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April 2009 Archives

Blogging on Peer-Reviewed Research I was vaguely contemplating writing about a question in last year's Schol paper, to do with antifreeze proteins in polar fishes, when a journal alert popped up in my in-box. It was for a paper entitled How do terrestrial Antarctic organisms survive in their harsh environment? (Wharton & Marshall, 2009). The uni has an extensive Antarctic research program, & in fact I was lucky enough to go down there myself (as an 'extra' on a botany study) a few years ago, so I was easily distracted. The fish aren't going anywhere, after all :-)

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By now the fact that senior NIWA scientist Jim Salinger lost his job last week has made global headlines (in the blogosphere at least). Apparently, he spoke to the media without approval from his superiors. OK, NIWA is a commercial entity & there are a lot of checks & balances to ensure that commercially sensitive information doesn't get out when it shouldn't - but it's hard to imagine how commenting on the weather faills into that category. And I would argue that there's a need for more scientists to communicate with everyone else about what they do (by talking with reporters, giving lectures, coming to Cafe Scientifque, or writing a blog) - but a move like this will only make many scientists even less inclined to take part in these increasingly important conversations.

Makes me glad my blog's hosted by the University, where the whole 'critic & conscience of society' thing is a key part of what we do :-)


Update: you might be interested in Peter Griffin's commentary, on the Science Media Centre site.

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The front page of the Herald this morning was pretty much given over to swine flu - how many cases there might be in NZ, various public health concerns, that sort of thing. I thought it was a bit excitable, but still, understandable I guess & hopefully will raise public awareness of some of the issues associated with any potential disease outbreak.

Page 2 has a bit more (well, quite a lot more), including some of the science. One cause for concern with this virus, for example, is the fact that it appears to be a 'triple reassortant' - it contains genetic material from pig, bird & human flu viruses, which could mean it's more virulent than any of those on their own.

But I wanted more. And since this is the internet, I found it. It's the Aetiology blog, written by an epidemiologist, which has an excellent commentary on some of the key issues relating to this swine flu outbreak. I think I'll be a regular visitor there.

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Last week one of my students wrote to me about something they'd seen on TV:

My friend & I saw this on Breakfast this morning. Although we don't think it is all true, we are still interested because they talked a lot about the skull's morphology & how they believe it is the offspring from a female human & an alien. Here's the website on it:

It would be great to hear your thoughts 

So I went off & had a look at the website, & wrote back... 

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I've written previously on suposed 'trials' of the benefits of fish oil on kids' school performance. One was the 'Durham trial', where a large cohort of schoolchildren was given fish oil supplements without any real scientific basis for doing so; another was in New Zealand. As I said then, one of the many problems with this 'trial' was the absence of any proper control treatment. The Bad Science website written by Ben Goldacre had a very thorough analysis at the time.

Now Ben's just written about a subsequent trial which was properly controlled. I wasn't particularly surprised to hear that it showed no difference in outcome between 'oil' & 'control' groups. Unless - & this is actually the focus of Ben's post - you do a subgroup analysis. This is essentially where you cherry-pick a subgroup of the data set, because the members of that subgroup do appear to show a response to the treatment. And it's a Bad Thing, really. Ben explains why.

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Blogging on Peer-Reviewed Research I used to love Rudyard Kipling's Just So Stories when I was a kid - my favourite was the tale of How the elephant got his nose (cue crocodiles, the great grey green greasy Limpopo River, & the insatiable curiosity of the elephant's child). Charming stories & great fun, but of course no evidence that things actually happened that way :-) But what about the giraffe's long neck?

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I really enjoy reading Brian Switek's posts on his blog, Laelaps - especially those relating to mammalian evolution & to the history of science. He's just written a lovely piece about the evolution of seals, including the comment that this lovely fossil helps to explain why it is that seals (unlike whales & dolphins) swim using their limbs rather than their tails. As he says, the past is the key to the present. Go over there & see why.


& there's a most excellent website associated with this particular fossil discovery.

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By now some of you may be thinking about entering for the Scholarship exam at the end of the year. I thought it might be helpful to look at some of the material related to this exam, so that you can get a feel for the qualities that the examiner is looking for. (And in places I've linked to things I've posted previously on this topic.)

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Blogging on Peer-Reviewed Research Some of the many questions to do with human evolution centre on our way of getting around - just when did bipedalism evolve? Is bipedalism a derived state, found only in our own twig of the primate family tree? Or is it a feature seen in the last common ancestor that we share with our sister species, chimpanzees?

Bipedalism is certainly a feature that evolved fairly early in human history. A tibia attributed to Australopithecus anamensis is around 4 million years old, & indicates that this species was bipedal. Orrorin and Sahelanthropus are older, at around 6-7mya, and may also have walked on 2 legs at least part of the time, although the evidence here is more tentative. In the case of Sahelanthropus, it's based on a virtual reconstruction of the cranium that suggests the foramen magnum was further forwards underneath the skull than is the case in the great apes.

While things like the position of the foramen magnum, the form of the tibia where it articulates in the knee, and the presence of a valgus angle are all indications that an organism is bipedal, we shouldn't forget the ankle joint. In a just-published paper, Jeremy DeSilva has examined the form & function of the ankle in a variety of species and used this to draw some inferences about locomotion in early hominins.

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I thought this fitted rather well with some recent posts :-)

song chart memes

courtesy of GraphJam

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Reading the UK newspaper, the Telegraph, I see that social networking sites can be bad for your moral values. Scientists say so, so it must be true...

Only they didn't, & it's not. Ben Goldacre has picked up on this story (along with other examples of overblown reporting in the UK press). The paper on which it's based has yet to be published **, but he did a bit of digging & got hold of a copy. And contacted the lead researcher. Who said that the research paper didn't mention Facebook or Twitter, the two sites fingered by the media, at all. However, his institution's press officer did, in their media release, & the media picked this up & ran with it to create a story that's both sensational and completely inaccurate.

I do wonder how long it will be before our own media spread this one around as well...


** Putting out press releases before the work's been published in the scientific literature isn't particularly good practice, as it means that other researchers in the field haven't had a chance to read & evaluate it. But it does happen, as this case shows.

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Grant is a regular commenter here & occasionally I've twisted his arm & persuaded him to write a guest post for me. The following item is one of these - it was too good (&  too long!) for the comment thread. Grant begins:

Alison recently put up an article about epigenetics. Since I was in a bit of a writing mood, and this topic was close enough to some of my own work, I wrote to add a bit of my own about epigenetics in reply. Alison invited to put this in a guest blog. It is a bit long for a comment...! I wanted to add an aspect of epigenetics that interests me: specifying the use of genes through forming different chromatin loops depending on which parent the copy of the gene came from. I am going to introduce a few terms as I go along; I am writing thinking of those that already know a little about biology and might like to learn some of the new things we are learning about chromosomes.

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A little while back I wrote about epigenetics - & I've got a nice piece from Grant to put up for you too. But in the meantime - PZ has written about genetic imprinting, another example of how modification of the chromatin can affect gene expression. And he's included some nice diagrams of how it works. Enjoy.

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Horrakapotchkin! It seems that hsi is no longer available - something t do with a 'terms of use violation'. I do hope the problem - whatever it is - is cleared up as this really was rather cool.


and a useful introduction to some of the terminology used in phylogenetics. (Courtesy, as usual, of PZ - either he spends hours on YouTube, or some of his minions do!) I rather liked the comment that phylogenies often leave out the wholly extinct groups, & this can sometimes give a rather unrealistic impression of the true complexities of a group's evolutionary history.


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I'm a big fan of Ben Goldacre's - I read his coliumn regularly & thoroughly enjoyed his recent book, Bad Science. Except for the missing chapter - when the book was published, Ben was engaged in a court battle over the content of that particular part of the book.

Anyway, that's over, Ben (& the newspaper he writes for, the UK's Guardian) won the case - & he's made the this final chapter freely available on the internet, & encouraged others to spread it around. So I am. Bits of this are scarey reading - for what they have to tell us about human nature...

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You see some interesting things in the 'letters' pages of our local newspapers. A little while ago it was the suggestion that 'stabilised liquid oxygen' was the cure for all ills. This week: a statement that the recently-introduced Gardasil vaccine contains rat poison & aluminium, and that it's caused 29 deaths and 10,000+ adverse reactions. Just how accurate is this?

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On my recent epigenetics post, Heraclides pointed me in the direction of an article about polydactyly in cats. It contains the comment that these cats are also known as mitten or thumb cats because they can learn to pick up things, open latches or move objects with near-human dexterity.

Well, OK, we had a cat who was pretty dextrous. He regularly opened the fridge (yes, all right, it was old & the door seals weren't too great, but still...) & he eventually became quite good at manipulating those lever-type door handles. But he did all that without benefit of 'thumbs'.

In polydactylous cats the extra digits tend to be added on the inner (not the 'pinky') side of the paw. I guess it's possible that there's some degree of 'folding' possible along the axis between 'normal' & extra digits, so these cats could well have a bit more flexibility in paw movement than a normal cat. But 'near-human dexterity'?

Cats are digitigrades - they walk & run on their toes. (Humans & bears are plantigrade, walking on the soles of their feet, while horses and deer - & elephants - are unguligrades & run on the tips of their toes.) The muscles associated with kitty toes will be arranged a bit differently than those in people and deer. And that includes the muscles that give a wide range of precise movements to the first digits on our forelimbs - our thumbs.

So I suspect that the claims about the abilities of polydactylous cats should perhaps be taken with a grain of salt. Fortunately. Otherwise we could be in real trouble... 

I mean, from this...

funny pictures of cats with captions

to this? And our cats already think they rule the house!

 funny pictures of cats with captions

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Did you know that there are more bacterial cells on & in your body, than there are cells that are 'you'? Well, there are. And those bacterial cells don't live in isolation, endlessly dividing & dividing & dividing... They communicate with each other. (I did know that, having read Carl Zimmer's wonderful book Microcosm - but not that different species 'talk' with each other.)

Now here's an excellent video on the subject, featuring microbiologist Bonnie Bassler. She does talk about other organisms as well - there's a wonderful luminescent squid that glows because of the bacteria living in its body. (Which is one reason PZ has the video up on Pharyngula, which is where I found it...)



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This time, the daughter tells me, she's doing a project on a 'current issue' - & she's selected stem cells. Current, controversial, contentious - & extremely interesting. But again, I'm not an expert (although my colleague Bjorn Oback, at AgResearch, is doing some very interesting work in that area & in fact received a Kudos award for his research in 2007). So this time, I thought I'd just point you at a couple of places to get started, if you've chosen this topic too.

One is a fact sheet that Bjorn put together for us when he spoke at a Cafe Scientifique, a couple of years ago now. (It was a great Cafe session. We must get him back for an update...)

And the other is a post & its related discussion that fellow science blogger Ken Perrot has put up over at Open Parachute. I think this one's particularly valuable for when you're doing the 'social & ethical' aspects of your project, because the discussion that's going on presents opposing points of view very clearly.

There's plenty more out there on the web - just remember to apply your critical thinking skills to what you find, as the quality of what's available is (as my mother used to say) like the curate's egg: good in parts :-)

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and the nature of open-mindedness (via Pharyngula [as usual!]). Remember to turn the sound on.

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... from over at Open Parachute:

You should probably go over there & read the post that goes with it :-)

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The daughter came home from school on Thursday & annouced that she wanted to find 'stuff' on epigenetics. Things like, what is 'epigenetics' & why is it important? It's not a subject I know a lot about, but I did remember that I had a reference or two squirelled away. One is a great blog post on the subject by the inimitable PZ Myers; the other, a news feature published a couple of years ago in the journal Nature (Qiu, 2006). Both are good starting points if you're looking for something on this subject.

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I saw this cartoon on Pharyngula, a while ago, & thought I'd keep it for a slow day :-)

teaching natural selection.jpg

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Now here's an interesting little item: using magnets to remove pathogens from the bloodstream... I must admit that when I saw the topic on SciTechDaily my first thoughts were very sceptical. The idea that sleeping on magnets can cure whatever ails you, for example, has always been a bit much for me to swallow. But on reading the original story - it does sound possible.

A research team looked at the possibility of using magnets to help clear pathogens from samples of human blood - but it was nothing to do with somehow using magnetism to 'get' the baddies. Instead, they took tiny magnetic beads & coated them with antibodies to a disease-causing organism; in this case, the fungus Candida albicans. When the treated beads were mixed with contaminated blood, the antibodies linked with specific antigens on the surface of the Candida cells, so that each little bead became the centre of a cluster of fungus cells. The whole lot could then be removed using a larger magnet, drawing the beads+fungus clumps out of the blood & into a collecting fluid.

At the moment, this is at the stage of a bench-top experiment. But it has more science behind it than some of the other claims you hear about magnets... Out of curiosity I went looking & found that using tiny magnetic beads to grab substances out of solution has been done elsewhere - to separate specific RNA or DNA sequences, for example (Oster, Parker & Brassard, 2001). So this technique isn't novel, & has been tried & tested in other applications already.

And I've learned something new. A little curiosity can take you a long way!

J.Oster, J.Parker & L.a Brassard (2001) Polyvinyl-alcohol-based magnetic beads for rapid and efficient separation of specific or unspecific nucleic acid sequences. Journal of Magnetism and Magnetic Materials 225(1-2): 145-150. doi:10.1016/S0304-8853(00)01243-9

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... and very well written, too - yet more evidence that the ancients had it right...

No doubt New Scientist will be featuring this content shortly :-)






... I had trouble keeping my face straight when I wrote that :-)

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