,000 generations old. Because dog generations are shorter.

We created them, but they’re now older than us. Just like how my dog was younger than me when I got him, but aged right past me. Science!

Saturday, December 5, 2015

Teaching genetics

Summer before last, I taught my first online classes, in introductory and behavioral genetics. It was a ton of fun and I learned a lot about how to teach genetics online to students with a variety of backgrounds and interests. I have since been itching to try again after redesigning the courses to take what I learned into account. In addition to my own experiences, I’m drawing on advice from Rosie Redfield’s excellent and very approachable paper on how to design a modern genetics class. She teaches Useful Genetics for EdX based on these principles, so check that out, too!

DNA being repaired by an enzyme

So I’m hugely looking forward to teaching a series of genetics courses for the International Association of Animal Behavior Consultants (IAABC). The plan is to cover all the material that a college-level genetics course would cover, but to do it in a way that makes the material accessible to students who aren’t in college and can’t commit to a massive course all at once. So I’m planning to teach four separate courses. They will be completely modular: you can take them in any order, or take some but not all of them. If they prove popular, I hope to continue to offer them in coming years, so that students can enter and leave the flow of classes without worrying that there won’t be another chance to take a particular class.

Anyways, the first class in this series is starting January 11, 2016, online at IAABC. It’s a course in molecular genetics — what is DNA, what are genes, how in the world do these tiny little molecules deep inside your cells code for processes that make you who you are? (And your dog who he is, and your horse who he is, and...) The topic list for the class is:

  • the molecular structure of DNA
  • DNA replication and mutations
  • transcription of DNA to RNA
  • translation of RNA to proteins
  • protein structure and function
  • genome sequencing
  • variation between individual genomes
  • genetic testing for disease (how it works, how reliable it is)
  • new advances in gene editing
Future classes will cover heritability (how do your parents pass genetic information on to you?), population genetics (focusing on breeds, what it means to be a purebred, and the consequences of inbreeding), and oh yes, everyone’s favorite, behavoral genetics (which you’ll be able to take without taking the others — but you’ll get more out of it if you take the others first).

More info? Sign up? At IAABC.

Questions? Comments? Requests? Bring ’em on.