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June 2009 Archives

Last year's Schol Bio paper had a question about allelopathy. The context centred on Black Walnuts (Juglans nigra). These are large deciduous trees with an extensive root system - and they release an allelopathic chemical called juglone, which has a number of toxic effects on a range of other plant species. This ability to kill or weaken potential competitors is a significant advantage to J.nigra as it improves the survival of walnut seedlings, and reduces competition for resources such as water, light, and nutrients. 

Such allelopathic chemicals are relatively widespread in nature, although we may give them different names depending on the organism producing them. For example, the chemicals produced by fungi to inhibit bacterial growth are called antibiotics (some of which are the basis of many modern antibiotic treatments for infection - 'penicillin' was just the first of these). Similarly some bacteria produce substances that kill off fungi. The term 'antibiotic' was first coined to describe streptomycin, originally isolated from an organism called Streptomyces. (As an example of how science moves along: Streptomyces belongs to a group of microbes called actinomycetes. The suffix -myces suggests they are fungi, & in fact that's how they were described when I first encountered them. However, they're now classified as prokaryotes, along with other bacteria.)

For a long time we've regarded these allelopathic chemicals as a form of biological warfare, produced by one species to kill off or deter competitors. So I was intrigued to read an article (Mlot, 2009) that suggested that they could have other, quite different functions in the microbial world.

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Those of you who came to the WEB days a few weeks ago (WEB = Waikato Experience of Biology, for those who didn't) might remember me saying that the human family tree is quite a complex thing. Not only is it a branching tree, rather than the linear model of early palaeoanthropologists, but our understanding of the nature & relationships of the branches is a work in progress. (Which is what science is all about, after all! Contrary to a common misconception, science isn't about 'the truth' [whatever that is], and we constantly review & revise our models & hypotheses as new data come to hand.)

In that light I thought you might enjoy a couple of new posts by Brian Switek, on his blog Laelaps. The first, Mystery hominin turns into mystery hominoid, is an excellent example of just how our perceptions and interpretations can change. In this case, those interpretations were based on a few teeth & a jawbone (& teeth have got researchers into embarassing situations before, with 'Nebraska Man' being perhaps the best-known example).

The second, More hominin hype, is a brief comment on a 2001 BBC documentary which was recently added to YouTube. The focus of the doco is Kenyanthropus platyops (the name means the 'flat-faced man from Kenya'), a fossil described some years ago now by Maeve Leakey & her team.  Kenyanthropus lived at around the same time as 'Lucy' (Australopithecus afarensis), but there's not a lot of fossil material associated with this genus & its position in our phylogeny is not at all clear (contrary to statements made in the video). The discussion thread is also good, not least because a couple of commentators offer links to possible human/chimp phylogenies for you to have a look at.

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Via SciTechDaily - a trip through a library of mammalian biodiversity! This is a video tour through a 'bone room' & a 'skins room' belonging to the Museum of Vertebrate Zoology at the University of California at Berkley. It looks like a fascinating place to visit (although the sight of the skins & furs was a little close to the heart for me at the moment), but the video is the closest most of us will get as there's no public access.

Nor is this 'just' a museum - as the original 'Wired' article says, it's a premier research institution. Scientists there can use the museum's contents to study biodiversity, both at the whole-organism level and - using DNA technology - at the genetic level. Plus the material can be tested for things like heavy metals, to get a picture of human impacts on the environment.

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A friend of mine, a secondary bio teacher, sent me through a couple of questions from students that she thought might be useful for a blog piece. And I agreed, so here they are:

How do scientists know when a species finishes and a new one is formed?
Are there different species in between the formation of a new species or does a, for example, Homo habilis have a Homo erectus child? The second question is actually quite similar to the first.
They're good questions that show the student is giving thought to what it is that defines/delineates a species, & how we recognise a new species. The answer depends in part on what sort of speciation event you're considering.
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I've just been talking with a very dear friend who was diagnosed with cancer not so long ago. She was telling me the various things she was doing to stay positive as she begins her treatment, & I remembered an inspirational article I first read years ago, by Stephen Jay Gould. (As you might have gathered, he's one of my favourite authors.) The median is not the message is an excellent piece on statistics, told from a very personal point of view.

Gould wrote it when he he'd just been diagnosed with mesothelioma, a particularly nasty cancer that has a median survival time of only 8 months from first diagnosis. After the first shock, Gould remembered that if the median survival time was 8 months, then while 50% of those diagnosed would die in 8 months or less, the other 50% could - with treatment - live for much longer. As he did: he lived a further 20 years & when he died in 2002 it was of quite a different cancer.

Anyway, this is a very humane piece of writing that also does a lovely job of explaining some valuable statistical concepts. If you're interested, you can find a pdf of Gould's article here.

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And this is one of those times. Because over the weekend I did what is probably the hardest thing I've ever had to do - I made the decision to end my beloved dog's life.

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This follows on from my previous post on finding papers in the first place :-) Reading a paper is a bit of an art, in some ways, & going by my own experience something we're almost expected to pick up by osmosis. Well, I guess that's not completely true - at the Hons/Masters level, you're usually given a reading list to work through before each seminar, & then you sit around with the rest of the students in the class & your prof, & critique them. And that was where I really learned how to do it. But at school? Your teacher probably doesn't have time to spend on discussing the relative merits of a bunch of papers, or even on how to read them. And it's not just a matter of starting at the beginning & going on till you get to the end.

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The other day I was talking with a friend who happens to be a high school bio teacher, & she said that it could be quite difficult for her students to do their research on the 'contemporary issue' (AS 90714). Not least because of the difficulty of getting hold of peer-reviewed articles on a student's chosen topic. (This is in relation to the part of the standard - well, the explanatory note - that says "In research, the student collects and interprets information from mainly secondary sources. Use of primary sources is acceptable.) Hmmm, I thought, a good topic for a blog :-)

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Blogging on Peer-Reviewed Research One of the arguments commonly levelled against the idea of speciation is that we can never see it happening. That argument is simply incorrect, & some time soon I guess I should at least give you some links to evidence that supports my statement. But in the meantime, I've just come across another apparent example of speciation in the here-&-now. (I've written before about speciation in indigobirds.)

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When you're studying human evolution (AS 90719), one of the fossil hominins you'll learn about is Homo erectus. These days this designation includes fossils that were placed in separate taxa, such as H. pekinensis ("Peking man") & "Java man" (named Pithecanthropus erectus by its discoverer, Eugene Dubois, but now recognised as the first H.erectus fossil to be described).

The "Peking" remains were found at a place called Dragon Bone Hill (Zhoukoudian), & while most of the fossils were lost during World War II, casts of the bones survived. One of the notable things about these remains is how fragmentary they are. Most of the fossils are bits & pieces of crania, with some long bones. And most of them show evidence of trauma - skulls cracked with great force, for example.

How did they get that way, & what does this tell us about the lives of these hominins? Brian Switek has just written a great post on this, explaining how interpretations of the Zhoukoudian remains have changed over time. And the role of what sounds like a very nasty hyaena indeed!

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I've just seen an on-line report that some parents overseas have been organising 'swine flu parties' (more than just your average sleepover), deliberately exposing their kids to the virus in the belief that this will give them immunity to a future, more virulent strain. Something like the 'measles/chickenpox parties' which have also received some adverse comments on sites like Orac's.

Those adverse comments apply to swine flu get-togethers as well. This Influenza A (H1N1) virus seems to be reasonably benign, in the sense that most reported cases have involved a mild-medium dose of flu. But even that is unpleasant - why on earth would you deliberately make your kids that unwell? Quite apart from the fact that there will be individuals who develop severe illness, not least those who are immuno-compromised for some reason. (NB measles isn't a trivial disease either, & even chickenpox can be extremely unpleasant for some sufferers.)

And while it doesn't make most people seriously ill, the virus is extremely infectious - one colleague who works in this field confirms that press reports that roughly 30% of the population will get it, are pretty accurate. That's a lot of sick people. And since flu is often accompanied by other, secondary infections that can lead to further visits to the doctor, or in serious cases hospitalisation, it's quite possible that our health system will be overloaded as the illness spreads. Deliberately spreading it by holding these 'parties' is not exactly a smart thing to do in these circumstances - I can only hope that the idea doesn't catch on here.

There's another reason for concern. As ERV has pointed out, different viral strains are more than capable of exchanging genetic material. In fact, Influenza A (H1N1) has already done this at some time in the past, as it seems to contain an amalgam of human, swine, & avian viral DNA. There's a real worry that, if someone with a virulent form of 'seasonal influenza' also picks up swine flu, the latter will add virulence genes to its existing genome. A flu virus combining very high infectivity with high virulence would be a very nasty customer indeed.

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I began thinking about this post when I read a National Geographic article about the possibility of cloning a woolly mammoth. (The print version of the magazine is always good reading, & the on-line version has heaps of extra stuff.) But, just because this now seems to be on the verge of being possible, does that mean we should actually do it?

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I'm not sure how much time you spend on the 'non-human' primates these days; we got quite a bit of content in that area when I was a student, but I do know that things have changed!

Anyway, lemurs (prosimians) are part of that group. And one that's always fascinated me is the aye-aye - that strange little beast with the very long thin finger (used in hooking stuff out of holes in trees). I don't think I'll ever see one in the wild, though, so I was delighted to find that the Duke Primate Centre in the US has some footage available. (There are links to more DPC videos through this one.)


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Oh, now this is really cool. There's a new site available that lets you find out the divergence times for a whole lot of different species (anything that there is DNA sequence data available for, really - it's based on published data & gives the references along with results). It's called Time Tree, & it strikes me as a really useful tool for using when talking about evolutionary relationships. Easy to use; just don't let it think for you :-) I tried 'chimpanzee' & 'human' for my first search, & TimeTree initially wanted to compare humans to chimp pinworms, which are an intestinal parasite. Which would also give an interesting result - one with a much greater divergence time than my original chimp/human pairing, which comes in at between 5.78 & 7.28 million years ago. (Thanks to ERV for the original link.)

I could spend a lot of time there, but I really should get back to my marking...

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But I simply couldn't resist this particular headline from the Royal Society's news bulletin. (Not the RS's doing, they simply select science-y headlines & send them round):

Museum asks, what is greatest invention?  Science Museum in London choses the steam engine, the X-ray machine, the electric telegraph, the DNA double helix, Stephenson's Rocket train, the Apollo 10 rocket capsule, the Model T Ford car and the Pilot ACE computer.

To me the odd one out is the DNA double helix - it's simply not an invention! The discovery of the structure of DNA is an enormously significant scientific event, but the helix has always been there, so it surely can't be claimed as an invention. (This reminds me of various attempts to patent particular gene sequences. I've never quite been able to understand that one, as the sequences already exist. I guess I'll never make an entrepreneur!)

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... and a VERY happy me. Not to mention the rest of our team. Because -

- we won 'Best Premier Feature Site 2009' at Fieldays :-)

And it's been a very busy few days, hence my lack of anything substantial for you to really get your teeth into. But I promise, this will be rectified anon.


And now we have a photo to prove it :-)

swan girl & fieldays site for blog.JPG

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It's Fieldays time again (my excuse for not writing something 'solid'!). This time round the theme is 'my land, our environment'. Many of my colleagues are doing work on issues directly related to this theme - & they have an international reputation for the excellence of what they do.

Anyway, the challenge was to represent some of this on the stand - again, with the expert help of Adam from Station Creative. And to do it in a way that tells a bit of a story. So...

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I've written a couple of posts on 'Ida' (Darwinius massillae) - the 47-million-years-old fossil primate which has been the focus of so much media hoop-la. For those of you who would like to read more widely about this discovery, Laelaps has hosted a blog carnival where he's brought together links to some great writing by a large number of other commentators.

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I talk and write quite a bit about why science outreach is important, and it's always nice to hear what someone else has to say on this issue. So I was really pleased to find this commentary by Lawrence Kraus (thank you to Laelaps). Lawrence's post is on a rather cool new site called the Science & Entertainment Exchange, which includes a blog whose authors write about the interface between science & the entertainment industry (think entertaining movie fliers with a hit of science: just how many helium balloons would be needed to actually lift a house, as per the plot of Up??). What fun!

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Back in 2006 Hamilton held a referendum on the issue of whether or not the city's water supply should continue to be fluoridated. (We even held a Cafe Scientifique about it.) At that time 38% of eligible voters returned voting papers, & 70% of those voters wanted fluoride retained in our water. So I had a feeling of deja vu when I saw in Friday night's paper that there is a move afoot among some councillors to have fluoride removed.

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I've just started reading Donald Prothero's book Evolution: what the fossils say and why it matters. It looks good & certainly captured my attention right from the start. (However, it will probably take me a little while to get through the book as at the moment it's my pick for when I'm on the stationary bike at the gym. And I could do with getting there more often!)

Anyway, I thought I'd share a couple of paragraphs from right at the start of the book, because they set out so clearly what science is

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says it all, really :-)

song chart memes

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Back in February, after a close friend died of cancer, I commented briefly on the link between evolutionary principles and our understanding of cancer. This is an interesting field of research and now I see that there's another new paper out on the subject. And there's also a very thorough review (of both the paper and this whole interface between oncology and evolution) out today on Orac's website. As I've said before - he's the expert in this area - so go over there & check out his post.

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Both from the pen keyboard of Brian Switek, on his blog Laelaps.

The first begins with a quote from Charles Darwin's Voyage of the Beagle, recounting the genocidal approach of an Argentinian general towards some of the local indigenous tribes. Darwin found this approach horrifying, but also doubted that there was much that could be done about it. Brian goes on to propose an historical hypothesis about how these experiences might have influenced Darwin's thinking on extinction (which he recognised went hand-in-hand with evolution).

The second - on Saartje Baartman - rang a bell with me when I saw it, because some years ago I'd read an article about Saartje by Stephen Jay Gould. In fact, on checking my library just now I find that Gould wrote about Saartje at least twice: she gets a brief mention in The Mismeasure of Man - an excellent book that examines the history of our many attempts to measure 'intelligence', & makes it clear that the various hypotheses underpinning these efforts are often - too often? - informed by underlying prejudices. And there's a much longer treatment of her story in The Flamingo's Smile.

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I'm marking essays at the moment (& casting about for ways to procrastinate - I can mark only so many essays in a sitting!). This made me think about the essays those of you sitting Scholarship will be writing at the end of the year - try to avoid a few of these common errors.

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