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how a fungus avoids a plant’s immune system Alison Campbell Aug 26

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Your immune system is a wonderful, complex, multipartite mechanism that usually allows you to fight off the attentions of the various pathogenic organisms (bacterial, fungal, and viral) that you’ll meet during your life. I say ‘usually’ because it’s not always successful on its own, and even where it is, you can be laid low for quite some time – think of flu, but also think of measles, mumps, smallpox, polio… This is where vaccination comes in: this ‘primes’ your immune system so that it can react far more rapidly when it encounters the actual pathogens themselves. NB for a taste of some ‘alternative’ thinking on this concept, try this thread over on SciBlogsNZ.

Now, all multicellular animals have some form of immune system. Ours offers two modes of defence: an ‘innate’ immune system, plus the ‘adaptive’ system involving antibody production in response to the multitude of antigens we face each day. At the other end of the scale, things like jellyfish & sea anemones have only the innate component. For example, Hydra (a freshwater version of the more familiar sea anemones, greenish in colour due to the presence of green algae in the cells lining its gut) lacks any physical mechanisms to keep out pathogens – no thick skin, or anything along those lines. But its epithelial cells release antimicrobial chemicals & antiproteinase enzymes when they detect external antigens.

What about plants? They too have innate defence systems, including mechanical barriers against infection – waxy cuticles, and bark (cork), and also the trichomes (hairs) that you find on many leaves - that . But bark can split, & cuticles can be pierced eg by insect mouthparts – what do plants do then? It seems that when plants detect an invading organism, they release high levels of salicylic acid (the active ingredient in aspirin) in the affected tissues. This induces programmed cell death in the affected tissues, which restricts the spread of the pathogen, and also activates immune responses elsewhere in the plant – this in turn means the plant is now primed to resist futher attacks on other tissues. Salicylic acid isn’t the only chemical resonse to infection; it turns out that plants also produce an enzyme called nitric oxide synthase, which catalyses production of nitric oxide (NO) after an infection.

Now, a pathogen that can evade an organism’s immune system for any length of time is going to be at a selective advantage, and so you get a form of arms race, where hosts with the ability to detect & respond to such a pathogen are in turn likely to have better odds of survival, & so on. Some strains of the bacterium Staphylococcus, for example, are able to wrap themselves in strands of the protein fibrin (which they obtain from the host’s blood), which may make them much harder for the host’s immune cells to destroy. (Alas for the patient – this ability is also linked to clotting; Not Good at all.)

Like animals, plants use ‘pathogen-associated molecular patterns’, or PAMPS, as the basis for identifying pathogens (de Jonge et al., 2010), so a pathogen that can somehow hide these from a plant would be at an advantage. The range of potential PAMPS – detected by receptors on the plant cell surface - includes lipopolysaccharides, peptidoglycans, a protein called flagellin, sugars typically found in fungal cell walls – & chitin, a major constituent of cell walls in fungi. Plants with damaging mutations in these receptors would potentially be more susceptible to attack by bacteria & fungi.

De Jonge & his colleagues studied  the cause of leaf mould in tomatoes, a fungus called Cladosporium fulvan. When this fungus is moving into the inside of a leaf, among the proteins it releases is one that protects the fungal cells from plant enzymes called chitinases, which would otherwise break down the fungus cell walls. Actually there’s more to it than that – when chitinases hydrolyse fungal cell walls, this releases molecules that appear to act as PAMPs & so stimulate the plant’s immune defences.

Another protein, called Ecp6, seemed to be needed for the fungus to be really effective at infecting tomato plants. Looking this more closely, the team found that Ecp6 doesn’t affect chitinase release but appears to tidy up other proteins released by the fungus, so that they aren’t floating around & able to be detected by the plant’s defences. So, because the host’s immune system doesn’t kick in, C.fulvan is able to grow more rapidly within the plant’s tissues. And It turns out that the genes controlling Ecp6 production are widespread in fungi – perhaps one outcome of the plant-fungus arms race. (And other example of how plants are considerably more complex than many of us would think.)

de Jonge R, van Esse HP, Kombrink A, Shinya T, Desaki Y, Bours R, van der Krol S, Shibuya N, Joosten MH, & Thomma BP (2010). Conserved fungal LysM effector Ecp6 prevents chitin-triggered immunity in plants. Science (New York, N.Y.), 329 (5994), 953-5 PMID: 20724636

fungal parasites & zombie ants Alison Campbell Aug 23

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ResearchBlogging.org

Parasites are ubiquitous. I remember watching a video (years ago, while I was teaching at secondary school) about parasites that make humans their home. Lice, eyelash mites (yes, really!), various intestinal worms… I tell you, I had psychosomatic itching for days after seeing that! Then I got my hands on Carl Zimmer’s wonderful book, Parasite Rex – as well as learning all sorts of stuff about parasites & how they live, I also had it brought home to me that parasites aren’t just some sort of passive, undesirable house guest – in many cases they actively influence the host’s behaviour in ways that enhance the parasites’ ability to complete their life cycles.

I was alerted to a recent paper in this area by a blog post from another Kiwi blogger: his sub-header was ‘zombie ants controlled by parasitic fungus for 48 million years’, which reall y took my fancy (the link will take you to a story in the Guardian, of which more later in this post). The authors of this paper (Pontoppidan et al. 2010) point out that it’s not just a case of the parasite affecting individual ants – they can structure the entire host population in terms of its distribution in time and space & thus influence their own distribuiton: the parasite’s ‘extended phenotype’, if you will.

The authors kick off by listing some rather dramatic ways in which other host species are influenced by their parasites, such as behavoural changes that make them more susceptible to predation, thus enabling the parasite to move to its next host; or effectively drowning themselves, which lets the adult stage of the parasite reproduce. (Their full list’s available in the PLoSOne paper.) All this raises interesting questions about just how this manipulation of host behaviour is achieved, & the effects of such parasitism on the species’ population as a whole (it’s obviously a Bad Thing for the indivdiuals concerned). Pontoppidan & her colleagues asked a further topic: the impact of infection on the host species’ distribution in space & time. They chose to look at the fungal parasite Ophiocordyceps unilateralis , and a tropical species of carpenter ants (Camponotus leonardi.).

This is really cool stuff (in a gruesome sort of way). An ant picks up the sticky fungal spores by walking over them on the forest floor; fungal hyphae then penetrate the unfortunate animal’s cuticle & extend throughout its body. It can be just a few days from infection until death. Once the ant’s dead, the fungus grows a ‘fruiting body’ out the back of its host’s head. This produces large spores, too big & heavy to spread on the wind. Instead they fall to the forest floor, produce & release secondary spores, a hapless ant comes along… and the cycle repeats itself. So far, so good (for the fungus), but the really interesting part is that the ants don’t die just anywhere, nor do they simply turn up their toes & drop dead on the ground. 

An external file that holds a picture, illustration, etc.<br /> Object name is pone.0004835.g001.jpg Object name is pone.0004835.g001.jpg

Ants biting the underside of leaves as a result of infection by O. unilateralis. The top panel shows the whole leaf with the dense surrounding vegetation in the background and the lower panel shows a close up view of dead ant attached to a leaf vein. The stroma of the fungus emerges from the back of the ant’s head and the perithecia, from which spores are produced, grows from one side of this stroma, hence the species epithet. The photograph has been rotated 180 degrees to aid visualization.
 
From: Pontopiddan et al. PLoS ONE. 2009; 4(3): e4835. doi: 10.1371/journal.pone.0004835
 
Instead, before an ant actually dies it bites into the surface of whatever plant it’s standing on at the time. Pontopiddan et al. identify this behaviour as the fungus’s extended phenotype: it holds the ant’s corpse in place on the plant for long enough that the fungus can secrete a ‘glue’ that will stick the body there more permanently, which in turn gives time for the fungus to develop its fruiting body (the ’stroma’ & ‘perithecia’ in the images above). What’s more, the team had heard accounts of ‘graveyards’ containing large numbers of dead carpenter ants (cue images of zombie ants staggering along to some formicine cemetery). So they decided to determine whether these graveyards really do exist and, if they do, how various biotic & abiotic factors influenced the distribution of dead ants.
 
To do this they spent more than 5 weeks & >500 person-hours in a Thai rainforest, looking for ants. (This wasn’t quite needle-in-a-haystack territory as these ants can be >4mm long, but still…) In all this time they found 2243 dead ants in their study plots (the great majority of which were Camponotus leonardi), but only 2 live C.leonardi. But there were lots of living ants from other species, doing what ants do, in the study area – which suggested that leonardi was definitely the main host for Ophiochordyceps unilateralis. It was 3 weeks before they saw an active trail of leonardi, which descended one tree & travelled only 5m on the ground before heading up another trunk, followed by yet another descent before disappearing into the canopy again. That trail led to a single leonardi nest, high in the canopy (20-25m above ground), with a network of trails running along twigs & branches & extending up to 100m from the nest.
 
On the basis of these observations, the team hypothesised that ants of this particular species actively avoid descending to the forest floor unless it’s the only way to reach a new resource. (You can see how natural selection might achieve this: a colony where too many ants go down to the ground on an everyday basis is likely to lose large numbers of foragers.  So if there’s a genetic underpinning for such behaviour, a queen passing on a ‘go to ground’ gene would end up losing lots of her daughters & thus her nest would be at a competitive disadvantage to other colonies.)  It turns out that there is some evidence supporting this hypothesis: in an area of forest where the parasitic fungus isn’t present, C.leonardi is commonly found at ground level.
 
When the research team went on to look at just where the dead ants were found, it appeared that the bodies weren’t randomly distributed. Instead they were in large aggregations (the ‘graveyards’) of up to 26/m2, separated by corpse-free zones. The now-deceased had bitten onto the undersides of leaves, on average about 30cm above the ground – an example of how the fungus influences its host’s behaviour. The distribution of dead ants appeared to be related to temperature & absolute humidity – things which could influence the survival of fungal spores & thus the chances of an individual ant picking up the infection.
 
Zombie jokes aside, this really is a fascinating example of the complexity of ecosystem interrelationships. And their longevity.  It also turns out that this particular parasitic relationship may have been in place for a very  long time indeed. The ‘death bite’ leaves a characteristic scar on a leaf, and in a separate paper David Hughes & colleagues describe finding just such a scar on a leaf dating back 48 million years, from rocks in what is now Germany.
 
 
 
 

 
Hughes, DP,  Wappler , T & Lanadeira, CC (2010) Ancient death-grip leaf scars reveal ant-fungal parasitism. Biology Letters. Published online before print August 18, 2010, doi: 10.1098/rsbl.2010.0521
 

Pontoppidan MB, Himaman W, Hywel-Jones NL, Boomsma JJ, & Hughes DP (2009). Graveyards on the move: the spatio-temporal distribution of dead ophiocordyceps-infected ants. PloS one, 4 (3) PMID: 19279680

 

the skills of critical thinking Alison Campbell Jul 11

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Those of you who are thinking of entering for the Scholarship Biology exam at the end of the year may have had a look at the statement of just what is expected (the ‘performance descriptors’). If you have, you’ll have seen that one of the key attributes you need to demonstrate is an ability to think criticaly: about the question; about the supporting materials that the examiner may have provided; about your own knowledge (you don’t want to do a brain dump, after all – this will not impress the examiner one bit!).

I’ve written quite a bit about this in the past (here, here, & here, for example). Today I thought I’d add to that, with a closer look at some of the questions that you, as a critical thinker, might ask about a topic. (This is a modified version of something I’ve posted on the ‘other’ blog, Talking Teachingwihich I share with my colleagues Marcus & Fabiana.)

At the end of my last Talking Teaching post I mentioned critical thinking – & said I’d leave that topic till later. This is ‘later’ :-)

If you ask a teacher to list the attributes that they’d like to see in their students when they move on to further education, then ‘critical thinking’ will feature somewhere on that list. It’ll probably be in most tertiary institutions’ ‘graduate profiles’ as well. What I’d like to consider is, do our students measure up to that aspiration? How well do we help them to become critical thinkers?  (That last means, not just talking about it, but modelling critical thinking skills for our students - & giving them the opportunity to practice! They’ll only learn by doing.)

What is a critical thinker, anyway? I’ve heard it said that a critical thinker is someone who has an open mind on issues under discussion - but not so open that their brains fall out! When faced with a given position statement (‘therapeutic touch really works’; ‘intelligent design explains biodiversity better than evolution’; ‘scientists are wrong about global warming’; & so on), someone who thinks critically will ask things like:

  • What is the source of your information?
  • What assumptions are you making?
  • Is a different conclusion more consistent with the data?
  • What is an alternate explanation for this phenomenon?

These are ‘Socratic questions’ (if you’re working towards Schol exams, I’d suggest following that link & having a look at the entire list). Over at Skeptoid, Brian Dunning offers a good introduction to the use of these questions. And he makes a very important point. The end point of critical thinking (skepticism, if you like) should not be simply the debunking of a particular point of view. That’s not exactly helpful (even if it does provide temporary satisfaction to the debunker!) As Dunning says, “Skepticism is about applying the scientific method to arrive at a conclusion that is evidenced to be beneficial…” In other words, it’s not enough to demonstrate why a point of view is incorrect – you need to produce an interpretation or explanation that better fits the available evidence, and ideally one that can be usefully applied to solve a problem.

And learning to do that takes time. And practice.

And maybe listening to some of the Skeptoid podcasts - I know I’ve learned a lot from those myself :-)

positive allometry & the prehistory of sexual selection Alison Campbell Jul 06

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ResearchBlogging.org

Thanks to herr doktor bimler & the University’s science librarian, I now have my hands on two copies of the paper I mentioned a couple of posts agoPositive allometry & the prehistory of sexual selection (Tomkins et al., 2010). The term ‘allometry’ refers to the relationship between the size of an organism & the size of various parts of that organism. When scientists study allometry, they might do this for various stages in the growth of an individual, or they might compare different organisms of the same species, or individuals from separate species. ‘Positive’ allometry means that as body size increases, so does the size of whatever other feature’s being examined. (The Panda’s Thumb has an example of this, for body size: brain size ratios in primates.) The paper by Tomkins et al. looks at the spiny ’sails’ on the backs of pelycosaurs & the crests on pterosaurs’ heads, and suggests that differences in size between male & female individuals is related to sexual selection.

When I first saw the newspaper report on this article, I wondered: just how did the authors identify male & female pelycosaurs & pterosaurs? With modern reptiles size can be a cue, as can colours & crests & inflatable throat pouches. (Sexual dimorphism is widespread in reptiles, but unfortunately it’s not consistent: in some groups the males are larger, but in others it’s the females.) And of course, hypotheses about which sex you might be looking at can be confirmed by watching to see who’s on top during mating. And also by dissection: the ‘who’s on top’ method wouldn’t work for some whiptail lizard species, where all individuals are female & reproduction is by parthenogenesis. In these species, individuals take on the ‘male’ or ‘female’ role during mating depending on the levels of oestrogen & testosterone in their blood.  So I was interested to know how the authors determined whether they were looking at a male or female in dealing with any particular indivdiual.

The ’standard’ explanation for pteranodon crests & pelycosaur sails is that they were related to thermoregulation. Pelycosaurs were unlikely to be endotherms, generating heat internally as a side-effect of a high metabolic rate, & so like modern reptiles would have had to bask in the sun to warm their bodies before dashing around chasing prey (or avoiding being prey). As Tomkins & his colleagues point out, a ’sail’ of tissue supported by vertebral spines, with blood vessels running through it, could have warmed the animal’s blood more rapidly – a bit like a solar panel used to heat water. It could equally have acted like a car radiator & shed excess heat. (I need to add that not all pelycosaurs had these sails.) Something similar’s been proposed for pteranosaur crests, although here there are other hypotheses, including acting as rudders in flight, or in courtship displays - in which case there could have been sexual selection operating. Certainly sexual selection can generate some quite extreme traits – the peacock’s tail is just one example. Tomkins et al. comment that “[p]ositive interspecific allometry occurs in the sexually selected traits of a range of [living species]“, & hypothesise that significant allometry in these two extinct taxa may also be explained by sexual selection.

For their examination of allometry in pterosaurs they used 9 skulls from Pteranodon longiceps - none of these skulls were associated with other skeletal bits & pieces from which to obtain a measure of body size. So the assumption here must be that the bigger heads/crests came from bigger-bodied individuals. Some support for this assumption came from an examination of the size of the eye socket: as you might expect this increased in size as the skulls got bigger – but in living reptiles the diameter of the eye socket is directly correlated with an increase in body size as well. However, as herr doktor pointed out in my earlier post’s comments, the individual pterosaurs are described as ‘putative’ males (N = 6) & females (N = 3) i.e. they’ve been tentatively classified as male & female on an unspecified basis. If the classification was based on size, then this is something of an a priori assumption that could colour the results. In addition, the smallest ‘putatively male’ skull is the same size as the 3 ‘putatively female’ skulls, with the same sized crest. It’s hard to see strong evidence of sexual selection in these data. I wonder if an alternate possibility could be an age series? Reptiles do increase in size as they age, within species-specific limits, so smaller skulls & crests could simply be those of younger indivdiuals.

In their analysis of Dimetrodon, the team didn’t have access to enough individuals of one species to look at intraspecific allometry. Instead, they used data from 7 Dimetrodon species, & found that the sail size did increase with an increase in body size from one species to another. But sexual selection – again, I’d like to see an explanation of just how the authors determined the sex of the individual animals concerned, & how they ruled out the possibility that they were looking at age-related size differences within particular species. Having said that, the authors do note that the sails of smaller dimetrodonts would not have had much positive effect on thermoregulation & might actually have been a thermoregulatory liability, radiating heat so fast in cooler conditions that the animals would have chilled very rapidly.

Basically, the sexual selection hypothesis as an explanation for the adornments of DimetrodonPteranodon is an interesting one, but we need to see data from many more specimens, & a clear method of sexing the remains, to test it further.

Tomkins JL, Lebas NR, Witton MP, Martill DM, & Humphries S (2010). Positive Allometry and the Prehistory of Sexual Selection. The American naturalist PMID: 20565262 doi:10.1086/653001

And I see that Brian Switek has beaten me to it… 

kinky crayfish courtship Alison Campbell Jul 04

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(I did wonder about using all Ks for that title…)

In studying the animal behavior part of the curriculum, you may well have read about courtship & mating systems. In many cases it’s the male that initiates courtship, & sometimes they use very elaborate displays to catch the female’s eye. Think of birds-of-paradise and bower birds as examples. This elaborate behaviour, & the physical features that often go with it (such as brightly coloured plumage or massive racks of antlers) are viewed as the result of sexual selection. If an individual has a feature that enhances their chances of mating successfully, and that feature has a genetic underpinning, then it may be passed to some of their offspring & over time spread through the population. This tends to be a bit one-sided, in that females tend to be the ’selective’ sex & so sexual selection tends to affect males more than females. In fact, ’sexual selection theory predicts hat females… invest less in courtship signals than males’ (Berry & Breithaupt, 2010)

Now, visual displays & sounds are frequently part of courtship behaviour, but chemical signals also play a significant role: for example, in around 1600 species of moth, the female releases a pheromone that guides males to her position. An individual male detecting such a signal gains information about the sex of the ’sender’ and also of their physiological state. Chemical signals aren’t cheap to produce: the often-complex molecules involved can incur quite an energy cost in their manufacture. So this rather contradicts the aforementioned prediction by sexual selection theory: it’s called the ‘female pheromone fallacy’ (aren’t we into alliteration tonight?) It could be that the pheromones originally evolved for some other function & have subsequently been co-opted to attract males. In an attempt to clarify this conundrum, Fiona Berry & Breithaup (2010) studied chemical signalling by female signal crayfish (Pacifastacus leniusculus). Apparently female crays release urine in the presence of males – what the researchers wanted to know, was whether the pee of female crayfish has any effect on the males’ behaviour.

In order to do this they played the role of matchmaker, staging pairings between male & female crayfish during the reproductive season. Male crayfish can produce a series of spermatophores & thus can potentially mate with & inseminate many female partners. Having mated with a female they wander off to seek another partner, and don’t play any part in looking after any offspring that might eventuate – this is the role of the females alone. In other words, there’s a big imbalance between male & female crays in terms of their investment in producing little crayfish, & so females might benefit by discouraging males. In this context, you’d predict that females wouldn’t produce courtship signals as they’d have entirely the reverse effect. 

The researchers knew that in another crayfish species, both sexes release urine, & urine contains a whole range of chemicals that could act as signals. They started out with blindfolded crayfish pairs (the control condition) – the blindfolding was to remove any visual cues that might influence behaviour. (This was important, because Berry & Breithaupt used a fluorescent dye to allow them to visualise urine release, & they’d hardly want the swirling patterns of ‘visible’ urine to distract their study animals.) Seven of 15 males made attempts to mate with their partners. When the females were prevented from releasing urine, there were no mating attempts & all behaviour by the males was aggressive. If female pee was added to the water by the researchers, in 6 of the 15 pairs the males again attempted to mate.

Two crayfish fight in a cloud of visualized urine. Credit: Fiona Berry, BMC Biology.

It turned out that both sexes released urine, but they differed in the context & also the duration of release. Mating males produced less than males engaged in aggressive interactions, while females released urine for roughly the same amount of time regardless of whether they were fighting or courting. In fact, 1/3 of the males didn’t pee at all during courtship, which rather suggests that male urinary pheromones don’t act as an indicator of male quality. However, all the females in this study released urine before mating, mostly during precopulatory aggression; in fact, the researchers noted that “female urine release coincides with aggressive rather than reproductive or submissive behaviours”, and that male pee production is reduced, or stopped altogether, as they change from fighting to courting. Berry & Breithaupt (2010) concluded that during social interactions both male & female crays release urine as an aggressive display rather than an aphrodisiac. However, female urine also acted as a trigger to change the males’ behaviour, so that they became more likely to try to mate. It could well be that female urination sets up conditions that allow them to assess mate quality: perhaps only the stronger males will persist with courtship in the face of the female’s aggression.

F.C.Berry & T.Breithaupt (2010) To signal or not to signal? Chemical communication by urine-borne signals mirrors sexual conflict in crayfish. BMC Biology 8: 25 doi:10.1186/1741-7007-8-25 http://www.biomedcentral.com/1741-7007/8/25

 This story obviously captured bloggers’ imaginations (& I was rather late out of the blocks), & you can read more about it at (for example) Live Science, Not Exactly Rocket Science, Pharyngula,  & the University of Hull’s news site

the genetics of lactase persistence Alison Campbell Jun 25

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Some time ago now I wrote about lactose intolerance in humans & the domestication of cattle. Last year the Schol Bio exam included a question that looked more deeply into lactase non-persistence (which is the normal genetic condition: around 70% of all adults can’t digest the milk sugar lactose because the gene coding for the necessary enzyme is ’switched off’ in early childhood). The examiner asked students to 

[D]iscuss the presence & occurrence of lactase persistence in different regions of the world. In your discussion consider: the genetics & inheritance of the lactase persistence allele in humans; the role of cultural evolution in the selection of lactase persistence in only certain regions of the world; & the reasons for the current frequency distribution of lactase persistence.

It’s an interesting question & so I thought I’d talk more about the whole lactase thing here.

As I said in my previous post, people first domesticated cattle around 8000 years ago; probably the animals were first kept for meat but at some point farmers thought of using the milk as well. Now, in terms of the human population as a whole, most adults can’t digest the lactose that milk contains, & can be described as lactose-intolerant.. Rather than being broken down into the monosaccharide sugars glucose & galactose (which are small enough to be absorbed across the wall of the small intestine), the lactose passes on to the large intestine where bacteria use it as an energy source. Unfortunately this bacterial fermentation also produces a lot of gas (which can be a bit anti-social & more than a little uncomfortable) & a range of other by-products that can cause considerable discomfort to those concerned. (This includes diarrhoea: the sugars that remain in the gut raise its osmotic potential & this means that a lot of water’s retained in the faeces,with unpleasantly sloppy results.)

It turns out that human lactase production is under the control of a gene on chromosome 2 (which means that it’s not sex-linked). The gene’s switched on in babies – as for all young mammals – & as a result the lactase enzyme is produced in the infant’s small intestine, allowing them to completely digest their milky diet. And, as in all young mammals, there’s a developmental pattern of gene expression in the small intestine: the gene is turned ‘off’ (ie the DNA is altered in a way that means that the gene cannot be expressed) when the infant is weaned. In other words, this change in gene expression is induced by an environmental change – an example of epigenetics. The result is ‘lactase non-persistence’ in the majority of human adults. However, this non-persistence is neither universal nor distributed evenly in human populations. Instead, lactase persistence is the norm in some parts of the world, and for most people in these populatins the lactase gene remains active, continuing to express lactase in the small intestine.

It seems that the gene remains active in these individuals because they all carry a dominant mutation that prevents the permanent inactivation of the lactase gene. (’Dominant’ means that the mutation is expressed in everyone who carries at least a single copy of that allele. For a ‘recessive’ allele to be expressed you need to have 2 copies of it – unless it’s sex-linked, that is.) What’s really interesting, in terms of the early history of agriculture, is that this mutation has become fixed in more than one regional population. It appears to have occurred – quite independently – in populations in northern Europe & also in parts of Africa, around the same time that milk cattle were domesticated in these areas. Now, realistically this mutation could have occurred many times over. But it wouldn’t have become fixed in a population until environmental conditions meant that it conveyed a selective advantage – in this case, the ability to digest milk & milk products, & thus take advantage of a novel source of protein, vitamins, & calories not available to the rest of the population. Bear that in mind when you look at the following map.

The distribution of lactose-intolerance is shown on the image below (if you click on it you’ll get to a higher-res form), where bright red represents the highest frequency of lactase-intolerant individuals (91-100%) & hence the highest frequency of lactase non-persistence. Bright green shows the lowest frequency (0%) [& apologies to those of my readers who are colour-blind! Blame wikipedia...].

 File:LacIntol-World2.png

So, let’s look in a bit more detail at the distribution of lactase non-persistence (shades of red) & persistence (shades of green). The high frequency of lactase persistence in parts of Europe & North Africa is related to the fact that these are areas where dairy farming was independently ‘invented’. Once people thought of drinking milk, those with the mutant allele that allows lactase persistence would be at an advantage because of their ability to access a good-quality source of nutrients & calories. If they produced more children, on average, than non-milk-drinkers, & some of those children carried the mutant allele, then it would spread through the population & milk drinking would become more common.The similarly high frequency of the allele in North American and Australasian populations can be put down to high migration rates from Europe.

There are of course exceptions to that last statement. Indigenous populations in both North America & Australia have a high frequency of lactase non-persistence, as do African Americans. Not to mention Asia & southern Africa: for an excellent Schol answer you’d need to suggest a reason for all this.

For the indigenous populations of Australia & North America, lactase non-persistence (& thus lactose intolerance) would be expected to be at high frequency in the populations because these are areas where early human populations did not develop dairying. Thus there’d have been no selection pressure & no ‘fixing’ of any ‘persistence’ mutations that occurred. You could also suggest that until recently there’s been little gene flow into these countries from the areas where dairying developed (with the resultant high frequency of the lactase persistence allele). It’s also likely that until recently high gene flow didn’t equate to high levels of interbreeding (necessary to introduce the persistence allele into indigenous populations). And you could also suggest that, for African Americans, the source of Africans taken to the US by the slave trade would have something to do with it.

See? I said it was an interesting question :-)

a follow-up on bleeding for the cause Alison Campbell Jun 18

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A couple of days ago, on my post about World Blood Donor day, one of my commenters noted that the NZ Blood Service is apparently going to follow their Canadian & Australian counterparts in banning people from giving blood if they’ve ever had Chronic Fatigue Syndrome. (At the moment folks who’ve had CFS are OK to donate once they’re fully recovered.) The reason for doing so is a purported link between CFS & a particular retrovirus (XMRV, or xenotropic murine retrovirus). 

But the link between CFS & XMRV is not particularly clear-cut. A study in Nevada found that >60% of CFS sufferers (N=101) also had traces of XMRV in their blood, compared to <4% of healthy controls (N=218). (Sorry, the link is to Science & may not work for all.) This sounded like something that ERV would be interested in & I was fairly sure she’d written something on it earlier, so I checked. I was right: she’s got a very interesting commentary on the methods used by the Nevada researchers. But she’s aslo cautious about the overall conclusions: fairly obviously XMRV isn’t the sole agent involved in CFS (if it’ is an agent), given that 33% of CFS patients didn’t express it in their blood. It would also be important to know where the samples came from: if the individuals with CFS lived where XMRV infection is common, then this would skew the results & make any relationship appear stronger than it is. And It does look as if at least some other labs haven’t been able to replicate these findings.

I can understand the Blood Service wanting to err on the side of caution, given issues with contaminated blood in the past (the Hep C/haemophilia problem, for example). Consequently I have to disagree with Smut on this one – it probably is better to be safe than sorry. A ban can always be reversed if the apparent XMRV-CFS link turns out to be non-existent after all.

On the other hand, I find it concerning that various commenters, including the lead researcher in the Nevada study, have made statements explicityly linking CFS & XMRV – when a causal relationship has yet to be demonstrated. (It could equally well be an opportunistic infection.) A commercial test for XMRV is now available. While this is valuable as a research tool (in measuring the incidence of infection, for example), identifying a particular individual as +ve for the virus can’t at present assist in actually treating the patient. However, in at least some cases people with both CFS and an XMRV infection are taking powerful anti-retroviral drugs (commonly used against AIDS) that can themselves have significant side effects, in the hope that ridding themselves of the virus will also cure the CFS. This seems to be drawing a long bow indeed.

reflecting on teaching (& learning) about the nature of science Alison Campbell Jun 06

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This is a re-post of something I originally wrote for the ‘other’ blog that I share with Marcus & Fabiana.

A couple of days ago I took part in a discussion around reflective writing. It was organised by the University’s Student Learning Support team, with the intention of helping students working towards their PhDs to think – in a reflective way – about what they are writing. I was asked along because the organisers felt that some of my blog posts were a good example of reflective writing – showing in my writing how my thoughts about a particular topic develop. (This is the example they chose as a basis for the discussion.) It was an interesting & productive session, & I think I probably learned as much as the students (albeit about different things).

One of the students asked me how thinking about science & reflecting on research affected my teaching. There followed a brief pause for thought :-)

To my mind (I said), thinking about science must surely include thinking about the nature of science – & from there, to thinking about how we teach about the nature of science. This isn’t just idle day-dreaming: if someone is going on to a career in science, then I’d like to think that they have more than a passing understanding of what science actually is. This is something that the new NZ school science curriculum is intended to address (although, realistically, I believe teachers are going to need a lot more support & guidance in doing this). But at university, how do we teach our students about the nature of science? Or, more to the point, how are we going to help them learn about it? For sure, that learning is not going to be on the basis of ‘cook-book’ lab exercises, where students basically follow a recipe to a pre-determined end. (The tutor & I are seriously trying to move away from this, in our first-year bio labs. But that’s another story – perhaps, one that I should persuade her write about here…) We need to give them a lot more opportunities to think like scientists, & to reflect on how science is done.

Standard, ‘traditional’ teaching methods don’t achieve this particularly well. There’s an increasing body of evidence out there that shows this. That student’s original question reminded me of some work I did with a couple of colleagues (& we really must publish it!) looking at how well our students understood the nature of science. To our suprise – & concern – we found that our 3rd-year students had no better grasp of it than the first-years we surveyed. Of course those 3rd-years had a lot more scientific knowledge, but they were still quite shaky on how science worked. To me, this means that we need to be a lot more up-front in teaching the nature of science, & certainly this realisation had quite an impact on my own classroom practice.

Reworking labs is one way to give students more opportunity to ‘do’ some meaningful science, but I firmly believe you can give students the opportunity to practice thinking like scientists in lecture & tutorial classes as well. This is where some of the active engagement techniques I’ve written about earlier come into play. However, ‘thinking like a scientist’ isn’t something that’s picked up by osmosis – we also need to model how it’s done. Those of you who read my ‘other’ blog will know that I’m big on stories as a way of illustrating the way scientists develop their understanding of the world. As I said there, telling the occasional story lets students see scientists as people who are thinking; speculating – saying ‘what if?’; using hypotheses, looking at evidence, ultimately making those strong explanatory theories that tie it all together. They’re thinking creatively: science is a creative process & at its best involves imagination & creativity. They make mistakes! Most of the time we’re wrong but you don’t get to hear about that because it doesn’t make good journal articles; usually no-one publishes negative results. So you just hear about the ‘correct’ stuff. Scientists persist when challenged, when things aren’t always working well. And so on.

Another way to model ‘being a scientist’ for students is to actively show them how you arrive at an hypothesis or the answer to a question. I actively encourage students to ask questions in lectures (& it’s a given that this’ll happen in tutorials) – how else am I to know what they don’t understand, or whether I’ve explained something clearly enough. From time to time, someone will ask a question to which I don’t actually know the answer. (And reflecting on it -  :-) – this is one of the things that I really enjoy about teaching, because it spurs me to go and learn something new!)  And I’ll tell the class that, that I don’t know. They need to know that scientists aren’t infallible, that we don’t know all the answers. (The idea that scientists ‘know it all’, or think they do, is a fairly pervasive one in the media & not one that does us any favours.) But then, I’ll say: but this is what the answer might be, and this is how I arrive at that hypothesis – the information I’m basing my answer on, how it all fits together & so on. In other words, I model my thought processes for them.  Sometimes they’ll call me on that & propose their own explanations. And then, between that class & the next, I’ll go off & see what I can find in the literature that will let me give a better answer – or if it’s a tutorial class we might look it up on the spot, it depends how we’re going for time. (Occasionally someone in the class will do that too – remember, these are first-year students & I think for many of them the prospect of maybe showing me I have got things wrong is more than a little daunting…) Then I can put the information on-line via Moodle, or use it to kick off the next lecture, & hopefully we’ve all gained something from it.

I hope all that helped the ‘reflective writing’ group; that they could take something from it to inform their own thinking & reviews of their work. I know that the reflection spurred by their initial questions, certainly helped me.

on craig venter & his new life form Alison Campbell May 25

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There’s been a lot of hype – & some overwrought responses – surrounding the announcement that Craig Venter & his research team have ‘created’ a novel life form (a mycobacterium with a completely artificial genome). I wasn’t going to weigh into it.

And I’m still not – but I am going to reproduce in full an excellent comment by PZ Myers. (Go back to Pharyngula if you’d like to join in the comments there.) If after reading it you want more, then here’s the place to go: the ‘Reality Club’ at The Edge has an extensive & high-powered discussion around the issue.

I have to address one narrow point that is being discussed in the popular press and here on Edge: is Venter’s technological tour de force a threat to humanity, another atom bomb in the hands of children?

No.

There is a threat, but this isn’t it. If you want to worry, think about the teeming swarms of viruses, bacteria, fungi, and parasites that all want to eat you, that are aided (as we are defended) by the powers of natural selection–we are a delectable feast, and nature will inevitably lead to opportunistic dining. That is a far, far bigger threat to Homo sapiens, since they are the product of a few billion years of evolutionary refinement, not a brief tinkering probe into creation.

Nature’s constant attempts to kill us are often neglected in these kinds of discussions as a kind of omnipresent background noise. Technology sometimes seems more dangerous because it moves fast and creates novelty at an amazing pace, but again, Venter’s technology isn’t the big worry. It’s much easier and much cheaper to take an existing, ecologically successful bug and splice in a few new genes than to create a whole new creature from scratch…and unlike the de novo synthesis of life, that’s a technology that’s almost within the reach of garage-bound bio-hackers, and is definitely within the capacity of many foreign and domestic institutions. Frankenstein bacteria are harmless compared to the possibilities of hijacking E. coli or a flu virus to nefarious ends.

The promise and the long-term peril of the ability to synthesize new life is that it will lead to deeper understanding of basic biology. That, to me, is the real potential here: the ability to experimentally reduce the chemistry of life to a minimum, and use it as a reductionist platform to tease apart the poorly understood substrates of life. It’s a poor strategy for building a bioweapon, but a great one for understanding how biochemistry and biology work. That is the grand hope that we believe will give humanity an edge in its ongoing struggle with a dangerous nature: that we can bring forethought and deliberate, directed opposition to our fellow organisms that bring harm to us, and assistance to those that benefit us. And we need greater knowledge to do that.

Of course more knowledge brings more power, and more possibility of catastrophe. But to worry over a development that is far less immediately dangerous than, say, site-directed mutagenesis, is to have misplaced priorities and to be basically recoiling from the progress of science. We either embrace the forward rush to greater knowledge, or we stand still and die. Alea iacta est; I look forward to decades of revolutionary new ideas and discoveries and technologies. May we have many more refinements of Venter’s innovation, a flowering of novel life forms, and deeper analyses of the genome.

academic language & learning about science Alison Campbell May 03

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One of the biggest challenges faced by students of biology (or any science, really) is coming to terms with the language of science. Scientific language is precise, it’s concise, and it uses a dauntingly large number of new terms. (I saw it written somewhere – sorry, too much marking & the memory’s gone bad! – that learning the last is like learning French or some other foreign language.) Going by the conversations I’ve had with some of my first-year students, just that overwhelming number of new words can be enough to make some people seriously reconsider taking the subject. Which is kind of sad, really – & one reason why I always take a great deal of care in my lectures to introduce new terms carefully & explain what they mean & how we use them. (OK, maybe not every new word, but at the very least, the ones that I know they have trouble with.) It also highlights the fact that it’s so very important to be meticulously careful in how you use words, when communicating about science with a wider audience. While the language can add precision, its sophistication & complexity can also be a real barrier to understanding (Snow, 2010).

Catherine Snow (2010) comments that what we call ‘academic language’ – something that all university students are expected to master, albeit in the form required by their own particular discipline – tends to be concise, lacking in repetition, with a high number of ‘information-bearing’ words that allow it to be very precise, and wtih a particular set of grammaticial rules. (Most of which I break, here, on a regular basis LOL). This works just fine when you’re communicating with someone else who understands the rules of engagement, but it can be a long way from the ease & simplicity of everyday speech patterns.

Thinking about it, this is probably one of the reasons that the Cafe Scientifique movement is successful – because the organisers take care that the scientists who speak at these events are well aware that they need to present to a general audience, & to keep the jargon to a minimum. In some ways the lack fo powerpoints & so forth probably aids this, too, as it’s all to easy to fill a screen with lovely long scientific words & totally lose your audience in the process. But I digress…

Well, no, I don’t really, Because Snow points out that the habits & characteristics of oral language probably are more accessible to the non-scientist. Sentences often begin with pronouns, so the listener/reader can be drawn in  rather than held stiffly at arm’s length. Verbs really are ‘doing’ words, and if you’re getting a lot of information across, it tends to be in a sequence of ideas rather than a whole bunch of embedded clauses. (OK, I know I do that sometimes.) All too often, perhaps, a piece of written academic scientific prose can come across as impersonal, distanced, authoritative, & too full of those scary new words – this can be off-putting to newcomers, & I know from experience that it’s extremely hard for new students to produce their own written work in the same register (desirable though that may be to their lecturers). They actually need a lot of support and multiple opportunities to practice, if we want them to be able to deliver the desired standard of work on a regular basis.

And it’s not just enough to teach the vocab. This is particularly the case if the definition of a new term includes other, widely-used scientific words that the student doesn’t know either! Snow gives the example of a piece of physics text: ‘Torque is the product of the magnitude of the force and the lever arm of the force.’ Now, I have a fairly good grasp of terms like ‘magnitude’, & I know what a ‘lever’ is, so I can work that one out. But to a new student, ‘product’ & ‘arm’ & ‘force’ have other, general meanings, & if they apply those meanings to the academic definition, they will be in all sorts of strife and misunderstandings & misconceptions will almost certainly follow.

Yet students who are going to progress in science really do need, eventually, to learn to write (& speak, in oral presentations anyway) in the complex formal register of science. The devil, of course, is in the detail of how we get them there. Snow argues – & I agree completely – that this needs to be embedded in the science curriculum (ideally, before students arrive at uni, but certainly at university level). The obvious questions are, how, and what do we leave out in order to do this? (Myself, I’m not convinced that we necessarily have to leave things out, but do have to change the way we teach. Material for another post, methinks.)

And hopefully the best of those students will end up with the best of both worlds – an ability to communicate within the science community, and the skills to translate from that to the wider community beyond the walls of academe.

C.E.Snow (2010) Academic language and the challenge of reading for learning about science. Science 328: 150-452. doi: 10.1126/science.1182597