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October 2008 Archives

This is totally off my usual topics, but I'm not really in the mood for a proper blog today - I've just got back from taking our oldest cat, Milo, on a one-way trip to our vet.

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I know from spending time with the Bio scholarship students at Hamilton Girls High that xenotransplantation is an issue that some of you might have discussed. It seems that ERV is also interested - not surprising given her focus on endogenous retroviruses. In her latest post, she says:

Why the hell was I interested in pig organs? Well, pigs can be genetically engineered to be almost perfect organ donors for humans that need transplants. Perfect... except for the fact pigs have PERVs like humans have HERVs. Read on... it's good stuff :-)

There are some excellent links here, & the item even has a New Zealand touch, because she's talking about research by Prof Bob Elliott & his team up at Auckland University.

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Here's a really interesting story that I picked up on while reading ERV's blog. We hear about 2-way symbioses/mutualisms (fungus+alga & fungus+cyanobacterium in lichens, & the mycorrhizal relationship between plants & fungi) - but here's something special: a three-way symbiosis between a fungus, a grass - & a virus (Marquez et al., 2008).

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I was just reading Charles Darwin's latest blogposts (it seems he's off to sea again - I hope he's over the seasickness that plagued him on his first Beagle voyage) & followed his 'science education' tag to this little gem: what everyone should know about science. What else do you think should be on the list?

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This topic's one that I use when I'm talking with year 10 students about critical thinking: ear candling. It involves the close approach of ears & candles. Hollow, burning candles.

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The Beagle Project aims to build a replica of HMS Beagle and retrace Darwin's famous voyage. The intention is that this will inspire global audiences through unique public engagement and learning programmes, and original scientific research in evolutionary biology, biodiversity and climate change. I think it's great! I've been keeping half an eye on the website, & recently had an e-mail discussion with a film maker who's following the project & was keen to hear about some of the evolutionary biology that's being done here at Waikato.

And now I see that the voyage will be tracked by the International Space Station. The idea is that scientists & students on the Beagle will work with astronauts on the Station, looking at a range of ecosystems that includes plankton blooms and coral reefs - most appropriate, given Darwin's own fascination with the development of coral reefs. As the press release says: Space stations, square riggers and marine biology: science does not get more exciting than this.

And I see that Charles himself approves :-)

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The question in question was about the proposed use of the herb pau d'arco as a prophylactic against MRSA: Evaluate the claims of the therapist, then use your biological knowledge to discuss the advice given. What are the possible evolutionary & ecological outcomes of the proposed treatment?

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I've just remembered (well, Ken reminded me) that today's the Earth's birthday. According, that is, to the chronology proposed by Archbishop James Ussher, way back in 1650. So, Happy Birthday, Earth!

Back in 2005 we celebrated this happy event with a Cafe Scientifque - we had a cake & everything. Of course, we also talked about the science involved in determining, as well as we can, the actual age of our planet. So this time round I thought I'd present some of that information here. (You can find the original version - written by Penny Cooke - in our Cafe Scientifique archives.)

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If you studied animal form & function in year 12, you may well have looked at gas exchange systems. Most first-year bio courses will build on that, & at Waikato we introduce a whole range: skin surface, external & internal gills, the tracheal system in insects, & lungs. Including bird lungs.

Now, bird lungs are cool - they're really rather small relative to the animal's size, tucked away at the front end of the body cavity. And they're quite unlike our own lungs in the way they operate. Ours work on a tidal flow system - but birds have a one-way flow that allows them to maximise their extraction of oxygen from the air that they breathe. And birds evolved from a lineage of dinosaurs - so what, if anything, can we infer about dinosaur lungs?

Quite a lot, it seems :-) I've just happened across a post by PZ Myers, on Pharyngula, in which he looks at this very question. While the lungs and their interconnecting air sacs wouldn't fossilise, nevertheless they leave evidence of their presence in the organism's bones. The post includes some excellent illustrations & the comments thread is also well worth a read, not least for the way that it shows how scientific arguments play out.

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We spend quite a bit of time on critical thinking during the Schol preparation days. This is because of the need - identified by the examiner's report every year - for candidates to think critically about both the question (just what is the examiner asking me to do?) and their response to it (what, of all the information I have at my fingertips, is relevant here?). I thought it might be good to revisit one of the exercises I use.

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I spent this morning over at the School of Education, talking with trainee secondary teachers and their lecturer about the curriculum & achievement standards & teaching evolution. Over lunch a couple of the staff continued with this, talking particularly about the fact that, whether we like it or not, the issue of evolution is seen as controversial by many students.

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A very quick one tonight (I've just got back from a Schol Bio session in Hawkes Bay & the brain's not up to much!) - PZ Myers has an excellent post critiquing a paper that suggested that human evolution could be affected by the increasing incidence of caesarian deliveries. This is an idea that's cropped up from time to time when I've been speaking in schools. You should go over to Pharyngula & read PZ's post; the comments & discussion are good too :-)

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A little while back I put up a brief post about Steve Jones' hypothesis that human evolution is slowing. At the time this proposal was on the receiving end of a fair bit of critical discussion on various science blogs.

Now here's an article by Benjamin Phelan, in Seed magazine, that suggests that the reverse is true - that human evolution is accelerating. (Not in the sense of large-scale morphological changes, but at the level of the genome.) It's quite a lengthy post, but really interesting & easy to read.

And this debate is an excellent example of how science proceeds - by people putting forward hypotheses & data & seeing them critically analysed by others.

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I first read Stephen Jay Gould's book, Wonderful Life, not long after it was first published in 1989. The book centres on the Burgess Shale, a wonderfully rich source of of different fossils (a Lagerstätte) from the Cambrian, around 530 million years ago. The Burgess Shale is unusual in that it contains an array of soft-bodied organisms, as well as those with shells and exoskeletons - & they are exquisitely preserved in 3-D detail. The book gives a sense of the excitement that scientists felt as they extracted these fossils from their rocky matrix and realised what they were dealing with.

Many of the Burgess Shale fossils are from arthropods - animals with a an exoskeleton & jointed legs. One of these is called Waptia - it looks vaguely like a shrimp. Now I see from PZ Myers, over on Pharyngula, that researchers studying the Chengjiang Lagerstätte, in China, have found some most unusual fossils of a Waptia-like creature - they're joined together, head to tail, like beads on a strange necklace. The paper's authors suggest that this may represent feeding behaviour, but this sounds a bit odd. As PZ says, the animals are joined nose-to-tail, so the last one in the chain is going to be getting a very unsavoury meal indeed!

waptia.jpg
(Click for larger image)

Waptia-like arthropod, Lower Cambrian, Haikou, Yunnan. (A) Individual with twisted abdomen, part of chain, Yunnan Key Laboratory for Palaeontology, YKLP 11020a. (B) Chain, about 20 individuals, various dorsoventral-lateral orientations, composite image (joined at cpt/p arrow), YKLP 11020a and YKLP 11020b. (C) Individual linked to carapace behind, lateral view, part of chain of nine individuals, YKLP 11021. (D) Isolated individual, subventral view, YKLP 11019. (E to G) Reconstruction shown in dorsal, ventral, and right lateral views, respectively. Scale bars in (A), (C), and (D) indicate 1 mm; in (B) and (E) to (G), 5 mm. b, s, and t indicate bent, stretched, and telescoped individuals, respectively; cpt, counterpart; f, facing direction; p, part; and tw, twisted. (from Pharyngula - original image is in Hou X-G, Siveter DJ, Aldridge RJ, Siveter DJ (2008) Collective Behavior in an Early Cambrian Arthropod. Science 322(5899):224.

 

 

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Takahe (Porphyrio hochstetteri) are one of the world's most endangered birds. There are only around 120 still surviving in Fiordland, although a few more now live on predator-free islands off the New Zealand coast. (If you go to Tiritiri Matangi Island in the Hauraki Gulf you'll be bound to see them.) But while the birds are intensively managed, there hasn't been a lot of research into their breeding systems. 

tiri - takahe.jpg

A takahe on Tiri

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One of the benefits of reading (& marking) students' essays is that  you find a whole pile of new papers that are worth reading. (I expect them to go to the scientific literature for information & examples, and support for their ideas, & I will confess to getting just a leetle tetchy when they don't....) Why is this a benefit, you ask? Well, it's just that there's so much new material being published in scientific journals all the time - it's next to impossible to keep up & this is one of the reasons that people tend to specialise. At least that way you can make a shot at keeping up to date in your own field! Most of the time I tend to see the same references, but now & then someone surprises me with something new & exciting. Like this paper...

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Well, yes, apparently they do - of a sort. ERV is a grad student studying retroviruses, and she's just put up a great post on genetic recombination in HIV. You learn something new every day :-)

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Cedric's suggested that I should collate all my answers to Wells' "10 questions to ask your biology teacher" all in one place. It hadn't even occurred to me, so - thanks, Cedric, & here you are :-)

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I thought it was time to check my readability once more - looks like I could slip in a few polysyllabics now & again :-)

blog readability test

 

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I was eating my muesli & idly flicking through the 'lifestyle' insert that comes with the morning paper when I happened on a page of ways to get oneself healthy for summer. Since at the moment my preparation for summer consists of walking the dog every morning & pedalling madly on the exercycle in the evening, I must confess that I wondered if there is a better way.

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The other day I mentioned I was reading Steve Jones' book, Coral. He's a good writer & I've enjoyed Coral, just as I've enjoyed most of his other books (although The single helix didn't quite work so well for me).

Anyway, yesterday a friend sent me a link to a report about a talk Jones had given - & it sounded really strange. Full of all sorts of assertions about how human evolution has stopped. I read it & thought, hang on, this all sounds a bit odd. I was going to write something on it when I got a chance, but now I see that PZ Myers has already done an excellent job over on Pharyngula (aided & abetted by his readers).

So read the two articles & weigh up their arguments - what do you think?

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I know I've said this before. And your teachers will have said it too. But - read the question!

Why am I saying this again? Because I'm marking essays at the moment & I seem to be writing that phrase rather more often than I'd like. When I set a question, whether it's for a test, an exam, or an assignment, I always try to delimit it - to write it in a way that outlines what direction I'm expecting the student to take, or the sorts of things that I'd like them to consider in an answer. (You've seen the same in L3 & Schol papers.)

So it saddens me when people don't take that on board, & go off at a tangent or include stuff that might well be interesting but is also irrelevant to the question at hand. In other words, if asked for examples from New Zealand, don't tell me about cases from Africa or Australia. If asked to discuss applications of today's technology, don't talk about the possibilities of future, untried technologies. And so on.

Don't get me wrong - I love it when students come up with novel, insightful, perceptive answers, things that I might not have anticipated myself. That's great, & I encourage it. But that insight & perception still has to be applied to the question that was asked. (If enough students go off the beaten track in their answer, that would suggest to me that I'd set a bad question in the first place. But that's a separate issue.)

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Last night I watched - & thoroughly enjoyed - the first episode in David Attenborough's series Life in cold blood. It was the first time I'd seen really good footage of chameleons hunting - their tongues are amazing! (& I hope that when I'm in my 80s I'm still finding life as much fun, & as exciting, as Attenborough obviously is!)

Anyway, the next in the series examines the evolution of amphibians & tetrapod colonisation of the land. This is something I've written on before (here & here, for example) & it looks set to be a fascinating 60 minutes of television. So - Sunday 12 October, 8.35pm on Prime - don't miss it :-)

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A couple of weeks ago one of the commenters on Ken Perrott's Open Parachute pointed me at a paper about blogging (& in fact Ken's already written about it). Shelley Batts & her colleagues have looked at the benefits of 'institutional' blogging - to the institution, the bloggers, and those reading the blog. I found it helpful & thought-provoking, & it sparked a conversation between me & some colleagues elsewhere on campus.

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Blogging on Peer-Reviewed ResearchFish with fingers, whales with legs - the sub-title of Carl Zimmer's 1998 book on the evolution of amphibians & whales - seems even more apt with the announcement of a new fossil find: a fish whose pectoral fins contained bones homologous to tetrapod fingers (Boisvert et al. 2008).

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A while ago my friend Heather, who's a biology teacher, asked if I would write something on answering questions in the 'processes & patterns of evolution' paper (AS90717). Here you are, Heather - I finally got around to it :-)

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In the last couple of days I seem to have accumulated a pile of lovely enticing books to read. (& I didn't even buy them - our wonderful science librarian sends new books through from time to time). I'm spoilt for choice, in fact. And I still haven't finished Microcosm!

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