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March 2009 Archives

From time to time I natter on about proper use of statistics. Now I see that Marcus is joining in, over at Physics Stop - he's written a rather nice little piece on the (mis)use of 'average'. Pop over & read it, & have a look through his other posts while you're there :-)

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Blogging on Peer-Reviewed Research Before I got sidetracked into mating behaviour in slugs & snails, I was mulling over the idea of writing about something equally complex - the area of male polymorphisms & mating systems. So here we go.

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Blogging on Peer-Reviewed Research This tale follows on from that piece on leopard slug courtship from a few days ago. I commented then that copulation in garden snails is generally preceded by (among other things) pushing 'darts' into each other's bodies. There've been various explanations for this odd behaviour (I mean, it sounds painful!), including the suggestion that the dart acts as some sort of 'wedding present' (nuptial gift), which might make the pierced partner more inclined to mating. Or that it indicates how ready the dart-shooting snail is to mate. But data from a 2001 study (Pomiankowski& Reguera) suggests another reason for this behaviour.

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The Burgess Shale fossils come from what's known as a lagerstatte - a locality containing a rich variety of fossils, where often even the soft tissues of organisms are preserved. Normally these bits would be the first to go during the processes of decomposition & decay, but the lagerstatte fossils formed when the creatures fell to an area of the seabed where the water was anoxic - no oxygen present, & hence very little decay. The bodies were then rapidly covered in fine-grained silt, which preserved the shape & often the details of the soft tisses as they fossilised.

The Burgess Shale isn't unique: other lagerstatten include the Solnhofen limestones, which provided the scientific community's first sight of Archaeopteryx, not to mention some of the sites in China that have yielded other beautiful fossils of feathered dinosaurs & early birds, not to mention some lovely Cambrian arthropods. And to those sites we can add another in Lebanon, where palaeontologists have found some absolutely stunning fossils of 95-million-year-old octopuses. Stunning for their beauty, their completeness, and for the presence of many transitional features that will help to unravel the tale of octopus evolution.

And as usual, PZ has done a great job of writing about them. But you'd expect that, from someone who's mad about cephalopods! (The comments section is also enjoyable.)

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Blogging on Peer-Reviewed Research Humans first domesticated cattle about 8.000 years ago. Possibly this was first for the meat, but at some point someone (or rather, several someones in several different regions) started also making use of the milk given by lactating cows. Which raises some interesting questions, as many people can't digest the milk sugar, lactose, found in cows' milk. Some of these were addressed in a recent study that examined the variation in cattle milk protein genes, lactose tolerance in modern humans, & stone-age cattle-farming sites (Beja-Pereira et al. 2003). The authors concluded that their data showed evidence of a 'gene-culture evolution between cattle and humans.'

In their study of lactose tolerance in Europeans, Beja-Pereira et al. found a high level of genetic diversity in Northern European native cattle. The distribution of this diversity was similar to the distribution of the allele that gives the ability to digetst lactose - and also with the distribution of Stone-Age cattle farms. Their explanation? 'Gene-culture' evolution between cattle & human culture. The ability to digest lactose opened up a new energy source to human populations with that ability. These populations kept larger dairy herds and actively selected for higher milk yields, changing the frequency of the milk protein genes in cattle - and this in turn would have affected the frequency of the lactase gene in humans. Gibbons notes that the same process led to the evolution of lactose tolerance in at least three different African groups in response to the domestication of dairy cattle.

A point to remember: the mutation allowing lactose digestion would have popped up multiple times in the past - but it was highly unlikely to be established in any human population in the absence of a selective advantage (the ability to make use of a novel food source). Unless, that is, it was carried along with some other feature under selection pressure, which doesn't seem to have been the case here.

A. Beja-Pereira, G. Luikart, P.R. England, D.G. Bradley, O.C. Jann, G. Bertorelle, A.T. Chamberlain, T.P. Nunues, S. Metodiev, N. Ferrand & G. Erhardt (2003) Nature Genetics 35: 311-313

A. Gibbons (2006) There's more than one way to have your milk and drink it too. Science 314: 1672

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This post uses material that was originally written for an item on the Science on the Farm website.

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Blogging on Peer-Reviewed Research One of the things that distinguishes medical science from what is often called 'complementary & alternative medicine' (aka CAM) is the willingness of the former to carry out careful, well-designed tests of various therapies. Those treatments shown to have some therapeutic value are added to the tools available to doctors & surgeons; those which don't, aren't. 

Over the years, a number of therapies that might once have been seen more as folk medicine have entered the mainstream. One of these is the use of leeches: once the tool of 'barber-surgeons' at a time when one of the main treatments for just about anything was to bleed the patient, leeches are now part of mainstream medical practice. (Frankly, if I'd lived back then & couldn't avoid a good bleeding, I'd have much preferred the leeches to the barber-surgeon's non-sterile knife! Although I suspect you could still pick up a bacterial or viral infection acquired up by the leech from the last person it sucked on.) They can be used after surgery to reattach skin and underlying tissues, to enhance blood flow to the affected area until veins have regrown.

More recently the use of maggots has become reasonably common as a tool for clearing dead (necrotic) tissue from in & around open wounds. Maggots are fly larvae; the ones used in wound treatment are typically blowfly larvae. But there's no danger of them gorging endlessly on the patient's flesh as they really only go for dead tissue. However, despite their increasing popularity, there hasn't been much in the way of a clinical trial of maggots & wound healing (if you have a weak stomach there are some high-ick-factor images here; they lack a good explanation but essentially show the progression of an ulcer under maggot treatment). That is, until the one described in a just-published paper in the British Medical Journal.

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... or something like it anyway!

Leopard slugs, like other terrestrial slugs & snails, are hermaphrodites. They produce both eggs & sperm, but must exchange sperm with another slug in order to fertilise their eggs. (This reproductive strategy means that an amorous snail doesn't have to find a partner of the opposite sex, it needs only to meet another snail. Of the same species, of course.) Actual copulation is preceded by a range of somewhat slimy courtship & precopulatory displays - in garden snails this involves (among other things) piercing one's partner with crystalline darts... Sounds painful, I know, but this part of the ritual apparently enhances uptake of the piercer's sperm by its partner.

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Who'd have thought it - a rap about the function & significance of Hox genes? But this is seriously good! (Thanks toOrac for spotting it.)

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Over at his BadScience blog, Ben Goldacre has had a close look at yet another dubious use of basic statistics. It's to do with the provision of carbon monoxide monitors in council housing in the UK. Carbon monoxide (CO) is a nasty thing - you can't smell it, & it can kill you very dead quite quickly: CO binds very strongly to the haemoglobin in your bloodstream - more strongly than oxygen, & each haemoglobin molecule that's clutchng a CO molecule is thus unavailable to carry oxygen to your cells. Anyway, a factoid released to the UK press (as part of a sales pitch, perhaps) claimed that an alarmingly high number of British council-owned flats weren't fitted with CO detectors. However, this claim was based on some rather creative mathematics, which Ben proceeds to pull to pieces.

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But not by me. I've just come across another rather good website, 'The naked scientists': covers all the sciences, with podcasts, articles, science stories, experiments you can do at home (I want to try the chip packet fireworks some time) & question & discussion pages. I thought you might be interested in this one: RNA interference explained: a concise. interesting explanation of what RNA interference is, its significance, & how we can apply this knowledge.

This is a site I'll be dipping into on a regular basis :-)

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Blogging on Peer-Reviewed Research

But not, says a press release, for the usual reasons.

Over my muesli this morning I read an item in the Herald (sorry, the link's to the identical item in a UK paper cos the Herald website doesn't carry it) saying that a group of scientists had 'disproved the theory' that competition for pollinators led to the evolution of brightly coloured flowers in many flowering plants. And it specifically mentioned red roses, saying in the sub-headline: Scientists have discovered why roses are red, claiming their striking colour has evolved to deter predators.

This was of course a red rag to a bull, so I went off to find the original paper on which this press release was based (Hanley et al. 2009).

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A while ago now I wrote something on common logical fallacies. I've just come across an e-book that talks about this area in rather more detail than I did. If you're interested, you can read the digital version of Humbug on-line, & it's also available to download. (And thanks to the Millenium Project for the heads-up.)

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Recently the journalist Amanda Gefter wrote an article for New Scientist on how to recognise 'science' books with a hidden (anti-evolutionary) agenda. While that's still available in the print version, the journal has now removed the on-line version - apparently, due to a complaint or complaints from readers. This strikes me as more than a tad hypocritical, since the NS cover 'Darwin was wrong' attracted considerable negative commentary & complaint (I wrote to the editors myself on that one) but remains with us. However, the web is a place where nothing, once posted, ever really disappears (scary thought! and all the more reason to take care with what you post there). So you can find the text of Amanda's article here.

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Blogging on Peer-Reviewed Research My colleague Brendan Hicks heads a research team that, among other things, has been looking at the evolution of some of New Zealand's freshwater fishes.  A number of these fish species belong to the bully family - & it seems that they arrived here relatively recently (in terms of the geological timescale, that is!). Using mtDNA techniques (Stevens & Hicks 2009) Brendan & his team have found that the ancestor of our modern-day bully speices probably arrived in New Zealand about 20 million years ago - & that their closest living relatives are bullies found in southeastern Australia. (that 20mya date fits well with the fossil evidence: the oldest bully fossil in New Zealand is between 60 & 20 million years old.)
 
Now hang on a minute - these are freshwater fish. Yet New Zealand sits in the ocean - it separated from Australia about 70 million years ago, as Gondwanaland began to break up under the influence of plate tectonics. How can bullies (well, an ancestral bully) possibly have arrived here so recently?
 
Well, bullies have a marine life stage, & Brendan says that South-East Asia is the most likely origin for both Australian & New Zealand bullies. What seems to have happened is that the fish arrived in Australian waters as marine larvae, and then subsequently crossed the Tasman Sea in the same way before moving up into our waterways.
 
This is borne out by genetic analyses by the resarch group. These trees indicate that our bullies evolved from a single ancestor that arrived from Australia & radiated into different species as it adapted to the range of new niches available to it (Stevens & Hicks, 2009). One factor underlying bully speciation appears to be loss of migratory behaviour, resulting in populations becoming isolated in individual catchments (Michel et al, 2008).  And this process isn't finished yet. As Brendan says, "Bully evolution appears to be a work in progress. While some are of New Zealand's bully species are clearly genetically distinct, others are not. This suggests that this genus is still evolving in New Zealand, and [our] research... on the common bully in the Bay of Plenty confirms this."
 
C. Michel, B.J. Hicks, K.N. Stolting, A.C. Clarke, M.I. Stevens, R. Tana, A. Meyer & M.R.van den Heuvel (2008) Distinct migratory and non-migratory ecotypes of an endemic New Zealand eleotrid (Gobiomorphus cotidianus) - implications for incipient speciation in island freshwater fish species. BMC Evolutionary Biology 8: 49. doi.10.1186/1471-2148-8-49
 
M.Stevens & B.Hicks (2009) Mitochondrial DNA reveals monophyly of New Zealand's Gobiomorphus (Teleostei: Eleotridae) amongst a morphological complex. Evolutionary Ecology Research 11:109-123 
 
My thanks to Brendan for providing me with the basis of this post :-)

 

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After reading & commenting on that letter, which attributed health benefits to sodium chlorite, I found my interest had been piqued. Just what has been claimed for this chemical? So I went looking...

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From time to time, someone will make the comment that evolution is totally irrelevant to everyday life in general, & to medicine in particular.

Today ERV's got a post detailing just how evolutionary theory has been & is being applied by medical researchers working on development of an HIV vaccine. Great stuff!

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A letter in our local free newspaper caught my eye tonight. Along with the rather outrageous statement that medical pharmaceuticals are 'just toxic pills and potions' pushed as medicines by marketing types (sorry, what? Does this person really think that drug companies & doctors are out to poison people?), there were some other interesting claims that I just couldn't resist...

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Reading Simon Ing's book, The eye, I was intrigued to hear about the possibility of learning to 'see' through the skin on your back. It involved a 'vest' bearing a set of rods with little actuators, controlled by a camera & computer. An image from the camera was converted into a fairly low-res image in the computer, & the rods were then moved to press against the person's skin in a pattern that reflected light & dark pixels.

Now it seems that a similar thing has been attempted with sound. Speakers embedded in the back & arms of a specially-built chair vibrate, stimulating touch sensors in the skin & allowing a deaf person sitting in the chair to 'hear' music through their skin. Different speakers are set up to transmit sound from different instruments & the system also modulates frequencies - very high-frequency sound vibrations can't be detected in this way.

Sitting in such a chair would certainly be an interesting experience - & surely a more pleasant one than standing close to a car with one of those infuriating boom-box stereo systems blasting at full volume. (Or does that just reflect the prejudices of advancing age?)

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A couple of posts ago I linked to a post by PZ on the fact that it's populations that evolve, not individuals.

Now he's written an extended article that starts there - & morphs into a lovely piece on the evolutionary history of elephants. Complete with great illustrations of their phylogenies. Superb stuff.

PS to put it in context, this whole elephant thing was kicked off (as alluded to in one of the comments threads) by a creationist argument that evolution couldn't really work because how could it produce both male & female elephants... Which shows a lack of understanding of that original point, that it's populations that evolve.

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One of the things I expect my students to understand, when we're talking about evolution, is that populations evolve, & not individuals.

PZ has said it rather well: Populations evolve, not individuals, and male and female elephants evolved from populations of pre-elephants that contained males and females. Species do not arise from single new mutant males that then have to find a corresponding mutant female — they arise by the diffusion of variation through a whole population, male and female.

Well worth remembering.

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We've 'got' ants at our place at the moment - the other day we came home to a thick black column that stretched from a chink in the woodwork around the french doors, all the way across the dining room & into the pantry. Determined little beggars! I suppose we should count ourselves lucky, as most of the time they confine their activities to the garden & the area round my goldfish ponds. (Yes - ponds, plural. I like goldfish. & the ponds are proper little ecosystems too - even have dragonfly larvae gobbling up the invertebrates that the fish miss.)

Anyway, the daughter & I have long been fascinated by ants - watching what happens when you stir up a nest, or changing their pheromone-laced trails & noting what happens. (We are in good company there - Richard Feynmann wrote how he did much the same, as a university student.) So I know she'll enjoy this article - a review of a book co-authored by one of the giants of sociobiology, E.O.Wilson. (Though perhaps not the book itself, as the reviewer - Tim Flannery - notes that it's rather heavy on the jargon.) But the review is great :-)

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Blogging on Peer-Reviewed Research A couple of years ago I sat in on a colleague's botany lectures & was enchanted to hear about a green sea slug - green, because it eats algae & sequesters the algal chloroplasts within its own cells. A solar-powered sea slug!

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As you'll have gathered (if you read this blog regularly), last week was an incredibly busy one for me, because I was heavily involved in the process of enrolling students for their 2009 studies. This was a new thing for me & it gave me the opportunity to think about ways to ease the enrolment process, from the student point of view. (I'm assuming that many of you are planning on university study of some sort.) So I thought I'd put some of those thoughts here.

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... & other devotees of things that go 'bang!'

Years ago now, I stood in for the HoD Science at a Manawatu high school. He was a chemist, & loved doing demonstrations. So before he went on leave, he walked me through some of his party tricks so that I'd get them right. I still remember him asking me if my hands sweated when I got nervious. Why? I said. Well, he said, if they do you won't be able to do this... & proceeded to roll a little bit of sodium into a ball before putting it into a deflagrating spoon! (He then proceeded to ignite the stuff & lower it into a gas jar full of chlorine.) I thought, ulp! His piece de resistance was to fill several condoms with hydrogen, attach them by strings to the ends of the seat rows in the assembly hall, & then proceed down the aisle & light them one by one. The kids loved it.

He probably wouldn't do these 'tricks' these days, though. In some ways this is probably a good thing (the memory of the balls of sodium is still with me!), & there are good arguments for not using bangs & explosions just for their own sake in the classroom. Students will remember them, but there doesn't seem much point if they don't also gain an understanding of the underlying scientific principles. But at the same time, chemistry could get a bit staid without them :-)

Where is this going? Well, I've just come across (courtesy of Ben Goldacre again) the most wonderful set of chemistry & physics demonstrations, all on video. Equipment, methods, explanations, it's all there. As Ben says, it's a bit tedious having to sit through the same introductory clip on each of them, but it's only for 20 seconds or so. My current favourite isthe balding gentleman with a stack of foil cupcake cases on his head - he touches a van der Graaf generator (while standing on a rubber mat), it's then turned on, & the cake cases fly off his head in a steady stream! (Apparently you need a bald volunteer to help with this one. I imagine that in someone with a full head of hair, the cake cases & the hair could develop an entanglement problem.) Mind you, the whoosh! bottle isn't bad either :-)

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I remember seeing a headline about Facebook being Bad For You because it causes cancer, a few days back. Unfortunately I was so busy with enrolment (& I might comment a bit on that in a separate post) that I didn't have time (or energy!) to chase it up. As I recall, the story had something to do with people sitting round all day chatting on Facebook, rather than going round doing 'healthy' things, & so leaving themselves open to cancer & other ills of the flesh.

And then today here I am, indulging in a pleasant spot of net-surfing, & I find that Ben Goldacre has done his usual excellent job of examining this claim, along with the related one that people who spend all their time on-line are more prone to loneliness, depression, & so on. For which it seems there is no convincing evidence, & in fact there are published studies which suggest no link exists.

So - visit Ben's place & read what he has to say. (You can watch/listen as well, as he's linked to a UK TV 'debate' on the subject. Great stuff.

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