Posts Tagged new science stories

today’s big earthquake in chile Alison Campbell Feb 28

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Friends rang us in great excitement this morning to ask if we were following the news about the big earthquake in Chile, and of tsunami alerts that had been issued for coastal areas around NZ. (The answer was actually ‘no’; I’d just got in from a walk with the puppy & hadn’t turned the radio on.)

Anyway, the Science Media Centre has some very good commentary & resources centred on this seismic event, & I thought that those teachers with students who’ll be working on ‘Planet Earth’ standards this year might find them extremely useful. There’s a media briefing here, and a post by Peter Griffin, that includes a presentation by Victoria University’s Dr John Townsend, here.

Big quakes are not uncommon in Chile, given that it sits above the boundary of two big tectonic plates. Charles Darwin wrote about the aftermath of one such event in his Beagle diary, and it’s still worth a read today. He also complained, in a letter to his sister Catherine, about how he’d experienced ‘just’ one little earthquake himself – he almost sounds disappointed! Those looking for some other reading material might enjoy Perils of a restless planet by Ernest Zebrowski. I found it fascinating, although my Significant Other laments that there a are no colour pictures (hardly surprising when you consider that the book covers past events, some of which occurred well & truly before cameras were invented, much less colour film!)

meta-analyses – testing relationships Alison Campbell Feb 16

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One of the nice things about working at a university is that there is almost always an interesting talk to go to (supposing you have the time…). Yesterday I managed to go to a fascinating discussion of the use of meta-analyses by a Waikato graduate, Shinichi Nakagawa. (I suspect that Grant knows much more about this technique than I do, but Shinichi’s talk was very post-provoking.)

Shinichi began his studies here a year or so after I joined the University staff. He was invited to do a BSc(Hons), something reserved for the really able students, & it’s a sign of the quality of his research project (on zebra finches) that he’s since published five papers from it. After gaining his PhD at a UK university, Shinichi’s come back to New Zealand to work at the Universit of Otago. Over the last few years he’s begun to use meta-analyses more & more to identify relationships (or the lack of them) between data sets, & this particular research tool & its applications were the subject of his enthusiastic presentation. (He recommended Morton Hunt’s 1997 book How science takes stock: the story of metanalysis as an excellent introduction to the area, written by a journalist for a lay audience.)

I’ve referred to meta-analyses myself, from time to time. The Cochrane Collaboration, for example, makes use of them in examining the (claims for) efficacy of various medical treatments. Essentially the technique involves combining the data from a range of studies (allowing for sample sizes & so on), producing summary results that may allow recognition of a statistically significant pattern in the data. (It may equally show that there’s no real relationship between a set of factors, as Shinichi noted. Alternative treatment modalities such as acupuncture & homeopathy, for example, have been shown to perform no better than placebo as an outcome of  meta-analyses.) The larger sample size afforded by a meta-analysis allows greater confidence about the results.

The technique does have its disadvantages: you could be accused of comparing apples with oranges, for example, although this could be overcome by proper selection of the studies for inclusion in the analysis. There’s perhaps a greater problem (Shinichi described it as the ‘file drawer’ problem) whereby studies with a non-significant result are less likely to be published, thus biasing the pool of studies available for inclusion in a meta-analysis. Shinichi described how he’d had difficulty publishing a paper on sparrow parental care because it had a negative result. Now, there’s nothing wrong with this, & a fairly large proportion of experiments would come up with such an outcome, but unfortunately this doesn’t make good headlines:-) And the editorial attitude described here both skews publications in a particular direction & also skews public perceptions of how science is done.

We then heard about a few research areas where meta-analysis had been applied to a large body of data to test prevailing views. Should we take antioxidant supplements, for example? Not according to a 2007 study, that found an increased mortality rate associated with their use. While this particular study had its critics, a paper published last year in Nature found evidence that antioxidants can actually help cancerous cells to grow. (Mind you, there is a need for caution in interpreting studies like this last one, given that it was done on cancer cells in vitro – there needs to be a fair bit of follow-up work to see if this holds true in the body.)

The final example in Shinichi’s talk looked at the widespread view that a restricted calorie intake can prolong life. (Obviously there would be limits to this one & it’s not a case of living longer & longer on less & less. Eventually there’d be a point in which the lifespan was shortened rather abruptly. And terminally.  Rather like the work of Famine in the wonderful Good Omens by Terry Pratchett & Neil Gaiman.)

Anyway, individual studies of rats & monkeys, fruit flies & nematodes, & even yeast, seem to bear out this idea – it looks like a general biological phenomenon. Our speaker seems to enjoy doing meta-analyses – he commented that a preliminary review f the literature, & an introductory analysis, shows no conclusive evidence that calorie restriction has any positive effect on the length of life, not as a general principle. He found there was no consistency in the data for different species. In the discussion at the end, someone pointed out that almost all the work in the area of dietary restriction’s been done in lab-bred animals, and might not reflect what happens in ‘wild-type’ individuals. And it’s more important to look at the carbohydrate/protein balance in the diet, rather than the overall reduction in calories.

And, of course, the sting in the tail – from an evolutionary point of view, if you don’t produce fertile offspring & thus pass on your genes, the length of life is actually irrelevant. If you lived to 120, but left no fertile children, you’d be an evolutionary non-event…

an update on facilitated communication Alison Campbell Feb 16

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A while ago now I wrote about Rom Houben, who’d been in a vegetative state for 23 years but who, it was claimed, was really conscious inside an immobile body & now able to communicate via something known as ‘facilitated communication’. I and many others were sceptical of this claim – it looked too much as if the ‘facilitator’ was controlling what was going on. (That’s not to say they didn’t genuinely believe that they were assisting Mr Houben to communicate.) And there were simple ways to test this, which at the time the lead researcher in the case seemed to feel unnecessary.

Now Steve Novella reports that such a test has been done. Mr Houben was shown several objects while the ‘facilitator’ was out of the room, & subsequently asked to name them with her assistance. He got none of them right. Not one. This very strongly suggests that the facilitator, consciously or otherwise, was imposing her own words & understandings on Mr Houben, and supports Dr Novella’s characterisation of ‘facilitated communication’ as a pseudoscience. (My fellow Sciblogger Darcy Cowan has also posted something about this.)

I feel intensely sorry for Mr Houben & his family in all this. If Mr Houben really does suffer from ‘locked-in syndrome’ (one possible diagnosis), then imagine how that must be for him, day after day. And imagine how profoundly frustrated you would be, in that context, if some well-intentioned person began claiming to help you to ’speak’ – and got it all wrong. And his family – his mother had insisted for years that her son really was alert inside his unresponsive body. To be told that he was, to have him ’speak’ to her, and then to have all that taken away by the lead researcher’s admission that he’d got it all wrong – to me this is indescribably sad.

It also saddens me that people will continue to cling to the hope – exemplified by one of the commenters on Dr Novella’s post – that facilitated communication really does offer the chance of communicating with people who are otherwise cut off from their loved ones (eg children – & adults – with severe autism). But, as the Houben case shows, the words will be those of the facilitator, regardless of their beliefs or intent. (And in case you think I’m being too harsh here, the Houben case is not the only one where the idea of facilitated communication has been shown to be false.)

grumpiness is best? Alison Campbell Feb 02

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ResearchBlogging.org

Today’s Herald carried a story from the UK’s Telegraph, which looked at some research into the social behaviour of chimpanzees & bonobos (’pigmy’ chimanzees). And – as usual – extrapolated from this to people… Grumpiness, it told is, was a sign of a more ‘advanced’ nature, whereas the happier, more peaceable bonobos were ‘less evolved’.

The article doesn’t begin well: Researchers looked at two different kinds of monkey – the familiar chimpanzee and the less evolved but much more easy going bonobo. Chimps are monkeys??? Arrggghhh! And the ‘less evolved’ really grates. Humans & chimps last shared a common ancestor around 5-7 million years ago and, as the recent swag of publications about ‘Ardi’ have shown, the two lineages have followed different evolutionary paths since then. (Bonobos & chimps subsequently diverged from each other 0.85-2.5 million years ago – & are as ‘evolved’ as each other.) I did wonder if there was a bit of wish-fulfillment there – chimps can be grumpy, & chimps are ‘more evolved’ than bonobos, so grumpiness is a ‘more evolved’ state – good news for all those grumpy human prima donnas :-)

The newspaper story was based on a paper in Current Biology entitled Bonobos exhibit delayed development of social behavior and cognition relative to chimpanzees (Wobber et al. 2010). The researchers compared chimpanzees (Pan troglodytes) & bonobos (Pan paniscus), looking at differences in the animals’ social behaviour & also their cognition in order to test the hypothesis that certain aspects of behaviour or cognition in adult bonobos represent developmentally delayed forms of the traits found in chimpanzees (Wobber et al, 2010:1). In other words – that differences in behaviour could be related to differences in development: adult bonobos show some ‘juvenile’ behaviour patterns (eg play, & non-reproductive sex) compared to adult chimps, & also show a degree of paedomorphism in their cranial structure.

In particular, the team looked at behaviours to do with sharing/competing for food: for each species they gave the animals a food-sharing task, using male:male, male:female & female:female pairs, for a total of 30 chimps and 24 bonobos. The results: older bonobos were as tolerant as juvenile animals when it came to sharing food, but adult chimps were much less so. The adult bonobos were also more playful (including sexual play), which the authors thought might affect their tolerance for sharing food. A subsequent trial of infant & juvenile bonobos & chimps found that pre-weaning bonobos were less adept at social behaviours related to feeding competition than pre-weaning chimps. And finally they looked at the ability of the two species to adapt to ‘role reversal’, where human experimenters switched roles in terms of which possessed a hidden food reward: young bonobos were slower than juvenile chimps, and adults of both species, to adapt each time a researcher switched roles. (It would be nice, though, to see some data from observational field work here – using a human experimenter does introduce new variables that might not apply in the wild.)

Overall, the authors concluded that [u]nderstanding the evolutionary processes by which ontogenetic changes occurred in bonobos may provide insight into our own species’ evolution. [It's been] proposed that the crucial cognitive adaptation of humans relative to other apes is the accelerated development of social skills in infants. Althought the genetic changes that produce such developmental shifts are not well understood, if we can determine the process by which the ontogeny of bonobos evolved, inference can be made regarding analogous evolution in our own species (Wobber et al. 2010: 4) In other words, having an understanding of the control of behaviour development in bonobos may tell us something about the evolution of our own social behaviour.

But it’s a big jump to suggest (as the Telegraph does) that the heightened intolerance for food sharing shown by adult chimps is a ‘higher’ form of behaviour (with the implication that grouchy behaviour in humans is somehow a ‘more evolved’ trait). After all, like bonobos, humans show a reasonable level of paedomorphism in their general appearance, resembling young chimps in their relative facial proportions & in their lighter body hair. But this apparent similarity between humans & bonobos is the result of parallel evolution. Similarly, humans & P.troglodytes have an equally long history of separate evolutionary development, such that any apparent similarities in behaviour (eg grouchiness as a successful food-competition strategy) may well be more perceived than actual.

V.Wobber, R.Wrangham & B. Hare (2010). Bonobos exhibit delayed development of social behaivour and cognition relative to chimpanzees current biology, 20 : 10/1016/j.cub.2009.11.070

rocket science & testosterone Alison Campbell Dec 14

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No, I’m not trying to suggest that spaceship designers/engineers have to be male. That would be a) stereotypical & b) incorrect as well, given that women also produce a certain amount of this hormone. But I wanted to catch your attention & direct it to a post by Ed Yong on Not exactly rocket science, where he discusses a recent bit of research on the influence of testosterone on behaviour. I first saw this story in the NZ Herald (there’s a copy of the article here) when the husband drew my attention to it. This is an interesting piece of research because it shows (again) just how strong the power of placebo can be: women who believed that they’d received testosterone (even if they’d actually received a placebo) behaved in the stereotypical belligerent way – but women actually under the influence of testosterone behaved more altruistically than expected. Fascinating stuff.

an update on xenotransplantation Alison Campbell Dec 11

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This one’s really for those teachers who might be thinking of getting their year 13 students to look into xenotransplantation. I’ve written a bit about this previously, but you might also be interested in the following, from the Science Media Centre:

Animal-human transplants OKed
Auckland-based Pig cell therapy pioneer Living Cell Technologies looks set to expand its trials across the Tasman in the near future, following a move by the Australian Government to lift a ban on animal to human tissue transplants.

LCT’s Professor Bob Elliot told NZPA last night that "…some trials of its implants for type-1 diabetics may be tested in Australia when the company needs multi-site clinical trials. And eventually, the company might establish a quarantine colony of the pigs it breeds to slaughter for tissues that can be implanted in human patients."

The AusSMC wrapped up reaction from scientists in Australia to the news of the five year ban being lifted.

do flies do housework? Alison Campbell Dec 08

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Some more entertaining & educational reading for you while I’m away :-) This time it’s from the Bug Girl’s Blog, where the eponymous Bug Girl describes as ‘egregious’ the headline  Fruit Fly Sperm Makes Females Do Housework After Sex. Visit the Bug Girl’s place to find out not only what egregious means, but also why she’s so annoyed about the headline. (I would have written an ‘annoyed’ something too, if I’d found the news item myself!)

some interesting links to follow Alison Campbell Dec 05

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Casting around for something to read, I’ve come across several interesting posts on various blogs. So I thought I’d share them with you :-)

For those interested in competition & its effects on plant growth forms & also plant diversity, check out Taking below-ground processes seriously: plant coexistence and soil depth at The EEB & flow. We do tend to focus on ‘above-ground’ plant relationships – this is a timely reminder that there’s a whole other world beneath our feet :-)

Our family is occasionally lucky enough to have a fishing friend present us with a crayfish. A live crayfish. I hate the way they try to climb out of the stockpot when they’re put in there – but is there a better way to kill a crustacean than by boiling it? The Neuro Dojo has a look at some recent research & says, mmm, perhaps not…

And for those of you interested in endosymbiosis, the Lab Rat talks about some recent genomic research into the question of just where did plastids come from.

That should keep you quiet for a little while :-)

gannet monogamy model moot Alison Campbell Dec 01

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When you studied animal behaviour in year 13 you probably learned about the different mating systems: polygamy (polygyny & polyandry), promiscuity – & monogamy: a bond between a single male & a single female. You may also have heard that in some species, such as swans, that bond is life-long.

It turns out things are more complex than that. My first inkling of this came back when I was working on the literature survey for my PhD on behaviour in black swans, & found (rather to my surprise – I was probably too naive for my own good back then) that swans indulged in some definitely non-standard breeding practices, with more than one paper describing a menage a trois (one female, 2 males). Cuckoldry wasn’t unknown, either. Plus, our own stitchbirds are known to practice polyandry, polygyny, and monogamy as well; homosexuality’s been documented in a large number of animal species; & of course there’s that recent example of oral sex in fruit bats. Anyway, the concept of variations on monogamy in swans got me thinking & I realised that for monogamy the idea of life-long fidelity probably didn’t hold either – after all, if your current partner is incapable of producing offspring, or turns out to be a lousy parent, it’s probably worth your while (in genetic & evolutionary terms) to divorce them & find a new one. Plus, if one partner dies, the other is unlikely to sit around doing nothing (in the reproductive sense) for the rest of their life. But it wasn’t something I investigated further at the time.

A new paper by Stefanie Ismar & her colleagues (Ismar et al. 2009 – based on Ismar’s PhD research) looks at the frequency & costs of divorce in Australasian gannets. (Not the costs of a settlement – the reproductive & hence evolutionary costs!). Gannets have long been another example of life-long fidelity in animals. They nest in large colonies (the best-known in New Zealand are probably those at Cape Kidnappers & Muriwai beach) & are highly territorial within those colonies, aggressively defending the small area immediately around their nest site. Each breeding season the males arrive at the breeding colony first, re-establishing their territories & waiting for the females to turn up – the birds are philopatric, which means that they are strongly attached to the colony where they were hatched & will return there to breed themselves. Although this set-up is described as monogamous, Ismar et al. cite genetic research showing at least some chicks have ‘extra-pair parentage’ – they’re produced by matings between one partner & an outsider (I’d suggest sneaky copulations between the female & a roaming, possibly neighbouring, male, as it would be harder for a strange female to come in & lay eggs in an established pair’s nest).

The study population comprised individually-banded gannets in part of the Cape Kidnappers colony. Ismar recorded the presence/absence of individuals, the presence of pair bonds, & the reproductive success of breeding pairs (where possible comparing her data with those from previous breeding seasons). From this the team was able to determine if members of a pair had divorced (one living with a new partner but the previous mate also present in the colony) or if a mate had been lost (ie didn’t reappear at all in the subsequent breeding season).

They found that divorce rates ranged between 40-43% – so much for gannets faithful unto death :-) This sounds high – were the birds accruing any reproductive advantage through their fickleness? Well, over the 2-year study period, pairs that remained together had significantly higher reproductive success (they fledged more chicks) than individuals who’d lost a mate & subsequently re-mated. Similarly, divorcees fledged fewer chicks than birds who retained their mates from the previous season (although the difference was statistically significant only for the 2008-09 season). These results suggest that there’s a benefit to sticking with the same mate when you can, perhaps because it takes a bit of experience to learn to cooperate with a partner in rearing the chicks. This would explain why first-time breeding pairs often have a lower breeding success than long-established pairs.

So why the high divorce rate? The researchers suggest that this may reflect delays in partners arriving at the colony. A bird who waits too long for their beloved to turn up may end up not breeding at all, so divorce could represent a compromise that offers at least a chance of reproductive success (the entertainingly-named ‘musical chairs hypothesis’). However, it’s still too early to completely rule out the idea of divorce as a way of minimising mate incompatibility, or perhaps minimising inbreeding  - as the authors say, more research is needed to unweave the ecological & behavioural determinants of breeding success in long-lived seabirds. 

Ismar, S., Daniel, C., Stephenson, B., & Hauber, M. (2009). Mate replacement entails a fitness cost for a socially monogamous seabird Naturwissenschaften DOI: 10.1007/s00114-009-0618-6

moa evolution & new zealand’s geological past Alison Campbell Nov 30

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The Level 3 & Scholarship examiners often ask you to discuss the evolutionary history of a group of organisms (Hebe, cockroaches, cicadas etc) in relation to the geological history of New Zealand. Geological changes such as the widening of the Tasman Sea, and the uplift of mountain ranges including the Kaikoura ranges & the Southern Alps, can drive evolutionary change through the isolation of populations (the Founder effect, genetic drift) & changes in selection pressures.

A new paper just out  has done just this for the moa (Bunce et al., 2009), combining "mitochondrial phylogenetic information from 263 subfossil moa specimens from across NZ with morphological, ecological, and new geological data to create the first comprehensive phylogeny, taxonomy, and evolutionary timeframe for all of the species of an extinct order." This includes evidence that for much of the last 30 million years or so, the North & South islands were geographically isolated, which would have provided the basis for allopatric speciation of the fauna & flora on those 2 landmasses.

You may be reasonably familiar with the idea of adaptive radiation in relation to moa & other ratites, as it’s a common example of this pattern of evolution in senior biology textbooks in NZ. At the moment scientists think that ratites first evolved around 80 million years ago (mya) in Gondwanaland, diverging – as the supercontinent broke up – into groups that gave rise to the modern ostrich, emu, rhea, cassowary, kiwi, & the extinct elephant birds and moa. As a taxon, moa also show considerable adaptive radiation, although until recently it was difficult to tell just how many species there actually were. On the basis of morphological & aDNA data, Bunce & his colleagues suggest some changes from the till-now current taxonomy for moa, shown in the following figure (they reduce the number of species from 11 to 9, for example).moa systematics bunce et al.png

Fig.1 from Bunce et al. (2009): Systematics, dimensions and approximate distributions of moa in the three family, six genera, nine species taxonomy advocated in this study. doi/10.1073/pnas.0906660106

The data from ancient mitochondrial DNA also allowed the team to study the time-frame of moa evolution. Earlier studies have suggested that the moa radiation occurred about 15 mya, but Bunce et al.’s data indicate that the two main groups of moa (the Dinornithidae & Emeidae) happened just 5.27 mya - much more recently. (The 2009 paper discusses the reasons why their figure differs so significantly from the earlier one, which was also based on aDNA, & suggest this is related to how the data were calibrated.)

What was happening in NZ during that period, in ecological terms, that might have driven this divergence? One factor is the rapid orogeny (mountain-building) that we know was happening at around that time. This would have provided a range of new, untapped habitats for moa & other species to exploit – and new selection pressures as well. For example, as the Southern Alps rose up, they increasingly blocked the predominant westerly airflows, favouring the development of wet rainforests on the West Coast and a warmer, drier environment on the eastern side of the mountains, opening the way for niche specialisation and speciation. This could have been quite complex, as during glacial periods glaciers extended to the coast on the western side of the island & well down into the eastern low country, further subdividing habitats & providing additional barriers to gene flow.

In addition, from about 2 mya relatively short-lived land bridges linked the main land masses, allowing movement between the two islands. (This partly reflects the impact of glacials during the last ‘ice age’, at their peak lowering sea levels around NZ by at least 100m.)

moa evolution & changes in NZ geography.png

Fig.2 from Bunce et al. (2009) A spatial & temporal context for the evolution of moa. Molecular phylogeny and date estimates of the moa radiation… compared with the new paleogeographic model of Neogene New Zealand. doi/10.1073/pnas.0906660106 NB the authors caution that the timings of divergence for the various species are provisional – it would be useful to have data from many more moa specimens, to improve the accuracy of the calculations.

A great deal of new work has gone into developing those maps, particularly in the King Country, Taranaki, & central Hawkes Bay, plus data from exposed onshore marine sediments and oil exploration drill sites. During the Oligocene (> 25mya), the New Zealand land mass was reduced to a string of low, well-separated islands. Bunce et al. comment that, even when the northern landmass was re-emerging, it was still completely separated from the South Island by the Manawatu Strait (see maps above) until roughly 1.5-2 mya. Thus any land animals (& plants!) that couldn’t cross the strait were geographically isolated for that entire time. But – the moa genetic data don’t show any indication of divergence that far back, which means that the various lineages probably descended from ancestors on a single island. Fossil evidence fingers the South Island as the ancestral home, which means that moa couldn’t have colonised the North Island until less than 2 mya, only to be isolated again when Cook Strait first formed 450,000 years ago. (This interpretation is supported by data from other vertebrate remains.)

But there’s still a lot to learn! The authors conclude by saying that this "important new geological model of Neogene NZ emphasises our current lack of knowledge about the pre-Pliocene landscape, and raises important questions about the role of marine barriers and the biotic diversity of the north and south islands. The combined geological and genetic data suggests that the NZ Neogene terrestrial record is likely to have been marked by the significant loss of terrestrial endemics from a highly unusual environment, which is only just beginning to be characterised."

Bunce, M., Worthy, T., Phillips, M., Holdaway, R., Willerslev, E., Haile, J., Shapiro, B., Scofield, R., Drummond, A., Kamp, P., & Cooper, A. (2009). The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0906660106

 

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