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March 2010 Archives

This is another re-post from Talking Teaching. I know that whole interactive-engagement thing is becoming the norm in schools, but I thought it might be interesting (for teachers, in particular) to see some of the back-story :-)

After my lecture today one of the students said, "I like your lectures, they're interactive. You make me want to come to class."

I'm really rapt about this; I've worked hard over the last few years to make my lectures more interactive: creating an atmosphere where the students feel comfortable & confident about asking questions; where we can maybe begin a dialogue around the topic du jour; where we can spend a bit of time working around a concept. I guess this reflects my own teaching philosophy: I've never felt happy with the 'standard' model. (I can hear some of you saying, but what's that? I guess you could say, the stereotypical, teacher-focused model of lecture delivery.) Way back when I was a trainee secondary teacher, my then-HoD was very big on me talking & the kids writing; we had to agree to disagree... Anyway, as time's gone on my teaching's become more & more 'research-informed', in the sense that I've increasingly delved into the education literature & applied various bits & pieces to what I do in the classroom. Anyway, to cut what could become a very long story a bit shorter, there's good support for the interactive approach in the literature.

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The latest edition of Nature carries an item that raises the possibility of another new - & recent - new hominin species, this time from Siberia (Krasuse et al., 2010). A few years ago, when the story about Homo floresiensis first broke, I remember commenting to my classes that it was probably only a matter of time until another recent relative popped up. After all, all the evidence to date shows that our family tree is much bushier than scientists used to think - when I was in high school that tree was presented as essentially linear in nature. But Siberia?

My mother used to say (when asked by importunate students how old she was), 'I'm as old as my little finger & older than my teeth.' In the case of this possible new hominin, that would make her very old indeed. The new find consists of a finger bone - the tip of a pinky, in fact - and the mitochondrial DNA (mDNA) extracted from it. (For 'pinky' read 'distal manual phalanx of the fifth digit'...)

The bone was found in Denisova Cave, which is in the Altai mountains of Russia & which has been occupied (on & off) by hominins for around 125,000 years. The finger bone wsa found in a layer of sediment dated at 48-30,000 years ago, & which has also yielded a range of other artefacts. Krause & his team decided to see if they could extract & sequence mtDNA from the bone; they felt this was at least a possibility as the cool conditions in the cave are better for long-term preservation of DNA than the tropics. They expected that - if their extraction was successful - the bone would be from a Neandertal or a modern H.sapiens individual, on the basis of the tool assemblages from the site and the geographic range of both species.

Using 30mg of powdered finger bone (this sounds like something Macbeth's witches would have liked...), the research t3eam were able to extract & sequence mtDNA. They then made a section extract & compared the two sequences: they turned out to be identical. The team hen checked that their sequences came from a single individual (if one bone yielded evidence of more than individual, then there could be questions about contamination). It did.  The degradation patterns of all the mtDNA fragments were also typical of ancient, not modern DNA: further evidence that the sample was not contaminated.

The next step was to compare the mtDNA from the Denisova cave individual with sequences from  modern human mtDNA, a sample from an individual who lived in late-Pleaistcene Russia, Neandertal mtDNA, and sequences from a chimp and a bonobo. There must have been a certain amount of excitement in the lab when the results of this came out - becaue the Denisova hominin's DNA had nearly twice as many differences from modern DNA as that of Neandertals (385 base-pair differences for Denisova/sapiens compared to 202 for the Neandertal/sapiens comparison). 

This suggests that the most recent common mtDNA ancestor for modern humans, Neandertals, & the Denisova individual lived about a million years ago.There's a certain amount of uncertainty around the dates, but nonetheless this is a long time ago. Krause's team comment that  'the divergence of the Denisova mtDNA lineage on the order of one million years shows that it was distinct from the initial radiation of H.erectus that first left Africa 1.9 million yeers ago.'  Remember, though, that we really need DNA (ideally both mitochondrial & nuclear) from more complete skeletal remains before it's possible to 'place' the Denisova hominin with any degree of confidence.

Getting back to my original comment - it's entirely possible that multiple hominin lineages co-existed in this part of the world as recently as 40,000 years ago. If the Denisova individual is confirmed as a new species, then it would have had both Neandertal & anatomically-modern humans as close neighbours in space & time. The apparent temporal overlap of floresiensis and sapiens in Indonesia may not have been an isolated event, and our family tree will then be even bushier than my teachers ever imagined :-) 

Krause, J., Fu, Q., Good, J., Viola, B., Shunkov, M., Derevianko, A., & Pääbo, S. (2010). The complete mitochondrial DNA genome of an unknown hominin from southern Siberia Nature DOI: 10.1038/nature08976

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From time to time the 'debate' around vaccinations re-surfaces in the headlines. A number of other NZ bloggers have addressed this (here, & here, for example). It's a much hotter topic as in the US, where a number of high-profile 'anti-' groups keep vaccines in the public eye for all the wrong reasons. 

Don't get me wrong - I have an enormous amount of sympathy for people whose children have become ill some period of time after receiving a vaccine. But apparent correlations in time do not equate to causation, a fact that lies at the heart of this issue and makes me wonder how effective we are at communicating about the nature of science to the community at large.

This is a real concern. Following Andrew Wakefield's now thoroughly discredited claims about a link between the MMR vaccine and autism, vaccination rates in the UK dropped to the point that measles in particular is again widespread in some communities. And while it can be a 'trivial' illness in most children, measles carries a real risk of serious illness & in some cases death (a risk that is several orders of magnitude higher than the risk of severe adverse effects from the vaccination itself).

Anyway, a very recent Downfall parody takes aim at the US opponents of vaccination - most of the names mentioned in this clip are those of prominent players in this group. The 'Paul Thoresen' mentioned first up is a scientist associated with a couple of research groups who may or may not have been involved in a misappropriation of funds - whether or not this is true has absolutely no bearing on the quality of the research done by those groups, something that seems to have escaped the 'anti-' commenters.


PS readers might also be interested in this post at ScienceBased Medicine, which examines some of the 'vaccines don't work' claims.


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The Darwin Awards have been around for a few years now. They're given to those people who - by some act of breath-taking stupidity - have removed themselves from the gene pool. (Though you could argue that most of the recipients should be excluded due to age....)


 Humorous Pictures

The (definitely posthunous) winner of this year's awards:

When his .38-calibre revolver failed to fire at his intended victim during a hold-up in Long Beach, California, a would-be robber did something that can only inspire wonder. He peered down the barrel and tried the trigger again. This time it worked.



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I listen to quite a lot of podcasts. Lately I've been listening to more than usual. I've had the flu (I'm assuming that's what it was, since colds tend not to come with fever, chills, & sore joints) & listening to stuff was easier than reading. Anyway, I digress.

One of my current favourite podcasts is Brian Dunning's - excellent primers in critical thinking, nicely presented, & not too long. One of these concerned the 'Scole experiment' - supposedly an excercise in which scientists tested the claims of mediums (people claiming to communicate with the spirit world) and  - gasp! - found the claims justified. I've been interested in claims about the paranormal ever since reading (& re-reading, multiple times) Martin Gardner's book Science: good, bad & bogus.

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I suspect that for many of my first-year Biology students, the sheer weight of new terms they come across is perhaps the most daunting thing about the course. In some ways learning biology is rather like learning a new language - with several thousand new words swamping the page (& the brain) over the course of a 3-year degree.

But there's more than just the new words - there's the meaning of the words to come to terms with. This is the focus of Helen Quinn's 2007 paper, Belief and knowledge - a plea about language. There are many words where their meaning to a scientist may be quite different from what they mean to a lay person. Quinn feels, & I agree, that some words 'are the root of considerable public misunderstanding about science: belief, hypothesis, theory and knowledge.'

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Creationism is a recurring issue for teachers of biology. It can come in many forms (eg young-Earth creationism, old-Earth creationism, & so on) but - despite what many 'IDers' would say - its most recent incarnation is as intelligent Design 'theory', or IDT. (I use the quote marks advisedly; Intelligent Design doesn't offer any evidence that can be explained by a coherent scientific theory, instead preferring to generate a false dichotomy between IDT and evolution: if evolution is wrong about 'x', then IDT is correct.) While IDT received a resounding defeat in the Dover trial of 2005, it continues to be promoted around the world as a 'scientific' alternative to evolution.

Anyway, a colleague has just sent me Jim Mackenzie's paper, How biology teachers can respond to Intelligent Design, which I thought I'd talk about here. As Mackenzie says, a significant number of authors have already argued convincingly that IDT is bankrupt as far as scientific theories are concerned. He proposes several strategies that science teachers can use in dealing with attempts to introduce IDT into their classrooms, and comments that it's possible to use these with younger children. I think this is particularly useful given that the 2010 NZ science curriculum makes evolution an organising theme for biology (aka the 'Living World') from the earliest years of primary schooling. Mackenzie's strategies are drawn from a case dating back more than 20 years, from an attempt to mandate the teaching of creation 'science' - surely an oxymoron - in Arkansas schools. I found this a little surprising given the more recent Dover case, but then it is all creationism under the skin, despite attempts by various ID proponents to claim otherwise.

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I blog a fair bit about the way science stories are (mis)represented in the press. And when I do, I always wonder what the original press release (from the intitution to the media) would have been like. Now Ben Goldacre's posted an excellent item on one such release.

The release in question came from a UK pest control firm, & it contained 'data' that seemed to show alarmingly high levels of pest infestation on London public transport. (Or, in the case of dust mites, surprisingly low. Only 500 of these tiny critters in a whole railway carriage?) Things like cockroaches, bedbugs, fleas. (Apparently bedbugs are raising their nasty little heads in New Zealand - not something I'd want to see gain a significant foothold here!). Cue a number of rather hysterical media articles.

Ben has done his usual thorough job of investigating this one. And he found - that the company did no studies whatsoever of in-service public transport vehicles. None. Zero. Zilch. Their scary figures were based on a model, which made a whole lot of unsupported & highly unlikely assumptions. As Ben hasn't been able to track down the original release, we can't be certain of its contents. But I have to say - to pretend some sort of scientific support for the numbers sent out to the media is to misrepresent what was done as good science. And that does none of us any favours.


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This is a re-post of something I've written for Talking Teaching. I've reproduced it here because I think the notion of teaching things like critical thinking & the nature of science are just as relevant here as they are in a discussion about teaching itself.

I've just been reading a post by Tim Kreider, over at Science-Based Medicine. Tim's talking about the learning experiences of medical students, but a particular phrase caught my eye. I''m reproducing it here because I think it can be applied much more widely: students are in the habit of transcribing and commiting to memory everything uttered by the professors who grade them.

I've seen this happen myself. I remember talking with a class about fungi & saying that while most fungi are saprophytes (consuming dead material), some are predatory. And they all (well, all those I could see, anyway) wrote this down unquestioningly. 'Hang on a minute,' I said; 'does this sound likely to you?' They agreed that no, it didn't really, it didn't match with what they already knew about fungi. 'Well then,' I said; 'why didn't any of you call me on it?' 'Because,' they said, 'you wouldn't tell us anything incorrect, would you?' Which showed a touching faith but also a worrying lack of willingness to question things that didn't sound right.

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My first-year students & I are currently studying plants. This is actually something of a balancing act from my perspective as a reasonably large proportion of the class didn't study the 'diversity in plant structure & function' standard back in year 12 (or don't remember doing so), so I've got to bring them up to speed without boring the others.

Anyway, when we get on to talking about flowering plants, one of the topics is adaptations for pollination. Some flowering plants (eg grasses) simply shed their pollen to the wind, but for many successful pollination has required the establishment of a plant-animal relationship. And some of those involve some very kinky activity indeed - the animal 'vector' comes to a flower, not for a nectar reward, but because in its eyes the flower looks like a member of the opposite sex...

And thanks to PZ, who always finds these things first!

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This is a very relevant question in the light of the government's recent announcement of its intention to tie a proportion of tertiary funding to student completion and retention rates. (This decision is presumably driven, among other things, by relatively low rates of retention and passing papers/courses, which lead to questions about whether we're getting value for money from our tertiary system.) Speaking personally, I find this a rather blunt instrument for rewarding performance as at least some of the factors affecting this are beyond the institutions' control (e.g. Zepke et al. 2005). There's quite a lot of literature around dealing with the whole issue of student retention, but I thought I'd be self-indulgent for once & discuss a study done here, examining the factors affecting completion & retention of students in science & engineering (Otrel-Cass et al., 2009).

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Found this today (while procrastinating...)

funny graphs and charts

Now, while the cartoon is funny, the message is not (& hopefully some of my first-year students are reading this - pay attention, guys!). Leaving an assignment to the last minute is not a good strategy for success - not in science, & not in any other area either.

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This is really an advertorial, I guess :-) But Marcus, Fabiana & I have got together to set up a blog for talking about teaching, called - fairly predictably I guess! - Talking Teaching. So for those of my readers who are teachers (secondary, tertiary, whatever) - please feel free to join us there. We're hoping to get some interesting discussions going, & maybe some sort of on-line teaching community. To give you a bit of background, so you can see where we're coming from - I've got a Trained Teacher Certificate (which has since been eclipsed by the Dip.Tching I think) & both Marcus & Fabiana are working towards a tertiary teaching qualification, & we're all university lecturers. And science bloggers as well :-)

So maybe we'll see you there some time soon?

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The last 65 million years have sometimes been called 'the Age of Mammals' (although I'm inclined to think it should be the Age of Insects, or perhaps - as it's always been - the Age of Bacteria; after all, in terms of sheer number of individuals, bacteria have got to be the dominant life form on the planet...). This gives the impression that mammals are a relatively recent evolutionary novelty.  But just how old is this class of organisms? Just what is the 'age' of the mammals?

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Over the last few months many science bloggers have been watching - with considerable interest - a libel case taken agains science writer Simon Singh by the British Chiropractic Association. Singh had used the word 'bogus' in describing treatments offered for a range of ailments, including asthma and ear infections. (Similar claims-by-implication are made in NZ.) While the UK's libel laws allowed the case to proceed (it's still before the courts), Singh's view is supported by a number of meta-analyses of availble good-quality studies: for conditions other than musculoskeletal pain (eg asthma, & a range of childhood conditions)  such treatments perform no better than placebo .

Now it seems that the case appears to have sparked somethng of a backlash in the UK, with chiropractors advised by their professional body to remove from their websites & other publicity material any claims of the ability to treat conditions such as whiplash and colic. This is interesting given that the BCA had previously released what it described as a 'plethora' of evidence supporting those claims. However, as Edzard Ernst has noted, of the 19 references included in that list, it seems that 4 didn't even contain data relating to chiropractic treatment. A further 8 are not based on controlled clinical trials, and the remaining 7 are flawed in methodology or conclusion - for example, a lack of double-blinding that doesn't allow us to rule out the placebo effect, in a comparison of chiropractic vs an anti-colic drug.  (Ernst also points out that several robust, rigorous trials of chiropractic interventions, that don't show any effect better than placebo, aren't included in the BCA list.)

If the BCA is now advising that claims concerning ailments other than back pain should not be made, where to next for the case against Singh?

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While searching for some background on another post, I happened across this headline on the Herald site: University denies author's PhD claim. I went on to read the story, as it's always a bit of a concern to see people claiming credentials and the supposed awarding institution denying that this is the case. And a statement from the person making the claims caught my eye.

"During a period in which 'evolution' became a bad word [in New Zealand] punishable by revocation of credentials and confiscation of property [the 1980's], I refused an order from a department chairman to withdraw my books Darwin's Universe and Time Gate from press," he told a contemporary writers' website.

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