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Archive April 2010

theorists of the lost ark Alison Campbell Apr 28

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 From today’s Royal Society compendium of science-related headlines comes this newsflash:

Evangelists claim Noah’s Ark discovery on Turkish mountain: Archaeologists have recovered 4,800-year-old pieces of wood from a structure 4,000 metres up Mount Ararat.
Well. Claims like this crop up fairly regularly, & then disappear without trace. And I have to say, I’m rather underwhelmed by this one, as well. Not least by the nature of the evidence.
 
For example, you can find pictures from the expedition on-line (& thanks to PZ for the link) – it’s news to me that the Ark had stone steps and squared-off stone walls, for example… That & the wooden structures shown suggest to my untutored eye that we’re looking at the remains of a land-based settlement rather than a floating bestiary. It’s also intriguing that carbon-dating data are being claimed as evidence for the veracity of this interpretation, given the way in which many creationists reject any form of radioisotope dating mechanism as inherently flawed. There’s a contradication there somewhere.
 
And – the supposed ‘Ark’ in the images looks awfully like a mountain ridge with an oval drawn round it. Outlines like that do a lot to help the eye ‘see’ something that isn’t there; something to do with the fact that we are pattern-seeking animals. (This also explains why some people see the ‘man in the moon’, and a giant ‘face’ on Mars.) Nup. Not convinced.
 
(If it is the Ark, shouldn’t it contain an awful lot of, well, sub-fossil poo? A ship full of animals would generate an awful lot of organic waste over the duration of the voyage…)
 

think before you write (or at least, before you hand it in) Alison Campbell Apr 26

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I’ve spent a lot of time lately marking essays from my first-year students. For many of them, this may be the first essay they’ve written in a while, & along with getting their heads around the essay-writing process, they’ve also got to come to terms with the academic environment that they’re working in. That means: making sure that they research the topic; read reasonably widely around the question they’ve chosen to work on (I always give a choice); make sure that as they write they cite the sources that they’ve used; include a properly-formatted References section; choose good-quality sources of information, & so on & so forth.

All that is probably a fairly daunting task if you’re new to the game, so I try to give as much guidance & direction as possible. There’s an outline of some of the key ideas i’ll be looking for, for example. And we give a lot of instruction, in the Study Guide & in tutorials, on things like references, proper citations, how to paraphrase, together with the really basic stuff like double-spacing, wide left-hand margins (for marker’s comments)…

Now, if you’re given that sort of support, use it! Follow instructions! I have lost count of the number of times I’ve written ‘please follow instructions’ on these essays, but overall far too many people have lost marks that they didn’t need to…

But going beyond that, it’s also necessary to think carefully & critically about the question & how you’re intending to answer it – the meaty stuff, that goes beyond issues of presentation. If you’ve been following this blog for a while, & you’re preparing for Scholarship Biology at the end of the year, you might remember me saying that a common problem for schol candidates is a tendency to do a ‘brain dump’: to write down anything and everything that might seem remotely relevant to the topic. This doesn’t do you any favours, because it does rather suggest that you haven’t thought your answer through – and skills such as critical thinking & the ability to integrate information into a coherent whole are some of the attributes that the examiner is looking for in successful candidates.

To take one of my essay topics as an example (I’ll blog about the science itself later on, cos it’s really very cool and interesting stuff): the question was based on a research paper looking at the relationship between a species of marine crustacean called Santia and the algae that grow on the animal’s exoskeleton. I asked my students to explain the nature fo the relationship and to discuss its advantages and disadvantages to the organisms involved.

Now, the relationship is essentially a symbiosis (where 2 different species live in close contact for part or all of their life cycles) or, more specifically, a mutualism, because there are advantages to both species. So the first thing I’m looking for is some definitions, and an explanation of why it’s a mutualism. But you wouldn’t include a whole lot of stuff on endosymbiosis & the origins of mitochondria & chloroplasts, for example, because that’s not relevant to the question in the form I set. (I could have asked my students to place the Santia/algal relationship in the wider context of the evolution of symbioses, but that would be a whole different ballgame.)

Similarly, once you got into discussing the advantages/disadvantages, you should be focusing on the two organisms involved in this particular example. Yes, there are a lot of other symbioses around, and perhaps fewer mutualistic relationships, but I don’t want to hear about those in a lot of detail. What you could do is point out that the whole symbiosis-mutualism thing isn’t actually all that clear-cut, and whereSantia & its carapace-dwelling algae fit on the spectrum.

But you might well include material on what closely-related species do, because the relationship we’re talking about is unique. How do other species of isopods & algae get by? What sets Santia apart? Attention to that sort of detail turns an otherwise OK essay into a very good one.

But it does require careful thought :-) So take the time to do that (yes, even in the pressure-filled context of a Scholarship exam!); it’ll repay you in the end.

chemo vs cancer, science vs disease Alison Campbell Apr 24

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In another few weeks it’ll be 27 years since my mother died of metastatic breast cancer. Not a nice way to go – but eased by a very caring family GP and the wonderful people at the local hospice, who helped her die with dignity at home.

I was reminded of this by reading David Gorski’s recent post on Science-Based Medicine: chemotherapy vs death from cancer. In the US at least (although I suspect here as well), ‘alternative practitioners’ offer a wide range of ‘therapies’ for people with cancer, claiming ‘natural cures’ & the option of ‘dying healthy’ if you must die at all. Unfortunately for those choosing this option, modern chemotherapy really is the best treatment option for many cancers (alongside radiotherapy & surgery, depending on how the disease manifests itself). If those alternative therapies worked they’d have become part of the mainstream pharmacopaeia by now. Dr Gorski agrees that yes, chemo can be quite brutal in its effects – but the cancers it is aimed at are at least as bad. (The reason chemo can have serious side effects is that it’s a fine line between killing the cancerous cells & killing normal tissues.)

Anyway, Dr Gorski’s article led me to think about the way that other proponents of ‘alternative therapies’ make special claims for their own products, and level all sorts of accusations against mainstream medicine. Over on SciBlogs, for example, a local anti-vaccination advocate was quoted in the comments thread for an article on vaccination that the sooner New Zealand drops all vaccinations, the better. In support of their views that vaccinations are Bad, Bad, Bad, the commenters on that thread trotted out all the usual claims: that vaccines cause autism (false – there are no data to support this claim); that vaccines contain ‘neurotoxic’ materials including formaldehyde (true, but our bodies make far more of this, during normal metabolic processes, than is contained in any dose of a vaccine); that vaccines contain ‘aborted foetal tissues’ & ‘monkey kidneys’ (serious scare tactics, these, & also false). These claims have been ably addressed elsewhere, both on SciBlogs & on overseas sites such as Science-Based Medicine & Orac’s Respectful Insolence.

But I wonder - do the people advocating a complete cessation of vaccination really seriously think about the consequences of this? My mother contracted polio as a teenager in the 1930s. She was lucky – the virus ‘only’ paralysed nerves in her hand and leg. She recovered, but for the rest of her life the muscles in those areas were smaller & weaker than on the unaffected side. She never had to spend time in an iron lung – and at the height of polio epidemics, some overseas hospitals had entire wards devoted to patients in these machines, which ‘breathed’ for people who could no longer breathe for themselves because the necessary muscles were paralysed. Mortality rates from polio – before the widespread availability of a reliable vaccine – were around 5%, with a further 35% of those infected suffering some level of paralysis.

Or what about diphtheria? The mortality rate for this bacterial disease is between 5 & 10%, & outbreaks still occur, even in industrialised nations. Diphtheria often has respiratory symptoms, due in part to severely swollen lymph nodes in the neck. But the bacterium (Clostridium diphtheriae) also produces metabolic by-products that can lead to damage to the heart & nerves, & it can sometimes cause serious secondary infections in the skin.

And there’s measles, whooping cough, rubella – while in the industrialised world, with its generally good provision of health care, most of those who contract these infections go on to recover, they are not trivial diseases. (I couldn’t believe one comment I read a few months ago, where the writer commented that whooping cough was a trivial illness; her child had ‘only’ had a serious cough for a week… & was unwell for several more.) All have a rate of serious complications, including death, that is several orders of magnitude higher than the unquestioned rate of complications due to vaccination.

And I wonder – are people so ready to advocate a return to a world where these diseases are common because they’ve never had first-hand experience of the effects? After all, the highest rates of illness occur in the ‘third world’, which is a long way from the experiences of most people in comfortably first-world New Zealand. And is part of it due to a failure on the part of scientists, doctors, the education system at large to help people understand things like relative risk, and how science-based medicine operates? And – a key part of this – how well do we communicate the idea that correlation does not equal causation: that because B happens soon after A, for example, this is not proof that A caused B?

I think we still have a long way to go on these things.

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PS And those with a genuine interest on what <i>is</i> in vaccines (as opposed to the wilder claims being made over at Sciblogs) might like to read this post from ERV:  – basically a group of researchers did DNA analysis on most of the main vaccines, looking for evidence of contamination from other sources (monkey tissue, foetal tissue, etc etc). The result: modern vaccines are clean.

what evolution is Alison Campbell Apr 22

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The issue of who’s going to coordinate our 2nd-year evolutionary biology paper came up the other day. (I haven’t done it for the last couple of years as my ‘other’ job - in the Dean’s office – takes up a fair proportion of my time. But at some point I’d like to get back into it.

We’ve had that paper, Evolution and Diversity of Life, on the books for a long time. When I first came here it was more of a diversity course, looking at the different plant & animal taxa, & while the topic of evolution was there it was more implicit than explicit at times. When I took over as coordinator I left things as they were for the first year or so, while I looked at content, curriculum & all that. And then, with several colleagues, I brought in changes that meant that we are now much more explicit in our teaching of evolution. This is because we’d found that many students weren’t really clear on what the word evolution actually means.

So we changed things to help them find out – there’s a lot of research out there showing that simply telling students ‘stuff’ (be that concepts in electronics or ideas in evolution) has hardly any effect on their understanding of the material. Getting them interactively involved, on the other hand, can work wonders. Story-telling’s good, too – with a concept like evolution, simply telling students ‘this is what it is’ isn’t particularly helpful in enhancing their understanding. But using narrative to show the history of how the theory of evolution developed, now that can make a difference.

And for a major concept like evolution, which underpins all of modern biology, it’s really important that students have a good understanding of what it means.

Evolution can be used in three inter-related ways. First up, evolution is a fact. There is now a very large body of evidence supporting the understanding that all living things have evolved through a process that Darwin characterised as ‘descent with modification’ from some common ancestor. Biogeography, palaeontology, embryology, molecular biology; all provide evidence of the fact of evolution.

People can also talk about evolutionary history – the pathways by which organisms arrived in their current state. I’ve written before about the evolutionary pathway of vision (here & here, for example) and of the tiny middle-ear bones in mammals (which are derived from bones in the reptilian jaw articulation). These days a lot of those evolutionary relationships are elucidated using comparisons of DNA sequences (& those of you sitting L3 Biology this year will have seen some of the cladograms, or ‘family trees’, that this work generates), but the fossil record has provided & continues to provide a significant amount of information. For example, both fossil evidence & DNA data support the idea that the most recent common ancestor of humans and chimps lived around 5-7 million years ago.

And of course, there’s the theory of evolution. Theory in the strong scientific sense of a cohesive explanation for a large body of data, which is consistent with those data and which provides testable predictions. The theory of evolution offers a mechanism by which the fact of evolution has occurred and which underlies those evolutionary pathways. (That should read ‘mechanisms’ really: while Darwin’s original mechanism, natural selection, is a key player, genetic drift also has a role to play.)

So there you are: what evolution is. And why we should take care to teach it carefully and well.

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Anyone interested in a bit of extra reading might want to have a look at Evolution: the first four billion years. Haven’t read it myself yet (apart from the intro, which shaped my thinking for this post) but it’s been recommended to me.

M. Ruse & J. Travis (eds.) (2009) Evolution: The First Four Billion Years. Belknap Press

why don’t students study plants? Alison Campbell Apr 21

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was going to write about yesterday’s dreadful Herald headline on the risks of multivitamin pills (which implied that women taking multi-vits are at a hugely increased risk of breast cancer) – but Jim McVeagh beat me to it.

So…

I’ve just finished giving my first-year ‘plants’ lectures. I really enjoy them & so, judging by appearances, do most of the students :-) But every year, when I ask for an indication of where they might be in terms of prior knowledge, then judging by the show of hands at least a third (& sometimes more) of the class tell me that they didn’t study the plant-related standards in year 12 of secondary school. (Either that, or they don’t remember studying them, which is much the same for my purposes.) This means I get to tread the fine line between losing that third of the class & boring the rest, who remember at least some of what they learned. And I don’t get any complaints to that effect in the end-of-semester paper appraisals, so I guess I manage to do that OK.

But it is a bit of a concern. I mean, plants are wonderful organisms in their own right, quite apart from the fact that the flowering plants, in particular, can be the inspiration for some beautiful works of art:

 New York City, NY: Metropolitan Museum of Art: Autumn Landscape (c1923, Tiffany Studios, New York City)

 This one’s a Tiffany window (Autumn Landscape) from the Cambridge 2000 image gallery. And then there’s this quilt (which I want!) by Leonore Crawford, which my brother saw & photographed in an exhibition in Beaujolais, France:

And of course plants, like all living things, have a natural beauty all their own. This shows the transport tissues in the root of a plant called Smilax:

This is a cross-section through the tissues of a leaf:

And I could go on & on.

But quite apart from all of that, plants – with their ancient ancestors, the blue-green algae – changed the nature of our planet. Without aerobic photosynthesis churning out oxygen as a waste product, there’d be no oxygen-rich atmosphere, no biosphere as we know it, and the complex plant, animal, & fungal life around us could not have evolved. They underpin most food chains & are of enormous economic and ecological significance. It’s hard to see how you could study ecological restoration, for example, without at least a passing acquaintance with the plant kingdom.

So – back to my initial question: why don’t more students study plants?

what science is Alison Campbell Apr 18

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“Science can give us answers, but they are not true just because science says so. They are true or at least a usefully accurate approximation of reality because anyone (at least with training and equipment) can perform the same tests or experiments and replicate the results for themselves.”

From a commenter over at Science-Based Medicine. Says it all, really.

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and also, from the same thread (different ‘speaker’):

“You can have faith in religion, you can have faith in leadership, you can have faith that a treatment will help you since it is based on scientific study, but you cannot have faith in science. In science, you should only have skepticism and curiosity. The only faith that you should be asked to accept in Science-Based Medicine (which is not science), is that what has been observed in the past, will likely be observed in the present.

“You need only believe in a part of science when you repeatedly observe that part of science being correct. That belief is justified so long as you continue to observe the same results. Science should be belief in what you observe, not faith. There are questions that science cannot answer, faith can be applied to those questions.

“In a scientific argument, the better argument will lead to a better hypothesis or experiment, not to a change in policy or lifestyle. Scientific arguments are often obtuse to anybody who has not been involved in the study of a particular subject. There are many who take advantage of that obtuse nature, and use sounding sciency to sway opinion without having the data to back it up.”

what’s in a name Alison Campbell Apr 16

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This is only sort of science - but it’s fun (& also Friday). But the secretary came in with a document & pointed out that one of the names – Goodbehere – looked really old. ‘Must be a bit of history behind that one,’ she said.

Names often have a story to tell. In science they can be extremely informative – the names of chemical compounds, for example, often tell you a lot about the structure of that compound. DNA (deoxyribose nucleic acid) anyone? And as a zoologist, I often reflect on the fact that if I hadn’t learned Latin at school – as the only kid at school learning it, I studied with the Correspondence School – then getting a handle on the names of muscles, bones & other anatomical bits & pieces, let alone the ‘proper’ names of living things, would have been more difficult for me. (By ‘proper names’ I mean the Latin ‘binomial’ names that were first developed by the Swedish taxonomist Carolus Linnaeus, aka Carl von Linne: things like Homo sapiens and  Zea mays. Before this, an organism with a wide geographical range might have had several different ‘common’ names depending on where you were, which must have made it hard to know if you were talking about the same beast or several different ones.)

Family names – surnames, or patronymics – can tell you something of a person’s past. Cooper, Smith, Baker, Cook, Mason, Fletcher… These are all names where the ancestor’s name reflected their occupation. What about the one that caught Karla’s eye: Goodbehere? We speculated: perhaps an ancestor had done something awfully good – in the sense of doing good for others – & the name commemorated that? Hmmm. Maybe it used to be ‘Godbehere’, either in the form of a prayer (‘Lord, please help us; God, be here’) or because it marked the site of a church, or shrine, or some other holy place?

In the end we did what very many other people would do – we googled the word. (Speculation is fun, but we wanted answers!) The corruption of ‘Godbehere’ did come up as one possibility, but so did another, more surprising answer: the long-ago ancestor might have been a woodsman. Apparently the original name was Woodyer, & over time that’s been corrupted (I suppose you could say, it’s ‘evolved’) into Goodair, Goodbeer – and Goodbehere.

What’s in a name, indeed? (Have a look at the etymology of ‘Bottom’, for example, as in Higginsbottom etc. Not what you might think!)

i get mail… Alison Campbell Apr 14

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… although I have to say, it’s nothing like as interesting (!) as some of PZ’s correspondence :-)

However, I thought I’d reproduce it here (despite the fact it isn’t really ‘science’) as it could form a useful basis for a critical thinking exercise (& possibly one in creative writing…). I’ve included my correspondent’s name as I very much doubt that it’s her (?) real one.

Subject: hello, dear

Greetings,

 I would like you to permit me to apply through this medium for your co-operation and to secure an opportunity to invest with you in your country.

 I have a substantial concealed capital honorably inherited from my late father (Mr. Timothy Cohen); He was killed by the rebels in the ongoing political crisis in our country that have resulted to war since this past few years.

 I intend to invest this money in profitable and lucrative business venture of which you are to advise and execute the said venture over there for the mutual benefits of both of us. I shall be glad to reserve this respect and opportunity for you, if you so desire, I want you to be rest assured that everything is in order and legitimate.

 I am 19years old, an orphan presently living with a family that I never knew from Adam, Imaging being alone at this tender age.

 I will give you all information?s needed as soon as I hear from you to further this transaction immediately.

 Best Regards,

 Miss Janet Cohen

 

OK, for a start, e-mails with subject lines like that go straight in my junk folder & often don’t see the light of day. (I have to check the folder occasionally as for some reason the system also junks e-mails from my students if they aren’t using their Uni e-mail addresses.) If you want me to look at a message, at least give it an informative title! Even my Significant Other doesn’t write like that :-) So, ‘another scamming e-mail’, I thought to myself.

I’m not quite sure how one could dishonourably inherit something. Short of nefarious activity on the part of the inheritor, that is. But I notice that while Janet (?) names her ‘father’(?) she has somehow forgotten to identify the country they lived in. I’m sure that was accidental… But of course this makes it a) harder to check her bona fides & b) increasingly likely that her intentions are dishonorable.

The spelling? Well, that could be excused from someone who (genuine or otherwise) doesn’t have English as their first language. It’s interestingly inconsistent, isn’t it?

What are they offering? Unusually, this particular letter-writer doesn’t say (they generally wave the carrot of 10% – or some similar proportion – of a rather large sum of money). I guess s/he wants me to be sufficiently intrigued to write back for these all-important details, & then s/he’d be able to string me along some more. And then get me to commit – because the punchline is generally that I need to either make a ‘small’ enabling payment, or hand over my bank account details, in order to expedite the deal. It’s often a few hundred US dollars – might seem like small bikkies, but it would rapidly add up if enough people were foolish enough to send the cash. (And of course, they’d never see it again.)

But – why on Earth, if this person is up-front, would they make an offer like this to someone they’ve never had contact with before? Surely, if they’re genuine, they’d be dealing with a mainstream financial institution? Would you be following through on this wonderful offer from someone completely unknown to you, one which seems almost too good to be true?

Well, unfortunately, far too many gullible people do just that every year. despite warnings from government and other agencies. I guess the lure of what looks like easy money, at ridiculously high rates of return, is just too hard to resist. Just remember – if something looks too good to be true, then it almost certainly is.

(I mentioned creative writing… The Scambuster419 site, based in the UK, contains some excellent examples. And of course there’s the very creative Scamming the Scammers site. However, I would recommend that you don’t try this at home; leave it to the professionals! Seriously – look at the examples for interest, education, & amusement. But some of the scammers can turn a bit nasty when they realise the tables have been turned.)

more bad stats & other stories Alison Campbell Apr 12

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I have a pile of marking to get through this week, & so that I can make a good start today I thought I might just point you at some interesting posts from other science bloggers.

Another tale of statistics from Ben Goldacre: this time it’s the frankly appalling story of where the lack of understanding cases of statistics can take us. The ‘comments’ section of Ben’s post is also well worth reading.

From Brian Switek: the potential link between forensic science and left-over leopard dinners

And from Orac: a thorough critical examination of a recent NZ press release that announced a study of chiropractic as a means of improving labour….

Enjoy. And hopefully I will have more time tomorrow!

nature by numbers Alison Campbell Apr 09

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I was having tea with very good friends of ours, a couple of evenings ago now, & they showed me this stunningly beautiful short film clip called Nature by numbers. The film-maker, Christobal Vila, describes it as a ‘movie inspired by numbers, geometry and nature.’ Absolutely gorgeous!

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