Tuesday, July 31, 2012

Shows ... potential

And if that potential was transformed into action, I would very much like to see David Cunliffe as part of the next government. On the basis of speeches like this: The Dolphin and the Dole Queue and the speech a while ago to the New Lynn Womens branch of the Labour party a while ago.

I would be reassured that there would be somebody who appears to understand large chunks of the world in largely similar terms as I do.

This is why ... shit is cool.

for those of you who don't know, the PhD that I am currently engaged with is on the gene regulatory networks that form between host and pathogen. Basically how two organisms interact down at the genetic level. Which, while the day to day operations can be a bit hum drum (especially if there are large morning teas with meringues and cakes that make me stop thinking for a day) is absurdly cool. Part of why I think this is fascinating is that this interaction between different organisms happens almost everywhere. A lot of it is symbiotic rather than pathogenic - there's whole systems in your body which are reliant on the ecosystem of bacteria that are living in your gut. So if we want to figure out how we or the plants and animals around us work, we have to understand how the micro-organisms work as well. And more specifically how they interact with whatever organism it is that they are attached to.
In the interactions that we know about, there are a sufficient number of components involved that the complexity of the system as a whole is ... absurd. The amount of data is ... absurd. And I get to dive in to all that data like Scrooge McDuck in his money tank and try and find patterns in it. Then to make it better, we just keep finding more ways in which we interact with micro-organisms. Like this study from the National Institute of Allergy and Infectious Diseases in Maryland. We've know for ages about the gut flora and their interactions. We're years away from understanding it all. And now we find that the micro-organisms on the skin (of which there are many) are playing a role in the regulation of our immune systems. The skin has long been known as one of the primary lines of defence in our immune system (stop, think about it, it makes sense really). To find that there's a whole system of communication between our skin and the micro-organisms that live on it that aids in the regulation of of the immune system is, that word once more, absurdly cool.

The skin’s secret surveillance system : Nature News & Comment

What a signature means

There was a case in the news a week or so ago, a director of a finance company has been charged with producing a false prospectus. Or something like that. Her defence was that her husband at the time had told here everything was alright, so she had signed it. Which, I don't think is a viable defence. The same thing has been in the news the past few days since the police decided not to charge John Banks with filing a false return. I accept that the police can't charge him because of the time lapsed - that's an issue I have with the laxity of the law rather than with the police or Banks. What I do have an issue with is Banks seeming to think that the fact that a volunteer had assured him that the return was alright was a viable defence. It's not. If any authority is to be put in legal documents, then the affixing your signature to a document has to mean that you are ready to stand behind everything said in the document. If it doesn't then we're left with the situation as described in the editorial of the dom-post this morning:
The minister's signature signifies nothing other than that he knows how to write his name. By no stretch of the imagination should its presence on a document be taken as evidence that he has read the document or stands by its contents
It doesn't matter if you're a company director, a pleb in the street or a minister of the crown. A large part of the day to day workings of our society is based on your signature signifying your understanding and acceptance of the document it is inscribed upon. It's why forgery is such a big deal - it abuses the trust that we place in signed documents. Banks's defence doesn't seek to fool us a a forged signature does. It does however suggest that his is a signature that we can little faith in.

Monday, July 30, 2012

That glaring omission.

Finally, someone (Bryce Edwards) with an audience other than hardcore politics junkies brings this out:
"It's important to remember that National's record levels of support in 2011 were actually a result of non-National voters staying home rather than any real increase in the number of National voters. If the negatives become enough to drive those 2011 abstainers back to the polls then it will spell real trouble for the Government, irrespective of how the opposition is perceived."
Time and time again, you get commentators going on about the high levels of support that National has. Or had. And these are people who are paid to report on political matter to the population as a whole or those  who are paid to advise political parties (Pagini). Yeah, sure, national got the largest share of the votes at the last election. This does not mean that a majority of the country supports them. It means that the number of voters who supported National is more than the combined total of those who supported other parties and those who did not care enough to vote. The key to getting a left leaning government back in power is not to win over the center as Pagini would have you believe, that's already where Labour are. The key is in reducing the number of voters who do not care.
How can we be sure that these non-caring voters are left leaning? If you take the total number of voters (not as a percentage, the raw number) for National for the last several elections, taking into account population growth, you'll find they haven't changed much. If you do the same for Labour, you'll find that its raw numbers have been dropping. Most likely explanation - a large percentage of the non-caring voters are from the left.

Sunday, July 29, 2012

Well that's torn it then.

So I've got speakers and a venue confirmed for the first chapter of Nerdnite in Auckland. About which, I have to say, I am quite pleased. Quite nervous as well though.

August the 14th, Nectar Bar in Kingsland. Beer. Food. Talks for the public geek. We have Siouxsie Wiles, a microbiologist an bioluminescence enthusiast. We have Thomas Lumley from statschat.org.nz - and I have to say I was quite pleased when he sent me the title of his talk: Science in the media: can pointing and laughing help? I do a lot of pointing and laughing at science reporting in a variety of media (you have to, it's either that or die a little nit inside every day), while it may help me cope it'll be interesting to see whether it helps in the greater scheme of things. And there's one more speaker, who I'm waiting on a confirmation email from. All in all, should be a good evening though. 

So. Come along if you're in Auckland. Details are on the facebook page, and will shortly be up on the Auckland Nerdnite page

Rock on.

Friday, July 27, 2012


Every so often you get a story like this pop up. One of those, "that's a beautifully simple idea, why didn't I think of that" ideas. I don't mean the execution of it is simple, for a 17 year old coder, it's a significant achievement. the idea though is simple, elegant even. Neural network machine learning applied to cancer diagnosis. Superb idea.

Thursday, July 26, 2012

Courses to the left of them, courses to the right of them.

It's not brand spanking new, but for some reason over the past week, from about 5 different directions Coursera has appeared on my radar. It's a bunch of open courses run out of a collection of (some pretty good) universities in the states, Stanford, Duke, John Hopkins, the list goes on. I've been humming and hrring about these - is it worth the time that I would have to take away from other activities to do them. I am going to give it a go I think though, at least to see what I get out of 1 or 2 courses. A lot of the ones that I would have chosen have already started, so I ended up with a R course (data analysis) to brush up on a few things, Drugs and the brain because it sounds interesting and the Introductory Human Physiology, again, just because it sounds interesting. There's some interesting humanities courses there as well, though the ones that seem most interesting haven't got a scheduled date yet, so I'll leave them be for now - don't want to have too much on my plate.

I'll keep a track of how they go before offering a deifnite opinion. On the chance that they are good courses though, I would recommend the Introduction to Genetics and Evolution. Just becuase it's something I think everybody should at least know the basics of. If anyone does have a crack at it, I'd be interested to know what they think of it.

Wednesday, July 25, 2012

Not understanding. Really not understanding.

For the record, this is primarily about me not understanding something. A few days ago I commented on a post about Julian Assange of wikileaks fame. I haven't followed the case in detail so there may be some obscure legal reason, but as one of the other comments said, why is there a fear that Sweden will more readily extradite Assange to the US than the UK would. There's a much bigger history of extradition between the US and the UK.
So the general gist of the comments I made was that Assange should go back to Sweden to answer questions and if need be, stand trial. Good works in one field do not cancel out unrelated crimes. You don't (or shouldn't) let a child abuser off because they work tirelessly to feed the homeless.

I will admit that the QoT (the post's author) uses strong language and plenty of invective. Can put some people off I suppose, but it doesn't usually get in the way of the sense that she (mostly) talks. The tone of the comments had been polite I think. I would have thought that given it had been noted that the commenter's did not know why it was more likely that Sweden would extradite Assange than the UK, then it would have been an opportune time for someone to enlighten us as to the obscure point of law that we had been missing. Instead (and I'm putting this behind the jump because it's unpleasant) we got this massive, massive disconnect:

Tuesday, July 24, 2012

What exactly, is politics.

The two main ways of thinking about politics are that it is either what politicians do or it is the sum total of everyones actions. I find most people hold to the former view, politics is considered something that you stay vaguely aware of, and once every three years, you wander down to the polling booth and tick a box. I tend to have more sympathy with the later view, that actions of an individual, in as much as they require interactions with others, are political. What we buy, where we go, who we support, are all political actions. Even attempting to opt out of political action is in itself a political action - opting out hands more power to those who choose not to opt out. For most though, politics is the nasty, grubby interactions of politicians and bureaucrats, attempting to run our lives.

Ill Doctrine breaks this down superbly. Politics at it's core he says, is not just about the grubby self serving actions of politicians. It is about the systems and institutions that make it possible for millions of us to coexist, have food and get shelter. It follows from this, that we have that involves how we as a society gets along, should be accepted as a poltical conversation. When people (and bloggers) start railing at the lastest fiasco by a government department, that's politics. When we start ranting about the inanities of the justice system, it's a poltical rant. When we start pointing out the damage being done to our environment, it's a poltical discussion. Poltical discussions are ones that involve the systems and institutions that society uses to get along. Poltics at it's core, is not a bad thing, it's an ongoing discussion about how we live our lives and how we want our lives to be. Opting out, is not an option. Or at least, not a sensible one.

Friday, July 20, 2012

She turned me into a newt!

And while you're contemplating that Daiquiri that's only a few hours away, also contemplate this: researchers have now (in vitro) been able to coax HIV out of hiding so it can be eliminated.One of the big problems with HIV is that once it's in, it stays in. It settles down into the patients DNA and waits. There's no way for the immune system to get in, activate and excise the virus DNA and then attack it. Now, we've got scientist looking and succeeding in finding ways of reactivating selected bit of DNA.
This is not a cure. It's not even in clinical trials. It is absurdly cool though. So if you feel like a bit of optimisim as you head home for the day, think about what scientists are now capable of doing that we had no idea how to do 20 years ago, had no idea it was even possible 50 years ago and 200 years ago would have got someone accused of witchcraft.

Sort of right for a Friday.

Though sadly I won't be making one this evening - don't have the rum at the moment <sad face>. So there's this chap called Jeffery Morgenthaler. Amongst cocktail geeks he's a bit of a legend. I'm rather fond of him for a couple of reasons, though primarily because he can talk about cocktails without slipping over into the pretentiousness that can so easily afflict bartenders when they actually get to know their craft. Also, he writes well, though nowhere near often enough. He offers a snippet today on How to Not Fuck Up a Daiquiri. While this may not seem important to you, it is to me. I'm rather fond of the classics. Or rather the simplicity of the classics.Some of the flashy drinks with 8 different ingredients can be nice, don't get me wrong. It's hard to beat having just 2 or maybe 3 flavours that naturally fit together in the correct proportions to create pure loveliness.

A martini with all sorts of weird flavours in in is just as bad as the ones some idiots serve up with barely a whiff of vermouth in it. Daiquiri's are lovely lovely drinks - not the big things in a blender with lots of fruit (though I will admit I used to called that a frozen daiquiri), that should more accurately be called a icy/fruity/alcohol drink. Nice, but not a patch on the original daiquiri. 3 ingredients, a nice rum, some fresh lime and some simple syrup. <sighs wistfully>

Now go and spend your Friday working and occasionally stopping to think about having a daiquiri when you get home.

Wednesday, July 18, 2012

Morally superior food - in a word, ick.

I've always (or at least, for as long as I can remember) thought the whole "organic" movement to be a bit smug. Which wasn't to say that I didn't initially think it was a good idea. Just a bit to self satisfied for it's own good. I've no doubt the intent behind the movement is good, but when you get to the shop. especially at places like Harvest Wholefoods in Grey Lynn and Commonsense Organics in Wellington, the prices make it a bit exclusive. Which in turn, as Giovanni Tiso notes, is one of the things that risks turning it into a moral issue - a holier than thou thing.
Which is, I would have though, a bad thing. Surely if you're out to save the world then you want as many people to buy your supposedly good for the environment food as possible. I initially thought that the high price was due to the small amount of produce being grown. While supermarkets may have started getting in on the organic thing, with prices getting lower there for organic produce, it doesn't seem to have happened elsewhere. If anything the prices seem to have risen. The only message that I can see from that is "save the world, at a premium". And when large chunks of the population can't afford a premuim, you have a problem, becuase they are going to dominate the market place, thus preventing the saving of the world.Giovanni actually manages to draw a few threads together in this vien such that when you sit down and think about it, the expensive organic stores actually seem rather ... creepy.

My primary problem with the industry is the lack of distinction made between organic and sustainable. Sustainable is the one that is good for the environment (and hence, in the long term, us). Organic is not automatically sustainable, nor automatically good. When you start taking the social exclusion/moral superiority factors into account, the problems I have with the organics industry become somewhat excessive.

Monday, July 16, 2012

This, I have to applaud

It's a list of 100 education academics who have signed a letter against league tables. I should (but probably won't) do some digging, but I imagine that has to constitute a significant chunk of our academics who are working in education. It would be interesting to know how many of our education academics are pro-league tables.
This though, should give any politician cause to pause. They might not be perfect all the time, but at the very least you should listen to the experts, the people who dedicate lives to figuring out how things work rather than just steam rolling ahead with your own version of "common sense". Not that I expect that this will give anyone in the current government will take note. Or if they do it will be to write it off as a disgruntled minority.

The comments section is no place for a politics discussion.

It's obvious really. Every time one of my friends has said something boneheaded about politics on the book of face I've had to bite my tongue or risk having the comments thread turn into something horrendous and not easy to read. It works sometimes when there's only a few commenter's and it's a quick back and forth between them - pundit.co.nz is a good example of this. On the pages of the herald website though, every single time I read the comments (I don't do it often) the head suddenly feels an inexplicable need to find a hard surface with which to hit itself. From people declaring that attempts to initiate a referendum to negate the tenuous mandate the government insists it has is undemocratic (i.e. those collecting signatures are sore losers) on Matt McCarten's opinion piece. Or the commenters agreeing with Rodney that the ETS and climate change is a scam - it's bad enough that they're applauding the presence of an "alternative" view as if that actually validates it. Sigh.
note to self: stop reading the comments.

Saturday, July 14, 2012

Some guide lines. Good ones.

Someone I've never heard of before has posted what I think is a pretty good starting place, not just for telling the difference between science and pseudoscience, but in life in general. It provides a bunch of red flags which should immediately start you looking closer. The same sort of flags could apply for politics or business. When it sounds to good to be true, when it makes you smarter than people who have spent years looking at the topic, look more closely. And when there's sod all work backing the claims up, treat them with suspicion.

Thursday, July 12, 2012

No surprises there.

Speaking on Radio New Zealand last week, Steven Joyce, New Zealand's science and innovation minister, called scientists' concerns over data quality “juvenile”. He added that researchers should respect NIWA's ability to make its own staffing decisions.

This from an article in Nature reproting on the downsizing of staff and reduction in measurements at the Lauder atmospheric observatory in the South Island. A minsiter of science (sort of, the science part is fading into the background of the new super ministry that he's going to be in charge of) calling concerns regarding atmospheric measurments, voiced by people who spend their lives studying the atmosphere, "juvenile".  I would have hoped for at least a discussion of the rationale behind NIWA's decision, even a sound bite. Dismissing concerns as juvenile is ... depressing. Though not surprising.

Failure to comprehend.

This is an image that the Greens just shared. It illustrates perfectly to me, why I don't understand those people who claim to like driving and oppose public transport. In this case, not only public transport but putting money into intercity rail freight.

If those who like driving can get more people and more freight off the road, then surely that gives them a better driving experience. Especially since spending more on building yet bigger roads tends to lead to ... more people driving. If there is a sane/halfway logical retort to this argument, I'm yet to hear it.

Wednesday, July 11, 2012


I've not dropped to many hints on the blog (I think), or at least, not for a while, but I am a fan of beer. I wasn't particularly until I came back from England and Germany. I went from decidedly average NZ beer (Macs gold iirc) to drinking some superb ales in England and Lagers in Germany. I never really appreciated them though, until I got back to New Zealand and found there was .... nothing. A desolate wasteland of beer. Happily, things have changed. And while it's a tad more expensive, there are actually some good beers around these days. Though for some reason that I haven't quite figured yet, most of the good breweries tend to be clustered around Wellington or Otago.
We've got Hallertau up here in Auckland, but it's by no means common. The good breweries aren't making enough beer yet. And with the breweries all down the line, we run into some supply problems. Take Tuatara. Currently far and away my favorite New Zealand brewery. I had to start making trips to Wellington just to find out that they're making a superb belgian style called Ardennes. And since they ship to a distributor in Wellington with Auckland getting what's leftover after the Wellingtonians have had their fill, it requires special ordering to get it to Auckland. Their APA is a delight, but in Wellington, you can buy it buy the flagon. It's enough to make you spit. The frustration. <sigh> 

I see this :

And they have no idea if/when it will get to Auckland. It's just not fair.

Monday, July 9, 2012


No, I'm not making a correction (yet). I'd like to draw your attention to this though. The independent in the UK is reporting on the differences in educational results across various schools. The few studies they reference indicate that for a student from wealthy backgrounds, there is little difference in results between those who attend a private school and those who attended a state school. Or even that there is a small benefit to be gained from attending a state school.
I point this out, not to promote state schools over private (though the studies tend to indcate that the extra money the private sector soaks up is wasted). it does demonstrate however, the importance of correcting for as many factors as possible in your work to get at the core, the mechanisms by which the world works. As the author points out, one of the common percpetions is that the school makes a huge difference to educational results. And most people would go, yeah, that makes sense and leave it at that.

What correlates well with the better schools though? Wealth. So the better schools have access to more/better resources/teachers right? Well yes, but at this stage it's correlation only and confusing correlation with causation is an opportunity to visit a world opf statistical hurt. So you do what the authors of the OECD report did and compare children of similar backgrounds at different schools. That way you can tease out whether it is the extra resources that the school has access to or the childs background or the background of the actual child. In this case it looks likely that the background of the child is more important, so it makes more sense to fight against the poverty that children live in than to pump more money into schools (assuming it's an either or proposition). So ideally you'd get a government forming it's policies around important focal points (reducing poverty) with larger effects rather than those with lesser effects (charter schools, increaing class sizes).
What's important though, is that you've looked at that correlation, tested it for causation and corrected your view based on the data that comes back. And if the lesson has been leanrt, then the idea that it's the childs socio economic circumstances that are more important will also be tested.

Saturday, July 7, 2012

Twin absurdities

So I was pointed to John Roughans column in the herald this morning, by various people. A depressing read to say the least. It reminded me somewhat of Shane Jones weird-arsed (from my point of view) that we should be exploring mineral, oil and gas reserves and that we shouldn't be taken in by the greens rhetoric. Roughan on the other hand, suggests that science has "succumbed to environmental hubris" and because of that, no longer inspires.

Nature is what inspires, science is a tool with which we can see nature better. To dismiss what we see because it's unpleasant is dishonest. Which puts both of these opinions in the willfully ignorant or dishonest category.

If Jones and Roughan are aware of the damage that extraction and oil are doing to our environment, then we have dishonesty. It is in essence suggesting that whatever we do, the earth is big enough to handle it, . In one sense, this is correct. Though it completely ignores the question of whether we will survive alongside the earth or if we do, how difficult we will be making our descendants lives.

If they aren't aware of the damage that will result from their suggested course of action, then given the amount of evidence that suggests otherwise, you've got willful ignorance.
Either way Roughans column is so chock full of arrogance that it's just not funny. Remind me at some point, I'd like to expand on this one day.

I'd also note that I'm not against exploration for mineral wealth, provided it's not on schedule 4 land. It is technically possible to do it with a minimum of damage to the environment, it's not going to cause long term damage to the planet as a whole and we need it. Though my position is not set on this, I am interested in arguments against this position. Extracting carbon for fuel though is unnecessary and damaging.

Friday, July 6, 2012

An oddly quiet week.

I'll probably be proved wrong in a short number of minutes after I post this, but for a busy week, there's been very little that has moved me to write. Locally there's been a lot of discussion about education, there's been a murder trial with an unexpected (by some) result, which I didn't follow. And seriously, the speculation of "how he got away with it" from around the coffee table on Thursday was just ... painful. I signed up to twitter for a look. So far it looks like it good for following public conversations that other people are having.
Internationally, we got the discovery of the Higgs boson, which was just absurdly cool. It's not my field though, so while I think I have a working knowledge of what it means, it's not my place to try and explain it. There's enough bad reporting on the matter without me confusing things further.
And I've managed to confirm my first speaker for Nerdnite -Auckland

As I say, lots of stuff happening and little of it has actually moved me to write. Odd.

Wednesday, July 4, 2012

A thought - not an evil one.

One of the comments this opinion piece in the herald (the IT editor thinks that Apple is become a bit of a bully) got me thinking. Someone contrasted it with Google (sarcasticly I presume), with Google being the other all pervasive entity on the blocks these days. Especially ironic apparently given Google's tag line of don't be evil". Which got me asking is it possible to be all pervasive and not evil. Does access to that much data automatically make you evil? My initial reaction is no, not necessarily. For me, for Google to cross the evil line, they would have have to stop being able to admit they were wrong. Yes they've bollocked things up a few times, and not always admitted it. Still, they appear to be able to admit they're wrong. This doesn't make them the good guys, but I'm not so sure they've crossed the line into evil. T'would be interesting to hear what others think.

Tuesday, July 3, 2012

Arse backwards but facing the right way. Sort of.

The PM is apparently against a minimum price for alcohol. Which is good. Whilst he may be against it, he doesn't appear to know what it actually is though. And having an MP (let alone the PM) arguing against something that they're not able to identify, that is worrying. Or it would be worrying if one weren't quite so worried already.

And to make it even weirder (for me anyway) is the fact that I'm sort of in agreement with the anti-minimum price stance. Key's argument is that it would just get the poor drinking lower queality alcohol. This is the bit that's arse backwards by the way. A minimum price on alcohol would mean the price of the low quality, cheap alcohol would rise, while most probably meaning that the price of the higher quality alcohol's would stay the same.


The problem that occurs to me with a minimum price policy is that it will make no difference to those heavy drinkers who can already afford to drink. For those on lower incomes, alcohol is already a luxury and I suspect those heavy drinkers who would be put off by a price rise are probably already drinking less. Which leaves those on low incomes who aren't willing to give up their booze. Where does their money come from then? The power bill? The kids lunch money? I could be convinced otherwise with some hard data from actual studies, but straight off the bat, I'm not convinced that a minimum price policy is necessarily a good thing.

Monday, July 2, 2012

Freedom is a zero sum game.

I totally stole the title for this post. It was , I think, a throw away phrase in the middle of an argument putting forth the idea that there are two types of rich in the states - those who still labor under the code of conduct imparted by the idea of  noblesse oblige  - the idea that the rich owe something to the community from which they gathered their riches, and those for whom freedom is defined as the right to, as an individual, do whatever you damn well please. Up to and including beating the crap out of your slaves, servants, wives and children.
For the latter group, freedom is very obviously a zero sum game - that is for any freedom that the peasants gain, it removes a freedom that the rich currently have. Give a slave the freedom to walk safely down the street and you remove the freedom of the slave owner to beat the crap out of the slave at will.
For the former group, it's not quite so obvious, but it's still the case. It is reliant on the realization that if you operate as part of a community, you put limits on your own individual freedoms. Which (and this isn't a contradiction) leads to a free society, though one should note that this is not the same as totally subjugating oneself to a society - limits don't need to be all encompassing. That is, the society is free, self imposed limits on individual freedoms stops the society from becoming subject to the control of the few.

The argument is illustrated using two sets of elites in the states - with those currently in control of the Republicans being an example of those pursuing absolute individual freedom. While the scale of elite may be significantly smaller, the same attitudes exist here in New Zealand. Chris Trotter looks on, I suspect in horror or despair (though not surprise) as some of New Zealand's rich make the same arguments here - that the poor must not rely on help from the state and if that means that the poor must suffer, then so be it. Anna Stretton argues that strict limits must be placed on the assistance our society should offer to the poor, that there is a culture of entitlement amongst the poor that must be eradicated. This is the end result of idolizing the absolute freedom of the individual. Eradicating a supposed culture of entitlement without regard for the consequences is reduces a societies ability to care for it's own and it skews the distribution of freedoms within a society towards those who have the resources to take care of them selves. Freedom becomes unequally distributed.

And what you get is this. Societies where no matter how hard those trying to get ahead struggle, they just can't get started. Things are there yet. but when they get bad enough, those at the bottom tear it up and try and rebuild or slip away and set up their own, new one. Those insisting on the absolute freedom of the individual are time and time again, either brought low or left behind. Which is not surprising, we're social animals.

In the end, the absolute freedom of the individual is only achievable by one person at a time.