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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.

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I find much of the information that comes to me via various science feeds interesting, informative, & useful. But sometimes I see a headline & an article that give me a serious facepalm moment. And this headline on ScienceAlert was one of them: 

This app promises to read your DNA and give you personalised health advice.

Except that the app (under development) doesn't 'read' your DNA at all. It turns out, when one reads the actual article, that interested users must first send a DNA sample to a lab that will analyse your DNA, before feeding the information into an IBM computer program (called Watson), which will then provide that advice.

We're told we can trust the app because

it also provides references from medical journals and clinical trials.

Surely we need rather more than that! I would need to have a great deal of confidence in the security of the system's processes - this is, after all, highly personal information that would be handed over to a third party.

I'd also be wanting to know exactly what information the analytical lab was obtaining. Yes, DNA sequence; yes, differences in overall sequence, non-coding sequences, & probably sequence differences in many coding and regulatory regions. But what about the influence of epigenetics, for example? 

Sorry, ScienceAlert, but I would have hoped for a more careful discussion of this particular topic - and the headline really lets your readers down.

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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

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This is one impressive lyrebird - laser guns and kookaburras! (Not quite at the same time.) I found him on a ScienceAlert page, which has more info and also links to other videos of these vocally talented birds.

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I spent much of the weekend marking first-year biology exam papers. It was a lovely weekend & I really didn't want to miss all the nice weather, so I ended up finishing the task well after midnight last night. And in the process I identified evidence of what is, on the surface, a really puzzling misconception, one that relates to the effects of X-chromosome inactivation.

Now, we'd spent quite a while in class discussing X-chromosome inactivation in female mammals: why it happens, how it happens, & its phenotypic effects (anhydrotic ectodermal dysplasia, anyone?). One of the images I used in this discussion was of Venus, a tortoiseshell cat with an extremely unusual colour pattern:

This image comes from the NBC News site, but Venus is a very famous purrball who even has her own Facebook page, and I've blogged about her previously. She's either a chimera, or we're seeing a most unusual (but not unique) example of the typical X-inactivation tortoiseshell coat pattern. Anyway, I used a similar image of Venus and asked

What is the most likely explanation for the colour pattern shown in the coat of this female cat?

And about 90% of the class answered, "co-dominance". Which really made me stop & think.

Why? Because it suggests that, while I'm sure they could quote me chapter and verse regarding a definition of co-dominance, they haven't really thought any further about what that means in phenotypic terms. For if codominance were in play here, with both alleles for coat colour being expressed in each cell where the gene's active, then we shouldn't see that clear definition of the two halves of the cat's face. Instead, both should be a fleckled mix (is 'fleckled' a word? Yes, it is; Shakespeare for the win once more) of black & golden hairs (rather like roan coats in cattle & horses).

And this gives me pause - & cause - for thought, because this isn't a mix-up that I'd have even considered before. Is 'codominance' their shorthand for one gene, or the other, being expressed (due to X-inactivation)? Or do they really think that's how codominance works? If so, it does suggest that a) I didn't really explain codominance (or X-inactivation) all that well this year, & b) I need to review what I do before teaching that particular session again.

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Recently I went to a couple of seminars/tutorials on using AdobeConnect in teaching & learning. As I vaguely remember saying somewhere else, this bit of software looked a bit like panopto might, if it were on steroids, & I could see how it could be a very useful tool for use in my classes. Not least because (as you'll have gathered from my last post), there's some concern around student engagement, particularly among those who don't actually come to lectures, & AdobeConnect seemed to offer a means of enhancing engagement even if students aren't physically present.

I decided that I'd like to trial it in the two pre-exam tutorials I'm running this week (my class has its Bio exam on Friday - the last day of the exam period. No prizes for guessing what I'll be doing for most of the upcoming weekend :( ) I would really, really like to use it during lectures, so that students not physically on campus can still join in, but, small steps...

So, first I set up my 'meeting'. Work has made this easy by adding an AdobeConnect widget to the 'activity' options in Moodle, so that was pretty straightforward; I just needed to make the session 'private' so that students signed in using their moodle identity. The harder part of the exercise lay in deciding what to actually do when in the meeting room. In the end I set it up with a welcome from me, a 'chat' area, so students could 'talk' with each other & ask questions, and a 'whiteboard' so that I could draw (& type) in response to those questions. And, when the class actually started, I spent a few minutes showing everyone there (the 20 or so who were there in the flesh, & the 8 present via the net) what each of those 'pods' was for & how to use them.

You certainly have to keep on your toes when interacting with a mix of actual & virtual class members! My thoughts & observations, in no particular order:

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  • remember to press 'record' right at the start, if you're intending to record a session!
  • next time (ie tomorrow) I'll remind those physically present that they can log into the meeting room too - this could, I suppose, be distracting, but it also means that they would be able to participate in polls, for example. I did it myself, at the launch of our 'connect week', just to see what everything looked like from the on-line perspective.
  • it was really, really good to see the 'virtual' students not only commenting & asking questions, but also answering each other's questions. I hadn't expected that and it was a very positive experience.
  • but do make sure that you encourage this cohort to take part; they need to know that you welcome their participation.
  • the rest of the class seemed to quite enjoy having others interacting from a distance.
  • next time, I'll bring & wire in my tablet, & use that rather than the room computer. This is because I do a lot of drawings when I'm running a tut, and while you can draw on the AC whiteboards, using a mouse to do this is not conducive to nice smooth lines & clear, precise writing. I <3 touchscreens!
  • it's very important to remember to repeat questions asked by those in the room: the microphone's not likely to pick their voices up, & if you don't repeat the question then the poor virtual attendees won't have a clue as to what you're talking about.
  • with a pre-exam tut it's hard to predict what resources might be used, in terms of powerpoints, web links & so on. For a lecture I'd be uploading the relevant files right at the start (ppts, video links & so on), but today I was pretty much doing things on the fly. However, I'm running another tut tomorrow & have put links to a couple of likely youtube videos into the meeting page already.
  • Internet Explorer seems to 'like' some AC actions more than Chrome; the latter wasn't all that cooperative about 'sharing my screen', which seemed to me to be a better option than uploading at one point in proceedings.
  • as a colleague said, doing it this way meant that overall I had more people in class than would have been the case if I'd only run it kanohi ki te kanohi (face to face) - what's not to like?
  • for me, the whole session was quite invigorating, & I thoroughly enjoyed the challenge of learning to use a new piece of software to improve the classroom experience.
  • Mind you, on that last - it was my impression that the classroom experience was improved. And you'll have gathered that I truly did have fun. But I'm not a learner in the way that my students are. So I asked them for feedback (interestingly, so far I've had only one comment + my response on Moodle, but as you'll see we've had a reasonable dialogue on Facebook) - and here's what they said:

    BIOL101 Adobe Connect tutorial

    So next year I will definitely be using this during lectures, and to interact with my Schol Bio group & their teachers - and I think we'll definitely have one tut a week (out of the total of 6 that we offer) that's via AC, so that students that can't come onto campus can still  get the benefits of that sort of learning environment.

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    I came across this story on Science's 'science sifter' page:

    The next CEO of Australia’s leading research agency, the Commonwealth Scientific and Industrial Research Organisation (CSIRO), is in hot water after suggesting the cash-strapped organization spend scarce research dollars investigating water divining, or dowsing.

    The editors at Science do have a sense of humour & my first thought was to check the date, but no, the story didn't break April 1st. 

    Before any science funders start spending their scarce funds on this particular brand of woo (for dowsing is not based on any known physical principles), those making the funding decisions might be best considering the fact that it doesn't stack up in controlled conditions. First up, James Randi (in Australia) - and note that those participating all agreed to the methods used before the test began.

    Richard Dawkins did something similar, & again, those taking part agreed to the methods before beginning (which makes the special pleading in the comments thread rather amusing)

    I feel a facepalm coming on.

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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.

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    Evolutionary change can be fast - Peter and Rosemary Grant's long-term & ongoing research project on the Galapagos finches documented rapid responses to environmental changes, for example, as does the  recent work on cane toads in Australia. And biologists have known since Darwin's time that competition can be a strong driver of evolutionary change. (Take Gause's principle of competitive exclusion & its implications, for example.) A just-published paper about Anolis lizards demonstrates this very well (Stuart et al., 2014).

    The way in which different species of this little lizard divvy up their habitat is used as an illustration of niche partitioning by many textbooks (you'll find an example here). Stuart & his co-authors describe some elegant experimental work over a period of 15 years, on artificial islands in a Florida lagoon. Initially they used six of these islands, all of which were already colonised by the green native anole, Anolis carolinensis: three of the islands acted as controls, while brown anoles from Cuba (Anolis sagrei) were introduced to the other three. The two species are described as being "very similar in habitat use and ecology", including diet, so they'd be expected to compete fairly strongly when brought together.

    In other areas where the two species are found together, A.sagrei perches lower in trees than carolinensis, which left to itself would occupy most of the tree. So the prediction was that on islands where sagrei was introduced the same thing would happen: carolinensis would come to occupy a reduced niche, perching higher than the 'invader'. And this is indeed what happened, in the space of three months: 

    by August 1995,on treatment islands already showed a significant perch height increase relative to controls, which was maintained through the study.

    The researchers also predicted that this change in niche would be accompanied by a change in morphology; specifically, that there would be selection for larger, sticker feet in A.carolinensis, on the basis that 

    [toepad] area and lamella number (body-size corrected) correlate positively with perch height among anole species, and larger and better-developed toepads improve clinging ability, permitting anoles to better grasp unstable, narrow, and smooth arboreal perches.

    This prediction was tested through observations on 11 islands, five with only the native species and six with both the native and the Cuban invader. Again, carolinensis perched significantly higher in trees on islands where sagrei was also present - and on those islands carolinensis anoles also had "larger toepads and more lamellae" than were found on the same species living without the competitor (an example of character displacement) - and this happened within about 20 lizard generations.

    Careful analyses allowed the researchers to rule out other explanations: 

    In sum, alternative hypotheses of phenotypic plasticity, environmental heterogeneity, ecological sorting, nonrandom migration, and chance are not supported; our data suggest strongly that interactions with A. sagrei have led to evolution of adaptive toepad divergence in A. carolinensis.

    So, just as with the cane toads, we are seeing rapid evolutionary change in real time.

    Y.E.Stuart, T.S.Campbell, P.A.Hohenlohe, R.G.Reynolds, L.J.Revell & J.B.Losos (2014) Rapid evolution of a native species following invasion by a congener. Science 346 (6208): 463-466. doi: 10.1126/science.1257008 

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    This was first posted over on TalkingTeaching.

    This blog post at SkepticalScalpel really struck a chord. Entitled "Should social media accomplishments be recognised by academia", it compares the number of citations the author's received for published papers with the number of hits on a blog post reviewing original research. And finds there's no contest:

    Three years ago, I wrote "Statistical vs. Clinical Significance: They Are Not the Same," which reviewed a paper on sleep apnea ...

    That post has received over 13,400 page views, certainly far exceeding the number of people who have read my 97 peer-reviewed papers, case reports, review articles, book chapters, editorials, and letters to journal editors.

    The SkepticalScalpel author also notes that this sort of on-line peer-review and discussion of data can have rapid, effective results:

    Last year, some Australians, blogging at the Intensive Care Network, found that the number needed to treat stated in a New England Journal paper on targeted vs. universal decolonization to prevent ICU infection was wrong. They blogged about it and contacted the lead author who acknowledged the error within 11 days. It took the journal 5 months to make the correction online.

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