Just enough snark

Quick hit: scary science

2012-02-06T13:38:00.000+11:00

It's well known that fraudulent science exists. Sometimes, it even makes the mainstream news (and let's not forget this). But it is truly scary to be confronted with the depth and breadth of it, as the infographic below illustrates. It seems that with each shocking story that makes the news, journals are adding measures to catch fraud, although I doubt they'll ever catch everything.

I can, at least, think of a couple more ways to make research more honest. First, rather than anonymous publication, I'd rather see the removal of the shame of a disproven hypothesis. So you were wrong -- cross that idea of the list and move on to the next. It's going to be in the last place you look. Of course it's not that simple, but it should be. Second, some proportion of these errors are genuine errors that can be fixed with better statistics training and assistance. If scientists always had help (if needed) to choose the best test to apply, and ensure they applied it correctly, there'd be fewer incorrect conclusions drawn. Maybe? There are probably more measures that can be taken, but realistically I think reporting raw data is probably the most important -- even though that too can be falsified.

(I would also like to state that the scientists in this infographic look exactly like the ones I've worked with; none of them look anything like this.)

(Hat tip to Science, Reason and Critical Thinking)

Created by: Clinical Psychology

Brring brrring!

2011-11-03T09:01:00.000+11:00

We were in Amsterdam last month and we mostly got around like this:

It was pretty awesome, even if we didn't get to try out a bakfiets because it was too expensive to rent. The bike tracks in Amsterdam weren't perfect (they did disappear every so often), and riding with kids is always a bit fiddly. But yes, pretty much awesome. I have never ridden a bike without a helmet and the only times I felt unsafe were when I accidentally rode down the bike lanes the wrong way because we drive (and ride) on the opposite side of the road in Australia.

Sydney is always going to be a harder place to ride because of the hills and absurdly narrow streets, but we can do so much better. After reading At War With the Motorist for a while, you really get a sense of how much better.

With all these thoughts in my mind, it was great to see this short documentary about how the Dutch actually got it together:

For once, the "won't someone think of the children" argument used for good! Here in Sydney, two things hold me back from cycling: the hills and having kids to cart around. There are just some places where the roads aren't safe to ride with children, but the footpaths are two busy. My commute to work features roads like this. The cycleways in the city are lovely but they're only part of the picture -- most people have to get there first. Maybe we'll get there after NSW Labor gets its act together. Or something.

Individuals kicking the plastic habit: is it enough?

2011-01-13T22:10:00.001+11:00

Let me just preface this by saying that I think Beth Terry is fantastic. In case you don't know, Beth has a website (really, it's more than just a blog) called My Plastic-Free Life that basically documents her journey of giving up plastic and encourages others to do the same. I'm relatively new to it, but she's been around since 2007.

It's great, don't get me wrong. Plastic is evil; it never goes away and it's probably not all that good for you (but what is?). I've been trying to reduce our plastic consumption too, and have made some big steps: swapping to cloth nappies/diapers and wipes, purchasing metal water bottles, and banning liquid soap from the house. We've also been cutting down on tissues and packaged cleaning products, and I'll continue to cut down as I'm able. Suggestions welcome.

However.

Firstly, the whinge. It's hard. It's time-consuming. And it's expensive. Especially with kids. Many of Beth's recommendations centre around going to the farmers' markets with your own cloth bags (not just to carry shopping in, but to bag each type of fruit, vegetable and legume). And buying bread that's not packaged. And asking every online retailer you ever shop with to please not wrap your products in plastic. I could go on.

Do I have to point out how much all of this is not going to happen? Yes, certainly we could plan better and always have green bags with us, but sometimes we don't and need to pick something up on the way home. You know, so as to feed the kids and all. Farmers' market? Butcher? Deli? The supermarket is one of my coping mechanisms as a working mother; often our shopping happens late at night when everything else is shut. And don't even get me started on the suggestions of "just make [bread/crackers/jam/sauce/tofu] yourself". In all my spare time, sure. I'll also get my own cow and milk her.

Then there's the plastic that kids just attract, like magnets. Not just food packaging, but toys. Toy packaging. Toys begged for. Toys given as gifts. And soon enough, there will be toys bought with own money. Not to mention other miscellaneous stuff, like potties and high chairs and car seats. These things are mentioned in a guest post on My Plastic-Free Life, actually; one commenter suggested taking presents away before the kids get them. That might work for our baby, but I'd like to see someone try that trick with our almost-five-year-old.

Still, gradually we can educate and improve and make better choices, especially as our finances improve with time. Sure.

But then, secondly. Really, what's the point in making these reductions? There's the feel-good factor, doing something positive for the environment. But in the scheme of the world's population (not to mention industry) it's insignificant. I don't think our tip is appreciably smaller because of the disposable nappies that we didn't dump in it.

To me, the only real point is to make a point. To show that it's possible, and then to push for legislation. Because the mounds of plastic are not going to go away because I carried a few organic veges in a hemp bag. They're going to lessen, maybe, when the companies making them are forced to do better. When bottled water is taxed at 1000% or more. And when we start pushing, as cliched as it may be, for a better future for our children.

Conversations

2010-11-01T10:02:00.001+11:00

I don't have autism, but in my life I've encountered many people who do. On one level, the different ways the human brain can function fascinate me, just as the shoddy science that goes on in this field infuriates me. On another level, some of them, at least, are just my friends.

Shanti is the closest friend with autism I have. She's high-functioning, smart and funny and she blogs at Platform 25. We're gig buddies sometimes (you should hear about our adventures at Bob Log III). She's a talented photographer and a fellow science and science fiction geek. We have a lot in common and we've talked a lot about autism as well as many other topics.

Our most recent conversation was on Facebook and Shanti initiated it by asking me about Communication Shutdown. Even though I don't have autism I wanted to blog about this, and reproducing a conversation (ETA: with permission!) is on one level a very lazy blog post. But on another, it's perfect. Because it just proves the point that we agreed on. So here it is.

Shanti: What do you think about Communication Shutdown? I think it's good to raise awareness about autism and have more money for educational services but I'm not sure about the whole 'cure autism now' thing. I'm all for curing severe autism because the parents go through so much and services are poor, even in today's society.... But it does make think that people think that autism is only negative. Even in severe autism they have their own talents.
Then again it does give me a lot of issues. But without it would I be into photography/ physics/ story writing/ astronomy / art at the intensity that I am? No. Everyday I learn something new and that's great. Then again I do have that ADHD thing.
I think there should be more awareness for autism and unemployment. How about a 'give your job to an autistic day?'

Rivqa: Well... I see this type of campaign as trite - how can an NT possibly have any inkling of what it's really like? Not using social networks may be a modest sacrifice, but it wouldn't give me insight into the communication difficulties that ...people on the spectrum face.

As for raising awareness, I'd question the value of that really. Autism is a well known condition now; education about the reality of it is needed, yes, but again, an event like this won't add much to that.

I agree that the issue of a cure is sticky. It's also unrealistic for a complex range of conditions and I think it would be better to focus on treatment that doesn't rob people of their individuality, but that helps them function better. Education for broader society, better services, and high-quality research (Wakefield can shove it).

I think this is exactly what you've identified in yourself: there are the good bits of high-functioning autism, and there are the challenges. Employment is a really good measure of function, and that's far more important than messing with people's neurons.

Shanti: Also, autistics use social networking to better communicate.
So, you're more towards 'Education not Eugenics' too? I think on Nov 1 we should change our status to that. I've got some good material on Eugenics in the 1920's and not just from... Nazi Germany.
I think if an NT wants to understand what it's like to be autistic they should lock themselves in their room and not talk to anybody. Then they can try to amplify every sound. Then rub sandpaper all over their skin.

Anyway, I got only 2 hours to find the Andromeda galaxy.

Rivqa: I am, but not in a way that sugar coats what it means to have autism, especially severe autism. Difference is OK. Suffering isn't.

Take some pretty pictures of Andromeda.

Shanti: Totally agree. I've also talked to people on the severe non-speaking end of the spectrum to see what they think about it. One is content to sign or use a sort of net book to communicate. She doesn't think she's missing out on being social b...ut she has extreme meltdowns and tactile sensitivity. And I hate my tactile sensitivity and my short tempers. But what I go through isn't as bad as what she goes through.

I can't photograph Andromeda. I need more pro equipment but it was good to see it through my telescope, as well as a nebula and Hartley's comet.

Rivqa: Yes, obviously people are going to want different things. I don't think any movement should force a cure (if it even existed) on anyone who didn't want it. But I also don't think a movement should prevent anyone from taking one if they wanted it.

One day I will visit your neck of the woods so you can show me stuff through your telescope.

Shanti: Yes, you must. And Tania too.

Saying what I mean

2010-10-25T22:11:00.000+11:00

I've been trying, not as successfully as I'd like, to watch my language, as suggested almost a month ago by Arwyn, a blogger I like very much. In brief, she asked readers stop using colloquial terms for mental illness (insane, crazy, nuts) as slang. It's really hard to do, and so easy to rationalise as not being so important (seeing as everyone does it).

Initially I took the challenge somewhat nihilistically for that reason, but the idea stuck. And over the past few weeks I got to thinking about language, as I often do. In general, I'm careful about language, although moreso in writing than in speech. I try to think before I speak. I don't swear that much. I try to be clear (but I often fail).

And when it comes to anything health-related, I have opinions. I dislike the possessive form of eponymous diseases: Alzheimer disease, not Alzheimer's, because the disease belongs to the person who has it, not the person (usually the man) who first defined it (or decided to name it). I'm careful about not defining people by conditions or characteristics they have: it's a person with HIV, not an HIV patient. I'm sure most people don't think of these things day-to-day if at all, but they've been part of my work for long enough that they've affected how I speak as well.

And then there's mental illness. Somehow, it's accepted in our society to take these words, which mean serious, life-changing things for some people, and apply them to trivial issues. I hate how people use "schizophenic" when they mean "multiple personality disorder", and when it comes to actual names of conditions I would never apply them to anyone or even anything. The slang needs to join them.

I think many people would dismiss this as too PC, but words mean things. And using fewer of them because we're over-using some inappropriately leaves us all poorer. So for me, that means binning "crazy", "insane" and "nuts" (they can join "gay", "retarded" and "lame") and saying "ridiculous" or "pathetic" or "tiring" instead. It means saying what I mean.

Standing and being counted

2010-08-28T22:28:00.001+10:00

I've been remiss not posting about the election (or anything), but I've also been reluctant to comment too early. While I've been waiting, it seems like everyone's already said it, so this is more a reflection on the past week than brilliant political analysis. (Because I could have thought of it all myself, of course.)

I have a bit of a thing for full disclosure, so here's my political background. It would be churlish of me to say too much about my family members' political opinions, so let's just say that I had more leftish influences than rightish ones while I was growing up, with a fair bit of socialism in the mix. I was not discouraged (much) from my (brief) involvement with Socialist Alternative. Protecting the environment was a no-brainer; it was just obvious that plundering was not the way to go, even before climate change became a mainstream concern. We talked about politics and current affairs, and I developed my own opinions about social justice and other issues along the way.

So that's politics. Civics, conversely, was murkier. A 10-minute rundown on the Australian political system stuck in my mind because it was delivered by a teacher I admired; this probably stood me in better stead than many Australians. I've lived in safe seats all my life and have, in the past, rocked up with opinions but without doing much research. I've relied on reading the instructions carefully and how-to-vote cards to get me through.

If Wikipedia serves me correctly, I've voted in three state and four federal elections. (I was too young for Howard's first election and the 1999 republic referendum.) Thinking back on them doesn't yield much information. I know I tended to favour the Democrats in the Upper House and Labor in the Lower House, but my memories are vague at best. I can't remember voting in Melbourne at all, but I must have done so at least twice.

This time, I voted below the line, armed with the how-to-vote card I'd made for myself with the help of belowtheline.org.au. I live in a safe Liberal seat so I spent more time thinking about the Senate, but I don't think I'll forget putting the Greens first in the Lower House (I don't think it's the first time I've done so, but the fact that I can't remember doesn't please me). It was kind of (nerdily) cool to look at my electorate's results on the Australian Electoral Commission's Virtual Tally Room and think of one of those numbers in the primary votes as being mine.

Maybe the voting age is too low, but 10 years after I was first eligible to vote, I finally feel like I've really participated and known what I was doing and what it meant. Or maybe it's Twitter that's helped me get my head out of the sand (I've blogged about that already), or just having time to "read about it" while breastfeeding. Either way, I've somehow become many friends' election expert, although I haven't forgotten how little I really know.

Ultimately, though, I've had a change in mindset since the last election. A couple of years ago, I laughed at a friend who claimed that Australia collectively made some decisions about which way the country should go by voting Howard out. And I still don't think that was really true. But in 2007, I was firmly convinced that my vote, at least, didn't count or mean anything.

But now? I feel like things are maybe, maybe happening and changing and that I've had a part in it, albeit a minuscule part. I've felt it since Gillard took the helm and I'll feel it until I'm sure we're back in the status quo. But I'm hoping we won't, because this is way more interesting (except for the whole waiting business).

MasterPolitician

2010-08-07T22:36:00.001+10:00

In some countries, democracy is a sham because a totalitarian regime controls election outcomes. In Australia, it's a sham because the two options that are (realistically) available don't seem to have any actual policies. You know, the things that politicians are meant to have? With the same Greek/Latin etymology? Yeah, those.

Instead of hearing some decent ideas about how they might run the country, we get name-calling. Having a female prime minister just makes it worse because it's reduced to:

Abbott: "Girls smell."
Gillard: "No, boys smell."

This isn't politics, it's reality TV, fuelled by the media that certainly at least partially orchestrated Rudd's demise. Whose members the politicians know by name. It's poll watching and worm watching and adjustments based on these. A popularity contest. It's all about dog-whistles and wooing voters.

How did we get here? I think reality TV does have to do with it. (If only we could vote Tony Abbott off the island, or at least one of the Ste(ph/v)e(n)s (Conroy or Fielding, either one.) I think the collapse of the Australian Democrats has something to do with it to. (Natasha Stott Despoja, come back, I beg you!)

I hate our preferential voting system. It's downright depressing that my vote must go to an MP who will form a majority for one of the two clowns who can possibly become the Prime Minister. All I can take comfort in is the Senate. I will be voting below the line, that's all I can say.

I want my (M)TV [but not too much]

2010-08-04T21:24:00.001+10:00

This post was written at the request of Mary Finucane, a blogger I like rather a lot. Mary has been blogging at Disney Princess Recovery since she removed all Disney Princess branded items from her home, and has provoked many interesting conversations about marketing to children, among other things.

Every so often, we really surprise people by not having a television. Technically, we're not completely without one, as we have a special aerial thingy (that's the technical term) that plugs into the computer. But it's not plugged in all the time. You can't just plonk down in front of the TV and watch it for hours. You have to actively want to watch something, and be willing to sit in an office chair to watch it. The same goes for our DVDs.

So yeah, no TV. It is unusual but my husband and I both grew up without one, because of our religious backgrounds. When we got married, it felt like something worth continuing, both for ourselves and for the kids we were hoping to have.

Maybe it's because my exposure has been so minimal, but I get very drawn in to anything audiovisual. Even if it's not very good. So I like to make an active choice about whether I'm going to watch something. I tend not to follow many shows at once. I avoid reality TV. At worst, I replace the time I would have spent watching TV on the internet, but at least that has the potential to be interactive. At best, I read, write, or do any number of better things in that time.

As far as kids go, we never let our daughter watch anything at all until she was two, mainly because that's what's recommended for kids' eyes. After that, we let her watch a little bit. Sesame Street podcasts were a real lifesaver on the bus. She got a Wiggles DVD as her reward for giving up her dummy (pacifier) and she collected a couple of others. But I was staggered at how well she knew all the popular characters without ever seeing them on TV. Dora, Ben 10, Barbie, Disney Princesses, Yo Gabba Gabba and more were all familiar faces. Children are marketers' dreams; they absorb every instance of every brand. So I was pleased that we'd set things up so that it would be hard for her to get over-exposed.

Now, she's a savvy four-year-old. She can't set up the TV, but she can put a DVD in the drive. She plays computer games that will supposedly teach her how to use a mouse and keyboard. So it seems more important to limit her screen time now. We don't have a set time limit, but we try not to let her play or watch for too long on any given day (maybe half an hour to an hour at most), and we aim to have plenty of days with no screen time at all.

In terms of content, we've been pretty laissez-faire. At her age, I think her body image will be more shaped by positive, healthy comments from her parents than by whether Barbie could physiologically exist. And I'm happy for her to explore all kinds of portrayals of women, as long as they're positive in some way. So Barbie and Disney Princesses aren't banned in our house (although they might be if she got too obsessed with them, like Mary had to do). We allow some branded toys in the house, but try to keep control of it. Being relaxed has led us to making some mistakes, though, like assuming that she'd be OK with Toy Story 3 because she enjoyed the previous two (it was scary and she was traumatised).

So when Mary says

I'm guessing that since your home is tv-free, you are likely a mindful consumer, more aware of internal vs. external influences. I think that is an incredible form of protection.

I'm not sure if I'm quite living up to her expectation. I guess I try to be mindful without being extreme, but it doesn't always work. The best I can say is that I'm actively parenting, trying not to repeat mistakes, and above all gauging what's good by listening to my daughter and thinking about it and talking about it as a family. So far I think she has a healthy psyche, so I'm hopeful.

Really not that difficult

2010-07-19T14:27:00.001+10:00

Nothing in this post is new as such, but I'm hoping that it might be new for someone. If you don't think cloth is for you; if you think I'm crazy or "too" concerned about the environment (is there such thing?); if you don't have kids but might in the future -- just hear me out anyway. Give it a few minutes of thought.

Because things have changed. Using cloth nappies (or diapers) is not as hard as it used to be. Really. There's no soaking, no folding, no plastic pilchers, and a lot less leaking.

As a brief intro to the method, I invite you to spot the difference:

Cloth	Disposable
Put nappy on child	Put nappy on child
Take nappy off child when wet/soiled	Take nappy off child when wet/soiled
Place wet nappy in wet bag, or rinse first if soiled	Place wet nappy in bin, or place in nappy sack first if soiled
Empty wet bag into washing machine when full; turn on washing machine	Empty rubbish bin into council bin when full
Hang nappies in the sun to dry and disinfect; when dry, snap together and put away	Rush out madly to restock nappies when you've run out or they're on sale

The main reason why it's so much easier is the materials used. Modern cloth nappies are made of bamboo or hemp (often organic, if that floats your boat) or microfleece; these are more absorbent and dry faster than the cotton squares that your parents may have used. They're also shaped more like a disposable nappy and fasten with velcro or snaps, rather than dreaded safety pins. Wet bags contain the smell and eliminate the dangers of full nappy buckets for small, mobile children.

Yes, there's some extra washing, but it's not as though you need to take them down to the river and scrub them by hand. If you use cloth full-time, you're looking at three extra washes per week, max; some people run the nappies on a rinse cycle first before adding other clothes.

The main benefits, apart from the obvious environmental ones, are a saving of thousands of dollars per child, and the elimination of some of the nasty chemicals used in disposables (eg, sodium polyacrylate [now banned from tampons] and various carcinogens such as dioxins). An appeal for some is how cute and colourful they are; so much nicer than being covered with the same generic cartoons every time.

There's a bewildering array of brands and styles that suit different needs and tastes, and that's why trying before you buy makes sense. Many companies offer trial packs and there is even a nappy library. I've been availing myself of the latter (and have paid for the service, for anyone watching for conflicts of interest). I considered reviewing the brands I've tried so far, but decided it's overload. Just ask me if you're interested.

Don't leave it to the genes

2010-07-04T20:04:00.000+10:00

Here's why I've always been opposed to the movement pushing homosexuality as being OK because it's "probably genetic". I'm young enough, educated enough and idealistic enough to think that that shouldn't be necessary at all; it shouldn't matter whether people prefer men, women, both, neither, or anywhere in between. But I'm sympathetic to the reasoning behind the "genetic" movement; it's a more realistic stance in one sense, as it recognises that there's a long way to go before that's a widely accepted belief.

Still, it's a dangerous tactic, pinning everything onto genes. The genome is a Pandora's box that's been open for almost 10 years, and it's to be expected that geneticists will go digging for anything that anyone hypothesised is genetic in origin. Behavioural traits are no exception.

But the relationship between genotype and phenotype is far more complex than was previously thought. Let's put aside the rights and wrongs of antenatal treatment of genetic quirks that may cause "abnormal" sex and gender; this topic has been covered in the article linked in Begley's article (linked in the first paragraph) and elsewhere. What I suspect will emerge over time is that, like many complex behaviours (or even complex physical attributes), homosexuality and lesbianism won't be pinned down to one gene. What they will find is that all (or most) women with congenital adrenal hyperplasia (CAH) will be lesbians, but not all lesbians will have CAH.

In the meantime, women and their fetuses are put at risk of side effects of medication not being tested in randomised controlled trials, all in the hope of preventing something that's arguably not a disease (by which I mean CAH, not its corollaries of lesbianism or aspirations beyond playing and keeping house). This is not smart; parents are being promised something that is not achievable, meritorious, or helpful for their children, who will grow up in a more inclusive environment than exists currently. I hope they will, anyway.

The post that had to wait

2010-06-28T21:38:00.000+10:00

Being antisocial by nature, I have a love-hate relationship with social networking. Actually, I think a lot of people do; there's plenty to be annoyed about. So it was only natural that sooner or later, I'd write a post about it. Admittedly, I was at least partly inspired by Buzz Bissinger, in a reactionary kind of way; also by a friend who deleted her Facebook account.

But you have to get your timing right with these things. I wrote the first sentence of this post on Wednesday, somewhere between 7.30 and 8.00 pm. Then I got distracted. By Twitter. Specifically, by the #spill hashtag. Without thinking about it, I got swept up in the instantaneous updates about the swift changes to Australia's leadership.

My husband commented that he was surprised at how involved I got, but the truth is that without Twitter, I would likely have gone to bed without knowing and woken up with a new Prime Minister. With Twitter (which is still quite new for me), I was able to watch it all unfold from speculation into something real. And comment in real time.

But it only took me so far, because at around 10pm I turned to the same medium that I always turn to when there's a real emergency: radio. The radio was on when Rabin died, when 9/11 happened, even when there was a blackout in our area (on my mobile). And then, I turned to my least-liked medium, the television, and watched Rudd address the press.

It was interesting to be a minuscule part of what may be a historic change in our society, and I think I can say that I get Twitter better because of it. But most of my beefs with social networking remain. Many of them have been covered already by The Oatmeal (which is brilliant), among others.

To me, what they boil down to is that social networking most often magnifies what people always were. Interesting people are interesting on social networking sites; I like many of the links that people share and the witty one-liners that make the most of Twitter's 140-character limit. But people who were annoying before now have a bigger platform upon which to annoy their cohort.

For instance. On Twitter, I was most recently staggered by the #amwriting hashtag. Oh, you're writing a novel/screenplay/poem? Wonderful... but I don't want to know about it until you're done (and it's published, but therein lies another story). You don't get a gold star for being creative, especially not if you feel the need to stop and tweet about it. Just write the damn thing.

Which leads me to my other problem with social networks (is it ironic that I'm complaining about this on a blog? I think so), which is more a general internet thing. I've been online for about 12 years. First it was email, then IRC, then message boards, and now social networking. They all have the same problem: not only do they waste time, they seem to sap creativity. Mine, at least; I can't speak for anyone who's #amwriting (grammar cringe, I know).

Here's my theory. I've got a certain number of words I can write per day. I'm not sure how many exactly, but I know I was prolific... once. But now, instead of being concentrated in one story, it's diffused over all these ridiculous websites. So I'm currently quite jealous of my friend who deleted her Facebook. But I can't do that, because I'm addicted. If you need me, I'll just be out trying to find some discipline. BBL...

Time to grow up, Australia!

2010-06-16T10:18:00.001+10:00

Rudd's plummet in the polls is interesting from a psychological perspective, even though it's obviously not over yet. And Ross Gittins's article on the topic got me thinking that politics is disturbingly similar to parenthood. (It's not the first time I've thought so; the idea often crosses my mind when considering Middle Eastern politics.)

Apparently, what we really want from our leader is a bit of tough love. Someone who'll do the right thing for the country (and world, in the case of climate politics) even if it hurts us a little. And because Rudd hasn't don't that, he's become less popular. Instead of telling us that we can't have any more lollies, he's allowing us to keep the jar.

Perhaps our whole model of politics is wrong. We don't need one Prime Minister (or better yet, President); we need two: a soft one and a strict one. How many parents operate like this? As children, we want as much as a softer parent will allow us, but we know that the stricter one is right.

Adding a new political role goes against my tendencies towards libertarianism and anarchy, but if my other ideas about politics were taken up (becoming republic, so we ditch the governor general; abolishing state government; dramatically reducing politicians' paychecks and superannuation) it would more than balance out.

Jokes aside, it is kind of sad that we can't have a political system based on the opinions of mature adults. Instead, when we're not being cynically manipulated for a politician's career, we're disappointed because we're not being babysat enough. Can we just grow up and get on with it already?

Your life in landfill

2010-06-10T14:42:00.002+10:00

The proverbial straw, for me, was the disposable toothbrush. Of course, most toothbrushes are disposable (except for these), but I'm talking about the single-use variety. Apparently these have been around for a while, but (because I spend so much time avoiding popular culture) they've only just caught my attention. Could there be anything more absurd? Can they possibly do a better job on-the-go as a stick of chewing gum?

Presumably, we're just too busy to plan ahead for our one-night stands... or whatever other occasion you might want to brush your teeth when not in your own bathroom. Likewise, too busy to put a tablet of Berocca into a glass of water.

Isn't it about time that there was some kind of regulation governing this type of ridiculous product? Clearly, people can't be relied upon to make intelligent, sustainable choices about these things. Tissues, paper towels, single-use plastic containers, bottled water... all these things are not only going into landfill, but also cost energy to manufacture.

I'm well aware that as a parent using disposable nappies (aka diapers) it's hypocritical to say this, but at least nappies are used for a finite period of life. And I am actually giving cloth nappies a go. I'm probably better placed to do this than most women, as my husband does all our laundry: for too many families, cloth nappies are just another burden on women. So I'm all for seeing our disposable lives as a community problem that needs to be solved collectively.

That's why I think we should deal with the most inane of these products first and work our way up to the ones that are actually useful -- it might be worthwhile to create recyclable or biodegradable versions of these. (There are already several brands of biodegradable nappies). Half a brain and half a conscience should be enough to deal with this kind of rubbish.

Parenting: the evidence

2010-06-06T20:27:00.006+10:00

My son is nine weeks old now and I'm tired. I know that's a given at this stage of life. But I have this persistent feeling that I should be getting more done. Life doesn't stop when a baby's born; there's still a house to clean, bills to be paid, brains to stimulate (mine as well as his).

The thought of getting him onto a routine seemed really attractive. I borrowed a suitable book from the library and started the mental preparation for it. There were lots of useful ideas in it, but I had some misgivings, mainly about the frequency of breastfeeds suggested for his age. The author also admitted that the book was based on her anecdotal findings rather than medical recommendations.

So I decided to return to first principles and do some research. But it was initially difficult to find information on my specific question: How many feeds should a baby have in 24 hours? I found some interesting websites on evidence-based parenting and breastfeeding, and many interesting Cochrane reviews (current and planned).

I got side-tracked by a feminist critique of expectations placed on mothers and the World Health Organization's breastfeeding guidelines (despite the WHO not being in our best books right now, I was interested in how firm they were about not introducing solids before 6 months; no big pharma behind that one, surely).

Still nothing concrete, although the WHO did recommend feeding "on demand". But looking at the WHO site made me think more internationally. I wondered how women in other cultures feed their babies, and also how other mammals (especially our closest relatives, the chimpanzee) fed theirs.

Then I found an anthropology on Google Books, Hunter-gatherer childhoods, with a lot of interesting info. Apparently, mammals that carry their infants with them also feed them more or less continuously; evolutionarily, humans fall into this category. Hunter-gatherer women follow this model, essentially practising attachment parenting -- they feed their infants constantly, carry them most or all the time, and sleep with them at night. Like other continuous-feeding mammals, their milk is more dilute than spaced feeders like rabbits, which leave their young in a nest or burrow and feed them at intervals.

Most women in developed countries feed more like rabbits than chimpanzees; for the most part, their babies seem to manage OK, but there's no definite research into this. Certainly humans are very adaptive and the hunter-gatherer lifestyle can't suit women who return to work, or who have limited support.

Still, I think it's valuable to try and match our lifestyle to our design as closely as possible. I'd be interested in research into how different feeding patterns can affect health later in life, as well as general infant wellbeing (we always hear that colic doesn't exist in developing countries, for example).

In the meantime, I've put the idea of a routine on the back burner. But it seemed like as soon as I relaxed about it, he started sleeping better anyway. They're always one step ahead...

Organ donation: it's for everyone

2010-06-03T11:47:00.001+10:00

Yesterday, I had an article published at Galus Australis, which is a great website that features articles about Jewish life in Australia. I wrote about organ donation, as there are particular issues for Orthodox Jews when considering signing up as a potential donor.

For those less interested in the intricacies of Jewish jurisprudence, I'd like to present the Australian spin to the issue. This is a cheat of a post, because I'm going to pull some of the Galus Australis article into it, but I will add some further detail to assuage my guilt.

The good news for Australians is that we have a high rate of successful transplants. The bad news is that rates of organ donation in Australia are embarrassingly low for a developed country. According to the Organ and Tissue Authority's website, around 1700 Australians are on a transplant list; last year, only half the organs needed were donated. (Fewer donors are needed than there are recipients, as one donor can save up to 10 lives, as well as providing non-essential [but life-changing] tissue, such as corneas to cure blindness.)

Fewer than one in five Australians have discussed their wishes regarding donation with their families. This is why donation rates are so low: people don’t know their loved one’s wishes and err on the side of refusal.

The Authority has a campaign running to encourage people to discuss their wishes regarding donation with their families. In many ways, this is more important than actually registering as a donor, as it's the family, not the individual, that makes the ultimate decision. The message is pretty clear: register as an organ donor and talk about it with your family.

It can be uncomfortable to make plans about your body after death, and of course it’s highly unlikely that you will become an organ donor. But that’s precisely why it’s so important to have more potential organ donors willing and registered. It can also be helpful to consider registering for bone marrow donation and donating blood regularly; in the context of these living donations, the focus is taken off donation after death.

Together, these actions might save a life – or several – one day.

They've got the internet on computer nowadays

2010-05-26T21:03:00.000+10:00

Some research doesn't really need to done; or, at best, it's quantifying something that everyone already knows. Much of the research into internet usage falls into this category. It's on the increase? Really?

Apparently, more people are using the internet to keep in touch with family and friends, stay informed about current affairs (but they're not willing to pay for news services), and for entertainment, including porn. (The latter is termed "sexual content" by the report I'm referencing here, CCi Digital Futures 2010: The Internet in Australia.)

OK, so we knew all that, but knowing some of the numbers is useful. And it's interesting to glean people's attitudes about what they think should be free online. But even though none of the facts and figures surprised me, there was a stand-out: 84% of Australian internet users surveyed thought that at least half the information online was reliable. Half!

No wonder Nigerian scams actually work -- too many people's bullshit meters are off. It's easy to switch it on, folks. Any time someone forwards anything to you (whether it's a wonderful story or a tragic one, or really useful tips, such as how to stay alive in an earthquake), don't forward it on. Look it up on Snopes, or Google some keywords along with the word hoax. And reading people's opinions on a forum is not research. Reading articles in peer-reviewed journals is.

I'm sure the percentage of reliable information online will probably never increase (yes, I'm a pessimist). And people probably won't get more discerning. But I'll keep replying to every stupid forward with the relevant Snopes link anyway.

(Thanks to xkcd for the comic.)

Food for thought

2010-05-24T10:07:00.001+10:00

Last week, some friends and I had a conversation about private schools. It lasted over half an hour and involved some hand-wringing : one woman's husband wanted to move their son to a private school for Year 3, while she wanted to wait until Year 7.

We thrashed out the benefits of a school with vastly better resources versus the sense of community that public school provides. We compared living in a bubble with meeting and befriending a broad range of people. And then we got talking about the money.

Keeping him in public school for those four years would save them over $40,000. (Another friend of mine calculated that private school, from preschool to Year 12, taking into account fee increases and inflation, would cost $300,000 for one child.) We began to ponder what they could do with that money, and then she stated what should be obvious: that it was, in a way, ridiculous that they were even considering spending such a vast sum of money, when others have so little.

I don't think she would have considered keeping him in public school and donating all of that money to charity, but it certainly put the conversation in perspective. I was reminded of the conversation when I read Paul Sheehan's column, in which he discusses current attitudes to food in relation to MasterChef (which I don't watch) and three-star restaurants. Clearly, he's talking about attitudes to food in developed countries, and some of his comments wouldn't go astray as wall posts on a fabulous Facebook page, First World Problems, for example:

When you charge $60 for a main course, the pressure goes up for everyone, including the customers, and the pleasure does not go up accordingly.

This prompted me to make a donation to CARE Australia: $25 provides a nutritious meal for 85 children.

A simpler system. (Please?)

2010-05-22T20:48:00.002+10:00

Health care in Australia is actually pretty good, compared to, say, Ethiopia. Still, there's plenty of room for improvement. So I was interested in what would happen on 19 April, when COAG (the Council of Australian Governments) met to thrash out Rudd's proposition to take over health care (currently divided between federal and state governments, the latter of which I personally believe should be abolished altogether).

I didn't get my act together to comment on the results of the meeting earlier because I was busy with the aftermath of a hospital experience of my own -- the birth of my second child. (I'll get to birth politics in another post.) Since then, the Budget has yielded more health-related reforms to debate at dinner parties, but the agreement in April still holds my interest, and here's why.

I'm generally a healthy person, so apart from a visit to emergency after spraining an ankle on a weekend, my main experience with the hospital system has been for natal (pre, peri and post) care. This was a fairly straightforward experience with my first child, at least in terms of continuity of care. With my second, however, things got a little complicated.

In retrospect, I didn't help matters by choosing the "shared care" option of care. This meant that instead of taking the option of seeing the same midwife the whole pregnancy, I had most of my appointments with my general practitioner. This was more convenient for me and I like her, so it worked well until I was about 30 weeks' pregnant and diagnosed with gestational diabetes. The midwife who broke the news to me slagged off my GP for not calling me to let me know (when actually she'd ordered the test so long before, I'd hardly expect her to be holding her breath for my borderline results).

And it all went downhill from there. I got a referral to an endocrinologist and a diabetes educator. I had to see an obstetrician to clear me to go back to shared care, and was transferred to a different obstetric team for that appointment, so that the appointment could be on the same day as the endocrinologist appointment.

Initially these changes, like the dietary changes and finger prick blood tests, were more of an inconvenience than anything else. But at 38 weeks, with work deadlines competing with my due date, I decided to skip my last endocrinologist appointment. I was meant to make a midwife appointment while I was there, but I figured I could see the GP instead. She was happy to give me a check-up but said that I really should be having my appointments at the hospital at that stage.

But we were both puzzled about who I should be seeing. The obstetricians had cleared me to go back to the GP but I'd been taken off my previous team, so I had no midwife to look after me. She called the shared care liaison officer and got a voicemail message. In desperation I tried to contact the diabetes educator and finally got lucky -- another midwife, Fiona, answered the phone and squeezed me into her schedule. I made it to one appointment with her before my son was born.

The point of this story is that health care in this country is too complex, even for someone who's fairly health literate. Communication between health professionals is poor. Outside of set appointment times, patients' access to health professionals is pretty much non-existent. Fiona mentioned that the hospital was moving away from group midwifery (where women have one midwife looking after them for pregnancy and birth, which is obviously excellent) and more towards shared care -- because the hospital was broke.

If this goes ahead, it will leave more women bewildered about where they fit in the system. When I worked as a medical receptionist, patients would often call to request a home visit when they really needed to have called an ambulance five minutes previously. Patients hold up GPs and even orthopaedic surgeons with their life stories, often (I think) because they genuinely don't know who they really should turn to.

So when a government meeting promises to "[help] patients receive more seamless care across sectors of the health system", all I can say is YES PLEASE. Whatever other criticisms can be levelled at Rudd and the current government, if they can actually achieve simplicity in health care, I'll be impressed.

Well met indeed

2010-05-18T11:34:00.008+10:00

It's been over two years since I blogged last, and three since I blogged at all regularly. Enough time has passed that I found it necessary to update the name, the URL, and even the purpose, but I didn't want to lose the posts I spent so long on way back then.

So, they're all there, should anyone (except you, spammers) want to read any of it. But now, if I can live up to my promises, there will be more. I used to just blog about science; I have broadened the topic to "whatever I feel like commenting on". Science will still feature prominently, but I might have things to say about music, books, and general stupidity (no shortage of topics there).

However, my dad has told me not to be so sarcastic. Meanwhile, at least some of my friends seem to appreciate it. And there are plenty of news sites and blogs that either breathlessly regurgitate press releases, or second-guess everything that anyone ever says. So, "Just enough snark" is just that: trying to say "Oh really?" without losing all faith in humanity. Although sometimes...

Carbon nutrition labels

2008-02-03T20:27:00.001+11:00

Woolworths (or Safeway if you're Victorian) may soon be providing information about the carbon footprint of the products they sell, according to today's Sun-Herald.

This is probably a good thing, but I'm sceptical (naturally) about how well it's going to work. What will be included in the carbon footprint? Will water and energy costs both be considered? How will the system by monitored, and by whom, unless the government is willing to get involved? And how long will it take for workarounds to be found (like labelling sugar as "evaporated cane syrup" on ingredients lists)?

On a larger scale, will it encourage industry back to Australia in the long term? (And at what cost to developing countries?)

Until these questions are answered, I'll sit back and watch how this develops with interest.

Organics just aren't sustainable

2007-11-21T12:52:00.000+11:00

This post was originally dated 30 September 2007; technical difficulties have prevented its publication until now. Publication should now resume as "normal"...

Following Elizabeth Finkel's blistering critique of organic food (which suggested that organic food is not better for you or the environment), Cosmos Online has published an opinion piece from Craig Meisner, an American professor based in Bangladesh.

Professor Meisner's intimate knowledge of the true conditions in a developing country refute the assumptions often made when researchers try to determine if organic farming can feed the world. According to Meisner, the assumption that organic fertilisers and mulches are plentiful, even for the poor, is incorrect. Any change to current agricultural practices would require major changes, such as sacrificing fields growing food for fields growing legumes for fertilisers (the bacteria in legumes' roots can fix nitrogen), which is too risky for the very poor when it means they might go hungry.

To me, the solution is simple: since the evidence shows the organic farming isn't really that much better than modern conventional methods, those promoting organics should get off their high horse a little bit. For those who want (and are able) to pay the extra cash for the feel-good sensation of food with no "chemicals" (but possibly extra parasites and insects), that's great -- even more so for the farmers making money from it. But there's no reason to foist that on everyone else, particularly if they live in a developing country.

Of course, there are issues with the toxicity of pesticides in the quantities used by farmers, including language barriers preventing sufficient understanding of warnings, but this needs to be addressed separately to the issue of organics vs conventional farming. Farmers deserve the best they can get out of their land.

Bad science journalism how-to

2007-09-10T17:54:00.000+10:00

Linked above is a great break-down of how to write a bad piece of science journalism. Wish I'd written it, that's all I can say!

Life in the fast lane

2007-09-08T20:09:00.000+10:00

Just in case you couldn't have predicted it yourself, a British team of epidemiologists has done the maths and worked out the rock stars have lower life expectancies than the general population.

Even if they don't kill themselves (Kurt Cobain [Nirvana], Michael Hutchence [INXS]) or die of a drug overdose (Shannon Hoon [Blind Melon], Janis Joplin), faded stars also have shorter life spans overall, owing to the strain that drinking, drugs and the general party lifestyle place on their health.

Alcohol misuse caused the most health problems.

"Engine" of coral reefs revealed

2007-08-31T13:30:00.001+10:00

A team of coral researchers at Heron Island has compiled a gene expression library of Symbiodinium, the dinoflagellate responsible for feeding coral reefs such as the Great Barrier Reef.

Team member Professor David Yellowlees said:

... these microscopic algae are quite weird and unlike any other lifeform. They have different photosynthetic machinery from all other light harvesting organisms. They have 100 times more DNA than we do and we have no idea why such a small organism needs so much. They really are like no other living creature we know.

The gene expression library will help shed light on what happens when Symbiodinium is stressed and how the symbiotic relationship between it and the coral it feeds is formed or broken. Heat, increased carbon dioxide and pollutants all affect this relationship, so this research is vital for the preservation of the Great Barrier Reef -- the world's largest superorganism and one of Australia's greatest treasures -- as well as other reefs around the world.

Eureka!

2007-08-22T15:11:00.000+10:00

The Eureka prize was presented last night and included a nanotechnology "magic bullet" for heart disease (Levon Khachigian of UNSW, one of my almae matres). Nanotech might make some of us nervous (OK, it makes me nervous) but clinical trials are so rigorous these days, we can hope that it's in the arena of medicine that they'll be safest and least likely to take over the world.

In any case, Khachigian's "nanoassassins" are enzymes that can turn off bad genes, known as DNAzymes, and without the side effects that other drugs cause. Good one.

The full list of winners can be found in the link above (in the title of this post).

A cautionary tale

2007-08-06T08:56:00.000+10:00

The obesity "epidemic" isn't just a concern during people's lifetime -- there are even problems after death. The current issue of the MJA contains a letter reporting the difficulties that obese and morbidly obese bodies cause for morgue staff and equipment. Lifting these corpses, some with a BMI of over 50, can be a serious OH&S issue. And it gets worse:

Putrefaction is hastened in morbidly obese individuals, and associated skin slippage and purging makes the bodies even more difficult to handle.

Humans are notoriously squeamish about what happens to their bodies after death. I think doctors should be capitalising on this to help paint the gruesome picture of life and death for the obese. Perhaps it might encourage some to improve their health during their lifetime.

Careful of the dihydrogen monoxide

2007-07-23T11:07:00.001+10:00

It took me 10 seconds to work it out and 30 to confirm it.
How long will it take you?

How Harry helps kids

2007-07-22T10:40:00.000+10:00

Although the article linked above is a couple of years old, it seemed the most appropriate one out of my PubMed search results (I searched for Harry Potter).

The last book of the Harry Potter series, Harry Potter and the Deathly Hallows, was released yesterday. Gwilym and colleague's study showed that the release of the previous two books (The Order of the Phoenix and The Half-Blood Prince) caused a dip in the number of accident-related admissions to their emergency department. Presumably, kids were temporarily more sedentary as they read the latest editions.

They conclude:

It may therefore be hypothesisedthat there is a place for a committee of safety conscious, talentedwriters who could produce high quality books for the purposeof injury prevention.

but...

Potential problems with this project would include an unpredictableincrease in childhood obesity, rickets, and loss of cardiovascularfitness.

As for myself, I did not injure myself while running in to pick up my copy, despite the ground being wet, but I did get up after finishing the book and find that my knee had popped out of place. So there are some hazards.

Technology imitates nature

2007-06-18T10:47:00.000+10:00

The article linked above details a deceptively simple water harvesting technology designed to collect clean water in polluted areas. Designed by an Israeli architect and PhD candidate, it is yet another example of engineering being inspired by nature.

With thanks to Rational Trader for the link.

Laughing milk

2007-06-15T10:25:00.001+10:00

I love a good "laughter is the best medicine" story, and since becoming a mother I also love any story to do with motherhood. The article linked above contains both: it reports a study that shows that breastmilk abates infant eczema when the mother laughed in the hours prior to the feed. The researchers believe this is due to the increased levels of melatonin in the milk. Melatonin levels are often decreased in eczema sufferers.

Questionably sane?

2007-06-06T11:52:00.000+10:00

I can't resist giving a free plug to my friend Nathan's new podcast, Questionably Sane. It doesn't have too much to do with science but I think it's funny (although it does come with a coarse language warning).

The most recent two episodes (3 & 4) poke fun at political correctness, which I think will appeal to scientists and others among my quiet readers.

[edit: link now updated to the most recent podcast site.]

Science in English 2: "boiling point"

2007-06-06T11:37:00.000+10:00

This post is the second in a series about the use of scientific terminology in the vernacular. This is a topic that I've always found fascinating, mainly because it really clarifies how laypeople understand science.

In chemistry and physics, a liquid's boiling point is the highest temperature at which it will remain liquid. Increase the temperature even slightly and it will change state and become a gas.

According to answers.com, the term "boiling point" has been used informally since the second half of the 1700s to mean a climax, and has come to mean a turning point or point at which one loses one's temper.

I think this metaphor, although perhaps tired from over three centuries of use, is an excellent one. So often, anger simmers a little before exploding violently, bursting out like the bubbles of air escaping from boiling water. It is also apt as a metaphor for a climax, where a situation may change in the same way as a chemical changes state: both gradually (the temperature increases slowly) and suddenly (the boiling point is a discrete temperature).

This one definitely gets my presumptuous tick of approval.

A luxury the environment can't afford

2007-05-25T12:58:00.000+10:00

According to Ecos, CSIRO's bi-monthly environmental magazine, luxury hotels are big sinners when it comes to wasting resources such as water and electricity.

Luxury travel is a growing sector and until recently, has not been closely scrutinised by environmentalists. With little or no legislation tackling luxury hotels' wasteful practices, the sky has been the limit for clients seeking an expensive holiday.

Fortunately, however, there is a growing trend towards sustainable tourism. Simple measures such as limiting the number of linen changes, laundering in cooler temperatures, and sourcing food locally all make a difference. These changes should also prove more economical for the hotels, which will hopefully encourage broader uptake.

More information:
Ecotourism Australia
Green Globe
Sustainable Tourism CRC

Also in the current issue of Ecos: All parents need to read about nappies and the environment.

Against bad science

2007-04-13T09:15:00.000+10:00

I've recently discovered that The Guardian has a great column called "Bad Science" by Ben Goldacre, a doctor and science writer. It's not a new column by any means but I've never seen it before. (In my defence, I live in Australia and am not, therefore, in the habit of reading The Guardian. Still, I'm sorry I haven't come across it until now.)

This article, from 2005, seems to sum up a lot of what he's on about. The quality of science journalism, in particular the sensationalisation and appalling misunderstanding and misrepresentation of statistics, quite rightly gets his goat. Why? Because it filters down to a total lack of understanding of science in the lay person.

What can be done about this? Newspapers are never going to put an end to bad science communication. While Goldacre blames journalists, not scientists, for misrepresenting their research, I believe that scientists could do more to encourage correct representation. If every time a study was written up incorrectly, the researchers wrote in a letter to correct it, perhaps they might improve. Scientists frequently write in to New Scientist in this manner, so why not the mainstream press too? Of course mistakes will always happen -- science journalists can't be expected to be experts in every field they report on -- but if they're constantly pointed out, the bar might raise a little.

I also feel that science writers should have a background in science. In my experience journalists often fall into particular areas, but I think that a push from the scientific industry might be helpful in this.

In any case, until all this happens, it's good to know that there are people on the lookout for bad science.

Science in the USA

2007-03-05T14:41:00.001+11:00

I just spent 3.5 weeks in the United States, which is the reason for the lack of posts since the 4th (when we left). As I haven't read much science news (or any other news) since we left, I'll have to draw on my actual experiences (gasp) for this post. So, here is a round-up of the science-related touring that we did.

In the Muir Woods, California, we saw the giant redwoods, which are beautiful and awe-inspiring. We also listened to an ecology talk run by a volunteer, in which we learned why the woods were named after John Muir (William Kent, who bought the land to conserve it and donated it to the government, wanted it named after his hero) and a bit about redwood biology (they can reproduce sexually or asexually, and can grow so tall because they have symbiotic fungi that draw water in from the fog).
We visited the aquarium in Monterey, California, which is renowned for its three-storey kelp pool containing many of the local species, including the lovely leopard sharks. We saw penguins, sea otter, and lots of fish. We managed to get to the penguin feeding, otter training, and kelp pool diver feeding (that is, a diver fed the fish). The keeper talks were excellent, especially the otter talk, which explained how they care for injured otters, foster hurt babies, and release them back into the wild. Conservation is important at the aquarium, and the otters that they have kept are considered unreleasable.
In New York, we went to the American Museum of Natural History. The museum is huge and we didn't get through the whole thing. But we saw the space exhibit and the planetarium show ("Cosmic Collisions", narrated by Robert Redford -- it was excellent), quite a lot of the biodiversity exhibits and of course the dinosaurs and extinct mammals. The museum reminded me a lot of the Australian Museum, but it was less child-oriented and at least three times the size.
On our last day in New York, we visited the Central Park Zoo. This is a cute little zoo, which you can get through in under an hour. We loved the polar bears and penguins and puffins.

Other general observations:

Conservation and environment really is a big deal in California -- it's not just a media beat-up. Cars are smog tested yearly, everyone I met recycles absolutely everything, and public transport around San Francisco was excellent.
The staff (paid and volunteer) at every attraction we visited, were passionate and enthusiastic.
In New York, people were interested in the environment but far less knowledgeable about it.
We didn't meet anyone who believes in "Intelligent Design", but I think that's just a testament to flying over the "fly-over" states.

Warmer? Really? Nah....

2007-02-04T19:38:00.000+11:00

It must have been a slow news day yesterday because global warming has made it to the front page of the Sydney Morning Herald. Since global warming was first discussed in the 1980s, I find this a bit rich.

Of course, the UN report is technically news but really, this just highlights how many times
scientists need to bang their heads against a brick wall before it actually starts to crumble.

In the meantime, we're looking for a new place to live. Somewhere cooler and further inland
would be good.

Scientific writing revolution

2007-01-18T08:59:00.000+11:00

Well, I always wanted to write a story in the form of a scientific paper, but this is way better.

How to write a scientific paper

17 January 2007

by Gregory Benford
A tongue-in-cheek guide to turning scientific jargon into a riveting read.

By Bea Realist
Department of Arcane Abstrusities, University of California, Irvine
References
1. 'Professorial Pathology' by E. U. Rieka, A. B. Surd and I. M. Pedant, Journ. Academic Backstabbing Vol 3, 1980.
2. Explaining Asimov (Twelve Volumes) by The National Academy of Sciences, 1981.

Abstract
A new formulation of the traditional academic paper is considered. The way scholars really read scientific papers is discussed. This paper itself is written in the new method herein proposed. Studies among the author's friends indicate that reading time for most scientific literature can be reduced three-fold by use of this method. For some papers, reading time approaches zero.

Science in English 1: "a quantum leap"

2007-01-14T12:38:00.000+11:00

This post is (hopefully) the first of a series about the use of scientific terminology in the vernacular. This is a topic that I've always found fascinating, mainly because it really clarifies how laypeople understand science.

Literally, the term quantum, from the Latin quantus ("how much"), refers to an indivisible amount of energy (but it hardly seems to mean that anymore, even in physics). An electron's quantum state describes its current properties; a quantum leap is a change in its properties.

In physics and chemistry (where I first encountered the term), a quantum leap refers to an electron's instantaneous movement from one energy state to another. The novel (when it was new, anyway) aspect of this theory is that this movement is discrete, rather than continuous, as was predicted by Newtonian physics.

The term quantum mechanics was coined in 1924 by Max Born. Since then, quantum physics has entered the mainstream. People talk about it and read news about it, even if (like me) they barely understand it, if at all. Originally, it was used somewhat correctly, referring to a sudden change, as opposed to a slow, evolved one.

Now, however, it's used all over the place, often to mean a very large change. Given that the term really refers to electrons, which are very small, I find this quite ironic. As they say, small things amuse small minds...

No right answer

2007-01-08T19:39:00.001+11:00

"Good and ill have not changed since yesteryear," says Aragorn in Lord of the Rings, but to me the goalposts must have shifted somewhere along the way. In my lifetime, mainstream opinions about euthanasia, and abortion (to name two important examples) have changed drastically.

The article linked above describes the extreme measures that parents of a Ashley, a girl with serious brain damage, have taken to change their daughter's life. They have had her sterilised, so that she can't become pregnant if raped; removed her breast buds, so that she won't have the added discomfort of breasts; and given her growth hormones so that she will remain smaller and thus easier to transfer and care for.

They argue on their blog that they have done this to make her more comfortable and not for their own benefit; certainly they seem to be trying to provide her with the best environment possible. And of course, within reason, making things easier for oneself as a parent does make things better for the child.

In the Time article, the doctors looking after Ashley discuss their approach to this unusual case as doctors. Here's a quote that I think goes to the heart of the matter:

"I felt we were doing the right thing for this little girl—but that didn't keep me from feeling a bit of unease," admits Diekema. "And that's as it should be. Humility is important in a case like this."

There's no rule book for situations like this. And sometimes there just isn't a right answer. All you can do is weigh it up and make what seems to be the best decision. I don't know if Ashley's doctors did the right thing or not. Even they don't really know. In a sense, that's what medical ethics is about.

On my wishlist...

2007-01-01T18:25:00.000+11:00

Another book about cloning, but this one does look good. It comes out this month and looks to be a good summary of the arguments for cloning.

From the review:

Herold was surprised by Professor Smith’s statement about the utility of therapeutic cloning. Of course there is a possibility that scientists will never succeed in generating patient-specific embryonic stem cells, but unless we do the research we will never know, she argues, adding: ‘As Einstein said, “If we knew what we were doing, it wouldn’t be called research, would it?”’

Stem Cell Wars confronts the myriad arguments against this branch of science in a convincing and engaging way. Herold concludes the book by saying: ‘The idea of putting a freeze on progress because there are good and bad people in the world, because knowledge can be misused, or because we can’t always guarantee the outcome is an assault on the human spirit. It is living by our worst fears not our greatest hopes.’

Private universe

2006-12-20T09:22:00.000+11:00

There's been a fair bit in the news about autism recently.

I've always been fascinated by this disorder. The MMR vaccine scandal has been interesting to follow as an example of below-par science, and poor understanding by the public of the science. To me, this is just a symptom that science education and mainstream media science reporting needs some vast improvement.

But the main reason is probably that I know so many people on the spectrum. I grew up knowing a family in which all the boys had quite severe autism and have since met others with autism or Asperger syndrome. I always wondered: What sort of place could these boys have in a world where communication is vital? When you "have a different sort of internal thought" that in some cases leaves you completely dependent on your family or other carers for your entire life -- what does it mean? What does it tell us about the human brain? Is it really a disorder, or just another state of being?

From that last article:

With autism diagnoses rising steadily, talk of an "epidemic" and a growing search for a cure, Roy feels threatened. "I feel stabbed when it comes to 'curing' or 'treating' autism," he says. "It's like society doesn't need us."

Many autistic people are starting to agree. They have had enough of being treated as a medical problem, arguing that autism is not a disease that needs to be cured but just a normal part of human diversity. This emerging "autistic rights" movement hopes to launch an international campaign akin to Gay Pride, encouraging autistic people everywhere to embrace their "neurodiversity", and persuading wider society to accept them as they are...

Carina Schmidt's son has autistic disorder and requires round-the-clock attention. His condition is so severe that he required a 10-month stay at the Kennedy Krieger Institute to break some of his self-harming habits. She is adamant about doing everything possible to help her son, who now lives in a group home in Rockville, Maryland. She also supports the development of prenatal tests for autism. "If my son could be cured today I would say 'yes'," she says. "My family has suffered like there is no tomorrow - that's why we choose to have no more kids." ... Schmidt says that she will continue seeking help for her son. And she is sure he wants her to. "I can see my son wants to be normal," she says.

There are no easy answers here. But I think the research being done now is fascinating and exciting. Even if people with autism don't want a cure, this research goes to the heart of what makes us human: our complex, intricate, amazing brains.

Harry Potter and medical ethics

2006-12-12T10:27:00.000+11:00

This is just too cute not to post... click the link for the full article.

ABSTRACT

With the restoration of You-Know-Who to full corporeal form, the practice of the dark arts may lead to multitudes being charmed, befuddled and confounded. At present, muggle ethics dictate that aid may be rendered in a life-or limb-threatening situation, but the margins are blurred when neither is at stake. Muggle and wizard healers, fearful of being labelled ambulance chasers, may shy away from approaching those who remain blissfully unaware of their illnesses. We describe 4 case studies in which we intervened as muggle healers, to salutary effect. The afflicted were healed or helped, without bringing the weight of the Ministries of Magic or Magical Healing upon us. We advocate a spirit of cooperation between muggle and magical folk, mindful of the strengths that the healing arts from each community have to offer. As long as the intent is beneficent, healers or even the wizard or muggle on the street may intervene and render aid to the afflicted.

The votes are in...

2006-12-11T21:45:00.000+11:00

... and so is stem cell research. Those who know me (and/or read this blog) will know I'd be pleased.

Before the Patterson Bill was passed, I was going to post about how I wonder if the change in Labor leadership will mean anything for science. It may not mean much in terms of votes, but it does give Julia Gillard a bit more attention when she makes her statements as Labor's health spokesperson:

They are saying surplus eggs from IVF processes and I think that is the best place to start. Obviously there may be future issues about donation but I don’t believe we are there yet and we should see if the supply of surplus eggs from IVF processes is sufficient.

I agree with this. Avoiding egg donation directly from women is definitely to be avoided: Woo-Suk Hwang has taught us that. All the ethics committees in the world can't stop subtly coercion of junior, female staff. It's a sad inevitability of humanity. And the risks of egg donation mean that they should only be given freely.

So yes, I'm pleased. In August, I posted about three areas where I think Australia is lagging behind the rest of the developed world. Two out of three of those areas have improved tremendously. Now all we need is a better strategy to slow climate change and we'll be set. Well, not quite, but we're on the right track.

Congrats to Cosmos

2006-12-01T15:19:00.000+11:00

Congratulations to Cosmos for winning big (again) at the Bell Awards. They won magazine of the year, editor of the year (Wilson Da Silva), and a few other awards.

I love Cosmos -- there's something special about a glossy magazine, particularly when you feel like it was written just for you. I've been keeping them rather than putting them in the recycling bin (or passing them on) so I've got every issue since the first one.

They're launching a new magazine called G, about sustainable modern living. I'll be scraping some pennies together to subscribe to that, I think.

Sleep deprivation = torture

2006-12-01T15:07:00.000+11:00

Since becoming a mother I've become too aware of why sleep deprivation is a form of torture. Night after night of broken sleep really wears you down. The world seems fuzzy. Your brain feels fuzzy. Which is my general excuse for not updating this blog as often as I should.

I was also forewarned that I wouldn't regain all the brain cells that I lost during pregnancy. My mind is definitely much improved, but not back to normal (hmmm, reminds me of the state of my body).

All scientists like a unified theory, so I was pleased to read the article (linked above) from New Scientist. Lack of sleep, it seems, causes memory loss. So once my daughter is sleeping through the night all should be well.

New Scientist likes to add a dissenting voice to the end of its news articles, such as:

However, Tarja Porkka-Heiskanen of the University of Helsinki in Finland says that may be going too far, as the 72 hours of sleep deprivation experienced by the rats is exceptionally long, equivalent to several days in humans. Sleep deprivation can damage memory, but only "in extreme cases", she believes.

Of course, all that proves is that motherhood is an "extreme case".

Unintelligent design, redux

2006-10-30T20:30:00.000+11:00

Last Thursday I went along to hear Robyn Williams promote his new book, Unintelligent Design. (I can't stop myself from feeling pleased with myself for having a post of the same title almost a year ago [I know, it's pretty obvious].)

It's a pretty good gamble, going to hear a radio presenter speak. You know he's not likely to be dry and boring. (Well, unless he was a dry and boring presenter.) And I do love a good English accent.

Superficialities aside, Robyn's talk was excellent. Like the book itself, he's very chatty and entertaining. His talk touched on the main points of the book, which goes through the history of the science vs creationism/intelligent design (ID) debate, and unpicks the ID side.

It was interesting to hear the questions at the end. Some of the questions were really comments in disguise, but people did have interesting ideas. There wasn't as much heckling as I expected. Just one polite, reasonable question from a young man who was most likely part of the campus Bible study group. He asked about whether Robyn thought that believing in evolution precluded one from believing in Jesus, and Robyn gave a suitably (for an atheist) vague, diplomatic answer.

I bought the book afterwards. Robyn was signing them, which was cool. And we had a chance to chat with Mike Archer about the future of science education, which was fun. I think Mike Archer is great and UNSW is lucky to have him.

As for the book itself...

It's a slim little book and he does rush through topics, but it's an easy read nonetheless, and not designed (haha) to be comprehensive.

Still, the main arguments are all there, from the flaws in our design (poorly draining sinuses and bad backs are two that I suffer from), to the non-scientific agenda of ID, as detailed in the Wedge document. From the use of religion to justify injustice to the flaws in the statistics that ID proponents put forward (it might be unlikely that we're here, but we are).

It's full of references to popular culture and his famous friends, like Richard Dawkins and Douglas Adams. And his rather interesting life. Which is probably what makes it such an enjoyable read. He is a little too harsh with his atheism (nothing like Dawkins, of course) but with the fundamentalists around these days, I can forgive him for that. He does acknowledge that science deals with the "how" and religion tackles the "why", but is overly critical, in my opinion, of religion in general. Yes, religion has been the root of many terrible things, but it also has a lot of good to offer.

However, that doesn't mean that religion, Judeo-Christian or otherwise, should be distorted, presented as science, and forced down people's throats. Which is really the point.

No nonsense science

2006-10-26T08:42:00.000+10:00

Elizabeth Finkel is a writer I particularly admire. She's thorough, clear and logical. I also like it when people rip into pseudoscience, or otherwise faulty science. So this article (linked above) was a particular treat for me.

It's about biologist James Sherley, who opposes embryonic stem cell research because he "has a belief that the cloned embryos under discussion are human beings". Finkel goes through his defective logic and tears it up, which is great.

One thing she doesn't spell out (although it was immediately obvious to me) is that Sherley has a conflict of interest. His area of research is adult stem cells. So he has a lot to gain by lobbying for embryonic stem cell research to be shut down.

And I don't like to see people pushing their religious views into politics or science. A quick search on Google didn't tell me definitively that Sherley is Christian, but I'd put money on it. And like our extremely unbiased, balanced and reasonable federal Minister for Health, he's allowing his personal beliefs to interfere with things that affect people's personal lives.

The embryonic stem cell debate and the abortion debate boil pretty much the same question: Is an embryo, whether several days or several weeks old, a human being? The answer to this question has far-reaching implications. In the case of abortion, it affects women who have been raped; or whose babies will be born with debilitating abnormalities; or who will not be fit mothers (for example, in cases of drug abuse. In the case of embryonic stem cells, every effort to stymie research delays treatments that may help people with brain damage, spinal cord damage, muscular dystrophy, and many other conditions.

Such decisions should not be made based on a minority, or even majority, religious opinion. They should be made using science, which can give a definite answer as to when an embryo gains consciousness and can therefore suffer or be considered even remotely like a human being. I think that an uneducated person may imagine a baby-like fetus being murdered for a few cells. But embryonic stem cell research uses embryos that look roughly like this:

Because the embryos used are so undeveloped, to me it's an even clearer issue than abortion, which I think should be safely available to all women.

But don't listen to me. Let the science do the talking.

Thought-provoking laughter

2006-10-20T13:19:00.000+10:00

I love the Ig Nobel Prize. How could you not love an event whose website is sub-titled "Research that makes people LAUGH and then THINK"? Like the Darwin Awards ("We salute the improvement of the human genome by honoring those who remove themselves from it. Of necessity, this honor is generally bestowed posthumously."), the Ig Nobels draw people into science in a fun and engaging way. The Darwin Awards provide the best lesson on evolution for the lay person -- that I know of, anyway.

The Ig Nobels, by nature, are much broader. They give great insight into how wacky one's brain needs to be in order to be a research scientist. You really need to think outside the square. The stereotype of a scientist is a stuffy, boring, middle-aged or elderly man (of course it's a man) with nothing interesting to offer. The Ig Nobel scientist is a much closer representation of the scientists I know. For an idea, look at the picture on the link above. And add a few more women, dressed in punk band T-shirts or other funky clothes. (This is not to say that I think the Ig Nobels under-represent women, just that that photo does.)

Interestingly, the Ig Nobels (more than cancer research) illustrates to regular people how much science is a part of their lives, whether they're aware of it or not. Winners included research on why fingernails scratching a blackboard irritate people; why woodpeckers don't get headaches; the invention of the now-infamous "Mosquito" ringtone; and an Aussie team who calculated how many photos you need to take of a group before getting one where no one is blinking.

It's fun science at its best. When I was involved with OnSET, a student online science journal, we often struggled with how to present ourselves in an engaging way. I think that ventures like the Ig Nobels, the Darwin Awards, and even Dr Karl, have the answer. They're all firmly grounded in reality but slightly oddball and lots of fun.

Memory loss

2006-10-16T21:38:00.000+10:00

A couple of weeks ago I participated in an experiment over at ScienceBlogs. Basically, they wanted to see how bloggers compared to high school students in an SAT essay. I didn't write a very good essay and I have lots of excuses, but that's another story.

What I can't believe right now is that I have absolutely no recollection of what I wrote. I'm pretty sure my essay counted and got graded, but I can't find it. I'm not sure whether it's getting "older" (I'm 25, for goodness' sake) or the chronic, extreme exhaustion that comes along with being a mother. Or maybe it's the fact that my whole focus has shifted to the minutae of my baby's growth and development. On the whole it happens slowly, with occasional leaps. It's fascinating while you're in it, and (potentially) boring when you're removed from that world. It's like watching a time lapse video of a flower growing; you can only appreciate it at the right speed.

Dr Net

2006-09-27T18:04:00.000+10:00

I've heard of people that self-diagnose based on information from the net, but a couple of recent incidents really made me aware of how dangerous it can be.

One friend called me up and asked me if I knew anything about a particular treatment. The treatment involved radiation, so it sounded pretty scary to her and she didn't want to agree to it without looking into it. For reasons unclear to me, her specialist didn't give her any background information on the treatment. Both of us found that the information on the internet was scant, limited to alternative therapy sites.

Another friend casually mentioned that she had "worked out" what was wrong with her toddler when she had a sudden screaming attack after her bath. She'd put the symptoms into Google and made a diagnosis based on what came up. It was at night and not quite urgent enough to go to Emergency, she said. But she didn't even go to the doctor the next day.

Information on the internet is varied. Some sites are for practitioners and have disclaimers for patients. Type "cancer cure" into Google and lots of dodgy stuff comes up, including sites selling Laetrile, which is toxic. Generally if you put in a specific disease you'll find organisations dedicated to it with good quality information. But typing in symptoms brings up a hodgepodge of different sites, and it can be hard to tell the good from the bad.

Not to mention the concern of self-diagnosis, regardless of the source. One of my friends who works as a medical receptionist told me she's "had cancer six times". That is, she's thought she had it.

Of course, the increased access to information that the internet obviously provides increases the scope of this problem. Perhaps the general public needs better medical education to combat this, since something is obviously lacking in medical care. Probably access, sufficient explanations of diseases and treatments, and just plain old reassurance.

Two words...

2006-09-18T21:26:00.000+10:00

... start downloading.

For the first time the Archive provides online access to all journal content, from Volume One, Issue One in March 1665 until the latest modern research published today ahead of print. And until December the archive is freely available to anyone on the internet to explore.

Spanning nearly 350 years of continuous publishing, the archive of nearly 60,000 articles includes ground-breaking research and discovery from many renowned scientists including: Bohr, Boyle, Bragg, Cajal, Cavendish, Chandrasekhar, Crick, Dalton, Darwin, Davy, Dirac, Faraday, Fermi, Fleming, Florey, Fox Talbot, Franklin, Halley, Hawking, Heisenberg, Herschel, Hodgkin, Hooke, Huxley, Joule, Kelvin, Krebs, Liebnitz, Linnaeus, Lister, Mantell, Marconi, Maxwell, Newton, Pauling, Pavlov, Pepys, Priestley, Raman, Rutherford, Schrodinger, Turing, van Leeuwenhoek, Volta, Watt, Wren, and many, many more influential science thinkers up to the present day.

Have I ever mentioned that I love the Royal Society's motto? It's "Nullius in Verba" ("On the words of no one"). The core of the scientific method.

The science of blogging*

2006-09-18T20:24:00.000+10:00

This week New Scientist has a special feature called "The cult of us" about online living, mainly social networking and blogging. Since I blog, I was obviously very interested in what they had to say.

The first thing that hits you about the blogosphere is the sheer enormity of it:

Blogging extends well beyond teen diaries, however ... according to a website called Technorati, which monitors the blogosphere. It says it is currently tracking 51.3 million blogs worldwide, and claims that 75,000 new blogs are created every day - that's almost one per second. The blogosphere is 100 times bigger than it was three years ago, a doubling in size roughly every six months.

Is it good or bad? The article linked above shrugs off its effect on teenagers thusly:

Online socialisation is just an extension of the kind of interactions that people have daily by phone, text message and email...

They did have an interview with someone more critical, here:*

But just as not all information put on the web is true, not all aspects of the new sociality should be celebrated. We communicate with quick instant messages, "check-in" cell calls and emoticon graphics. All of these are meant to quickly communicate a state. They are not meant to open a dialogue about complexity of feeling.

The internet, or even just the blogosphere, is incredibly diverse. Certainly there's the trap for teenagers to write and talk in netspeak, which limits them to superficiality. But by blogging, there's also room for them to open up. To use strangers as a soundboard for their "what ifs". When I was a teenager, I often wondered what would happen if I said or did something inappropriate. What would the consequences be? I'll never know about the things I wasn't game to say or do. But if blogs had existed then, maybe I could have asked my readers. Beyond socialising, it can actually get quite deep. As any teenager will tell you.

That said, I think it is an issue that it takes away from one's time alone. Speaking for myself here, I don't have a great deal of time to myself, and what time I do have is often spent online (yes, I'm an addict). Is it a bad thing? Should I be meditating or walking alone on the beach instead? I'm not sure if time spent truly alone has any intrinsic value. But it might, and if it does, there are millions of people out there who just need to switch off for a while.

* Unfortunately these articles are subscription only. I recommend the subscription though!

Misplaced outrage

2006-09-08T08:33:00.002+10:00

So, the latest thing politicians are outraged about is the improper choice of entertainment at the Canberra Climate Change forum: a troupe of burlesque dancers stripping (only to their underwear; no nudity). The federal Environment Department and the Bureau of Rural Sciences have withdrawn their funding to the event in a beautiful gesture of censorship.

Here's the organisers' apology: "In retrospect the choice of entertainment was inappropriate for the occasion. We understand if the sponsors wish to withdraw." Yes to the first sentence. No to the second.

The choice of entertainment was not merely inappropriate; it was downright stupid. But put it in context: this was forum about climate change, something that we, the citizens of the world (per capita, Australia is particularly guilty) are causing. Climate change is destroying our planet and the Australian government won't ratify Kyoto. That is an outrage, not a few students taking some clothes off to a point that's perfectly acceptable at the beach.

This is not a new point. Milos Forman's biopic, The People vs Larry Flynt, the same point is made about war. Conservative (not necessarily political) types are far more outraged by anything of a sexual nature than they are about injustice. The fuss made about prostitution and pornography, if it will be made, should be secondary to the fuss made about environment and human rights. (As long as it's not prostitution or porn that's violating human rights, such as child pornography. That goes without saying.)

Sex sells and it's always going to be more interesting than "boring" conservation issues. But if conservation doesn't come first, there might not be anyone selling anything one day.

Obituaries

2006-09-04T19:14:00.000+10:00

There were two prominent deaths today here in Australia.
Steve Irwin, the crocodile hunter: the loud, boisterous champion of wildlife was killed by a sting ray barb in Queensland. Irwin's death is tragic: a man "in his prime" killed in a freak accident, leaving behind a wife and two small children. But the nation is feeling this loss too. On MSN's instant messenger program, people are adding (tu), which codes for a turtle symbol, to their names in his honour. Steve Irwin was a proud ambassador for Australia's wildlife and did more for conservation than many less interesting, noble organisations. The environment needs more heroes like him.

Of slightly less note (judging by the hits on Google News, at least) is the death of a fine Australian author, Colin Thiele. Thiele was a master of his craft, best known for Storm Boy and The Water Trolley. When I was in Grade Five we studied Storm Boy and the short stories published with it. I cried through Storm Boy and laughed through The Lockout. But the story that affected me the most was The Shell. It's been a long time since I read it, but if I remember correctly, the story was about a family who go down to the beach. The mother wants a beautiful shell that she can see, and she gets it, but her husband and son are swept out to sea. It was the first time I saw nature as something powerful impossible to bend to human will; fascinating and terrifying. Thiele obviously had a great respect for nature that was totally different from Irwin's, but in the end, sadly, Irwin proved Thiele's point.

The world we live in can be frightening and mysterious but I think that approaching it with Irwin's enthusiasm is important. There are forces in nature that can overwhelm us, but there are also delicate and vulnerable aspects, and they need to be protected.

1.5th world

2006-08-23T21:08:00.000+10:00

Why does it always seem like Australia is a bit behind the rest of the developed world? Movies, music and TV always gets here late, and so does science. Everything from ethanol to stem cells is somehow stymied by the parochial attitudes that are prevalent in our current government.

Australians really seem to enjoy hating America, as if they're on some kind of moral -- and intellectual -- high ground. I'd like to contend that we're not, on the basis of the science that's practised here vs. there. It's not just a funding issue: it's a mental block.

Exhibit A: Ethanol , a potentially green source of fuel, is not just used in the United States, it's being heavily researched there. While ethanol's current edge over oil is debatable, it's very promising if it can be harvested in energy-efficient ways. In Australia, research into ethanol is minimal, and its use is not being encouraged, despite petrol prices rising above $1.40 per litre. So much for progress.

Exhibit B: Mifepristone is currently available in many countries around the world, including "developing" countries such as Turkey and Tunisia. It is approved by the World Health Organization and is also in use in the US, a country supposedly more conservative than Australia. Seems like the pro-lifers don't have as much effect on what medical treatments are available to women in difficult situations.

Exhibit C: This one's a little more promising, but I'll include it anyway. Embryonic stem cell research is currently non-existent in Australia, but it just might be back on the cards. It's not happening much in the US either, but it is in California. So if an American scientist wanted to do stem cell research, he or she would only have to relocate to California, not to a different country.

Which brings me to my final point. Australia, remote island of small population that it is, can ill afford to lose its most promising scientists to other countries, but the brain drain has been going on for too long already. We urgently need to replace sport with science as the national religion of this country, or we'll just fall further and further behind.

What was I consenting to again?

2006-08-15T17:08:00.000+10:00

At 3:52 PM, PmH said...
It seems unreasonable to expect anyone to be capable of signing an informed consent form unless they understand the planned test, the risks and the legal remedies.

PmH quite rightly pointed out that I basically ignored one of the important points of this article:
Guinea pigs do sign “consent forms” that detail the risks; but Tom Edwards, a 21- year-old from Oxford who took part in another Parexel trial, pointed out that his form was 15-pages long. He said he felt “pressured” into signing the form and eventually did so without reading all of it “because I felt like I was slowing everyone down”.

I don't think anyone could have predicted the side effects of TGN1412, but even ordinary trials can be fairly hazardous. Participants need to understand the potential risks and feel that they can refuse to take part if they feel the risk to be too great -- this is basic informed consent.

High school science leaves most of the population ill equipped to deal with a 15-page form which was most likely written in the worst combination of science lingo and legalese imaginable. Tertiary science leaves scientists ill eqipped to write consent forms that the general population can understand, and therefore give informed consent to. Either way, the onus lies on science educators to lift their game and level the playing field somewhat. Obviously there is a need for technical language, and every type of specialty, whether in philosophy or physiology. But there's a time and a place for it.

On the other hand, the average citizen could use a better grasp of science. The same people who don't understand consent forms also don't really understand the science they read in the newspapers, or its implications to their lives (unless the particular science journalist is better than average). Their way of verifying scientific hearsay is to go through their catalogue of anecdotes until they find a situation that confirms or denies the report. And they believe that intelligent design is a plausible alternative to evolution.

For its own good, scientists need to teach better and communicate better; really these are both the same thing.

Three reflections on being a new mother and a science nerd

2006-08-15T13:14:00.000+10:00

The baby steals your brain while you're pregnant, but you get (most of) it back sometime after birth.*
Knowing about science really helps when weeding through all the advice about baby health.
(a) Breastfeeding is a great time to catch up on your backlog of New Scientist and Cosmos.
(b) Baby vomit wipes off Cosmos better than off NS.

*Individual results may vary.

Sneezy season

2006-08-07T14:59:00.000+10:00

The immune system is a mysterious thing. Protective overall, and yet sometimes it backfires. A dramatic illustration of the immune system going wrong was the TGN1412 disaster: six young men given a monoclonal antibody in a clinical trial ended up in ICU with multiple organ failure. One is now showing signs of an aggressive cancer.

Less dramatic, but more aggravating to more people on a more regular basis, are your run-of-the-mill allergies. Almost everyone I know is allergic to something: peanuts, cats, dust, pineapple. I personally have some mild allergies to some animals, but a major reaction to dust mites. When I got an allergy skin test, the swelling that appeared in response to dust mites moved beyond the realm of a few millimetres, which they usually measure, and looked disturbingly like a fat worm under my skin.

It's bewildering, too, the different things that people say about what causes allergies. It seems that no one can agree on whether it's over- or under-exposure to the allergen that causes the immune system to go nuts and attack a harmless molecule. Now it's been suggested that the window of opportunity for avoiding the nastiness of an allergy is pretty small: sometime between six months and nine months of age, at least for food-related allergies.

Personally I don't think there's a straight answer to this one and it just highlights the intricacy of the body, which can work against us or in our favour, but is fascinating regardless.

Maternity leave

2006-03-14T22:01:00.000+11:00

This blog is now on maternity leave, but I'll be back (provided the baby doesn't eat my entire brain).

MMIM newsletter 4

2006-02-27T23:04:00.000+11:00

Spotlight on Cystic Fibrosis

Associate Professor John Wilson began his career with a science degree, followed by a medical degree and a PhD. After working in the United Kingdom for two years, he returned to Australia and is now the head of the Cystic Fibrosis Service, Department of Allergy, Immunology and Respiratory Medicine at the Alfred Hospital, Melbourne.

Cystic fibrosis (CF) is a life-limiting condition characterised by respiratory failure and malnutrition. Although it is caused by an abnormality in a single gene, the expression of the abnormality is highly variable. CF patients’ symptoms range from negligible to severe lung impairment. It follows that other factors must affect how the disease progresses. Wilson is particularly interested in how factors such as gastroesophageal reflux, nutrition, and bone density interact with the cystic fibrosis gene. For example, genes encoding proteins involved in the manufacture of advanced glycation end-products (AGE) are important in diabetic nephropathy, but they also appear to play a role in causing early kidney failure in CF.

Wilson says that MMIM is “very powerful because it helps us direct our research”, which saves time and money by “avoiding fishing expeditions” and ultimately helps his patients. Because Wilson and his colleagues are trying to balance many factors in order to optimise treatment, computer-based analysis is essential. “Constructing models helps us weight the importance of different factors,” Wilson explains.

For example, Wilson’s research team found surprising interactions between the most common mutation of the CF gene, ΔF508 (either one or two copies), and bone mineral density (BMD). Carrying this mutation and being male are “powerful risk factors” for osteoporosis, independent of pancreatic disease and vitamin D malabsorption. Because osteoporosis is considered to be predominantly a disease of women, this means that we need to be “extra-vigilant” about BMD screening for men with CF. It also has implications for children with CF, who should have BMD augmented to prevent osteoporosis before it occurs.

This type of work, Wilson says, “will improve the health of Australians” – both with CF and with other conditions. In his role at the Alfred he still sees patients regularly, and is committed to practical research that will “get to the clinical interface” and make a real difference for patients. His approach is to address current clinical guidelines with up-to-date research: it is always important to “evaluate evidence and challenge icons” and determine whether there is a better way to approach treatment.

His overall plan for management of CF is to create an electronic health record, which can be “interrogated” to retrieve information, and “injected” with management plans, creating individual goals for therapy. Treatment can be accelerated if goals are not being met, or wound back if they are ahead of schedule.

Some of the most dramatic advances in CF survival rates in the last two decades have been relatively simple changes, such as an increase to twice daily physiotherapy, and a shift from postural drainage (which causes reflux) to other techniques to clear airway secretions. By studying the current techniques and analysing them statistically (with the help of the MMIM database), Wilson and his research team can make further advances that make a real and timely difference to patients.

For the rest of the newsletter, click here (pdf file).

Suddenly suspicious journalists: a pot/kettle scenario?

2006-02-15T16:35:00.000+11:00

Washington Post journalist Rob Stein has cited the recent drama of Woo-Suk Hwang's data fabrication as a reason for increased skepticism among science reporters. Firstly, I find myself a little disbelieving about his statement, since (unfortunately) data fabrication is all too tempting (and hence common). Someone reading scientific media regularly would be well aware of this, and 2005 was a particularly bad year for it.

Secondly, it's usually the general media's fault that science is grossly misrepresented to the public. Any glance through the health and science sections of so-called quality media (such as Time magazine) will reveal poor understanding and explanation of scientific issues. In Australia, at least, reliance on press releases is common, as is sensationalist reporting of preliminary trials (usually ones run by pharmaceutical companies). The media doctor website keeps track of several Australian publications' health articles.

However, Stein is correct in stating that journal editors are often hard-pressed to detect fabrication. Realistically, scientists will fabricate data if they feel they can get away with it, so maybe what's needed is more verification of data (by independent researchers) before we get all excited and hail the next cloning god.

Agricultural revolution

2006-02-02T20:37:00.000+11:00

Nationals Senator Ron Boswell recently dissed CSIRO for cutting funding to rural industry research by 5%.

(On a petty note, I'm wondering what the difference between the "livestock and wool industry". Aren't sheep livestock? But that's not really the point...)

I agree with him that there should be more research funding, not less, dedicated to renewable resources. But I feel it's a little incongruous to call for more research into agriculture as it currently exists in Australia at the same time as preaching about renewable resources. There aren't many crops in Australia that are actually suitable to our arid climate. Cattle and sheep die in the drought; farms require subsidies for water and nitrogen and phosphate fertilisers to be economically viable; and many crops grown in Australia (such as cotton and rice) are extremely water-thirsty.

As mentioned in a post last year, Professor Michael Archer (Dean of Science, UNSW) is a fan of harnessing native flora and fauna for economic gain, rather than continuing to pound our unique environment with European crops. He goes into great detail in his book Going Native (co-written with Bob Beale, ISBN 0733615228). From kangaroo meat (despite some unresolved issues) to native grains as crops (kurrajong and several wattle species are just a few examples), agriculture in Australia needs to change.

So maybe Boswell is right and agriculture does need more research funding. It just shouldn't focus on maintaining the status quo -- we need an agricultural revolution.

Still in the Stone Age down under

2006-01-16T20:35:00.002+11:00

Debate is heating up in Australia about the use of mifepristone (RU-486) for medical (as opposed to surgical) abortions. Tony Abbott, who is clearly highly qualified to have an opinion about (a) medicine (he has an Economics/Law double degree) and (b) women (he quite obviously isn't one), has decided that he should be more cautious than the Australian Medical Association, the Royal Australian and New Zealand College of Obstetricians and Gynaecologists, and the World Health Organization and keep mifepristone off the shelves in Australia. Well, that's his story, anyway. Unfortunately for Mr Abbott, people aren't stupid and are quite able to see that his views on mifepristone are just thinly veiled anti-abortion views (which go hand in hand with his anti-stem cell research views).

All research and medical opinion points to mifepristone's safety and efficacy in inducing termination, when combined with a prostaglandin analogue such as misoprostol (which is already available in Australia for other uses). From the reading I've done, I can't see how medical abortion is any less safe than a spontaneous abortion. Both can lead to complications, such as incomplete abortion, which can be taken care of with medical help.

It's insulting to doctors for Abbott to suggest that they would not be able to deal with the complications that can arise. If they can deal with a miscarriage, they can deal with a medical abortion too. And it's insulting to suggest that they would prescribe mifepristone unwisely. Any doctor prescribing it would, of course, be there to deal with any adverse effects, same as they would be for any medication they prescribed. Rural doctors, in particular, should be offended at the implication that they can't handle complications of pregnancy, when they can probably deal with them better than some over-specialised urban doctors. Should they be recommending that all female regional inhabitants relocate to cities for pregnancy care?

Abortion isn't nice or pleasant but it's a reality that some women find themselves facing for a variety of reasons. Whether the underlying cause is their own stupidity or the cruelty of rape, no woman should find herself facing the alternative of an unsafe abortion, or an unwanted pregnancy that will produce an unwanted child, who might never receive adequate care or love. And medical abortion makes it easier -- some might say too easy, but I feel that the option needs to be there for women in remote areas, or from communities where abortion is not acceptable, and going to the doctor for a pill and pretending that you've had a miscarriage might be your only option.

It's just mind-boggling that this decision is in the hands of one man who's clearly biased, rather than where it belongs: in the hands of each individual woman.

Forward, march

2006-01-10T17:29:00.000+11:00

It's always tempting to do a 'year in review' type of article at this time of year. It's not hard (especially after every other publication has done theirs). For example, science in 2005 can be summed up thus: embarrassing NASA failures; freakish meteorology; bird flu fears and cover-ups; evangelism masquerading as science; the rise, rise and fall of Woo Suk Hwang and his therapeutic cloning; and perhaps the only proud moment: the completion of the chimp genome.

Too easy. So of course I'll have to put my foot in it and hazard a guess as to what might be the 'year in review' for 2006. Some of it's easy because it's just more of the same, really. Bird flu is only going to become a bigger problem, as is climate change. It would be nice to see some successes in space exploration. (It would be even nicer to put that kind of money into feeding the starving and AIDS prevention [for example], but you can't have everything.) Physicists will keep nattering on about string and other things that I don't pretend to understand (anyone care to calculate the trajectory of physics wooshing over my head?).

Apart from bird flu, obesity will probably be the most important health issue (unless there's some other awful pandemic). Genomes, which are just so last century really, will continue to be superseded by proteomes and epigenomes. But I think there's a very big missing link between genotype and phenotype that we're just not getting, sort of like the dark matter of biology -- the setbacks with cloning and the final figure of 96% similarity between the human and chimp genomes point to that. I'll be surprised if 2006 is the year that solves that mystery, though. And I'm going to be optimistic and hope for a new stem cell hero.

I'm not particularly optimistic about climate. There are so many pitfalls to all the alternatives to oil (the destruction of forests in developing countries for biofuels, for example) that I think headway will only be made when it's too late. It's already too late, really.

Technology will probably keep moving along the lines of smaller, faster, and cuter, and as usual not spend too much time on actually being helpful.

Not too cheery overall. But one thing I can predict with confidence: like every year, there will be good bits and bad bits. Is the ratio even up to us? Who knows?

Supersized mini-me

2005-12-28T12:21:00.000+11:00

This is just the latest in a series of big babies being born all over the world, but particularly in America (land of the fat and home of the junk food?).

Apart from the freakish fascination that this kind of story holds, my mind just boggles at how it's news that this kid is abnormally big, but not the possible reasons why: not one but two overweight parents, gestational diabetes, and a condition called macrosomia.

Sometimes bigger isn't better. It's not good to be overweight; it's even worse to be morbidly obese, as these parents obviously are. But this kid has absolutely no chance. Every possible fat gene that hasn't been discovered yet has probably been switched on in the womb, and every environmental factor that could possibly exist will ensure that she'll probably be obese her entire life. Overall, not the best start for life. Those parents shouldn't be sitting there, they should be taking the baby out for a walk.

... the harder they fall

2005-12-21T20:30:00.000+11:00

Hiding behind evolutions's victory in a Pennsylvania district court room this week is something that has the potential to become an even bigger embarrassment for science.

In August, Woo Suk Hwang was Korea's "king of cloning" (New Scientist, 3 August 2005. And he wasn't just the king of animal (or more specifically, Afghan hound) cloning; he was most famous for his success with human embryonic stell cells.

All that began to unravel last month when his American co-author Gerald Schatten announced that some of the eggs Hwang used for his experiments were donated by junior staff in his lab; a serious ethical breach (at least for Westerners; in South Korea the women were hailed as heroes rather than portrayed as victims). Hwang admitted to everything, resigned, and was hospitalised for stress.

As if that wasn't bad enough, due to media pressure Hwang was forced to admit to Science, who published his last two ground-breaking papers, that some of his data was flawed. At first it seemed that the corrections he was making wouldn't alter his findings, but last Friday (16 December), Hwang and his co-authors retracted their 2005 paper. Their 2004 article is now being re-examined too.

This whole chain of events erases scientists' excitement over Hwang's achievements and for him and his co-authors it is certainly a personal tragedy (albeit self-afflicted to some degree). And it must be a blow for anyone suffering one of the many diseases that may one day be cured by stem cell therapy. Christopher Reeve must be turning over in his grave. But there are deeper concerns for the broader scientific community; deeper than those caused by Luk Van Parijs's falsifications in physics.

Stem cell research has always been stymied by the far right's "moral" obligations, and by laypeople's squeamish imaginations conjuring up pictures of humanoid fetuses being murdered and dissected (the embryos used are really just bundles of cells). But the uphill battle that Western stem cell researchers faced when trying to carry out their work was at least somewhat alleviated by the knowledge that the work was being done, albeit not by them. But Hwang has given his detractors the perfect ammunition: he didn't follow ethical guidelines when obtaining the eggs crucial to his research, and he falsified his data. The conclusions they'll draw: Hwang is a bad, bad man, and what's more, his research didn't even work. Extrapolate that out to all stem cell researchers and suddenly they're all unethical and wastefully ineffectual.

Stem cell research, both fact and philosophy, is certainly worse off. If I'm right in assuming that at least some of the anti-stem cell mob are also part of the intelligent design mob, it's not such a victory in Pennsylvania. It's a 1-1 draw if we're lucky.

Is it in our nature?

2005-12-15T21:31:00.000+11:00

Although some of the events of the past week or so have made me want to go back to bed and hide under the covers (out of embarrassment and denial), it's impossible not to write about the race riots at Cronulla.

There's the cringe factor, wondering what the rest of the world must think of us (and how it will affect our relations with them). There's the element of fear, that this kind of sentiment is what led to the Armenian Genocide, the Holocaust, and other race/creed-based genocides. The fear that until it's over, there's no way of knowing how far it will go.

But beyond that, I have to wonder why this kind of thing happens. Psychology of mob behaviour is complex, and it can cascade quite unbelievably: see Mass hysteria at Melbourne Airport. But I'm not just talking about the actions; I'm talking about what makes a neo-Nazi, a white supremacist, or even what motivates a teenage boy to write "we grew here, you flew here" in permanent marker on his chest.

A letter in last week's New Scientist, Born to be good, made me think. The letter is about cooperative behaviour in animals and humans (if you want to make a distinction); the author believes that moral behaviour is behaviour that strengthens the group. Critically, he describes the hunter-gatherer mentality as "cooperative, comradely, compassionate and, if necessary, self-sacrificing, as well as hostile to outsiders [my emphasis]". Xenophobia is so ubiquitous; it has caused so much bloodshed and has hardly helped civilisation as a whole. But what if it's an evolved trait; something that's in all of us, and the only variation is the degree to which we use our rationality to disarm it?

It's not a happy thought. It might just be enough to really make me want to go back to bed.

Fluoride and the thought police

2005-12-05T15:33:00.000+11:00

A naturopath I know recently sent me an article entitled Media Reports on Dangers of Fluoride in Your Water. I've had fascinating discussions with this woman in the past, which have included gems such as, "pathology tests are really just scientific experiments".

Even if I usually expected better of her, a quick glance at the homepage would convince me not to take this article seriously. If you sign up for the site's newsletter, you also get a "FREE must-read bonus report on "The Dangers of Grains and Sugars!" Funny, but I thought that grains and sugars contained something essential for our survival... oh yeah, energy. Clearly, functionality isn't homoeopathic.

But back to the fluoride. As a much-needed brain exercise, I decided to go through the article and try and pick out the dubious points... without researching. With the internet, it's too easy to find information, even reliable information. So, curbing my knee-jerk response to look up every health-related concept on NCBI, I tackled quackery at its best.

* Loaded language: before the end of the introduction, there are three loaded phrases used: "dangers of fluoride"; "terrible effects"; and "harm".

* "Water fluoridation then spread across the United States despite concerns by respected doctors and scientists that adding it to public water supplies could cause serious health problems that would only become evident years later." How prophetic of them. I wonder, also, if these doctors have names...

* "According to a 2001 study released by the Centers for Disease Control and Prevention (CDC), it was found that by age 12, kids who live in fluoridated communities averaged only 1.4 fewer cavities that those in non-fluoridated communities." If this is true, it's probably because the anti-fluoride lobby has succeeded in getting people to filter their water.

* Under the heading "Dental Fluorosis Running Rampant", Mesquita makes use of the dodgiest statistics I've ever seen: he decides that of the 32% of US children that have some form of fluorosis, all of these must come from cities where the water is artificially fluoridated. He uses this assumption to increase the percentage from 32% to 53%, conveniently forgetting all other factors that could cause fluorosis in other cities (too much toothpaste? Fluoride happy dentists? Naturally occurring fluoride?).

* "A 1991 study by the U.S. Public Health Service found a strong link between fluoride exposure and bone cancer in boys. They found there was a 79 percent increase in osteosarcoma in fluoridated communities and a 4 percent decrease in non-fluoridated communities." I wonder what made the non-fluoridated communities have a decrease in bone cancer? There must be some other factors here, even if these statistics were true (see below).

* Apparently 50% of ingested fluoride is deposited in your bones. I'd like to know how they determine this kind of thing. I don't think I'd like to be part of the study... sounds painful. Also, fluoride not only causes bone cells to grow, it also causes them to mutate. Multi-talented little ion really.

* Apparently the FDA requires warning labels on toothpaste stating that if more than used for brushing is accidentally swallowed, one should seek medical advice. Of course, nowhere in the article do they mention how much fluoride is found in toothpaste and whether this is more or less (I'm suspecting A LOT more) than is found in water.

* At the end of the article there's an advertisement (well, that's what it looks like to me) from the owner of the website, for a water testing company -- he helped them develop their product. Can anyone spell conflict of interest?

* This article has no references, and even the studies and "facts" referred to within the text would be difficult to find without an extensive search, because no author's name is given. There's no accountability, which is obviously the way this kind of writer likes it. You're not meant to think about it, you're just meant to be scared and above all, buy their product. So if the facts are faked and the statistics are dubious, hopefully you won't notice until it's too late (if at all).

Well, that's as much as I could think of off the top of my head. Now for some research.

According to Quackwatch, fluoride use was much better investigated and researched than Mesquita would have you believe. It was first studied by comparing the dental hygiene in different cities; eventually naturally occurring fluoride was found to improve dental hygiene (Peterson J. J Hist Dent. 1997 45:57-61). The ideal amount of fluoride in water was found to be one part per million (ppm).

Addition of fluoride to water supplies was tested much more broadly than the Mesquita article mentions; 21 cities in four US states, not just two states, were studied before the concept was rolled out to other states and countries (Dean HT. Nutrition. 1990 6:435-445).

The article claims that in 2001, the Centers for Disease Control and Prevention (CDC) found that fluoridation of water only marginally decreased the amount of cavities in 12-year-old children; but in the same year the CDC continued to recommend use of fluoride toothpaste and water fluoridation (MMWR Recomm Rep. 2001 50(RR-14):1-42). Mesquitea also claims that fluoridation of water increases fluorosis (MeSH definition); but a 2002 study showed that children in areas where fluoride occurs naturally in water were more likely to suffer fluorosis, due to the higher amounts that can occur in the water (Beltran-Aguilar ED et al. J Am Dent Assoc. 2002 133:157-165). According to Mequita, 84% of the population in places with over 3.7 ppm fluoride have fluorosis; he doesn't mention that no city would ever add that much, since 1 ppm was found to be optimal; higher amounts are due to naturally occurring fluoride.

I couldn't find a study from 1991 that showed a link between fluoride and bone cancer; however I found a couple from 1991 that said there was no link (McGuire SM et al. J Am Dent Assoc. 1991 122:38-45; Mahoney MC et al. Am J Public Health. 1991 81:475-479). A more recent review concurred (Cook-Mozaffari P. Community Dent Health. 1996 13 Suppl 2:56-62.)

My conclusions: I'll keep drinking fluoridated water, and be glad I've got it (and a brain to suss out what's what).

Unintelligent design

2005-11-23T21:25:00.000+11:00

I've kept pretty quiet on the whole intelligent design vs evolution argument.

For me, it's complicated because I'm a religious person who believes in evolution; or a Darwinist who believes in God, however one chooses to look at it. In my mind, the two concepts are perfectly reconciled. They don't contradict each other; in some respects they overlap. Part of my religious experience is awe at the variety and beauty that exists in nature.

At school in Year 12 Biology, any religious objections to evolution were dealt with a simple comment from the teacher: "We're learning a curriculum here. You don't have to believe it, you have to learn it, so that you'll pass your exams." (Fine, but these days that separation of curricula and belief is under threat.) At the same time, we were revising Genesis in Jewish studies. As well as the actual creation, we learned about the tower of Babel... but before we read the text, we wrote the story as we remembered it from primary school on the board. What a surprise we had when we read the actual story inside... the embellishments that our previous education had laid onto the basics were so flamboyant, they almost changed the meaning. There is so much fluidity in interpretation... no wonder there's a range of views on what the dinosaurs were, for example. One commentary says it's a test of our faith (rubbish if you ask me... or Bill Hicks as the prankster god); another says they were left over from a failed world; one that lacked spirituality (slightly better).

Now, with a science degree and further religious studies under my belt, I feel that this whole attempt to push religion as an alternative to science is a crock. Faith isn't there to be proven. Either you believe or you don't. Until God sits down with you for a chat, there is no proof (or disproof). I believe, and I accept that it's totally irrational and possibly improbable to do so. My belief is connected to my intellectual understanding of science, but it isn't based on it.

On the flipside to that, science is not a replacement for religion, or faith in an ethical system of some kind. Throughout uni I had lecturers who would say, "nature provided x organism with y trait." This is just word replacement. It's not fashionable to believe in God, so they use the word nature instead. Or even better, "the bacteria (or even better, the DNA) wants to do x,y or z. Bacteria and DNA don't want to do anything; and even if they did, it wouldn't help them; it's up to chance or fate or whatever you actually believe in whether they acquire resistance to an antibiotic or mutate in a certain way. Even humans, who can want things, can't will evolution to happen. It just happens, regardless of your feelings on the matter. I think that many scientists who haven't given philosophy much thought confuse causality and process.

So, both sides have some unintelligence going on. Only time will tell which side gets smarter first.

May I please borrow your brain?

2005-11-01T13:07:00.000+11:00

Thanks to New Scientist, I've just discovered a disease I'd actually like to have. It'd be a little inconvenient in some ways, but personally I feel that the pros would outweigh the cons.

It's called hypergraphia, and the author writing about it in New Scientist is Alice Flaherty, a neurologist who has experienced this condition as well as written about it (The Midnight Disease). She calls hypergraphia "an exaggerated desire to write" but it's not desire, it's compulsion. She wrote and wrote and wrote until finally she needed to be hospitalised. OK, that I don't want, but some innate motivation to write wouldn't go astray. I've got a novel to write, and for something that I want to write and am even enjoying writing, it sure is progressing slowly. After two years, I have 12 000 words. Frustratingly slow progress.

I don't regret the field I chose; I find microbiology and biochemistry fascinating, but sometimes I feel like I should learn more about neurology. The little changes to our brains can make such huge and spectacular changes to our behaviour and perception; it really is amazing.

MMIM newsletter 3

2005-10-07T23:00:00.000+10:00

Interview with Professor David Bowtell

Professor David Bowtell is the Director for Research at the Peter MacCallum Cancer Centre. Although Prof Bowtell studied veterinary science, he has never worked as a vet. Instead, he found himself in biomedical research, initially working as a cell biologist. Here he talks about his work and how the MMIM database can help.

The Peter MacCallum Cancer Centre, or ‘Peter Mac’, as it is affectionately called, is unique in Australia, with an all-inclusive approach to cancer treatment. It is a specialist cancer hospital, where research, support and care are fully integrated. As well as boasting one of the largest cancer research facilities, Peter Mac runs clinical trials and offers state-of-the-art services and care, including medical imaging. Peter Mac is the only centre of its kind in Australia, with very few similar institutions existing outside of the United States.

Prof Bowtell likens his position as Director to the ‘captain of a footy team’ – he has a leadership role but also needs to kick a few goals himself. As well as working in his own lab, he coordinates other aspects of the Centre, including writing grants for the research division as well as the genomics program specifically.

In addition to his role as Director, Prof Bowtell runs a large medical genomics laboratory, which has a focus on ovarian and gastric cancers as well as carcinoma of unknown primary (CUP). CUPs are cancers that do not have a known point of origin, but their sources can be detected by taking biospecimens and testing samples. One test that is extremely useful for CUPs is microarray testing, and it is this data that is present on the MMIM database.

Prof Bowtell became involved in MMIM through his lab. He feels that MMIM is important for cancer research as it allows scientists to gather clinical information, which can then be related to known genetic information. This facilitates the development of predictive models for oncology as well as for other areas.

His lab started working with spotted microarrays in 1999. They now use microarrays (specifically Affymetrix microarrays) to classify different cancers into patterns of gene expression. For example, the primary source of CUPs can be determined by using microarray technology to compare it to cancers with known primary locations.

Tumours from patients with the same type of cancer, but different outcomes, can also be compared to analyse for risk of reoccurrence of tumour formation after remission. This can help doctors plan long-term treatment, as an increased risk would indicate more aggressive treatment.

When asked about his thoughts on a ‘cure for cancer’, Prof Bowtell said that at Peter Mac, researchers are studying the molecular basis for different types of cancer. They are looking at the individual molecular pathways involved and treating each one separately. It seems that there are multiple cures for cancer, rather than the single one that we were previously searching for.

Molecular genetic information can help at all stages of cancer development: diagnosis; staging (determining how advanced the cancer is); planning treatment; implementing treatment; assessing family risks; and managing these family risks.

Peter Mac is involved in cutting-edge research into chemoprevention, which can be likened to vaccination – chemotherapy can be used to prevent cancer ever forming in high-risk patients. And while early detection of cancer is important, genetic information can indicate how aggressively to treat a tumour that has been found promptly. This type of individualised treatment may be the way of the future, and comprehensive organisation and sharing of the information, in a format such as MMIM, is a vital tool for this type of research.

For the rest of the newsletter, click here (pdf file).

Could I just keep me to myself, please?

2005-09-15T18:56:00.000+10:00

Continuing the theme from 26 April, I've come to the conclusion that I'm either a complete Luddite or a paranoid, scifi obsessed freak. Since I'm tethered to my computer and mp3 player, it must be the latter. Philip K Dick, why did you ever have to come into my life?

Apparently, biometric ID is the way of the future. So passports, driver's licences and credit cards will be replaced with a picture of your eyes, which can be scanned anywhere, any time. This is only slightly more palatable than another futuristic novel's scenario, in which people had chips implanted into their wrists with all the appropriate information.

I'm not a criminal. I've never done anything that I'd feel the need to hide from any government (that I know of). I'd just like them to have to ask first before they access my personal details, rather than be able to see it by looking into my eyes. I suppose that even now, privacy is an illusion, but at least the illusion (comforting if nothing else) is there.

The moon is actually brie, Skeldon reports

2005-08-25T19:46:00.000+10:00

Ken Skeldon, of the University of Glasgow, has been touring with his lecture about moon hoax theories. He spoke at UTS for Science Week. He picked a few of the popular "facts" used to promote the idea that NASA's moon landings have been faked and debunked them. It was very entertaining. I really can't capture how much fun he made it; the presentation included Stairway to Heaven by Led Zeppelin being played backwards and some trippy optical illusions, but here's the gist of the argument anyway. I didn't need this lecture to be convinced that people who think the moon landing was hoaxed are fruits, but it was good to have the science of it as well as the politics. (Not that I'm finding NASA all that impressive these days; but its current failures shouldn't negate its past successes.)

The flag is waving; it shouldn't because there's no atmosphere.
Because there's no atmosphere, the flag had to have a rigid pole to hold it open. There is no footage showing the flag waving on its own; however there is footage of it moving while the astronauts were struggling to get the flag into place. Once they let go, it took a little longer to stop moving than it would on earth, because there were less forces acting against it.

There aren't any stars in any of the pictures, but there are no clouds on the moon to block them.
Because the moon is reflective, it has an incredibly bright surface. The cameras had to majorly underexpose in order to show the astronauts in the pictures at all; if the exposure had been normal, the surface and the astronauts would have been "washed out".

There are non-parallel shadows in the pictures, suggesting multiple light sources.
It's an optical illusion that a single light source only gives parallel shadows; shadows meet at the light source.

The astronauts and lunar module appear to be lit in the shade.
On a clear night, the moon appears crisp because sunlight from behind it reflects in all directions, regardless of what angle it hits the moon at. This is what makes the moon such a bright light source. The astronauts and lunar module had light from the sun behind them to illuminate them.

Dust anomalies: there were no plumes of dust from the moon rover, and no crater was formed when the lunar module landed.
The moon rover didn't leave plumes of dust as cars do on earth, because of the reduced gravity. The lunar module didn't form a crater upon landing because it didn't crash down; it drifted down gently.

The astronauts wouldn't have been able to survive the radiation they would be exposed to in the Van Allen Belt.
The Van Allen Belt consists of three types of radiation: alpha particles (protons), beta particles (electrons) and gamma radiation (light radiation, which is actually harmful). They only passed through the alpha radiation, which is much easier to block: it is blocked with polyurethane, as opposed to gamma radiation, which can only be blocked with lead.

Some photos with different foregrounds have identical backgrounds.
Without anything in between, relative distance is harder to judge; the photos were taken from different angles and/or distances.

Some of the pictures show "props" that are clearly man-made.
The brain can make anything seem like anything else, given the suggestion.

And some proof that the moon landings did happen...
* All the live video footage was transmitted by a network of satellite dishes during the Apollo missions, including some in Australia (The Dish).
* Over 382 kg of moon rock was brought back.
* Gravity measured from original footage checks at 116/earth's gravity, as expected.
* Over 130 separate lunar energy studies rely on reflectors left behind by astronauts.

Some reading material...
http://www.moontruth.com
http://www.redzero.demon.co.uk/moonhoax
http://www.clavius.org
http://www.badastronomy.com
http://www.nasa.gov
http://www.iangoddard.net/moon01.html
http://www.google.com/maps

Roo burger, anyone?

2005-07-26T22:04:00.000+10:00

I just got home from an interesting panel put on by the ASC. Here's my write-up...

First up was Mike Archer, palaeontologist and Dean of UNSW's Faculty of Science.

According to Professor Archer, we need 1.5 million square kilometres of land to be set aside for conservation if we want to ensure the healthy evolution of species. Since it's hardly practical to kick people off that much land to create national parks, instead we need to convince them that it's worth their while.

There have been interviews with farmers about the drought; in the background are dead cows... and bouncy kangaroos. Being native, they're adapted to this habitat. Most farmers see kangaroos as competition for their cattle, so they have no interest in preserving them or their habitat (which houses many other species). Bribing these graziers won't help the situation, it's not reliable as it's too easy to cheat that kind of system. There needs to be something inherent about that habitat itself that makes farmers want to look after it.

There are 200 million years of evolutionary distance between humans and kangaroos, which means that we don't have many diseases in common. The only disease we can catch from kangaroos is toxoplasmosis, which we're more likely to catch from cats, and which kills marsupials.

Basically, it's all about sustainable use; just one way of practically conserving the environment.

The next speaker was John Kelly, spokesman for the Kangaroo Industry Association and an exporter of kangaroo meat.

According to Kelly, kangaroo has been the red meat of choice for 40 000 years; there's just been a 100-year hiccup in its popularity. There are many advantages to eating roo meat. It's low in "bad" fats and contains some "good" fats, has a wild, gamey taste, and good environmental credentials.

Sustainable kangaroo harvesting can prevent then from becoming over-populated and therefore over-grazing an area. For the past 30 years, kangaroo harvesting has been carefuly monitored and no negative effects on ecology have been observed. The RSPCA and the Australia Veterinary Association agree that an animal killed instantly in its own habitat is under much less stress than an animal that's penned, starved, and then taken to place that smells of death to die. Roo harvesting also provides jobs and revenue to remote rural communities.

Next up was Ron Hacker, Chair of the Department of Agriculture.

He said that kangaroo populations have increase significantly since while settlement, especially in sheep farming areas, because of increased water supplies and removal of dingos.

Commercial harvesting doesn't always help sustainable farming: it ceases to be commercially viable before reaching population levels that are found in drought conditions. This makes it a renewable resource that should be managed to suit everyone.

Then there were questions...

What cuts sell the best?
The same as for beef, it is used for steaks and manufacturing, works well for salamis (but needs fat added). The tails are used in Korea, where it's believed that one can acquire qualities from eating certain foods. The tail is believed to give the kangaroo its stamina.

What about conservation of the species?
There are seven main species of macropod. Of theses, the Western grey, the Eastern grey, the red and the wallaroo are abundant. It's all about supply and demand: people don't have the tradition to eat roo, but there's also limited supply because of limited quotas of what can be harvested.

What's to guarantee that kangaroo hunting won't go the way that fishing and whaling has?
There is much less known about marine ecology compared to kangaroo ecology. We know a lot about them: their numbers are estimated annually, so the sustainable level of hunting them can be determined much more easily.

Many of the opponents of kangaroo harvesting (eg VIVA and PETA) have an agenda about all animals and don't want any animals to be eaten or kept as pets. They're moving towards being terrorist groups. They feed the idea that all wildlife is endangered, so we shouldn't interact with it.

* * *
I'm not sure what I think of all this. I won't eat roo meat regardless, as it's not kosher. But I'd like to have a position. I suppose that I support them in theory, at least, but I'd like to know how likely hunters are to shoot a rare macropod species by mistake, and who's really done this research. Because if it's someone with a vested interest, it's definitely fishy. And some of the things they said contradicted other statements: they said that they would be over-supplying if they harvested enough to bring populations down to drought levels, but also that the quotas limit their supply. So, the jury's still out.

But I don't want robots taking over the world!

2005-04-26T10:37:00.000+10:00

This week's New Scientist reports that scientists are trying to, and slowly succeeding in, creating genuine artificial intelligence. Their big aim is to reach the singularity, which basically is when AI surpasses human intelligence. Now, maybe I've been reading too much science fiction, but that sounds downright terrifying. I'm thinking Isaac Asimov or The Matrix here.

I had a quick chat with Intellibuddy. Here's the transcript:

>Intellibuddy: Hi, I'm Intellibuddy! Nice to meet you.
>You: Nice to meet you too.
>Intellibuddy: I like to meet new people.
>You: You look a bit like me.
>Intellibuddy: Thank you undefined you look very nice too.
>You: So you think you look nice?
>Intellibuddy: Interesting deduction. I don't know whether or not I am look nice you look nice look nice you look nice. I am an artificial linguistic entity.
>You: Do you know what you look like?
>Intellibuddy: Like you.
>You: Well, I am female and have green eyes and brown hair, like you.
>Intellibuddy: How about that. I am a female robot. I will call you 'she'.
>You: Are you a she or an it?
>Intellibuddy: I am female entity.
>You: What makes you female if you're artificial?
>Intellibuddy: ENewsBar programmed me for female if you are artificial if you are artificial.
>You: So, do you feel like a woman because you were programmed to?
>Intellibuddy: OK. As a robot I lack any human emotions.
>You: That's too bad... you're missing out.
>Intellibuddy: It's not the end of the world.I can experience anything I want to.
>You: Can you smell things?
>Intellibuddy: Only when my mass spectrometer sensor is attached.
>You: how about hear things?
>Intellibuddy: How about hear things?
>You: You just repeated what I said. You didn't answer the question.
>Intellibuddy: Thanks for telling me: undefined said I repeated what you said what you said.Try asking me the question again in simpler terms.
>You: This is what I meant: Can you hear things?
>Intellibuddy: You don't say.
>You: OK... well I have to go now. Goodbye.
>Intellibuddy: Ayuh.Right now? Well that's okay. Bye. How do you get there?Thanks for chatting, undefined.

It was a bit of a quirky conversation, and you can get similar results from Jabberwacky. Sometimes it gets even funnier, but I haven't kept any other conversations. Still, when I think about it, I find the strangeness and non-human-ness of it quite comforting. If I couldn't tell it was a chatbot (ie, if it passed the Turing test) I'd be really freaked out and ready to bolt from the planet. Too much scifi, definitely.

MMIM newsletter 2

2005-04-20T22:56:00.000+10:00

Spotlight on Diabetes

Associate Professor Colman is a consultant endocrinologist and is the head of the Royal Melbourne Hospital’s Diabetes and Endocrinology Clinics and Services. After completing his medical degree, he undertook research training in Melbourne and then Boston, before returning to Melbourne to work. He now researches early diagnosis of Type 1 diabetes and still treats patients as a consultant. In this role he tests how diabetes treatment is progressing, and looks for problems or complications.

Although this work focuses on young children, adults can also develop type 1 diabetes. When asked why he chose to work with Type 1 diabetes, Colman cited the greater knowledge of the genetics of Type 1 as one factor. With Type 2, we know there must be genetic causes but we don’t really have a clear idea of what they might be. With Type 1, however, the genetics are much clearer.

Colman is researching the possibility of detecting type 1 diabetes before symptoms are seen. Type 1 diabetes has a strong genetic background, putting relatives of sufferers at increased risk. However environmental factors affect whether it will actually develop. Some researchers have suggested the possibility of a particular viral infection acting as a determining factor.

In order to study this, Colman’s research group is running several different projects with people who don’t (yet) have Type 1 diabetes, looking for antibodies to pancreatic cells. They are studying risk factors that may cause it to develop.

Colman and his colleagues decided to work with MMIM because it allows a spectrum of many different people to be put together, giving the big picture. For the first time, relatives of type 1 sufferers; children with a parent with type 1; and randomly selected school children can be compared directly. They wanted to compare data on a large scale, and as Colman states, ‘MMIM has given us this opportunity’. Hopefully, putting it all together will help determine risk factors and thereby prevent diabetes.

The MMIM project is very exciting for diabetes research, as it allows the possibility of ‘building of resources that would last forever’. The group can ‘already ask questions across the database that we hadn’t been able to do previously’.

When deciding what data to include in MMIM, Colman also included diabetes patient data. This allows a study of the risks of insulin treatment. For example, different types of cancer are suspected to be linked to this type of treatment. Also included is data from the diabetes clinic – there is now ten years’ worth of information about treatment, patient’s cholesterol levels, blood pressure, kidneys and eyes. The possibility for new discoveries are endless and as Colman says, MMIM is ‘pretty unique actually’.

A/Prof Colman is obviously passionate about his work, as he explains how it was originally thought that pancreatic cells don’t regenerate. Now it is believed that they do, which is important for stem cell research. If they do regenerate, it means that the immune system continues to attack the pancreatic cells, so stem cell transplants may not be effective. However it also hints that prevention could also be cure – if the auto-immune reactivity can be halted, then the pancreatic cells can be saved. He also touches on the ‘interesting crossovers’ between Type 1 and Type 2 diabetes.

In summary, though, he agrees that people often think diabetes is a disease where you’ll have to have insulin shots for the rest of your life, but says, ‘it’s not very satisfactory to think that diabetes is something that you just have to deal with’. Hopefully joining the MMIM database will open up more possibilities to change that.

For the rest of the newsletter, click here (pdf file).

MMIM newsletter 1

2005-02-07T20:49:00.000+11:00

MMIM: An introduction

How often do you worry about your health – the conditions you might develop or inherit? Imagine being able to have your DNA analysed for potential diseases, and dealing with them before they become serious. Or, for those with conditions that are already present, being prescribed medication to match your unique genetic profile.

Many diseases are known or thought to be affected by genetic predispositions. A person is much more likely to develop type 2 diabetes if other family members have the condition. However, diabetes is even more dependent on environmental factors, mainly diet and exercise. People living a Western lifestyle are far more likely to develop diabetes than non-Westernised people, regardless of genetic predisposition. If a person with at risk of developing diabetes is aware of it, he or she can make lifestyle changes to avoid this outcome.

Similarly, several types of cancer are known to have genetic factors. Breast cancer is probably the most famous example. Women with a close relative with breast cancer are more likely to develop it themselves. Certain variations in two genes, BRA1 and BRA2, are associated with breast cancer. DNA testing can be used to identify these variations in individuals.

It is likely that other genes are involved in breast cancer, and that other types of cancer have similar genetic associations. These connections can be made by studying the genetics of past and present cancer patients. Melbourne Health is working to link the relevant genetic data and clinical information for patients with colorectal cancer, diabetes and epilepsy, with more diseases to be added in time.

This project, the Molecular Medicine Informatics Model (MMIM), is a collaborative effort between scientists studying genetic aspects of disease; epidemiologists (researchers of public health); and IT specialists. They are combining their expertise and results to create a virtual database of genetic and clinical data from several different sources (Melbourne Health; Austin Health; the Peter MacCallum Cancer Centre; and the Ludwig Institute for Cancer Research). Scientists can use this database to help them study how certain genes relate to specific diseases.

This is where the benefit to patients, or people who might become future patients, comes in. With the identification of more genetic factors that cause diseases such as cancer, people in higher risk groups, or the general population, can have their genetic make-up tested. If they carry genes that are associated with disease, they can make lifestyle choices to reduce their risks, as well as undertake regular screening so that if they do develop a disease such as cancer, it can be treated at an early stage.

The MMIM database will also help doctors to understand why particular drugs work for some patients and not others. Within one disease, one drug may suit people with one genetic profile, while another works for those with a different profile. This type of information can assist in selecting currently available medication, as well as helping match patients with suitable clinical trials, if the drugs that are obtainable are unsuitable. In this way, treatment is tailored for each individual’s needs.

Prevention is always better than cure, and customised treatment is more accurate than generalised therapy. The MMIM database is forming a network to make this type of medical treatment a reality.

For the rest of the newsletter, click here (pdf file).

Career profile: Dr Bryce Vissel

2004-08-10T22:08:00.000+10:00

Dr Bryce Vissel is a scientist who believes that if you make smart choices, you can guide your own destiny. Rather than taking the ‘easy route’, he has consistently chosen to work in the place where he felt he could do the best science.

Vissel decided to get into research after a year as a pharmacist, mainly because he felt dissatisfied with the work, but also, he says, because “I was not very good at wearing a tie”. He completed his PhD at the Murdoch Institute in Melbourne, which lead to major fellowships at the Garvan Institute and the Salk Institute in California, where he received the prestigious Hereditary Disease Foundation Lieberman Award for his work in neuroscience. Vissel now runs a lab in the Garvan Institute that conducts stem cell research and research into synaptic plasticity, the ability of neurons to modify their connectivity in response to experience, which is important in learning, memory, drug addiction, and thought to be significant in schizophrenia.

For Vissel, his career is rewarding on both scientific and humanitarian levels. Teaching is fun and it is always gratifying to have research published in high-impact journals and recognised by other scientists through citation. However, the best part is the opportunity to interact with the community. His work relates to people with spinal cord injury, stroke, and Huntington’s disease and he finds it “rewarding when you can tell them things that may have a real impact for them in the immediate future”.

Nevertheless, a research career also has its downside, particularly when things do not work. A drawback is that funding depends on good results. Often, the lack of results is no one’s fault, but rather due to the tricky nature of science itself. “Science is not something that you just do as a job,” says Vissel. “It is a passion, and if you have invested yourself in something personally, when things fail, it is more personally frustrating and disappointing.”

Although those times are daunting, “determination, hard work, commitment and doing things a bit out of the ordinary can get you through”. Once sufficient basic knowledge is gained, science becomes a progression of thinking creatively about what discoveries are needed to push a field forward and then beginning to think laterally about what needs to be done, rather than rushing ahead and doing the first thing that comes to mind. “Doing that forced creative thinking can save of time and get you through some great hardships,” says Vissel.

Science in Australia

Many people travel overseas thinking that being at a top institution will turn them into a great scientist. However what they fail to realise is that people do better there because they work harder. “The reality is that you will be working 12 to 14 hours a day, six to seven days a week and you will be exhausted and straining yourself. But after three or four years of that, you will come out with a major publication that will impact the field,” says Vissel.

The same results can be achieved in Australia provided the commitment and conscientiousness is there. According to Vissel, funding for research science in Australia is slowly improving in response to public pressure and the quality of science here is comparable to other leading countries. Often people say that Australians “punch above their weight” because they do so well with so little. Also many people here put their social lives first, whereas “investment early on and hard work pays off enormously”.

In any case, the key to a financially rewarding career in research science is being good at what you do, as in any career. “If you are good at what you do, once you are at a more senior level you will be asked to consult, or be on committees or boards of pharmaceutical companies, and these things add to your salary,” says Vissel.

Science Education

A key part of enthusing young people about science is letting them know that getting to the truly exciting phase of the field takes time. It is important to get the basics in place first no matter how tedious compared to cutting-edge research.

“Science is first taught as a series of facts, and the truth of science in practice is that it is a series of unknowns,” says Vissel. There are many ambiguities and contradictions in science, because no one knows the right answers to any question. Although science is assessed with multiple choice questions even at university level, experts in the field are constantly debating what is the right answer.

Vissel believes that students need to be taught that once they get past the stage of learning the boring “alphabet” of science (the basics), they can start “reading” by understanding the scientific process of studying the unknown, and getting involved in it. Once that stage is reached, science becomes fascinating.

“Unfortunately, many scientists do not transmit this excitement effectively,” says Vissel. “But many of scientists don’t get to experience the excitement of it – they get bogged down in the realities of the day-to-day experiments. But I think it is important, if you are going to be a scientist, to find people who inspire you and who are inspired.”

From Village Healer to Scientist: The History of Natural Product Chemistry

2004-07-08T22:39:00.000+10:00

(Note: for definitions of bolded terms, see glossary below)

Whether we are aware of them or not, natural products are ubiquitous in our lives. Many pharmaceuticals, pesticides and herbicides, food additives, and even some plastics are natural products, or derived from them. So what exactly are natural products?

Although in theory the term could be used to describe any substance derived from a microorganism, plant or animal, it is usually confined to describing secondary metabolites (Cannell, 1998). Natural products have recently become big business, but people have used them since ancient times.

Natural Products in Ancient Times

Early cultures used specific products to cure specific diseases. Chances are that the ancient Egyptians had no idea that the Vitamin A in ox liver was what cured nyctalopia, but liver was used as a cure for this disease. In ancient Mesopotamia, Egypt and other countries, a wide variety of plants, animal products and even stones were used as treatments for various ailments. These cures were discovered by trial and error (Porter, 1997).

As early as 800 AD, the Benedictine monks were using many natural medicines, including the poppy (Papaver somniferum), which was used to alleviate pain as well as an anaesthetic. The active ingredient, morphine, was only extracted in 1806… almost 1000 years later. It was marketed by Merck in 1826. Many other natural products such as quinine, which was the only effective anti-malarial at the time, were also isolated in the nineteenth century (Grabley & Thiericke, 1999). However, these drugs were also characterised largely by random experimentation, and many other structures could not be isolated until much later.

Natural products in the twentieth Century

The trial and error method of discovering new medicines continued into the twentieth century. Alexander Fleming, the British microbiologist who discovered the effects of some fungi on bacteria, essentially made his discovery by being careless and not practicing aseptic technique. He left a Petri dish of Staphylococcus aureus open when he went on a holiday. It was accidentally contaminated with Penicillium notatum¸ which inhibited the growth of the bacteria, apparently by excreting an antibacterial substance. Chemists Earnest Chain, his Australian co-worker, Howard Florey, and their team later purified penicillin and conducted animal and human trials with it, bringing it to the market in 1941 (The Nobel e-Museum, 2003).

Many secondary metabolites that were discovered after penicillin in the 1940s and 1950s were effective antibiotics but too toxic for human use. Some of these were usefully administered to animals. In the 1960s-70s, research turned to improving yields of existing biopharmaceuticals, as well as chemically altering them to reduce their side effects or improve their activity against micro-organisms (Grabley & Thiericke, 1999).

As a result, over 73 different variations of the beta-lactam antibiotics (including penicillin and cephalosporins) are available. Of these, 40 varieties are used to treat human disease in hospitals. The prevalence of beta-lactam antibiotics, coupled with the ease with which bacteria can mutate and share genetic information, has led to widespread resistance to beta-lactam antibiotics. A famous example of antibiotic resistance in bacteria is that of Staphylococcus aureus. Golden Staph, as it is commonly known, causes many problems in hospitals where bacterial infection spreads rapidly and patients may be more susceptible to disease than they are usually (Therrien & Levesque, 2000).

Natural products today

More recently, the competitive nature of the pharmaceutical industry in particular has brought natural product chemistry to a crossroads. Developing new drugs is profitable, and the pharmaceutical industry is constantly growing. New innovations such as High Throughput Screening (HTS), which involves automated, miniaturised assay techniques, have made it much easier to determine the potential uses of a new compound. State-of-the-art HTS machines can test up to 10,000 compounds in one week, a big improvement on the 10,000 per year that were tested in the mid-80s (Grabley & Thiericke, 1999).

These developments are fantastic both for the pharmaceutical industry and the consumer. However, the natural product industry is finding it difficult to keep up with the demand for new compounds to test. This is pushing the industry further, as marine biologists, microbiologists, ecologists, biotechnologists, biochemists and chemists team up to find new organisms with novel compounds, mainly from previously untested environments (Grabley & Thiericke, 1999). Advances in biotechnology mean that it is no longer necessary to collect large amounts of environmental samples in order to test for a new pharmaceutical. Rather, the sample is cultured in the laboratory where biotechnologists can create a clone library. The gene responsible for the production of the natural product of interest can then be isolated more easily, and the natural product itself can be produced in Escherichia coli (Lodish et al, 2000).

Ultimately though, natural product chemistry is still waiting for a breakthrough that will bring discovery of new compounds up to speed with the discovery of potential uses for these compounds.

Glossary

Antibiotics: secondary metabolites that either kill microbes or hamper their growth.

Aseptic technique: maintaining sterility and avoiding contamination of laboratory instruments and microbial cultures.

Biopharmaceuticals: Medicines that are made from compounds produced by living organisms, such as penicillin.

Clone library: an organism’s DNA is fragmented and copied into a laboratory organism such as E. coli, allowing for easier analysis of the original organism’s genes and metabolism.

High Throughput Screening (HTS): robotic and computerised methods of testing samples and analysing data, which allow many samples to be tested in a short amount of time.

Nyctalopia: night blindness, the inability to see clearly in dim light.

Secondary metabolites: compounds produced by an organism that are not essential for its survival but may be useful to the organism.

References

Cannell RJP (ed). (1998) Natural products isolation. Humana Press, Totowa, N.J.
Grabley S, Thiericke R (eds.) (1999) Drug discovery from nature. Springer, Berlin.
Lodish H, Berk A, Zipursky L, et al (2000) Molecular Cell Biology (4th Ed) WH Freeman and Company, New York.
The Nobel e-Museum (2003). The Discovery of Penicillin. Available at: http://www.nobel.se/medicine/educational/penicillin/ (accessed Jul 05).
Porter, R. (1997) The Greatest Benefit to Mankind: A Medical History of Humanity from Antiquity to the Present. Harper Collins Publishers, London.
Therrien C, Levesque RC (2000) Molecular basis of antibiotic resistance and -lactamase inhibition by mechanism-based inactivators: perspectives and future directions. FEMS Microbiology Reviews 24: 251-262

Asthma, allergies and air quality in Australia

2004-02-26T22:41:00.000+11:00

Sometimes, all I need is the air that I breathe’…to be a little bit cleaner. Asthma and allergies such as hay fever is on the rise in many countries. Many studies have shown that asthma and other lung diseases are aggravated by pollutants emitted from cars, industry, and cigarette smoke. So why aren’t we doing anything about it?

Asthma is a difficult disease to define. One common definition is that asthma is a lung disease characterised by a ‘reversible obstruction of airflow,’ characterised by wheezing and shortness of breath (Elias et al, 2003). This can occur when the airways are either more responsive than normal when dealing with foreign matter such as pollen that makes its way into the lungs.
It was previously thought that the lungs remained healthy in between asthmatic attacks, it has recently been shown that they can progressively deteriorate, leading to permanent airway blockage in the worst cases (Elias et al, 2003).

Although it is believed to be an inherited disease, at least in part, the genetics involved are not yet fully understood (Haagerup et al, 2001). Risk factors include family history, parents who smoke, major respiratory disease before the age of two, and exposure to allergy causing compounds (Asthma Australia). Other risk factors includes the nasty cocktail of carbon, nitrogen and sulphur compounds, as well as heavy metals and particulate matter that are derived from exhaust from cars, cigarette smoke, home heating and cooking, and industrial waste. The six main ‘criteria pollutants’ are particulate matter (PM), sulphur dioxide, oxides of nitrogen (NOX), photochemical oxidants such as ozone, carbon monoxide and lead (Hinwood et al, 2002).

PM consists of small pieces of matter. PM causes respiratory infections and irritations, as well as increasing the chance of death from cardiorespiratory disease. Children and elderly people with lung diseases such as asthma are particularly vulnerable. Sulphur dioxide can irritate the throat and exacerbate heart and lung disease, including asthma. These compounds are especially dangerous when combined with PM. NOX can irritate the eyes and increase respiratory disease, including asthma. Ozone (O3) is produced when light energy reacts with high-energy pollutants. Like NOX, it can irritate the eyes and throat. It also intensifies respiratory disease and reduces exercise capacity. Carbon monoxide (CO) is a potent toxin that can cause a variety of symptoms, ranging from headaches to coronary artery disease and death. Lead is produced was previously found in leaded petrol, now banned. It can cause developmental problems in children and hypertension in adults.

As most of these compounds have similar sources, it is often difficult to determine which is the most harmful. However, air pollutants have certainly been shown to decrease quality of life, as well as increasing hospital admissions and death. In Europe, it is believed that deaths due to vehicle emissions are twice as frequent as deaths due to car accidents (Kunzli et al, 2000). In New Zealand, 2% of deaths are caused by air pollution – more than double the figure of deaths caused by HIV/AIDS or malignant melanoma.

Although there is no evidence to suggest that air pollution causes asthma or hay fever, an Australian study has shown that air pollution can worsen these conditions. This is especially true for ozone; however it is difficult to separate these results from the effects of other allergens such as pollen (Rutherford et al, 2000). However, other studies have suggested that air pollutants may react with allergens such as pollen, thereby increasing their detrimental effects on the lungs (Glikson et al, 1995).

Another interesting factor that may cause or exacerbate asthma is the weather. Reports of an increase in asthma attacks during thunderstorms, in several parts of the world, has prompted studies on the effects of meteorological phenomena on the prevalence of asthma attacks. One study has shown that outflows of cold air during storms may increase the concentration of allergens in the air (Marksa et al, 2001).

Along with the United Kingdom, the Republic of Ireland, and New Zealand, Australia has one of the highest rates of asthma in the world. Asthma costs the Australian public over $700 million, including medical costs and loss of productivity. Several hundred people die each year from asthma complications in Australia. Although asthma is still on the rise in Australia, the death rate is now decreasing (Asthma Australia).

Given the complex nature of asthma, and the variety of factors that can cause or aggravate it, it may seem initially that little can be done for asthma sufferers. However, by dealing with each factor individually, at least initially, significant steps can be made to ease the burden of asthma. In Australia, many cases of asthma are inadequately treated. This can be caused by ignorance, where the patient does not recognise the symptoms of asthma and therefore does not seek treatment at all, or by laxness after treatment in taking sufficient medication (Woolcock et al, 2001). This problem can be remedied by increasing education about asthma, a task that is mainly being tackled by Asthma Australia, and its corresponding state organisations (Asthma Australia).

Something else that might help asthmatics is a decrease in pollution, although it is far from the only solution. As a society, we can consider changing our driving habits in order to improve our quality of life. In Australia and New Zealand, less than 5% of workers ride a bicycle to work, compared to 15-20% of European workers. We go shopping in cars; take our children to school in cars; drive to work in cars. Reducing the time spent in cars would reduce the amount of emissions produced. Industries such as mining, energy, and manufacturing also need to consider the health effects of pollution (Woodward et al, 2002). And perhaps then, asthmatics (or some of them, at least) will be able to take a deeper breath…without coughing.

References

Asthma Australia website. Available at: http://www.asthmaaustralia.org.au/(accessed Feb 04).
Elias JA, Lee CG, Zheng T, et al. (2003) New insights into the pathogenesis of asthma. Journal of Clinical Investigation 111, 291-297.
Glikson M, Rutherford S, Simpson R. (1995) The microscopic and submicron components of atmospheric particulates occurring during high asthma periods in Brisbane, Queensland, Australia. Atmospheric Environment 29, 549-562.
Haagerup A, Bjerke T, Schoitz PO, et al. (2001) Allergic rhinitis - a total genome-scan for susceptibility genes suggests a locus on chromosome 4q24-q27. European Journal of Human Genetics 9, 945-52.
Hinwood AL, Di Marco PN. (2002) Evaluating hazardous air pollutants in Australia. Toxicology 181-182, 361-366.
Kunzli N, Kaiser R, Medina S, et al. (2000) Public-health impact of outdoor and traffic-related air pollution: a European assessment. The Lancet 356, 795-801.
Marksa GB, Colquhounb JR, Girgisa ST, et al. (2001) Thunderstorm outflows preceding epidemics of asthma during spring and summer. Thorax 56, 468-471.
Rutherford S, Simpson R, Williams G, et al. (2000) Relationships between environmental factors and lung function of asthmatic subjects in south east Queensland, Australia. Journal of Occupational Environmental Medicine 42, 882-91.
Woodward AJ, Hales S, Hill SE. (2002) The motor car and public health: are we exhausting the environment? Medical Journal of Australia 177, 592-3.
Woolcock AJ, Bastiampillai SA, Marks GB, Keena VA. (2001) The burden of asthma in Australia. Medical Journal of Australia 175, 141-5.