Archive May 2010

it’s not a miracle Alison Campbell May 31

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From time to time the media present us with reports of ‘miracles’: the most recent is probably that of the 9-year-old Dutch boy who was the sole survivor of a plane crash in Libya. Frankly I would have thought it more miraculous if everyone on board had survived… But anyway, ‘miracles’ are often presented in the context of medicine. The thing is – they aren’t the result of some miraculous intervention, but of the skill & dedication of a whole range of medical practitioners (surgeons, nurses, anaesthetists, oncologists; the list goes on).

Why are some people so ready to ascribe these outcomes to some other cause?

female genital mutilation – hideous whichever way you look at it Alison Campbell May 28

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I’ve just been sent through an article from an Australian news site, which suggests that the Royal Australian New Zealand College of Obstetrics will next month be discussing the possibility of doctors offering ‘ritual nick’ – a form of female genital mutilation that entails a small incision on the clitoris. (In this they seem to be following in the footsteps of the American Academy of Paediatrics.)

I am commenting as both a biologist & a woman when I say that I find this practice abhorrent. At its most extreme, female genital mutilation (FGM, sometimes called ‘female circumcision’, presumably in an attempt to make it sound more acceptable) sees the removal of the clitoris & the labia minora & majora; women are often also infibulated ie the wound is stitched to heal in such a way that only a small opening is available for the passage of urine & menstrual fluids. I say ‘women’ but the whole process is performed on young girls. The outcome of this extreme mutilation – if the child doesn’t die of infection – is complete loss of any pleasurable sexual sensation and the real potential for further damage during intercourse & childbirth, not to mention an increased risk of urinary tract infection. The ‘ritual nick’ is far less extreme, but it still involves damage to a particularly personal part of a girl’s anatomy for no good medical reason.

The rationale for the doctors’ consideration of this issue appears to be that it’s already done in a ‘backdoor’ way by various ethnic communities in Australia, without anaesthesia or proper surgical tools, & making the less extreme ‘ritual nick’ legitimate might stop the whole backdoor thing in its tracks. (In some cases families take their daughters overseas & the FGM is done there. It’s hard to see how people who feel so strongly about subjecting their daughters to this would settle for ‘just’ a nick…)The problem I have with this is that it legitimises the idea that it’s OK to scar young women in this way. The practice may have a lengthy cultural history but that doesn’t make it right. Nor is there any good biological or health-related reason why it should be encouraged – I fail to see, for example, how cutting away any tissue around a woman’s genitals can is some way improve personal hygiene. Yet it’s sometimes justified (ha!) as making a young woman ‘more beautiful.‘ More tellingly perhaps, in many proponents of the practice feel that it reduces the young woman’s libido, making it less likely that she will engage in ‘illicit’ (ie outside of marriage) sexual intercourse. This is an incredibly misogynistic view. (And no, I don’t see the point of male circumcision either.)

OK, if an adult genuinely consents to such a procedure, & knows what the outcomes are, then it’s their decision (although I find it hard to imagine why a woman would wish to go ahead with it). But not a child. Children cannot possibly give informed consent for this.

And – for the doctors – whatever happened to ‘first, do no harm’?


PS (29th July): the College has put out a press release saying that it does not support the use of the ‘ritual nick’. Thanks to Mark for passing this on.

slightly more than half of everything i am is thanks to you (thanks, mum) Alison Campbell May 26

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For teachers (& students): a biologist’s song for Mother’s Day. (Yes, I know it’s late, but my wonderful tutor just found the video!) It makes the point that, thanks to cytoplasmic inheritance & the nature of what goes on in the womb, slightly more than half of every mammal is due to the mother: we’re not simply the result of a 50:50 genetic combination of maternal & paternal DNA :-)

on craig venter & his new life form Alison Campbell May 25

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There’s been a lot of hype – & some overwrought responses – surrounding the announcement that Craig Venter & his research team have ‘created’ a novel life form (a mycobacterium with a completely artificial genome). I wasn’t going to weigh into it.

And I’m still not – but I am going to reproduce in full an excellent comment by PZ Myers. (Go back to Pharyngula if you’d like to join in the comments there.) If after reading it you want more, then here’s the place to go: the ‘Reality Club’ at The Edge has an extensive & high-powered discussion around the issue.

I have to address one narrow point that is being discussed in the popular press and here on Edge: is Venter’s technological tour de force a threat to humanity, another atom bomb in the hands of children?


There is a threat, but this isn’t it. If you want to worry, think about the teeming swarms of viruses, bacteria, fungi, and parasites that all want to eat you, that are aided (as we are defended) by the powers of natural selection–we are a delectable feast, and nature will inevitably lead to opportunistic dining. That is a far, far bigger threat to Homo sapiens, since they are the product of a few billion years of evolutionary refinement, not a brief tinkering probe into creation.

Nature’s constant attempts to kill us are often neglected in these kinds of discussions as a kind of omnipresent background noise. Technology sometimes seems more dangerous because it moves fast and creates novelty at an amazing pace, but again, Venter’s technology isn’t the big worry. It’s much easier and much cheaper to take an existing, ecologically successful bug and splice in a few new genes than to create a whole new creature from scratch…and unlike the de novo synthesis of life, that’s a technology that’s almost within the reach of garage-bound bio-hackers, and is definitely within the capacity of many foreign and domestic institutions. Frankenstein bacteria are harmless compared to the possibilities of hijacking E. coli or a flu virus to nefarious ends.

The promise and the long-term peril of the ability to synthesize new life is that it will lead to deeper understanding of basic biology. That, to me, is the real potential here: the ability to experimentally reduce the chemistry of life to a minimum, and use it as a reductionist platform to tease apart the poorly understood substrates of life. It’s a poor strategy for building a bioweapon, but a great one for understanding how biochemistry and biology work. That is the grand hope that we believe will give humanity an edge in its ongoing struggle with a dangerous nature: that we can bring forethought and deliberate, directed opposition to our fellow organisms that bring harm to us, and assistance to those that benefit us. And we need greater knowledge to do that.

Of course more knowledge brings more power, and more possibility of catastrophe. But to worry over a development that is far less immediately dangerous than, say, site-directed mutagenesis, is to have misplaced priorities and to be basically recoiling from the progress of science. We either embrace the forward rush to greater knowledge, or we stand still and die. Alea iacta est; I look forward to decades of revolutionary new ideas and discoveries and technologies. May we have many more refinements of Venter’s innovation, a flowering of novel life forms, and deeper analyses of the genome.

sequencing the neandertal genome Alison Campbell May 23

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I’ve had this one in my ‘must write about’ file for a little while: in the May 7th edition of Science, a large research team announced that they’d produced a draft sequence of Neandertal DNA (Green et al. 2010). Using DNA from 3 individual Neadertals, the multi-institutional team managed to decipher more than 4 billion nucleotides from the Neandertal genome. Considering that Neandertals disappeared 30,000 years ago, this is a stunning achievement.

Stunning, because DNA so old is always going to be highly degraded, & in this case the researchers were recovering fragments averaging only 200 base pairs long. What’s more, when you die the decomposers take over, & the team was faced with the challenge of distinguishing between Homo neandertalensis DNA & that from the microbes involved in decomposition. This was done by comparing the various DNA fragments with chimpanzee & modern human genomes. (Up until now just 4 fragmentary sequences of Neandertal DNA had been decoded, from loci involved in skin colour, blood groups, speech, & taste. Again, the nature of these fragments was determined by comparing them with modern human DNA sequences. The results of the Human Genome Project are not restricted to modern humans but have allowed us to look far into our past.)

Neandertals first appear in the European fossil record around 400,000 years ago & subsequently spread into Asia, as far as southern Siberia & the MIddle East. They’re regarded as the sister species of Homo sapiens. Anatomically-modern humans moved into the Middle East around 80,000 years ago & it’s long been assumed that the two species would have come into contact, then & later when sapiens moved west into Europe & also into Asia. And a question that’s often asked when I’m talking with school students is, could Neandertals & modern humans have interbred?

Up until now it hasn’t been possible to rule out the possibility. This is because, while the available Neandertal mitochondrial DNA (mtDNA) sequences fall outside the range of modern human mtDNA, this doesn’t rule out interbreeding. (If you can’t see why not, remember that mtDNA is almost always passed down along the maternal line. The absence of any mtDNA apparently belonging to Neandertals may simply mean that no female Neandertal lineages have survived to the present day.)

Green et al. extracted their DNA samples from bones from 3 different individuals, found in a cave in Croatia. (They used mtDNA comparisons to confirm that the remains were indeed from 3 different people.) And they found that yes, there probably was a certain amount of interbreeding between resident Neandertals and the new, younger species moving in from Africa. How much, is hard to say, but it appears that modern human populations from Europe, Asia & the South Pacific have 1-4% ‘Neandertal’ DNA. (But not Africa: only modern human populations moving out of Africa would have had the opportunity to meet up with Neandertals.) The authors also note that any gene flow between the 2 species probably occurred before the divergence of those modern human populations.

There’s much more to the story, though, than simply cataloguing early inter-species matings. There’s enough information in the draft Neandertal sequence to look for variants of genes that are shared by both neandertalensissapiens & those that are unique to one or the other. And it turns out that there are just 78 genes where a ‘novel’ variant has become fixed (either by positive selection or by drift) in the human population (although there are rather more novel non-coding sequences in the modern genome as well). Some of these are implicated in brain development & functioning in modern humans. Mutations in another gene affect the cranium, shoulder girdle & ribcage – all features where sapiensneandertalensis skeletons differ. This is really exciting stuff, where palaeontology and genetics come together to unravel the details of a fascinating time in our past.

You can read much more about this on John Hawks’ weblogPharyngula (of course!), & in Carl Zimmer’s piece in Discover magazine, & there’s a video interview here on the Dolan DNA Learning Centre page.

R.E.Green, J.Krause, A.W.Briggs, T.Maricic, U.Stenzel, M.Kircher, N.Patterson, H.Li, W.Zhai, M.H.Fritz, N.F.Hansen, E.Y.Durand, A-S.Malaspinas, J.D.Jensen, T.Marques-Bonet, C.Alkan, K.Prufer, M.Meyer, H.A.Burbano, J.M.Good, R.Schultz, A.Aximu-Petri, A.Butthof, B.Hober, B.Hoffner, M.Siegemund, A.Weihmann, C.Nusbaum, E.S.Lander, C.Russ, N.Novod, J.Affourtit, M.Egholm, C.Verna, P.Rudan, D.Brajkovic, Z.Kucan, I.Gusic, V.B.Doronichev, L.V.Golovanova C.Lalueza-Fox, la Rasilla, J.Fortea, A.Rosas, R.W.Schmitz, P.L.F.Johnson, E.E.Eichler, D.Falush, E.Birney, J.C.Mullikin, M.Slatkin, R.Nielsen, J.Kelso,, M.Lachmann, D.Reich & S.Paabo (2010) A draft sequence of the Neandertal genome. Science 328: 710-722 doi:10.1126/science.1188021

flashes in the eye Alison Campbell May 20

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I’ve just spent an interesting hour down at my optometrist’s rooms, having my eyes looked into. And learning a whole lot of new stuff.

I’ve had glasses for years, since I was 10 or so. (My primary school teacher picked up the fact that I was having trouble seeing the blackboard & sent a note home with me for my parents. I was horrified at the prospect of wearing glasses – that ‘four-eyes’ name really stings when you’re 10 – & hid the note in the hedge. Which of course led to all sorts of trouble when the teacher followed up on my parents’ apparent inaction…) Over the years my myopia (short-sightedness) has stabilised & in fact these days I don’t need to use specs for close work.

Anyway, I trundled off to the optometrist because yesterday I started getting these weird flashes of light in one eye: quite bright arcs of light off to the side, usually when I moved my head quickly. They were a bit like what you get when you press on your eyeball gently – that sort of pressure-generated flash of coloured light. Very puzzling & also very distracting (& a bit of a worry: an elderly neighbour of ours, years ago, had suffered from a detached retina & of course you tend to think the worst when something odd happens to your own eye).

After putting some drops in my eye to dilate the pupil (& I’m still going round with uneven pupils!) the optometrist had a good look around inside, using lenses & some very bright lights – so bright in fact that I was seeing after-images of the blood vessels over my own retina. A bit like cracked mud on the bottom of a dried-out pond, with the blood vessels being the cracks. She was able to tell me that it wasn’t the retina coming away that was causing the strange arcs of light, which was a big relief. Instead, the jelly in my eye is going goopy.

Structure of human eye and refion of retina

The main part of your eye, back of the lens, is filled with a firm jelly-like substance called the vitreous humour (to distinguish it from the aqueous humour between lens & cornea, which as its name suggests is watery). Apparently what can happen as you age is that the vitreous humour can begin to liquefy, pulling away from the ‘wall’ of the eye & folding in on itself. (My optometrist was quick to reassure me that this wouldn’t necessarily result in any deterioration of my vision.) However, this mass of dense jelly is attached to the retina, most firmly at the blind spot & also around the anterior edge of the retina (towards the front of the eye). And when it pulls away from the retina, the pressure changes can generate nerve impulses that your brain interprets as arc-like flashes of light (like the pressure-induced flashes I mentioned earlier). Which is kind of cool, really. There’s a name for it too: posterior vitreous detachment.

Apparently the whole process can take up a few weeks, so I guess I’ll be having my own intermittent private light show for a while yet :-)

(It seems there’s a small risk of retinal detachment following on from vitreous detachment, especially along that front edge of the retina. My friendly optometrist told me that this can manifest as a shower of ‘floaters’ – she described it most graphically as looking through a shaken snow-globe. Now that’s a light show I can do without, & hopefully will never experience!)

let it grow, let it grow… Alison Campbell May 20

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The tutor running our first-year labs does a wonderful job of seeking out quirky little video clips that she can use to illustrate a particular point & pique her students’ interest. But I think I might have beaten her to this one (courtesy as usual of PZ): a time-lapse sequence of germination & growth of maize.


One of the reasons I was glad to find the clip relates back to an earlier post on the dearth of students who are really keenly interested in botany. The tutor wondered if perhaps it’s because plants just don’t seem to do anything: they sit there & photosynthesise, you can eat bits of them (as long as the bits aren’t brussels sprouts), but they don’t seem to behave in the same fascinating, multifaceted way that animals do.

Of course, people who are ‘into’ plants know that plants do behave, but their behaviour patterns tend to be visible only on a longer time-scale than we’re used to. Tropisms – growth movements, & in particular thigmatropism – can look almost balletic when filmed in time-lapse & speeded up. Flowering, root growth, development of fruit – all look wonderful viewed in this way, in a way that daily classroom observation of germinating seeds can’t capture.

Maybe we need to provide more links to material like this?


milk & health: there aren’t always two (equal) sides to a story Alison Campbell May 18


 I had another learning experience down at the gym this afternoon. There I was, happily pedalling away on the exercycle (I believe in varying my cardio, otherwise it gets boring!) & reading a fitness magazine (what else?) when I came across an article on whether or not drinking/eating dairy products is bad for you.

It started out with comments from dieticians to the effect that ‘lactose intolerance’ tends to be self-diagnosed, which probably over-inflates estimates of the actual prevalence of this problem. (From a biological perspective, it should be less common among those of European & perhaps African descent, something that’s related to the repeated ‘discovery’ of dairy farming around 9,000 years ago.)

The article then gave gave another point of view, with a nutritionist commenting that milk today is quite different from what it would have been like 100 years ago, in the sense that animals are farmed more intensively & with greater use of various pharmaceuticals, which are likely to come through into the human diet. She also noted, in a rather shocked tone, that much of the milk comes from pregnant cows, so it likely has higher levels of oestrogens & other pregnancy-related hormones. The implication was that this could be linked to various cancers in humans.

What was the evidence for this? The article tried to be even-handed, looking at information from both sides (milk causes cancer/doesn’t cause cancer). For the ’no cancer link’ side it cited a study of around 9,000 women, published in a research journal, which found no correlation, let alone causal relationship, between women’s dairy intake & the incidence of breast cancer. Because it was the gym, I didn’t have pen & paper handy to take down the details, but I’m fairly sure it was a 2002 paper by M-H Shin & colleagues, which concludes: We found no association between intake of dairy products and breast cancer in postmenopausal women. Among premenopausal women, high intake of low-fact dairy foods… was associated with reduced risk of breast cancer. 

Searching some more I found this paper (Knektl et al. 1996), & this one (Parodi, 2005), both of which present data supporting the conclusions of Shin et al.. Parodi (2005) also points out that the amount of hormones taken in via dairy products is extremely small compared to a woman’s own endogenous hormone production: about 0.05µg/day from dairy intake against up to 1mg/day in pre-menopausal women & between 40 & 200µg/day in post-menopausal women.

On the ‘milk is implicated in cancer’ side we got a paper in the journal Medical Hypotheses. The paper looks at apparent correlations between diet & the incidence of various cancers, including breast cancer, & suggests that hormones in milk may be implicated in cancer . However, correlation is not the same as causation, & while the suggestion that cows’ milk contributes to some cancers due to its high hormone titre is an interesting hypothesis, again there is no direct evidence presented in support of this. To counter this argument, as noted by Parodi the hormone contribution from dairy products is insubstantial compared to that produced within the body.

The problem I have with the oriiginal magazine article is that it presented both sources as of equal importance & validity. And they’re not. The first three papers I’ve linked to (including the one cited by the article) are from peer-reviewed journals & they’re evidence-based ie they contain data from fairly large cohorts of patients. Medical Hypotheses, as I’ve commented before, isn’t peer-reviewed and the papers it contains are often published because they offer provocative hypotheses. In this case the hypothesis – based on data on cancer rates & diets, but not examining particular cohorts of patients – is an interesting one but the apparent correlations need to be examined in a lot more depth.Sometimes there really aren’t two equal sides to a story.

D.Ganmaa & A.Sato (2005) The possible role of female sex hormones in milk from pregnant cows in the development of breast, ovarian and corpus uteri cancers. Medical Hypotheses 65(6): 1028-1037. doi: 10/1016/j.mehy.2005.06.026

P.Knektl, R.Jarvinen, R.Seppinen, E.Pukkala & A.Aromaal (1996) Intake of dairy products and the risk of breast cancer. British Journal of Cancer 73:687-691

P.Parodi (2005) Dairy product consumption and the risk of breast cancer. Journal of the American College of Nutrition 24: 556S-568S

M-H.Shin, M.D.Holmes, S.E.Hankinson, K.Wu, G.A.Colditz & W.C.Willett (2002) Intake of dairy products, calcium and vitamin D and risk of breast cancer. Journal of the National Cancer Institute 94(17): 1301-1310. doi: 10.1093/jcni/94.17.1301

helping students engage with maths & physics Alison Campbell May 17


OK, not biology :-) But what follows could equally well apply to teaching problem-solving in any of the sciences.

A colleague of mine (thanks, Jonathan!) sent me through the link to a talk by Dan Meyer, on teaching maths & physics. Dan’s talking about how to engage students with the subjects he teaches; how to put them on a level playing field – where they can all understand what a question’s about; how to get them talking about the question in a way that guides them to understanding how to get at the answer in a meaningful way. His aim: for all his students to become ‘patient problem-solvers’. His hope: for textbook authors to develop resources that support this aim instead of obfuscating it. Enjoy.

PS while the lecture’s aimed at high-school teachers, I would argue that university lecturers teaching in maths & physics should also be watching it. After all, they teach the teachers :-)

knowledge vs certainty Alison Campbell May 16

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From time to time (well, OK, quite often!) I write something about the nature of science. One of the things that I think is often misunderstood is that science is not about certainty, it’s about knowledge. Because we are constantly adding to our understanding of how the world works, we’re never 100% certain about our findings. 99.9%, maybe, but there’s always the possibility that new data may make us question that :-) The trouble is that humans seem to want certainty, & if you’re craving that certainty, & don’t understand why science can’t give it to you, then it’s easy to deny the science in favour of some other ‘way of knowing’.

Anyway, Orac has just written a great post entitled Knowledge versus certainty in skepticism, medicine, & science. It’s based on a research paper examining people’s reluctance to change particular beliefs when presented with ‘belief-challenging’ scientific information. I found it a fascinating read :-)

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