SciBlogs

Archive October 2009

a tale of several fishes Alison Campbell Oct 31

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Well, Marcus & I have just completed a Scholarship preparation session in New Plymouth – it was (I hope!) a useful & enjoyable time for all involved. Marcus & I enjoyed it anyway – we both get a buzz out of working with groups like this (one of the reasons, as far as I’m concerned anyway, is the very perceptive questions & suggestions that students come up with.)

Anyway, my group spent a fair bit of time working through last year’s Schol Bio paper, including this question: Identify  and discuss the patterns and processes of antifreeze glycoprotein (AFGP) evolution in polar fishes. The question also provides quite a bit of contextual information – and it’s really important that you read this carefully! It contains a lot of useful data that you can integrate into your answer (& the markers would have been looking for this).

Antifreeze compounds are, as you might perhaps expect, not uncommon in organisms living in polar regions. Most, but not all, are glycoproteins – proteins with saccharide sidegroups. They function to lower the organism’s freezing point, reducing the risk of ice crystals forming within the tissues (& thus rendering cells leaky,squishy, & generally dead). More precisely, according to the US National Science Foundtation, they ‘plug gaps in existing small ice crystals, … [preventing] the attachment of more ice molecules’, thus stopping the ice crystals from growing large enough to be damaging.

Two groups of animals possessing antifreeze glycoproteins (AFGPs) are the arctic cod (found, as the name suggests, in northern polar waters) and the notothenioid fishes of the Antarctic seas. While these fish groups are poles apart (sorry! couldn’t resist that one!), as the Schol paper says, ‘the AFGPs [they produce] are virtually identical and they both contain the same repeating sequence of three amino acids (threonine-alanine-alanine).’

So, what pattern of evolution are we seeing here, and how might it have evolved?

You’ve probably said, convergent evolution, & you’d be right. But this wouldn’t be enough to keep the examiner happy. You’d also need to explain what you understand by the term ‘convergent evolution’, and the evidence you used to come to this decision. In convergent evolution, organisms which are only distantly related – & whose last common ancestor lacks the trait in question – independently evolve the same or very similar adaptation in response to similar selection pressures. Sharks, dolphins, and the extinct ichthyosaurs all show convergence in body shape, for example. In the case of the polar fishes, there are two lines of evidence that you could cite. The context material included the information that the AFGP genes are found in quite different chromosomal locations in the two groups and have different origins, and yet the proteins are essentially the same, which suggests an independent origin followed by convergent evolution.

There is also the issue of when this particular gene evolved. Again, the contextual info is helpful here. Antarctic waters are to some degree thermally isolated by a circumpolar current, which formed around 30 million years ago after the final separation of Antarctica from South America, Once this happened water temperatures started to drop, getting down to around freezing point about 10-15mya. (Scientists can date these events using oxygen isotope ratios from sea-floor sediment cores – and ‘well done!’ to the student today who knew about that.) Scientists think that at this time there was probably only a single notothenioid species, and that this species acquired the AFGP mutation. (You shouldn’t think that this was the first time this particular mutation occurred, as it almost certainly wasn’t – but it would have been the first time that a fish bearing the mutation was likely to be at a selective advantage from it.) The Arctic Sea, on the other hand, didn’t freeze over until about 4-5 million years ago, and so that’s the earliest point at which an AFGP would be subject to strong selective pressure in its favour- strong evidence for independent origins of the AFGPs. (It also gives us the earliest likely time for polar bear evolution, although many scientists think they evolved much more recently than that.)

As for the part of the question that asks about processes of evolution – here the examiner’s asking you to integrate your knowledge of how natural selection operates with specific information about the ice fish. (That is, you wouldn’t get a lot of credit for talking about natural selection only in very general terms.) You could also talk about speciation within the notothenioid fishes of the Southern Ocean, given that the question identifies two particular species (‘bald notothen’ & ‘threadfin pinhead’) and also tells us that there are more than 100 species of notothens.

Natural selection requires that there be some heritable veriation among the members of a population, so you’d start off by reiterating that some individual(s) in a single species would have to gain the AFGP mutation. (If it had happened independently in more than one notothen species, you’d expect to see some evidence of that, in terms of chromosomal location and origin of the gene(s) concerned.) As the oceans cooled, those individuals possessing the mutation would have been at a selective advantage compared to those without – they’d be more likely to survive & reproduce, and at least some of their offspring would possiess this beneficial mutation and pass it on in turn to their own offspring. Combined with continuing directional selection (progressively cooler waters) this would see the AFGP allele spread throughout the ancestral species population. At the same time, those fish species lacking AFGPs would become locally or globally (if they couldn’t migrate to more sutiable habitat), thus leaving a range of ecological niches. And this in turn could drive further speciation of that ancestral ‘ice-fish’.

An excellent question, & it generated some excellent ideas today. And now I’m off for a walk :-)

wolves in the cross-fire Alison Campbell Oct 30

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A while back I wrote about the wolves of Yellowstone & what they can tell us about the ecological impacts of a top predator. Wolves were reintroduced to the US’s Yellowstone National Park in 1995, after an absence of around 50 years, & wildlife biologists were having a field day (pardon the pun!) examining the ecological impact of this reintroduction.

Since their reintroduction, wolf numbers in the park have grown to in excess of 100. One researcher had radio-collared a number of wolves in order to track their movements & identify their ranges – which were found to extend beyond the park’s boundaries. After all, animals can’t read signs**. And this placed the wolves at risk – outside the park they are viewed (by the local farmers & in legislative terms) as animals in need of control, just like moose & other deer.

So that researcher was doubtless devastated when two of his collared wolves were shot by hunters during the ‘open’ season in rough country surrounding Yellowstone (Morell, 2009). The wolves were caught by a double whammy – their own behaviour & the perceptions and attitudes of the human populations surrounding the park. Wolves from Yellowstone are naive as far as human intentions go – within the park they are fully protected & the focus of a lot of tourist attention, so in terms of behaviour they would not have learned aversive/avoidance behaviour patterns that would stand them in good stead outside the park’s boundaries. And they need those behaviours: ranchers living around the park opposed the initial reintroduction on the grounds that the wolves would target livestock, & are allowed to shoot those that do (or are claimed to). And hunters pushed successfully for a hunting season this year, albeit one with a seemingly limited quota of 12 animals. ‘Seemingly’, because 12 is a large chunk out of the total population, and since one of the dead wolf was known to have 5 five-month-old pups, unlikely to survive on their own, the total mortality will be even higher.

The loss of these wolves, & the manner of their deaths, will have a significant negative impact on the various research projects centred on these large predators. The ecological ramifications are also significant. Scientists worry that if the wolf hunt is an annual event, this will have the effect of skewing the population’s age structure towards the younger age classes. This in turn will affect the park’s elk population, because younger wolves apparently kill more elk, although you could argue that this will be good for the area’s vegetation. In addition, removal of wolves from the area surrounding the park may cause that area to act as a ‘sink’, drawing into it wolves that might otherwise have remained within the park boundaries and making them targets in their turn, with an overall negative effect on the population. For the wolves, all the news is bad.

V.Morell (2009) Research wolves of Yellowstone killed in hunt. Science 326: 506-507  

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And for something a little more cheerful, on the issue of animals reading signs:

ask for directions.jpg

another contender for ‘best blog post title’ Alison Campbell Oct 30

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I thought it would be hard to beat ‘When zombies attack’. That was, until Grant alerted me to this one: ‘Fellatio by fruit bats prolongs copulation time’. The fiend! How did he beat me to this?? Ed Yong has written all about it on his blog, Not Exactly Rocket Science, and you can find the original PLoS paper here. (Now I come to think of it, I did see a male fruit bat doing a spot of what looked awfully like masturbation against the mesh of his cage, when we were in Vanuatu last year…)

people can believe some very strange things… Alison Campbell Oct 27

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I was spurred to write this by reading the latest post on the Quackometer. Dr Luc Montagnier shared the 2008 Nobel prize for medicine or physiology, for the discovery of the human immunodeficiency virus, a discovery with a significant impact on our understanding of the evolution and spread of Acquired Immune Deficiency Syndrome (AIDS).

However, as the Quackometer notes, he’s recently published in a different area. A rather strange area…

Earlier this year Dr Montagnier, along with several colleagues, published a paper entitled Electromagnetic signals are produced by aqueous nanostructures derived from bacterial DNA. (The term ‘aqueous nanostructures’ rings an alarm bell as it sounds awfully like some of the claims made about homeopathy.) The paper abstract states that

A novel property of DNA is described: the capacity of some bacterial DNA sequences to induce electromagnetic waves at high aqueous dilutions. It appears to be a resonance phenomenon triggered by the ambient electromagnetic background of very low frequency waves. The genomic DNA of most pathogenic bacteria contains sequences which are able to generate such signals.

The paper goes on to claim that these electromagnetic waves are associated with some unspecified ‘nanostructures’ in water (hence the title of the paper), & to suggest that these EM waves in some manner allow a re-creation of the microorganisms that originally produced them – even when the solution is so dilute that it can contain none of the original DNA!. This second claim seems to be based on the following finding:

 

filtration of a culture supernatant of human lymphocytes infected with Mycoplasma pirum, a microorganism of about 300 nM in size, through filters of 100 nM or 20 nM porosities, yielded apparently sterile fluid. The latter however was able to regenerate the original mycoplasma when incubated with a mycoplasma negative culture of human lymphocytes within 2 to 3 weeks.

Extraordinary claims require extraordinary evidence. And the first evidence I’d be looking for, with regard to the above quote, is absence of any possible sources of Mycoplasma contamination…

Anyway, you can see why I thought of homeopathy. Basically, this paper is suggesting that you can take the DNA from some pathogen, dilute it (with regular shaking at each dilution, and a thorough filtering after the first couple of dilutions) beyond the point where any of the original substance can be present – & somehow set up ‘nanostructures’ in the water that manage to emit particular EM frequencies that indicate the original presence of the pathogen. This is supposed to work for a range of different human pathogens, both bacterial & viral. Considering the differences in their DNA, I would have expected that – in the extremely (very, very extremely) unlikely event of this being a real effect – you’d expect to see differences in the EM waves detected. Tellingly, the authors report that the frequencies emitted are all alike, regardless of the bacterial species involved, although they do put this down to a lack of sensitivity in their equipment. (While I’m not a physicist, I do wonder about their equipment, & so did a number of the Quackometer’s commenters – perhaps Marcus could say whether it would be capable of what’s claimed for it.)

Now, there are a lot of questions that spring to mind about this paper. Why do only pathogens emit these EM waves? And only human pathogens, at that: why don’t all microorganisms do it? What’s more – as the Quackometer says – where’s the evidence of any mechanism by which DNA could emit such radiation (given what’s normally needed to generate radio waves)? Our chromosomes are not miniature radio transmitters.

If you’ve seen my earlier comments around reliability of sources, you’ll also know that another question we should be asking is, who published this material? ScienceNature? The Quackometer reveals that the paper was published in the Journal of Interdisciplinary Sciences: Computational Life Sciences, 3 days after submission - which is a pretty clear signal that it wasn’t subject to normal peer-review processes  ie no-one’s had a good critical look at the methodology & results prior to publication. Peer review isn’t perfect, but it does help us to be fairly sure that the quality of the work being presented is reasonably good.

The worry here is that, because Dr Montagnier has done some excellent science in the past, and rightly been honored for it, some people will think that this latest bit of work is equally good. Indeed, one suspects that, somewhere, these results are already being put forward as an explanation for the supposed effects of homeopathy. Unfortunately they are no such thing – simply evidence that, while we can all be spectacularly right some of the time, we can also be spectacularly wrong.

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PS Those interested in a more detailed analysis of the paper, including the methods used to obtain the claimed results, should read this post – & the comments – at Science-Based Medicine. (Thanks to Grant for pointing it out.)

self-grooming in cows Alison Campbell Oct 26

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From time to time my Significant Other’s thoughts turn to life in the country. This can manifest itself in the purchase of lifestyle-block magazines. I was flipping through one this morning & came across an item on self-grooming in cows, & thought I’d look into it a bit further as it seemed to fit with my last post on cows learning to run mazes. Also I thought it was a rather neat idea :-)

The article was based on a study done by Yute Schukken & G. Young (2009), looking at cows’ use of a self-brushing device & its effect on their health. The project looks like it was contracted by the manufacturers of the device, & it was carried out on a working farm in the US. Remember that cattle there, particularly in the northern states, spend the winter indoors in huge barns, so a lot of their normal ‘in-paddock’ behaviour patterns are quite restricted. The Swinging Cow Brush is a patented device, mounted on a post, that cows can rub up against to groom all those hard-to-reach places.

The study used 4 pens, each containing around 100 cows. Two of the pens held cows in their first lactation: one pen acted as the control & the other contained 2 of the brushes; animals were randomly allocated to a pen. The other 2 pens followed the same set-up, except that the cows were in their second (or higher) lactation. The researchers collected data on milk production, beginning roughly 3 months before use of the brushes was begun & continuing for 6 months from that point. Cows, like many (most?) other animals, do a lot of grooming, & the authors cite an earlier study that found a 5-fold increase in grooming when cows had access to a suitable brush. Schukken & Young’s animals certainly seemed to enjoy the opportunity to use the brush :-) 

 

And they did seem to gain some benefits from the self-grooming. For second-lactation cows – but, surprisingly – not for younger or older animals, there was a statistically significant increase in daily milk production. The authors suggest that cows might be more likely to visit a feed station en route to the brushes, but this doesn’t explain the differences between the age groups.

In addition, cows in the second cow-brush pen (the second/higher lactation group) showed a marked decrease in clinical mastitis. For some reason (please feel free to comment!) younger animals had much lower rates of mastitis to begin with. Presumably grooming enhances the animals’ cleanliness, either directly or because they are more active & so spend less time lying around in their pens. This is an important consideration given that they spend so much time inside in relatively cramped conditions. In other words, this device would appear to have some animal welfare applications, as well as the potential to boost production. It would be interesting to see how much use it received in NZ conditions, where animals spend most of their time outside. Would cows come to the bovine equivalent of a scratching post, rather than rubbing up against trees & fences?

(I was rather surprised, on searching ‘self-grooming’, to find a range of patents for self-grooming devices, many intended for companion animals like cats & dogs. I guess that in your absence, your pet might get some comfort out of something that simulates patting, but I can’t help thinking it would be a real pity if someone spent so much time away from their pet that they couldn’t indulge in a fair bit of real hand-on-fur interaction each day. It’s good for both partners in the relationship, after all!)

Y.H.Schukken & G.D.Young (2009) Field study on milk production and mastitis effect of the DeLaval Swinging Cow Brush. Final research report, August 5, 2009.

teaching old cows new tricks Alison Campbell Oct 25

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I originally wrote the material in this post for the Science on the Farm websiteIt’s re-posted here because I thought it might be an interesting extension for those of you currently studying animal behaviour.

Automatic milking is an exciting technological innovation facing the dairy industry in New Zealand, with the potential to affect farming lifestyles and boost productivity. This technology is quite well-established in Europe, where it’s fairly straightforward to train cows to move from an indoors feedlot to a robotic milking system. However, in New Zealand, with its pasture-based farming systems, things are not quite so simple.  Tania Blackmore, whose PhD research is examining how best to help cows find their way to the milking robot, comments that “It’s not so easy to ensure that individual animals flow smoothly from the paddock to the shed and back to fresh pasture.” Automatic milking requires cows to find their own way to the milking shed, without being driven by humans and often on their own, without herd-mates to follow. This means they are faced with learning how to do this, as well as a range of new behaviours distinctly separate from conventional milking. 

With existing research indicating that cows can perceive the colour yellow, a Waikato University research project looked at whether cows could learn to approach a yellow stimulus (“sign”) as a visual cue to the correct path that they should follow. Firstly, cows learned to distinguish between yellow & grey signs, learning to approach only the yellow stimulus. Why? Because it was associated with a food reward (an example of operant conditioning).

cow & transponder.JPG

This cow is wearing a transponder (blue box) on its left foreleg, so that its movements through the automatic milking system can be tracked by computer.
 

Cows then successfully learned to follow the yellow sign when it was randomly located in simple mazes. Finally, cows used the yellow sign to learn the correct path in a series of more complex mazes, involving multiple turns and the sort of one-way gates that the animals would have to push through on an automated farm. What’s more, once they’d learned the visual cue, the cows were able to generalise that learning to a quite different maze layout.

associating sign with food.JPG

A cow learns to associate the yellow sign with a food reward.

The researchers found that the yellow signs could indeed be used as a visual cue, and that cows could successfully solve mazes when yellow signs were provided – but had difficulty with this task when the signs were removed. The training was successful, showing the potential for cows to learn to follow signs that would make it easier for them to find their way to the milking shed.

 
following a sign.JPG
A cow uses yellow signs to help her to navigate through a maze.

Interestingly, while heifers learned faster, older cows remembered what they’d learned for longer. So you can teach old cows new tricks. But this project involved intensive training – up to 30 days for each cow, with 50 tirials a day. This really would be impractical on a working farm. But there are ways to apply this knowledge. Tania suggests that one option would be to put signs on gates that can be opened: once cows have got through them a few times they would learn that it’s not possible to push through gates that don’t have signs on them.  

 

two ends of the science spectrum Alison Campbell Oct 23

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Today the Science Media Centre carried an item about the just-announced Prime Minister’s science prizes (blogged about here by Peter Griffin). These awards (for a top research team, an emerging researcher, the MacDiarmid Young Scientist of the Year, a science teacher, & a science media communicator) carry a lot of money. They’re sure to be hotly contested & will draw out & showcase some of the best that New Zealand has to offer. And this is a Good Thing.

But at the same time, we hear that next year, primary schools won’t get any additional support for teaching science (or music, or the arts): any additional funding they receive will be tied to bedding in & supporting the new national standards in numeracy & literacy (the three ‘R’s).  Yes, our children need to be literate & numerate – but we also need to be ensuring that schools can help them to see the passion, creativity, joy & excitement of science. Where else are our future emerging scientists going to come from?

(And besides, literacy & numeracy aren’t stand-alone subjects; they can be taugjht across the curriculum. Think of that report you had to write on a current issue, or the Schol examiner’s comments about the need for good communication skills!)

conspiracy theories & the electricity supply Alison Campbell Oct 22

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Apologies in advance – this is way off my usual beaten track but it’s been a hard week & I am in need of diversion :-)

Over the last few days there’ve been a couple of letters to the editor of the Waikato Times, talking about our electricity supply. The first suggested that Nikola Tesla had invented a way of transmitting electricity without wires and without loss of much energy – but that the secret of this was being suppressed by the electricity supply companies (the naughty people!). Tonight we learned that money given to a variety of Marsden fund projects would be much better spent on investigating this lost discovery,due to its enormous significance to our economy (with the implication that much of what scientists & other researchers do is a total waste of time & money).

Now, Tesla is rightly regarded as one of the key players in the development of electricity as an energy source (Marcus could tell you much more!), and he certainly gave more than a little thought to the concept of transmitting energy without wires (the basis of today’s induction coils, for example), but the idea of evil Big Business suppressing key discoveries as a way of making money sounds awfully like a conspiracy theory to me :-) After all, no-one’s hiding the fact that he investigated the idea (you can find it on wikipedia, after all!), & the eponymous Tesla coil is based on the idea of resonant induction. (Apparently their discharges could be described as ‘man-made lightning‘ – not something to try in your bedroom, then…)

Certainly there are some wild claims out there about Tesla – that he was able to somehow harness the Earth’s magnetic field to generate electriciity enough to power an electric car (this is back in 1931). And I suspect that the letter-writer’s claims are based on statements such as thiswhen Tesla was determining the resonant frequencies of the earth to potentially transmit unlimited electric power… (And, regretably, pedlars of all sorts of woo have used Tesla’s name & work as a way to add a science-y stamp to their out-there claims.)

But anyway, back to the evil Big Electricity Companies – surely they’d be as interested as anyone in this technology? After all, any mechanism by which they could sell us more energy, rather than lose it via resistance in the power lines, would represent profits for them, wouldn’t it? (But perhaps I’m being hopelessly naive!) No, it sounds like a conspiracy theory all right: shadowy powerful players (Illuminati, anyone? – warning: don’t read too much of this site or your brain cells may suffer uncontrolled apoptosis!), un-named sources, misunderstood geniuses, lack of credible published sources, huge benefits for mankind if only we knew The Truth…

seeing the world through blindsight Alison Campbell Oct 20

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While driving home on Sunday I listened to another Skeptics Guide podcast. The ‘science, or fiction?’ segment included the statement that ‘scientists had found that a blind man was able to navigate flawlessly around obstacles without using any other senses.’ Science, or fiction, indeed. I was inclined to pick it as the ‘fiction’ statement, until I remembered reading something about the phenomenon known as ‘blindsight’.

Blindsight? It’s where someone who is clinically blind, & has no conscious recollection of seeing anything, nonetheless shows evidence of ‘seeing’ things at some subconscious level. Their blindness has to be due to some damage at the level of the brain ie their eyes function just fine, but the message doesn’t get through to the visual cortex.

And indeed, that’s just what the SG segment was about. (For once I got one right!) The patient they were describing, who’s identified as TN by the researchers – unfortunately our institutional subscription won’t let me access the original paper so all I can see is the abstract, very sad – has what’s known as ‘cortical blindness’, which means that his blindness is due to damage (from two strokes) to his visual cortex. His eyes and optic nerves function just fine, but the information they gather & transmit is not being processed in the part of the brain responsible for interpreting visual signals – the researchers confirmed this using brain imaging.

After confirming that TN really is clinically blind, here’s what the researchers did next:

They then persuaded TN to set his stick aside and walk down a corridor strewn with lab equipment. He was able to do so flawlessly, despite being unable to consciously see any of the obstacles. Head down and hands loose by his side, he twisted his body to slalom slowly but surely between a camera tripod and a swingbin, and neatly stepped around a random series of smaller items.

(The quote’s from NatureNews, so my apologies in advance if you can’t access it directly.)

It’s unusual to have an example of blindsight where the patient has damage to the visual cortex in both hemispheres of their brain. I’ve read other studies where scientists have tested the phenomenon in people who are affected on just one side. When such individuals are shown a picture, to their blind side only, they can often give at least some information about that picture, which suggests that some data from the retina are being processed by another, subconscious, part of the brain.

Apparently TN is able to interpret facial expressions – which he can’t ‘see’ in the normal sense – but the finding that he can also navigate his way around obstacles with a high degree of accuracy was unexpected. You could argue that he’s using echolocation, but the research team said ‘no’, becuase he was so accurate in his movement down a cluttered corridor. That doesn’t entirely rule echolocation out, because TN wasn’t blindfolded to block out all input from his eyes. It would be really interesting to know if he’d consent to repeating the corridor walk under such conditions.

But if TN is definitely using blindsight, think what this suggests about the subconscious goings-on in our brains. And after all, who hasn’t gone for a walk & arrived at the destination without any clear memory of what happened between A & B? (Or is that just me? That’s a worry!)

it couldn’t happen here. could it? Alison Campbell Oct 19

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I hope not.

Some of my fellow Sciblings have written quite a bit lately about various ‘alternative & complementary’ health claims. And I’ve thoroughly enjoyed reading their posts (here & here, for example). So I wonder what their take would be on a story from the UK, helpfully publicised by the Quackometer. Not only is a British MP calling for more & better public health funding for various ‘complementary & alternative’ therapies – but their Minister of Health is reported as saying ’that the Government’s position on complementary and alternative medicines, which I shall refer to as CAM, is the same as our position on mainstream medicines. ’ In other words, that homeopathy, iridology, relexology & all the other non-scientific, lacking-in-evidence-of-effectiveness modalities should be treated the same as mainstream medical practice when it comes to funding & publicity, and the euros/pounds sterling allocated to health should stretch even further than they have to now. As the Quackometer says, “[to] treat the claims of pseudo-medical cults in the same way as you treat the claims of scientific medical research is an absurdity.”

If I was a health consumer in the UK, I’d be worried. But it couldn’t happen here. Could it? I hope not.

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