Friday, December 21, 2012

Required reading.

Got a few minutes to spare? Read this piece from Brian Cox and Robin Ince.



Just that. Carry on.

Wednesday, December 19, 2012

An optimistic view

One that, I imagine, Steven Pinker would approve of. Whilst civilization is not exactly crumbling, it does seem, sometimes, that things are at least a little bit grim. And if I'm talking specifically about what I want to be doing with my life in the next 5-10 years, then yeah, things aren't the best. Which tends to bring the mood down.

It's all relative though. I start off from a very lucky place. Very. Lucky. All the doom and gloom that I read about every day is only doom and gloom compared to the bright and shiny places that I want life to go. When you raise your eyes from your own life to the rest of the world though, things aren't necessarily so bad.   There's even a reasonable chance that things are pretty good. Which is not to say that things are perfect. The Spectator's editorial notes that world wide, poverty is decreasing, but it was at a fairly horrific starting point, so there's still a long way to go.

There's some pretty serious diseases that we're making inroads against, malaria for one. Death rates for some fairly serious cancers are down. The number of deaths attributed to war over the last decade has been the lowest for quite some time. The world is far from a perfect place and we have a lot of work to do. there's a case to made for saying we're making some progress though.

Monday, December 17, 2012

Still small. Very small.

It's nice to be reminded that we're quite small in scheme of things, even when we're talking on the relatively small scale of our planet.

The Hurricane Research Division of the US National Oceanic and Atmospheric Administration (their version of our NIWA)  actually has a dedicated page spelling out why exploding a nuclear bomb in the eye of hurricane so as to stop it wouldn't work. Though I'm having a hard enough time entertaining the notion that this is a sufficiently frequently asked question so as to warrant a dedicated page. The short of it being that we don't have a nuke anywhere where capable of even disturbing a hurricane - the total mechanical energy generated by the human race might have a shot at disturbing a single hurricane if it wasn't to big.  In other words, compared to nature, we are still, very, very small.

Apart from it not working it ignores the whole it being a terrible idea in the first place thing - large amounts of radioactive waste anyone?

One of the lines that is often trotted out with regards to climate change is that we're killing the planet. This I think, is a reminder that we're not killing the planet, the planet will tick along quite nicely without us. We're just stacking the deck against ourselves.

Wednesday, December 12, 2012

A balancing act.

There's been a series of posts about housing, employment and liveability the Auckland Transport Blog recently that have made interesting reading. If for no other reason than that it demonstrates the problems that the much maligned planners of Auckland City are trying to deal with.

The intensification of employment in certain areas in other cities appears to be a key driver of economic growth - a good argument is made for this. In our case, intensification is happening in several places, most notably the CBD. We're going to have problems getting everyone to work pretty soon if we want to grow it though. So transport has to be incorporated into the equation. There's two ends of any journey which brings housing into the equation. The council gets bagged regularly - often it deserves it, but I do think it's an incredibly hard job, balancing just those three facets of the community.

And I have to say that it's thoroughly refreshing to see commentators not treating Aucklanders (and New Zealanders as one amorphous mass - note the warnings against generalizations in the housing posts where it is noted that not all  New Zealanders want to buy a house.

Wednesday, December 5, 2012

A bright and shiny place.

Sure, an actual colony on Mars is still many years away, but quite frankly, I love the fact that someone is thinking about it. Elon Musk of the Tesla Motors and Space X appears to be seriously thinking about how we go about landing a sizable, permanent colony on mars and how much it going to cost.

And it is going to cost a lot. Once everything is establish and the initial costs have been taken care of, he reckons it'll get down to about half a million dollars per person. Still, it's something that I don't think we've had, as a species for a while now - something to look forward to or aspire to. It's a bright and shiny future in the making. I think the last time we had that was probably when the space race was at it's height, when massive efforts were being made to send people to the moon.

The one criticism I've heard of this was that we should shouldn't be spending so much money on something like this when there are so many problems here at the moment. I don't hold with this for a number of reasons. Fixing the problems here on Earth or going to Mars is not an either/or proposition. And if you think we shouldn't go anywhere until everything is fixed on earth, then we'll never go anywhere. There's always going to be another set of problems somewhere.
And to top it off, the benefits that will accrue from what we learn and the investments that will have to be made will, I think, outweigh the cost and provide benefits for everyone.

Either way, it's part of a bright and shiny future that I want to happen. So it makes me happy to know someone is getting on with it.

Monday, December 3, 2012

Tired but optimistic.

It's been a hellish couple of weeks. By which I mean very, very busy. Long days at work, extra shifts at the 2nd job, a party to organize, tomorrows nerdnite to organize (it's all about beer), a new flatmate to find, a landlord to coral, shipping my RNA samples to Korea for sequencing, that sort of thing. Mostly self inflicted I'll admit, but hellish nonetheless.

So it was nice to walk into the office this morning, glance over the news feed and almost immediately spot three pieces that made me feel all relaxed and optimistic about the world. It won't last and they're all quite different so I'm going to drag them out over the week.

I had an English flatmate once, odd girl. She was doing biology at university, which is a fairly diverse school. We found out sometime after she moved in that she really couldn't stand "all those asians taking the good marks". In other words, racist. Very, very racist. I find racism an odd thing at the best of times. Most of the time, apart from it being unbelievably stupid in the first place, I just don't see how people who are racist operate in the world today. Even more so, given it's very international nature, scientists.
I continue to hope that with the drive that I believe most scientists share (finding shit out is awesome, in the original sense of the word, i.e. awe inspiring) that differences in race or gender and the like wouldn't actually matter - only the finding stuff out would matter. It's not always the case, science is done by human beings and as I'm sure you're aware, much has been said on the nature of human beings being perfect.

Sometimes however, humans are good. Sesame is a project that is being put together in Jordan in the middle east. It has scientists from all over the region, from Turkey, Pakistan, Bahrain, Egypt, Iran and Israel. There's a whole bunch of countries of countries in there that have a fairly significant history of hating the crap out of each other. And here's a bunch of them sitting in the same room, not worrying about where they all came from and getting busy finding stuff out.

Provisional warm fuzzies for the day everyone.

Thursday, November 29, 2012

Now this worries me

Has anyone else noticed the change in the background noise of climate change chatter the past few weeks? The prevailing undertone that I've noticed over the past few months is that restricting the change in temperature to 2 degrees is no longer an option.
The past couple of weeks though, the narrative has changed. Now it's we have to prepare for a change of 4 degrees celsius. Which is going to require adaptation. Major adaption. And given the records of various governments around the world in tackling climate change so far, I don't have the same amount of faith that the world bank has in our worlds leadership.
4 degrees looks like its going to be pretty awful. Any thing over that, I'm seriously not looking forward to.

Friday, November 23, 2012

Something to read.

I was listening to the Guardians weekly science podcast last night, they were discussing the Royal Society science book prize short list candidates. Six books, all of which I'd like to have a crack at but for one reason or another (time/money) I'm probably not going to get to. Of the six though, The Information by one James Gleick sounded the most interesting. Alok Jha, the chap who does the podcasts offers a review here.

It reminds me of the History of Computing paper I did way back when I was doing my Comp Sci masters, before I switched to biology. It a spectacularly interesting paper run by a curmudgeonly old chap by the name of Gary Tee. One of those papers that it was sometimes difficult to pay attention in class, but as soon as you walk out, you realize that you've just had another hours worth of really interesting pieces of history dumped in your brain.

The paper started, if I recall correctly, with the revolution of cutting a reed at an angle so as to allow an Abyssinian scribe to easily make either a dot or a dash on the wet clay tablets they were recording production on. And moved steadily through to the code breakers at Bletchly Park in world war II. In other words, it covered a huge amount of ground. I seriously might have to make the effort and track down a copy of The Information.

Wednesday, November 21, 2012

An odd thing.

Writing is an odd thing. I don't dislike it. When you get on a roll for a couple of hours it can be quite rewarding. It's hard though or rather, consuming. I have been finding that trying to write one thing, in this case, the literature review for my PhD's provisional year reports tends to make a lot of everything else fall by the wayside.

The whole Labour leadership debacle? Can't be arsed. Something interesting come through the science feeds, can't be bothered. Even the news that the Mars exploration teams at NASA have big news coming up in the next week or so barely raised any idle speculation from me. Which is annoying, I recall rather liking being interested by the many and varied things that float past me of an afternoon.

It's least rewarding though, would have to be spending an afternoon sitting, looking at what you've written and not having the foggiest where to start editing.

Tuesday, November 20, 2012

The Monkey Cage is back!

And it's still infinite. I speak of course of the Infinite Monkey Cage, a half hour show on the BBC's radio 4. Also, fortunately available as a podcast. Brian Cox you should all know as latest in the line of English science stars presents it with a comedian by the name of Robert Ince. Ince, if you haven't heard him before is, in my (very humble) opinion on of the best comedian's the English have at the moment. Alongside Dara O'Brian, Josie Long and Mark Watson of course.

As an aside, has anyone else noticed that the famous scientist meme is something that the English do quite well - there is always someone in the public eye, someone like David Attenborough or Patrick Moore, all the way back to Robert Boyle.

The Infinite Monkey Cage is a superb half hours distraction, where the occasionally have a crack at the big questions - Art vs Science for example (hint: Science wins, he said with a grin) but more often it's a light hearted ramble through a variety of the interesting aspects of the worlds that scientists immerse themselves in.

Listen to it. All of them if you haven't already.

Tuesday, November 13, 2012

A reference post.

A month or two ago, there was a study of rats feed GE corn in France. It was widely criticised at the time. Recently it's started being referenced in scary pictures the flick through my book of face feed, upon which I commented. In the comments I was asked to elaborate on my position that a seriously flawed study, which I'm going to do there, because facebook comments are an annoying place to try and lay out something like this. So apologies to those of you for whom this is a rehash.

The study was touted as being a long term (2 year) study as opposed to the more common 90 day test. On the face of it, this sounds like a good thing and it could very well have been. If you were going to do a long term study and report on the incidence of tumours though, I would suggest not using a strain of rats (Sprague-Dawley rats, a particular strain of lab rat) that are highly prone to get tumours after 2 years anyway - that's living a life without being experimented on. Something that has been known about for many, many years.

On top of that the number of rats used in each group was woefully small - 10 rats in each group. This brings a large amount of statistical variability into play. The paper linked to in the last paragraph gave 86%  chance of tumour development for males and 72% for females - without treatment of any kind. If you take 10 rats from a population, getting the results that Seralini did due to chance alone is very very high. To be able to say that any deaths/tumours were the result of the rats diet of GM and GM+roundup corn they would have had to have much, much larger numbers of rats per sample, somewhere north of 60. The best discussion of why the Seralini paper was statistically rubbish, is from Andrew Kniss at weed control freaks. For a detailed discussion of the myriad of other problems with the study, Emily Willingham has a pretty good overview.

The picture the started all this off was using a Russian ban of GM corn as an exemplar. I opined that the ban was political and not based on the science. This I may very well be wrong about. The paper was widely and rightly criticized before the Russian ban though, anyone making a decision based on it's results, especially at the international trade level would have been being disingenuous at best. Which leads me to believe that there was a political or economic motive being it, with the study being used as an excuse.

I've said it before and I'll say it again. GE is not inherently bad. It's a tool to be used when and where appropriate. I've got no problem with people having problems with Monsanto's business practices but Monsanto is not GE and GE is not Monsanto. GE can be used to prevent dietary deficiencies, create drought resistant crops or possibly one day provide sustainable fuels and plastics. Sure we should study the effects GE food has on people, just as much as we should study the effects that non-GE food has on us. The Seralini study was seriously not the way to do it though.

And that's without mentioning the unethical abuse of journalists and press embargoes used to hype the paper to the mainstream press.

Friday, November 9, 2012

Generating trust.

A few weeks ago the Ministry of Social Development story broke - there were kiosks in the Work and Income offices that were open to the public, connected to the departments servers effectively allowing anyone to walk in off the street and access sensitive information that was being held on citizens currently using the service. It was all fairly horrendous.

At some point Ira Bailey got a bit of criticism for attempting blackmail Winz. Brendon Boyle, the head head of MSD said "Mr Bailey had asked for cash in order to tell the Ministry where the problem was.", an idea reiterated by John Key. From where I was sitting it was sounding very much like an attempt to cast Bailey as a criminal.

There are people who do this for a living though. It's not an uncommon practice for companies to pay individuals a bounty for bugs. And there's evidence to suggest that it's a practice that's paying dividends - there are a limited number of bugs in a given product and Google is finding fewer and fewer. Every time one is reported, it is fixed, and the end product becomes more secure. Rather than vilify those who find weaknesses in their systems Google has recognized the value of the time people have invested in finding bugs and have used them to make it's product better. It's a good deal I think, certainly something that would make me more inclined to use and trust their products over a similar product that doesn't have such a scheme attached.

Thursday, November 8, 2012

Life is ... not bad.

There are some who would take that as a pessimistic statement. It is sincerely not. There is something quite nice, almost relaxing about sitting down with your workmates at 1 in the morning in a bar after a 7 hour shift with a beer and a whisky.
This is after having the best of the Nerdnite's so far yesterday evening, a moderately productive day at work despite an hour or two spent clicking refresh on the American elections results (waves fist angrily at Florida for being so bloody contrary). And the knowledge that I don't have to get up first thing tomorrow, that I can head out to my weekly coffee tasting before getting to spend another day doing some solid science (as well as some writing - it's not all fun and games) and a games evening with the lads tomorrow to look forward to.

My life is not perfect. Compared with many though, I have no cause to complain. And sitting down at the end of a good night behind the bar with a beer and a whisky - puts life into perspective. Mine is most definitely  not a bad one.

Tuesday, November 6, 2012

Nerdnite Auckland - Chapter 3.

I've been quiet here for the past couple of days. Trying to organise Auckland's 3rd Nerdnite and not be completely frazzled by the time we kick off. Fingers crossed it'll work this time. We've got speakers talking about the relationship between the size and shape of birds, why we should treat conspiracy theories more seriously than we currently do (I'll report back on this one) and lasers.

Seriously, who doesn't love lasers?

Doors open at 6:30pm at Nectar in Kingsland for anyone who feels like sitting back with a beer and listening to something interesting for an evening.

Tally ho. 

Thursday, November 1, 2012

Weasel words if ever I saw them.

New legislation will require companies making health claims for their products to provide scientific proof to back their claim. Brilliant. Continue reading ... " or traditional evidence to back their claims". What exactly is traditional evidence. Evidence of a health claim, not backed up by science is not evidence. It's story telling.

Wednesday, October 31, 2012

Beer yes, IPA? no not really.

This lunchtime I had occasion to try one of Monteith's "Brewers Series". Which I presume is Monteith's attempt at trying to appeal to the surging craft beer market. I can't pass an opinion on the porter, the wheat beer or the ginger beer. If the IPA is anything to go by, they won't really be worth bothering with.

"There’s plenty of rich maltiness from this Pale Ale and higher-kilned malt combination. The Cascade and special New Zealand hops create a fruity aroma with a dose of bitterness to drive home the hop flavour. A beer for the IPA aficionado with a distinctly Kiwi style. Perfect for a moment spent catching up with old mates."

Rich maltiness? More ... lemonadey I would have said. It's Monteith's original with a few extra hops chucked in. "Special New Zealand hops". Which ones? One of the things I suspect Monteith's doesn't get about the craft beer market is that those who take an interest in their beer, take an interest in their beer. Bland marketing blurbs do not help inform the drinker. I suppose you could describe it as hoppy. If your normal beer is the urinary extract of Mustelinae Mustela. It's not as if the big breweries can't do good beer. The Macs seasonal ranges are by and large, good and even their day to day range has some good beers, namely Hop Rocker and the Sassy Red.

It's drinkable, I'll give it that. It's not horrible. With so much other good beer coming out locally though, I don't see why you would bother drinking this. It demonstrates a complete lack of understanding of craft beer and as such, is but a pale imitation. 3/10 for the beer, 1/10 for effort.

And alcohol sites insisting on entering a birth-date? Please, it's insulting.

Tuesday, October 30, 2012

Nerdnite and stuff.

I've now got the talk titles and summaries in for the next Auckland Nerdnite. There's a talk on why birds aren't any bigger than they are. One on conspiracy theories and why we should take them seriously - not the actual theories but the existence of the theories (and theorists). And one on lasers. Should hopefully, with the lessons I've learnt over the past couple of sessions, be good (seriously, who doesn't like lasers).

 It's also Open Access Week, promoting open access in scholarship. When research is published in open access journals, for those that don't know, it is freely accessible to the public. This is view by many (including me) as a sensible thing. Not only because in many cases it's the public that pays for a lot of the research in the end, but because it makes it easier for researchers to get to and build upon others work.

When Siouxsie Wiles was talking about it recently, she was asked what her role was. it got her thinking about her role in communicating science to the public. After all, having research available to those of the public who are interested is part of the battle. That doesn't necessarily make it comprehensible, thus the suggestion of adding an easily understandable summary of the main findings of papers. Something which I think also has potential. The dense language that scientists use in many papers can be (and is) used badly by many, but it can also be a method of condensing work down to make it more easily communicable to others in the same field. A step back from that in a summary would probably be a good thing both for inter-disciplinary communication and communication with the world at large.

I popped up with my standard question, which I'm almost sick of me asking. That being how do you engage with the adult population who don't really care? And I'm beginning to think there isn't really an answer. The best we can do I suspect, is tell people about the science and why it's absurdly cool. Hopefully some of those people will end up talking to those who aren't engaged and getting them enthused. Or at least curious. Which is partly what I hope nerdnite will do. It's preaching to the choir with the hope that the choir will do the work.

There's a distinct lack of initiatives that reach out to those who don't particularly care about what science is doing. And I can't go and talk to them all, so I talk to those who want to listen and hope they talk to others. It all I've got. And besides, as David Winter says, he “doesn’t quite understand how anyone can do science without wanting to tell the world about it ”. 

Thursday, October 25, 2012

Shouldn't it though?

This "will have 'serious ramifications' for employers"

I see this trope relatively often. In this case, the supreme court in England has ruled that it has jurisdiction and will hear cases related to equal pay compensation claims for up to six years prior to the commencement of the case as opposed to the current six month time limit. And there's a bunch of people muttering about how this has serious implications for employers as if this is obviously a bad thing. Well, yes, it has serious implications for employers who have been screwing their workers. I'm firmly of the opinion that there should be serious implications for employers like that though. Employers acting in a fair and reasonable manner aren't going to have a problem.

The other place this pops up quite often is in conversations about minimum wage. An increase in minimum wage "will have serious implications for employers". If the minimum wage is not sufficient to live on, then employers who only pay the minimum wage are screwing their employees and there damn well should be some serious implications. It's not as if those paying the lowest possible wages actually value their staff, as Chris Rock once said : "Do you know what your boss is telling you when he pays you the minimum wage? He's telling you, 'I would pay you less, but I can't.'".

Wednesday, October 24, 2012

GE for sustainability.

Late last week there we had the reports of engineered algae possibly being used to produce the ethylene for plastic - something that would reduce our dependence on fossil fuel sources. Well here's another use of genetic engineering that could help us with that.

Vast swathes of corn are grown in the US for use in the production of biofuel. One of the problems with this is that parts of the plant that we currently use for producing fuel is the bit with easily accessible sugars for the yeasts that produce the food. This is otherwise known as the edible bit. The rest of the plant, the stalks, the foliage are wasted. The stalks and foliage of the plants contain to much cellulose, a component of the cell walls, made of sugar, that is incredibly hard to break down. As a result there's a lot of arable land being used for fuel production that could otherwise be being used for food production - something we're going to need a lot more of in the coming decades.

A group in Massachusetts has engineered corn so that the enzyme to break down the cellulose is already inside the cell where it can get easy access to the cellulose. On the face of it, it's a silly thing to do, if you have an enzyme in the plant cells that break down cell walls, there will be enzymes inside the cells, crippling the plant as it tries to grow. Which is where they get clever. When the plant is growing, the enzyme is produced in an inactive state. They've inserted a protein sequence called an intein that that excises itself out of a larger protein, specifically one that only works at high temperatures. The plant grows normally, you harvest the edible bits for food and ship the rest off to the fuel processing plant where it is heated, the intein activates, cut's itself out of the enzyme which then goes to work on the cellulose in the cell walls, breaking it down and freeing up all the sugar for the yeasts.

And you get the same benefit that you get with the ethylene producing bacteria, you're not introducing any new carbon into the atmosphere. It's not production ready and even when it is there a number of other factors to consider when trying to make farming more sustainable, but it's an ideal example of how GE technology can help.

Unless of course you consider GE is to be inherently evil.

Tuesday, October 23, 2012

Go directly to jail.

Well, not quite directly. In 2009 on the 6th of April, after a series minor quakes and a shock of 4.1 on the 30th of March,  there was an earthquake in Italy. People died. In this case though there had been a meeting of the Italian National Commission for the Forecast and Prevention of Major Risks. The commission included several geophysicists. In the meeting there had been disagreement amongst the scientists, some thought that the minor shocks might have relieved tension and that no more shocks would be forthcoming. Some disagreed. The conclusion "was anything but reassuring"

A press conference was held ostensibly to report the commissions findings, though in fact to counter the publics unease  being caused by predictions being generated using an unreliable and unproven technique. The press conference reported that the "seismic situation in L'Aquila was certainly normal" and that there was "no danger".

Saying there is was no danger is the only point that I would find fault with the commission. If they had said "no danger other than what there normally is" I don't think I'd have any problems with their press conference. It doesn't follow though that the scientists who concluded that "It is unlikely that an earthquake like the one in 1703 could occur in the short term, but the possibility cannot be totally excluded"* should then be held accountable for the deaths caused by people not leaving their homes (supposedly because they were comforted and reassured by the commission).

I've been told that the idea that these scientists are being prosecuted because they didn't predict the earthquake on the 6th of April is stupid. It's not. The people who are finding fault with the commissions public statements acknowledge that the scientists cannot predict earthquakes. "People aren't stupid," he says. "They know we can't predict earthquakes." [1].

So when a commission comes out and says that there is no danger, i.e. that there is no chance of an earthquake then the only sensible interpretation is that there is no danger over and above the normal danger. Yes, the commission could have spelt it out better. To throw your normal precautions to the wind after a lifetime living in the area, because of the commissions statements is an abrogation of responsibility. It requires the assumption that the geophysicists are now capable of forecasting when there isn't going to be an earthquake. Which is the same thing as predicting when they will strike as well. On the assumption that people aren't stupid, if they know that the geophysicists can't predict quakes then the whole argument falls apart.

Which leaves the only reasonable interpretation that I can see being one big blame game that isn't going to help anyone. It might even end up hurting people in the long run by reducing scientists willingness to engage in public assessment of risk.

[1] John Mutter seismologist at Columbia University's Lamont-Doherty Earth Observatory, who declined to sign the open letter circulated to support the Italian scientists.

Friday, October 19, 2012

Convenience and sustainability.

From the cool file. Plastic is evil right? All those fossil fuels being dug up and used to pollute and kill birds and cute little baby seals? Pity it can be such a convenient material.
How about, instead of digging up all that oil and using it to make plastic, we engineer some bacteria  to produce ethylene and use that to make all our plastics?

The problem with using oil to get the ethylene for plastics, apart from the general littering and it's knock on effects on the environment, is that we are reintroducing a lot of extra carbon into the atmosphere that would otherwise be locked up underground. Which is where it should be if we want our children to live in a world that vaguely resembles the one we have. Using GE bacteria to produce plastics doesn't involve the introduction of any more carbon into the cycle - it both takes up carbon from the cycle and means that we would have to use less of the liquefied dead dinosaurs than we currently do.

And as they rightly point out, there are solutions (probably not perfect - very few things are). We can dispose of the plastics by feeding it to the mushrooms that eat plastic. A bit of tinkering and we can probably make those work even better as well. Convenience and sustainability all in one nice little package. Unless of course the GE is to inherently evil for you.

Tuesday, October 16, 2012

Well that's just ....

I'm not sure how to sum all this up. Farce possibly?
The source of the MSD vulnerability turns out to be Ira Bailey. Source has previously been arrested on terrorism charges.
Keith Ng releases information on said vulnerability exposing gaping hole in MSD's security.
New Zealand National Cyber Security Council is strangely ... quiet.
New Zealand National Cyber Security Coulncil turns out to be part of the GCSB.
GCSB part of the bollocks, over the top raid on Kim Dotcom, a raid which was more suited to taking down an actual terrorist.
Dotcom upon whom the GCSB was eavesdropping had made donations to John Banks.
Current PM refused to read police report that incriminates Banks.
GCSB which PM is responsible for, fails to communicate said PM.


*update: Read Scott Yorke's assessment, he says it much more eloquently than I.

Monday, October 15, 2012

Support vs replace.

I have this picture in my head, of economists of yesteryear, jealous or envious or lacking confidence in their craft or ... something. Eager to bring their craft to the fore they formulated their theories of markets and insisted that everything was market driven. It's wildly inaccurate yes, I know there have been plenty of economists who haven't invested their all in the supremacy of the market. It amuses me though. It's either that or be horribly depressed. And given the continuing move towards a commercial footing of our universities (CEO salaries for vice chancellors etc) it's definitely one or the other. The longer you think about it, the more it's the latter.

Just as the physicists who insist that everything is reducible to a physics problem*, you get economists who insist that everything is reducible to a market. They're both wrong of course.
Markets as we know them are not the creators and inventors of all we see around us. Sometimes they will create something new but for the most part they draw on the knowledge that science has uncovered, the structures that mathematics have discovered. New things are created by people who are interested in how things work, who are interested in tinkering and making things better. Markets are valuable yes, they are tools that can be used to bring the fruits of science to the general population. It a balance though. If you suborn education and research to markets then the markets will lose the pool of innovation that they currently draw on.

Take computers for instance. It wasn't the market that created computers. It was people who were trying to figure out how to compute gunnery tables or break codes. Even the personal computer wasn't created by market forces. It was created by a bunch of geeks in garages who wanted to be able to tell machines what to do. Markets enabled the personal computer to grow, yes, but the seed didn't come from the market. Markets aren't everything, they're a tool, something that should be used to boost and support education, not replace it.

*Some things might be reducible to a physics problem if you had a sufficiently big computer, but the computers big enough for the biggest problems are quite frankly, impossible to build.

Sunday, October 14, 2012

The end of a beer

Or at least I hope so. On Friday afternoon I was rather taken with the #momentsofmanhood tag on twitter. It accompanied tweets which were taking the piss out of the prospectus issued by Moa  beer last week. And quite frankly, it deserved it. The IPO/prospectus that it, the beer, when I've drunk it in the past has been good. Overpriced, but good.

The most obvious failing was the complete dismissal of women. As potential investors, as part of the beer drinking community*, as people really. That's bad enough on it's own, something that is enough to make me object to the whole venture on its own. The subtext that I'm going to personally take offence at though is the idea that it's built around the presumption that I, as a guy, am going to think this bleak dismissal of women is something that I would support. Moments of manhood my arse. If there's anything antithetical to my conception of manhood, it's the empty-ness and isolation that things like this embody.  For the record, Hayden Green's piece on this is well worth reading. Even better is Emma Hart's piece (short version - even if the were going for a dom/sub vibe with the silly human ash tray stands, they fucked it up).

This is pretty much a straw that breaks the proverbial camels back. I love the rising craft beer scene in New Zealand and I will continue to support it. I'll drink Heineken or Beck's when  it's free, they lack flavor. They are inoffensive. At best. Steinlager and Stella, not my cup of tea, I don't actually like the taste all that much. I really don'y like Moa's taste in advertising, so I don't think I'll be drinking it again. Even if it's free.

Monday, October 8, 2012

A question.

Very very quiet on the blogging front at the moment. You may have noticed if you're the sort of person who pays attention to that sort of thing. Thing is I've been writing for the past week, My literature review is due in in a few weeks time and it's time to massage that horrendous lump of text that I've been accumulating over the past year into a coherent whole. And to tell the truth, I'd forgotten how consuming writing can be. It's hard, yes, but the ability to get any enthusiasm up about anything else is, well, severely impaired.

So I'm farming my other thinking patterns out to the void. There's a festival of sorts that I'm attending in January, goes by the name of Kiwiburn. A New Zealand version of burning man, only it's in a paddock rather than in the desert. Every year Kiwiburn has a them and this year, since It's the tenth anniversary the theme is "EnlighTENment". Get it? Ten. Subtle isn't it? There's a fairly strong hippie contingent at Kiwiburn and I suspect most people attending will think of this theme in the "spiritual" vein.
I got to thinking though. The age of Enlightenment. The birth of the age of reason, the advancement of society through the use of science. It would be nice to do something to showcase that side of enlightenment. I don't know how to go about it though, the only idea I have so far would be to construct a Foucault pendulum of the power pylon that's on site. And while that would be cool, I don't really see me being able to get permission from Transpower to be able to do it. Myself and a few others are already planning on cutting a mini in half and fitting it out as a mini bar, but I don't really see that as showcasing the ideals of the enlightenment. Any other ideas?

Wednesday, October 3, 2012

Lessons learned (work in progress)

The 2nd Auckland nerdnite happened last night. About the same number of people turned up though it felt like slightly fewer to me. I suspect that was because the seating was actually organised this time as opposed to being a hodge podge of seats and tables jammed in at the last minute like last time. 

I don't think it went as smoothly as the first either. Our first speaker was late, so I delayed the beginning rather than immediately swapping the 2nd speaker for the 1st. In the end it was getting to late so I did in the end, swap them. I really should have done it sooner. The delay ended up making the whole night go to late, which meant that there was a number of people who had to duck out before the 3rd speaker got completely underway - they missed a good talk.

The sound system really needs sorting out. The mikes worked fine when we tested them before hand but kept cutting out during questions and the like. The only solution I can figure for that is to work up a little set of guidelines for the speakers that includes getting them to repeat the questions. 

And I really have to work on my introductions I think. 

Monday, October 1, 2012

An example.

I don't believe for a minute that it will be taken as such, but the debacle around the release of the so called national standards data (NSD) for our schools provides an illustrative example of how science works. Granted, it's not usually carried out in such a public forum but I think it's a fair example. With one major exception.

ScienceNational Standards
-ExperimentSurvey/data collection
-Peer review to ensure coherence
-Publish Publish
-Work is attacked by the scientific communityWork attacked by people who know basic statistics
-Work becomes valued and retained or is found lacking and is forgottenWork is found lacking

Ideally your experimental design gets thrashed about before you start. The NSD equivalent would have been the government listening to the people who study education.  Peer review would have been equivalent to getting some statisticians to curate the data and verify what conclusions can and cannot be drawn from the data. I've argued before that peer review is a basic hurdle, not definitive of good science. Over the years there's been a fair amount of work that's got past the peer review process that really shouldn't have. Wakefields paper linking the MMR vaccine and autism for one. More recently the appalling rats feeding on GMOs out of France. Without that basic coherence check we would have chaos.

Which is amply demonstrated by the current reporting of the NSD. The data is currently being disassembled by a number of people who know their statistics. Result: there's precious little information in there and it does an okay-ish job of reporting something that we already knew, that there is a correlation between poor performance and decile.

The difference being that the chances of the NSD being quietly forgotten and not acted upon is small.

Friday, September 28, 2012

Nerdnite - Chapter 2.

For those who don't already know via other channels, the 2nd Auckland Nerdnite is happening next Tuesday at Nectar in Kingsland. I'm heading in on the weekend to make sure the projector and the sound are working - the projector especially, we don't want it to be all fuzzy like last time.

Our three speakers are Daniel Hurley, talking on the history of tango (the dance), Steven Galbraith, talking about some of the fun things you can do with cryptography and one Brendon Moyle talking about black markets, poachers of endangered wildlife and economics. All of which I'm very happy about. Come along if you can, feel free to bring friends who might be interested.

Tally ho.


One of the things that's fairly central to my PhD is the extraction of RNA. For most biologists, not a particularly complex task. Having been primarily a computational biologist in recent years, I find it's actually quite a lot of fun pottering around in the lab, learning a new process. Even now a couple of months after learning the process, I find there is always a moment of looking at the falcon tube in a concerned manner because there is nothing there when you rather hoped there would be something.

And a few hours later, there of moment of quiet, smug satisfaction when out of the centrifuge come a nice set of pellets in the bottom of the eppendorf tubes.

Tuesday, September 25, 2012

Open source science - equipment.

Oh for the time and money. I'm not sure if that I actually want to have a lab at home (I'm pretty sure I do) or if I just want to spend time putting together the various gadgets. Sadly it all costs money that isn't currently available on a PhD students stipend. At the very least it would be nice to see the labs here start to take an interest - the cost of some of the equipment in our labs is horrendous. And we don't even have the latest or flashiest machines that go ping.The prices of some pieces of machinery are justified, they are high complex and need to be incredibly accurate. As precision and available materials for 3d printing gets better it would be nice to see some of the cheaper pieces, less complex pieces of machinery being maintained in house.

The kickstarter project that is building home spectrometry kits is fully funded, which is a good thing to see. I would still urge you to got and support it if you are able, the more we see of people creating the basic equipment from readily available technology the less money we will have to spend on equipment and the more money we have to spend on scientists doing science.

Monday, September 24, 2012

Surprisingly relevant

The big news in blogland today, locally at least, has been the release of the so called National Standards data. I say so called because as best I can tell, they are not actually standardized.

The National Standards data (NSD) are problematic. There's a number of problems with presenting the NSD in the form that have been. For a start they don't actually say anything. An attempt was made to justify the release, claiming that it wasn't about selling paper. Journalists claim to have released the data to drive discussion on National Standards. This defence is weak at best, on one hand claiming that no measure of quality can be extracted from the data released : "Anyone who read the National Standards results as a proxy for quality would be quite foolish". Four paragraphs later they declare that they there are problems with National Standards: "If there are problems with the National Standards - and it's pretty clear that there are". How they reach this conclusion with no data regarding the quality of National Standards is a mystery. I can only surmise that the journalists who did this are either ignorant of what the job of a journalist actually is or that they are incompetent. Publishing data like this with no attempt to interpret it reduces journalism to stenography.

There are two very large problems with releasing data like this. The first is that it can be very easily be used to support unjustified claims. This sort of behaviour has been well demonstrated today with the herald reporting larger class sizes produce better educational results. A claim that just does not stand up. The second problem is that most people are going to trust what the herald and say. Some of us will look closer and understand that the claims put forth by employees of the herald pretending to be journalists are complete tosh. Most will not - they're to busy living their lives and still have a soupçon of faith in our media. And because its the journalists who are making up these stories in the first place then the chances of their unjustified claims of larger class sizes being better are unlikely to ever be reported to the public that they have already misled.

It also illustrates the point I was trying to make last week about transparency and process. In some ways the ideal journalist is similar to a scientist. Journalists are bound a lot looser than scientists but both have a responsibility to sort through the raw data and report on what is actually there rather than what is superficially evident. Journalists do this by attempting to be vaguely competent and consulting those with relevant expertise before publishing something. Scientists generally go through the peer-review process. This makes the peer review process, not an arbiter of what is significant and what is not, but an assurance that a basic level of rigour has been used. Both journalists and scientists have, relatively speaking, positions of authority in today's society. If reporters start putting out raw data without even attempting to explain what it means then they are failing as journalists. And I this is why scientist don't release their data directly to the public before they have published - there is a responsibility to dig through the data and be sure about what it says. And we do this because most people do not have the time or the desire to acquire the statistical background necessary to look any deeper than is required for basic day to day operation.

Thursday, September 20, 2012

When is a good time to talk?

One of the things I like about blogging (seriously), is that occasionally I write about something that I think is rational and reasonable and shortly after that I realise that it conflicts with something else that I think is rational and reasonable. Or at least appears to conflict. It makes you think about your opinions with a little more depth than usual, I'm aware of cognitive dissonance, but not a fan.
Releasing un-reviewed papers or risk assessments direct to the public, places an unnecessary burden on not only a specific GE product, but on GE research in general. I am also of the opinion that scientists should try and engage more with the public - I seriously don't like the idea of demarcating science and saying "this bit is for scientists, that bit is for release to the general public", an attitude that is both underestimates those who are interested in science and distances science from public life where I think it belongs.

The question becomes then, when is it appropriate for scientists to engage more directly with the public? I'm new at this whole writing scientific papers business, but I get the impression that few scientists put pre-published results out to the general public. I would go so far as to say that results don't generally get discussed outside of a very small group. Results get talked about widely after peer review, if they make it past. Any results that do make it past should be open for the public to access - whatever problems there are with the peer review process.
A lot of the communication of science that I have seen and the method that I try (not always successfully) to emulate is speculative. Telling people about what this particular piece of research might mean, how something that we're doing might help with a particular problem. This is a good thing, long gone are the days of the scientist who can answer every question with authority. It needs to conveyed that the larger part of what we do is question. Its not as much about the message then but at about what stage in the process you decide you have a message is it when you start to question or is it when you have poured over the other research and your own data for months on end, discussed it with some of those who have done similar work?

After some thought, I don't think my two positions are in conflict. The results science produces should be open to all, public and scientists alike. As should the process. I'm not so sure that a result can or should be released without some independent checking, i.e. peer review.
This all changes when the commercial world rears it's head. The commercial world doesn't want to let everybody know their secrets lest someone copy them.  I think it's overdone and quite silly sometimes, but I'm generally fine with that. Prof. Heinemann suggests that "This boundary has long ago been transgressed by the commercial sector, using scientists and writings of scientists in ads and other ways". And I am tempted to agree. I think the commercial sector has gone a step further though. They use the appearance of scientists and imitations of the writings of scientists. And it's not just the commercial sector that does it, special interest groups that use these tactics as well (using both scientists and the appearance of scientists).

This causes a problem. Without a transparent regulatory process then it becomes difficult for the public to tell good science from the appearance of good science. When it comes to products that have potential for harm, then regulatory agencies need to both put their assessments through review and publish the results. Prof. Heinemann suggests that this might slow the progress of good products and differentially penalise small business. This doesn't hold up in my mind. If a product has potential for harm, then there is cause to believe that it might not be a good product - something that should be checked. And the time compared to the cost of developing a GMO, I don't see the time and cost of an independent, reviewed risk assessment being that onerous (I could quite easily be wrong here).

All of this boils down to three points:
  1. Open, transparent regulatory processes
  2. Full and open communication of how the risks and results are being assessed over the whole process.
  3. Full and open communication of risks and results after review - there's enough confusion about from commercial and special interest groups already, best practice should be to reduce it if at all possible.

This is still a work in progress in my head, so criticisms would be welcome.

Tuesday, September 18, 2012

Where's a good place to talk?

There's been a bit discussion over at sciblogs and a few other places that have got me thinking. Recently Prof. Jack Heinemann released a report, being a risk assessment of a form of GE wheat that the CSIRO in Australia has developed. It has been criticized, for amongst other things being presented direct to the public rather than appearing in a peer reviewed journal. Which in some peoples opinion makes it an attempt at science by public opinion. The response to this argument is (and was made) that neither are the risk assessment regulators reports. And I agree that it's a good idea that risk assessments made by the regulators should be both peer reviewed and published. I'm not sure though, that this is an adequate defense against the criticism.

To fully appreciate a risk assessment, I think you need some background in the area. Prof. Heinemann certainly has this. I'm not sure that the general public does. I'm not suggesting that risk assessments should be locked up for privileged eyes only, that's pretty much what's causing the problem in the first place. Presenting them to the general public rather than in an appropriate venue after blind peer review is counter-productive though.

Presenting it to the general public sans peer review, even if it gets reviewed after it is made public, allows it to be presented without criticism, as indeed I believe it has been, as a tool to enable an argument from authority. Which I shouldn't have to say, is a terrible thing. In this case, even more so because Prof. Heinemann raises potential problems that should (and could easily) be addressed.

There is merit to the idea that a risk assessment should be published. I am firmly of the opinion that the argument we should be having is with the regulators - that risk assessments should be both peer reviewed and published in a suitable venue. That way valid risk assessments are a lot harder to dismiss as populist science by public opinion. And scare mongering press releases can be more easily dismissed. This is not suggesting that Prof. Heinemann's assessment is the latter btw. It is however suggesting that published where and how it has been, it loses credibility (as Prof. Dearden of Southern Genetics suggests). It becomes less useful as a piece of science used to help us mange our tools and our world and more useful as a PR tool, a piece of spin. Which, I think is unfortunate.

Prof. Heinemann says:
Science routinely shows prevailing assumptions, such as those made earlier about dsRNA, to have been wrong.  The proper response to challenges to assumptions is further research.  This, not denunciation of the challengers, is the way to maintain public trust in the regulatory system, and in science.
With this I concur. Further, open research is the proper response. Questions raised by research should be answered. Questions raised by press release though?  That imposes extra unneeded burdens on legitimate research.

One little thing.

Via Twitter:

Working to keep NZ GE free

This GE fixation is the one and I mean single issue that I take with the Greens. The link takes you to page where Steffan Browning chronicles his work on behalf of the Green Party to keep NZ GE free. As best I can tell, the Greens aren't strictly speaking against GE
"GE needs to stay in lab, releasing it would destroy our clean green image which is so important to our economy."
I have enough difficulty coping with the cognitive dissonance generated by a party that seems sane, articulate, intelligent and well reasoned on every other topic yet seemingly unable to understand what GE is actually is. The least they could do would be to stop using blanket dismissals of this incredibly useful tool that science uses. If they don't like it, fair enough, want it labelled, as silly as I think that is, no problem with it. For the love of bob though, I would ask the Greens to please stop attempting to characterize this piece of science as evil that must be stopped at all costs.

Friday, September 14, 2012

Some thoughts about crowd-funding

So we all know about crowd-funding right? The thing where you put your project, be it an album, a documentary or knitted kitten covers for albino pumas on a website like kickstarter and people, if they think your project is worthy, pledge money. Normally you offer rewards, so that if someone gives you $5 you get a picture of a kitten in a hat, if you give $100 you get to play with a kitten, that sort of thing. If you get to the sum of money that you were aiming for, kickstarter take money out of all the accounts of people who pledged money and give it to you.

Amanda Plamer, who I talked about yesterday, ran a kickstarter project with a whole bunch of rewards. She managed to raise ... ooodles of money. Approximately $1.2 million US. Which is both a lot and not very much. In a post a while ago, she told everyone roughly speaking, where all the money was going. Which is a) a good thing and b) the sort of thing you'd expect Amanda Palmer to do if you've followed her at all - she is very open with her fans.
A short while ago, she asked for some volunteer musicians to help in a few of the gigs that she had planned. This got some artists very annoyed. Annoyed, because artists, musicians especially have a long history of being asked to play for free, the trade off being that they will supposedly be gaining "exposure". This is in short, crap, musicians work at their craft and should be paid, just like plumbers and electricians. Some people did think this is what Amanda Palmer was doing though. I thought it odd, given the number of random free gigs that young Palmer has done over the years and the way that she interacts with her fanbase.  Then someone pointed out that in the initial distribution of funds post she had finished by suggesting that :
"investing not just in the future of my little record and band, but in an idea whose time has come."
and that this concept of investing in an idea rather than a specific project was ... disturbing. I don't think Palmer was referring to this particular project specifically, rather, she was referring to crowd-funding being an idea whose time, if not come, then was at least arriving. That's not the point though as it got me to thinking. I'm a student with fuck all money, so I don't really have money to give to crowd-funding projects, as much as I would like to. I would have given to Palmers one, I would have given to the Oatmeals campaign to build a Tesla Museum (seriously, how cool a project was that) and I would, if I had money give to Ethan Perlsteins "Crowdfund my Methlab" project - he's an academic with a proper lab who wants to do some work figuring out exactly how amphetamines interact with receptors in the brain, strange we don't already know that, but we don't.

Crowd funding is beginning to raise it's head as a possibility in the sciences. Only for small projects at the moment, Ethan's project is the biggest one I've seen. And more so in science funding, people are investing in an idea, not a person. Primarily because scientists don't (yet) have the same presence in peoples lives as musicians do. I don't think investing in an idea is necessarily a bad thing. In fact, it's almost unnecessary. If we get people investing in crowd-funded science projects, they are investing in ideas, both in the individual project and in the larger sense that Palmer meant it: a new, alternative (not replacement) way of doing things.

One of the comments Palmer made in her defense of asking musicians to play for free (and I accept the reasoning of her post as a whole) was essentially that it is an issue of trust. She has been incredibly giving over the past several years, working sometimes for free, sometimes not, sometimes asking for help, sometimes having help offered. In the end, I think it's perfectly acceptable for her to ask for volunteers as she has
"worked my ass off for years to build the kind of trust that built me that line of credit with people."
It's a trust thing.  It would be different, I suspect were someone planning a birthday party and wanted the band to play for free - they're not part of that community, they haven't given, they have no right to expect to receive. Palmer has, not that she thinks she has a right to expect people to help, she doesn't, but she has given enough, built enough trust for people to want to help her when she asks.

This is something that I wish the science community had more of. Maybe it will as the crowd-funding idea grows. There are numerous projects that I hear about, that sounds really cool and I'd love to offer the use of my skill set in my somewhat limited free time. It's not really the done thing though from what I can see though or at least, I'm not at the point in being comfortable doing that yet. As (I hope) a community grows, we will build trust between the scientists and the funders. That however, requires both a lot of communication and a willingness to invest in new ideas.

Thursday, September 13, 2012

A fine distinction maybe?

I'm possibly drawing to fine a distinction here, I'm not sure. There's a bit of ... flurry, around Amanda Palmer not paying her backup band. And it's an odd one. On the one hand, musicians definitely deserve to get paid. The whole "do it for the exposure" thing is complete bollocks.

On the other hand, when Amanda Palmers kickstarter was wildly successful, she did lay out where all the money was going, demonstrating quite well, I thought, how much it actually costs to put together a record and a world tour. In other words, she might have raised 1.2 million dollars, but she is by no means going to get rich off that, so calling her a stingy moneybags is not ... accurate.
The distinction that I'm attempting to make here is that when artists get asked to do it for the exposure, it's asking for a service to be provided for free. In this case, having followed Amanda for a while, I'm guessing that she's asked for volunteers and said that there's no money in it. Even without volunteers though, she would still play and the show would probably be grand. The concert tickets were iirc, part of the kickstarter rewards - so everyone already knows where the money has gone for that. So in the end, the service that was contracted (via kickstarter) will be provided, with or without a volunteer backup band.

It's a tricky question. One I'm at the moment going to, tentatively, come down on Palmers side on. She has built up a lot of trust with her fans over the years, I just don't see her squandering it like this. I could be wrong though.

Tuesday, September 11, 2012

Cue spin ....

An opinion piece in the herald today, supposedly talking about the recent judgement against the he New Zealand Climate Science Education Trust in their attempt to cast doubt upon the integrity of NIWA's researchers. It's interesting to note that it doesn't really say anything about it other than the fact that the temperature record as presented by NIWA was contested. In fact, it doesn't really say anything at all. "The science of climate change depends entirely on reliable data, quality controlled and homogenised rigorously" ... well, yeah, that's pretty obvious. "Climate services of various countries provide clients with statistical information on climatic variables that is based on long-term observations at a collection of different weather stations."... again, no surprises there. And apparently after a long and expensive court case, the NZCSET wasn't actually out to cast doubt on the NIWA's climate record at all, they just wanted to "make sure that evidence of this for New Zealanders is accurate". Indeed, their pre-court spin was: "We’re saying (and proving) they made serious mistakes in their reconstruction of the national temperature record."  Which is, if you think about it ... casting doubt on NIWA's climate record. Calling the record into question is exactly what they were doing.

The interesting part though is, I think, in the first paragraph.
"One assumes scientific analysis is objective, so it may come as a surprise that this was challenged in a New Zealand High Court case, the results of which were released last week."
With absolutely no mention of the result of said challenge. The result of course was that they got spanked by the judge and told they had essentially no credibility and no idea what they were on about.

Friday, September 7, 2012

And a smile for Friday.

It's only a small smile though. I imagine the annoying little sods will wind up their trust and declare it bankrupt, leaving us to foot the bill for their absurd little bit of theater.For those of who that don't know, our climate change "skeptics" (cranks) took NIWA to court a while ago over the climate record, claiming it wasn't accurate.

NIWA, if I recall had made some adjustments to records where climate recording sites had moved. So if the  recording station's position or environment changed, they changed the record. This is a perfectly legitimate thing to do, there are well documented differences depending on the terrain. Cities will often record a degree or two higher  that the surrounding countryside due to the heat absorption from comparatively higher amounts of concrete and asphalt. If an area around a recording station becomes built up, adjustments may need to be made. When you're talking about climate change, you're looking at trends in the data. These trends have to take into account changes in the environment of the recording stations.

What it boiled down to though, was that our local cranks couldn't stand the idea that we have a bunch of hard working scientists who know what they're doing looking after the temperature record. Surely the must be past of "teh global conzspyracey!". So they set up a trust with the express intention of taking NIWA to court. The judge found against them, noting two points
a) being a clever person with an interest in a field does not make you an expert and more importantly:
b) the courtroom is not the place to decide issues of science you do that in peer review publications (where, btw, the discussion is not of whether climate change is happening, but of how badly have we underestimated it).
The downside being that now that they've lost, as I said at the beginning, they'll probably wind up the trust and leave us footing the bill.

Thursday, September 6, 2012

Who stole the editors?

Today is one of those rare days when the herald editorial actually makes sense. GE crops have been present in the worlds food supply for quite some time now, with no obvious harm arising. We should be looking at individual crops on a case by case basis, deciding if a GE crops makes sense or not in our circumstances. At the very least we should be doing the science here. The fail though at understanding why we need to be investigating new crops and new ways of doing things.
The gene modification industry does its case no favours with apocalyptic predictions of population growth and food shortages. It is enough that genetics can increase crop yields, reduce the need for insecticides and make farming more profitable.
Look at farming as only a way to make more money and you end up with companies like Monsanto - companies which are almost universally reviled - even if they have done good in some places around the world, no one is ever going to give them any credit for, given the reputation they have saddled themselves with. How is using increased profit going to put those who oppose GE at ease? It's not. I find it difficult to believe that there are people who are opposed to GE on the basis that it's not profitable enough.
We should be moving ahead with GE science despite opposition. That doesn't mean that the concerns of those opposed or the researchers motives for doing so should be ignored, they shouldn't. Appeal on humanitarian grounds at least has a chance of assuaging some fears. Feeding and controlling the population so that future generations can have enjoy something like the lifestyle we have now is important. Profit is secondary at best. Putting profit first shows the ugly side of the heralds world view.

Wednesday, September 5, 2012

Fighting the forces of evil.

I'm not sure if I've mentioned Jeffrey Morgenthaler on here before. He's a bartender in the states who likes his job. He takes his time and takes care with the drinks that he makes. and he has an appreciation of the classics. To the point that he will defend them against the forces of evil.
Those who care about the alcohol we drink are fighting a battle on two fronts at the moment.Those such as Morgenthaler is battling, those who really don't care what we drink as long as buy something. And those who think we shouldn't drink at all. The craft brewery industry in New Zealand is currently battling on both fronts - though the battle against the temperance movement is to the fore at the moment.
The drinking of alcohol is not something that is going to go away. Unless humanity suddenly generates a highly beneficial mutation that has a side effect of discouraging alcohol consumption. In other words, not. going. to. happen. Some harm is always going to be caused by alcohol, in as much as alcohol consumption is a problem, the goal should be to reduce that damage. And a big part of reducing that damage is to have a healthy relationship with your booze. We shouldn't be telling people not to drink - we should be telling them to care about what they drink.

An example.

Or rather, how I would like to see policy being made. A few people have reposted links to Ben Goldacres submission to the UK cabinet office on the use of randomized controlled trials in policy making recently. Which has got me thinking about the whole evidenced based policy mindset again. And then in the paper this morning was this: Child poverty costs NZ $10b a year.

Which is a fine place to lay out an example of how I wish policy was made. Really.
First, identification of the problem. In this case, a study is bringing child poverty and it's associated costs to the publics attention. The first thing to do is to have a look at the source of the report, in this case an independent researcher by the name of John Pearce. Is he a crackpot? Or is he someone with a relevant background and experience who has done the relevant work? In this case the Children’s Commissioner’s Expert Advisory Group (EAG) appear to rate him, so, if we are interested in doing something about the problem, then we should pay attention. Does the work stack up against other works of a similar nature here or overseas? More weight should probably be given to the problem if similar conclusions are being reached by local studies - for the sake of this example, I'm assuming it does stack up with similar work (likely but I can't be bothered going and finding sources to back me up on this atm, it's beside the point)

What's next? A problem has been identified. It's not good for people and it's costing us money. Get some of the people who have done the work in a room with people from the appropriate ministries. In this case, I would guess the Ministries of Work and Income, Housing and Finance. Lock them in a room with a statistician until they have identified at least 3 or 4 areas that can be tested and compared, 3 or 4 possible policies that could alleviate poverty, and a series of concrete measures. Things like, how much less is poverty costing us in a particular area, how does the number of people below the poverty line compare, before and after - taking into account population changes.
Implement the measures in a the different areas, 1 treatment per area. Wait. Years if need be. Build something into legislation that will protect the trials if need be. Compare the results against the measures proposed at the beginning and then implement the policy that produced the best results.

It's probably one of the reasons I'll never be good at politics. I wouldn't want to push for one particular policy over another. I'd rather push for a trial composed of a number of different measures and select the best based on the results.

Tuesday, September 4, 2012

One size doesn't fit all.

Neil MIller points out the absurdity of the unintended consequences of the Auckland Council attempting to get liquor stores to stop selling single bottles of beer. I agree with the post, up to a point. The removal of craft beer from the shelves would be an appalling loss for Auckland. Our craft beer scence is already years behind Wellington's. Or at least it feels like it sometimes.
The craft beer movement promotes the drinking of beer for personal enjoyment - taking pleasure in the variety of styles and flavours that can be found. This is exactly the sort attitude towards drinking that needs to be promoted in new Zealand - you don't drink to get pissed, you drink to enjoy whatever it is that you are drinking. Len's response is a complete non-answer. It may have decreased pre-loading in some areas but it's a stupid, one size fits all approach that harms the part of the industry that is trying to promote the very attitude you want to encourage. Pathetic really.
On the other hand, I have no idea why Miller veers off into a discussion about the councils Maori policies and rail loops. There has been cross over between central and government rolls, which requires clarification, though I wouldn't include the councils public transport planning in this. It's enough to point out that what the council is doing is, at least in part, counter productive.

Nerdnite - Chapter 2.

The first Nerdnite in Auckland that I organised (a few weeks ago now) went, from my point of view, superbly well. The projector was a little fuzzy and the sound could have been a bit better, but everyone enjoyed themselves and we had way more people than expected turn up.

I've just gone and booked the venue for the 2nd Nerdnite. It's the same place, but I'll be getting a friend who specializes in this sort of thing to come look over the projector beforehand. The speakers haven't confirmed - though they have nominally said they are keen. Details will be on the website and the book of face when they confirm. Fingers crossed it all goes as well as last time.


Thursday, August 30, 2012

Another (18) bite the dust.

Via Lactia is a research company owned by Fonterra. They are, to the best of my knowledge, well respected in New Zealand Biotech, doing some good science. The news then, that they are losing 18 science positions is not ... encouraging. Rather than generating ideas themselves, they will apparently be looking for science done overseas and using that to advance their interests in New Zealand.

New Zealand has abysmally low levels of research done by industry in the first place. And now Fonterra, one of our largest companies is apparently no longer willing to support basic research into their own industry which is just depressing.


Wednesday, August 29, 2012

Now we're getting somewhere.

The fluff that keeps getting announced by the Ministry of Everything has been getting me down. There's been some nice things in there (increased recognition of the science etc.) but overall, I don't really think most of it has done or will do much, either for science in New Zealand or for New Zealand itself.
So it's nice to see something that sets a bit of direction and will, I think help: funding. The ministry has released their first round of investment. This is where how you get scientists and innovators interested - show them what you want to work on. It provides direction and will get people thinking about what they want to work on that could possibly contribute to the goals.
The biological industries fund - seems good. There are projects attempting to build on (or save) what we have. And I like the Hazards/Infrastructure section and it's particularly relevant with the whole Christchurch thing - putting thought into how we live as a society is always a good thing. The Energy minerals sections has some good points, there's a decent chunk of money for renewables research and grid storage. The focus on ageing puzzles me a bit in the health/society fund, but it's not a bad thing.
Ideally the fund as a whole could have been bigger, but that's a complaint that could be made no matter what the size. It's unfortunate I think, that they're looking at spending money on researching offshore mining. A couple of the biology projects seem ... overly focused maybe. There's two grants for the "Leather and Shoe Research Association" which at first glance to me seem like they should be being funded by industry. Especially since we don't, to the best of my knowledge, actually have a shoe industry here any more. Is this an attempt to create one or is it to improve the hides we presumably send offshore?
All in all, on the assumption that this is new funding and not old funding shuffled around, it's not a bad start. Not spectacular, but definitely not bad.

Tuesday, August 28, 2012

Targeted is better.

I don't actually agree with a universal child payment. It's a bit of a waste really. If we're trying to have a poverty baseline under which no one falls then money should be targeted. I don't see the point in giving money to parents who are either swimming in it or even just coping. I'd rather money be spent on those most in need. It's the whole point of have a welfare state - having a safety net for those that need it, not to make life a little bit easier for those who are already coping.
And from a larger societal point of view, giving money to those who don't need it is silly, it takes money out of circulation - it'll get put into a savings account or some such. Whereas if you give it to those who needed it, they'll spend it - more money in the system, better all round. That's not really the point though. The point is that that if it's not targetted, then there's more wastage than there needs to be.


Going through the progress indicators in the Ministry of Everything's "Building Innovation"  progress report. Specifically in the section "growing the innovation workforce: - important to me because I'm going to want a job one day. Preferably one where I get to be a scientist. There's nine points, of which 4 are marked as completed:
  • Lift the profile of science through the appointment of the Prime Minister’s Chief Science Advisor
  • Institute the Rutherford Fellowships to provide greater opportunities for early stage researchers
  • Establish the annual Prime Minister’s Science Prizes to acknowledge and reward scientific achievement
  • Maintain internationally competitive personal tax rates that encourage highly-skilled workers to work from New Zealand
Can't say as I'm overwhelmed with optimism. Appointment of a science advisor. Cool. It's done some good - brought a little sanity to the discussion of some topics. How's it's meant to grow the innovation workforce though, I'm not sure. Maybe it's meant to have inspired some sprogs to take up science as a career. Maybe it has. who knows. the Rutherford Fellowships - grand for them that can get them. 10 per year. And it's for early/mid stage researchers. Competition will be - fierce. Same thing with the PM's Science prize - it's for a few people who have done particularly well and while that recognition is a good thing, I don't see how it's grow the workforce. And the last one just completely misses the boat. Very few scientist will look at the personal tax rate and decide that that's the thing that's going to stop them from working somewhere. They will go where the work is interesting. There are larger economic arguments for low tax rates (not saying they're valid arguments) - but it's not going to the thing that innovators will look at and decide to move country because of.
So what's in progress then?
  • Complete a stock take of post-PhD employment opportunities in New Zealand and make policy changes if required
  • Increase investment in engineering studies at tertiary institutions and lift graduate numbers by 500 per annum by 2017
  • Collect and provide better information on career prospects to students and the tertiary sector
  • Highlight the role of entrepreneurship in business innovation through annual Prime Minister’s Business Scholarships
  • Investigate highlighting innovation careers in science, design, engineering and maths to school students and their families
A stock take, that's good, it's easier to make changes when you know where you're starting from. I don't imagine the results of that stock take will be particularly encouraging though. Increasing investment at engineering faculties is probably the high point on this list. I would be nice to see a corresponding increase in the sciences so the scientists can give the engineers new and better things to play with. I don't see how providing information on the limited job prospects to students is going to make things better - surely that will only send more people to study law. Business scholarships - again for a few, the recognition may be nice but it's not something that any researcher is specifically going to strive for. And investigation of highlighting innovation careers? That's not even highlighting science/engineering/design to prospective students. Again it's sounds like they're attempting to take an evidence based approach to building things up, which is good, but I just don't see how anything is going to change that will keep me in New Zealand when I finish my PhD. I would like to stay and be part of an innovative workforce, but it will be availability of interesting work that keeps me here. It certainly won't be the tax rate.

Friday, August 24, 2012

Ummm .... okay

From the PM's speech at the presentation of the Transit of Venus Forum report last night:
"The first thing I would highlight is that we have been actively working to lift the profile of science in New Zealand."
Seriously? How? Whilst I'll admit that I'm somewhat biased, in as much as I'm already in the field and am thus possibly less likely to see the reaction of the public to "measures to lift the profile of science".

So there's:
On becoming Prime Minister I established the position of Chief Science Advisor, reporting to me personally, which Sir Peter has filled admirably.
This is something I suspect most people in the science community are aware of. And a limited number of the general public. And whilst it's been a good thing, I'm at best unsure as to it's benefit in lifting the profile of  science in NZ.
I also launched the Prime Minister’s Science Prizes, with total prize money of $1 million, because I think our scientists deserve their share of public acknowledgement and acclaim.
Oh? That's nice. If I've barely registered this, I seriously doubt anyone else has
And we are continuing to improve the way the science system operates. Sir Peter’s Forum report highlights some opportunities in this regard and we’ll continue to work on those.
Over the last year, I've seen many pictures, nice diagrams with generic high levels statements about what is being done for science. I've not seen any perceptible change in the general public's perception though.

Someone remind me, I'd like to say something positive about the public perception of science in NZ at some point. It's Friday and late though. And the Malthouse has done me in with Tuatara's Double trouble.

Where's the blue sky?

Back in June there was a forum held in Tologa Bay, aptly, for historical reasons (go look them up, transits, Captain Cook etc), called the Transit of Venus forum. Originally the brain child of Sir Paul Callaghan, it was curated by Sir Peter Gluckman. The idea was to discuss how science can be a part of making society better - I like that part, the recognition that science isn't separate/distinct from society, but part of it.
Anyway. So Sir Peter  distilled the themes that were running through the various discussions and presented them to the Prime Minister last night at a Royal Society gig. Whilst I wasn't there, I did watch what was being said via twitter. It was sort of depressing. The general feeling that emerged whilst the politicians were talking was there there is little place in science in this country for just figuring things out - that's what gives scientist a buzz btw if you hadn't been paying attention. It appears that we must focus on science that has specific outcomes that can be turned into economically viable businesses. Which is just ... wrong.

Someone in the twitter feed linked to this this, which I think is pertinent. There is a crisis of perception, if not here, then approaching. The innovative technology that our leaders want us to go looking for is not generally foreseeable  As in you can't go looking for it. Maxwells descriptions of how electricity work didn't arise from him trying to construct a toaster. Yet toasters arose as a by product of Maxwell understanding and aiding others in harnessing the power of electricity. And the contestable funding model that we have for most science funding in New Zealand supports this idea that you should be able to predict what you are looking for and of what benefit it will be. This is not an approach that leads to new and innovative ideas that can be commercialized. 

And to compound the problem, some of the problems that we are being asked to find problems for already have answers. Apparently we must develop a vaccine for rheumatic fever. Yet we already no that one of the biggest causes is poverty and the lack of adequate housing. There's a solution already there, it's apparently not sophisticated enough. This is not an ambulance at the bottom of the cliff type approach. It's someone standing next to the ambulance at the top of the cliff yelling down to the bottom asking if everything is alright.

Thursday, August 23, 2012

At least we're talking about it.

It's an hour long, but if you haven't done much in the way of reading about David Nutt and the whole Drugs advisory committee saga in the UK from a year or so ago, then it's worth listening to. Professor Nutt is a neuropsychopharmacologist Bit of a mouthful I know. He was also the head of the UK's drug advisory committee who got fired after he came out publicly stating that cannabis and E and a whole bunch of other drugs that are currently illegal are, when you look at the evidence, significantly less harmful to both the individual and society than alcohol and tobacco. He provides a good overview of the saga on this science podcast from the Guardian. Near the end of it he is asked if he thinks there will ever be change, will be ever have evidence based drug policy aimed at reducing the harm to society? His answer is basically when we get the next generation of politicians. it might have been difficult even 10 years ago for him to be talking about drug policy reform. It's nice to see that things have changed sufficiently that we can at least talk about evidence based policy reform - still sad that we're not quite at the point of enacting it.