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April 2010 Archives

 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...)
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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...

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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.)

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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.

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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.


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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.


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."

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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!)

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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.

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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!

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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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I wrote a few days ago about the over-hyped media stories around the then-upcoming release of a new Science paper about a possible new hominin species. At the time is seemed really strange & definitely a spoiler rather than a teaser - by the time the actual paper came out, there'd already be a set of public perceptions around the story that the actual science would be unlikely to change. Anyway, here - courtesy of Grant - is an excellent take on the various goings-on & what seems to be a less-than-optimal response by Science to whoever broke the original press embargo. Fascinating insight into the world of journalism.

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Today & tomorrow I'm down in Wellington. This year Victoria University is hosting the training camp for New Zealand's Biology Olympiad aspirants, but I got invited to come down & help out at some of the lab classes. Which is great, because I don't want to lose contact with the IBO organisation (or the the wider umbrella group. Science OlympiaNZ).

For me, the highlight of these training camps (which up until this year were hosted at Waikato Waikato & UniTech) is the interaction with a bunch of gifted and talented young New Zealanders. But I also value the opportunity to talk with the rest of the team of dedicated individuals who make the camps possible. This afternoon I had a lengthy session with my friend Angela Sharples, who leads the Biology organising team & is also Chair of the Science OlympiaNZ Council. One of the things up for discussion was the question: what do universities gain from their association with the movement?  After all, we're talking fairly small numbers of students here - 19 at this year's camp - and they're not all going to go on to study at the host institution. And these camps do cost a lot to run, in terms of materials, resources, & staff time.

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The earliest forms of life on Earth were prokaryotes, & they dominated the biosphere for around 2.5 billion years. And slowly they changed it - aerobic photosynthesis by cyanobacteria ('blue-green algae') led first to the oxygenation of the oceans & then to the development of an oxygen-rich atmosphere (incidentally making life impossible for many anaerobic bacteria). Then, beginning about 1 billion years ago, we start to see evidence of eukaryote organisms in the fossil record. Perhaps the best-known are the (relatively) recent animals of the Cambrian (c. 540 million years ago), but there are also the strange organisms of the Ediacaran fauna. And, from fine-grained Chinese sandstones dating to between 635 & 551 mya, come what may be the earliest microscopic animal fossils (eggs, embryos & cysts), many of them preserved in beautiful detail. (There was some disagreement about the nature of these fossils, with a suggestion that they might actually represent prokaryote cells, but other discoveries seem to have ruled this out. NB that last link might not work for all.)

So what happened, around 1 billion years ago, that saw eukaryote animals begin to flourish? The increasing availability of oxygen must have been part of it. However, other changes in ocean chemistry may have been key to the evolution of multicellular animals (Narbonne, 2010) & researchers have been able to identify these changes by examining changes in the nature of sediments that formed in those ancient oceans. Examination of strata from the Doushantuo Formation (635-551 mya) in China indicate that the waters in which these sediments were laid down were anoxic (lacking in oxygen) & also strongly stratified, with chemically-different layers of water sitting one on top of the other. The researchers also inferred that there'd have been a thin layer of oxygenated water sitting on top of those anoxic layers.

Up to about 740 mya such oxygenated layers were apparently rare, which would have reduced the odds of any animals evolving - after all, animals need oxygen. It's assumed that the Doushanto organisms lived in a thin surface layer of oxygenated water & were deposited in anoxic sediments when they died (the lack of oxygen in those sediments helps to explain their excellent preservation). It seems that the world's oceans didn't start to become oxygenated at depth until about 580 mya, a change that would have set the stage for the subsequent evolution of the much larger, multicellular animals of the late Ediacaran & following Cambrian periods.

G.Narbonne (2010) Ocean chemistry and early animals. Science 328: 53-54

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This morning's NZ Herald carried a story from the UK Telegraph under the headline "Child's skeleton missing link to man's ape-like forebears.' It could have been worse: the Telegraph's headline was 'Missing link between man & apes found' (sigh). I read the article & have to confess a certain amount of disappointment - because this seems to be another case of the press release pre-dating the actual scientific paper describing the remains. (A bit like all the hoo-rah surrounding 'Ida', really. And one has to wonder why this is so.)

The new fossil appears to be contemporaneous with Homo habilis, & in fact the story suggests that it may provide a link between habilis & the more 'ape-like' australopiths (an interesting idea, given that habilis is itself fairly similar to the australopiths in many ways). Regardless of this, it does sound like an interesting specimen, given that it's described as 'an almost-complete skeleton' in the Telegraph story.

But some of the statements seem rather overblown - we're told that the skeleton 'will allow scientists to answer key questions... [such as] when they began walking upright on two legs.'  Yet we already know that the trend to bipedalism began much earlier than this (& may even have been a trait found in the most recent common ancestor between chimps and humans), so this is not really a biggie. And while the new fossil may well prove to fill some gaps in our knowledge of our family tree, it is not going to have us 'rewrite the story of human evolution'! (Several of the experts quoted in the story qualify their statements with 'may' & 'if' &  'could': they too will be waiting with interest for the actual release of the full scientific description of this find.)

I would love for this new fossil to be a clear window into our past. But I wish, oh how I wish, that press release and scientific paper could have appeared together, instead of the media flurry preceding the information that would let us make sense of it all. Not least because, by the time the actual paper comes out - later this week, according to the Telegraph release - the 'yet another missing link' idea will be firmly at the front of people's minds, with all the polarisation of opinion that this implies. (Read the comments following the news story, to get a feel for what I mean.)

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A while back I wrote about some fascinating little deep-sea creatures - the 'bone-eating snot-worms' (Osedax sp.) that colonise the corpses of dead whales falling to the ocean floor. Now Brian Switek, over on Laelaps, has reviewed a paper suggesting that this bone-boring habit has been around for millions of years. The evidence is in the form of trace fossils: vertical tunnels bored in the skull of a 3-5 million-year-old whale. Fascinating stuff, & it helps broaden our understanding of the ecology of the Pliocene seas. Well worth a read :-)

(Brian's title - The worms go in, the worms go out - brought back memories of a song my mother taught us when we were littlies, to do with graveyards, bodies, & worms crawling in & out... Deliciously icky for small persons :-) - we loved it!)

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One of our first-year bio labs sees our students using potometers to determine how transpiration is affected by things like light, humidity, & wind movement. Those of my readers who are school students may well have done something similar, but for those who arent - a potometer allows you to measure the rate of water uptake by a leafy shoot.


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A few posts ago I wrote something about 'research' into psychic phenomena, & why it was bad science. Now Orac has posted a sign that says it all:

 This highlights something that has always puzzled me about the claims made by various psychic practitioners, regarding their abilty to predict future events. Surely they'd have known?

(I am equally bemused by claims - such as those by the psychics involved in the Scole experiment - that it's possible to speak to the dead. If it is, then why don't the dead ever seem to say anything useful? Where the will is hidden, perhaps. Or that diamond ring that was lost? Or - in the case of claims to solve murders - surely they could give accurate information on where the body is, or whodunnit?? Is that too much to ask?)

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