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February 2018 Archives

Prof Karen Burke da Silva was the keynote speaker at Day 1 of the 2017 First-Year Science Educators' Colloquium, held in Wellington. Her topic:Transforming large first year science classes: A comprehensive approach to student engagement. Currently at Flinders University, she's been instrumental in setting up an 'integrated teaching environment' that's seen a drop in withdrawals, and a marked increase in engagement, among their first-year STEM students. 

If you've read my earlier FYSEC-focused post, you'll know that student engagement was a hot topic at last year's colloquium. Which isn't surprising; as Karen noted, both NZ and Australian universities have trouble with attention, engagement, retention, and performance of their first-years, who face some significant challenges in transitioning from their smaller high-school classes to the large lecture rooms of universities. She commented that

how best to build a first-year program in sciences that allows for different student backgrounds, abilities and interests is a task that all first-year coordinators face.

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Pangolins are strange little creatures, with their diet of ants and termites, and the entire outer surface of their bodies covered with armour-like scales (face, belly & the inner surfaces of the limbs are either hairy or naked). When in danger, pangolins are able to roll up in a ball, presenting only that armoured surface to a predator.

Actually, some of them aren't so little: from nose tip to tail tip, they range from 75 cm to more than 1.5 m in length, with their strong tails making up about half of that. Arboreal species tend to be smaller, just a couple of kilos in weight, but apparently the giant pangolin can weigh in at over 30kg. 

Ground Pangolin at Madikwe Game Reserve

Image by David Brossard (Scaly Anteater exits stage left) [CC BY-SA 2.0 (https://creativecommons.org/licenses/by-sa/2.0)], via Wikimedia Commons

In taxonomic terms pangolins have their own order (Pholidota), with a single family (Manidae) and genus, Manis; there are 4 species in Africa and 4 in Asia. Like giant anteaters they are toothless (edentate), & indeed, they converge with the giant anteaters in a number of ways and for a while the two groups were thought to be closely related. However, it seems that molecular data (from DNA & amino acids) places the pangolins' order as a sister group to the carnivores. So, the toothless state characteristic of both types of anteater has evolved more than once, as has the heavy musculature and massive claws of their forelimbs. 

I hadn't really thought before about how pangolins manage to digest their diets of termites and ants, after licking them up with those sticky, extrusible tongues. (Here's something else I didn't know: a pangolin's tongue is as long as head & body combined ie half their total body/tail length. It's folded back into a throat pouch when not in use, and the animals produce so much sticky saliva that they have to drink frequently.) It turns out that the stomach is rather like a bird's gizzard: its walls are hardened and it contains sand or very small pebbles, which help to grind up those crunchy meals as the muscles in the stomach wall contract and relax.

It seems that yesterday was World Pangolin Day. It would be nice to think that drawing attention to the plight of these strange little creatures would change the fact that they are currently the most trafficked mammal in the world. After all, they range from vulnerable to critically endangered status and are supposedly protected by both national and international legislation. Sadly I think that greed & stupidity will push them over the edge. 

Why? Because, as this article in The Independent says, pangolins are poached on a huge scale 

for their meat, which is considered a delicacy in China and Vietnam, and their scales, which are used as ingredients in traditional Asian medicine. 

Practitioners believe scales are capable of treating a range of ailments including asthma, rheumatism and arthritis.

That defensive habit of rolling up in a ball is useless against poachers, who can just pick the animals up. So, people are prepared to pay a lot of money for the meat and the scales of these creatures, which is where both greed and stupidity come into it.

Greed: well, money talks. In December 2016, Chinese customs made their largest-ever confiscation of scales - a mind-boggling 3.1 tons from an estimated 7,200 pangolins. Their worth: about $US2 million. Research by TRAFFIC, a network that monitors the international wildlife trade, suggests that around 20 tonnes of pangolins, & pangolin parts, are trafficked each year.

And stupidity, because those hugely expensive scales are made of keratin - nothing more and nothing less than the protein that makes up our own hair and nails. People consuming the pangolin's scales might as well chew their own fingernails, for all the good it would do them. I guess they'll have to, when the pangolins (and rhinos, whose horns are keratin too) are gone from the world.

 

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I've written about MMS - the "Miracle Mineral Supplement" - several times beforeA (here and here, for example). I guess it's a useful thing to hold up to show how something can clearly be woo - eg claims that it kills/cures practically everythingB under the sun - and yet people still buy the stuff. Buy it, & potentially do real harm using it. Because MMS is essentially bleach: 28% sodium chlorite in distilled water. Those using it typically 'activate' it by mixing it with lemon or orange juice, which gives the strong bleach, chlorine dioxide. And then they drink it, or - even worse - feed it to their children...

Because it's popped up again in this news story, I thought I'd point out the ridiculousness of the claims for how MMS 'works', before weighing in on the story itself. Sad to say, the NZ-based website where I first found those claims is still around today, Quack Miranda warning & all. That site notes that ClO2 is "a proven pathogen killing mineralB used extensively in the hygiene and water treatment industriesC to destroy bacteria, viruses, pathogens and other harmful organisms in water" and helpfully points out that "the human body is 60-70% water". Their implication is that thus it works just as well in the body - in fact, it's not even implied; further down the page they actually say that "you could class the human body as being a 'water system'! As a biologist I'm gobsmacked: there is a world of difference between water treatment and reticulation systems, and the human body.  

Anyway, here's how it's claimed to work: 

When a chlorine dioxide ion contacts a harmful pathogen in a water system, it instantly rips up to five electrons from the pathogen, in what can be likened to a microscopic explosion; harmless to us, but terminal for pathogens. The pathogen - an electron donor - is rendered harmless due to the involuntary surrendering of its electrons to the chlorine dioxide - an electron acceptor - and the resulting release of energy. Oxidised by the chlorine ion, the former pathogen becomes a harmless salt.

Once it encounters various pathogens in water systems, chlorine dioxide performs a highly energetic acceptance of four electrons when it comes across any cell that is below a pH value of 7. This means that diseased cells are essentially vaporised (i.e., oxidised) while healthy cells are unaffected.

Now, ignoring the differences in the number of electrons cruelly ripped from ... somewhere... this claim also obviously buys into the nonsense about needing to alkalise one's body (because acid conditions cause disease, donchaknow). It's also wrong: here's the actual mode of action

Compounds within the cells and on the surface of cell membranes that contain oxidisable material react with chlorine dioxide, causing cell metabolism to be disrupted. Chlorine dioxide also reacts directly with disulphide bonds in the amino acids and the RNA in the cell.

That is, ClO2 will attack any oxidisable material on or in any cell; it's not selective in its action. Which is precisely why consuming MMS (either by mouth or rectally; more on that in a minute) has the potential to be quite harmful. 

Anyway, back to the original news story, which tells us that a mother in the US was arrested for feeding MMS to her child - after 'activating' it, not with the usual lemon juice, but with hydrochloric acid. As Orac has noted (reasonably often), in addition to the usual claims that MMS will cure AIDS, malaria, & even cancer, there are also people who promote it as a 'cure' for autism. Worse, not only do they advise that parents of autistic children get them to drink the stuff, they also advocate using it in enemas - apparently in the belief that autism is due to intestinal parasites. Parents who do this often share photos of what they find in their children's faeces - what they're actually seeing is mucus, plus bits of mucosa ie the tissue that lines the gut. (If you want an idea of what the children are subjected to, read this post by one mother. I did - & felt like throwing up. That poor little boy.)

The only words I have for the people selling this stuff are not really printable. 

 

A Just realised that my first post on this topic was back in 2008. How time flies! A pity the woo doesn't fly away with it. 

B including, supposedly, cancer. The wooster at this site seems to have bought into the pseudoscientific claim that cancer is a form of fungus. 

C Minerals are usually defined as inorganic & crystalline in structure, so I guess the purveyors are right on the inorganic part. Chlorine dioxide, alas, is a gas under normal conditions.

D Sadly for this argument, many things kill pathogens in the petri dish, but fail to do so internally.

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At FYSEC2017, Gerry Rayner led a session called "Undergraduate science education in the 21st century: issues, needs, opportunities". 

Gerry kicked off by commenting that education has a greater impact - on students, teachers, and the wider society in which education systems are embedded - when people work together across a range of disciplines. What are the issues currently facing undergraduate science in NZ & Australia, he asked, and how do we address them? This was something that generated quite a bit of subsequent discussion. On the list: 

  • rising enrolments: Gerry commented that in Australia, the removal of caps on enrolment, together with international demand, meant that some predictions of student numbers saw growth of perhaps 30% over the next few years'
  • increased diversity - not only cultural and ethnic diversity, but also a wider range of prior knowledge and academic achievement on entry; 
  • as fees increase, and with that, student debt, we're already seeing a change in attitude: students see themselves as customers, paying for a product, and can expect particular outcomes;
  • lower on-campus attendance may well have an effect on student engagement (and comments from attendees showed that this is something we all face) - but, to support increased numbers, we are pushed to provide more on-line delivery;
  • this means that educators need to provide not only more on-line content and assessment, but also the sort of meaningful interactions that enhance student engagement; 
  • the need - Gerry described it as a moral obligation, & I agree that the obligation is there - to provice meaningful opportunities for students to enhance their employability. That is, it's not all about mastery of content, and students also need to gain a whole range of work-related competencies and capabilities.
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Polyploidy - the duplication of chromosome sets - is relatively common in plants, and can result in the development of new species. (Many modern food crops are polyploids.) It's much less common in animals, although found in some frogs & salamanders (amphibians) & leeches (annelids). 

So it was with a mix of excitement, surprise, & alarm that I read about a triploid crayfish species: excitement, because I hadn't heard about a polyploid crustacean; surprise, because it's a triploid organism; & alarm, because it's an invasive pest across its range.

File:Procambarus fallax forma virginalis.jpg

Image: Wikimedia commons; photo by Zfaulkes

Procambarus virginalis, the marbled crayfish, was first found in Germany in the mid-1990s but is now widespread in Europe & Africa, including Madagascar. In a paper published this month, Frank Lyko & his colleagues reported on their study of the species' genome (Gutekunst, Andriantsoa, Falckenhayn, Hanna et al., 2017). They found that it has 3 copies of each of its 92 chromosomes (276 chromosomes in total), and that all the chromosomes come from the slough crayfish (Procambarus fallax), but from two individuals that weren't closely related. The team suggested that the marbled crayfish originated from a mating between 2 slough crayfish, where one parent contributed a normal, haploid, gamete (one copy of each chromosome) & the other, a diploid gamete with 2 copies of each chromosome, produced by non-disjunction during meiosis. Their genomic analysis pointed to the aquarium trade in Germany as the source of the new species. 

Now, triploid organisms are usually sterile, because they're not able to produce viable gametes via meiosis. (The same would be true of a pentaploid, with 5 copies of every chromosome.) Yet this crayfish has rapidly become an invasive species, & that means it makes lots of baby crayfish. How does it do this? 

By parthenogenesis. That is, this is a clonal species. (The researchers describe the Madagascan population of P.virginalis as "genetically homogeneous and extremely similar to the oldest known stock of marbled crayfish founded in Germany in 1995.)

Every marbled crayfish is female, producing 'apomictic' eggs by mitosis. No sperm necessary. And because every individual is capable of producing eggs and - in this species, a lot of them - in ideal conditions the species' population can grow much faster than that of a sexually-reproducing species. This gives the marbled crayfish quite an advantage over other, competing, species when it's introduced into a new ecosystem, which is why it has been able to expand quickly across Europe & Africa - having likely arrived in these countries via the aquarium trade. And again, because they are parthenogenetic, you need just a single individual to begin a new invasive population. In Madagascar their spread was enhanced by human activity in terms of moving animals around to establish new food populations, the warmer temperatures (compared to those in Europe), and the ready availability of suitable freshwater habitats, and there's concern that endemic crayfish species, and their unique ecosystems, are threatened by the exotic invader.

But there's much more to this story than a tale of an unusual crayfish. I found it fascinating that that understanding how the marbled crayfish genome evolves over time may have applications to cancer research:

The generation of genetic diversity will be shaped by a complex set of factors, including the intrinsic mutability of the genome, environmental mutagens, genetic drift and selective pressure. All these factors are known to play an important role in the evolution of tumour genomes. The analysis of mutations in marbled crayfish populations provides an opportunity to detect the generation, fixation and elimination of genetic changes with particularly high sensitivity and robustness and could therefore disentangle the specific contributions of individual factors. As such, it will be interesting to further explore marbled crayfish as a model system for clonal genome evolution in cancer.

 

J.Gutekunst, R.Andriantsoa, C.Falckenhayn, K.Hanna, W.Stein, J.Rasamy & F.Lyko (2017) Clonal genome evolution and rapid invasive spread of the marbled crayfish. Nature Ecology & Evolution doi:10.1038/s41559-018-0467-9

 

Interested readers will also enjoy this summary of the paper, with commentary from other scientists. 

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Students often get to look at hydras - tiny, fresh-water members of the group that includes sea anemones, jellyfish, corals, and the Portuguese man'o'war. All these cnidarians have a simple body-plan: two layers of true tissue with a jelly-like layer between them, a sac-like gut with a single opening that acts as both mouth and anus, and the characteristic stinging cells - cnidocytes - that give the taxon its name. And many of them rely on endosymbiotic algae for their survival, using some of the sugars that the algae produce by photosynthesis. The image below shows part of a hydra's tentacle - you can see not only its green algal symbionts, but also a halo of discharged stings.