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September 2009 Archives

As I left the office this afternoon I said to my colleagues, 'I'll be in a bit later tomorrow, I have an interview with a vampire.' At which they all laughed, because they know this means I'm off to my regular appointment at the NZ Blood Service centre, over by the hospital.

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Commenting on my last post about plant behaviour, Jim mentioned a paper by Marian Smith on plant responses to being touched or shaken. Unfortunately I couldn't get the link to work, but I did a Google Scholar search on the name & topic & got this: Plant growth responses to touch - literally a 'hands-on' exercise! It's in JSTOR so should be accessible for teachers & students interested in this paper, published in The American Biology Teacher (the link's to the JSTOR backfiles of this journal).

Most people would be familiar with the rapid responses to touch shown by venus flytraps & mimosa plants (one being what you could describe as a 'predatory' response, & the other quite possibly an adaptive response that reduces damage from herbivory - fascinating stuff & I must write something more about it). But that would be it. However, it seems that most plants have a distinct, measurable growth-response to mechanical stimulation (Smith, 1991). This response tends to be a reduction in vertical growth in response to a range of environmental stresses: grazing would be the obvious one but there's also wind (by itself or driving movement of one plant or plant part against another) & perhaps rain. If a plant is exposed to one of these stimuli & its stem grows shorter & thicker than in an undisturbed plant, this adaptive response would leave the plant less susceptible to future damage.

Smith's paper goes on to describe how to investigate & analyse this growth response to touch - very interesting & also very doable, if you're interested in having a go yourselves :-)

M.Smith (1991) Plant growth responses to touch - literally a 'hands-on' exercise! The American Biology Teacher 53 (2): 111-114 

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A couple of weeks ago Brian Switek's blog Laelaps included a post on transitional fossils (those things that some creationists will tell you simply don't exist... ) Brian's post was sparked by this story (OK, maybe the writer of was aiming for 'balance', but really!) & he suggested that others might like to emulate him & write something about their own favourite transitional fossil. The idea's been simmering away in my mind since then.

Brian's challenge required some pause for thought - what is my favourite transitional fossil? I do like the whales, but he beat me to it on that one. And then I thought, what about Diarthrognathus???

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One of the Biology Standards year 13 students study is called 'Describe animal behaviour & plant responses'. Now, if 'behaviour' = response to a stimulus, then that's really what plants are doing too. I guess it's just hard to think that something (usually) green, (usually) fixed in place, & with no nerves or muscles is able to behave - but plants do, & some of their behaviour is really quite subtle. You're probably familiar with plant responses to stimuli, including tropisms, circadian rhythms, & flowering in response to changes in photoperiod. But there's more: not only are there plants that actively hunt, but plants can also communicate - with each other, & in some cases with animals as well.

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I've been blogging for 2 years now & following other people's blogs for rather longer than that. But I've only ever been aware of a few other NZ science bloggers; there's so much material out there that unless you go looking for something specific, an individual blog can get lost in all the 'noise'. But this is set to change next week, thanks to the Science Media Centre:

From the keyboards of scientists...

Are scientists blogging in New Zealand? They sure are - but it is relatively tricky to find them.

That will change on September 30 when the Science Media Centre launches Sciblogs.co.nz, a blogging network bringing together some of the best science blogs in the country and launching a good few new ones.

Sciblogs will kick off with 25 bloggers from universities, CRIs and private research institutions covering everything from healthcare to climate change. Our bloggers know their stuff - they have two dozen PhDs between them and they aren't afraid to tackle the big science-related issues affecting society.

Sciblogs will become an on-line hub for discussion of scientific topics and will grow to include other bloggers. if you would like to enquire about hosting a science blog on Sciblogs, contact the SMC.

Sciblogs will be live on Wednesday September 30 and you will be able to keep tabs on our Scibloggers via RSS, email updates and by following Sciblogs on Twitter.

I'm looking forward to this with considerable excitement - it has the potential to raise the profile of science blogging in this country & make a whole lot of good writing much more widely available.



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A fellow blogger drew my attention to a recent decision by the Broadcasting Standards Authority.  It seems that Dr Shaun Holt, a medical doctor who appears regularly on TV1's Breakfast show, has been slated by the BSA over some comments he made (several months back now) concerning chiropractic. The BSA found that the show - & by extension Dr Holt - had breached standards of accuracy, impartiality & objectiveness, & that the coverage was neither fair nor balanced.

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This week a very dear friend of mine is having surgery for bowel cancer, having already gone through a course of comibined chemo/radiotherapy in preparation. When I was talking with her last week, she commented that she wasn't looking forward to the operation, but the prospect of a few more years of reasonably comfortable life as a result of it was infinitely preferable to the alternative..

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You've probably gathered by now that I get quite irritated by the way that some news reports portray science. But it's not always easy to know what to look for, in terms of the tell-tale signs that let you know that all may not be as it first appears.

Fortunately the inestimable Ben Goldacre has just republished a guide on How to read stories about health and healthcare (this is a link to a pdf of the guide, written by Dr Alicia White) that applies equally well to other areas of science. I wish I'd read it before that Schol tutorial, as it would have made an excellent handout....

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I ran a Schol Bio tutorial out at the uni yesterday & the last exercise we did involved going over a question from last year's paper. This question looked at sickle-cell disease (SCD), which is seen in individuals who are homozygous for a recessive mutation - on chromosome 11 - that affects the haemoglobin molecule. The mutant molecule differs in just one amino acid from the normal one, but this is enough for it to have significant health effects. When red blood cells containing the mutant form of haemoglobin are placed in a low oxygen environment, then they collapse into a rigid, jagged, sickle shape that clogs capillaries. This in turn has a range of physical effects on organ systems throughout the body - this is an example of pleiotropy. Individuals affected by SCD usually die early, before they reach reproductive age. (People who are heterozygous have the less-severe sickle-cell trait.) Overall, sickle-cell is a Bad Thing for those who have it, so you'd expect that its frequency in a population would decline rather quickly. And yet - that's not the case, & in parts of the world (notably equatorial Africa, India, Asia & around the Mediterranean the frequency of the Hbs allele can reach 70%. (In comparison, its frequency is around 1% in the NZ population.) So what's going on?

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This post's about another of the papers a teacher sent to me recently, with the subject line 'science can be fun'. The title of this one is Parachute use to prevent death and major trauma related to gravitational challenge: systematic review of randomised controlled trials (Smith & Pell, 2003). I have to say that I chuckled when I read this - a common charge levelled agains current medical practice by the 'alternative health' lobby is that many medical techniques haven't been subjected to randomised controlled trials (with the corollary that it's thus unfair to demand evidence from such trials on alternative practices).

And indeed this strikes me as an article written with tongue firmly in cheek. The authors state that they conducted a literature search of some of the major science sources: Medline, Web of Science, the Cochrane Library, and various others, using the search words 'parachute' and 'trial'. However (& unsurprisingly), they found no randomised controlled trials (RCTs) of parachute use. Smith & Pell begin their discussion with the following inspired statement: It is a truth universally acknowledged that a medical intervention justified by observational data must be in want of verification through a randomised controlled trial. Many medical interventions probably fall into this category - for example, I doubt that surgery for severe appendicitis has ever been subjected to such a trial. That's not to say that, where appropriate (& in the case of appendicitis it almost certainly isn't!) such trials shouldn't be performed. As Smith & Pell point out, hormone therapy for post-menopausal women seemed - on thebasis of observational studies - to convey a number of health benefits. But RCTs showed that hormone replacement therapy actually increased the risk of ischaemic heart disease.

As the authors point out, RCTs avoid a major weakness of observational studies: that of bias (eg selection bias & reporting bias). They note that individuals jumping from aircraft without the help of a parachute are likely to have a high prevalence of pre-existing psychiatirci morbidity (ie they are probably not in their right minds when they jump. You have got to love this paper!). So any study of parachute use could well be subject to selection bias, in that those using them are likely to have fewer psychiatric problems than those who don't. Smith & Pell also put forward the possibiliy that enforced parachute use is simply a case of mass medicalisation of the population by out-of-control doctors - or worse, by evil multinational corporations :-) (These are, of course, charges frequently levelled at the medical world eg by those who are against interventions such as vaccination.)

This little gem of a paper (& I continued to chuckle as I read it) contains some valuable lessons on the nature of science (& more particularly, science-based medicine). And it should be read by anyone who doubts that scientists have both creativity and a good sense of humour.

G.S.S.Smith & J.P.Pell (2003) Parachute use to prevent death and major trauma related to gravitational challenge: systematic review of randomised controlled trials. British Medical Journal 327: 1459-1460.

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A couple of years ago now (before I got into this blogging thing, anyway) there was a brief flurry of media interest over a study that - according to various stories in the press - showed that the Maori population has a higher frequency of a 'warrior gene' & that this explained all sorts of negative behaviour. I thought at the time that the reports seemed overblown, but I didn't look into it further at the time. Now there's been another spurt of interest, with claims that new research has debunked the old. As it turns out - and is explained very well at The chicken or the egg - a) the original research never made these claims, so b) the original media reports were completely off the ball, & c) the 'new research' is not a scientific examination of the original data, so 'debunked' is hardly the term to use. The chicken or the egg gives an excellent explanation of this & also of the original genetics work & its findings, so well worth going over there to read it all :-)

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I was moved to wonder about this after seeing another article in today's Herald about ageing. Or, more particularly, about slowing/stopping the ageing process & thereby extending the period of our natural lifespan. Rapamycin got a look-in as well. And there was something about how the French manage to lead long & presumably healthy lives. (Having experienced my brother's creamy, rich cooking while staying with them last year, I have no idea how he & his family remain a) healthy & b) slim!)

On the global level, average life expectancy is around 66-67 years (depending on whose figures you use). Metropolitan France (excluding its various territories/protectorates around the world) is placed 9th or 10th in terms of life expectancy at birth (81 years - New Zealand, on 80, isn't that far behind). While 66 may not sound too flash, remember that a couple of hundred years ago life expectancies were even lower - we've come a long way in some parts of the world, thanks to modern medicine & other technological advances. But, given that some fortunate individuals do live much longer - 120 years or more - maybe there's something in the research by various groups into ways to further postpone the Grim Reaper's visit? (Like some other countries, the US even has a National Institute on Ageing, dealing in part with just this sort of research.)

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I do love the fact that there is always something new to learn. And often, to pass on to my students. Like the 'Lost City' - a surreal landscape of ghostly white towers that's formed around alkaline vents deep under the Atlantic Ocean. Now, I know about the 'black smokers' - fragile black towers belching superheated, chemical-rich waters into the icy ocean depths of the mid-Atlantic ridge, and the amazing biological communities associated with them. I talk about them in lectures, as (among other things) an example of ecosystems that don't rely on inputs from the sun to power their producers. And colleagues of mine have the privilege of regularly diving to study these pockets of life. But alkaline vents?

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I've been marking essays a lot of the day & there are still a fair few waiting for me to give them some attention, so this is going to be brief. But reading through them all has spurred me to make a couple of comments relevant to your Schol preparation.

One is something I've said before - read the question! It is so important to be clear on what the examiner is asking, and to focus on answering that. I've just had to give a couple of papers quite low marks. They were well-written; the students had made good use of diagrams to show what they were talking about; references were cited correctly; & so on. So what was wrong? They hadn't answered the question that I'd set.  Their essays made perfect sense & they obviously knew what they were talking about, but they hadn't addressed the question that I'd set.

And in some other cases, I've put lines through whole paragraphs & written 'irrelevant' next to them. Well, scribbled it, actually. (And the more frustrated I get, the scribblier my writing becomes. Even with a fountain pen. Which I use because it forces me to write legibly - most of the time...) In other words, these students haven't thought critically about the information available to them, in terms of what is relevant to their answer & what isn't. Comments on this sort of 'brain dumping' are a constant refrain in the Schol bio examiner's report. My students don't lose marks for this, not directly - but their essays have a word limit, & if this is partly taken up with irrelevant content, that leaves less space & words to cover the essentials. And of course, in the Schol exams (& in uni exams) you are up against a time limit, so putting in unnecessary bits & pieces is also chewing through the time available to you to complete the paper. And since the Schol examiner is looking for evidence of criitcal thinking, someone piling on the waffle is not doing themselves any favours.

Cutting a too-long story short is a learned skill, but it's one that will stand you in good stead. That, & paying careful attention to which story you are being asked to tell :-)

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I got an e-mail yesterday from a biology teacher (thanks, Ayelet!) with three pdfs & the subject line 'science can be fun after all!'. And the three attached papers definitely showed that :-) 'Excellent blog material,' I thought to myself...

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A comment on my post about human pheromones got me thinking a bit more about the topic :-) Just how much do we know about these signalling chemicals & our ability to detect them?

Many animals use scent as a basis for communication. Many female moths release a sexual pheromone that males can detect from a considerable distance (using their featherlike antennae), flying up the 'odour stream' in the air as they seek a mate. Cats & dogs use urine sprays to mark territories & also to communicate about their social status - my old dog used to react quite differently to different scent marks, getting hugely excited by some & carefully backing off & walking around others.  Bushbabies pee on their hands & then wipe urine on various surfaces (this, according to David Attenborough, is a black mark against otherwise adorable pets), while ring-tailed lemurs wipe pheromones from wrist glands onto their tails and then use these as scent wands during bouts of what are known as 'stink fights'.

Ring-tailed Lemur

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From time to time I've heard it said (by those in the creationist camp) that evolution has no relevance to modern medicine. Um... hello? antibiotic resistance in bacteria, anyone? And an understanding of evolution can also be put to good use in examining possibilities for new treatments, as ERV describes in her latest post.

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I've just finished reading The Science of Sherlock Holmes, an engaging little book that has the subtitle: from Baskerville Hall to the Valley of Fear, the real forensics behind the Great Detective's greatest cases. I'm a sucker for CSI, so when I saw that title in the library, I simply couldn't resist.

(At this point I should add that being a sucker for CSI extended only to the original program - & my interest waned when Grissom (William Andersen) left the series... And, despite my enjoyment of the series, I do feel that it's quite possibly done a real disservice to science. Those investigators get their DNA results in hours, rather than days or weeks, & they tend to see things in black & white, rather than shades of grey. And that's not because they work at night! Anyway, if jurors - say - get their information about forensic science from programs like this, then they could have quite unrealistic expectations of real forensic scientists when they are providing evidence for trials or acting as expert witnesses.)

I quite enjoyed the Sherlock Holmes stories when I was a kid, although I haven't read them recently. The plot-lines were ingenious & Holmes was a wonderful hero, complex & clever. & with an analytical, scientific mind. In this book, author E.J.Wagner takes a number of criminal cases over the last couple of hundred years & gives the reader the scientific back-story, interweaving this with quotes & examples from the Holmes stories to show not only how the eponymous detective applied scientific reasoning to his work, but also how he made the most of modern scientific discoveries in working out whodunnit. This includes such innovations as early scientific tests for blood, which would allow investigators to determine first of all whether they were dealing with blood at all (& not some other rusty stain on an item of clothing), then if it was human blood, & then - with the advent first of blood typing & then of DNA, just which human it might belong to.

Then there's the history of identifying individuals - by tattoos (which Cesare Lombroso firmly believed to be 'a sign of atavism, criminality, & insensitivity to pain'), fingerprints & photography. And the fine art of disguise, of which Holmes was apparently a master. And so on. I have to say, I enjoyed the book for its history as well as the science it contained. And the author's occasional flashes of dry humour just added to the enjoyment.

E.J. Wagner (2006) The Science of Sherlock Holmes. John Wiley & Sons Inc.

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Like other animals, humans produce pheromones - chemical signals released by one individual that carry information to another. (Unlike other animals, we also spend a lot of time & money modifiying those pheromones: bathing, deodorants, perfumes...) However, while the significance of pheromones in other animal taxa has been studied fairly thoroughly, there's been less scientific research into our own signalling chemicals, & in fact it's sometimes said that we can't detect them. So, some of the questions about human pheromones include: can we actually detect them? and, how do we react to these signals?

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I was in a schol bio tutorial the other day & one of the students asked a really intriguing question - one that I hadn't really thought about before. Apparently the class had watched the series Walking with cavemen a few weeks ago, & at some point (she couldn't remember which species it was) the narrator said that this particular species was the first to have whites to their eyes. The student said, I was wondering what the significance of that is.  Do you have any ideas?

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From one of those intra-office 'junk' e-mails:

I cnudolt blveiee taht I cluod aulaclty uesdnatnrd waht I was rdanieg. The phaonmneal pweor of the hmuan mnid! Aoccdrnig to rsceearh at Cmabrigde Uinervtisy, it deosn't mttaer in waht oredr the ltteers in a wrod are, the olny iprmoatnt tihng is taht the frist and lsat ltteer be in the rghit pclae. The rset can be a taotl mses and you can sitll raed it wouthit a porbelm. Tihs is bcuseae the huamn mnid deos not raed ervey lteter by istlef, but the wrod as a wlohe. Amzanig huh?

Well, yes, it is rather neat that I could read & understand all that. Rather hard to type though! (Even though I am one of thost people who types 'taht' for 'that' from time to time.) But what they're not telling you is that you still have to be able to read first! If you don't already know what each individual word is supposed to look like, your mind will see only nonsense in that paragraph. 

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September 1. Spring is (officially) sprung, the grass is riz, & the puppy is jumping all over the place. (In quite a different way from Bella - Ben gets up on his hind legs & prances. Must be a poodle thing.) But his arrival has rather upset the social order.

Having pets of two different species (the goldfish don't count here) sets the stage for the development of some interesting social hierarchies. The interspecies communication is good to watch as well.  When Bella joined us nearly 15 years ago, Milo was our only cat. Well, there was Possum, but he was old & gaga & didn't really notice the pup. Milo very soon taught our little lab that cats rule, OK? In fact, when things happened that Milo didn't like, such as him being groomed, when it was all over he'd go off quite deliberately to find & hit the dog!

So when the other cats came along, one by one, Bella already knew that dogs were at the bottom of the hierarchy. (Which went: Milo>Fidget>Merry=Ginger>Bella, in case you were wondering.) In any case, she adored kittens & was hugely protective of  them all. This didn't stop her wanting to play - & I was fascinated to see that the 'play bow' dogs use to signal this was understood by the cats as well. So we'd get these hilarious sessions where the dog chased a cat up the hall, & then at the end of the passage things were reversed & the cat chased the dog back down :-)

Milo's death upset the kitty hierarchy somewhat, although that's now settled down again, but it didn't alter their attitudes to Bella. Cats still ruled. But I'm afraid their noses are now well & truly out of joint. Ben doesn't really know how to deal with cats, I think, although he was certainly very cautious around the vet's cat, Patrick, this morning. But from the cats, it's a combination of peering suspiciously round corners, full-frontal fluffed-up back-arched threats on bumping into Ben in the garden (he whines & backs down, which is a good start), & giving us the complete cold shoulder.

Knowing how hierarchies develop, I'm confident it will all work out in the end. We may even see the cats stealing the dog's bed, just as they used to with the old girl... (Disclamer - neither of the two below is/was ours!)

lunch money.jpg

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  • Alison Campbell: Hi Nicole - apologies for the delay in posting your read more
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  • David Williams: Ruptured sinuses due to exposure to a series of rapidly read more
  • Nicole: On Renee's question: In a way, it may be true read more
  • herr doktor bimler: Worst horror movie EVAH. Mind you, there's a horror movie read more
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