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May 2009 Archives

The daughter & I love reading Elizabeth Peters' 'Amelia Peabody' books: lovely rollicking yarns with a leavening of actual historical events, likeable characters, and a delightful, gentle poke at Victorian standards (of writing & other behaviour). And, as they're set in Egypt, the occasional mummy. We're fascinated by mummies as well :-)

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In today's Science journal there's an update (Gibbons, 2009) on all the hoop-la associated with the unveiling of 47-million-year-old Darwinius massillae (aka 'Ida). I commented earlier that the hugely overblown press coverage that accompanied the publication of Ida's description in PLoS One was a worrying thing.  It described Ida as a 'missing link' (a claim that the authors of the paper itself wisely chose not to make).

As an example of 'framing' science for public consumption this is not good. Jorn Hurum, a co-author of the formal paper, remarked that the scientific work involved in describing D.massillae & determining her place in our family tree is too hard to discuss in a press release. He says that If you want kids to be interested in science, we need to start packaging it in many different ways (Gibbons, 2009), using this to justify all the hype. I certainly agree that we need to look at how we communicate about science (& I disagree that the underlying science is 'too hard' to get across: look at Carl Zimmer's wonderful article) - but he's really taking a calculated risk with this particular approach.

You don't think so? The risk is that when the dust settles, & the scientific consensus turns out to be that Ida's a lovely fossil but really nothing special, the public will have yet another example of 'scientists getting it wrong'. And this is important, because it will only add to the perception that science often doesn't really know what it's doing & is, after all, just another way of looking at the world & of no particular worth. Which is a very long way indeed from the reality & significance of scientific endeavour.

A.Gibbons (2009) Celebrity fossil primate: missing link or weak link? Science 324(5931): 1124-1125 doi: 10.1126/science.324_1124

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Here's a really interesting quote from Ryan, commenting over on Orac's blog:

Sometime in the 60s, education in America started putting a greater emphasis on skepticism. For the first time, kids were encouraged to question what they were told. This is a good thing, or course. But I wonder - have we been encouraging people to distrust and challenge authoritative voices without properly equipping them to properly judge authoritative voices?

Orac speaks authoritatively and quotes research papers as his sources. The anti-vax movement also has authoritative-sounding voices who are able to quote research papers:

How are people from outside the medical and scientific community supposed to parse this? At what point in High School were we supposed to have been taught how to properly evaluate the findings in research papers? I don't recall that chapter. I was made to memorize the periodic table, but I don't recall that anyone ever taught me how to tell the difference between good science and bad science.

It's a good point, isn't it? Just how well do we teach students these things - to tell the difference between good science & bad science?

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At least a couple of times I've made a comment along the lines of "the plural of anecdote is not data". Now here's an excellent video (courtesy of Evidence-Based Thought) that explains why not:


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Well, I got a giggle from it  :-)

It is sort of true, though - there are an awful lot of blogs out there, & one thing that puts me off returning to some of them is a distinct lack of regular updates. The husband complained over the weekend that I take blogging far too seriously (I'd just written 3 posts in a row, to have something in hand). But, I said, I don't want to become what I don't like - & besides, it's fun! (It's also quite a good discipline, actually, as you have to sit down & write something most days.)

song chart memes

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Achievement Standard 90716 expects you to know something about a range of animal behaviours, including intraspecific relationships (territoriality, cooperative interactions, reproductive behaviours, hierarchical behaviour, competition for resources) - & the relationship between behaviour patterns & environmental factors.

Quite a range of stuff there - although it's worth remembering that these are not isolated, stand-alone categories. With my swans, for example, territoriality, competition & reproductive behaviours were quite closely linked. On Pukepuke Lagoon, black swans breed on territories, & the size of those territories reflects (among other things) the outcome of competition for resources. And there was something of a hierarchy - one particular pair was dominant over all their neighbours & could pretty much be guaranteed to win any boundary encounters they might have. And there's a strong environmental influence at play - at the local level, competition for areas where young cygnets can feed is significant in shaping territories, while on a country-wide scale, birds breed in territories or in colonies depending (again) on availability of resources.

All in all, behaviours associated with reproduction are quite fascinating, & ethologists have devoted what some may see as an unhealthy amount of time to documenting & explaining these key facets of animal life. So I was rather pleased to find a post on Pharyngula, from around 3 years ago, dealing with reproductive behaviour in zebrafish - a common lab animal, but not one I know a whole heap about. PZ talks about his own work, the things he has to do to keep his zebra fish happy, the things they need if they're going to breed successfully, & also talks about a paper that includes some lovely illustrations of courtship behaviour in these cute little fish. A good resource, I think, for this particular area of your studies :-)

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In the Herald today (I'm not picking on them! It's just that this is our morning paper) is a headline: Having sons will turn fathers right-wing, study suggests. The ensuing item is from a UK research project that also suggest that if a man has daughters, his voting preferences will trend to the left. (Presumably someone with one of each will be middle-of-the-road?)

Well, it sounded interesting. But I can't go & read the research paper itself - because it hasn't been published yet. It's described as having been submitted to an economics journal. This rings the odd alarm bell, because it's not good practice to announce your findings to the world before the paper's been through the process of peer review.

Anyway, why would the gender of your kids have this effect? According to the researchers, the answer - which is 'scientifically attractive' (!) - is because men become more sympathetic to female viewpoints as the number of females in their families increases. This may be true, but without access to the paper, it's hard to assess. Unfortunately, the article (which I hasten to add comes from the UK paper the Observer, & not the Herald's reporters) says that although there are those who dispute the interpretation of the findings, ...evidence nonetheless abounds of daughters who have tamed the most manly of men. The reporter goes on to quote rapper Sean Combs as saying that having daughters changes things for the better. But this is actually irrelevant: just because someone is 'manly' doesn't mean that they'll lean to the right in their voting preferences. Nor do we know anything about the gentleman's voting preferences before & after his daughters were born. And if we did, would this change make any difference? No, because this is simply a single anecdote.

There does seem to be a rash of this stuff these days. Or perhaps I'm just getting more sensitive to it...

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In a couple of weeks it'll be time for Fieldays again. We've lived in Hamilton for 13 years now, but last year was the first time I'd ever been out to this major agricultural event. And I went out there every day - because I'd been closely involved in the development of the Univesity's stand at the show, so I had a deep interest in seeing how it was received.

Where is this heading? Well, I want to make the point that science communication can take many forms, that it can involve quite a bit of creativity, & that it is fun. Last year's theme was 'Science on the Farm' (& yes, there's a website of that name as well; now, that was a lot of work!). While Waikato's not an ag-focused university, we do have an awful lot of research going on that has direct links to what's happening in the land-based industries. So the trick was to come up with a way of communicating about some of that science in a way that was not only accurate but quirky, attention-grabbing, & entertaining.

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Just a quickie & a link: Ben Goldacre's got an interesting post on the total misreporting of several bits of research, in the UK media. (Having read one of the 'news' items, on 'man-flu', I have to say that in that case the reporter was pointed in the right direction by the researchers themselves. But not even the researchers stated that their research, on immune responses in mice, could be generalised to human flu in any shape or form.) It just goes to confirm my perception that, all too often, a perfectly good science story will be sensationalised in the media - whether because of a feeling that that's what sells, or because the reporter doesn't know enough about science to ask some good searching questions, it's hard to say.Sigh...

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Blogging on Peer-Reviewed Research You've probably already seen the following image, as it's been splashed all over the media recently:

From Franzen et al. (2009) PLoS One 4(5): e5723 doi:10.1371/journal.pone.0005723.g001

NB 'Plate B' is the 'counterplate' of A; while A is complete & genuine, it seems that B was altered to make it appear more complete (& thus more attractive to prospective purchasers) while in private ownership. The parts of B marked '1' & '2' are the genuine article.

Meet 'Ida' (Darwinius masillae), a juvenile female primate who died when she was less than a year old, to become an exquisite fossil in Eocene rocks that are 47 million years old . So complete is her preservation that even the remains of her last meal are present, while the dark material surrounding the skeleton is the remains of soft tissues (muscles & skin). And while the skeleton is described as 'lightly crushed' by the research team, the only bit that's actually missing is the lower left leg & foot. But how can we be so sure about details such as age & sex?

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At least, that's how those working in medicine/health were characterised in a letter to one of our local papers. The writer seems to see the whole vaccines/pandemic warnings issue as a conspiracy to drive up profits for doctors, scientists, & pharmaceutical companies.

Personally I always thought doctors & health researchers were in the business of helping people, but perhaps I'm just naive..... But no, I just don't buy this conspiracy thing. (Yes, pharmaceutical companies make money from their products - so does anyone else succeeding in their business. And yes, they make errors from time to time & have been caught out - usually as a result of scientific scrutiny. But this is not the same as some global conspiracy to make outrageous profits from others' ill-health.)

But I have heard people saying that the latest pandemic 'scare' - the one over Human Influenza A H1N1 (more commonly called 'swine flu') - has been rather overblown. After all, it seems to have turned out to be a storm in a teacup. Have we done ourselves a disservice in this? Will it make people more inclined to ignore the next warning.

I hope not - at the very least it has raised awareness of the public health steps needed to deal with any flu outbreak: the handwashing, use of tissues, & so on. And things could so easily have turned out differently. Apparently the H1N1 strain has already acquired the ability to spread between humans more easily than other strains of seasonal influenza. If this had been combined with virulence factors, so that H1N1 made people really seriously sick, then we would indeed be looking at a serious global health issue. The early & rapid response to 'swine flu' coming out of Mexico meant that we had a breathing space; if this virus does turn out to be less harmful than first expected, doesn't mean it will be the same next time. (And that remains a big 'if', given that this does seem to be a rapidly-evolving strain.)

And if that breathing space gives people the luxury of time to complain, well, that's human nature I guess.


You might be interested in this article from the NYTimes - the World Health Organisation is changing its 'rules' to do with warning the world about imminent pandemics. (Thanks, Grant!)

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Well, viral recombination anyway. I mentioned in an earlier post that viruses can pick up sections of DNA from each other, while within the host's cells. Now ERV has a post on this, in a lot more detail (& really well explained - she is a great science communicator!).

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By the time you read this I'll be on the way down to Palmerston North (to give a public lecture & a seminar & talk with students); all that travel & chat leaves little time for blogging, although if I get a bit of time between talks I'll see if I can pull something together :-) Looking forward to being there but not to the getting there - the weather forecast is the pits & I suspect I will have to avoid the Desert Road. But there's always the Brown Sugar Cafe in Taihape for a very pleasant break in the journey :-)

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Some years ago I read the whole series of 'Thomas Covenant' books by Stephen Donaldson. (I have to say that I found them a bit overblown - & I got seriously annoyed with the protagonist, Covenant, on more than one occasion.) Anyway, one of the plot lines was that Covenant suffered from Hansen's disease - more commonly known as leprosy - & because of this was pretty much an outcast from his community. Which was in the modern United States. I was reminded of this when I read Kathy Reich's Bones to ashes (I could never be a forensic anthropologist; I just don't think I have a sufficiently strong stomach!)

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Blogging on Peer-Reviewed Research She has enormous, protuberant breasts, huge buttocks, exaggerated genitalia, and no head. Oh, yes, and she's 35,000 years old - the oldest 'Venus' figurine to date (Conard, 2009).

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Blogging on Peer-Reviewed Research When I first heard the name 'tree lobster', I had an immediate mental image of crayfish climbing trees... But I was wrong - while they're both arthropods, that's about as close as the relationship between crayfish & tree lobsters gets.

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Or rather, why people may choose not to go with chemotherapy as a cancer treatment. Orac has a great post on this. The context: a sad case in the US where a 13-year-old has rejected chemo for a cancer (Hodgkins lymphoma) where chemo has an excellent track record in terms of cure/remission. The underlying motivations are quite complex & I think Orac's done a superb job of teasing them out.

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It's been hectic at work lately (in fact, things seem to be that way most of the time!) & tomorrow I'm off to Taranaki with my Dean & the VC for a couple of days. Why? To meet with teachers & principals of schools there, so that we can find out more about the needs of teachers & students, & how we can support them. This sort of thing is really important - we do a better job of teaching our uni students if we understand where they're coming from, plus we're at the cutting edge of new science & can offer a lot of new knowledge that hasn't made it into the textbooks yet :-)

Anyway, basically what this means is that service may be interrupted for a couple of days. I could sit down & write something in my motel room tomorrow night - but there are some excellent restaurants in New Plymouth!

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The daughter said today that having done stem cells, I should also look at some of the other topics you can choose from for your research exercise. She suggested xenotransplantation, as it seems quite a few of her friends have chosen that one. So I'll have a go :-)

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In this morning's Herald there's an item entitled 'Call to save hilltop boulders'. According to the people doing the calling, the boulders were placed at the top of what is now an Auckland hillock prior to Maori settlement by a group of fair-skinned people, claimed to be Celtic voyagers. Hmmm. One of those campaigning for the boulders to be saved is quoted as saying [It] sparked a lot of mystery over how they got there. They were concretion boulders, which can only form in sea sediments, yet they had made it to the top of this high, yellow clay hill. More hmmm - this makes it sound as if human agency is the only way for these big boulders to have reached the top of the hillock.

But there are other, simpler explanations. As Geological Society spokesman Bruce Hayward says (in the same article), there's no mystery about how the rocks got there. After all, the land mass that is now New Zealand formed from sediments deposited on the sea bed, on top of much older rocks, off the east coast of what's now Australia. The boulders themselves are 70 million years old & formed on the sea floor, to be raised up during the tectonic events that produced New Zealand. Over time, the sediments that they were enclosed in eroded away, leaving the boulders in their apparently anomalous position on an Auckland hilltop. (These geological processes are well-documented and well-understood, which is rather more than one can say for the alternative hypothesis involving Celtic seafarers & their calendar system.)

The scientific explanation for the placement of marine concretions - & of fossils - isn't new. Back in the late 1600s Nicholas Steno recognised that these objects could be buried in marine sediments & subsequently raised up above sea level by land movements & then exposed to view by erosion. And before him the polymath Leonardo da Vinci offered the same explanation for the observation that fossils of marine organisms can be found on mountain-tops far above the sea: fossils were once-living organisms that had been buried at a time before the mountains were raised. He wrote "it must be presumed that in those places [mountains] there were sea coasts, where all the shells were thrown up, broken, and divided. . ." The overwhelming weight of evidence is in favour of these early interpretations. And yet for some reason these elegant, insightful, evidence-based explanations can still be rejected in favour of hypotheses that seem to fit a somewhat romanticised and more than slightly unlikely view of the past.


Update: you might like to read this post on the All Embracing blog.

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I wrote a post a while ago on what made for a 'good' (as in reliable) journal, in terms of the nature & quality of the research reported in it. Now it seems that there's a new low on the scale - in 2003 a pharmacological company paid a publishing house to produce a 'fake' medical journal: much advertising, & reprints of papers that had appeared in other journals in the publisher's stable. Orac provides a very thorough commentary on this - valuable reading if you're interested in how publication works & what makes for a good place to publish. As he points out, the quality of the reprinted articles isn't in question - but the fact that they were in a 'pseudojournal' stuffed with the drug company's advertising, is just downright wrong. As one of Orac's commenters notes:

A fake academic journal creates the appearance of a conflict of interest. It is designed to look like legitimate peer reviewed research published by a nominally independent publisher (Elsevier) who in fact is being paid to publish research in this journal which supports the products of the particular medical products company that is paying Elsevier to do it. Thus there is a conflict between Elsevier's ostensible role as a leading publisher of peer-reviewed scientific research and their actual role of being paid to produce advertisements for a particular company. And it was ethically wrong for Merck to suborn Elsevier's conflict of interest.


It's one thing to create a throwaway journal that is clearly identified as such and kept at arm's length from any academic journals published by the same company. It's another thing to create a throwaway journal that is specifically designed to look like another of the many academic journals published by the same company. The arm's length relationship between marketing and scientific publishing is key: without it, we scientists cannot trust the scientific publishing.

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Now, here's an interesting family pedigree:


See if you can work out what's going on, & then go here to read the full story. (It's not quite what you might expect.)

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My students & I have talked a bit about swine flu (sorry, Human Influenza A H1N1) in classes over the last week. Probably a lot of other teachers are doing the same thing. Anyway, I've come across a rather nice post on the subject by uni lecturer in the US, which anyone interested in the subject would enjoy reading, I think. (I didn't know that Google has a swine flu map - very nifty!) He's included a number of very informative links, including one to a site that offers a range of (free!) teaching resources, including lectures on flu & other topics :-)

And Ben Goldacre has an interesting piece on Tamiflu. (I can't quite get my head around the way Tamiflu is now available to the public in NZ: from apharmacist, provided an individual suffering from flu turns up for it in person. Certainly, we need to be sure that those receiving the drug actually have the flu, not least because mis-use of it is a first step on the road to resistance to the drug. So I can see why we don't want to be handing it out to someone who's 'come in to get it for mum'. But at the same time, to have people with the flu coming in to a pharmacy seems a good way to help spread the virus around. Bit of a catch-22, really.)

Anyway, the Cochrane Library (as Ben says, a wondrous institution) has looked at data on the effectiveness of two antiviral drugs, Tamiflu & Relenza, in treating & preventing influenza. On the treatment front, it seems that someone taking the drugs will have the course of their illness shortened by roughly one day. Not spectacular. But they do appear to work quite well in preventing symptomatic influenza. On the other hand, they also have some unpleasant side-effects (& the Cochrane authors note there's no evidence they work against avian flu - the review was completed before this 'swine flu' scare came along).

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Over at Open Parachute, Ken has posted an item on 'why is science important?' It includes a series of brief videos showing a range of scientists giving their answers to this question. Well worth viewing.

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