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So, I own a pocket wolf.



Oh, OK, I own a little black mini-poodle. But, like all dogs, he has the same number of chromosomes as a wolf!

There've been several articles posted recently about the evolution of domestic dogs. While we've tended to think that domestication didn't begin until humans began to settle down & develop agriculture, DNA analysis suggests that wolves and humans may have begun a relationship up to 100,000 years ago. And a paper published in Science back in June presents evidence that there were two domestication events, one in Asia and once in either the Near East or Europe. There's a nice visualisation and explanation of the doggy family tree here.

A few weeks ago, I was discussing domestication with RadioLive's Graeme Hill, and one of the questions he asked was, why do we have so many different body forms in domestic dogs, and so little variation in form in cats? Was it because the dog genome is more 'plastic' & susceptible to change? My answer was that I suspected it had more to do with the length of the species' association with humans. Cats are sometimes described as 'semi-domesticated', and our shared history may go back just 10,000 years (with the possibility, again, of at least two separate domestication events). Whereas 100,000 years gives a lot of time for selective breeding by humans to produce all those different dog breeds.

Which takes us to bulldogs - the subject of a Scholarship Biology question in 2014. Bulldogs were originally bred to drive cattle, and had the strength and the ferocity (and presumably also a high pain threshold!) to subdue an animal by grabbing its muzzle and hanging on. They were subsequently used in bull-baiting, a cruel 'sport' that the UK banned in 1835.

Instead, the dogs were then bred for show. While their physical characteristics remained pretty much the same (short & squat, very muscular, the familiar very short face/muzzle with deeply folded skin) - by 1860 they had already begun to develop, as a result of selective breeding, their now-familiar gentle, non-aggressive temperament.

Unfortunately, selection for that very distinctive body form has brought with it a whole host of inherited disorders. You've probably met a bulldog with that snorfling, stertorous breathing - this respiratory problem is called brachycephalic syndrome, due to the very short face & nasal passage. Other heritable disorders include:

  • hip dysplasia (seen too in other breeds, such as labradors), where the hip joint can partially dislocate - this one is due to polygenic inheritance ie there are a number of different genes involved. 
  • a hole between the two ventricles of the heart. This is called ventricular septal defect (VSD), and an animal must inherit 2 copies of a recessive allele to express this disorder. It's autosomal, which means that male and female bulldogs are equaliy likely to express it.
  • cryptorchidism - one or both testes remains up in the body cavity instead of descending to the scrotum. This one is an autosomal dominant trait - only one copy of the allele is required. 
  • and - with all those wrinkles - dermatitis, also considered to be an autosomal dominant trait. The dermatitis often leads to bacterial infections. 

Poor bulldogs :( 

The actual exam question gave this background information & asked students to discuss two things: how humans may have manipulated the evolution of bulldogs from wolves; and how further selective breeding could be used to try to eliminate EACH of the named disorders AND evaluate how effective this might be. For students intending to sit these exams: remember that when you're answering these questions you need to provide both 'evidential' statements and justifications for them. And to do that, you'll need to integrate the resource materials provided in the exam paper with your own biological knowledge. 

The first part's pretty straightforward: you might consider, for example, why humans would want to select for non-aggressive wolves (eg for help in protecting a human or group of humans from other predators). Or what about the founder effect, which would come into play because of that small population of proto-dogs? The small sample of the wolf gene pool found in those first 'dogs' could mean that particular alleles were simply lost in the dog population, while others could become much more common.

You'd then want to address the sort of things a breeder would focus on to get from generalised doggy form to the highly specialised bulldog: insensitivity to pain; the short, powerful, upwards-facing jaw; the squat, heavily-muscled body. Don't forget the explanation: that the physical features would allow the dog to drive or subdue much larger animals, and that selection for those traits, if they had a genetic component, would see those particular alleles to increase in frequency in the bulldog gene pool.

And of course, once bull-baiting was banned, selection for gentleness/docility came into play. Because that called for further inbreeding in the existing bulldog population, it would likely result in a higher frequency of any existing harmful alleles as well.

The second part of the question tests understanding of students' knowledge of concepts around inheritance. In some cases it's probably possible to remove the deleterious alleles from the bulldog gene pool - but as a result the dogs would diverge from what's currently viewed as the breed standard. For example, selective breeding for a longer, less-wrinkled face could reduce the frequency of brachycephalic syndrome and dermatitis - but the resulting animals would be much less bulldog-like!

The same approach is less likely to be effective for hip dysplasia, however, due to the polygenic nature of this disorder, because it involves multiple genes rather than a single gene locus.

But selective breeding could help with VSD & cryptorchidism. For example, a dog that doesn't express VSD is either homozgyous dominant (with 2 copies of the normal allele) or heterozygous. So at the population level, breeding heterozygous individuals will on average produce 25% of pups with VSD, with the rest not expressing the disorder. Using a test-cross would allow you to breed only from parents homozygous for the normal allele, but it would take more time.  

And with cryptorchidism, you'd avoid breeding from males who had the disorder (which would have very poor fertility anyway, I'm guessing), and from females whose sons had undescended testes (because these females would be 'carriers' for the allele - while cryptorchidism is a dominant trait, you're only going to see it in males). 

Of course, you could also try out-breeding with other dog breeds - but then, the resultant pups may well not conform to the bulldog 'standard'. 

I must say, it does bother me that adhering to a breed standard - a human construct - can perpetuate known health problems in a breed such as this.

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The National government is proposing a number of amendments to the NZ Education Act. One, which has already received quite a lot of press, sounds rather like a return to bulk funding under another name. But the latest one to hit the news is more like an untried social experiment with the potential for a lot of brown stuff to hit the fan.

And what is this proposal? They've certainly come up with a catchy title: COOLs - Communities of On-line Learning. The NZ Herald covered yesterday's announcement by the Minister of Education, Hekia Parata, with its reporter stating that

any registered school, tertiary provider such as a polytechnic or an approved body corporate be able to apply to be a "community of online learning" (COOL).

Any student of compulsory schooling age will be able to enrol in a COOL - and that provider will determine whether students will need to physically attend for all or some of the school day.

Sounds cool? Not really. I try hard to be a glass-half-full sort of person, but I can see too many fishhooks in this proposal to be in any way confident that it should be rolled out in this fashion. 

Yes, I understand that there are some children for whom regular schooling really, really doesn't work. But we already have a range of alternatives in place for this cohort. Where is the evidence that going on-line is a better option? We also have the Correspondence School, Te Kura - surely we should be looking at how it operates in the digital space and enhance that if needed, before going full open slather?

The Minister is reported as saying 

This innovative way of delivering education offers a digital option to engage students, grow their digital fluency, and connect them even more to 21st century opportunities.

Yet digital options already exist in mainstream schooling & have been used very successfully to engage students, with notable successes - including for students at low-decile schools. So we should be encouraging & supporting teachers in all schools to investigate ways of doing these things, rather than setting up yet another layer of schooling - presumably also funded by the public purse - to 'fix' a perceived problem in an untried way. After all, a range of resources already exist - see here, here, & here, for example. 

There are other reasons for caution. COOLs sound a lot like MOOCs (Massive Open On-line Communities), which offer many good things to their potential users but which also have an impressively high drop-out rate - on average 80-90% of those beginning a course, fail to finish it. And that figure includes data from very high-quality options, such as those available through Coursera. Student motivation probably plays a large role in this - it can be quite hard to maintain motivation when contact with tutors and classmates is solely digital. Before the Minister's proposal is implemented, we need to be very sure indeed that any providers are able to maintain student engagement & motivation to succeed. 

There's certainly mixed evidence that digital learning, alone, can contribute to learner success. For instance, this study found that on-line learners - especially those where there was also an element of face-to-face contact - did tend to do better, but pointed out that 

conditions often included additional learning time and instructional elements not received by students in control conditions. This finding suggests that the positive effects associated with blended learning should not be attributed to the media per se.

Plus there's evidence that on-line learning suits abstract thinkers more than those who need and use concrete examples in their learning: 

Successful telecourse students also preferred to look for abstract concepts to help explain the concrete experiences associated with their learning. That is, they wanted to know 'why' certain things happened in conceptual or theoretical terms. This more abstract approach clearly favoured success ... [while] those who needed concrete experience and were not able to think abstractly were more high-risk in a telecourse.

There is also a significant social element to successful learning for most students. In fact, learning is about far more than acquiring factual information; there are a wide range of social attributes and what are commonly called 'soft skills' that students also need to gain. Indeed, in the tertiary sector the emphasis is more and more on institutions being able to demonstrate that they are producing work-ready graduates with a range of competencies and capabilities, including communication and teamwork skills, and other social skills that are difficult to come by in a digital context. 

And finally, it's difficult these days for many families to cope financially unless both parents are employed. Which leads me to ask: if students are able to spend part or all of their day learning on line and at a distance from their education provider, just who is going to be supervising them?

I'm sorry, Minister, but we need - and our children and students deserve - to see the actual evidence that this proposal works before it's put into action.

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There's a lovely, life-size bronze sculpture of a Powelliphanta land snail sitting on my china cabinet. I love it because a friend made it for us - and because snails in this genus are rather special, for they are all carnivorous.

Now, I 'knew' this fact, but I'd never actually seen one feeding. Snails being normally rather slow, sedate creatures, it was hard to imagine how they'd ever catch anything other than even slower prey. That was until I saw this video

Every earthworm's nightmare!

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The semester's begun, teaching has started, admin isn't letting up any time soon, & there are days when I feel like a zombie by home-time. So it seems entirely appropriate to revivify a post I wrote 3 years ago, on that very subject.

Honestly, sometimes I think the zombie apocalypse is already here. Certainly zombies seem to be flavour of the month (& whatever friends say, I still can't bring myself to watch Walking Dead). And I've written about them myself: well, the insect variety, anyway.

But our developing understanding of how parasites 'zombify' their hosts has been developing since well before the latest iteration of human zombies grabbed the popular imagination. I was reminded of this when I saw the video below (in all its over-the-top hyperbolic glory), for I was first introduced to the concept of zombie snails years & years ago by one of David Attenborough's TV programs**. (According to my aging memory, it would have been an episode of Life on Earth.) 

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Tunicates are more commonly known as 'sea squirts' - little blobby marine creatures that squirt water when you touch them (hence the name). We don't hear about them often, except perhaps when they make the news for all the wrong reasons. But from an evolutionary perspective they are fascinating little creatures - and it's largely due to their larvae.

As an aside: why do we call them tunicates? Because the body of the adult organism is enclosed in an outer sheath, aka a tunic. The majority of tunicate species belong to a group known as ascidians, which as adults live in shallow waters, attached to rocks or maritime structures (including boats). The remainder are planktonic & found out in the open ocean.

The larvae of many ascidians are free-swimming and, because of their body form, are often described as 'tadpole larvae'. (Some of the non-ascidian tunicates have adults with the same morphology.) These little animals have a number of features (shared with creatures such as the cephalochordate formerly known as Amphioxus) that link them with the chordates: a hollow dorsal nerve cord, a post-anal tail, a pharynx with slits in it (which feeds into the gut), and a living cartilaginous rod known as the notochord, against which the animal's muscles work. (The larvae, and the adults of some non-ascidian tunicates, are basically little swimming filtration units.)

In fact, because of their rather simple structure, tunicates have long been viewed as representing the likely common ancestor of both chordates (a group that includes us) and the slightly-more-complex cephalochordates like Amphioxus. However, a newly-published & fascinating article by Linda Holland (2016) looks at 

the highly derived body plans and life styles of the tunicate classes, their importance in the marine food web and their genomics [with an] emphasis ... on the impact of their especially rapid evolutionary rates on understanding how vertebrates evolved from their invertebrate ancestors.

It turns out that a genomic comparison, using nuclear genes from chordates, cephalochordates and tunicates, indicates that it's actually Amphioxus that sits at the base of this particular group. This in turn means that tunicates

have lost a lot of what the long extinct ancestral tunicate once possessed. 

This genomic work is fascinating on a number of levels. For example, the 'textbook wisdom' is only bacteria (ie Prokaryotes) have their genome organised into operons, where a single mRNA transcript contains several genes. But it turns out that tunicates, which have a rather small genome.

[have] a high percentage of genes in operons

something that Holland states they share with roundworms (nematodes) and some flatworms, which apparently also have "reduced genomes". In tunicates, it seems that among the genes that have been lost are some of the 'Hox' genes - genes that control the development and patterning of body form. 

I learned heaps of new things from this paper: tunicates are able to regenerate most of their bodies, for example (makes sense, I guess, as the sessile adult sea squirt can't exactly avoid being snacked on by predators). Apparently this is achieved by pluripotent stem cells in the animals' blood, though how it's done is still something of a mystery. And I had no idea at all that the animal's 'tunic'

contains cellulose, synthesized by a cellulose synthase that was evidently acquired in an ancestral tunicate by horizontal gene transfer from a bacterium. 

An animal that produces cellulose! Nature never ceases to surprise :)

L.Z.Holland (2016) Tunicates. Current Biology 26: 4 pR146–R152 DOI:

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This is an amended re-post of something I first wrote back in 2012.

We're in the lead-up to the start of the A semester & lately I've spent a lot of time lately advising students on their programs of study. (Consequently I'm a bit short of the time needed to give attention to serious posts on Serious Subjects.) One of the things we often talk about is which major(s) a student should study, where a 'major' is the subject that they will devote most time to over the second & third years of their degree.

This is an important decision for first-year students as it pretty much determines how they're going to spend much of their study time in the ensuing years, and so we take quite a bit of time to talk about the various options, and I often find myself asking 'where do you see yourself in in 5 years' time? It's serious stuff as you don't want to get it wrong, and sometimes I encounter someone who is just a bit confused by the various majors on offer & how they're structured - but happily I have yet to meet anyone with the views parodied by the good folks at xkcd :-) (Thanks to my friends at Number8Network for passing this on, and yes - someone has already had a go at singing it!)

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So, last night I was asked how hedgehogs mate. 

The obvious answer was, carefully! My interlocutor suggested that perhaps face-to-face was most likely, but as far as I know, very few species (& that short list includes our own) do that. It turns out that care is indeed needed, for the male approaches the female from behind, & she must adopt what's coyly called a 'special posture' and flatten her spines so that the sensitive portion of his anatomy doesn't take on the appearance of a kebab.

The question was actually part of a wider discussion around the architecture of sexual reproduction: the mechanics of how the bits fit. If you'd like to hear the entire thing, it's here on the RadioLive site.) Entomologists, in particular, seem to spend quite a bit of time studying this architecture, not least because these details may help them distinguish between species that are otherwise pretty much identical in their appearance. (There's a lovely story about Michael May's work on dragonflies here, complete with etchings illustrations.)

In many cases the structures - which can be quite bizarre - are driven by competition. Competition between the males, but also between males and females. So in those dragonflies, for example, the males' penes have all sorts of features that are related to sperm competition - they allow a male to scoop out, scrape out, or otherwise displace semen deposited by another male, and replace it with their own. And in mallard ducks, which are highly promiscuous, a sort of male/female arms race has driven the evolution of extremely complex genital anatomy in both males & females, discussed here by Ed Yong. Incidentally, that link also includes a video - perhaps not for the faint-hearted! - of the rather explosive uncoiling of & ejaculation from the drake's corkscrew penis.

Some of these structures can be rather large: we're talking a metre long for male African elephants, for example (according to wikipedia), around 2.7m in right whales, and up to 3m in Blue whales (the largest animals alive). And as one might expect, this has been attracting human attention for a long, long time. Sadly, some of that attention has been seriously harmful to the survival of some species - witness the aphrodisiac claims made for the sex organs of tigers by Traditional Chinese Medicine, for example. But there's also the point-&-wink sort of interest, shown in a painting of a dead sperm whale dating from 1606 and described by Menno Schilthuizen in the excellent book, Nature's Nether Regions:

On an otherwise nondescript Dutch beach likes the Leviathan, its beak agape, its limp tongue touching the sand. A smattering of well-dressed seventeeth-century Dutchmen stand around the beast. Prominently located, and closest to the dead whale, stand a gentleman and his lady. With a lewd smile, face turned towards his companion, he points at the two-metre-long penis of the whale that sticks out obscenely from the corpse. Centuries of smoke-tanned varnish cannot conceal the look of bewilderment in her eyes.

These few square feet of canvas ... [exemplify]... the unassailable fact (supported by millenia of bathroom graffiti, centuries of suggestive postcards, and decades of internet images) that humans find genitals endlessly fascinating.

However, it's only relatively recently that this fascination has really been reflected by scientific interest: interest in the structures, their function, and their evolutionary history. But, as Brian Switek points out in his book My Beloved Brontosaurus (which is also an excellent read), we still have no idea how dinosaurs - especially the big ones - actually mananged to mate. Particularly the big spiny ones. This may well remain one of life's not-so-little mysteries. 


It has occurred to me that the search history on my computer will look really, really odd as a result of doing a spot of research for this post!

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Demodex mites are tiny little creatures that live in mammals' hair follicles. I first heard about them years ago, when I watched a documentary with my science class back at PN Girls' High. It was about animals that are parasitic on humans, and after the segment on eyelash mites, I don't know about the girls but I felt itchy for days!

For eyelash mites live where the name suggests, in the follicles of our eyelashes. (There are 2 species: Demodex folliculorum and D. brevis.) The common name gives an idea of just how small they are: adult length is 0.3 to 0.4 mm. They spend a lot of time inside the eyelash follicles, snacking on the sebum and dead cells (or maybe the bacteria) that accumulate there. But at night... at night, they come out and wander across our faces as we sleep, achieving a speed of 10cm/hr or more. Which doesn't sound much, but when you remember how small they are, that's quite an achievement. Presumably that's also when they mate, which they do where an eyelash follicle opens to the skin's surface. 

I was surprised to discover that these mites lack an anus. This sounds somewhat problematic, but the eyelash mites have survived, with their human hosts, for at least tens of thousands of years, so they obviously cope somehow. And when they die, their little bodies degrade and release their contents. On your face. Or in the follicles where they spent most of their lives.

Though demodex mites are tiny, there are an awful lot of them. There may be only one or two per hair follicle (they don't restrict themselves to the eyelashes), but an individual human has around 5,000,000 hairs on their body (Thoemmes et al., 2014), so that's an awful lot of available places for a mite to set up home in.

Thoemmes & her co-workers were interested in the genetic diversity of these mites. They predicted there'd be geographically-distinct lineages, because the tiny animals are very closely associated with their hosts and don't seem to be particularly mobile between hosts. However,

if Demodex lack strong geographic structure, it suggests the movement of mites among humans must occur very frequently (perhaps even with social greeting rituals) and across large geographic distances.

To test this hypothesis, the team examined adults (from a single North American population) visually, but also tested skin scrapings for the presence of mite DNA. The results showed that despite being able to see mites on only 23% of their sample population, 16S rDNA sequencing indicated that 100% of those sampled actually had mites present. The latter matched other research showing that 100% of dead bodies tested positive for the presence of Demodex.

Figure 2 from Thoemmes et al. (2014): Maximum likelihood (ML) phylogeny of mites based on 18S rDNA sequences.

While the results of their phylogenetic analysis of the mite DNA are based on samples from only 29 people, they're interesting nonetheless. It appears from that analysis that the 2 species, D.folliculorum & D.brevis, probably colonised humans at different times. Because D.brevis' DNA indicates that their nearest living relatives are mites living on dogs, then the researchers suggest that we acquired this species from our doggy friends, perhaps as recently as 11,000 years ago but possibly as many as 40,000 years ago. There does appear to be some regional variation (based on a comparison of the US data with earlier sequencing results from Chinese populations), but there's also quite a bit of variation within populations, due perhaps to individual humans picking up different mites on different occasions as individual humans came into close physical contact.

And after reading all this & watching a few videos, I feel itchy again!

Thoemmes MS, Fergus DJ, Urban J, Trautwein M, Dunn RR (2014) Ubiquity and Diversity of Human-Associated Demodex Mites. PLoS ONE 9(8): e106265. doi:10.1371/journal.pone.0106265

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Occasionally it's nice to just post a pretty picture. This is one that I took back in July 2015, while we were in France. We'd gone to visit the ruins of of an old Cathar castle called Peyrepertuse and there, on one of the scraggly plants growing on a patch of gravel by the side of the track, was this butterfly. It's a European Swallowtail, and oh how I love the camera in my phone!

Thumbnail image for butterfly  closeup.jpg


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A friend recently pointed me (via donotlink - well done, Nicky!) at a post on healthnutnews (which reads a bit like an offshoot of - this, it turns out, is hardly surprising). It's a while since I've read anything so full of total nonsense - well, a few days, anyway! 

The post, by one Erin Elizabeth, is a paean to someone called Johanna Budwig & her 'life-saving cancer protocol'. I hadn't heard of this particular person before, & according to Erin, this is because all knowledge of her work has been censored by teh ebil Western medical establishment, along with Big Pharma & the nuclear industry, all of whom would be, like, totally out of a job if everyone followed Budwig's advice. Being curious, I thought I'd check - surely there'd be time for a search before the men in black arrived...

To my complete surprise (I was shocked! Shocked, I say!!!), typing 'budwig protocol' into google brought up 142,000 results. Some, like Cancer Research UK, are obviously trying to repress knowledge of the dietary protocol (or at least, advising that It Doesn't Work), but an awful lot of the others provide recipes, advice, and testimonials about miracle cures.

Not a lot of repression going on there, then.

In fact, the entire post is a concatenation of quackery, woo, & mythinformation. Plus an appeal to authority: 

This German doctor was nominated six times for the Nobel Prize for medicine, which means that it would be wise to take her health work seriously. 

Really? Nominations are secret & by invitation, and nominees need to have a fairly solid body of research under their belt. However, a quick pubmed search didn't come up with anything by Budwig, but did give a number of papers whose authors had looked into this & similarly restrictive dietary protocols and concluded that It Doesn't Work (see here, and here, for example). 

Erin also trots out this standard cliche: 

Any researcher who found a cure would quickly find himself looking for another job, and at some level, all of them know it.

Here is a simple answer to that particularly offensive statement:

Image via The Credible Hulk and sheeple.

What else do we have?

Cancer is ... a modern man-made epidemic? Apparently so, evidence from antiquity notwithstanding: in the world according to Erin, the reason ancient Eyptians suffered from cancer, for example, was mass heavy-metal poisoning.

Medicine is the 3rd leading cause of death in the United States? Well, that one's easy to check, and it's not correct - you'll find the list here. Erin, could it be that you are being just a leetle creative in your narrative?

Surveys show that most oncologists would refuse their own treatments if they had a cancer themselves? Nope. This is cherry-picking, pure and simple. A 1985 survey about the then-new drug cisplatin, which has significant side-effects,did find about 67% of the oncologists surveyed would be reluctant to use it. A follow-up survey in 1997 found a significant reversal: 64% would now use the drug if they needed it. And why? Because science-based medicine moves on & those side-effects can now be minimised or better controlled, or different drugs may be available.

There's also a misrepresentation of Otto Warburg's work around tumour formation and physiology (work for which he really did receive a Nobel Prize), and the rather startling statement that

The secret to beating cancer is that life-giving breath of God: oxygen.

Apparently all that is needed to cure cancer - any cancer - is to provide cells with sufficient oxygen again. My immediate response was, so why is lung cancer so common, then?

And how do you get your tissues back into that oxygen-rich state? With a rather complicated and restrictive diet, of course!

At least Budwig's patients were spared coffee enemas, but they did get flaxseed oil via the back passage if too far gone to take it by mouth. And champagne was on the list of OK things to ingest!

Frankly, the only reason to repress this nonsense would be to reduce the harm done to people gullible enough, and desperate enough, to invest time and money into following it.

Was that a knock at the door ... ? 

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