The University of Waikato - Te Whare Wānanga o Waikato
Faculty of Science and Engineering - Te Mātauranga Pūtaiao me te Pūkaha
Waikato Home Waikato Home > Science & Engineering > BioBlog
Staff + Student Login

January 2016 Archives

Following on from the private lives of snails, I bring you: slugs! (The first part of this post is largely a repost of something I wrote back in 2009.)


Leopard slugs, like other terrestrial slugs & snails, are hermaphrodites. They produce both eggs & sperm, but must exchange sperm with another slug in order to fertilise their eggs. (This reproductive strategy means that an amorous snail or slug doesn't have to find a partner of the opposite sex, it needs only to meet another snail. Or slug. Of the same species, of course.) Actual copulation is preceded by a range of somewhat slimy courtship & precopulatory displays - in garden snails this involves (among other things) piercing one's partner with crystalline darts... Sounds painful, I know, but this part of the ritual apparently enhances uptake of the piercer's sperm by its partner.

| | Comments (0)

I love words (to the extent that I've been known to peruse dictionaries for pleasure). The Story of English was one of my favourite TV programs, back (long way back) in the day. So of course when I saw positive reviews for Robert Macfarlane's book, Landmarks, of course I had to get hold of a copy. For, as the author says, 

This is a book about the power of language,... It is a field guide to literature I love, and it is a word hoard of the astonishing lexis for landscape that exists in the comparison of islands, rivers, strands, fells, lochs, cities, towns, corries, hedgerows, fields and edgelands uneasily known as the British Isles.

I could tell I was going to enjoy the book as soon as I read that first paragraph. This isn't going to be a book review, because I haven't finished it yet. But I do want to share my thoughts on something else that Macfarlane says, very early on (in explaining his reasons for writing it). 

For he dicovered that a new edition of the Oxford Junior Dictionary (my kids had to have their own copies for school) had removed a number of words from its lexicon:

A sharp-eyed reader noticed that there had been a culling of words concerning nature. Under pressure, Oxford University Press revealed a list of the entries it lno longer felt to be relevant to a modern-day childhood. The deletions included acorn, adder, ash, beech, bluebell, buttercup, catkin, conker, cowslip, cygnet, dandelion*, fern, hazel, heather, heron, ivy, kingfisher, lark, mistletoe, nectar, newt, otter, pasture and willow.

In their place, the editors had added terms bearing on modern technology, including "attachment, block-graph, blog, broadband, bullet-point, celebrity, chatroom, committee, cut-and-paste, MP3 player and voice-mail".

Now, I'm not someone who resists changes to the language. I know words change their meaning over time (which is why etymology is so much fun), and I know that words fall out of favour and into disuse, eventually to be lost. But that's different from an editorial board making a conscious decision on what words are more, or less, important for children to know and understand. 

The OUP editors were happy to explain the changes to Macfarlane: earlier editions had a reasonably large contingent of 'nature' words because a larger proportion of the population lived in semi-rural areas and would see plants, animals and the seasons on a regular basis.

"Nowadays the environment has changed." There is a realisim to her response - but also an alarming acceptance of the idea that children might no longer see the seasons, or that the rural environment might be so unproblematically disposable.

Now, words have a certain power. Of course you can convey a powerful message in relatively few short words! But a complex vocabulary allows precision in description, and (Macfarlane thinks, and I agree) also allows a sense of connection with the world. Not only is it sad to think that children may see less of the natural world these days, but it's a concern if with the loss of vocabulary comes a reduction in the ability to engage with any precision in describing and understanding the natural world.

There is, after all, a big difference between knowing that something's a tree, and knowing that it's a particular type of tree with its own particular niche. If we lose the feeling of the specific that's associated with the ability to name plants or animals with exactitude, do we also lose some amount of care for their individual survival, and for their wider environment? Macfarlane certainly thinks so, & says it far more eloquently than I can.

He quotes a colleague's observation that 

as people's 'working relationship with teh moorland [of Lewis] has changed, [so] the keen sense of conservation that went with it has atrophied, as has the language which accompanied that sense.


there are fewer people able to name [the features of the natural world], and that once they go unnamed they go to some degree unseen... As we further deplete our ability to name, describe and figure particular aspects of our places, our competence for understanding and imagining possible relationships with non-human nature is correspondingly depleted ... Or as Tim Dee neatyly puts it, 'Without a name made in our mouths, an animal or a place struggles to find purchase in our minds or our hearts.'

And so the loss of these words diminishes us all.


* Dandelion's gone? Really? Dandelions pop up even in concrete jungles. If  there was one flower I might expect city kids to see, it would be that.

R.Macfarlane (2015) Landmarks. pub. Hamilton Hamilton

| | Comments (2)

Once I started paying attention to the woo around milk I realised how much of it there is. And how ready people are to accept it.

I've written about the notoriously non-scientific Food Babe before. Someone with a high pain threshold could probably manage a daily blog post on this young woman and the way she manipulates opinion, and sometimes sells the very things she inveighs against... But I digress!

Today I noticed she's shared a link about how drinking milk encourages the development of osteoporosis. I was mildly suspicious about the source (' but before taking a look I skimmed the comments. Oh dear.

Have you ever noticed how mucus forming milk is when you drink it? It's because the pasturation process has made the protiens in the milk unhealthy for your body. So what does your body do? It surrounds the protiens with mucus and rids them from your body thru the lymphatic system. 

That 'thud' was my head meeting my desk.

Following the link (& I've used 'donotlink' as I don't want to up their page traffic) induced several more thuds. Apparently the reason pasteurised milk is Bad (and they're clearly OK with 'raw' milk) is that 

the pasteurization process only creates calcium carbonate, which has absolutely no way of entering the cells without a chelating agent. So what the body does is pull the calcium from the bones and other tissues in order to buffer the calcium carbonate in the blood. This process actually causes osteoporosis.

Funnily enough, I couldn't find any data suggesting that fresh milk contains calcium carbonate (see here, for example, for the chemical constituents you'd expect). The next sentence is chemical word salad, which I suppose someone had fun making up.

And the focus on pasteurised milk is disingenuously misleading as the paper they've sort-of-cited (no actual details given, but you'll find it here) didn't distinguish between pasteurised & raw. It's also notable that holistic-living omitted the authors' conclusion - hardly surprising as it doesn't support their narrative (my emphasis):

Given the observational study designs with the inherent possibility of residual confounding and reverse causation phenomena, a cautious interpretation of the results is recommended.

Caution is needed all right, not least because the data were gathered on the basis of food diary surveys.

Caution is also needed on the holistic-living page, because it just goes on & on - including claiming that the enzymes in raw milk are essential for us to absorb the other nutrients in the milk. And conveniently forgetting that those enzymes may well not survive the stomach. And proposing links between hormones in milk & cancer, which I've blogged about before & for which there appears to be little supporting evidence. (As I said back in 2010, Medical Hypotheses doesn't count.)

Le sigh. Plus ça change, plus c'est la même chose .

| | Comments (0)

This image popped up again on FB the other day. It was originally posted, with the comments I've pasted below, on a page run by/for someone called 'Dr Sebi'. I do not recommend asking his advice. After all, I'm doubtful that someone who could say something like this, in advising people what not to eat

Cauliflower - It is worse than broccoli. It will rob you of your minerals. It has no carbon.

has a particularly good grasp on biology, chemistry, nutrition - or science, really. And in case you were wondering, here's the advice around brocolli: 

Broccoli – Being that broccoli is hybrid, unnatural, incomplete molecular structure, it should not be consumed by humans. It’s an acid based vegetable. It has no nutritional value and is worse than okra and spinach.

This is what followed the image; sadly, it does not seem to be a poe :( There do appear to be people out there who believe this nonsense. 

Cow is a hybrid between a Yak and Buffalo. Meaning they mated a Yak and Buffalo and out comes a hybrid that we know of as a cow.

No. Not even close. Those interested in the origins of domestic cattle will find a wealth of information on the Berkeley evolution page, but basically they're derived from aurochs via a number of independent domestication events. (Interestingly, it appears that a breeding program has led to the production of animals that more closely resemble what we know of aurochs than they do modern cows, with some of those animals released into the wild in several European countries.)

If God made it, the milk would be on the alkaline side of 7 or higher. The pH of cow milk is between 5.5 and 6.0 while the buffalo's and yak's milk has a pH of 9.

Now, how on earth would they know what a designer intended? But wait - the focus on an alkaline food makes it fairly clear (as does a perusal of some of 'Dr' Sebi's claims) that this is aimed at people who buy into the nonsense that is the alkaline diet. It is also aimed at people who don't understand what pH really means - and who presumably do no fact-checking of their own. For cow's milk is slightly acidic, with a pH of around 6.7,  while human milk varies between 7 & 7.4, depending on the stage of lactation. (Perhaps 'Dr' Sebi's adherents should oppose breast-feeding too?) The pH of yak milk is around 6.4, and while I couldn't find any data on buffalo milk there's no reason to expect it to be much different. 

What do you have in milk? penicillin, puss, blood, and steroids. Milk is heated up over 212°F because you don't want bacteria in it (they take the cow and hook it up to a machine to milk the cow, but the machine doesn't know when the cow is done and it keeps pumping and puss and blood gets into it). So now you have white plastic puss and blood in your body.

I'm not sure whether their concerns around penicillin relate to human ingestion via milk, or to the development of antibiotic resistance in bacteria found in farm animals that can then be passed on to human pathogens. But anyway, in NZ and many other countries there are very strict guidelines about the use of antibiotics, and their presence in milk can lead to farmers being penalised and the rejection of an entire tank of milk. For this reason, milk from animals suffering from mastitis and which are being treated with antibiotics, must be handled separately and can't be sold for human consumption.

Milk doesn't have 'pus' in it1 but it may contain a certain level of 'somatic cells'. These may include damaged cells from the udder but are mainly white blood cells, which increase in number if the cow is suffering from an infection. (In fact, somatic cells counts and bacterial2 cell counts are two indicators of milk quality. They are not inherently a bad thing, and I can only assume that our writer gets most of his information from sites such as and, both of which push the idea of pus and blood in milk quite stridently. (I am not going to link as they don't deserve the traffic.)

Cows milk is made for the bulk of the calf sooo immediately humans are gonna get bigger from that because we're drinking something that's molecular structure is so large. This is why we don't promote cows milk or any other animals milk in this group. Homemade hemp, coconut, brazil nut, and walnut milk are all ok to use.

So, humans get bigger (fatter?) because the molecules in cows' milk are bigger than those in alternative fluids? Bwahahahaha. No, seriously, this is just fantasy. While the molecular weight of caseins found in milk varies from 19 to 24 kiloDaltons, the main protein in almond milk comes in at around 63 kDa, while in coconut milk the molecular weights can get up to 52 kDa

And finally, there's the claim on the poster itself that casein is 'toxic' and causes a range of serious ailments. Unfortunately for this claim, caseins are found in human milk too. Again, this is a claim shared by mercola and naturalnews; its origins are unclear but it may go back to the book discussed here. The discussion is interesting and provides links to the scientific literature, which show that humans can digest caseins and also that the study supposedly demonstrating toxicity used doses way way waaaaay above what one might even remotely approach in real life. Plus, you do have to wonder how the Masai have survived so long.

1 As for the white plastic and puss, I have no idea. Naughty kitty!

2 And this is why we have pasteurisation.




| | Comments (5)

This morning when I went out to feed the goldfish, I encountered a pair of snails in flagrante delicto. I resisted the urge to step on them :)

However, I was reminded of a post that I wrote several years ago, on the sexual habits of snails, and thought it was worth a repost. So here goes:

Copulation in garden snails is generally preceded by (among other things) pushing 'darts' into each other's bodies. There've been various explanations for this odd behaviour (I mean, it sounds painful!), including the suggestion that the dart acts as some sort of 'wedding present' (nuptial gift), which might make the pierced partner more inclined to mating. Or that it indicates how ready the dart-shooting snail is to mate. But data from a 2001 study (Pomiankowski& Reguera) suggests another reason for this behaviour.

Snails have quite intimate, elaborate courtship rituals that involve a lot of close physical contact before actually mating. After about 30 minutes of mutual stimulation, one snail pushes a sharp pointed dart into the other. (This is often described as 'shooting', but it isn't - it's more of a hard push.) The darts aren't essential for copulation - virgin snails don't have darts, but still mate successfully. (As do snails that miss the mark - apparently around 33% of darts either don't hit the partner at all, or fail to enter their body.) So why go to the trouble of making darts (which aren't re-used, so an amorous snail must be constantly making new ones)?

It seems that the dart carries mucus along with it, & this mucus seems to paralyse the partner's female reproductive tubing. This lets more sperm make it to the sperm storage organs, where they're stored until needed to fertilise the eggs. This is important - when garden snails (Helix aspersa) mate they produce & pass to their partner a spermatophore containing 1-10 million sperm, but only about 0.025% survive in the partner's female reproductive tract (Pomiankowski & Reguera, 2001). Most of them end up in the no-return area of the bursa copulatrix, where they're digested & absorbed. But in a study of mating pairs, virgin snails that were firmly pierced by their partner's dart contained twice the stored sperm of non-stabbed virgins. And yet 

successful shooters appeard to transfer fewer sperm than did unsuccessful shooters. This suggests that successful shooters can afford to reduce the amount of sperm transferred because the penetration of dart mucus ensures a higher rate of sperm storage.

Koene & Schulenburg (2005) suggested that this may well lead to something of an arms race between the manufacture of a 'love dart' that maximises the shooter's success, and the female spermatophore-receiving organs (because the 'female' partner's reproductive success may benefit by using sperm from as wide a range of partners as possible).

But there's a lot we don't know about the finer details of snail reproduction. For example, snails may vary in how their female tracts respond to the paralysing mucus. And what's the story in those snail species that don't shoot their partners during foreplay? Hard questions to answer...

A. Pomiankowski & P. Reguera (2001) The point of love. Trends in Ecology & Evolution 16(10) 533-34

J.M.Koene & H.Schulenburg (2005) Shooting darts: co-evolution and counter-adaptation in hermaphroditic snails. BMC Evolutionary Biology 5:25 doi:10.1186/1471-2148-5-25

Mind you, the inimitable "True Facts" also does a good line on this tale :)


| | Comments (0)

Black salve. A slightly ominous name, but to some people it seems to be the best thing since sliced bread.

A colleague has just pointed me at a discussion (on FB, where else?) around the use of 'black salve' to heal a self-diagnosed melanoma. (That bit's important - the person concerned never saw a doctor & never had a biopsy, but nonetheless is describing a 'cure'.) Sadly, a lot of commenters were weighing in on how wonderful this 'treatment' was & how it does a great job of 'drawing out' the cancer, and the original discussant made this 100% incorrect claim (which I am quoting here as the page is a public one, open to anyone to view and to comment):

Black Salve only kills the cancer cells. If you put it on a spot thet is not doesn't do anything.

This is a repeated claim: that the salve will not damage healthy tissue. Yet a bit later they say: 

I overdid it on the Black Salve... piled it on... overall it [the 'cancer'] turned out to be much larger than I had anticipated.

So the large ensuing wound (& it's a nasty one) was entirely cancer, in their view.

This is what Medsafe has to say about black salve: 

Black salve and related products are promoted as an alternative to conventional medicine for treating skin problems including skin cancer. These products work by ‘burning away’ (destroying) the skin (both healthy and potentially diseased) to form a thick black scab which eventually falls off. There is no scientific evidence that black salve and similar products are effective at treating disease/skin conditions.

In other words, the user had burned away both healthy and possibly diseased tissue, creating a large open wound. (If you really want to see what this would look like, google 'black salve' and click on images - but only if you have a strong stomach as the images are nauseating. And I do have a strong stomach, and was nauseated1.)

Now, this stuff is actively promoted as a 'natural' treatment that is ever so much better2 than the 'cutting, poisoning and burning' used by the surgery and radio- & chemotherapy of science-based medicine. The irony, it burns (no pun intended): remember that we're talking about uncontrolled use of something that delivers 3rd-degree chemical burns, which indiscriminately destroy healthy and unhealthy cells alike (here's Medsafe again):

Use of Sanguinarine [the active ingredient] leads to the indiscriminate death of normal and cancerous cells and results in extensive tissue necrosis with possible secondary necrotising vasculitis.

On being challenged on their promotion of this highly dubious therapy, the original poster answered that

I did my research and I feel you are not crediting others with doing theirs.

Some responses attempted to show that using this potion - and advising others to use it - is unlikely to cure much (especially something like the claimed melanoma) and highly likely to do harm. 

Where has anyone discredited people's research? I'm sorry you think that. What concerns me is people promoting their methods and processes to other people who may be so scared and vulnerable about going to a medical person that they embark on inappropriate treatments ... Well-meaning people would be better off advising [that they] go to a trained medical person.

  But to no avail:

There are others out there that have used this method. Their you tubes were what gave me faith that it would work. 

Youtube videos = research?! [Incredulous squeak!]

Black salve has years of use, positive results, and its [sic] only the pharma trolls that go out and make it look fake/scary/dangerous.

That one has surely avoided looking at the images, which in many cases are posted by bloodroot users. And then the echo chamber starts, with others thanking the original poster for 

having the courage to go beyond and outside of the conventional method of treatment. Fear stops many from stepping outside of what 'the doctor' often prescribes. You have now left footprints for others to follow.

I can only hope that the spot this person 'treated' was neither melanoma nor metastatic, because then they may have struck it lucky, albeit by going through weeks of pain & discomfort from an escharotic wound (be warned that there is a rather graphically-unpleasant image at that link). 

I also hope that others aren't influenced by this to avoid medical care and try this 'all-natural' remedy instead; the endpoints may not be as pleasant.


1 I was even more nauseated when I got to the commenter who was advising that swallowing capsules of bloodroot - remember, this is a highly caustic burning agent - to treat internal cancers.

2 And I'm sure that it must be ever so cheap, if not free, given the way Big Pharma is so often dissed for making money through its drugs... (/snark)

Those who would like to read more about the harm that this 'treatment' can do should have a look at this article on Respectful Insolence. It includes links to images that I'm also not going to directly share here as some of them are quite literally stomach-churning in their effect. 

| | Comments (0)

Given the fuss occasioned by her PhD thesis, I was interested to look at the document produced for Judy Wilyman's MSc (available here on-line), largely to see what attention had been given to the science content and perspectives. Having examined or adjudicated a number of Masters theses in the sciences, I've a reasonably good idea of the standards of scholarship and scientific knowledge expected from this level of graduate research.

The section around research questions is interesting, in that it describes the purpose of the research project as

to provide supportive evidence for the Australian Government’s Pertussis Immunisation Policy.

This sounds a little like an a priori argument; I'd have expected something more like "to assess the evidence for..." (although one would have hoped that the Australian Government had assessed the evidence itself before implementing its policy). The author goes on to say (p.7) that

Vaccination is a medical intervention that introduces a suspension of live (attenuated) or inactivated microorganisms and chemical substances into a healthy body to induce immunity to a particular disease (Stern A. and Markel H, 2005).

The article by Stern & Markel actually identifies more than just live or inactivated micro-organisms as being used to elicit an immune response. As also noted here, the antigenic component of vaccines (the part that elicits an immune response) may be of four types: 'live attenuated', 'inactivated' (where the microbe has been killed), 'sub-unit' (ie only an antigenic protein or other molecule is used; there is no actual bacterium or virus present), and 'toxoid' (inactivated form of a toxin produced by the microbe). It's clear that Wilyman is not talking about the latter two in her description of vaccination, as she then lists the 'chemical substances' as

preservatives, antibiotics and adjuvants that are contained in a vaccine carrier.

She goes on to say (p.8) that

Therefore it is important to consider the cumulative and synergistic effects of chemicals in vaccines and any other drugs taken at the same time. This policy applies to all individuals so consideration should also be given to the knowledge that exists on genetic factors that predispose some children to greater risks. This risk must be weighed against an accurate knowledge of the chances of harm being caused by the disease itself.

On the surface this sounds reasonable. I'd therefore expect, in an MSc thesis, a section setting out the current state of knowledge about the workings of the immune system, a brief explanation of how vaccine safety is assessed, and data on morbidity and mortality associated with pertussis (the Vaccine-Preventable Disease, VPD, that is the subject of the thesis).

So it was disconcerting to find that at least some references are rather outdated. The discussion of immunity, for example, appears to be based on a textbook published in 1952. This is unusual, given the advances in our understanding that have occurred in the intervening 60+ years. This is also true for the source of a statement (citation published in 1956) that VPDs are no longer a cause of infant mortality.

No-one disputes that hygiene and living standards play a significant role in enhancing public health, but the current scientific consensus is that vaccines also play a significant role in reducing both mortality and morbidity related to VPDs. The data presented here are quite instructive in that regard: while they are from the US there is no good reason to expect that the Australian situation is different. Not only deaths, but also rates of significant illness, fell with the introduction of vaccines for the various VPDs. Chapter 3 of the thesis includes only mortality data, although the author also notes in an earlier section (p.11) that

Complications or morbidity from pertussis disease include:  1) Pneumonia - resulting from B.pertussis itself or secondary infections. 2) Atelectasis – a failure of part of the lung to expand due to mucus plugs. 3) Otitis media and sinusitis are common and usually due to S.pneumoniae.  4) Ruptured alveoli and emphysema. 5) Bronchiectasis – widening of the bronchi in which pus forms. 6) Convulsions and encephalopathy (Behrman et al, 1998).  

Wilyman goes on to say that

Celermajer J, and Brown J, (1966) studied the morbidity due to pertussis over an eleven year period from 1953 – 1964 and concluded pertussis in the Sydney community appears to be only infrequently associated with neurological complications and these tend to be mild in nature.

This does rather gloss over all the other forms of morbidity identified above, and raises some concerns about special pleading. In addition, there is again some concern around the date of the reference; is this statement supported by more recent reviews of the data (the thesis was submitted in 2007)?

In that regard it's also notable that discussion around the waning of immunity provided by the whole-cell pertussis vaccine clouds the waters a little as this vaccine was removed from use in Australia in the 2000s, to be replaced by an acellular vaccine containing key antigens. It's never been a live-cell vaccine, so the comment about reversion to virulence (p.39) is a little odd. (There's some really interesting science in the linked article, which discusses research findings examining the possibility that the pertussis bacterium may have evolved in such a way that some strains no longer express one of the key antigens in the vaccine. This means that the vaccine may be less effective in eliciting an appropriate immune response; however, it seems this may possibly be offset by a loss of the bacterium's ability to cause severe disease, and overall the study found pertussis vaccination to be effective.)

Incidentally, the scientific and medical communities agree that no vaccination is 100% effective; around 70-90% of those receiving the pertussis vaccine acquire full immunity. However, it is an interesting use of stats to suggest (p. 40) that because approximately 1/3 of children presenting with pertussis to one hospital in 1964 were fully vaccinated, that 1/3 of the fully-vaccinated cohort will still get the disease. There is a good analysis of this concept here.

At this point I began to feel that the approach taken in the thesis was intended less to provide 'supportive evidence' and more to develop arguments against the use of vaccines. For that reason I skipped ahead to the Conclusions section, because this is often a very informative section of any thesis, where the author's findings and recommendations are to found.

I'm afraid that this section really did confirm my developing impression. Here is one paragraph (p.69), broken down to include my own comments.

Prior to the implementation of mass vaccination programs, Burnet M, (1952) indicated that there were many gaps in scientist’s knowledge about the functioning of the human immune system. 

As I said earlier, the science has moved on & it's unfortunate that this isn't reflected in the references. A 62-year-old immunology textbook is going to be more than a little out of date & it seems somewhat disingenuous to rely on this for information on the immune system's functioning.
Fifty years on it is known that vaccination doesn’t provide lasting immunity
The accuracy of this statement depends on the vaccine; it is true for pertussis but measles seems to confer life-long immunity in the majority of those vaccinated (no vaccine confers protection on 100% of those receiving it).
 and a ‘modified infection’ means bacteria or virus’s that are treated with preservatives, antibiotics and stabilizers that parents are not informed about. 
Well, no, especially in the context of pertussis. Only a live vaccine can induce a 'modified infection', and the pertussis vaccine is not a live vaccine. The implication that it is, is of concern in a thesis on this subject. Antibiotics may be used during manufacture of some vaccines but are not ingredients per se, so if present this will only be in extremely small amounts. Preservatives are there to prevent the growth of other, potentially-harmful microbes while the vaccines are in storage; similarly stabilisers reduce loss of function over time.
These chemicals are known allergens and neurotoxins such as mercury, formaldehyde and aluminium. 
At this point the thesis commits distinct errors of omission. The first is that ethyl mercury, in the form of thimerosal, was phased out of pediatric vaccines at the turn of the century. The second is that this form of mercury is readily excreted by the body, unlike methyl mercury, which bioaccumulates (think, Minamata disease). Thirdly, humans produce formaldehyde in their tissues every day as a result of normal metabolic processes, at much higher concentrations than are contained in vaccines ie dose is important. (One might as well argue for banning pears from children's diets on the basis of their formaldehyde content1. Similarly the stabiliser, polysorbate-80, is also an ingredient in icecream2.) And fourthly, aluminium is ubiquitous in air and water. (Aluminium salts are present in vaccines in tiny quantities as adjuvants, to enhance the immune response.) A thorough literature review should have uncovered this information; as it is, a statement like that cited above could have come directly from anti-vaccination literature.
In the twenty-first century the effects of these chemicals on biological cells are well known 
but see my previous comment in regard to dose. We know the effects, and the doses at which those effects occur. (And 'biological cells'? What are the cells in our bodies, if not 'biological'?)
and parents are trying to avoid them in their children’s diet. Yet parents are not being told they are injecting them into their babies bodies at the most vulnerable stage in their development. 
But again, see above. In addition the language here has moved away from what would expect and into the area of advocacy for a particular point of view - one that appears to be distinctly against the use of vaccination, and where arguments are based on an incomplete presentation of available information. Not really what one would expect of a thesis at this level.
J.Wilyman (2007) An Analysis of the Federal Government's Pertussis Immunisation Policy. A major research project submitted in (partial) fulfilment of the requirement for the award of the degree of Master of Science, University of Wollongong
2 Similarly, a dose of the flu vaccine contains 25 μg of polysorbate 80. A typical adult European ingests around 100 mg of polysorbate 80 mu;g in their daily diet.
| | Comments (4)

Dragonflies are ancient: with damsel flies, they were among the earliest flying insects. An analysis based on molecular data and fossil evidence suggests a date of 480mya for the first insects, around the same time that land plants evolved, and includes a rather impressive family tree for the taxon; the earliest dragonfly fossils are around 325my old.

Back when I was doing my Hons year at uni, a friend was studying feeding in nymphal dragonflies, which was quite something to watch! (The feeding, not the friend.) If you look at them head-on - there's a good view in this video - they've got a well-developed set of mandibles. But the thing to watch out for, if you're something dinner-sized, is the big, extensible labium (analogous to a lower jaw) - this shoots out at great speed to catch passing water boatmen, mosquito larvae, or other suitable prey.

So, they're active predators, and this means that they need excellent vision. Like all insects, dragonfly eyes are based on units called ommatidia. However, dragonfly eyes are hugeMost of the animal's head is covered by the two compound eyes, each of which is made up of roughly 28,000 of those ommatidia. Much of their brain must be given over to processing that information, given the speed at which they move and the accuracy of their attacks (apparently up to 95% of attempts on prey are successful).

And since I mentioned speed, here's a video from the BBC on just how quickly dragonflies react to the sight of potential prey.

| | Comments (2)

I had another head-desk moment today, on reading a bit more of Judy Wilyman's PhD thesis (a bit at a time is quite enough). The document has quite a bit to say about smallpox. I've already noted the ill-considered statement that the vaccine has never been subject to clinical trials - a statement unaccompanied by any "now, I wonder why not?" explanation.

Incidentally, in commenting on that post, Tsu Do Nimh pointed out that there have been quite a few natural experiments that allow a comparison of morbidity and mortality between the vaccinated and non-vaccinated, beginning back in 18th-century Boston. In this instance the practice of variolation (using pus or scab material from someone recently infected) was used to protect people from smallpox; it was not as effective as modern vaccines and there were concerns that people still became ill and died. However, the comparative statistics are compelling. There were 3 outbreaks of smallpox in Boston, in 1721, 1764, & 1792, During those outbreaks the deaths per thousand cases of smallpox among the non-variolated ranged from 146 to 298. For the variolated group, deaths/1000 cases ranged from 9 to 20.

Wilyman must have missed this somehow.

But it gets worse. 

It's quite evident that Wilyman would prefer to attribute declines in rates of infection from diseases such as measles, polio & smallpox solely to 'environmental' factors, such as isolation of patients, along with better hygiene and nutrition. No-one would deny that these are important, but it's also worth noting that 1950s America (ie the US) had high standards of both hygiene and nutrition - and fairly high rates of morbidity and mortality from measles. Nonetheless, she claims (p128 of the thesis proper) for smallpox that 

isolation of the cases alone could have stopped the circulation of the virus and eradicated this disease
Why? Because, in her view
smallpox is only transferrable by direct skin-to-skin contact.
Now, while it's true that the main route of transmission is face-to-face contact (and not skin-to-skin - the World Health Organisation notes that the virus can travel in saliva droplets on the breath of an infected person), that's by no means the only route. As the Centres for Disease Control point out
Smallpox can also be spread through direct contact with infected bodily fluids or contaminated objects such as bedding or clothing. Rarely, smallpox has been spread by virus carried in the air in enclosed settings such as buildings, buses, and trains.

That information was extremely easy to find. It's surprising, to say the least, that the usual rigorous literature review required for a PhD thesis did not turn up the same information. And that the examiners didn't notice its absence.

| | Comments (5)

This is the human face of smallpox:

Child with Smallpox Bangladesh.jpg

Photo Credit: Content Providers(s): CDC/James Hicks This media comes from the Centers for Disease Control and Prevention's Public Health Image Library (PHIL), with identification number #3265.

Smallpox is now extinct in the wild: the last known case was in 1977.

And this is what Judy Wilyman has to say about the vaccine that eradicated smallpox virus, in her strongly anti-vaccine PhD thesis - you'll find the quote on page 15 of the main document

Vaccination as a preventative public health strategy was first used by Edward Jenner in the late 18th century (Hays 2000). It was used in the fight against smallpox for ~150 years but its efficacy was never tested in controlled clinical trials that exposed a large number of participants to the smallpox virus and compared the outcome to a control group (Wallace 1898).

This is simply unbelieveable. Does Wilyman genuinely think that this would be an ethical approach to addressing the development of a smallpox vaccine? Really? And equally unbelieveable is that this was not regarded as a signficant issue by either her supervisor or those who examined the thesis.
Smallpox is now extinct in the wild, so many people will never have seen a case of it. (This was possible partly because humans are the only known reservoir for the virus.) It's hard to imagine, given the rigorous literature reviews normally expected of a PhD candidate that Wilyman might be ignorant of the disease and its effects1: the most common, severe form of the disease killed a large proportion of those infected with it. Wikipedia tells us this:
The disease killed an estimated 400,000 Europeans annually during the closing years of the 18th century (including five reigning monarchs), and was responsible for a third of all blindness. Of those infected, 20-60 percent - and over 80 percent of infected children - died from the disease. 
Survivors were scarred for life.
It is frankly appalling to see that a PhD candidate thinks it would be in any way ethical to carry out a controlled trial of a vaccine against a virus where the known outcome would have been death for up to 60% of those involved. And yet the supervisor and examiners let this pass?

1 Mind you, she also has this to say (also on page 15):

The fact that developing countries are still rife with infectious diseases today suggests that depending on vaccines to prevent disease in countries with poor environmental and nutritional conditions is questionable
It's almost as if she doesn't know why smallpox is extinct, and polio nearly so.
| | Comments (2)

One of today's big stories, in the blogosphere and elsewhere, is of the University of Wollongong's decision to award a PhD to a thesis that promotes a strongly anti-vaccination take on the policies and science relating to immunisation. Fellow NZ scibloggers Helen Petousis Harris and Grant Jacobs have already commented on it, and over on Respectful Insolence Orac has his usual thorough take on the issue.

The University of Wollongong has defended the awarding of the PhD to this particular thesis:

The university says it accepted a PhD thesis from a controversial anti-vaccine advocate on the basis that universities promote freedom of thought and it adhered to international standard protocol.

"As a leading research-intensive university, the University of Wollongong values intellectual openness, freedom of opinion, diversity of ideas, equity, and mutual respect," a spokesperson from the University of Wollongong said in an official statement.

"UOW does not restrict the subjects into which research may be undertaken just because they involve public controversy or because individuals or groups oppose the topic or the findings."

The spokesperson provided a form that outlines the requirements that must be met in order for a PhD to be accepted and which they said the university complied. "UOW ensures research is undertaken according to strict ethical and quality standards," they said.

And therein lies the rub. Universities do value diversity and freedom of opinion (it would be a sad state of affairs if they did not), but that opinion should be evidence-based. Academic freedom (another phrase aired in this and similar contexts) is not the freedom to say whatever one likes, whenever one likes, without considering the quality of the opinions being expressed.

New Zealand's Academic Audit Unit has discussed this concept at some length. It notes that academic freedom is an important contribution to the community. And for that reason, again, it's important that the opinions expressed under the aegis of academic freedom are accurate and research-based - because if they are otherwise there is the potential to do real harm in the community.

I am not flying a kite here. Helen has already commented on how the views expressed in this thesis, as exemplified by (but in no way restricted to) the abstract, are not based on current best practice and understanding around vaccination. But the thesis is highly likely to be held up by organisations such as the 'Australian Vaccination Network' and the 'Vaccine Resistance Movement' as evidence that vaccines are not only useless but in fact bad for us. If this then results in a drop in vaccination rates, then vaccine-preventable diseases will increase in frequency in the community: this is just what happened in the UK after the publication of the now-retracted report that linked MMR vaccination with autism.

The authors of the AAU monograph go on to note the links between that critic and conscience role in universities and the quality of the research (& teaching) done at the institutions. And this is, I think, the key here: those opinions which we express should be underpinned by good-quality research. In the case of the thesis discussed here, the quality of that research, and the degree to which it was scrutinised by both the supervisory panel and the external examiners, must - as Helen, Orac, and others have already shown - be called into question.

One pressing question is whether the thesis was subject to expert scientific scrutiny in both the development and examination phases. This is because a considerable portion of it discusses not policy but issues of actual science (Chapters 7 through 10), and as Helen's said, quite a bit of that discussion is not based on the modern mainstream scientific literature. For example, as Orac's already noted, the thesis claims that there is a plausible link between vaccination and the development of autism. No such link has been demonstrated, but it's a frequent claim on many antivaccination websites and social media pages. And sadly, it appears that even the offer of scienfitic review and commentary was rejected:

John Dwyer, emeritus professor of medicine and president of the group Friends of Science in Medicine, says Ms Wilyman has challenged well-established concepts in science without the data to support her conclusions. Peter McIntyre, director of the National Centre of Immunisation Research and a WHO adviser, said he had offered to discuss the research with Ms Wilyman but found her “not willing to entertain” evidence contrary to her views.

And then there's the statement that vaccine-preventable diseases have not been shown to be a serious risk to the majority of children in Australia. This runs against the actual historical evidence. I suppose that between 10 & 20 cases of paralytic polio per 100,000, the figures reached during epidemics, don't sound all that much, but that doesn't include non-paralytic forms of the disease. Children under 5 are at greater risk than anyone else. Or pertussis (whooping cough): Australia had around 10,000 cases in 2009. Most cases of this disease are in children under 10, and every year infants die from it; those too young to be immunised are at particular risk, and rely on herd immunity. And let's not forget measles: this remains a significant cause of death in young children, on a global basis, and is easily spread across open borders.

All this information is readily available and it's staggering that it was glossed over in this way, or went unchallenged during the writing and examination of the thesis. Freedom of opinion is one thing; freedom to ignore or misrepresent information that doesn't fit one's narrative, in the development of a PhD thesis, is something else.

EDIT: Orac has added a further commentary, hot off the press.

| | Comments (7)

In 2012 the world was introduced to some of the smallest-known vertebrates: tiny chameleons. My good friend Grant wrote about them at the time, & I set an essay assignment for my first-years on these tiny beasties. How tiny is tiny? The following images are from the original paper, published in PLoS one by Glaw, Kohler, Townsend & Vences, 2012.


Brookesia micra sp. n. from Nosy Hara, northern Madagascar. (A) adult male on black background, showing orange tail colouration; (B) juvenile on finger tip; (C) juvenile on had of a match; (D) habitat along a small creek on western flank of Nosy Hara, where part of the type series was collected. doi: 10.1371/journal.pone.0031314.g008

Anyway,Science News has an article on the speed with which chameleons shoot out their tongues to capture prey. It's based on this paper by Christopher Anderson, published in Scientific Reports.

When a chameleon shoots out its tongue, the movement's driven not only by muscle contraction but by utilising the potential energy stored in stretched elastic tissues. This allows the animal

to release energy more rapidly than by muscle contraction directly, thus amplifying power output. Chameleons employ such a mechanism to ballistically project their tongue up to two body lengths, achieving power outputs nearly three times greater than those possible via muscle contraction.

Noting that small animals are often capable of greater performance in the same feat than larger ones (think about the relative heights that fleas can jump, for example, or the loads that ants are capable of carrying), Anderson hypothesised that smaller chameleons would be able to outperform larger ones when it came to thrusting out their tongues.

To test this, he watched feeding by chameleons from 20 different species, and found that smaller species could indeed reach further: 2.5 times  body length in an individual just 47mm long. And they also achieved much greater accelerations: while larger species send forth their tongues at accelerations as high as 486 m s-2, the smaller ones Anderson studied managed far greater acceleration and power:

peak accelerations of 2,590 m s-2, or 264 g, and peak power output values of 14,040 W kg-1

The interesting question here is, why? Why can smaller chameleons shoot their tongues our further & faster? The answer may lie in the animals' metabolic rates: smaller chameleons will have higher mass-specific metabolic rates, and better feeding effectiveness could mitigate the impact of this. Anderson's data support this: because they also have proportionately longer jaws, larger tongues & associated structures, and higher relative tongue projection distances, 

small chameleons have effectively increased the relative size of their entire feeding apparatus. In doing so, small chameleons have increased the functional range of their prey capture mechanism, and are likely able to capture and process larger prey items than they would otherwise be able to if their muscle cross sections and jaws were not disproportionately large for their body size. This inference is supported by the selection of proportionately larger prey items by the smaller of two morphological forms in Bradypodion. These patterns are thus consistent with those that would be predicted for mitigating metabolic scaling constraints, which may be involved in driving the observed morphological scaling patterns.

Dr Anderson has produced a number of videos showing just what happens when a chameleon strikes, and has kindly given permission for me to use one of them here: 

C.V.Anderson (2016) Off like a shot: scaling of ballistic tongue projection reveals extremely high performance in small chameleons. Scientific Reports 6, article number 18625. doi: 10.1038/srep18625


| | Comments (0)

A few days ago there was a story in the Herald about an Australian huntsman spider that had been found by NZ's border security workers at Auckland airport. With a legspan of up to 15cm these are not small creatures! And yes, we do have them in NZ as well, but they're a different genus: NZ readers may know them as the Avondale spider. 'Our' version was most famously used - and viewed - in the film Arachnophobia

I was reminded of that story when my Facebook feed brought up an article, complete with video, about how the Australian spiders are used by parasitic wasps as incubators for their babies. (A photo in the linked article will give you a good idea of just how big both wasps and spiders are.) Once a spider's been paralysed and dragged back to the wasp's nest, its stuffed into the cavity and a single egg is laid in its body. Once hatched, the growing wasp larva eats its paralysed host, avoiding any vital organs until the last minute (after all, no self-respecting larva would want to dine on rotting spider if that were avoidable!).

Many people would probably find this quite gruesome, but it is simply the wasp's natural behaviour, and something that Darwin himself commented on in a letter to Asa Gray in explaining his thoughts on evolution and religion (it's a most interesting letter to read):

I cannot persuade myself that a beneficent & omnipotent God would have designedly created the Ichneumonidæ with the express intention of their feeding within the living bodies of caterpillars.

Ickily fascinating.

| | Comments (0)

Well, probably not1, in the sense that most would place on the term 'tummy bug' (where a close proximity to the toilet is a Good Thing), but it turns out that he did have some rather interesting intestinal bacteria.

Ötzi is perhaps better known as the 'Iceman', who died around 5,300 years ago in the Otztai Alps of the Italian Tyrol. (He's the subject of a fascinating web page & I have to say, I'd love to visit the museum, maybe when we next visit family in Europe.) His body, clothing, and equipment are exceptionally well-preserved & are yielding a great deal of information on life in Neolithic Europe - including, as described in the latest issue of Science, the nature of his microbiome. (You'll find the full paper here, but there's also an open-access summary here. I do have a gripe about the use of the term 'tummy bug' in the latter, though!)

In their just-published paper, Maixner's research team reports on their finding of a strain of Helicobacter pylori in Ötzi's stomach contents (he'd apparently eaten a full meal not long before he died). I've written about H.pylori before: while it's been found to be associated with development of gastritis, stomach ulcers, & sometimes cancer in a small proportion of those carrying it2, there's also evidence that it has a protective effect against other disorders, including acid reflux and oesophageal cancer. And it's been with us for a long time:

Predominant intrafamilial transmission of H. pylori and the long-term association with humans has resulted in a phylogeographic distribution pattern of H. pylori that is shared with its host. This observation suggests that the pathogen not only accompanied modern humans out of Africa, but that it has also been associated with its host for at least 100,000 years. Thus, the bacterium has been used as a marker for tracing complex demographic events in human prehistory.

Most modern Europeans carry one particular strain of this bacterium, which is believed to have originated via recombination of two earlier strains. However, the origins of these strains have been uncertain, & the researchers hoped that Ötzi's gut microbes might throw some light on this. The Iceman himself was born and lived in Southern Europe, and DNA comparisons link him to early European farmers. However, the strain of H.pylori found in his gut is most closely related to a haplotype now found in central and southern Asia, and not to those of Europe and Africa.

The detection of an hpAsia2 strain in the Iceman’s stomach is rather surprising because despite intensive sampling, only three hpAsia2 strains have ever been detected in modern Europeans. Stomachs of modern Europeans are predominantly colonized by recombinant hpEurope strains.

Maixner suggests that the Iceman's ancestors must have brought this Asian strain of H.pylori with them when they migrated to Europe. Well after Ötzi died, later immigrants from Africa brought their own strain of the bacterium, and subsequent recombination produced the modern European strain of this microbe. This is evidence for rapid evolution of H.pylori in Europe as waves of human migrants moved into and across the continent.

The researchers also noted that Ötzi's version of the bacterium represents a strain that's associated with stomach inflammation in modern humans - and that protein biomarkers expressed in his gut indicate that he had an inflammatory response to the infection. This may or may not have manifested in actual disease - his stomach lining was not sufficiently well-preserved to let them draw any conclusions on this.


1  Which is a real pity, as I was so going to steal my friend Grant's suggested phrase, "the Tyrolean trots", for my title :( 

 It's "found in approximately half the world’s human population, but fewer than 10% of carriers develop disease that manifests as stomach ulcers or gastric carcinoma" (Maixner, Krause-Kyora, Turaev, Hoopmann et al., 2016)

F.Maixner, B.Krause-Kyora, D.Turaev, A.Herbig, M.R.Hoopmann, J.L.Hallows, U.Kusebauch, E.Vigi, P.Malfertheiner, F.Megraud, N.O'Sullivan, G.Cipollini, V.Coia, M.Samadelli, L.Engstrand, B.Linz, R.L.Moritz, R.Grimm, J.Krause, A.Nebel, Y.Moodley, T.Rattei, & A.Zink (2016) The 5300-year-old Helicobacter pylori genome of the Iceman. Science 351 (6269):162-165 . DOI: 10.1126/science.aad2545

| | Comments (0)

February 2016

Sun Mon Tue Wed Thu Fri Sat
  1 2 3 4 5 6
7 8 9 10 11 12 13
14 15 16 17 18 19 20
21 22 23 24 25 26 27
28 29          

Recent Comments

  • herr doktor bimler: But there's also the point-&-wink sort of interest, shown in read more
  • Jj: If dmsa causes "lasting cognitive impairment" how is it possible read more
  • Alison Campbell: Yes, although I don't think Budwig went that far. read more
  • herr doktor bimler: And how do you get your tissues back into that read more
  • Alison Campbell: Quite so. I think it's a nice provocative talking point, read more
  • herr doktor bimler: Now, I'd be wanting to know how that estimate is read more
  • Alison Campbell: That was me having a brainfade. Thank you for the read more
  • herr doktor bimler: And also in comb jellies, marine arthropods, and cephalopods. This read more
  • Alison Campbell: 1/3 the size of a flea - I suspect most read more
  • herr doktor bimler: I should probably scan and send you Fig. 209 from read more