SciBlogs

Archive August 2012

science – it’s not magic! Alison Campbell Aug 31

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One of the things I like about my job is that there’s always the opportunity to learn new things. Today I learned about episomes. Not being an actual geneticist & all, it was a novel term to me. An episome is defined as:

a portion of genetic material that can exist independent of the main body of genetic material (called the chromosome) at some times, while at other times is able to integrate into the chromosome.

By that definition, transposons and viruses would both be episomes, while bacterial plasmids aren’t, because they don’t insert themselves into the main bacterial chromosome.

I learned about them as a result of discovering that Bad Science Reporting is always out there somewhere, courtesy of my blogging buddy Aimee, who sent me this link to a report on how scientists have cleared a path to the fountain of youth. Yes, really.

It’s an article about some rather interesting research into the possibility of reprogramming adult cells so that they return to a pluripotent stem cell state. (You can read the original paper here at PLoS One: the genetics is a bit technical but the intro & discussion are reasonably straightforward.) Reprogramming somatic cells often uses viruses, which can be problematic if the viral DNA inserts into the ‘wrong’ place in the recipient cells’ genomes, but if transfection agents aren’t used then conversion of body cells to stem cells tends to have a very low success rate: the authors of the PLoS One paper give a figure of 0.001% to 0.5% (Park, Huo, Peters, Talbot, Verma, Zimmerlin, Kaplan & Zambidis, 2012).

However, the researchers report figures of around 50%, which is quite something. They did it using cord blood (ie umbilical cord blood), where the cells were ‘lineage committed’ ie they had already differentiated from the pluripotent state, and tweaking gene expression in those cells using ‘episomal nucleofection’ to carry a set of four key genes into the cells’ nuclei. (The earlier you catch cells post-differentiation, the easier it apparently is to nudge them back to pluripotency: ‘developmentally immature’ cells (Park et al., 2012) will revert at a higher rate than fully differentiated adult cells.)

So, preliminary proof of concept, but a long way from inducing adult tissue cells to re-enter a stem cell state.

Unfortunately, the writer of the article Aimee pointed me at seems to have been a little overenthusiastic in their reporting:

an efficient and totally safe method to turn adult blood cells [back to their embryonic state]. The discovery could be the key to cure the incurable – from heart attacks to severed spinal cord to cancer – and open the door, some day, to eternal youth.

For some reason the article talks of obtaining ‘adult blood cells’ from a patient’s spinal cord, when the original paper talks of cord blood from a cord blood bank (ie we are talking umbilical cords). It also mentions plasmids, when the paper talks of episomes. (I guess that one’s less obvious as I thought ‘plasmids’ on first reading & had to look up episomes for myself!).

As for ‘totally safe’ – hmmm, that one I would want to hear more about. Plasmids don’t integrate into host DNA, but episomes do – so the potential is still there for disruption of functional genes. But the phrase that nearly made me cough tea over the keyboard was this:

the cultivated cells magically turned to embryonic stem cells.

No, no, no! The researchers are able to describe the mechanism. They are pretty clear on what has happened. This is SCIENCE, not some magical intervention!

I will leave my readers to debate whether this final vision of a brave new world is necessarily one to look forward to:

Hypothetically, if you’re able to perpetually fix any part of your body, there’s no reason you wouldn’t be able to live as long as you wanted.

 

Park TS, Huo JS, Peters A, Talbot CC Jr, Verma K, et al. (2012) Growth Factor-Activated Stem Cell Circuits and Stromal Signals Cooperatively Accelerate Non-Integrated iPSC Reprogramming of Human Myeloid Progenitors. PLoS ONE 7(8): e42838. doi:10.1371/journal.pone.0042838

fostering is the cause… Alison Campbell Aug 27

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… of a lack of time for other things. (Like writing ‘proper’ posts.)

On Friday we became the foster parents of a tiny 4-year-old black toy poodle male (who’d previously been a stud dog). At least, we think he’s about four; could be a bit less or a bit more. Kanji (his new name) is one of several ‘toy’-breed dogs & bitches removed from a puppy-mill operation: kept in small pens and constantly bred to provide puppies for the pet trade. Some went to the pound, but several came out to the kennels where Ben goes for doggy daycare, in the hope that some of their ‘regulars’ could provide foster or permanent homes. Hence, because I am a sucker for sad little poodle faces, Kanji (who’ll be going to his forever home in a few weeks).

kanji (cropped).jpg

 

He’s wearing a coat (taped-up to make it fit – he’s that tiny) because when he arrived at the kennels, his coat – like that of the other little dogs who arrived with him – was way too long & hideously matted, so he needed a very short clip to get rid of all that and feels the cold. He’s off to the vet tomorrow, for desexing & a dental check: his teeth look in fairly good condition, but several of the others had terrible teeth & needed some removed.

Kanji is desperately eager to please, has never been in a house before (& despite that we’ve had only one accident to date, but we watch him carefully!) – and eats faster than a labrador that’s missed breakfast. He’s learned his name, & to come when called (although I definitely wouldn’t trust him at the park just yet), & walks well on the lead considering he’s not had a lot of experience at it. A bright little dog, & very easy to train. (Ben seems to be enjoying having a pack & being the leader of it. I guess it makes a change from being at the bottom of the pecking order, beneath all 3 cats! Kanji follows him like a shadow.)

But my goodness, after learning Kanji’s back-story I will always look sideways at puppies in pet shops. (Not the puppies’ fault, but nonetheless…)

charter schools (from letters to the editor) Alison Campbell Aug 21

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Usually when I choose to base a post on the ‘letters’ section of a newspaper, it’s because something that someone’s written has rather got my goat. This time - this time, it’s because I agree with the sentiments & feel they warrant a wider audience & further analysis.

The Government wants to introduce charter schools, apparently, to solve issues of under achievement. It points to students failing to achieve NCEA Level 2 as justification for this policy. In fact, if the Government actually bothered to look at NCEA data, it would see that pass rates have been rising over the past decade, something achieved without charter schools.

And in fact, the NZ Herald ran a story on this in early 2011.

Studies clearly show that the most effective way to assist schools to lift achievement levels is employing trained teachers and providing quality professional development. Charter schools can employ untrained teachers and the Government has cut funding for much of the professional development it offered.

As I’ve said previously, it’s hard to see how using untrained teachers is going to improve teacher quality.

New Zealand has a very good education system. In countries with poorer education systems than ours, with greater academic under achievement, charter schools have failed to make any significant improvement to under achievement. So, if the Government wants to make a dent in education under achievement, why import policies that have failed overseas. Failure simply replicates failure.

The evidence on success (or otherwise) of charter schools is mixed. In some US states, for example, they seem to have a marked positive effect on learning outcomes for their students. In others, not so much. We’re told that in NZ, charter – sorry, ‘partnership’ – schools will be run following best overseas practice; it would be useful to hear more about what that will entail, sooner rather than later.

In that last post, I also expressed concern about the potential for charter schools – which, let us remember, will be state-funded – to include subjects such as creationism in their curricula. A ‘Stuff’ piece by Kelsey Fletcher expands on this, describing the intention of one group keen to run a charter school to use the ‘In God’s Word’ philosophy (something that would somehow still be able to be ‘marked’ against the Cambridge curriculum – presumably only if the evolutionary underpinnings of the biology curriculum component are ignored). Associate Education Minister, John Banks, tells us we don’t need to worry (the following is from the ‘Stuff’ item):

John Banks said the ministry had received a lot of correspondence, including complaints about public funding of faith-based education. He would not comment on the trust’s charter plans. “There’s no proposed partnership to consider, because we haven’t received any formal applications, and none have been called for,” Banks said. “The first schools open in 2014, and expressions of interest will be called for next year.”

I would feel more sanguine about this whole process if the nature of charter schools, and what they can and cannot offer in their curriculum, was set out clearly well in advance. Finding out after the event is not an appropriate option.

 

academic olympics fail to gain government support Alison Campbell Aug 16

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This is a guest post – I’m running it on behalf of my friend & colleague Dr Angela Sharples. Angela is the current chair of OlympiaNZ (the umbrella organisation for the various NZ Olympiad committees) and leads NZ International Biology Olympiad. She received the Prime Minister’s Science Teacher Award in 2011.

At a time when we celebrate all things sporting we should reflect on our attitudes towards success in all forms of endeavour in New Zealand. The Olympics showcase the world’s best in sporting endeavour and we rightly look up to these elite athletes and admire the effort and dedication it took for each and every one of these athletes to reach the top of their field. The personal attributes required for them to even participate at the Olympics are transferable to all areas of performance in life and so we celebrate these athletes, admire them and aspire to like them. They are role models that encourage younger athletes from primary school to university level to participate in the sport of their choice and to dream that with hard work and dedication they too may reach Olympic level.

The government recognises this social benefit of elite sports and funds it accordingly, through SPARC and the high performance programmes. They have their eye on the long term benefits that participation in sport at the elite level provides to the wider New Zealand community. The government also recognises that New Zealand must foster innovation through a responsive, high performance education system if New Zealand is to remain globally competitive in a rapidly changing world.  Unfortunately, whilst the government has
published any number of reports on the importance of Science and innovation in New Zealand we see very little action on establishing and supporting programmes which foster such excellence.

Just last week, the New Zealand International Biology Olympiad withdrew from hosting the International Biology Olympiad here in New Zealand in July 2014. This prestigious international event challenges and inspires the brightest young secondary school students from 60 countries (and the number of member countries continues to grow) to deepen their understanding of biology and promotes a career in science. The focus is on the importance of biology for society, especially in areas such as biotech, agriculture and horticulture, environmental protection and biodiversity. These are all areas of academic endeavour crucial for New Zealand’s economic success in the future. Hosting this event in New Zealand was a chance to showcase our innovative education system and biological research to some of the world’s top academics and to inspire our own students to develop the dedication and put in the sheer hard work required to reach this highest level of academic endeavour. It is an opportunity lost!

Unlike our sporting Olympians our academic Olympians receive little support from the government and even less acknowledgement and celebration of their success. New Zealand has performed outstandingly well in the International competitions since we first competed in 2005, winning 16 Bronze medals, 7 Silver and 1 Gold Medal. These high performing students are New Zealand’s economic future and yet few in the country are even aware of their achievement.

Until we apply the same high performance strategies to our science and innovation system in New Zealand that we utilise in sports we will continue to talk about the importance of fostering excellence in science and innovation whilst we watch our competitors on the global stage outperform us. And we will continue to lose our best young minds to countries where their contribution is valued.

this is a poodle moth… Alison Campbell Aug 15

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… and I shall call it… no, not Ben. That name’s taken.

This is Ben.

Thephoto (2).JPG

And this is a poodle moth (via Animal Story):

The photo’s all over the internet (especially via pinterest: there’s a particularly lovely image collection here). However, neither scirus nor google scholar searches return a scientific name for this lovely fluffy insect (& so I’m hoping the entomologists on Sciblogs can help out.

I do wonder, though, if that fluffiness could be a problem for those who go ‘squeeee’ & would like one for themselves: in Venezuela another species of hairy moth has been linked with skin & respiratory symptoms.

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(This is a ‘lazy’ post as my brain is still virus-fogged. More normal service will resume as soon as possible.)

dodgy experts & gardasil – further questions Alison Campbell Aug 10

Perhaps the greatest fear for any parent is that their child will die before they do. Such events must be incredibly hard to bear, particularly if the death is unexplained and unexpected,  & my heart goes out to any parents in such a situation.

Sometimes, particularly where the death is unexplained, all sorts of alternative hypotheses can be put up, perhaps as a way of dealing with the grief. And unfortunately, sometimes those hypotheses can offer fertile ground for proponents of pseudoscience to put down roots. Grant and Orac have both posted on one such case, a young New Zealand woman whose untimely death has been attributed by her mother to the Gardasil vaccine that she received 6 months prior (despite the fact that other causes – some potentially heritable – may have come into play).

This death is currently the subject of a coroner’s inquiry, during which a couple of overseas ‘experts’ have had the opportunity to present their views to the coronial court. Expertise, and views, that require rather closer scrutiny than has yet been afforded by the media. Orac has already done his usual very thorough job but I wanted to add a couple of points.

In the Otago Daily Times* we read that

Neuroscientist Profefssor Christopher Shaw of the University of Columbia in Vancouver told the inquest … that he was sent Ms Renata’s brain tissue to test. He said there was aluminium in all the samples he tested and there were some abnrmalities in the samples. The human papillomavirus (HPV16) was found in her brain, which could only have got there through the vaccine, Prof Shaw said…He said there was a “biological plausibility” that [the vaccine caused her death] because of the abnormalities in her brain he had examined.

In addition,

Dr San Hang Lee, a pathologist at Milford Hospital in Connecticut, told the inquest … that he tested samples from Ms Renata’s blood and spleen. He also found aluminium and HPV in her system, from the vaccine. Dr Lee could not say for sure what caused Ms Renata’s death, but said the results he found from testing samples from her were “unnatural”.

Aluminium is the third most abundant element on Earth. It’s present in the food we eat and the liquids we drink. So it’s hardly surprising that either ‘expert’** would find aluminium in the dead woman’s tissues. (We’re not told whether either of them used control samples when doing their analyses.) Aluminium is used as an adjuvant in some vaccines – but there’s no way of distinguishing the various sources of Al in someone’s tissues and in addition, the quanitity of Al used as an adjuvant in Gardasil is comparable to that ingested daily via food and drink*** (& vaccines are not delivered on a daily basis).

Both men said that they found abnormal or “unnatural” results, but we’re not told (in this article anyway) what “unnatural” actually means. How does it compare with ‘normal’? Who knows?

And HPV in the brain, ‘which could only have got there through the vaccine’? First up, you’d want to know how the virus was detected: the amount of HPV DNA in Gardasil is tiny, and only a fraction of that would make it into the bloodstream, and a fraction of that again into the brain. Any testing regime would need to be extremelysensitive and also extremely robust, with suitable controls. Was this the case? We don’t know; certainly neither ‘expert’ is reported as giving this information. In addition, human papilloma virus isn’t spread only via intercourse. In fact, HPV – including the HPV16 strain – is also found in dermal warts. So there are other potential sources of HPV virus particles.

And as one of Orac’s regular commenters noted:

If tiny traces of HPV DNA cause sudden death, I would expect most warts (which are essentially HPV DNA factories) to be fatal.

Again, this is a very sad story – made even sadder by the fact that the focus on a vaccine as a potential cause of death is obscuring other possible causes.

 

* The ODT story also gives a more measured response from a pathologist, further down the page.

** A search of the staff at Milford Hospital, Connecticut, does not bring up Dr Lee’s name.

*** someone using antacid tablets would receive a much higher dose.

There’s a lot of information on the development and testing of the Gardasil vaccine here, and the US National Cancer Institute provides more general information.

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11/08/2012  Something else (courtesy of another of Orac’s commenters: the HPV virus infects squamous cells – the type you find in skin & other eplthelia. It does this by locking onto receptors that are peculiar to squamous cells. Neurons (the type of cell found in the brain & nervous system) are not squamous cells. (Which should be a case of ’nuff said.)

passionate biologists start early Alison Campbell Aug 08

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Today, 385  talented senior biology students from 67 secondary schools will sit the NZ International Biology Olympiad entrance exam. Dr Meikle, secretary NZIBO said “This is the largest number of students from the widest range of schools ever!” At Christ’s College, the students are so keen that they will sit this test at 7:15 am. The two hour multi-choice exam challenges students’ thinking skills and knowledge of biology.

It also gives them a sample of the type of question that they could face at the International Biology Olympiad in Bern, Switzerland in 2013. From the exam cohort, a group of 80 students will be selected to participate in the 8 month tutorial training programme. This year, the NZIBO team brought home 2 Bronze and 1 Silver medal from the International Biology Olympiad in Singapore, continuing New Zealand’s superb record in the competitions.

things to do with precious bodily fluids Alison Campbell Aug 08

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A couple of posts back I wrote about the dreadfulness that is ‘Fresh Cell Therapy’. As practiced by the German clinic offering it, FTC supposedly involves injecting foetal lamb cells into people as a ‘treatment’ for all sorts of ills. (I used the word ‘supposedly’ deliberately – the best one can hope is that in fact no lamb tissue actually ever goes near the fluid that’s injected.)

Over on Riddled, Smut Clyde has delved more deeply into the history & current use of FTC and related techniques – not a pleasant job, but someone’s gotta do it! (Chimp testes as a ‘rejuvenation’ technique I had heard of. But I really must read The_Adventure_of_the_Creeping_Man.)

quality counts – except when it doesn’t Alison Campbell Aug 06

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A few weeks ago, writing about the ‘great class size debate’, I also touched on the question of quality teaching. There’s no question – at least, there shouldn’t be – that children deserve the best possible learning experiences, and one of the requirements for that is quality teaching by excellent, expert teachers. It’s quite tricky to pin down just what defines that excellence, but at least our current system of state sector teacher training and subsequent registration goes some way to ensuring that the people teaching our youngsters have been trained in how to go about the multitude of tasks that teachers encounter every day: planning, classroom management, assessment, pastoral care & general admin, and have gained experience in said tasks…. (and that’s before we even get to the actual teaching!).

But a couple of days ago, Minister of Education Hekia Parata & Act MP John Banks announced that charter schools – oops, sorry, ‘partnership schools’ – would be able to employ at least some non-registered teachers, along with setting their own curricula & deciding on things like the length of the school day, term dates, & teacher pay rates. This is strange – to say the least! – following as it does on a recent meeting of the Ministerial Cross-Sector Forum on Raising achievement, which “discussed… improving teaching practice with a focus on priority learners.” As well that discussion, the meeting heard from the Chief Education Review Officer, who

presented the latest Education Review Office findings on how to raise the quality of practice in New Zealand Schools.

His remarks focused on three dimensions: assessment for learning; student centred learning; and responsive school level curriculum.

Minister Parata, who chairs the Forum, commented that

The Forum will continue to discuss ideas around how we can achieve quality teaching practice.

It’s not exactly clear how allowing charter schools to use some unspecified proportion of non-registered teachers will achieve this. Concepts and practices related to assessment for learning and student-centred learning are best acquired before arrival in the classroom, not on a learn-as-you-go-when-you get-there basis. (Yes, state schools can already employ non-registered staff, under a ‘limited authority to teach’ provision, but that’s temporary and for a limited period.)

Some real contradictions here…

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The freedom of charter schools to set their own curriculum also concerns me somewhat. We already have ‘special character’ schools which teach creationism in their classrooms, for example (see here, here, and here, for starters). It is rather irking to gain the impression that state funding could support the same in charter schools – and to date I’ve heard nothing to say this will not be possible.

 

 

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