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I met with a local biology teacher today to talk about setting up a Schol Bio preparation day in the Waikato, and we also discussed things like the need for critical thinking skills (in addition to a solid base of knowledge from students' year 12 & year 13 studies and time spent in reading more widely around the subject). So here are some thoughts on this, for those of my readers thinking of entering for the examination this year.

That critical thinking needs to be applied not only to the questions themselves (just what is the examiner asking me to do? what are the key points I must answer to do this), but also to the resource material (what inferences can I draw from this? which bits of information are relevant, and to which section(s) of the question) and to your own knowledge (which of the concepts I've learned about is directly relevant here?). Assessing your own knowledge with the same care that you apply to assessing the question and determining how to integrate the resource material with your answer is very important - it'll avoid you doing what I've heard examiners characterise as a "brain dump". That's when a student simply writes down everything they know that might be related to a particular question, in the hope that some of it will be relevant. 

And then look at the construction of your answer in the same way: for example, check to see that for each statement you make, you've also written a justification. That is, why is the point you've just made, relevant? What explanation can you provide to support it?  For example, in the 2015 paper there was that question around whether the moa could possibly be brought back into our bush. In answering the part asking about factors leading to a species' extinction, you might have written that a species might be more at risk of extinction if it's a specialist (eating a fairly specialised diet). That would be an 'evidence' statement, which you'd then need to justify: if environmental conditions change so that its particular food sources become rarer, or disappear completely, then the species is less likely to survive.

Critical thinking is a learned skill, & something that needs practice. It's something your teachers will probably work on with you. But there are also resources out there that you can use. For example, criticalthinking.org has rather a good model that encourages this sort of reflection:

  • what is the question I'm trying to answer?
  • what information do I need to answer it? Of all the information available to me, which bits are relevant?
  • now I've identified all the relevant facts, what is the best possible conclusion?
  • what assumptions am I making here, and are they justified?

Teachers are probably already aware of the resource on the tki website (and the material at this link is a "heavier" extension to that.) but for a student looking for additional study pointers focused on critical thinking then this webpage is a nicely written primer on the subject. 

Don't think that these thinking & reflective skills are needed only for the exam! They're the sort of skills that you'll use throughout life - a point made by the narrator of this video :)

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Today a science-minded friend posted a screenshot of a post by another individual to the FB group 1080 eyewitness. Because it is a) heavy on the innuendo, b) inaccurate, and c) decidedly unpleasant, I thought it worthy of a bit of additional attention.

Let's look at c) first. The original poster claimed to have written this on the Prime Minister's FB page; it's a particularly nasty attempt to sow fear & confusion in womens' minds by using a combination of overstatement, innuendo, & downright inaccuracy. Jacinda Ardern is level-headed enough to ignore the item as an ill-founded rant, but I see no reason why someone should attempt to frighten others in order to push their own point of view in this way.

and, a little later

That is really is nasty.

Now b) - he implies that 1080 is a teratogen of the same order as thalidomide,

which doesn't appear to be borne out by actual scientific evidence. For example, Eason et al. (1999) state that

1080 causes developmental defects in rats when pregnant females are exposed to relatively high doses (0.33 and 0.75 mg kg(-1) day(-1)) on a daily basis during the period of organogenesis (from days 6 through to 17 of gestation). The developmental abnormalities observed were mild skeletal effects: slightly curved forelimbs, and bent or "wavy" ribs. [The birth defects caused by thalidomide are much more severe.]

These concentrations are quite high. They are also much higher than the precautionary drinking water standard defined by the Ministry of Health (2 parts per billion), and much higher than has ever been detected in water flowing from watersheds where 1080 has been dropped (0.1 parts per billion). In addition, NIWA comments that

Importantly, no 1080 has been detected in drinking water supplies.

Similarly, in 2011 Eason & his colleagues pointed out that (my emphasis)

Results of the initial research and subsequent monitoring demonstrated that there has been no evidence of 1080 presence in reticulated water and no evidence of significant or prolonged 1080 contamination in surface waters

Brown also implies that teratogens can cross the placental barrier but other chemicals can't. This is incorrect: plenty of chemicals cross the placenta. I mean, oxygen, anyone? Nutrients? But, more seriously, if 'chemicals' couldn't cross the placenta then we wouldn't see neonates affected by meth (P) or with foetal alcohol syndrome.

So, Brown is correct that 1080 is a teratogen. What he carefully ignores is that it has these effects at concentrations far higher than have ever been measured in our drinking water. That is, his implication that the PM, or anyone else drinking water supplied from the Hunua catchment, is "heavily poisoned" by 1080 is both incorrect, and blatant scaremongering.

Which pretty much addresses a) as well.

Now tea, on the other hand, does contain small but measureable quantities of sodium monofluoroacetate, aka 1080. I wonder what Brown's take on that would be?

 

Please note: none of this should be taken to mean that 1080 is a benign substance. It's not. But it is the best currently-available mechanism for controlling pest species in those parts of New Zealand where other methods fail. And as Eason et al. (2011) comment

There has been no evidence of significant or prolonged 1080 contamination of surface waters... The risks associated with 1080 to human health are determined by the toxicity of 1080 and the potential for exposure: risk = hazard × exposure. The innate toxicity of 1080 is not in question, as there are clearly identified lethal and sub-lethal effects as illustrated above. However, exposure risk to humans is very low with the exception of the small group of workers in the pest control industry, a group that has been closely monitored to try to ensure minimal exposure (Beasley et al. 2009).

Because of this, they state that

the use of 1080 must continue to include safeguards that focus on those individually handling 1080 or 1080 baits to ensure they do not ingest, inhale or absorb 1080.

 

C.T.Eason, M.Wickstrom, P.Turck & G.R.G.Wright (1999) A review of recent regulatory and environmental toxicology studies on 1080: Results and implications. New Zealand Journal of Ecology 23(2): 129-137

C.Eason, A.Miller, S.Ogilvie & A.Fairweather (2011) An updated review of the toxicology and ecotoxicology of sodium fluoroacetate (1080) in relation to its use as a pest control agent in New Zealand. New Zealand Journal of Ecology 35(1): 1-20

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I was idly skimming the Herald's website when I came across an article with the headline "Is plant medicine really that effective?" Since the article appears to be in the nature of an advertorial, the answer is, it depends on who you ask.

Unlike man-made chemical drugs that have been developed as novel medicines from the 19th century onwards, plant medicines have been used in human healthcare for millennia. 

This is what's known as an appeal to antiquity - because something's been in use for ages, it must work. It's repeated later in the article, with the claim that 

[t]raditional plant medicines have a rich history of being effectively used for over 2500 years

A rich history of being used is not the same as a history of being used "effectively". In Hippocrates’ time, for example, ‘plant medicine’ & basic surgery were about all physicians had to work with. That doesn’t mean that they necessarily achieved a high cure rate. The implication that plants are somehow better than their modern pharmaceutical counterparts is an example of another logical fallacy, the appeal to nature. (Tim Minchin was spot-on when he said “You know what they call alternative medicine that's been proved to work? - Medicine.”)

They share a long co-evolution with humans and are the foundation of their modern chemistry-based counterparts.

There are certainly many examples of coevolution involving plants and animals. However, much of this coevolution has taken the form of an arms race: as mutations that make plants less attractive to eat (e.g. spiny, less palatable, or downright poisonous) spread through a species, this can act as a selective agent on herbivores: animals with gene combinations that allow them to process the poisons are more likely to survive and spread those own genes around, and so that species evolves in turn. Coevolution does not mean, as previous articles by Clair imply (see here, for example), that plants are thus well suited by coevolution to our own needs in terms of acting as medications. The defensive alkaloids produced by many plants can certainly have a physiological impact, but as part of the plant’s anti-herbivore armoury. We can make use of some of those chemicals, sure, but natural selection didn't design them for medical (or recreational) use in any directed way. (Deliberate selection by humans is another matter.) 

But yes, many modern pharmaceutical drugs are derived from plant extracts, and pharmaocognosy is an important field of research in the search for new drugs and investigation of how traditional treatments might work. The difference being that modern pharmacology means that we can control things like dose, concentration and purity, which isn't really possible if you're using the entire plant prepared fresh each time. The chemotherapy drug taxol (isolated from the Pacific yew tree) is a good example, but there are many others, including: digitalis (foxgloves), salicin/salicylic acid (meadowsweet and willow bark), vinblastine (derived from the Madagascar periwinkle), and quinine (chinchona bark). For some drugs (e.g. vinblastine) yields from the actual plants are low, and the cost of obtaining the drug is high, so modern production methods make the drugs available to far more people than could ever avail themselves of the natural source.

... research confirms their beneficial effects for rebalancing hormones, aiding sleep, dealing with stress, in depression or strengthening the immune system. 

"Rebalancing hormones" seems to be one of those 'catch-all' phrases - which hormones are we talking about, & why do they need "rebalancing"? How did they get out of whack in the first place? Similarly, "strengthening the immune system": it's a meaningless term and ignores the fact that in the great majority of people the immune system works just fine. Other than the use of vaccines, "strengthening" or "boosting" may not be such a good idea... And in some instances evidence for other uses is conflicting.

Plant medicine can provide you with essential building blocks for organ health that cannot be found through diet alone, and have a cumulative effect on the body to help build or restore your physiology to the optimal levels.

Sorry, what? Which 'building blocks' would those be? All the building blocks of life – amino acids, di- & monosaccharide sugars, fatty acids, nucleotides, vitamins & minerals – are provided in an average diet. So what are these things that diet supposedly doesn't deliver?

In fact, Western biomedicine is historically rooted in plant medicine, given that it was the main form of medicine until the establishment of the new economic order after the industrial revolution.

And why did medical practices change at that point? Perhaps, because it became much easier to identify the actual active ingredients, and produce standardised doses of known concentrations and purity? Perhaps because the ability to do this meant that some drugs, at least, could become more widely available? Certainly the use of lab-made ingredients would help to protect species such as the Madagascar periwinkle, or plants such as goldenseal & ginseng, which in the US anyway have become endangered in parts of their range due to overharvesting for 'traditional' uses. 

Since the mid-1980s there has been an explosion of research into complementary and alternative medicines (CAMs), driven by consumer demand for natural medicines. There have been over 40,000 studies conducted over the past three decades. This means that in addition to traditional empirical evidence, we have increasing evidence based on newer methodologiesA such as randomised controlled trials. They overwhelmingly confirm traditional medical applications of plants.

Some citations would be nice. This would enable us to answer questions such as: of these 40,000 studies, how many were randomised controlled trials (RCTs)B? How many of those were properly blinded? Were they in vitro studies, carried out in petri dish or test tube, or in vivo, using animal models? Were they studies based on whole plants, or on extracts thereof? And – what were their results? 

Traditionally, plant medicine incorporates the whole plant and its extracts, and with this it brings a full spectrum of active constituents that work synergistically on different parts of the body's physiological functions. 

There are certainly examples where different plant constituents can act in a synergistic manner. One such example, looking at antibacterial activity in extracts of the plant goldenseal, is discussed here. It identified the actual compounds, their structure, and their likely modes of actionC. (What’s not to like?) Notably, while the goldenseal article was written in 2011, evidence that the same action occurs in vivo is (as far as I could tell from a quick pubmed search) still lacking. It’s also worth pointing out – should this evidence eventuate – that a synthetic preparation of the 3 compounds would be a much more reliable source than a tisane or a poultice of the whole plant.

Plant medicines will only work if they have been expertly compounded – from harvesting the plant at the right time at their peak potency, to careful processing them to preserve their active constituents and then to the correct formulation.This means to reap the many benefits of plant medicine, you must ensure you are getting them form [sic] a trusted company or registered Medical Herbalist.

And thence, my comment on advertorials.

 

A The idea of RCTs isn’t actually a modern invention. Perhaps the first such trial (albeit an imperfect one) was run by James Lind, back in 1747, in seeking a treatment for scurvy. He subsequently followed this up with a systematic review of the subject.

B There are some good explanations & examples in terms of trial design at this link.

C Thus the statement in a 2015 op.ed by the same writer, that “we simply do not have the technology yet to understand exactly how they work”, is incorrect. (Nor, from that same article, is it accurate to say that there are no side-effects if you use a whole plant remedy: see here, here, & here, for example.)

 

 

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I subscribe to the Tertiary Insight newsletter (a great way to keep up with news of what's happening in the tertiary sector). Yesterday's edition  included a statement (& a link) about the NZQA's decision to cancel the registration of the Aromaflex Academy. It seems that this Private Training Establishment (PTE) was placed under strict conditions in January 2018, & has presumably failed to meet them. 

Now, if you go to the Academy's webpage, you'll see that it offers courses about "The Science of Aromatherapy, Reflexology, Holistic Massage, Anatomy & Physiology". Personally, I struggle to see how one could offer a course in the science of either aromatherapy or rellexology (of which, more at the end of this post), so my first thought was that the NZQA's decision was - from a scientific perspective - a Good Thing. However, the list of compliance requirements shows that they are regulatory in nature, and in fact this is how the NZQA processes are intended to work.

And so they should: we absolutely need to ensure that providers comply with the various regulations that ensure the quality of the learning experiences for students and the quality of the outcomes that they attain. But surely we should also be asking questions about whether the nature of what's taught in programs describing themselves as science-focused - the actual content side of the curriculum - is evidence-based as well?

In this particular case, the Academy's website lists a number of offerings. From a science perspective the anatomy & physiology certificate sounds OK (although without access to the study materials it's hard to say more than that). As currently described on the website

The Anatomy & Physiology award is the 'foundation' upon which all other Complementary, Beauty and Sports Therapy awards are based. It is comprised of 12 units encompassing all systems of the body: The Chemistry of Life & Pathology, Cells, Tissues and the Skin, Skeletal System, Muscular System, Nervous System, Human Senses, Endocrine System, Circulatory System, Lymphatic and Immune System, the Respiratory System, the Digestive System and the Urinary & Reproductive Systems.

However, I'm puzzled about how someone with an even an introductory understanding of those body systems and their functioning (it's described as a level 4 Certificate) could then go on to accept the idea of reflexology. Again from the website

The Diploma in Reflexology qualification is a study of the reflexes of the feet that relates to the various parts of the body. Hand Reflexology and Auricular Therapy (reflexes of the ears) are also taught over the various block week courses.  Students also learn about Zone Therapy and the Meridians relating back to the feet and hands.  

This statement appears to be using the word 'reflexes' in a rather non-scientific way; here's a definition that someone who's learned about the nervous system should be familiar with. In addition, since the 'meridians' relating to feet, ears & hands seem to be totally invisible to science (ie non-existent), it's hard to see how a course could reasonably claim to teach the science underlying them. Which leads to the next question: is that aspect of delivery something that NZQA considers in approving programs & papers? And if not, should that change?

The scientists & doctors at Science-Based Medicine have written quite a lot about reflexology and the fairly specific specific health claims made by some providers, They note that a 2011 systematic review found that there is no convincing evidence that relexology is effective against any medical condition. (The massage aspect of it may well make you feel better, in a general sense, but that's a different issue.)

It's the same for aromatherapy: nice fragrances can be relaxing, but as Steven Novella comments, "high quality studies are almost completely lacking in the published literature regarding essential oils." He goes on to explain that any studies demonstrating efficacy need 

to be properly blinded and adequate controls are essential. You can use pseudo-objective measures, like the need for additional pain medication, functional ratings, and other markers of their health outcome as appropriate. And of course, studies need to be large enough and carried out for long enough to get adequate data, and executed to prevent p-hacking.

Especially when dealing with a treatment for a subjective symptom like pain, one that we know to be highly modifiable by non-specific interventions (like distraction, mood, the introduction of a novel treatment, physical contact, the environment, interaction with the practitioner, and other variables), adequate controls are essential (pun intended).

Now, I understand that people believe in these modalities, regardless of whether or not there's empirical evidence that they work, and that the NZQA

approves training schemes if they are genuinely needed by learners and stakeholders,

but is that sufficient grounds for accrediting courses that claim to teach 'the science of...' but from a scientific perspective appear to be a combination of massage and magical thinking?

 

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I'm starting to gear up for some Schol Bio preparation days in the regions (hi, Hawkes Bay! See you in 4 weeks!) and realised that I haven't written anything specifically focused on those exams for a while. So I thought that putting something together would be a good way to spend a rather wet Sunday. At these days we usually put quite a bit of time into working on answers to the previous year's questions, so in this post let's look at one from the 2015 paper.

In 2015, the examiner based question #1 on a statement by then-Opposition MP Trevor Mallard that he felt that it could be possible to bring moa back to our national parks

... the moa will be a goer, but we're talking 50-100 years out

and expressed a desire to see

small ones that "don't weigh much more than turkeysA ... ones that I could pat on the head rather than ones that are going to bowl us over...

After providing some other contextual material (as is the norm for Scholarship Biology - be aware that you'll need to factor a reasonable amount of reading time into your planning on the day), the examiner asked students to

Analyse the information provided in the resource material and integrate it with your biological knowledgeB to discuss:

  • the evolutionary and ecological factors that contribute to declining population numbers that may result in the extinction of species AND account for the very large increase in the rate of extinction of species in modern times. Use named examples to support your discussion
  • how humans could manipulate the transfer of moa DNA to restore a moa population to the Rimutaka Forest Park AND analyse the biological implications of this. Give your justified opinion on whether the 'moa is a goer'.

There are a number of factors that could feed into a decline in population size. High on most lists would be a reduction in the genetic diversity of the population, something that could be due to genetic drift. If the population is isolated, there would be little or no gene flow due to migration or breeding with individuals from other populations, which would also have a negative impact on genetic diversity and result in the phenomenon of inbreeding depression. (Think of NZ's black robins, as an extreme example.) This is why those managing endangered species such as takahe & kakapo are careful to mix breeding up where possible.

Then, if a species is a specialist, environmental change could pose a problem if the resources the organisms rely on diminish or disappear; they may lack the flexibility to change to others. Specialists are then perhaps more likely to feel the effects of loss of habitat due to climate change or a natural disaster; if they're a non-migratory species then the problem is compounded. Either way, the population sizes of such species are likely to decline. That environmental change can include the arrival of exotic predators, competitors, & diseases - something that's certainly had a significant negative effect on NZ's native fauna & flora. Takahe, for example, have suffered from competition with deer, but were also badly affected by the arrival of stoats. Mustelids, rats, & feral cats kill native birds, reptiles, and insects much faster than the prey species can replace their losses. And chytrid fungus infections pose a threat to amphibian species worldwide, including our own ancient native frogs.

Ultimately their population size may become too small to be sustainable - this is where the concept of 'effective population size' comes into play. If the total size is large, but most individuals are past their normal breeding age, then the effective population size is small. This means that at the population level, reproductive outputs decline. And once death rate exceeds the birth rate, extinction is on the horizon. In addition, in a small, isolated population inbreeding becomes common, and any harmful recessive alleles may be more likely to be expressed. 

It may not be only that species that's affected, either. Removal of one species from an ecosystem can have ramifications for the entire ecosystem - this relates to the concept of a keystone species.

In all of this, we should not forget or underestimate the impact of our own species. Habitat destruction accompanies human settlement, as does the introduction of new species (in NZ, rabbits, possums and pigs along with the deer, rats, cats, dogs, and mustelids). Humans are reasonably efficient predators themselves: it's estimated that moa became extinct here within 200 years of first human arrival. (Research suggests that human arrival & expansion, coupled with climate change, is implicated in megafaunal extinction in Patagonia & elsewhere.)

So, could we bring 'the moa' back? (I really dislike this whole 'the' thing: there were around a dozen different species of moa in NZ, with their own ecological niches.) In theory, yes, we could. It's possible to extract DNA from moa bones, and Massey University researchers used this aDNA to work out how many species of moa once existed here. Mind you, to bring any species of moa back you'd need to ensure you had its full genome!

Then, you'd need to identify a suitable surrogate parent, remove the nuclear DNA from eggs from that host, replace it with your moa DNA, and implant the egg into the surrogate. What would that surrogate be? Perhaps another ratite, such as an emu? Or - if we're going with Mr Mallard's wish for small & manageable moa - perhaps a turkey, given the similarities in size. You'd need to do this multiple times, with the remains of multiple individuals of your target species, and to clone both male and female moa (using the sex chromosomes to identify them), in order to end up with a genetically-variable breeding population. 

Easy to say. But in reality things are likely to be more complex, & more difficult, than that. It's debatable, for example, whether scientists could find a large enough number of P.geranoides individuals to be able to reconstitute that genetically-variable population. In that case, the threats related to inbreeding & genetic drift would still be there, and the species could well spiral back into extinction. 

From an ecological perspective, moa were reasonably large, and each individual would eat a lot of vegetation each day. Given that the Rimutaka Forest probably isn't the same as it was when moa were in their hey-day, would re-introducing moa have a negative effect on the current ecosystem, particularly on the other herbivores? We need to be able to answer that one, to avoid inadvertently causing further changes to the forest community's species composition. 

So, what would be your final opinion? You could argue, along with Mr Mallard, that yes, "the moa is a goer". Remember that you need to justify that opinion: bringing moa species back could help to re-establish the natural biodiversity of ecosystems that human actions have damaged.

Or, you could say - as I would - that no, this isn't a viable proposal. Firstly, as far as I'm aware, birds have yet to be cloned successfully. (There's a list of cloned species, plus a lot more information, at this FDA link.) And secondly, this seems to be a diversion from a more pressing problem: the need to use that money & scientific effort to conserve those ecosystems and species that we currently have.

 

A Mr Mallard was wise to limit the size of the species he wanted resurrected. After all, the giant moa species, Dinornis robustus & D.novaezelandiae, stood over 2m tall & weighed around 250kg. The much smaller Mantell's moa, Pachyornis geranoides, was under 0.5m tall & would have tipped the scales at 20kg ie roughly turkey-sized. Much less alarming, should you meet one in the bush!

B This reminds me that I also need to write something on what the examiner is looking for, in giving an instruction like this.

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