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yes, we have some bananas – just not gm ones (yet) Alison Campbell Mar 09

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Back in 2010 I wrote a post about bananas, following on from a Schol Bio question the previous year. As well as looking at the genotypes of modern bananas, I highlighted the fact that the original wild banana was not a particularly appetising object, with little flesh and a lot of large, hard seeds. Selective breeding for the win!!!

Anyway, it seems like at least one anti-GMO Facebook group has got a case of the vapours about ‘GMO bananas’, this being the only explanation some of its members could think of for the fibres that you’ll often see in the skin of a not-completely-ripe banana when you twist & pull the stalk end. Kevin Folta picked this up in a blog post, noting the lack of knowledge of some of the commenters there (I haven’t quite decided if the one about Morgellon’s is a poe…) – but as Robert Sacerich notes, one of those commenters is giving an object lesson in how NOT to do science communication, & doesn’t help the cause.

And no, we have no GM bananas – at the moment. Sacerich points out that there’s work in progress on developing GM plants that are resistant to the major threats to banana production (Black Sigatoka disease, Banana Bunchy Top virus, and bacterial infections). So such plants may well become a reality in the relatively near future.

But that will have nothing to do with the fibres that so concerned those anti-GMO commenters; they’ve always been with us & were apparently used in cloth production in Japan as early as the 1200s, a practice that’s seen something of a recent resurgence. (I didn’t know that! You learn something new every day.)

rip frank’n'louie, the diprosopic cat Alison Campbell Feb 25

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Seeing this image of a fish with 2 mouths reminded me that I needed to finish writing about Frankenlouie, a janus-headed (diprosopic) cat. It’s funny how the mind works, because the fish definitely isn’t a janus-fish: that would require the mouths to be side-by-side rather than one above the other. (While this is a rather unsightly mutation, the fish seems to have survived in the wild until a fisherman hauled it out.)

Two-mouthed bream

Photo: Garry Warrick)

So – on to Frank’n'Louie.

Frank’n'Louie was (were?) described as a ‘janus cat’ because he had two faces that looked in different directions, like the Roman god Janus (as opposed to that fish, which has two mouths one atop the other). Many people would have found him rather hard to look at, as he had 3 eyes, the middle one of which was blind; two noses; two mouths; and but a single brain. The fact of that single brain means, I suppose, that this really was one, strange-looking, individual cat, rather than the two distinct individuals seen in dicephalic parapagous conjoined twins such as the Hensel sisters. Despite being expected to die soon after birth, Frank’n'Louie attained the ripe old age of 15 years before succumbing to cancer in 2014.

R.I.P.: 'Frankenlouie', the world's oldest Janus cat - a feline with two faces - died at the age of 15 on Thursday, Dec. 4, 2014. The Guinness World Record holder passed away at the Cummings School of Veterinary Medicine at Tuft's University in Grafton, Mass. according to owner Martha "Marty" Stevens of Worcester, Mass. (AP Photo/Worcester Telegram & Gazette, Jim Collins)

Frankenlouie’s features are the result of craniofacial duplication, or diprosopus: an individual with a single body and normal limbs, but a greater or lesser degree of duplication of the face. (He was lucky to survive so long as many janus individuals also have neural tube defects, including – at their most severe - anencephaly, or the absence of a brain, and die very young). When I first saw a picture of this cat I wondered if his features had something to do with conjoined twinning, and apparently that’s often put down as the underlying cause if the organism has two complete faces.

However, another possible cause is a mutation in the gene responsible for the Sonic Hedgehog protein (SHH), which among other roles is involved in the control of craniofacial development. Too much of that protein (overexpression of the mutant form of the gene) results in craniofacial duplication; too little can cause cyclopia, where there is just a single eye. (Infants with cyclopia die soon after birth as the condition is associated with severe brain abnormalities, so the Cyclops of the Ulysses stories would not have been modelled on an actual adult with the condition.)

In fact, SHH plays a crucial role in embryonic development, as this description on the National Institutes of Health gene database makes clear:

It has been implicated as the key inductive signal in patterning of the ventral neural tube, the anterior-posterior limb axis, and the ventral somites.

This means that mutations in the gene coding for SHH can have far-reaching impacts on the development of the brain and nerve cord, limbs, and body segments, while a mutation in one of the enhancer regions (an enhancer is a region on a chromosome that affects transcription of a particular DNA sequence) results in duplication of the thumb.

But there’s more: Sonic Hedgehog is one of a group of ‘evolutionarily conserved’ genes (others in this gene family include ‘Desert Hedgehog’ (!) and Indian Hedgehog) found in vertebrates, so SHH is involved in the patterning of embryo development in all vertebrates, not just in mammals like Frankenlouie. These ‘conserved’ regions of DNA tend to play crucial roles in development and functioning of an organism, and so are relatively unchanged over time: any significant alterations in their sequence, and so in their products, would probably be subject to strong negative selection.  And Sonic Hedgehog’s gene family is in turn related to the hedgehog gene that is involved in proper formation of body segments in Drosophila. So the chromosomal region that’s most likely to be implicated in Frankenlouie’s particular birth defect is one with a very long evolutionary history indeed, one that extends back beyond the split between invertebrate and vertebrate lineages.

why paper cuts hurt Alison Campbell Feb 16

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I suppose one of the benefits of e-readers & ‘paperless’ offices (haha) is a reduction in the risks of paper cuts. Because those cuts jolly well hurt! Part of that may just be because they usually involve fingers & those are in use so much that our attention is constantly drawn to the afflicted part. But there’s more to it than that, and this video from Scientific American explains why:

The comments thread over on youtube is rather fun!

food matters aotearoa – an opportunity for real debate? or muddying the waters? Alison Campbell Feb 08

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One of the big stories on my Facebook feed at the moment alerted me to Food Matters Aortearoa and its upcoming Wellington conference. The program for this conference has certainly generated a lot of interest among my friends.

The focus of that interest lies in the line-up of speakers & the agenda of their tour – something my friend & blog-buddy Grant has also written about. The blurb for the Christchurch event pretty much sets the scene: the speakers there (Seralini & Douzelet)

will reveal their experiences with the health problems that chemically grown food can generate

Er, ‘chemically grown food’??? All our food is comprised of chemicals!

But what of the speakers? As Grant notes, Dr Gilles Seralini is perhaps best-known in scientific circles for a now infamous study on the toxicity both of the herbicide Roundup and of maize treated with it. The original paper was retracted but subsequently re-published (seemingly, without any further peer review), without any real attempt to address any of the issues that led to the retraction: the small sample size and the appalling lack of ethical treatment of the study animals (which were allowed to live with extremely large tumours rather than being euthanized at an early stage of tumour development), among others.

Dr Vandana Shiva has done some admirable work around conservation and supporting women farmers in India. However, she has also made some highly questionable claims, including the incorrect but oft-quoted statement that the use of GM cotton led to a marked increase in suicides among Indian farmers. While people may oppose the use of GM technology for a variety of reasons, using demonstrably incorrect information doesn’t bolster their case. There’s an interesting article on Dr Shiva on the New Yorker website, and a discussion on ResearchGate links to a number of valuable resources that look at other claims (for example, the patenting of seeds pre-dates GM technology by some decades).

Similarly, the other major international speaker, Dr Huber, also opposes the use of GM technology & of genetically-modified organisms. I have to say that I continue to be puzzled to the opposition from some quarters to the use of modern genetic modification techniques, while the effects of other tools such as mutation breeding are ignored. Yet the first involves one to a few genes and is well-tested and highly regulated, while the second – which is not regulated in any way – is completely unpredictable and can affect a very large number of gene loci. (A 2008 study found that mutation breeding produced far more genetic change than did transgenesis, & concluded that “the safety assessment of improved plant varieties should be carried out on a case-by-case basis and not simply restricted to foods obtained through genetic engineering.”)

On the face of it, this conference and the associated publicity could offer the opportunity to have some valuable discussion on issues such as the future of agriculture in a time of climbing global population and widespread environmental change, and the safety of GMOs and the various techniques used to produce them. However, since the conference appears to have a strong anti-GMO slant, I doubt this will happen – although I’m prepared to be pleasantly surprised.

 

 

 

 

are ‘alternative medicines’ really free of side effects? Alison Campbell Dec 16

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Not necessarily. OK, most homeopathy’s just water (or sugar pills), but if a non-self-limiting disease goes untreated because someone is relying on homeopathy then, yes, this ‘remedy’ could be said to have side effects.

Similarly, using powdered rhinoceros horn – prescribed as an oral dose in Traditional Chinese Medicine – is unlikely to have side effects on the dosed individual; after all, we can’t digest keratin. Which makes this quote, from a post at visiblefriends.net, all the more poignant as it focuses attention on the wider impacts of magical thinking:

A common defense of Alternative Medicines is that they are side effect free. While the consumption of a tea made from a small piece of powdered rhinoceros horn may be as harmless and ineffective as biting your own fingernails, the side effects are far reaching and will be obvious for future generations who only know the rhinoceros from plaster molds along side those of dinosaurs in museums.

(via https://www.facebook.com/hatepseudoscience/posts/427349107412957)

credulous reporting around cancer Alison Campbell Dec 02

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This is a really difficult post to write. The word ‘cancer’ evokes any number of fears & unpleasant images, and I can’t imagine something worse than discovering that a child has cancer. (Nor can I be certain of my own reaction, if I should find myself in that position.) But that doesn’t excuse credulous reporting on the issue, most recently exemplified in this story (in the ‘Life & Style’ section) in the NZ Herald.

The story is about the use of plant-based compounds, called salvestrols, for children who’ve been diagnosed with a range of cancers. Now, a search for ‘salvestrols’ brings up a rather large number of websites making all sorts of claims for their efficacy, but a search for ‘scholarly articles’ narrows things down a bit. The first such paper to come up appears to be the one used to support the claims made by the Herald piece, & was published in the Journal of Orthomolecular Medicine in 2007. (It’s worth noting that this particular field of study is not widely supported by science-based medicine and that the journal itself isn’t indexed by Medline. I was intrigued to see that the editor of JOM has compared it to Medical Hypotheses, because really, that’s not a good advertisement.)

Those claims include the hypothesis that salvestrols are used by our bodies to destroy cancer cells (referencing an earlier study by the same authors) and that modern practices around food-growing & preparation reduce the amount of salvestrols in our diet (with little evidence for this cited in support). Unfortunately the Herald’s reporter simply presented these ideas as if they are widely-accepted facts:

they trigger a process in the body allowing it to kill diseased cells. But they have been depleted from food through modern farming and production techniques which have drastically altered diets.

The paper itself discusses case studies ie there are no controlled trials; while the case studies may suggest routes for future research they should be viewed as tentative, at best. Further, it makes the following claim:

First, it is not harmful. The toxins produced through the metabolism of Salvestrols by CYP1B1 are confined to the cancer cells and are exhausted through the destruction of the cell.

And yet GSK stopped a trial of a salvestrol (reservatrol) in cancer patients because not only was there no evidence of efficacy, there was evidence of harm (kidney damage). Hardly suprising as compounds such as reservatrol appear to have an effect on quite a range of metabolic pathways in our bodies.

Now, that information was fairly easy to find, so it was really, really disappointing to see the Herald’s reporter referencing the JOM – and the British Naturopathic Journal – as being the best source of information on this subject.

It’s also important to note that the people identified in the Herald story as successfully using salvestrols as a cancer treatment have also had surgery & in some cases chemotherapy as well. It’s entirely possible that the medical treatments alone have resulted in patients being in remission – and without properly-designed clinical trials there’s no way to identify any impact of the plant compounds. Nor is it enough to say that it’s “common sense” that they work; as a colleague’s said to me, blood-letting was also seen as a common-sense treatment for pretty much everything that ailed you.

This isn’t the first time that we’ve seen such poor reporting around such a serious issue; sadly, I suspect it won’t be the last.
 

weapons-grade foolishness from the ‘food babe’ Alison Campbell Nov 18

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Today, we move on to just plain, flaming, weapons-grade foolishness. Foolishness that is, unfortunately, spread to a rather wide audience.

Vani Hari is the self-described ‘Food Babe’, on a mission to ‘make America’s food safer’. According to Ms Hari, if you can’t pronounce a food item’s ingredients, you shouldn’t be eating it1. I guess she’s never seen information like this, then (graphic by the wonderful James Kennedy).

Ingredients of an All-Natural Banana

But I digress. Recently Ms Hari wrote a piece giving her advice around flying. (It’s since been removed from her site, but the internet has ways of ensuring that things don’t just disappear, so you can read the post in its entirety here – for as long as it remains there, or there’s a screen cap here.) The nature of some of her comments do not inspire me with confidence.

A few facts about what airplanes do to your body -

When your body is at seriously high altitude, your body under goes [sic] some serious pressure. Think about it – Airplaines thrive in places we don’t. You are traveling in a pressurized cabin, and when your body is pressurized, it gets really compressed!

I am still trying to get my head around the idea of inanimate objects like aeroplanes ‘thriving’. That aside, our bodies are not placed under greater pressure when at altitude. Yes, plane cabins are pressurised, but that pressure’s still less than what we’re exposed to at sea level.

Compression leads to all sorts of issues. First off your body’s digestive organs start to shrink, taxing your ability to digest large quantities of food. Secondly, this compression reduces the ability for your body to normally circulate blood through your blood vessels. Sitting down for long hours while this is happening, exacerbates these issues, leading to what they call “Economy Class Syndrome.” Economy Class Syndrome results the action [sic] of sitting in a cramped space for a long period of time, thus resulting in blood flow loss to the legs.

Yes, aeroplane passengers are subject to increased risks relating to poor circulation, but they’ve got nothing to do with ‘compression’ due to supposedly high cabin pressure & everything to do with simply sitting still in cramped conditions for prolonged periods of time. In fact, air travellers are advised to use compression stockings to help mitigate those risks. (Ms Hari does give some sensible advice on combatting this.)

The air you are breathing on an airplane is recycled from directly outside of your window. That means you are breathing everything that the airplanes gives off and is flying through. The air that is pumped in isn’t pure oxygen either, it’s mixed with nitrogen, sometimes almost at 50%. To pump a greater amount of oxygen in costs money in terms of fuel and the airlines know this! The nitrogen may affect the times and dosages of medications, make you feel bloated and cause your ankles and joints to swell.

This is such a basic science fail. Passengers don’t breathe in ‘everything the airplane gives off’ (details of where cabin air comes from are here). And Earth to Vani: the air you breathe has never been ‘pure oxygen’, whether you’re at ground level or 11,000m up in the air – probably just as well, really, given the reactivity of the pure stuff. This is so easily checked (image from geocraft.com):

Now, this may seem laughable. Someone is ill-informed & shares that lack of knowledge rather widely. But that’s not doing any actual harm, is it?

Except, I think it is. Why? Because the Food Babe is encouraging and pandering to chemophobia and scientific illiteracy (and, sad to say, has a wide audience for this nonsense: several hundred thousand followers on FB, for example). And when you’re also spreading anti-vaccine misinformation to that number of followers then yes, you have real potential to do harm.

 

1 Sad to say, one of our local NZ companies has bought into the ‘no long words’ meme. It’s worth remembering that some ‘nasties’ have very short names, while the names of many important proteins are multisyllabic.

but surely if it does no harm… Alison Campbell Nov 14

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With Acupuncture Week coming up, I thought it might be timely to revisit one of my earlier posts on the subject. Since I originally wrote this piece, there’s been at least one high-profile example of needles being found where they definitely shouldn’t have been: a 7cm needle found in the lung of a former president of South Korea.

There’s a lot been written in the blogosphere around what’s known as ‘complementary & alternative medicine.’ (I would argue that there’s no such thing – if it works ie improves/cures the patient’s health, then it’s medicine). In any debate around the use of CAM someone is likely to say that at least it does no harm. For things like homeopathy you could argue that since the client is swallowing only water or sugar pills, with no active principle present, then they’re highly unlikely to come to harm (witness the 10-21 homeopathic ‘overdose’). The counterargument here is that if the patient relies solely on homeopathy for anything beyond self-limiting conditions then there is in fact considerable potential for harm.

With other ‘treatments’ the potential for harm is more apparent. And in some cases the harm can be real. In a 2010 issue of the New Zealand Medical Journal, Brian Kennedy & Lutz Beckert reported on the case of a woman whose acupunturist  left her with a case of pneumothorax. This is not a trivial problem: pneumothoraxis where air builds up within the chest cavity, in the space round a lung, as the result of chest trauma or due to a spontaneous breach in the lung itself – or in this case, because an acupncture needle pierced the lung. This puts pressure on the lung, & as a result the lung collapses. (Pneumothorax has also had medical applications– in Sonja Davies‘ autobiography, Bread & Roses, she describes it as a treatment for tuberculosis. Apparently collapsing the affected lung makes it more difficult for the tuberculosis bacilli to survive & grow, so the lung has a chance to recover.)

In the case described by Kennedy & Beckert, the patient “became acutely short of breath, following introduction of an acupuncture needle into the right side of her chest posteriorly. She developed ‘tightness’ … and associated chest pain” & very sensibly left the clinic, went home, & called an ambulance when her symptoms (typical of pneumothorax) got worse. An X-ray showed that her lung had collapsed, & doctors used a needle to remove 450ml of air from the pleural space around the lung. The next morning the pneumothorax had recurred, which meant surgery to inset a ‘drain’ into her chest wall. After the lung reinflated the drain was removed (& presumably the opening was sealed) & she went home a day later.

Madsen, Gotzsche & Hrobjartsson (2009) performed a meta-analysis of clinical trials looking at acupuncture as a treatment for pain. They looked at data from a total of 3025 patients who received either ‘real’ acupuncture, ‘sham’ (placebo) acupuncture, & no treatment. Their conclusions: there was “a small analgesic effect of acupuncture …, which seems to lack clinical relevance and cannot be clearly distinguished from bias. Whether needling at acupuncture points, or at any site, reduces pain independently of the psychological impact of the treatment ritual is unclear.” (As Orac comments, on a related study, “the larger and better designed the study, the less likely it is to find a treatment effect greater than placebo due to the treatment.”)

Given the following that acupuncture appears to have, people will no doubt continue to seek it out for various ills, regardless of the fact that it performs no better than placebo. In which case, they need to be aware that adverse events like the one described by Kennedy & Beckert, although very rare, can still occur. (These authors list ”transmission of diseases, needle fragments left in the body, nerve damage, pneumothorax, pneumoperitoneum [air in the abdominal cavity], organ puncture, cardiac tamponade [accumulation of fluid around the heart] and osteomyelitis [a bone infection]” as major adverse events, albeit extremely rare ones.) They conclude that as these events are generally associated with poorly-trained practitioners, if people do seek out acupuncture treatment they should choose their practitioner carefully – and if treatment involves acupuncture of the chest wall, then the client should be warned about the risks of pneumothorax by the practitioner concerned.

But as Darcy says over on SciBlogs, why go down this route at all?

Brian Kennedy, & Lutz Beckert (2010). A case of acupuncture-induced pneumothorax The New Zealand Medical Journal, 123 (1320) http://www.nzma.org.nz/journal/123-1320/4258

M.V.Madsen, P.C.Gotzsche & A.Hrobjartsson (2009) Acupuncture treatment for pain: systematic review of randomised clinical trials with acupuncture, placebo acupuncture, and no acupuncture groups. BMJ 338: a3115

a tale of rare blood groups, or, ‘the man with the golden blood’ Alison Campbell Nov 03

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One of the topics we cover in first-year biology is human blood groups – it’s discussed during genetics classes & also touched on when looking at how immune systems function. I give the genetics classes and, being a regular blood donor myself, thought I knew a bit about at least the common blood groups and their inheritance. But there’s always more to learn, something I was reminded of when I read a fascinating story about people with truly rare blood types: “The man with the golden blood”.

There’s ‘Thomas’, for example: a man who lacks the Rhesus markers completely & so is classified as Rhnull  - in 2010 he was one of an exclusive global club of 43 individuals (of whom only 6 regularly donate their blood). And James, who is ‘Lutheran b negative’, and one of only 550 active donors for this blood type.

This makes known donors precious, in that if someone else with the same group needs a blood transfusion, there are very very few people around the globe who might be able to help them. And helping comes at a cost to the donors, for – as the story tells us – it’s actually easier in many cases to move people across borders than it is to move blood, but because many countries don’t pay donors, then that movement may well be at the donor’s expense. It’s also difficult for people like ‘Thomas’, with his vanishingly rare blood group: his blood can be used by anyone who’s Rhesus negative, but he can receive blood only from another Rhnull person, which means he has to be reasonably careful not to put himself in harm’s way (although he does still go skiing!).

Quite an eye-opener – and a tale I’ll be including in next year’s class.

‘alternative’ medicine – numbers using it =/= evidence it works Alison Campbell Oct 26

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Recently some friends & I were discussing the use of what might be called ‘Supplementary, Complementary, & Alternative Medicine’ – a group of ‘therapies’ that includes (but is not limited to) things like homeopathy, reiki, acupuncture, ear candling, and cranio-sacral therapy, and for which there is little or no evidence of efficacy.

One of the reasons given by those supporting their use is a form of the ‘argument from popularity’ logical fallacy: ‘but look at how many people use them. They can’t all be wrong!’ That viewpoint is exemplified here, in the claim that a large number of doctors are now recommending alternative therapies to their patients, or providing these therapies themselves. The list offered at one such practice includes

psychologists, naturopaths, nutritionists, cranio osteopaths, massage therapists, hypnotherapists, yoga practitioners, an acupuncturist and a breast thermography technician.

Now, massage, yoga (exercise), and psychology are hardly ‘alternative’, although including them in the list then allows one to inflate the number of people supposedly seeking out alternative health modalities. Most of the rest have been addressed far better than I could by Orac (see here, for example, and here) and the authors of the Science-Based Medicine site.

But let’s not get distracted. As my friend Renee said: the claim is that lots of people use these modalities, therefore they must be good; a claim supposedly supported by “the impressive statistics showing people are now willing en mass [sic] to spend their dollars on integrated health care”. What we should be asking to see are the statistics showing the efficacy of such care, before we start spending any more of our scarce health dollars on it.

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