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August 2009 Archives

A couple of days ago our local paper carried a letter that included the bald statement: "vaccines cause ear infections."

My first response to that one was: citations, please! That sort of statement is incredibly dangerous, because it's essentially saying, don't vaccinate if you don't want your kids to get ear infections. (The letter writer advocated avoiding antibiotics for such infections as well. Now, as you know there are issues surrounding the mis-use of antibiotics, but we'll come to that later.) And we are already seeing what you get when vaccination rates in a population drop.

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Well, I managed to go just over 2 months without a dog...

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In today's Royal Society news clippings was an item concerning a scientist's intention to manipulate chickens to get dinosaurs. Intriguing! A quick google search found a number of news items like this one - the researcher concerned believes that by flicking various switches during an embryo chicken's development, he'll be able to 'reproduce the dinosaur anatomy'.

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Sometimes scientific terminology can be quite confusing - everyday words like 'theory'  & 'law, for example, mean something different when used in a scientific context. And just what is a law in science, anyway? I've just stumbled across a brief excerpt from an interview with Richard Feynman, where he uses some great analogies to answer that question. (Gosh, he must have been a wonderful teacher!)


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A while ago, in one of my posts on pseudoscience (there's also some material on that on my Schol Bio moodle page, for those of you who have access), I commented on the issue of bacterial resistance to common antibiotics. This is a real problem & not one that's going to go away. (It's also an excellent example of evolution in action.)

Now Abbie has a post on her blog, ERV, looking at the use of bacteriophages as a way of stopping pathogenic bacterial infections in their tracks. Bacteriophages are viruses that kill bacteria. The suffix '-phage' means 'eater', & if you have a lawn of bacteria growing on an agar plate & infect them with the right phage, then you'll see clear areas develop on the plate as the bacteria are destroyed - on the macro scale it looks like they're being eaten :-) Bacteriophages are very host-specific, so are unlikely to kill off the 'good' bacteria living in your gut and, in the research paper that Abbie's talking about, they didn't appear to cause any side effects. OK. we're talking a mouse model here, but it's still a promising piece of research. Pop over to ERV & read the whole story

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A couple of years ago my father-in-law had an operation to remove a rather large gallstone, & with it his gall bladder. It had caused him a couple of urgent hospital admissions, through blocking the bile duct & causing a back-up of bile. He was quite seriously ill for a bit but is now fully recovered, although he has to watch his diet.

Anyway, he'd have been intrigued by an item I've just listened to on the Skeptics Guide podcast - a listener had written in asking about something that one of her relatives was trying to get rid of gallstones. Basically it involved drinking large quantities of apple cider for a couple of days, after which time the gallstones would be passed into the gut & come out with all the other undigested gunk. The person (website?) giving the advice had noted that these 'stones' would be greenish & 'soft to the touch'. Eewww - who goes around touching these things?

So, here's a question for you - based on your knowledge of the human digestive tract & maybe some chemistry, just how likely is it that drinking apple cider would soften gallstones to the point where you could pass them in your faeces?

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The human appendix is often held up as an example of a vestigial organ - something that is much reduced in form from the homologous structure in other organisms (though not necessarily also non-functional). Darwin wrote a little bit about our appendix in The descent of man. Now it seems that a research team has done a bit of molecular detective work & claims that appendices aren't vestigial at all. PZ Myers has the first part of a very thorough coverage of this over on Pharyngula, dealing with the suggestions that  'Darwin was wrong' (which are just begging to be quote-mined by the creationist lobby). (He says he'll post 'part II' soon - it would have been a mammoth post if he'd done the lot at once! PS & here it is.)

PZ starts off by quoting a press release from the research team's home institution:

Now, some of those same researchers are back, reporting on the first-ever study of the appendix through the ages. Writing in the Journal of Evolutionary Biology, Duke scientists and collaborators from the University of Arizona and Arizona State University conclude that Charles Darwin was wrong: The appendix is a whole lot more than an evolutionary remnant. Not only does it appear in nature much more frequently than previously acknowledged, but it has been around much longer than anyone had suspected.

"Maybe it's time to correct the textbooks," says William Parker, Ph.D., assistant professor of surgical sciences at Duke and the senior author of the study. "Many biology texts today still refer to the appendix as a 'vestigial organ.'"

Now, can you see the glaring straw man argument right there? Darwin mentioned the human vermiform appendix only, not the appendix as part of a generalised gut, & that rather briefly, saying that it was significantly reduced in size from the same organ in many other mammals.  

Yet another paper for me to try to find time to read :-)

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Every so often someone writes a paper with a really eye-catching title. I've come across two of these this week: When Zombies Attack! Mathematical modelling of an outbreak of zombie infection (no, honestly, I'm not making it up! You can read the original paper here) and Deep-sea, swimming worms with luminescent 'bombs' (Osborn, Haddock, Pleijel, Madin & Rouse, 2009). I'm not going to say anything more about the zombies - if you're interested, there is some commentary on this Respectful Insolence post. But I thought the worms were really cool.

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This afternoon, while I was sweating out my frustrations via one of the gym's cross-trainers, I listened to the May 20th podcast from The Skeptics Guide to the Universe. Among other things, they discussed the candiru, a small freshwater Amazon fish that allegedly swims up the urine stream of someone urinating (stories aren't clear as to whether you have to be waist-deep in the water, or above it). I've always been a bit suspicious of this one - I mean, why do the stories always talk of this odd little fish attacking men, & not women? - so I was interested to hear what the team had to say.

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 - it's the result of an intricate web of evolutionary relationships. Why'd I pick this topic? Because I came across Chet Raymo's musings on Sacculina, a barnacle that over time has become an internal parasite on crabs. Female Sacculina larvae settle on a crab's exoskeleton & injects a mass of cells that move to the crab's abdomen, whence they send a mass of tendrils throughout their host's body. If a male Sacculina larva comes along, it can enter via a pore opened (& subsequently sealed) by the female & provides its sperm to fertilise her eggs. The crab remains alive but its behaviour & physiology are hijacked by the barnacle - to the extent that both male & female crabs behave like gravid females, growing a broad abdomen containing not crab eggs but those of the parasite, & releasing them into the ocean when mature. Works well for the parasite, & enough non-parasitised crabs survive to procreate & ensure a future supply of hosts. (In fact, if that wasn't the case, Sacculina would eventually run out of hosts & would then itself become rare - nature is full of checks & balances.)

Now, people can regard this sort of thing as more than a tad distasteful. And they'd be in good company. Charles Darwin wrote (in a letter to his American friend & colleague, Asa Gray) that I cannot persuade myself that a beneficent and omnipotent God would have designedly created the Ichneumonidae with the express intention of their feeding within the living bodies of Caterpillars, or that a cat should play with mice. He went on to argue that this, & other examples of apparent cruelty in the world effectively argued against the existence of any form of designer (& used the term 'intelligent designer' in its modern sense). Richard Dawkins comments that [if] nature were kind, she would at least make the minor concession of anaesthetising caterpillars before they are eaten alive from within. But nature is neither kind nor unkind. She is neither against suffering, nor for it. Nature is not interested in suffering one way or the other unless it affects the survival of DNA

In the natural world there's no 'right' way to do things. And indeed, that humans can consider such concepts is itself the product of our own evolutionary history, shaped by natural selection in just the same way as that parasitic barnacle and its unfortunate hosts.

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A while ago now I blogged on comments that had been made in a letter to one of our local papers concerning gardasil, the vaccine currently offered to young women & offering protection against the four most common strains of Human Papilloma Virus (HPV). My main concern in writing then was to counter some rather inaccurate statements made in that letter (& by now you've probably realised that such things will continue to concern me...). Anyway, the Science Media Centre has just put out a release updating the current state of play with regard to reactions to gardasil.

The SMC report begins:

Three years after the Gardasil vaccine was licensed in the US to protect against the human papillomavirus, or HPV, research shows there have been few serious reactions to the 23 million doses administered to Americans. The research published today in the Journal of the American Medical Association reveals that fewer than 1 percent of patients - 54 people out of 100,000 vaccinated, experienced side effects most commonly including headaches, nausea and dizziness.

It also notes that the Centre for Adverse Reactions Monitoring (at the University of Otago) has come to a similar conclusion. And it's worth noting - again - that correlation is not causation; for example, someone may faint after the vaccination, but this is not necessarily a response to the vaccine itself (simply being poked with sharp pointy things can induce fainting in some people). Similarly, at least some of the deaths reported to the VAERS database involved car accidents & cancer...

You can read the whole report here.


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The concept of reductionism is something I've written on before. I was spurred to add this post after listening to a podcast interview (from The Skeptics' Guide to the Universe) with the wonderful science writer Carl Zimmer.

While the interview traverses a great deal of ground, including how Carl became an award-winning writer of science books, blogs & articles, it centres on his most recent book Microcosm: E.coli and the new science of life. In the interview (& the book) he gives an excellent example of why the reductionist view, that an organism is no more than the sum of the sequence of bases in its genetic codes, is far from the truth.

Colonies of E.coli are made up of thousands - millions! - of bacterial cells that are all clones: genetically identical. So you'd expect that they'd all react in the same way to various stimuli: the presence of a particular sugar, for example. But they don't. In the presence of that sugar, some of those cells will express the genes needed to metabolise it while others - with exactly the same genes - don't. The genes are regulated differently in those individuals, or their DNA is modified epigenetically; either way the responses differ between cells. And this is something that a purely reductionist approach would never have predicted.

(I didn't think I'd like podcasts as I've always preferred reading to broadcasts for my information - but I have to say that now I'm hooked. I can exercise my brain at the gym, as well as my muscles!)

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So many cool websites - so little time to enjoy them all!

The first is one my friend Marcus alerted me to (via Physics Stop): it's called Science - so what? so everything & there's an awful lot of fascinating material there - including the answers to questions such as, why do flamingos stand on one leg? And check out David Attenborough on why science is important. I can see I'll be returning regularly to this site :-) Thanks, Marcus!

And the second - Baba's World - has some excellent rap songs relating to evolution :-) (My kids will be impressed - their mother, listening to rap!)

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As I was skimming the headlines at SciTechDaily just now, the headline CT scans of 300-million-year-old fossils provide a frightening 3D portrait caught my eye. What could they be talking about? Something with claws & sharp pointy teeth, perhaps?

It turned out to be spiders. (Poor spiders, always getting a bad press.) Using computer-assisted tomography scans, scientists were able to build up a very detailed picture of what a couple of Permian spiders looked like - even down to the tiny tarsal hairs on their mouthparts that might have allowed them to manipulate their prey. Modern technology has certainly opened some very detailed windows into the past, & not for the first time.

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You might know that squid can change the colour patterns on their skin. But how does this happen? & if the changes are in relation to a changing colour in the environment, how do squid know about this - do they see the change, or sense it in their skin? (Hence the 'blindfold squid' of my title.)

Well, over on PZ's there's a lovely podcast which I enjoyed so much that I've embedded it here as well. Enjoy! (NB for teachers - 'Creature Cast' seems an excellent classroom resource.)


CreatureCast Episode 1 from Casey Dunn on Vimeo.

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In today's Waikato Times there's the following headline: Faith healers attack cancer, injuries with prayer.

Unfortunately it's not really possible to assess the claims being made for the power of prayer - because those attending this new clinic are advised to continue with regular medical treatment. So - in the event of someone's health improving, it's not really possible to assess which treatment modality did the work... For example, I'm always a bit sceptical of claims along the lines of 'I had X tumours prior to the clinic's treatment, & now I have only Y' (where Y<X). If the tumour numbers were confirmed (before & after the treatment) by radiography/surgery, then the outcome is good for the patient, however it was achieved - but I'd like to see the supporting evidence for the original claim. Plus some indication of what other treatements the patient was also having - you'd hope that someone diagnosed with a large number of tumours would be referred rather promptly for surgery, radiotherapy or chemotherapy (or a combination of those). In which case, which treatment modality actually had the desired effect? Without that sort of supporting evidence, these testimonials remain at the level of anecdote.

Similarly, claims that the clinic has high success rates for its 'treatment' of cancer are not backed up with any data, so again, they cannot be properly evaluated. (I guess this particular practice may not be covered by the Medicines Act as it offers a 'service' rather than a product...)

Note - prayer may well have a profound psychological effect for some people, & I'm not arguing against that. What I am saying is that extraordinary claims along the lines of 'prayer can cure cancer' do need to be backed up by extraordinary evidence.


Update: You might also be interested in this more extended discussion by the Silly Beliefs team.

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Blogging on Peer-Reviewed Research A little while ago, when I wrote a post on homeopathy, I mentioned the placebo effect. All the science-based commentaries I've read on homeopathy indicate that it achieves its apparent results via placebo: the patient expects to get better, & in some cases they do (eg report fewer symptoms, less pain, & so on). Now, the placebo effect could well be effective in cases where a friendly discussion of their problems & a homeopathic remedy contribute to a feeling of well-being, but what about something like surgery? Surely the placebo effect wouldn't be operating there as well?

The answer is - yes, yes it could.

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Well, I had a great time at the Junior Cafe in Tauranga yesterday :-) I always like to talk about things that interest me with other equally interested people, & the questions afterwards were really stimulating. As I've said before, I enjoy challenging questions because they stimulate my own learning :-)

Anyway, there was a question about mutations & whether they drive evolution. My answer was basically, no, but they provide some of the raw material (the genetic variation underlying the phenotype, which is the thing actually 'visible' to natural selection) that selection pressures can work on. And then came the deep question - when does something stop being a mutation & become 'normal'? What is 'normal', anyway?

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... a Junior Cafe, that is (you could sing that to the tune of 'we're off to see the wizard' from The Wizard of Oz, if you were inclined....). My friend & colleague Kathrin Otrel-Cass runs the Tauranga Cafe Scientifique, & has set up a couple of Junior Cafes as a related project. Tomorrow I'll be attending the Tauranga event at Otumoetai College, addressing the topic 'was Darwin wrong?'

The idea behind the Junior Cafes is - as for the more familiar 'adult' versions (which are, in fact, open to everyone) - is to enhance engagement with & understanding of science. Students get to talk with scientists about their work & learn about how they do that work - this includes developing a better understanding of concepts which can cause trouble. The idea that scientists don't know all the answers (we'd have nothing to do, if we did!). Or that science is a continually-evolving enterprise :-)

What's really neat about the Junior Cafes is that they're run by the students themselves. Each Cafe has a 'management team' of students from the school, & while Kathrin & their teachers are available for help & advice, the students set the program, organise publicity, & invite speakers. Kathrin's provided a list of possible speakers & I guess you could say that she acts as a liaison between the schools & the scientific community. But really it's the students' baby.

I think Junior Cafes are a great idea (& Kathrin deserves a huge vote of thanks for getting them off the ground in Tauranga & Hamilton!). And I'm really looking forward to tomorrow - it should be a really interesting & stimulating time for all concerned. As for my answer to that question, was Darwin wrong? Well, the answer (as for much in science) is, it depends: very wrong indeed about things like how inheritance works (with no concept of genes, how could it be otherwise?), but very right on the mechanism of natural selection as a driver of descent with modification. (And yes, there'll be more to my talk than that!)

PS if you're keen to find out more about the Junior Cafes, drop me a line & I'll put you in touch with Kathrin.

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In this particular case - yes. What else would be an apt outcome for a pharmaceutical company that had ghost-writers producing review papers for publication that promoted their own drugs as examples of best practice? This is actually an example of how science shouldn't be done - & also of the self-correcting nature of science, because it was subsequent research that showed that some of the claims being made didn't stack up.

The story centres on the promotion of Hormone Replacement Therapy for menopausal & post-menopausal women - not just to relieve hot flushes (which can be a downright pain, believe me!), but also to reduce the appearance of skin aging & also to reduce the risks of developing heart disease & dementia. (I could go off on a tangent here, because this medicalisation of a normal aging process is something that concerns me. This is not intended to trivialise the impact of dementia - I've seen it in members of my own family & it's not good. But aging happens to us all, so why in the last century or so has society as a whole become so obsessed with minimising or hiding its more cosmetic impacts?... no, no, I won't go there right now! Back to the story!)

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If you've seen today's papers (& I guess it's on TV/radio as well), you'll know that the outbreak of measles that began in Christchurch seems to have spread to Auckland (by the simple path of someone picking up the infection in Christchurch & then travelling north, I suspect). A measles expert quoted on the Science Media Centre site (I'll post the interview below) commented that this can probably be put down to lower-than-desirable vaccination rates, & that in some ways vaccination has been a victim of its own success: complications due to once-widespread diseases are now so rare that a generation of people has forgotten what they were like & why they were so serious.

This resonated with me. My mother had polio as a young woman in the 1930s. It left her with much smaller & weaker muscles in her right hand & right calf (her arm & leg were most affected by the illness.) And a very close friend spent months in an iron lung in the 1950s, completely paralysed by the virus & relying on the 'lung' to maintain her breathing. But these days the odds of meeting someone affected are really pretty small, due to the effectiveness of the modern vaccine - & so we tend to forget how bad the illness actually was. The same can be said of diptheria, whooping cough & yes, measles - while many children may escape with a mild infection, this is not a trivial disease.

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It's always bothered me to hear statements along the lines of 'now that we now the genome of [insert species name here], we know all about [insert species name here].' That's so far of the mark, because there is more to the genome than the string of As, Ts, Gs & Cs that make it up. Beginning his post on this issue, PZ Myers says

We miss something important when we just look at the genome as a string of nucleotides with scattered bits that will get translated into proteins — we miss the fact that the genome is a dynamically modified and expressed sequence, with patterns of activity in the living cell that are not readily discerned in a simple series of As, Ts, Gs, and Cs. What we can't see very well are gene regulatory networks (GRNs), the interlinked sets of genes that are regulated in a coordinated fashion in cells and tissues.

What this means is that if you look within a specific cell type at a specific gene, its state, whether off or on, will be correlated in a coherent way with a set of other genes. Look in a developing muscle cell, for instance, and you'll typically find a gene called MyoD is switched on, and also other genes, like Myf5 and myogenin. Look further, and you'll find others like C-jun and cyclin-dependent kinase 4, that also have their activity modulated in predictable ways. And when we start poking around experimentally, we discover that the relationships are often directly causal, with certain gene products binding to and modifying the expression of other genes.

You should read on, because he then goes on to explain how all this is done.

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I found the following on the Silly Beliefs website:

[Someone] popped up on the Stuff web-site last month the day after the interesting magnitude 7.8 earthquake in Fiordland, suggesting we should expect further big earthquakes around the globe in the following week, because it was no coincidence that the Fiordland earthquake occurred a mere 30 minutes before the "change of phase" of the moon at last quarter, because most big earthquakes occur "around new moons and full moons, and a week either side".

This prognosticator would appear to have covered all his bases - can you see why?


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A few days ago I read an article about the discovery of a new species of bird - a 'bald-faced bulbul'. It's easy to think that there isn't much more to discover in the world, with humans living in pretty much every habitable part, but in practice there arer still gaps in our knowledge & new things to find. As with the bulbul. OK, it's relatively rare to find somethng big, like a large mammal or bird, but the chances of finding a new arthropod (for example) are probably reasonably good.

Mind you, out in the wild is not the only place to find a new species - museum shelves probably hold large numbers of organisms that are new to science & haven't been properly described & named. Many of them - like the new & alas! probably extinct fruit bat described here - were collected in the 19th century, when there was a bit of a 'collecting mania', & stashed away in bottles & jars, pickled in alcohol or formalin, for someone to work on later. But for animals like this bat, 'later' took a long time to arrive.

The sad thing is that for many species, like this bat, extinction will arrive before the taxonomists do. There are at least two reasons for this. Firstly, scientists estimate that there are millions of species of living things - the estimates range from 1-2 million up to 80+, depending on the basis of their calculations. (And an awful lot of those species would be arthropods of one sort or another!) And since extinction is a fact of life, many species will go extinct without us ever knowing that they existed. The fact that we seem to be involved in an ongoing mass extinction event doesn't help there. And secondly - there simply aren't that many taxonomists! It's not seen as a particularly cool career path & isn't well funded either.

Either way, I find the idea that something can die without anyone ever knowing that it has lived, rather sad.

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One of the 2007 Scholarship exam questions sort of links to an earlier post I wrote, on xenotransplantation. It says

Human disorders are increasingly being diagnosed and treated using biotechnological applications such as:
        Genetic testing, including testing of adults through to pre-birth diagnosis (for example: pre-implantation genetic diagnosis (PIGD) of embryos, amniocentesis or chorionic villus testing)
        Gene therapy
        Stem cell research
And asks you to 
Discuss how the use of named biotechnological applications may impact on the gene pool and the future biological evolution of Homo sapiens.

Quite a meaty one, isn't it? But - as for all these questions - what you have to do is clearly set out for you. And the question doesn't ask for more knowledge than you might reasonably have gained over the course of your year 13 bio studies; it simply asks to you demonstrate that you can integrate what you might have learned in studying several different standards, into a coherent, well-argued whole.

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I've heard it said that the only 'real' science is experiment-based - things like palaeontology, astronomy & so on can't get it right because they are 'observational', looking back into the past, & so can't generate repeatable data. It's usually said as the preface to special pleading for some sort of supernatural influence on the world.

Now Ken has a great post on this rather pointless distinction, over at Open Parachute.

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Now here's a weird-looking little beastie:


It's a solenodon  (although to me it looks a bit like those big rats - the Rodents of Unusual Size - in the fire-swamp scences of The Princess Bride... gosh, I enjoyed that movie!). And its chief claim to fame is that it's a venomous mammal. Snakes, blue-ringed octopuses, spiders... there are a lot of venomous animals around, but venomous mammals are actually rather rare. (The only other one I can think of is the platypus.)

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What's wrong with catching the measles is the name of an excellent post over on Evidence-Based Thought. It was written following warnings from our Ministry of Health about the possibility of a measles epidemic - something which is already becoming a problem in parts of Europe & the US, where vaccination rates (& consequently herd immunity) have declined after a fair bit of scare-mongering about the risks of vaccination. (Evidence- Based-Thought has some useful things to say on risks & probabilities - a valuable antidote to some of the comments that follow the MoH warning. I must admit, I was gobsmacked to see claims there that homeopathic remedies could prevent or treat measles...)

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Recent Comments

  • Alison Campbell: Hi Nicole - apologies for the delay in posting your read more
  • Alison Campbell: "Ruptured sinuses due to exposure to a series of rapidly read more
  • David Williams: Ruptured sinuses due to exposure to a series of rapidly read more
  • Nicole: On Renee's question: In a way, it may be true read more
  • herr doktor bimler: Worst horror movie EVAH. Mind you, there's a horror movie read more
  • herr doktor bimler: But there's also the point-&-wink sort of interest, shown in read more
  • Jj: If dmsa causes "lasting cognitive impairment" how is it possible read more
  • Alison Campbell: Yes, although I don't think Budwig went that far. read more
  • herr doktor bimler: And how do you get your tissues back into that read more
  • Alison Campbell: Quite so. I think it's a nice provocative talking point, read more