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December 2008 Archives

Blogging on Peer-Reviewed ResearchMany year 13 Biology students will spend some time during the school year on a plant or animal study. Often the organisms you'll study will be something like slaters, or duckweed, because they are easy to keep & study in the classroom. But that's not always the case, & today I thought I'd write about one such study that was done on a different animal. Let me introduce you to...

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Insects and humans (& in fact all other animals with eyes) use the same visual pigment - rhodopsin. But in other ways, insect & mammal eyes are fundamentally different. The insect eye is a compound eye that comprises many individual units, while ours is a camera-type eye. And these structural differences have a considerable impact on just how the owners of those eyes perceive their world.

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Thankfully, the antivaccination lobby is (so far!) relatively small & quiet in New Zealand. It's another story in the US, where various celebrities lend their names to the anti- voices. A couple of days ago Orac posted another in his series on what's wrong with the US anti-vax groupings, & I thought I'd talk about some of the issues he highlights - they need to be made here too.

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When I did a plasma donation the other day, the blood-bank people put a note on my file so that the plasma would be fractionated & treated as necessary to prevent any recipients from getting malaria. (Not that I"ve got malaria!) This was because I'd just got back from Vanuatu, and malaria is relatively common on the outlying islands there, so you're advised to take anti-malarial drugs as a prophylactic measure (a preventative) if you're travelling in the region. (We didn't, because we were going only to the main island, & the resorts tend to have a fairly vigorous mosquito-control program. We never saw a mozzie while we were there.)

Now there's news (Enserink, 2008) that the malarial parasite, Plasmodium, is showing signs of developing resistance to the most commonly-used anti-malarial therapies - an example of evolution in action. Scientists working on the Thai-Cambodian border have found that these drugs, called artemesinins, are not clearing the parasites from patients' blood as quickly as they used to: a sign that the parasite is becoming tolerant of the drugs.

This isn't a new development, in the sense that artemesinins are only the latest anti-malarial drugs in our armoury. But evolution in Plasmodium has previously rendered all our earlier drugs useless (and again, this resistance evolved in the Thailand/Cambodia region before spreading round the world).

And why is this? One posible explanation is that people in that region either aren't getting the right drugs at the right doses, or they're getting fake drugs that aren't as effective as the real thing. In either case, this would mean that in these patients Plasmodium is being subjected to strong selection pressures, with the outcome an increase in resistance to the drugs. From there, it seems likely that travellers & migrants have taken their resistant parasites with them to other parts of South-East Asia, & thence to other continents. Not so good for us, but a real advantage for Plasmodium.

M. Enserink (2008) Signs of drug resistance rattle experts, trigger bold plan. Science 322: 1776

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Happy Holidays, have a great New Year -

- & may your days be filled with interesting things :-)



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Why is it important for people (scientists, journalists, science communicators, every woman & her dog) to talk about science? Does it really matter if NZ primary school students think science isn't fun, if secondary students seem to be showing less interest in the sciences, or if fewer & fewer students major in physics at university? As science writer Natalie Angier says (& I hasten to add that she's playing devil's advocate here!)

Does it matter if the great majority of people know little or nothing about science or the scientific mindset? If the average Joe or Sophie doesn't know the name of the closest star (the sun), or whether tomatoes have genes (they do), or why your hand can't go through a tabletop (because the electrons in each repel each other), what difference does it make?

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You learn something new every day.

One of the big talking points in palaeontology is the 'Cambrian explosion' - the seemingly rapid appearance (over 'just' a few million years!) of complex animal life, which occurred around 490-540 million years ago. Discussion ranges over the causes of this diversification and whether the apparent 'explosion' really happened at all.

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... it probably is.

The latest example of this comes from a newspaper story, wherein a visiting professor (I can't remember what he was a professor of) was expounding on what the world would be like in 2070. Among other predictions, he felt we'd have dishwashers that cleaned the dishes without detergent, water - or energy.

The dog pricked up her ears when I read this out - she rather fancies herself as a detergent-&-water-free dishwasher, & regrets that opportunities are far & few between. But hopefully your critical thinking faculties have also engaged.

Detergent-free, water-free - OK; maybe it's technically possible to do this using something like ultrasound, for example. Marcus might be able to explain whether that's possible. But energy-free? Sorry, but cleaning the dishes (however it's done) is going to involve work (whether by dog, man or machine), & that in turn takes energy. We could probably be rather more efficient in how that energy's used, but that's another story...

(Although, I suppose... you could always put the dishes in with some dermestid beetles... but no, the turnaround time would probably be too long for that one to really catch on! And besides, the dermestids don't like fresh food - they're late-stage decomposers & they like their meat fairly whiffy)

I think this one really was too good to be true.

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It seems the silly season is beginning early - I'm expecting a rash of 'letters to the editor' as the 200th anniversary of Darwin's birth gets closer (what are you doing for Darwin Day?), but this seems a little premature. The writer begins:

We've weathered a fair few scientific broadcasts lately authenticating Charles Darwin's findings. Effectively they explain how all life is the handiwork of animated primitive cells that inadvertently regrouped as butterflies, flowers, elephants, etcetera, which apparently proves there's no God and we should abandon that idea.

Hmmm, where shall I start?

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Blogging on Peer-Reviewed Research I've always been interested in dinosaurs, & I loved Jurassic Park. Especially the raptors - they reminded me of birds in many ways. Which makes sense, of course, given that the majority consensus is that birds evolved from maniraptor dinosaurs :-) Anyway, all this means that dino headlines are always going to make me look twice. As I did at an item in today's Royal Society news feed: the earliest known dromaeosaur from South America.

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Eyes seem to be flavour of the month at the moment :-) PZ has just put up a fascinating post - about using MRI technology to see the images forming in the visual cortex of volunteers as they look at pictures of letters of the alphabet.

Truly. But he points out that it's not like Big Brother will be using this technique to read your mind any time soon. For a start, it takes a fair bit of time, partly because the volunteers had to stare fixedly at the pictures for 12 seconds - that's a very long time to keep your eyes fixed on a single point. (Normally your eyes are constantly in motion, even if you're not aware of it.)

Anyway, go over there & read the whole thing. When I first saw it, it reminded me of the old (& I thought rather creepy) idea that the last thing someone saw as they died was imprinted on their retina. So if someone was murdered while looking the bad guy in the face, you had only to find some way of visualising that image & bingo! you had your man. Or woman. In one case this led to quite a lot of frogs (I think, from memory) dying rather abrupt deaths so that the researcher could 'develop' the retinal image. Think what he could have done with MRI!

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Blogging on Peer-Reviewed Research Time for look at another paper. This one's on something I think I referred to earlier - the use of ancient DNA to determine the sex of New Zealand's giant, flightless - & alas! extinct - moa.

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A headline in SciTechDaily caught my eye: If I'm not gullible and you're not gullible, how come some improbable stories take a long time to die? This reminded me of a comment by Ben Goldacre, along the lines that people aren't as good at assessing their own abilities (whether related to driving a car or passing an exam) as they'd like to think.

But the link took me instead to a story that ran in one of the Saturday papers last weekend - why some rumours have such a long shelf life. And this is itself an interesting look at the way our minds work, & why it's sometimes easier than you'd think to fool many of the people quite often, really.

It seems that we're more inclined to accept stories as factual if they:

  • play on our emotions and anxieties;
  • fit with our pre-existing biases, even if the story sounds a little odd or unusual (if you have experience of someone saying something a bit dopey, you'll be predisposed to believe something outlandish attributed to them by a third person);
  • appeal to people who are easily swayed by a story (apparently, a playground rumour about the explosive potential of a sherbert sweet combined with cola almost destroyed a confectionary product);
  • are heard so often that there just might be a grain of truth in them;
  • reflect what's currently on people's minds;
  • are simple, and sound 'real' (not abstract); are hard to disprove (look at the longevity of the Loch Ness monster story, for example);
  • and - if they reflect badly on individuals that we envy (something of the tall poppy syndrome in that one!).

And - if it sounds too good to be true, it probably is!

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I've written before about the evolution of the eye (here & here for example. Now there's a whole issue of the most excellent science education journal Evolution: education & outreach devoted to this very topic - & it's free on-line right here! So if you're interested in following up on some of the latest work on this topic, do follow the link & download what interests you. I've got several articles to read & think about at my leisure (bwahahaha - leisure!) & might write about one or two here.

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Well, it wasn't all lying around by the infinity pool while we were away in Vanuatu - although I must say, doing that was very pleasant... (& contrary to appearances, we had very little rain.)

infinity pool.JPG

But one of the attractions of going somewhere different is that there is so much new stuff to see and do. And given that we're both biologists, seeing some of the local wildlife was fairly high on the agenda...

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A little while ago now I wrote about the creationist take on a recent paper looking at chimp/human genetics - more specifically, copy-number variations in particular gene sequences. I intended to read the original paper & blog about it, because the Sensuous Curmudgeon made it sound so interesting. So you may imagine that I was just a tad annoyed to find that my institution doesn't have a subscription to that particular journal. (Not really surprising - there are an awful lot of journals out there & no one institution can possibly subscribe to the whole lot.)

But today I was pleasantly surprised to see that PZ Myers has done his usual good job on just that paper, over at Pharyngula. Thus both educating me & saving my bacon - pop across & read it :-)

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This post's based on another news item to do with postponing ageing (it sort of follows on quite well from that recent one about telomerase). There seems to be a bit of a run on this in the media - or maybe it's just because I'm getting older & more sensitive to this stuff?

It's an item in this morning's Herald: a US story on the rather extreme lengths that some people will go to in an attempt to postpone the ageing process. There's an eyecatching photo (well, actually, there's a before & an after photo) of a chap who's 69 years old but has the physique of someone decades younger. He runs a clinic that is described as specialising in 'age management' - promoting a regime that supposedly keeps you younger for longer. He's achieved this, and claims that his clients can too, by making significant changes in diet, exercising hard, and - most extreme - having daily injections of human growth hormone. (To me, this is over the top. Human growth hormone has its uses in treating children with extremely short stature - not just 'below average' either! After all, a reasonable proportion of the population is going to fall below the mean. And there are other clinical applications, some more controversial than others. But its use in clinically normal adults seems unjustifiable, & in fact use of human growth hormone in this way is banned in the US. But - not if it's prescribed for 'hormone deficiency'.)

Why am I writing this? Because I think the story raises some interesting ethical issues, which you might like to think about & which I'd like to have seen the paper give some consideration to as well. For starters, there's that (mis)use of human growth hormone. (I have absolutely no problem with the messages about exercise & healthy eating habits.) And aside from this ethical issue, what are the long-term effects, & side-effects of the treatment? The answer is, we don't actually know. And since it doesn't sound like there are any controlled studies being done, we're extremely unlikely to find out. (I see from a PubMed search that a 2007 study found that while treatment of elderly patients with HGH saw increases in weight & muscle mass, it had no impact on fitness, & did have several negative side effects. This hasn't stopped people making all sorts of wild claims for the benefits of HGH - you have only to do a google search to see that!)

Next, one I touched on in that earlier post - is it really a good thing to have a proportion of the population living even longer (if in fact this treatment lets you do that, rather than resulting in better health in old age but with no significant extension of life)? After all, humanity already places a significant and increasing burden on Earth's ecosystems - should we add to it? And this 'advance' is not going to be for everybody - those in the Western world, with an already high ecological footprint, are, I suspect, most likely to the beneficiaries of this particular innovation. If they can afford it.

And, what is it with this constant medicalisation of everything to do with our lives? "Going bald? Going through menopause? Don't worry, a pill will fix it." Please don't get me wrong - I'm not trying to trivialise the impact of, say, menopause on the women going through it. I'm at the age where I know what it's like at first-hand! But it's a normal part of life. This overemphasis on medicalising such normal life events runs the risk of people feeling that anything that ails them can - & should - be fixed by taking a nice little pill. At a price. Is that really healthy? Or desirable?


[PS to be fair, the paper does look briefly at this last point. But the overall tone of the article is extremely favourable.]

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I'm back. Yes, it was a great holiday - & no - it wasn't long enough :-) And yes, I did spend a lot of time lying around under an umbrella by the water, reading books & generally applying myself to relaxing.

Anyway, one of those books was Ben Goldacre's Bad Science, which follows on from his blog of the same name. If anyone's looking for a book which covers basic scientific principles, illustrates the nature of science, shoots down pseudoscience, & shows why science is so important - all in a lovely down-to-earth & entertaining way - then this should be at the top of your list. I'd recommend it not only as excellent reading for all interested people, but also as a great classroom resource. 

Need more convincing? Then read on...

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Completely off-topic but I had to share this one :-) It's another bread recipe - I had a day's leave before we left on this trip (I might share some photos if I can work them into a story somehow) & spent part of the morning trying out that bread book again (Ingram & Shapter, 2007). This time: Mallorcan ensaimadas...

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(Another little something I prepared earlier...)

Our daughter's just drawn my attention to a brief item in the Listener's Health page. It reports on claims by Spanish researchers that increasing the amount of telomerase in the body could result in less cell death - &, by extension, longer lives. (Telomerase is the enzyme that repairs the telomeres at the ends of chromosomes. Without it, telomeres get shorter each time a cell - & its chromosome - divides.) Sounds good, doesn't it? I mean, it would be good if we could live longer, wouldn't it?

Now, I'm not entirely sure I want to live longer - I have a sneaking suspicion boredom would set in at some point, & besides, there are  more than enough people on the planet already without us all living longer & consuming more resources/producing more wastes. (Mind you, it wouldn't be everybody, would it? More likely to be only those who could afford whatever treatment was necessary.) But there are a couple of other issues to consider as well.

First up - the claim is based on work done on genetically engineered mice, & mice are not always the best model for what will happen in humans. (We've seen this before - in the 1970s the FDA banned the use of the artificial sweetener, saccharin, because it caused bladder cancer in rats. But more work showed that it didn't have this effect in other test species, only in rats - & only in male rats. The ban was later removed.)

And secondly - there is already a class of cells which are to all intents & purposes immortal. Cancerous cells. Given the terrible damage that they can do, I'm not so sure that I would be keen to see the amount of telomerase in normal cells increased. (& it would have been interesting to hear more about those Spanish mice - what was the incidence of various cancers, compared to a non-GE group?)

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A while ago now I wrote something on the Dmanisi fossils - the remains of a few individuals that suggest that Homo erectus spread relatively quickly through Eurasia after leaving Africa. I've just come across an interesting post on the Panda's Thumb that I thought makes a good follow-up. Read it & see what you think.

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Just letting you know that I won't be monitoring the blog for the next few days - my Significant Other & I will be spending 4 days on a desert island. Well, an island. A tropical island. Where there may not be net access & even if there is, using it could prove to be a divorcing matter ;-) If posts magically appear during this time, it is because there was a last minute-rush on my part to schedule a few in advance...

Anyway, the point is that any comments you write won't be approved until I get back. So please be patient - & don't think I'm ignoring you!

ideal beach view.JPG

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For those interested in physics, my friend Marcus Wilson has recently started a blog on the subject: Physics Stop. Luging, the Large Hadron Collider, Star Trek transporter beams - all this & more. And his door's always open to visitors :-)

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I've just finished chairing the examiners' meeting that finalises grades for students in our School. (For those who might think that uni lecturers have nothing to do once the students have left - forgeddit! This is the time when we: finish exam-related admin, work with grad students, prepare for next year's teaching, write papers, do a bit of research... But I digress.) This was a new role for me & the several days' preparation for the meeting left me feeling a bit like this:

tired from work.jpg


So before the meeting I did what I suspect many do in this position - stocked up on 'V' & other commercial caffeine sources & made a pot of tea. (Green tea. Jasmine dragon pearl tea, actually - lovely stuff.) Only to be to told by my science colleagues that: this one contains ammoniated caramel (see if you can guess which product that's in!) & that's a neurotoxin, while that one will see me taking something for acid reflux in next to no time.

Am I worried? Not particularly. Because I'm pretty sure that, like many other things, the dose is what's important. Water, for example - you have to have it, but drink too much of it & you'll be a very sad (& possibly dead) puppy. Or vitamins - vitamin A's an essential part of your diet, but take it in megadoses (eg by eating carnivore liver...) & you'll discover the unpleasant effects of hypervitaminosis A.

So - I'll continue with the commercial stuff in moderation. And I certainly won't be giving up my nice pot of tea any time soon!

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A while back Ken gave a link to wordle, a rather neat site where you can build a word image for a piece of text or the content of a web page. I've just revisited and got a wordle for the last few posts here:

people do science 2.png


like wordle :-)

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Blogging on Peer-Reviewed ResearchTiktaalik roseae is a lovely example of a transitional fossil - it has a number of morphological features that clearly place it on the 'fish-to-tetrapod' transition.  The type specimen is a remarkably well-preserved fossil that's been very carefully analysed. A recent paper by Jason Downs & his co-workers described the results of their examination of the fossil's cranium (Downs et al. 2008).

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Or, one reason why teaching is good for teachers.

I've just got to the point in Richard Feynman's autobiography where he's talking about why he loves teaching. It really resonates with me & I thought I'd share this bit with you:

If you're teaching a class, you can think about the elementary thgns that you know very well. These things are kind of fun and delightful. It doesn't do any harm to think them over again. Is there a better way to present them? Are there any new problems associated with them? The elementary things are easy to think about: if you can't think of a new thought, no harm done; what you thought about it before is good enough for the class. If you do think of something new, you're rather pleased that you have a new way of looking at it.

The questions of the stduents are often the source of new research. They often ask profound questions that I've thought about at times and then given up on so to speak, for a while. It wouldn't do me any harm to think about them again and see if I can go any further now. The students may not be able to see the thing I want to answer, or the subtleties I want to think about, but they remind me of a  problem by asking questions in the neighbourhood of that problem. It's not easy to remind yourself of these things.

In a good classroom, everyone's learning.

R. Feynman (1985) Surely you're joking, Mr Feynman! Norton.

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