Diving Fit!

[Note: I was in New Zealand for a few days for work-related business, and at the moment I am wrestling with a particular blog post that requires more attention and editing and fancy pictures than I can generally churn out on short notice, so here is something I prepared earlier. -KN]

Before getting my dive ticket, I agonised over whether I was “diving fit”. I spent most of my childhood and adolescence being more-or-less sedentary, and had this notion in my head that people had to be extremely buff gymsters in order to be able to SCUBA dive.

This is… not the case. Of course, the more fit you are, the better: diving will be easier. Walking down the pier wearing weights and tank will be easier. You will be more efficient with air. You may be asked to carry other people’s tanks, and thus earn their eternal gratitude and numerous blackmailing opportunities. Your tendency to get fatigued and dehydrated and develop some form of DCI (decompression illness) will be reduced.

Fitness isn’t, as a concept, well defined. It is better to apply fitness to a particular goal.

Take yours truly. I am not spectacularly fit. I go to gym a few times a week, I do my weight training, I spend a lot of time on flexibility, and at the moment I am trying to get through the Zombies! Run! 5k training app. I am probably stronger than most of my cohort (age/sex/etc.) and have an advantage in terms of muscle mass. But if you watch me running, you will be appalled. I am slow. I am ungainly. I have bad feet. I have hypermobile joints. I am, basically, horrifying to watch. My podiatrist referred to me, in slightly awed tones, as “the most flaily runner I have ever seen.”

In short, I am not running fit.

Fortunately, I am diving fit.

To be basically diving fit means that you can accomplish the following things:

  • You can swim 200 metres (any stroke; I like backstroke) without stopping. You can take as long as you like to do this.
  • You can tread water for ten minutes (this can be quite soothing).
  • You can lift and carry your own tank (it’s okay to need help getting it on. That shit is heavy and awkward right there. Park benches, fence posts, retaining walls and dive buddies are popular aids for this process).
  • You can walk around wearing the unit and the weights that you need to descend (more on that in a moment).
  • You can climb ladders onto boats and piers wearing the unit and the weights.

A standard sized 12L steel tank weighs slightly under 14 kgs, although this varies depending on the manufacturer and how much air is actually in it at the time. For most people this is a bit uncomfortable, but not a major obstacle.

The real problem comes down to weighting.

If you are diving in warm, tropical waters, you may not need thermal protection. It’s warm and pleasant, so you might dive in a lycra suit or, if you’re not concerned about jellyfish and fire corals, a bikini. Bikinis and lycra suits are not particularly buoyant, so you won’t need much weight.

If you are diving in cold waters (Melbourne. Sigh), you need thermal protection. I dive with at least a 7mm neoprene semi-dry wetsuit. These are, to use a technical term, very floaty. In cold months, I wear a drysuit. These are even more buoyant, since they don’t take on water. You don’t sink in this gear; you just bob around on the surface of the water. That’s not diving. That’s just very expensive snorkelling.

Because of this flotatious thermal protection, I need to wear more weight. The amount of weight you need to use is reduced as you get more experience in diving: you relax, you breathe more slowly, you learn to control your buoyancy. I am down to about 7 kgs in my 7mm suit, which suits me just fine (I used to wear about 10 kgs). That means that, including the tank, I’ll be wearing over 20 kgs strapped to my person, not counting the wetsuit itself and other accoutrements; and let’s remember that it is not strapped on in a particularly ergonomic fashion. I can walk in that without getting exhausted, but it is a workout not to be sneezed at.

In my dry suit I wear about 11 kgs of lead – so over 24 kgs in total. That makes a difference. Again, I can walk in that, but I do so very slowly, and have a breather before I descend (note: descending while out of breath or with an above-resting heart rate is not a great idea. You’ll guzzle air on the way down).

This is me. I am of a very average build. You might think that if you put on weight, you’ll have to carry less lead – because, naturally, you’ll be heavier.

Unfortunately (and believe me that I curse this), fat is positively buoyant in water. So even if you are very heavy on land, if that heaviness is fat rather than muscle, you will need more weight. I’ve known people who wear upwards of 20 kgs of lead alone, not counting their tank. This doesn’t mean they can’t dive; on the contrary, people of all sizes and shapes can master our not-so-ancient art, since people of all sizes and shapes can be diving fit.

But it does mean they have to be very strong if they are going to do cold water diving, because they are going to be walking around wearing that gear. You don’t usually park on the pier. Generally, you walk at least a hundred metres from the carpark to the water entry, and frequently it’s further than that. Not only are you walking, though; you’re bending down to pick up things if you drop them, or put your fins on if you are doing a jump entry; you’re helping your dive buddy get their own gear on; you are still bending and moving and doing heavy work, it’s just that now you’re wearing a metric fuckton of weight. You need to be able to do these things and help your buddy do these things if they get stuck.

This is not meant to be discouraging. I found it embarrassingly difficult to do anything in full kit at first. You get stronger, and it gets easier, and then it feels fantastic. It’s better to go in with your eyes open, though.

This is the main reason why diving requires fitness – for the most part, it’s not the actual diving and swimming. You wear fins when diving, and most of the time people swim quite slowly so they can look at things. In fact, you are encouraged to be relaxed and breathe slowly; diving is exercise, but it’s not supposed to be work when you’re under water (unless you are actually diving as part of your employment, which may involve diving in crappy conditions). The biggest risk is before and after you get in the water.

My recommendation for “stay dive ready” exercise is weight training focusing on back, legs and core work. Those are the muscles you use to handle your gear, get it on, walk around in it, and swim against current if necessary. Cardio is obviously a net benefit, but that is always true, and it’s not everything. I’ve seen numerous divers with excellent cardio fitness struggle to get onto the boat at the end of the dive because, when gravity reasserts itself, their glutes and hamstrings start to give out.

That’s right. You need a strong arse. You can climb a ladder wearing weights, but you need to take it slowly and use the big muscles.

I nearly met my match on a particularly awful ladder in Albany, Western Australia. It was an old, slightly rusted ladder hanging from the town jetty, and only the bottom rung was in the water; this meant I had to hook my knee over it to even get leverage. There was a moment where my supervisor looked at me and offered to take my weight belt so I could get up the ladder. I am nothing if not bloody-minded and managed to get my feet under me and straighten my legs (not without some cost and limping and very sore muscles for the following couple of days), but it was touch and go for a moment. This was also back when I was wearing a lot more weight, and, not coincidentally, I had less muscle strength than I have now.

Essentially, if I can do it – even at the cost of some wincing and whimpering for a day or so afterwards – it is pretty much achievable for most people, barring some particular circumstances.

There are a few conditions and situations that make SCUBA diving a spectacularly bad idea, and some that merely make it slightly more tricky, including but not limited to asthma and diabetes, as well as some temporary advice. I am not a doyenne of diving health or general SCUBA safety, but I plan to do some research and post some more general and basic information on the above conditions and general Thing You Should Not Do but which some people do anyway (much of this would be covered in an Open Water course, but refreshers are always good). If you want a heads up in the mean time, I suggest contacting someone listed among the South Pacific Underwater Medical Society (www.spums.org.au).



On Modesty, Self-Respect, the Appropriate, and defining your terms before you open your mouth

I would be perfectly happy never again to hear the fusty, huffy catch-cry of “It’s about self-respect! What next?” when it comes to modesty, clothing or behaviour, because honestly, the answer to “What next?” is usually “Hotpants.”

I would be happy never again to hear, “They can do what they like, but I don’t want to have to see it” or “I don’t want to see anyone’s [body part]” or “I don’t want to see a [person of description] wearing [apparently objectionable clothing item].”

(I happily quote Ragen Chastaine’s blog in response to the latter: “Look over there! It’s a whole bunch of other stuff you can look at!”)

And I would be happy never to hear someone say, “It’s called being appropriate.”

I’m not sure if I get this from my general English major or my science major, or just being plain rigorous, but I get quite uncomfortable whenever anyone uses a term to proscribe someone else’s behaviour that they then cannot define.

Thus far, no-one has managed to provide me with a definition of modesty, the appropriate, or even the nebulous self-respect (in this context) without resorting to

(1) extraordinary sexism

(2) religious beliefs (see 1); or

(3) generalised sex-negativity (see also 1).

Appropriate may refer to “current societal norms” (which vary from place to place within the same city), but it more often refers to “the societal norms I grew up with.” You can not reasonably expect everyone to operate according to your specific personal preferences. You think your god doesn’t like people eating pies? Great! Don’t eat pies. Now explain that to all the people who don’t follow your god. Why, exactly, should they stop eating pies? Moving on from pies (it’s possible that I’m a bit hungry just now): you’re upset by seeing navels? That’s a shame. You should probably try not to look at people’s navels.

People do have a right to complain about their discomfort (I complain frequently, whether I’m being reasonable or not), and I have a right to sling it back at them. Sure, I wince a little when a friend refuses to wear pants that cover his butt-crack, but I have no objective standard for saying there is anything morally defunct about his butt-crack (we all have them. If we did not, our buttocks would be fused! Would that not be problematic, gentle reader?), nor do I imagine he is unaware of the problem (the air blows through the pass a wee bit cold), and I am not obligated to stare at the coin slot thus exposed (no matter how my eyes may be drawn to it, as unto a single stain on an otherwise pristine carpet).

If my butt-crack exposing friend were attempting to project an air of professionalism, I might let him know that his vulnerable crevice is working against him (assuming he did not already know). Otherwise, it’s his call.

I deliberately used a male example here. Should we now, perhaps, discuss young ladies who wear extremely short shorts, such that one can see, from certain angles, an exposed derriere? Oh, my stars, I feel quite faint. Should we discuss breastfeeding in public such that someone might see a nipple? Bring me my smelling salts! (wait, these aren’t smelling salts. This is Wizz Fizz)

Can anyone define modesty in such a way that it is a societal virtue?

Honestly, whenever someone says “modesty”, all I hear is, “Cover yourself, skin is bad,” and “Cover yourself, because people don’t want you to make them think about sex,” and “Cover yourself, because other people’s thoughts are your responsibility,” and, finally, “Cover yourself, because I was a bit surprised and now I have seen something that is out of context for me, and I’m being forced to deal with it, and it’s all a bit too difficult.”

Modesty, as near as I can tell, is somehow positioned and staged (with special effects and clever lighting) as being about self-respect. With glorious sleight-of-hand, people use the term “modesty” and then somehow manage to skip over the definition, where your body is something you actively restrict; self-respect means not letting other people see your parts which… are apparently bad? Self-respect means only letting certain people see your parts, otherwise… rain of toads? Because, if you respect yourself, that means hiding yourself away. Things are only worthy of respect if they are rare and offer restricted access.

Wait? What’s that you say? Oh, right, sexism. Alright, women are only worthy of respect if they are restricted. The minute you can see too much of a woman, you aren’t supposed to have respect for her, and it means she does not have respect for herself.

Now, please, stop for a minute, and think, because that shit right there is fucked up.

Stop, and just for a moment, swap the genders. I don’t assume my friend with the naked crevice lacks respect for himself. I don’t feel he’s immodest. I honestly think he probably just doesn’t give a donkey’s ball sac whether anyone can see his arse or not. I think it’s misguided when he’s trying to be professional, but when he’s not, I think it’s admirable.

Here’s another one: the notion that women who breastfeed in public are somehow being immodest plays into the idea that women with babies should enter into “confinement”. Women should be restricted whenever showing evidence of, ahem, biology. Biology is not appropriate, apparently.

And all people can tell me is, “Mumble, mumble, modesty,” and “Mumble, mumble, appropriate.” If a breastfeeding mother is uncomfortable potentially exposing the nipple, because there’s the possibility of being judged and stared at, and that is upsetting, sure, cover up, find another space, do what you need to do. I don’t like being stared at and judged either and it definitely informs my choices and anxieties. But if you don’t give the aforementioned donkey’s ball sac about other people’s hang-ups, then go forth and lactate.

If you like the short shorts and what must surely be a wedgy sort of feeling (I may be projecting; short shorts don’t deal with my hips), go forth! Expose the lower portion of thy buttocks. I don’t care – although, granted, I find it looks a bit odd – and if anyone does, it says more about them than about you.

The minute someone says, “But what about the elderly?” remind them that the elderly are adults, and that the world was in the process of changing as they grew up and isn’t going to abruptly stand still. If they say, “But what about children?” remind them that children not only have body parts, they tend to find them pretty fascinating. The fact that other people have body parts is not likely to confuse them. In fact, it’s a reassuring confirmation of logical expectation.

Lest anyone be confused, here: I reserve the right for anyone to make aesthetic judgments. I can subjectively say, “I don’t think that looks pretty”, and none can say me nay. I won’t say that to the person in question unless they actively seek my opinion (and even then I may dance around the issue in a clumsy not-wanting-to-hurt-feelings sort of way), but I have my preferences as does everyone. The difference is that I do not ascribe any moral relevance to my aesthetic preferences. The fact that I prefer A-line dresses to t-shirt dresses just means I like full skirts and a fitted waist (where that is comfortable for the body type in question); I don’t like t-shirt dresses because I think it looks like people just aren’t wearing any pants, and I’m used to the people with baggy tops wearing pants. You know what? It doesn’t matter that I think that. It doesn’t matter that I’m confused. It doesn’t matter that damn it, fashion changed since I was a teenager, and now these young-uns are wearing weird looking clothes and it’s not in line with the aesthetic I developed growing up; and that is all that is (this also applies to music in a serious way, but that’s another conversation).

No-one has the right for their subjective aesthetic preferences to be followed. In a similar vein, no-one has a particular right not to be exposed to flesh, or clothing they don’t like. No-one has a right to judge, by any objective standard, another person’s clothing, body type, or sexual behaviour (outside of causing harm).

People will judge anyway. So do I. We’re human. We should, however, take a step back, and remind ourselves that we have our own business we’re perfectly capable of minding, and we should get right on that. Why, when I was a lass, people didn’t… I don’t know what they didn’t do, but they didn’t do it, and now they do, and it’s wrong! What’s that? Why is it wrong? Because it’s disrespectful? Of what, exactly? Of… me and my expectations.

That’s it. Seriously, screw your expectations.

On Marine Biology Cred

Telling people you are a marine biologist is like injecting your ego with steroids. I’m not sure when or how it happened (the early 90s may ring a bell), but marine biologists are apparently – somehow – cool. We have cred. This is odd to me, since we are all nerds of the highest order, but I’ll roll with it.

It’s seen as an amazing and desirable job. People imagine we spend our research days on the beach, in the sun, in the water, while they are cramped up at desks or behind cash registers or stoves.

I actually feel a bit guilty at pointing out that, technically, I don’t have a job. I have contract work because my taxonomic training fills a particular niche. When people have crinoids (feather stars) that need identifying, and they are in Australia, and they have funding for taxonomic services, I get work. At the moment there is a bit of a boom going on, thanks to mining in the north west of the country and the associated marine ecological surveys, but honestly, there’s not usually a big call for that skill (not by people who can pay me, anyway, and it is really the kind of thing you should not do for free).

I feel like I might be a bit of a downer if I point out that, far from roaming the beach in the sun while gentle waves roll up the sand, fieldwork generally involves rough, cold, murky water, wriggling into wet neoprene, cutting one’s hands up on rocks and getting covered in bruises (that’s not including walking extensive distances carrying up to 26kgs of lead and steel on one’s back). I love fieldwork, don’t get me wrong, and sometimes the water is warmer, and calmer, and clearer, and sometimes I’m not getting rained on, and sometimes it’s a very short walk to the water and I may only be wearing about 20 kgs of lead and steel, but my point remains.

And I feel like I’m bursting the bubble of fun and dreams if I then point out that, far from being on fieldwork all the time, most of the time I am hunched over a lab bench or a computer just like everyone else, collecting data or analysing it, wrestling with niche software that was developed almost accidentally for someone else’s project and then subsequently released for other people to use, covered in bugs and with poor error-checking.

And then I feel like I’m just the party-pooper of all party-poopers if I point out that, not only are there very, very few jobs, the results of the recent Australian election have made it clear on several levels that there will be even less jobs in my field than there were before (cuts to research funding, cuts to conservation, suspension of marine parks, etc. etc.) and that, even if I am exceptionally lucky and successful, the longest term job security I will ever ever have is most likely to be about three years at a stretch; and I chose this path more or less knowing that this was going to be the result, so I don’t actually complain about it that often.

So often I don’t point these things out. I just smile, mention that it is pretty awesome (despite all that, it really is) and accept my brief moment in the slanting sunlight of cool.

Animal breeding, genetics abuse, and Powerpoint pedigrees

I’m about to tell a little story, here, and be aware that there are far worse and far more egregious cases of what I’m going to call “genetics abuse” than the situation I am about to describe.

After dog training the other day, as we were walking Amos (our purebred Rottweiler, for those who don’t know) back to our car, a woman stepped out of our car and went “Oh, he’s beautiful!” (thank you, we know our dog is gorgeous).

“What line is he from?”

This question, well-intentioned as it is, makes me twitch. While we did glance at Amos’s pedigree (in my case, and as I’ll explain below, it was to calculate his inbreeding coefficient) and look at his parents’ records for eye examinations and elbow and hip scores, we don’t care what line he is from. We’re not breeders. We won’t breed Amos for a number of reasons. We got Amos from Oscelly because his parents were healthy and good-natured, and the breeders were supportive.

“Oscelly,” Husband replied politely. “In Kyneton.”

“I used to breed Rottweilers, in Queensland,” the woman explained. “But I can’t have another one since my last one died.”

I flooded with sympathy. “Oh, that’s awful,” I said.

“Yes, and there was no sign! I line-bred him as close as I could-”

At this point the conflict between “It’s so sad to lose a dog” and “you fucking idiot” caused a blood vessel to pop somewhere in the tact-zone of my brain. I actually inhaled my own spit when I went, “Ah… ha?”

“-and I’d been wrestling with him the night before, and he was fine, and I went out to the garage in the morning and he was dead. He was only seven.”

A healthy Rottweiler has a good chance of making it to ten years old and beyond. Quietly I observed, “Sounds like a heart problem?”

“Yes, I thought so.”

Then she admired Amos some more while he wriggled in sociable happiness, particularly his beautifully shaped head (he does have a nice head), and we parted ways. As in all truly frustrating situations, it actually took a few hours for me to get angry enough to start composing this post in my head.

Let Auntie Kate explain line-breeding to you, as well as some basic genetics, and let’s get cracking on what happened to this poor dog and his owner.

Line breeding is where a particular breeder/stud decides that they want their dogs (or horses, or cats, or alpacas) to have a particular look and tendency. They basically want a genetic stamp that says “These are our dogs. You have a dog from Stud X!” They also want all the traits that will allow them to win more dog shows, which will get them more stud fees. In order to achieve that, they try to concentrate the particular desired traits in their dogs.

They do this by inbreeding. Let’s be clear here: line breeding is just another way of saying “inbreeding.” There is no fucking around. It is the same thing, and it is very, very bad for any population to have this happen.

I know a good deal about population genetics (the thesis is coming along nicely) and next to nothing about animal husbandry. All that I know about animal husbandry is based on breeders of any kind of animal delivering bone-headed pronouncements that make me want to smack them upside the head with a population genetics text book (heavy enough to concuss). Having said that, animal husbandry is one of the long arms of human agriculture. Humanity has been breeding animals to conform to their specifications for millennia, and we’ve become pretty good at it. Without an understanding of DNA, or complex inheritance patterns, we managed to work out that breeding too close was a bad idea.

We worked this out from a number of signs: deformed offspring is one obvious sign. Less obvious signs are infertility or reduced fertility. If, for example, you want to buy a puppy from a breeder, and they announce that the bitch only had one pup in that litter, do not buy that pup. That pup has a good chance of breaking your heart. If you do cave, and buy the pup that almost certainly carries a number of recessive defects, do not breed the pup. Ever. If you do, you’re part of the problem.

So some animal husbandry has limits as to how close they are willing to breed their animals. They draw these limits far, far closer than they should, and then cite some pretty random research to say that this is okay. This research does not say what they think it says, and I’m going to explain why.

In every cell of your body*, you have two copies of your master genome** – the 23 (usually) chromosomes that are tightly wound strings of DNA. You have one copy from your biological mother, and one from your biological father. In the simplest scenario, when you produce gametes (eggs and sperm), each gamete contains only one copy. They might have your paternal copy, or your maternal copy (they might have a slight mix of the two as your chromosomes cross over and recombine, which is how new combinations arise). The successful gamete will pass that copy on to the next generation. Odds of having a mostly paternal versus a mostly maternal copy are 50:50.

So we have two copies of every gene and every gene region. When these copies are different in any way, we refer to the different versions as “alleles”. For example, I have red hair. Red hair is what we call a recessive trait, which means that I have to have inherited alleles relating to red hair from both my mother and my father (hair colour is actually a polygenic trait, so it’s not that simple, but both parents have to be involved for my hair colour to express the way it does). This also means that, since I have two copies of the relevant alleles, I am guaranteed to pass on one redhead allele copy to any kidlets I one day have.

So we’ve got the background for simple recessive inheritance. Now we get to the scary part.


No, really, you are. DNA is self-replicating, and it even has proofreading systems to make sure it copies everything perfectly. It still screws up, and leads to mutations. We all have these mutations, every single one of us. Most of them are probably relatively benign on their own – after all, you’re reading this, right? – but in many cases if you had two copies, the result would be lethal. In fact, most of the time, if you have two copies that were flawed in the same way, you wouldn’t develop all the way to viability. You would be miscarried, maybe as a zygote, or an embryo, or a fetus.

Here’s the thing: because these mutations are so sparsely distributed throughout the genome, and so individual, and because there is so much diversity in the human genome (we have what is called a large effective population size, more on that later), it’s astoundingly rare that you will get two copies of a flawed allele (with the exception of some named recessive disorders that have persisted in the population – and there are some nasty ones out there).

Of course, if you’re closely related to someone, it’s much more likely that you both have that allele. I am now going to illustrate why cousins shouldn’t marry and have kids****, only in my example, they are DOG cousins.

(****early footnote to prevent offense also pasted in here: Of course, cousins are perfectly allowed to marry. It’s their right and their choice. It’s just that most of them seek genetic counselling to make sure that they are not going to pass on some deleterious recessive trait. In most cases, it’s perfectly fine.)

We begin with a basic pedigree.


Meet Lord Doggington and Princess Jemima. They are both perfectly healthy, show line dogs of the breed I just made up called Zimbabwean Slothhounds. They win awards for how amazingly pretty they look. Depending on the breeder, they may also be valued for their robust strength and good nature, or the breeder might just be interested in appearance. Let’s give them the benefit of the doubt: they are, after all, particularly good at chasing down sloths.

Like all dogs – and all DNA-bearing organisms – Lord Doggington is carrying a nasty secret in his genome. It’s okay, because it arose with him due to a point mutation in one of his parents’ gametes, so it doesn’t exist anywhere else in the Zimbabwean Slothhound population. We should be safe from anyone ending up with two copies of this allele.

Alas, Lord Doggington’s owners think he is super awesome, and they want their whole stud to be like him. They want to concentrate his traits.

Lord Doggington and Lady Jemima have a bunch of puppies (ideally around eight). The stud sells six, and keeps two, Daisy and Fido, whom they like the look of. Daisy and Fido each have a 50% chance of inheriting Lord Doggington’s crap-arse allele. However, they will only ever have one copy, because Princess Jemima does not have the crap-arse allele. She probably has her own deleterious alleles, but we’ll focus on the other one here.


Let’s imagine that both Daisy and Fido inherit the crap-arse allele. There is a 25% chance that this will happen (0.5 x 0.5 = 0.25, for those who forgot probability as soon as they graduated high school). Daisy and Fido are each bred to outstanding Slothhounds from other studs, and produce, respectively, Butcho and Miss Dogface, who are adorable puppies.


There is a further 50% chance each that Miss Dogface and Butcho respectively will inherit the crap-arse allele from Fido and Daisy. If we know that Fido and Daisy have each inherited the allele, then, again, there is a 25% chance that both Miss Dogface and Butcho will as well. If we don’t know the status of Fido and Daisy – i.e., we’re just guessing, which is the fun part of recessive trait pedigrees – then there is a 25% chance that each pup will have the allele, and a 6.25% chance that both of them will. That’s a more than 1 in 20 chance; it’s actually quite high.

Let’s say that this untoward event happens, and the breeders decide to breed Dogface to Butcho (some breeders won’t do this. Some will. It varies) to create the pure strain of awesome that descended from Lord Doggington, thus elevating the Zimbabwean Slothhound from relative obscurity as a breed to glorious renown.

If we know that Dogface and Butcho have the crap-arse allele, there’s a 50% chance that their pup will have one copy, a 25% chance that they will have no copies, and a whopping remaining 25% chance the pup will have two copies. If it is still unknown – if, in fact, all we know is that Lord Doggington is on both sides of the pedigree and that Butcho and Dogface are first cousins – then we have a 1.56% chance that their offspring will have two copies of any allele from Lord Doggington. This is what we call the probability of identity by descent (IBD).*****


In this last figure, I’ve now changed the colour to indicate that this unlikely event has happened, and we can see the carriers of the allele. The offspring of Miss Dogface and Butcho inherits both copies (something that is a 1.56% chance from the word go), and either aborts, or is born with a severe defect that may even require euthanasia. This is why you want to avoid dogs with tiny litter sizes – unless they’ve been bred for reduced ovulation, small litter sizes generally represent resorbed pups that did not develop or even useless gametes.

Lest you think 1.56% is vanishingly small, in a population-level analysis, it is huge. It is a matter of some concern, and this shit happens all the time. In livestock animals, offspring may often be bred back to their parents – now that you’ve got the basics, I’ll leave you to draw out the pedigree of all the shit that comes out of that.

When Amos’s breeder showed me his pedigree, he brought out a photo of his very own Lord Doggington, explained how fantastic that dog was, and that he was on both sides of Amos’s pedigree. This was stated to me as a good thing, and if I were not a geneticist, I would have been convinced by his superior knowledge. That is why I am writing this post and using too much bold typeface.

I gently pointed out that I was a population geneticist doing a PhD and that this was of some concern to me. The breeder told me about some research some fellow in the UK had done on plants where he experimented and showed that inbreeding wasn’t so bad.

I haven’t managed to find whatever research he was quoting, but here’s the question I want to ask: what sort of plant? Was it a native population? Because this, I think, is where animal husbandry and population geneticists part ways. Animal breeders know what I’ve just been explaining. These are not stupid people – they have a science all of their own. They’re just not updating it, and they are missing a crucial piece of the puzzle: the piece that comes from population genetics.

They are missing effective population size.

Effective population size is basically a way of describing the background genetic diversity in the population and what is passed on to the next generation. For example, you might have an enormous population of corals on a reef, but if the millions are all reproducing by cloning themselves, and if they are all descended from the same clone, the corals will have a very, very small population size (i.e.: 1). However, since they are clonal, they already have their two genome copies, and we already know that they are functional. There are advantages to clonality.

You might have a very large herd of deer, but if all the young males keep getting their arses handed to them by the boss male, he’s going to do all the mating. Because you have a large number of different females, the effective population size will be larger than 1, but it’s not going to be enormous. There’s going to be a lot of deer wandering around with that paternal genome copy.

The basic message is this: when you breed to concentrate physical traits in a population, you are removing variation from the genome, because you are not breeding the animals that don’t fit your requirements. These animals do not contribute to the next generation; therefore they are not included in your effective population size. You are concentrating the physical traits you desire, but you are also concentrating the invisible, deleterious alleles. You are increasing the likelihood that matings will result in double copies of the same rare, lethal allele. You are reducing your effective population size.

You are drying up your gene pool #nerdpun.

So inbreeding is tolerable and manageable when you have a large effective population size, although it is itself reducing your population diversity. It is a horrible thing to do when you have a small effective population size.

This just in: purebred dogs have a very small effective population size. We’re not talking clonal corals, but we’re definitely not talking human-grade levels either. It’s a closed system; generally they only breed purebreds of a breed to others. That’s the whole point. I decided to get a purebred dog despite knowing all this, because I grew up with and love the breed, and also because this way there is a measure of predictability regarding temperament (I like large dogs. Temperament is important) and disease (I want to know what to look for).

I decided to look at Amos’s pedigree myself. All up, his probability of any allele being identical by descent was less than 0.06%. Since I’d been told that the odds of finding a breeder who does not practice line breeding are slim to none, I decided that was an acceptable risk. Amos has an undershot jaw, so it would be irresponsible to breed him (it’s not a huge deal for him personally), but otherwise he is perfectly healthy.

I think. I’m not sure, because here’s the rub: Rottweilers became very fashionable at some point in the 1980s. Before that, they were known for the elbow and hip problems, and possibly the minor eye issues – and that was it. These are also common to many breeds of dog.

When a dog breed becomes fashionable, you get a lot of what is termed “backyard breeding” – people either breeding out of ignorance (because they like puppies), or greed (because purebred dogs are worth squagloads) or both. This means people didn’t necessarily check that their dogs were healthy before they bred them.

Rottweilers are now known for heart problems. This is a new thing. I now have to worry about my dog’s heart, because even though he has a 0.06% chance of identity by descent, the odds of these crappy heart alleles floating around are much higher (there’s also cancer. Don’t get me started).

And this woman I met in the parking lot – to come back to the point after a long and circuitous journey – line-bred her dog as close as she could, and she did it because she honestly believed that it would produce a healthier dog. She believed this because all the dogs she bred were outwardly healthy, with no consideration for or knowledge of what was hanging around unexpressed in their DNA. This is the problem. Because they don’t consider effective population size, because they don’t consider recessive traits, and because they do not acknowledge how common these mutations are, they only breed from the appearance and behaviour of the animal, i.e., from the phenotype, not the genotype (this is not universal: a number of recessive traits are very well understood and bred for, but this doesn’t connect with effective population size).

It’s possible that if she outbred her dogs with other studs – and you could even do this and keep a dog purebred – the resulting pup wouldn’t have had a congenital heart defect.

It’s just possible she wouldn’t have gone out to the garage and found her best mate dead on the floor at seven years old.

So, even in purebreeding systems, you can outbreed. Do that. Avoid genetic abuse. Reduce animal suffering. Avoid getting your heart broken.

*Except red blood cells. They need extra room for hauling around oxygen, so they don’t have a nucleus.

** We’re not talking about the mitochondrial genome. While that is important in its own way, it is only maternally inherited, it doesn’t recombine, and because cellular respiration is so crucial and you only have one copy rather than two, deleterious mutations don’t tend to survive.***

***Having said that, there are rare cases of species or individuals where a mitochondrion may be bi-parentally inherited and/or undergo recombination, and there are rare human diseases that are caused by mitochondrial mutations.

****Of course, cousins are perfectly allowed to marry. It’s their right and their choice. It’s just that most of them seek genetic counselling to make sure that they are not going to pass on some deleterious recessive trait. In most cases, it’s perfectly fine.

*****IBD! Identity by descent! Not to be confused with Isolation By Distance, or any other number of concepts for which IBD is an acronym…

(Backdated entry: Originally put together November 2012)

Sound check / Mission statement

I’m slightly taken aback. I was expecting WordPress to ask for my personal biography and breakfast habits, but instead received the enthusiastic suggestion to create a post. I’ve been mentally narrating that bio in the menu there (presuming I get around to creating it by the time this is read) for the last little while.

Introductory posts suck. It’s like stage banter before the first song. It should all be heavy drums at that point, but here I am, grinning vapidly at the audience.

I have other places on the internet where I vent my spleen, but they haven’t quite turned out the way I desired. This is the place where I plan to actually compose and consider entries (introductory posts excepted) and (gasp!) research them prior to tossing my opinions and tales to the wind. I’ve been writing various blog entries in preparation for a while, about various things – all of them, naturally, interesting to me – so for a while I will not be short on content.

Blogs tend to do better when they have a unified theme. I, however, don’t. My education and experience has been somewhat heterogenous to say the least, so you might find me waxing lyrical on anything from literary criticism to evolutionary biology. Or animal behaviour (with a likely focus on dog training and my dog, or simply cats). Or SCUBA diving (I plan to borrow Husband’s GoPro and add footage from time to time). Or exercise and hypermobility (I am perfectly healthy but suffer from somewhat odd biomechanical problems).

The fact is that I spend most of my life with a running commentary blathering through my skull, and it is frankly exhausting. I plan to add careful editing and research (where appropriate) to these mental screeds and find a home for them here; over the years it has turned out that these screeds seem to be interesting to people, so I should make them the very best screeds the world has ever seen.

Word of the day: screed.

Welcome. Please stick around.