Thursday, September 26, 2013

Just in case.

This has been out since yesterday and should hopefully have been seen by everyone who's going to vote in the Auckland local body elections. Just in case you haven't though, go here. It's a scorecard for the candidates for Mayor and Auckland Councillors. Sadly it doesn't go down to the level of community boards, but that would have been a huge task. we should be grateful to the folks of Generation Zero for even this.

For the record, I tend to pretty much agree with the political outlook of Generation Zero in as much as I think intensification, transport, sustainability, climate change and the like are all important, things that our politicians should at least have some form of plan for.

I'm told by the one person I know with the gumption to stand in the local body elections that Peter Haynes responses didn't do justice to his actual positions - i.e. that his ideas align more towards the Generation Zero ideals than would otherwise be indicated with his grade.

The one ranking on this that surprised me was that of Penny Bright in the Mayoral contest. I don't know much of her apart from the fact that she is an activist, generally speaking, on the left of the political spectrum. I can only presume that she didn't think Generation Zero were sufficiently important to respond properly to. Quite surprised.

Monday, September 23, 2013

It's easy. [waves hand's in the general direction of away]

So I've recently had a little setback wherein the samples I've gathered and been attempting to process for the past several months (nine, start to finish if I'm counting correctly) aren't fit for purpose. I can get perfectly good RNA out of them, but not RNA that is sufficiently good for sequencing.

Unfortunate really given that that's the entire basis of the data for my PhD. And that I need a good time course of host/pathogen sequence data around which to build my models. No worries! apparently. Just go and get some datasets from other studies that have been published and use them to build your models! This has been suggested to me several times over the past year or two. Each time I've dutifully gone off and looked for some of these magical published datasets. I've even gone searching a few times when no one has suggested it.

The only difference I found last time I went searching was that I actually found a relevant study with published data. I use the singular deliberately there. One. This one, if anyone is particularly interested.

There are institutions like NCBI that are collecting a large amount of data. Sequence data, protein structure data, metabolomic data. There are 13 databses focused on RNA listed by Wikipedia, but most of them are specialised on specific subsets of RNA - not the transcriptome in it's entirety. One thing I think we forget though is that even though we're collecting large amounts of data, the amount of data generated by biologists in last decade or two is significantly larger. Which means that even if there are people working on similar topics, there's a decent chance that the data is either a) difficult to find or b) hasn't been published in the first place*.

The other possibility that springs to mind is that there just haven't been many experiments of the sort that I am doing that have been done. One of the things that I have slowly gotten used to over the past year or two is the realisation that a lot of the work that I assume is fairly basic for understanding biological systems just hasn't been done. There's so much of it, it's only been possible to study whole systems as a whole fairly recently and there's a distinct lack of  both money and people to do the work. So when I go out looking for host/pathogen sequence data in plants, even though the conventional wisdom that seems to have seeped into the scientific mindset is that there is plenty of data out there, I find one useful example. 

So much to do, so little time (and money).

*Approaches like that proposed by the DNA Digest group will I think be quite useful in opening up access to the masses of data that's been backed up and then then not used on thousands of servers around the world. Fingers crossed.

Monday, September 2, 2013

Superb idea.

There were a few good talks on day 3 - I didn't get a chance to write about any of them yesterday because it was almost straight from the conference to the conference dinner and then home late. On the plus side, a couple of late nights appears to have got rid of the jet lag. Now I'm just tired.

The best talk thou, was a surprise. Literally, the speaker, Chris Voigt, hadn't told anyone what he was going to be talking about. In the end, he was talking about the nitrogen fixing system in plants. Or at least in some of them.

Some who know me, know that I'm liable to occasionally go on a rant about growth and sustainability. As in we're growing, we're not going to stop it,  it we need to control it and grow sustainably, especially when talking about feeding the word. Screw organics, it's a badly defined industry that isn't necessarily sustainable. Or even necessarily good for the environment. On the other hand, some of the industrial level farming that we currently do is not sustainable. Referring particularly to the large amounts of fertiliser that we produce and use. Why do we use so much? A lot of the plants that we grow for food, like grains etc, need nitrogen and they get it from the soil. They don't fix nitrogen out of the air. Some crops do, like legumes. Solution? Gt everyone to eat more beans. Good luck with that.

Another option, take the nitrogen fixing gene complex out of a plant that has it and put it into some of the plants that don't. Bam, there goes our need for large amounts of fertiliser. It's not that simple though, the complex of genes that regulate the nitrogen fixing process are, to be frank a mess. Evolution does't necessarily find the optimal solution, it finds a solution that works.

So Voigt's group took the complex out of Klebsellia - a bacteria that fixes nitrogen and have been re-factoring it. Re-factoring being a software engineering turn for taking something that doesn't work on a new platform, stripping it right back and building it back up again. It's a fairly complex system of 16 genes that are very much prone to stop working when there are minor changes in translation levels. They stripped out all the regulatory elements, even made a whole bunch of neutral mutations in the codon codes to remove any internal regulation and started modelling and experimenting with re-writing the regulatory process so that they would have a robust system that they can then put the whole shebang into a new system and get nitrogen fixation where previously, there was none.

And they've done it. They've gone from the base Klebsellia fixation system, essentially re-written it and put it into E. coli. It doesn't operate at the same efficiency (about 70% atm) but it does work. So a while before it gets put into plants and solves our fertiliser problems. Good idea though. And the work that they done to figure out how to control a specific system is quite frankly, superb.

Sunday, September 1, 2013

Talk of the day

Definitely goes to one Soren Vedal. And not just because he gave one of the two talks that came in under time - seriously, is it me or a cultural thing or something else entirely that makes me hate it when speakers go over time? It's not that they haven't know for several months how long their talk should be and haven't had time to practice. It wasn't terribly problematic today, but still.

Anyway. The talk was in the session about temporal phenomena on a biological time scale. It communicated a system level concept, cleanly and efficiently in an engaging manner.

Suppose you had a population of bacteria. At the population level (definitely not the individual level) it makes sense to sacrifice some of your, less fit populace, so that there are more resources for the better adapted to survive. This being a basic trade off called hedging your bets.

This can be improved upon though. When bacteria divide, they don't divide evenly. A disproportionate amount of any damage that a bacteria may have suffered is shunted off into one of the two offspring. This results in one bacteria in better shape and more able to reproduce than another. Which in the longer term means taking less time to replicate and the proportion of undamaged cells increases. More environmental pressure exacerbates this effect. It is basically diverting you damage that a population suffers off to into a redundant evolutionary side track and out of the population. The average damage goes down and the population growth rate also slowly increases. Which is better than static bet hedging.

And all backed up with experiments that fit the predicted patterns.

Nice theory. Nice system. Well communicated.

Thoughts for the day.

It's been a good day. Technically, my knees are still working after being treated to a superb dinner at a strangers house (friend of a friend I've never met before, I was delivering parcels, wine was exchanged in large quantities). Another drink or two though and I would have been seriously wobbling one the way back to the hotel.maybe being up this late will cure the jet-lag. Fingers crossed.

The talks at ICSB were almost all interesting. Which is not to say that the few that weren't were bad talks, just sufficiently outside my area of interest so as to me unable to hold my attention. Which is to be expected.

There were a couple of people that I semi-ran into in the foyer who I would very much have liked to have sat down and chatted do, which circumstances did not permit me to do so. Again, not to worry, with any luck I'll be able to find them tomorrow.

The big thought for the day though is that while the talks were interesting, they weren't, generally speaking, what I would call systems biology. They might well have used various aspects of systems biology to come to the conclusions that they did, but in primarily presenting their conclusions, it felt to me like it was more of a molecular biology conference. The talks weren't, for the most part, systems biology as I understand the term.
I may very well be wrong about this, it might very well just be the selection of talks that I have seen. Or it might very well be that my perception of the field is somewhat distorted having come from a somewhere without a strong systems biology community. As it stands though, the first full day of talks was interesting but not what I'd been hoping for. Some of the talk titles in later sessions indicate that we may very well be in for more systems focused talks though which would be a good thing.

And now, to bed. Before I fall asleep at the keyboard. Naughty friends of friends, feeding me and taking me to bars with beers called spymaster and evil twin hipster.

Night all.

Saturday, August 31, 2013

It has begun

The conference kicked off yesterday. I would have wrote about it last night, but afterwards I went and found some pizza for dinner, came back to the hotel, did the jet lag zombie thing and fell asleep. Still, it's getting better, I didn't wake up until just after 5 this morning and there was some cold pizza waiting for me.

First observation. It's a lot bigger than I thought it would be. I have no idea why but on the basis of no evidence what so ever, I had assumed that there would be 2, maybe 300 people. There's at least 500, probably closing in on 600.

Second observation, related to some of the tea room conversation I had just before I left NZ. Casual glance at the speaker list ~ 1 in 10 speakers are female. Casual glance at the audience, I'm guessing ~ 2 in 5 are female. I could be wrong with those numbers, but not sufficiently wrong to prevent me from asking what gives? Disappointing.

The first keynote speaker, Stuart Kauffmann was apparently in the building but had gone missing so we launched straight into the science. It took me a few minutes to realize that we had launched straight in with a talk on nucleosome mediated epi-genetics. Cis-regulation of genes (not transcription factor based). Interesting at the mechanism level yes, but it didn't really grab me.

Marc Vidal, the second speaker talked about exploring the unexplored regions of the human interactome. Of which funnily enough there is quite a bit. He was doing this multiple ways - text mining literature for protein protein interactions  was a big one, though I thought the fact that interactions mentioned only once weren't as trustworthy as interactions mentioned multiple times was a bit of stating the obvious.
So the immediate thing that I already have out of this conference is text mining. I've been aware of it's existence obviously, but not so much of it's utility applied to the field of systems biology.

Kauffmanns talk about personalized medicine had good points and bad. The bad being that he'd prepared it on the plane and it was a bit ... rambling or vague at times. Our health care system, or at least the US health care system is still in the mindset where you find one drug to treat one conditions while trying to minimize the side effects. So this talk for me, paralleled Sorens talk from the workshop. Kauffmann was talking more about extracting the data directly from the biology, something that I suspect is still a little out of our grasp, given the magnitude of the system involved (people). Sorens was a more realistic, data driven approach, extracting information from clinical reports at a coarser grain than desired by Kauffmann.

Of the industry keynotes, the chap from SGI, Eng Lim Goh was both entertaining and informative. Briefly (and humorously) comparing systems biologists to the NSA in our desire to collect all the information in case there is something that we don't know about that we don't know is in the data we currently collect. The amount of data SGI deals with is staggering - they deal with NASA and paypal and all sorts of other big data people as well. Though if I read one slide right, their 2nd biggest customer is the people who are working with the wheat genome. Also from the very random cool factoid box, when the square kilometer array gets turned on, it's going to be generating data equivalent to youtube. Every day.

Interesting if not mind bending keynotes. And a couple good of random conversations at the drinks afterwards. Productive first day. Can't help but feeling I won't be getting to the meat of the conference today. Not sure what I'm doing this afternoon, but I'm definitely hitting the Temporal Phenomena across biological timescales session this morning. For now, it's either ty and get another hours sleep or coffee. Can't decide.

Friday, August 30, 2013

While it's fresh-ish

There were four talks at the workshop that I went to yesterday. All of them were good - I was in what was essentially a classroom listening to talks for close to four hours and didn't once get drowsy, a very good sign. I wrote about one of them yesterday, one was from Jennifer Becq from Illumina, largely about exactly how fast they can go from taking a sample to finding variants in a persons genome - thinking finding the mutations that might be responsible for someones cancer. It's very fast, as in less than a week. Very cool stuff they're doing there.  And one was from Fiona Nielsen of DNAdigest, the people who were running the workshop. They've got some nice ideas about how to make it easier to share data, increasing the power of all the data that is currently locked up in various public institutions.

The stand out talk of the workshop for me though, was from Mette Nyegaard of Aarhus University. There is an extended family with a genetic predisposition towards deafness. Some of the family are born deaf. Some become deaf when they are six. Some become deaf in their twenties. She started off with linkage analysis to identify where in the genome the problem is - she started with 50 known genes and 80 loci (where the general area is known but not the actual gene is located) involved with hearing loss. Her analysis narrowed this down to 1 loci. Which was a nice start.

There were multiple false starts with candidate genes being misidentified - sequencing and analysis eventually knocking out various contenders. There were some interesting bits in here that I don't fully understand, I need to read up on her work, but there were candidate genes that looked iffy, which once sequenced were shown to be completely normal - there was a pseudo gene duplicated from the same gene, in the same region that was making it look damaged. And another one that appeared to be responsible but then turned out to be present in the greater population with no ill effect.

She finally tracked it down to a 18 base pair deletion which had initially been interpreted as a frame shift mutation. That 18bp deletion though appears to be a sorting signal responsible for moving the protein from the cell surface to the lysosome  (where it would normally be degraded). Even with all the work she's done, it's not guaranteed that this signal is the cause of the deafness. This is the only likely candidate in the coding region of the loci. If this doesn't pan out - then it will be off to look at the regulatory regions of the loci, to see if there's anything abnormal there. 

The next step is apparently an animal model (the signal part of the protein is highly conserved across many species) . Which could be tricky - another reason to be impressed is that none of this research has been externally funded in any way shape or form. It's taken a long time because of that. Animal models however require money. Imagine though if she did get an animal model, you could get a time course of expression in the cells in the ear where the problem occurs. And then possibly go further than identifying the mutation that causes the problem, but the process behind it.

Sigh. I don't really feel like I've done justice to her talk here, it was yesterday and I need coffee. I'm going to have to do some reading. It was a thoroughly good talk though. I'd like to try and make this clearer, but it'll have to wait. The conference proper starts today. And I have a sneaking suspicion that as of tomorrow I'm going to be inundated with things I'd like to write about.

Adventures in Daneland

So, I'm in Copenhagen for the International conference on Systems Biology (ICSB). The conference hasn't even started yet and I'm already having an (intellectual) ball. There was a workshop this afternoon I attended on the journey from bioinformatics to medical informatics run by a group called DNAdigest - a bunch of open data/open science enthusiast by the sounds of it.

First up was a chap by the name of Soren Brunak - apparently one of the founding fathers of bioinformatics in Denmark. Technically, I think the talk was about the intention to align fine grained phenotypic information with genomic overlays.

First off he asked us to consider that we do, in fact do large amounts of human experimentation - another description of hospitals. The trouble is that we don’t collect the data. Denmark has an advantage here, in that it has an opt-out system with regards to the collection of health related data. Even better, there is a standard international vocabulary ICE10 if I recall correctly, that is used to describe patient symptoms. Better still, the data is not anonymised, meaning that you can correlate incidence of disease with income level or environmental factors from where people live or work. My first thought here was obviously that this is a data scientists wet dream. There’s so much potentially relevant data here that is otherwise lost in the usual anonymization process.

My second thought was, I hope, equally obvious. This is a complete nightmare from the perspective of a privacy advocate. There’s significant amounts red tape that Soren’s lab has to go through to get the data and by all accounts, the data is stored by Soren’s group more securely than at the hospitals, but I just have a large amount of difficulty imagining the amount of trust that the population of Denmark have in their health system to allow the aggregation of such data in the first place let alone allowing it to be accessed by researchers. I certainly don’t have this amount of confidence in the NZ health system. I doubt they could coordinate to actually collect the data in the first place.

There are of course, problems with dealing with this sort of data. Soren described systems biology as the movement from a thinking about single genes to thinking about all the genes. A description that quite frankly, I like. One of the problems though is that in the messy environment of the real world, removed from the lab where you can isolate the effect of a single gene or its response to a single drug, there are often multiple diseases interacting with multiple drugs. Comorbidities, I believe he called them.

And there’s a number of natural language processing problems extracting the phenotypic data from doctors records. They think a lot of that has been sorted though. And they haven’t got the all the genomic data yet. Despite that, there is still utility in the processing of the data. Correlations between … I don’t know the word here - certain sub-genres of diseases and other diseases are being discovered. Between certain types of schizophrenia and say kidney disease. This could, conceivably suggest better treatments for people exhibiting similar comorbidities. Or alternatively suggest places to looking for genetic clues when ceratin comorbidities aren’t present.

There’s also the possibility of looking for adverse drug reactions (ADRs) amongst all this data. Often when a drug is tested it’s interaction is tested with some of the other drugs that it is likely to be prescribed with to look for ADRs. In reality though, drugs are often given with drugs that they haven’t been tested with. It’s actually an argument that I have heard before from woo-meisters as to exactly why drugs made by big pharma are all bad mmmkay? People who seem to think that every possible of interaction of a drug with every possible other drug and a given human should be tested before it’s considered safe.
In Denmark where there are almost 7500 different approved drugs, is a lot of testing. Using the data from doctors records - especially from mental patients who are often given significant drug cocktails they are attempting to identify possible combinations of drug interactions for certain types of patients that  haven’t previously been identified. The theory being that there might be drugs that work well for certain people for certain diseases that could actually be dangerous for others with other people with similar conditions that are interacting with another set of diseases.

And then there’s the whole trying to work in temporal data into the equation. Which disease arrived first? Making the patient susceptible to what other conditions. All very interesting stuff. It doesn’t sound like they’ve managed to integrate much in the way of sequence data yet, but there’s still some interesting correlations (stressing correlation rather than causal relationships) popping up.

And for my money, that was the 2nd most interesting talk of the workshop this afternoon. I’ll try and write about the one using linkage analysis, sequencing and mouse models to determine the genetic causes of deafness in an extended family this evening. Very cool stuff from a woman by the name of Mette Nyegaard. Apparently there’s a significant correlation between deafness and kidney disease. 

For now though I have to go find someplace for dinner.

Sunday, July 28, 2013

A lot of people are missing something wonderful.

Great minds discuss ideas; 
average minds discuss events; 
small minds discuss people.
Often attributed to Eleanor Roosevelt amongst many others, this is not something I regard as a truism. At different times of the day, we all spend time discussing people and events. It's the discussion of ideas though that brings me the greatest pleasure. With a few (treasured) exceptions, there are sod all people I spend much time discussing ideas with, at least in person. So much of of the discussion of ideas that I engage in, actively or passively, is via the written word.

There has been an idea floating around, for quite a long time now, that there is essentially a binary choice that people make between science vs culture.  It has seen a little light recently with a noted tech writer, one Virginia Heffernan, writing an essay on why she is a creationist. The whole argument boils down to "I like the stories better". This is someone consciously making a choice between science and culture. Strangely enough, whilst fully embracing the technological fruits of scientific endeavors. Making a choice that doesn't need to be made. The idea that science detracts from the sense of wonder we get from the stories that weave in and out of our various cultural practices is not only asinine, it's abhorrent. Science and the stories it tells continually allow us to understand more than we currently know. For every part of our culture that science forces us to re-examine, it opens up a dozen new avenues of inquiry - new ways of looking at the world, new levels of understanding. There are parts of the world where it doesn't make sense to apply the scientific method. Annalee Newitz gives the example of a painting. You can't ascertain whether a painting is true or false, it's a nonsensical question, a category error. There are some things that are currently well beyond our abilities and understanding such as why some people prefer blue to green. And then there is the rest of this vast, magnificent world - a world which on some levels, we know quite a lot about, but on others we are only just beginning to understand how little we know.

Evolution being the example that springs to my mind first. We know it happens and a lot about the mechanisms involved, but it's only in recent years we have come to understand exactly how complex the structures the evolution has built are. It has forced us to re-examine ourselves and our place in universe. Those who either have not taken the time or fear to understand it cling to old beliefs and bemoan the destruction of their stories, proclaiming to be soulless and bleak. And the miss out on a glimpse of how wonderful and complex life is and how appreciative we should be to be able to at least attempt to figure out how it all works.

The sifting of ideas, the sorting of the wheat from the chaff is, I think, one of the greatest pleasures in life. The realization that something you hadn't thought about and taken for granted has some fairly shoddy underpinnings and requires some examination which might very well influence how you live your life is an opportunity to change and move towards becoming the person you want to be. Even better is when an idea that you have thought about is attacked and withstands that attack. Often nothing comes of this, occasionally though you see your beliefs is a slightly different light and you can see why they hold true.

I understand that large numbers of people can't be bothered spending the time and effort to investigate the world around them, the work that people do to figure out the world and the various opinions that are developed as a result of that work. I don't think I will ever understand why they aren't excited though. And I think it's sad that they are missing out on the stories the world has to offer. I'll give the final word to Annalee Newitz though:
"What's infuriating is when we're presented with a false binary like science vs. culture and are forced to choose a side. If you want to find me, I'll be on the side of the people who are deconstructing the cultural binary and building a better world out of atoms."

Thursday, July 11, 2013

The duties of the 4th estate

The press like to tell us sometimes about how they are doing an important, necessary job - communicating the truth to the wider public. It is, I think, one of the reasons that you want a free press, so that you can have an informed citizenry, which is essential to a well run democracy. The press will, of occasion, descend into scandal and hyperbole, but the essential goal, so we are told is to deliver the truth.

Whose fault then is it, I wonder, when the public are not aware of the actual state of their nation? Admittedly the numbers that that article talks about are for Britain. Which is not surprising, given that it's in the Guardian. I wouldn't be surprised though to learn of similar misapprehensions occurring here in New Zealand. 

If the information is available, the most likely cause for the public's ignorance that I can think of is that there is a problem with the communication. And it is the press that is doing the communication. The press are the ones bringing us the news of crime, immigration and taxes. If what is real is  significantly different from the public understands the case to be then the conclusion that I am forced to draw is that the press isn't doing a particularly good job at presenting the truth.

Tuesday, June 11, 2013

A non linear relationship.

There's a number of people who have been yelling and screaming incoherently in the local media lately about the draft of the draft unitary plan that the council released for consultation and public feedback.

One of the more asinine objects to planning for an extra million people in Auckland over the the next forty years involved a bunch of people who seemed to think everything is just dandy as it is and that we don't want or need an extra million people. Besides, they said, it'll cost a lot and we don't have sufficient money.

There's several different types of stupidity gathered up in that objection. The only one that I one to draw attention to here is the fact that the relationship between economic growth and population growth is non-linear. The people from the Santa Fe institute that did the study found, roughly speaking, an increase of 130%  in economic productivty when the population increases by 100%. This is not the only place that I've seen research like this, I'm busy though and it's the only link you're getting from me today.

We had a speaker at Nerdnite a couple of months ago, one Shaun Hendy who was trying to get across a similar message - more people in a close proximity allows a greater number of connections per person than in a less densely populated area. Which leads to a lot more business being done. And if that leads to economic prosperity which allows council's and governments to gather a greater absolute amount of tax dollars, in turn allowing more development of public transport and other local amenities, then quite frankly, I'm all for welcoming another million people to my city. .

Friday, May 10, 2013

The bee thing.

When I'm in the kitchen baking my weekly loaf of bread, one of the podcasts that I often listen to is the Science Magazine podcast. One of the presenters continually makes "ah" noises when she listens to people explaining things, which is annoying, but apart from that it's pretty good listening.

This week the had a short segment on bees that led me to this PNAS paper. Bees, as you will probably be aware are suffering a decline in numbers. A decline that will potentially cause a significant impact on agriculture. The cause of this decline has for a long time, not been understood. Which hasn't stopped large numbers of people dispersing whackadoodle theories on facebook sadly.

Recently though, there have been indications that neonicotinoid insecticide may be a contributing factor to the problem. Which is unfortunate because neonicotinoid insecticides work quite well are are quite widespread. It's sufficiently serious that the EU is moving to ban them though. The recent PNAS study casts an interesting light on the matter though. Honey, as we all know is packed with good stuff. The interesting (and obvious in hindsight) is that some of the good stuff in honey helps the bees rudimentary immune system remove unwanted substances from their bodies. There is a compound called p-coumaric acid which is a component of pollen cell walls, which up regulates  genes that deal with the removal of unwanted chemicals, as well increasing the activity of a while bunch of antimicrobial peptide genes.
Something similar becomes evident when you look at the bees diet. A varied diet is required for bees to produce sufficient amounts of a hormone called glucose oxidase - used to sterilise the food fed to larvae. 

You might not think much of this given that bees have lots of honey. The problem being that commercially farmed bees (is farmed the right word there? hrrmm) don't get that much honey - the beekeepers take their honey and replace it with sugar syrup. And while sugar syrup might give the bees sufficient calories to stay alive, it doesn't have the compounds which help the bees immune system.

So while the neonicotinoid insecticides probably aren't helping, at the same time that we're dosing them with the insecticide, we're removing their ability to cope with it. Bees feeding largely on a single crop in mono-culture heartland, I imagine probably fare even worse.

It demonstrates quite nicely I think, that the quick, obvious answers are not always right. Or at least not always right for the reasons that we think we are. And that is important because that can influence how we deal with said problems. All in all, an interesting, important and nuanced problem. And one more reason to hide the feed of the next person who posts some unsubstantiated claim about power lines or cell phone towers being responsible for bees disappearing on my news feed. 

Monday, April 22, 2013

You call that an argument.

Worst argument against the Labour/Green energy sector reform goes to Colin Espiner:
"It's a long time since the Max Bradford power reforms of the early 90s. I remember them well - I covered them as a young reporter. There's little doubt turning electricity into a private commodity and setting up an electricity marketplace has led to higher power prices for residential consumers. And also lower prices for industry.
The reforms did make the whole industry much more complicated and possibly didn't work as intended. But that doesn't mean unpicking them is either desirable or even possible without creating far more upheaval than it's worth. "
In other words, the power industry has had a free ride for the past couple of decade and we're about to hand a decent chunk of that easy money to private investors. We shouldn't try to fix the imbalance because it's really really hard.

Since when has it been written that politicians are only allowed to tackle the easy problems?

Thursday, April 18, 2013

Sorry, what?

I have to admit to being taken somewhat by surprise. This, at a casual glance appears to be actual policy coming out of Labour. Yes, it's coming from the Green's as well, but that's not surprising, they've had actual policy policies for quite sometime.

The idea of a central buyer works for the pharmaceuticals industry - or rather, it works for us in curbing some of the excesses of the pharmaceutical industry. It's not perfect, but it's significantly  better than any alternative that I'm aware of. It'll be interesting to see how the idea of a central purchaser works for the electricity industry stands up to the economists and the pseudo-economist blogoshpere.

Another one or two of these and I might actually begin to consider the possibility that Labour could conceivably,at some point in the future, maybe get their shit together.

Tuesday, April 16, 2013

Throwing the baby out with the bathwater

I was asked for an opinion yesterday on a report by TV3 on a new diet proposed by a researcher in Auckland. Quickly following that in the conversation were references to a chap by the name of Dave Asprey, aka the bulletproof exec and a surgeon by the name of Peter Atia who runs a website called the eating academy. Both of these appear to be body hackers - customizing their diet and finding what works for them.

As far as science reporting goes, TV3 is probably one of our better media organizations, which means that I have exactly zero faith in them to not over hype the result of a single study. Despite this, my response to the TV3 report was, I believe a statement of there being insufficient research (that I could find) regarding the work the researcher proposed or the actual diet.

As for the bulletproof execs site - I am somewhat more dubious. This guy is a body hacker. There is absolutely nothing wrong with this. More power to him. Fair enough, his website documents his story, and even better his story is scattered with references to actual research. The science around nutrition is incredibly complex though. And my impression of the science referenced is that a lot of it is very specific, very focused, on small sample sizes and over limited time frames. Asserting recommendations at the level of diet from these is ... troublesome. My level of respect drops even further when there are references to causes and cures for autism, a fundamental misunderstanding or misrepresentation of epigenetics, and the site is selling a book suggesting that you can improve your babies genes whilst it's still in the womb (not to mention using the heading "Darwin was wrong" in a discussion of genes - Darwin didn't even know about genes for fucks sake - sorry, this one always bugs the crap out of me when it gets trotted out).

As for the Peter Atia website - I offer no thoughts, I haven't the time nor the inclination to look at it in depth. Though I will add that the fact that it's a surgeon writing it is no redeeming feature. Doctors can, but don't necessarily make good scientists. And over the years I've seen some doctors come out with some right clangers - surgeons being amongst the worst. Suggesting we should give them more credit because of a medical degree is similar to the logical fallacy presented in many arguments - the appeal to authority. As with pretty much all topics where I am able to offer an opinion, I will go and look at the other work related to the topic at hand that then individual has done and assess them based on that.

Look. These body hackers have found something that works for them. Using dribs and drabs of cherry picked studies and using them to back up their products - scientific, it is not. I'm not, in other words, throwing the baby out with the bath water. There might very well be something to the diets they propose - indeed, I would suggest that at the very least the actual diets they propose could very well deserve closer examination. The fact that they are referencing relevant science is to be applauded - the fact that they can't get some of the basic details right when they are using that science is being used to back up products, not so much. Read these body hackers blogs - take ideas from them and try them, see what works, what doesn't for you as an individual. It could be described as a process that takes inspiration from the scientific process (yay!), but without major work, it remains the experience of an individual (or small group of individuals) rather than solid science.

And yes researchers are beginning to look seriously at various diets and the consequences of different foods types on our health - I work with some of them and have have participated in at least one study looking at effects of given diets (as a subject). It's likely that our knowledge of nutrition and health is barely scratching the surface and a lot of what is currently considered common knowledge is at best woefully incomplete. My best guess at the moment given how diverse we are as a species, is that the answer is a damn site more complex than anyone who is selling something wants you to believe. Me, I'm eating a vaguely healthy diet and waiting for the Cochrane review.

Thursday, April 4, 2013

The big dreams are hidden

There is a need for projects that require exceeding our current abilities. When we are pushed, we can achieve great things. A prime example I think, was the space race. What the Americans especially pushed themselves to do when confronted by the possibility of Russian dominance of space was quite simply, awe inspiring. It was expensive yes, but the benefits that flowed from it far surpassed the money that was put into it. The political will faltered and now NASA seems to remain, perpetually 20 years away from putting a man on Mars.

It's not that these projects don't exist any more. They do - I'm thinking here of the various plans currently being formed to bring asteroids into earth or moon orbit and mined. The SpaceX challenge got us privately owned space flight. And I'm not just talking about space exploration. There are groups that would see us use our knowledge and abilities to decrease human suffering. There are projects aimed at bringing sustainable and non-polluting electricity and refrigeration to large areas that currently don't have it. The thing to notice though is that they all tend to be privately led rather than public ventures.

I'm not entirely sure whether this is a good thing or a bad thing. On the plus side, thing are getting done. On the downside though, these things are not in the public eye. Our societies are not looking to the better worlds that we can build. In the debates about climate change the general response of governments has been to submit to the primary source of activity, unfortunately in this case, opposed to any activity at all. It's as if the governments of the world have opted to follow rather than lead.

And it's not that it's not possible financially, for governments to lead the way. The choice is one of the distribution of funds. As much as I would like humanity to be striving outwards into space, I think it applies just as much to other projects - reducing the effects of poverty, living sustainably or making lives longer and better.
When someone says, “We don’t have enough money for this space probe,” I’m saying, “No, it’s not that you don’t have enough money. It’s that the distribution of the money that your spending is warped in some way that you are removing the only thing that gives people something to dream about tomorrow. You remember in the ‘60’s and 70’s, you didn’t have to go more than week before there was an article in LIFE magazine about, “The Home of Tomorrow,” “The City of Tomorrow,” or the “Transportation of Tomorrow.” All that ended. After we stopped going to the moon, it all ended. We stopped dreaming.
-Dr. Neil deGrasse Tyson on the defunding of NASA. 
The big projects are there, but because the governments are involved any more the public doesn't see them. Which means that we end up with the problems of everyday life as our focus, they become our life rather than problems we have to solve so as to be able to create a better world.

Thus ends my somewhat maudlin reflection for the day.

Tuesday, March 26, 2013

Exasperation coming on.

I have a lot of respect for the wisdom of Sir Bob Jones that he shares with us via his column in the herald. No, wait, that's a lie. I've got sod all.

The market will solve everything. That's this week's broken record message. In this case he's telling us that the market will take care of Auckland's housing crises. The government (local and national I presume) should butt out and let that holy of holies take care of everything. Seriously, has the man learnt nothing from the past 30 years. The market can be an efficient tool at times and it shouldn't be done away with completely.

It's not some bloody wondrous fix-everything type tool though. Like any system, it has it's own biases. For one thing, the market tends to follow the money. It doesn't really like to pay to much attention to the poor until such point in time as the poor, collectively, have enough money to make large investments worthwhile. So as much as Jones fantasises otherwise, the market is not going to step in and offer the poor better housing, there's not profit in it because, funnily enough, the poor have sod all money.

Of course, he could be imagining that the market will step in and build large numbers of expensive houses which flood the supply chain and bring the current medium value housing into affordability for the poor. That relies on more housing being built than our current growth rate requires. Eventually, we may be able to do that. It's going to take a long, long time though and in the meantime, the low and medium income earners just have to suck it.
Market systems indisputably produce the best outcomes but inherent in them is volatility, failing which they're not functioning properly. We need to recognise that and have less infantile handwringing when balances swing one way, confident that in the course of time they'll be self-correcting.
This is the bit that gets me. Let the market sort it out he says. Have confidence that any imbalances will be self correcting. 1) They not always self correcting and 2) that infantile hand-wringing? That's because it's it's actual people living in poverty, not just some bankers bottom line that is coping with that volatility.

What an arse.

Thursday, March 14, 2013

Well that's ... encouraging

I suspect I'll be reading a little more in days to come. Not that I'm enthralled with their reporting mind. It's more of an ... organisational thing. They have apparently just hired a chap called Harkanwal “Kamal” Singh, who, to be honest, I wouldn't know from a bar of soap. The capacity in which he has been hired though is "Data Journalist".

 There is a large amount of data floating around our world at the moment. And even though much of it might be technically accessible, very little is actually accessible by the general public. Primarily because of the sheer volume. I'm reasonably conversant with how to navigate large amounts of data but I have neither the time, nor the background to be able to ask the right questions. There has been for a while now, a small but noticeable movement in some journalism circles towards extracting stories from the large amounts of data that is available. Data driven journalists have even been putting together guides to help get more journalists trawling through the data.

Needless to say, I'm a large fan of the idea. In years to come I hope it becomes a core part of journalism - extracting what we need to know from bodies of data that the rest of us have neither the time nor the skill to navigate. The fact that there are people paying attention to this sort of thing gives me hope. Just as I suspect that the little burst of disappointment that comes along almost every time I read a story in our media that use statistics in anyway comes from how badly it is currently done.

Wednesday, March 13, 2013

See the link?

I saw this yesterday. Bill English, our Minister of Finance warning farmers that if we get the higher frequency of droughts and extreme weather that NIWA are suggesting we might get as a result of climate change.

Colour me surprised. Climate change might have an economic impact? It was pointed out on twitter this afternoon by @georgedarroch that some time ago, when our Minister of Finance was in opposition, he mounted both a tractor on the steps of parliament and an effective campaign against a proposed tax of 85c per year per cow that was meant to fund research into reducing emissions. Emissions that fuel climate change. The same climate change that is likely to lead to greater levels of extreme weather, to the extent that the government  probably won't be able to support farmers which is going to lead to farmers losing their livelihoods.
Bruce Wills, national president of Federated Farmers, said the industry had been dealing with wildly fluctuating weather for many years. 
Well that's lucky Bruce, because your industry is going to get a lot more practice at it. It's not necessarily the fault of all farmers - I have no doubt there are a decent chunk who have considered climate change a threat for some time. If I were a farmer though. I'd be a little pissed at those who represent the farmers, those that for some years have been amongst those who have resisted change.

A couple of things to note here. The proposed research wouldn't have, on it's own, prevented the increased climate variability that we're seeing. Even in 2003, there probably wasn't much we could have done to stop what is happening today. We could very well have made an impact on what will be happening in 2050. Blew that one. There is however, such a thing as getting your own house in order before going to the world at large to demand action. New Zealand has stood up and taken unpopular issues onto the world stage before, we could have done it again.

And I'm sure I rattled on about this before, but treating nature as part of the infrastructure of our economy is essential. To continually externalise the cost and assume that nature will sit there remaining unchanged is foolishness in the extreme. Nature is not just part of our economy, it is the base upon which it all rest. Without water in our dams electricity is not made, without rain on the fields, we have no dairy industry, if we fish with no regard for the oceans, we end up with no fishing industry. If you dig up more coal to power greater levels of industry, you release more carbon into the atmosphere, which is seriously, not going to help.

Friday, March 8, 2013


There's a movie coming out shortly, called Enders Game. It's based on a superb book,  a classic sci-fi novel by a chap called Orson Scott Card. It probably helped that I first read it when I was probably about 12. So I'm a little nervous about the movie. I regard the book being mostly about the psychology and the appalling situations that the main character (Ender) is put in. I'm not sure how that's going to translate to the big screen.

I might not go see it on the big screen though. When an author becomes outspoken on social issues (in a non literary capacity) it can become hard to separate your idea of them from their work. For example, over the past few years, I've not found the Dilbert cartoons to be particularly funny. Ever since I found out exactly what sort of anti science, rabid climate change denier type knob that the author Scott Adams is.

It's an odd thing this association. Emma Hart was talking about it yesterday - the idea that with art, it shouldn't matter how horrid the artists was, the piece of art itself remains beautiful, if it was beautiful to begin with etc. With writing though, Emma suggests, and I think I agree that it's different. I don't say this because it should be, I say this because this is what I have found to be the case for me.

Enders Game was and remains for me, a great book. I've read several of Card's other books, none of which have been as good. I'm moderately confident that they aren't as good because I can recall reading some of them before I found out a couple of years ago, what a major asshat Card is. I knew fairly early on he was a Mormon. That didn't bother me to much. Being a complete homophobe and  fully on board with the idea of overthrowing governments that legalize gay marriage - that bothers me.
 " Regardless of law, marriage has only one definition, and any government that attempts to change it is my mortal enemy. I will act to destroy that government and bring it down"
"Because when government is the enemy of marriage, then the people who are actually creating successful marriages have no choice but to change governments, by whatever means is made possible or necessary. "
Maybe his personal views shouldn't bother me and I should look on the movie as a piece of art detached from Card. I don't seem to be able to though. And as Emma points out, some of the money this movie makes is going to find it's way back to Card and support him in his endeavours. As a result of his stated views on gays and gay marriage there are, understandably I think, a large number of people who are not particularly fond of Card. A significant number of those people are geeks - by virtue of the fact that Card's audience prior to his activism was primarily sci-fi fans.

Then a short while ago, it was revealed that DC had retained the services of Mr Card to write a special edition of Superman. This news was not taken ... well, by many people. Having a hero who is meant to uphold the idea of a land free of hate (amongst other things) written by a writer so obviously full of it is disturbing. There were/are petitions calling on DC to not publish Cards story. The artist booked to draw Cards story withdrew.  There's even mutterings that the studio putting out Enders Game is getting a little nervous about fronting Card at various sci-fi conventions as part of the promotions for the movie.

Some have suggested that this is an abrogation of Card's right to free speech. You should all know where I stand on that particularly facile argument - the right to free speech does not guarantee a platform, it should only ensure that no governmental authority is able to censure what you. Besides, it works both ways. Claiming that protests against someone should stop because they violate that persons free speech are pretty much calling for the free speech of the protesters to be quashed. DC deciding not to publish the comic written by Card would DC listening to their customers who don't want to support a venture that supports Card and in turn supports his activism against either themselves or their friends and families. I really don't see anything wrong with that.

The best summary of the arguments against supporting either the Superman comic or the movie are here, read them. I won't be buying the comic - not that I would have anyway, but I don't think I'll go see the movie either. The total proportion of my money making it's way back to card would be small. I'm just not comfortable with any of it getting back to him.

Thursday, March 7, 2013

Where is the good news?

A better question would be, why does only bad news sell. An even better question would be does only bad news sell?I'm not going to argue against the need for bad news, we need to know when public servants or politicians are lying*. We need to be aware of trends in the greater world - i.e. climate change. The good news always seems to be fluffy and borderline meaningless. Or about sports. So the things that take the headlines are primarily bad things.

One possibility that is trotted out often enough is that it's the bad news that sells. And it obviously does. The counterpart to that argument though is that good news doesn't sell. I've been watching a cooking programme called River Cottage - this particular series of River Cottage is all vegetarian. An observation was made that there was and had only ever been only one vegetarian dish on the main menu because that's what the market wanted. Which immediately raised a logical fallacy type flag in head, how do you know that's what the market wants if that's all you've ever offered them?

The things that take the headlines are generally speaking either bad or sports related. Could we not offer the number 2 or 3 spot to some well thought out, well reported good news. I'll even offer a jumping off point :

 Not news in and off itself maybe, but we had William Shatner talking to one of the astronauts on the space station recently. How about an ongoing theme through our media for a couple of weeks about space exploration and the plans currently being made to bring asteroids into moon orbit so as to be able to mine them? Something for the public to be inspired by?

It occurs to me, as I write this that  the primary problem with reporting good news, might very well be that it's more expensive that reporting bad news. Bad news happens right in front of your face. Good news has to be sought out. And it requires retaining well trained and specialised journalists.
I will admit there is a possibility that there is good news in the news - a lot of it science related, which I don't see as good news because it's so poorly reported.
It also occurs to me that I may have made a related argument once before with respect to the need for grandiose projects. Things to inspire people, to get them talking. We still need to talk about all the bad stuff, it'd be nice though to have some larger, positive themes running through our public discourse.

*No, politicians do not lie all the time. Some of them are devoted to some pretty stupid, fundamentally detached from reality type policies, but I don't doubt that large numbers of our current National government are in politics because they think they are doing the right thing - reality be damned.

Wednesday, March 6, 2013

Withholding judgement

There's a new bar in Kingsland opening shortly. I find it sad that my first reaction to a new business in the area is to deadpan a completely unenthusiastic "oh yay". There's a certain amount of me being a snob in that reaction. There's also a large chunk of not being able to get excited by the same old things being trotted out as new and "cool".
Kingsland already has several bars. A couple of them are even pleasant places to hang out. Which is good. What I'm going to grump about is the beer.  We already have a large Monteiths bar and a large Macs bar. Which is Lion and DB taken care of. One of the smaller bars - the Portland Public House has a few decent brews in bottles but all their taps are taken by Monteiths beers.

So when this latest bar started being put together I was quietly hopeful in a cross my fingers and close my eyes really really tight kind of way. It looks like a nice place inside and it adds another sunny courtyard to Kingsland. There's lots of nice places and sunny courtyards in Kingsland already though. What I was really hoping for was some good beer - preferably on tap. not relying on the big breweries is not an impossible business model - Galbraiths have been doing it for years, Golden Dawn has been serving good (Hallertau) beer on tap for years now and O'Carrols in Vulcan Lane has so much good beer being served on tap that I can quite happily dither for several minutes whilst trying to decide what to drink.

My hopes have not completely died but they've at least taken a severe beating and are on their way to the emergency room. Walking past yesterday afternoon I see the new bar, Citizen Park being stocked. Couldn't see what beer was going on the taps, but the sun umbrellas in the courtyard ... Heineken. [deadpan]oh yay[/deadpan]. Same old, same old. Still, one must withhold judgement- the possibility of good beer* being served alongside the horrid stuff is still there. Fingers back to being crossed ... ow.

*For the record, Moa is good beer, but I hope this doesn't come in - it's marketed, in my opinion, by wankers, for wankers, not something I particularly want to support.

Tuesday, February 26, 2013

Food that leaves you feeling empty.

A week or so ago, myself and a friend met anther friend at the French markets in Parnell. I haven't been for a while, and it hasn't changed that much. It's a bit bigger now maybe. I don't recall being overly fond of it before, but this time, I found myself outright not liking it.

There's nothing wrong with the food. A lot of it looked very tasty. Some of the cheeses were quite lovely. One of my coffee companions asked if it reminded me of the Matakana markets, another market that I'm not particularly fond of. Indeed there are similarities between the two markets. My primary objection to the Matakana market is that it presents itself as a farmers market. I don't think it is, I'd be much happier if it was described as an artisan market. Everything is gourmet this, special handmade that or cold smoked something or other with wood cut down by virgins on the full moon after the winter solstice. An exaggeration, but you get what I'm getting at. Or at least I hope you do.

The markets down at the Silo cinemas aren't much better. It's all food for eating there and then but that same sort of marketing applies. It's all small portions for high prices of gourmet branded foods that elsewhere in the world are cheap and cheerful street food.  

Then, a few nights ago, I was attempting to watch one of Jaime Oliver's new cooking shows. Seriously, I lasted about 3/4 of the way through the 1st episode. It struck me as very similar to a Gordon Ramsay show I tried to watch about a month ago. Nothing wrong with the food, different styles between the two cooks obviously and some of it sounded quite nice. The problem I had was that everything was described as superb or astounding or spectacular. The amount of hyperbole was off putting.

Even after all of that, I probably wouldn't have written out it. Then last night, watching Hugh Fearnley Whittingstall's latest River cottage instalment, the differences became blinding. Food was described as good. Not spectacular. Not mind-blowing. Good. Occasionally with little burnt bits around the edges. Which is what cooking is to me and what I want food to be. Astounding is good every so often, but when you're immersed in it the words become empty. That association of emptiness and food I find disturbing. It's what I find on most cooking shows and it's what I find in a lot of Auckland markets. The food becomes not for everyone but only for those who can afford it. It almost feels like an attempt to partition food off into approved, good stuff that only the right sort of appreciative rich people can have) or icky food for the plebs. It might not be the intent but for me at least it endows food with moral qualities. A sort of backwards snobbery,  "look at me, I'm doing things the good, old fashioned way, which is superior to modern methods" sort of thing. 

The food might well be very nice, but the way they market it leaves me feeling empty. And also not particularly hungry for whatever it is they're selling.

Friday, February 22, 2013


This little snippet :
2.  When someone points out that you’ve totally innocently slipped up and thus contributed to [problem], saying “oh shit, you’re right.  I’ll work on that.”  No one necessarily expects you to be perfect, because this shit is internalized and subconscious, right?

comes from a QoT post. The post itself is a oft repeated (not by QoT, by many people) about how to be an actual ally to a cause. I'd just like to note though, that this one paragraph can be useful for life in general. Compared to many (most?) my life is pretty damned easy. And good. Which means that sometimes I get caught up in my own little problems and fail to take sufficient heed of others. Having someone to point out when you're being a bit of dick is very, very good thing.

One of the (numerous) ways that I consider myself lucky, is that my two closest friends at least are willing to tell me to rein myself in a bit when I'm being ... oblivious, is probably a good word. On the off chance that you have friends like this, treasure them, you're bloody lucky.

That's all.
Carry on.

Wednesday, January 30, 2013

Toe in the water.

It's been a long, long January. A lot of it in a paddock a long way away from a computer. Which, while lovely, is making it a little difficult to get back into the swing of things. The world does not stop when I'm gone (where's your sense of priorities world?) which means that there's so much to catch up on. My rss feeder apparently stops counting at 1000 items to read. It's taken me a few days but I've got it back down to 3-400.

So in the interest of putting my toe back in the water of the happenings of the greater world, I'd care to offer you this. The Greens new housing policy. A while ago, Labour released one which basically said, we're going to build a bunch of low cost homes, yay!. Which was all well and good. There was however no real means of targeting those homes to lower income groups - the ones that need good solid homes the most and are currently excluded from the housing market.

The Greens have added to this by offering a scheme wherein the government builds the low cost homes and the tenants then pay the costs associated with the governments borrowing and if and when they can, make extra payments to purchase equity in the house. Superb idea. Nicely summarized here.

I think it's a good idea to target new low cost housing to low income groups. From what I hear from my town planner acquaintances, the whole idea of the market taking care of this particular problem just isn't working because all the developers building new houses (especially out of the fringes) are trafficking in high cost developers - that where a developer gets their best returns. The only other objection I think I should mention is that the high cost of sections is going to prevent all this low cost housing - i.e. the cost of a section in parts of Auckland approaching $3-4,000,000 will make building houses for $300,000 difficult. To which I call bollocks. I've not seen anything yet to suggest that all this low cost housing is going to be individual houses on individual sections. If this scheme is going to work in with Auckland cities long term plans, I dare say a lot of the new low cost housing will be medium density at least, hopefully based around decent transport/rail corridors. 

Friday, January 18, 2013


So, I'm sitting in a shed in a paddock in almost the middle of nowhere (South Waikato, the beer selection is terrible, trust me). Given the ability of little things to trigger bouts of nostalgia, I offer my latest nostalgia inducing image.
Not so much the contents (beans, I'm cooking for large numbers of people, the food is cheap but nice). Rather the pot. Or more correctly the dutch oven that it's cooking in. It's the same pot that Dad used to cook meals and loaves of bread in when we went camping as sprogs. I managed to convince Dad to part with it for a couple of weeks, cleaned it up and got it back in service. And I have to say, it's a pleasure to cook with. Superb piece of cookware. And very nostalgia inducing. Very cool.

Friday, January 11, 2013


Whilst, as you may or may not have noticed, I am finding it difficult to write much at the moment, I will take this moment to note that, after a long day moving a friend into a new house, lying on bean bag with a gin in hand and more in the chilly bin, waiting for the outdoor movies to start and with cooked meats on the way ... life is good.

Hai everybody!