Friday, September 30, 2011

Life just gets better and better.

Your genome is the sum total of all your genetic information. That's the actual genes that code for proteins that do all the work as well as all the bits of DNA that are used to regulate the genes and the bits that are coded into RNA which then control the regulatory sequences. There is, to steal a line from Ben Goldacre, a metric fuckton of information encoded there. It is not however, the sum total of the information that controls your make up though.
DNA is normally stored all coiled up. There's a whole bunch of things that latch on to DNA that open up certain bits of the coils or tighten up the coils making them less accessible to the cell machinery, which in turn can turn genes on or off. All this extra control is called the Epigenome.
"Epi-: Prefix taken from the Greek that means "on, upon, at, by, near, over, on top of, toward, against, among."
Which is basically all the things that attach to the chomrosomes that also have a roll in controlling the cell (these can be changed by environmental factors which has led some to believe (and rattle on about) Darwin was wrong and the theory of evolution is wrong, which is, in short, bollocks).   Funnily enough, this extra layer of epigenetic control increases the amount of information involved in controlling the cell significantly. Which is brilliant for those of us who like disappearing into a morass of complex control networks. Even better, there's an initiative in Europe that's about to start mapping the human epigenome. More data, more stuff to figure out. <grin>

Thursday, September 29, 2011

Well if you look at it that way.

Danyl's got an interesting way of looking at the whole police pushing for urgent retroactive action to legalise their breaking of surveillance laws.
The police obviously consider Valerie Morse a risk to the community. They charged her with terrorism! That charge was thrown out by the Solicitor-General, and the Supreme Court dismissed the other charges against her because the police made an informed decision to break the law when they collected evidence against her. Because the police acted illegally, someone they consider a terrorist is at large! Haven’t they put us at terrible risk? When do we see some accountability on that score?

The fact that no one in the police is going to face recrimination for this bugs me somewhat. They've cocked up and rather than sort out where the cock up is and how to fix it in the short term, they're running round with their hands in the air shouting boogieman! I'd rather have a police force that takes responsibility for anything they've done wrong like a grown up and gets on with fixing it.
The argument has been made that they've been doing it for years and they thought what they were doing was legal doesn't really hold water with me. a) they're the police, they should damn well know what the laws they are enforcing are and b) pleading ignorance of the law doesn't work for the general population and damn well shouldn't for the police. I'm having a hard time deciding whether it would be worse to have a few more serious criminals on the street or a police force that is ignorant or willing to break the law.

Tuesday, September 27, 2011

It has begun.

So, he said, I've started my PhD. I thought I'd offer a little overview of what I'm going to be doing for the next few years.

There's a bacteria called Pseudomonas syringae, which is a plant pathogen. It has a number of different varieties or pathovars, which are quite specific in terms of which plants they use as hosts. One of these pathovars, P. syringae pv actinidiae, attacks kiwifruit. I'm essentially going to be spending the next few years looking at the interaction between the two organisms - various cultivars of kiwifruit and Psa.
I'm assuming that everyone knows about DNA, not necessarily it's exact structure or how it works, but at least that it exists and that it's where the instructions for a cell are kept. Proteins are the molecules in cells that do all the work, in addition to constructing and operating the cell around them, some of them make more copies of themselves, using the instructions in the DNA. An intermediate step in the process, between getting getting the information out of a piece of DNA and turning it into a protein is the production of RNA. RNA being a molecule very similar to DNA but a lot more mobile. So, as part of this PhD, we are going to be extracting large amounts of RNA from kiwifruit plant cells, some of which will have been infected with Psa. This will let me see which genes are in the process of being turned into proteins and various different times. If some genes are being turned on in infected plant cells but not in clean plant cells, there is a possibility that those genes might be involved in the plant attempting to fight off the pathogen. The long term goal is to build up a computer model of how the various genes interact and how the plants genes interact with the bacterial genes that are attacking.

All of this will hopefully let the plant breeders at Plant and Food Research identify genes that will improve the resistance of the plants to the bacteria. Which would be a good thing, given the damage this bug is currently doing to our kiwifruit industry. I'm going to try and pepper this blog with a more details over the coming months, which will involve posts at various levels of biology and maths, hopefully I won't bore anyone to much.

Monday, September 26, 2011

Estimating crowd numbers.

200,000 people right. Completely unexpected that, everyone predicted 50,000. And with so many more people than expected it can't really be anyone's fault that things failed right?

Several months ago, December I think, my attention was called to the work of one Tony Cooper, a man with a pretty damn good pedigree in stats and a vested interest in producing accurate numbers. I recall thinking that 300,000 people attending the Santa Parade, the number being bandied about was quite impressive. Then along comes Mr Cooper, does a little bit of applied maths and wh'hey - actually you'd only fit about 30,000 people in there. He's at it again, looking at the RWC crowds. his best estimate for opening night down on the viaduct - 70,000 max. Iiiiinnnntersting. If he's right then we have a situation where they got the expected numbers right and things still failed. Even if he's not completely bang on with his estimate, it casts serious doubt on the 200,000 number.

And actually, while I think about it, what sort of organisation allows claiming that it 300,000 people can get into and out of town with little or no problems for a Santa parade yet can't handle 200,000 rugby fans with 4 years of planning?

Friday, September 23, 2011

Hello hyperspace - fingers really really crossed

There's a nice summary on Miscience of the faster than light neutrino story that's doing the rounds in the mainstream press at the moment. Read it. The few mainstream articles I've seen also mention that these are not confirmed results, which is good as it means I don't have as much cause to rant today as I otherwise would have. They also mention that the researchers are appealing to the physics community to have a good look over the results to confirm things.
Aimee covers a couple of possibilities bandied about by in the know physicists, such as the speed of neutrino's possibly being the limiting factor rather than light or neutrino's taking shortcuts through other dimensions (hyperspace maybe!). None of which matters until the physics community makes sure no one has misplaced a decimal point and figures out what the hell is going on.
An interesting point she brings up at the end though - who's driving all the press coverage? Doesn't appear to be the scientists. The media has a long history of presenting provisional findings as fact though they appear to be acknowledging that it's all provisional at the moment. I wonder if they will conviently forget that point sometime soon.

Very small games.

Foldit has been going for a while now, it's a game that uses gamers spatial reasoning skills to figure out the shape of proteins - something computers are still a little ... slow at. And it appears to be working quite well. Ars sums up a paper recently published with both scientists and gamers listed as the paper's authors - they solved the structure of a protein involved in the life cycle of HIV that was thought to be a protease. The started off with a bunch of incorrect models and let the players tweak them. It took them 16 days apparently, though I'd be interested to know how many gamers there were doing the tweaking and how they got their initial models, just to compare to how long it traditionally takes to solve the structure of a protein.
Why is this sort of thing important? If we know the structure of a protein, we've got a better chance of finding a drug that targets it, which in turn may mean new treatments.

Thursday, September 22, 2011

Rule of law.

This is the other side of showboating politics, the more serious side. There's been a lot written in various places over the past couple of days about the circumstances which the current government is attempting to rectify by implementing retroactive legislation, namely turning illegally gathered evidence, retroactively into legally gathered evidence. There are two pieces that I think are worth reading on the topic, Mai Chen in the Herald today, and Andrew Geddis on Pundit yesterday. Andrew makes the point that if the crimes are serious enough, the courts can still use illegally gotten evidence so using "bad guys are going to get away" is poor justification for retrospective legislation.

There are a couple of larger, more important points made by both of these people, ones that I wholeheartedly concur with. One of the problems with retrospective legislation is that you can make something that was illegal legal. In this case the illegal actions were those of the police. Allowing those actions to be legalized gives the impression that the police are above the law, that they can break it with impunity and have parliament sort it out later. One of the most important things that distinguish a police force from an occupation force is that they are bound by the rule of law. Retroactively legalizing criminal actions on their part removes responsibility from the police removing them from the rule of law. Which is not to say that the police are about to descend into lawlessness. Two points though. If the general population think of the police as being able to operate outside the law, why should they be regarded as anything other than state sanctioned criminals. And if there actions are retroactively legalized once, what is to stop them from seeking to have it done again. Retroactive legalization of criminal actions on the part of the police, especially under urgency where no input from the public is allowed, in my opinion would weaken the trust the general populace have in the police. Which is a bad thing.

One of the things that annoys me the most about our current government is there seeming disregard for the rule of law. They give me the impression of people who think that the act of governing gives those in power carte blanche. It doesn't. Or it shouldn't. You don't go giving people broad powers via badly written legislation and say it'll be alright because those people will only ever use those powers in the manner intended. They will. Humans don't have a good history in that respect. I would prefer the legislation my government passes to take time, have been looked over by a bunch of incredibly devious lawyers to get rid of loopholes and to be prospective. Breaches of current laws should be prosecuted rather than amended.

Besides, if they can make something that was illegal legal, what's to stop them making something that was legal illegal. Not the sort of confidence I want to have in my legislature.

Wednesday, September 21, 2011

Showboating politics.

I'm beginning to think that there are two options. Either our current government has no idea of what it actually means to govern or they're deliberately trying to be overly showy about how they do things. Of course it could be both. Think about it though, The Christchurch recovery legislation that was put through in a such a hurry. As best I can recall, it was mostly already covered by other legislation, which left me thinking it was mostly about being seen to be doing something. Minister of Tantrums McCully stepping in and taking over a process that he was in charge of anyway to "make sure it all gets done", sum total benefit over and above what was already being done - 2 extra screens and 20 extra portaloos. John Key trying to get retroactive legislation to legalize illegal surveillance undertaken by the police so that nasty criminals don't get away with it - when if the crime is serious enough, the court already has the discretion to admit illegally obtained evidence. It's all about being seen to do something, no matter how ineffectual it actually is.

Extreme Weather.

A few weeks ago, we had snow in Auckland. Snow. It has apparently happened before but not while I've been alive.
It's hard to tie any specific wather event down to global warming. You can't say this particular flood or that particular hurricane was as a result of global warming. What you can do though, is look at the number and intensity of extreme wather events. If a region used to get 5 hurricanes a year and is now getting 8 or 9, you've got an increase in the frequency of extreme weather events that can be attributed to global warming - if it's what all the models we have have been predicting. There's a couple of papers out recently, summarized at Hot Topic, in which the researchers have gone back and looked at what the climate change models have been predicting and at recent weather trends. Surprise surprise, we can already see the effects of climate change.
And to top it all off, there's a decent chunk of the world that is likely to end up with their average summer becoming as hot as their hottest summers from the past 50 years. Which is unfortunate, I'm not a fan of stupidly hot weather.

Tuesday, September 20, 2011

Idle thoughts and trains.

I was wandering past the St Lukes mall on my way yo work this morning. It occurred to me that I can't actually recall every actually going to a mall in my 3 years in London. Mall's tend to be car friendly or at least require car friendly type places. In London where there was a lot more in the way of trains, what you had instead of mall's was little bunches of shops and apartments close to the train stations. So there was no running around with hands in the air declaiming against the big businesses killing the communities or the little businesses. Nothing concrete in that thought, merely an idle correlation. Possibly something for someone with a town planning background to look into maybe?

Monday, September 19, 2011

A glimmer of hope.

Only a glimmer at this stage, but it appears to be one of the better glimmers we've had of late. There's been a trial of an HIV vaccine in Thailand. Interestingly, it was a combination of two other attempted vaccines that don't appear to be very successful. It's not an entirely successful vaccine, the people who got the vaccine were only 30% less likely to get HIV compared to those who got the placebo. It is however, a noticeable immune response, that has given HIV researchers some promising leads in looking for a more effective vaccines. I don't think I really need to say much about an HIV vaccine being a big thing.

A glimmer of hope.

Only a glimmer at this stage, but it appears to be one of the better glimmers we've had of late. There's been a trial of an HIV vaccine in Thailand. Interestingly, it was a combination of two other attempted vaccines that don't appear to be very successful. It's not an entirely successful vaccine, the people who got the vaccine were only 30% less likely to get HIV compared to those who got the placebo. It is however, a noticeable immune response, that has given HIV researchers some promising leads in looking for a more effective vaccines. I don't think I really need to say much about an HIV vaccine being a big thing.

Friday, September 16, 2011

Diamonds in the sky

Floating round the edge of the news for a short while has been the news that some Australian astronomers have found an exo-planet that has large parts of it composed of diamond. Which is pretty cool. Though i'm still more impressed with the idea that we can now figure out the compostion of exo-planets.

Then I saw this. One of the astronomers wrote this brilliant wee piece talking about how it's been unvirsally positive for him (though not particularly significant in terms of astonomy) and how it could have been a lot worse. Short answer: They could have been climate sicentists. They've followed the same general process as climate scientists, studied their models, compared their models to obcservation, had everything peer reviewed and the press has lauded them. The climate scientists do the same thing and they get attacked and written off as people of dubious ethics in it for the money (ha!) amongst other things.

It's enough to give one the impression that people are willing to accept what science tells them, as long as it doesn't conflict with their world view. Which is a fundamental misunderstanding of what science is. It is about finding out about the world regardless of what we want the world to be.

Thursday, September 15, 2011

Another one bites the dust.

Not globally, but in India at least, Polio cases appear to have dropped considerably, to 1 case reported this year. It's cool that we're now at a stage where we can get rid of entire diseases (smallpox, last recorded case, 1978). Measles was pretty much gone in the US, though it's on it's way back now that there a bunch of people who shun vaccines, endangering everyone. Having polio gone would be a good thing as well. The measles case though show the need for worldwide, sustained cooperation in eradicating diseases though. Malaria is another one, there are parts of Africa that get quite successful at eliminating it for periods of time. After a while though, people become complacent, preventative measures fall by the wayside and the disease creeps back in from other places that haven't eradicated it.

Wednesday, September 14, 2011

Time for a tantrum

I've read a few different perspectives of McCully's take over of the world cup party. Russell's, Danyl's, even Fran O'Sullivan (yes, I'm having difficulty with the worrying idea that i'm finding O'Sullivan is vaguely sensible this morning). There's a couple of things that have been noted. Firstly, that in taking it over, McCully's trying to distance himself from a process he was very much in charge of in the first place. There were multiple failure's, McCully's disowning all of them. As a whole, it's a massive vote of no confidence in the organisational structure that central government put in in the first place. And rather than focus everything on the rugby and have a bit of fun, which rugby fans should be, while someone fixes stuff in the background, this just bumps the games (which should be the focus) off the front page.  *edit Also, how does this present a comforting picture to international businesses, it says that the administration of our major economic powerhouse is incompetent - comforting much?
In the end, I concur with Russell's summing up:
"Yet in the long term, the lesson is this: it's not just about the Rugby World Cup. Aucklanders have shown they will flock to their newly-opened waterfront precincts. We need to re-engineer our transport systems and the downtown CBD to make that work. And we need central government to help and not hinder that change."
Right, enough bloody transport stuff. I'm going to go read something interesting for a change (sciencey stuff). If you're lucky, I might even write about it.

Tuesday, September 13, 2011

Ummm..... what?

Seriously, I have no idea what this means. The government is taking over the waterfront? McCully is going to take over and sort everything  in a matter of weeks becuase the council (working with the government) couldn't sort it 4 years? Here I was figuring it would all get swept under the carpet and quietly ignored and then McCully starts having a tantrum and brings it to the fore.

Monday, September 12, 2011

Journalistic echo chamber.

I wonder sometimes, if, in New Zealand at least, given the small size of our media industry, if there is some sort of echo chamber that journalists can't see out of. One in which they think they are well respected by the general population who admire them for their journalistic integrity. Does anyone outside of NZ journalists actually think they are any good? Danyl expresses a little disbelief that the Dom-post are having a go at Nicky Hager. You might not agree with Hager's conclusions (I have no idea, haven't read his books so I only know his conclusions via hearsay) but at least he's having a go at finding out the things our mainstream press should be looking at -i.e. presenting more than just the official press releases.
I don't doubt we have some hard working journalists, the one who report on the day to day stuff, the fires the robberies and the murders. And the sports journalists I suppose. I can't recall meeting anybody who actually trusts the political or business press though or the press as whole to do the big stories (like the one's Hager has a go at).

Look on the bright side. If you're a rugby fan.

Forget about the traffic woes, look on the bright side and get on with having fun at the tournament appears to be the general feeling around my slightly rugby mad workplace this morning. And I agree, wholeheartedly, that this is probably a good course of action for those who are rugby fans.

Some of us though, don't care about the rugby. And a smaller overlapping subset of us are quite concerned about the shoddy state of public transport in Auckland. For those in that position, the failures last Friday and the washing of hands from the national government are important and we should be focusing on them becuase one day soon the rugby will be over. And our shoddy train system will still be here. Now that it's been exposed (a little more than it already was), it would be nice if once the rugby is over there is still a some people reminding everyone of what it is actually like. There are some solutions that keep getting ignored by central government in favour of building roads.

Sunday, September 11, 2011

Public transport fail at the RWC.

If you read the tail end of one of the few articles
the that is being published in NZ about this at the moment, you'll see
that the head of Veoila, the people who runs the trains has apologised
to the public, while attempting to plead extenuating circumstances in
that Friday night was an "exceptional situation". 4 years. 4 years this
company has had to plan for this and he comes up with "exceptional
situation". The other word for it of course, is incompetence. And not just from Veoila. Fair enough, there's been 50 odd years of public transport fail to deal with, but with the amount of money that was being thrown around on stadium's and party venues, did no one actually stop and make sure the transport system was going to be able to get everyone to the various places? There should have been more trains than there were when the system was tested on smaller games ... actually, I'm not going to get on what they could have done. This post would be interminable.

First off it was 50,000 people expected in the city. The number being bandied about today was 100,000. That I can believe. Now all of a sudden, it's 200,000 people. Seriously. Someone needs to do some maths and figure out what the maximum possible crowd size was before it becomes 300,000. If we're not careful, the blame will start to be get shifted from commuters pushing the emergency buttons (thus apparently bringing trains and thus the entire network to a stop) to the fact that there were 500,000 floating around. And I'm sorry, but what sort of buffonery is passing for management when they turn round and say "oh, Saturday transport to North Harbour went alright" as if to make it seem as if all the problems had been sorted? It's not the opening night with a ceremony, nor is it the home team (and a semi-home team) playing. And I can just see some idiot blaming all this on Len Brown (our last best hope for halfway competent public transport) because he drove rather than trained and using it as an argument against building/maintaining the trains <sigh>.

Friday, September 9, 2011

Algorithm for the RWC

Step 1) Spokesperson steps forward from the crowd of hundreds. "We are all terribly excited about the RWC and ensuing party!"
Step 2) 4 or 5 people down the back step forward and say, "um.... actually, we're not that excited about it at all really"
Step 3) Cue inital spokesperson and various other persons calling the un-interested ones churlish, unpatriotic and accuse them of acting like a persecuted minority. And telling them that even if they don't like rugby they have to be happy about the big party.
Step 4) Back to the 4 or 5 people "...ummmm..... all we said was we're not particularly interested. You're welcome to go enjoy the game, but it'd be nice if you stopped telling us how we feel, thanks". Add 1 frustration factor for each time this step is reached. Any thing over 10 and you're allowed to seethe.
Step 5) Return to step 1.

Adapted from the comments on Danyl's post.

Thursday, September 8, 2011

Patents Galore.

Most people, will, I think be aware of the fact that a lot of large technology companies hold swathes of patents, which are quite often used offensively to stamp on small potential rivals. A side effect of this is that you don't often see the big companies going at each other hammer and tongs, because it would lead to all out patent war and for each patent the big companies infringe, they probably hold one that is being infringed upon. Personally, I think the whole system is silly, which makes it entertaining when war does break out, as in this case. Technically it's HTC vs. Apple, but one of the other bigger forces is backing up HTC, providing patents (weapons) for their battle against Apple. Maybe not a war, but certainly an entertaining patent battle.

Continuing a theme.

Sort of. This piece at Ars Technica is worth a read if you follow politics at a global level at all. As much as we'd like it to not be the case, the American political sphere influences our own, Doesn't matter who's in charge over there, our government will probably be seeking trade deals or signing treaties that bring elements of other jurisdictions into our own. Some of the things that are being brought into the country aren't necessarily bad, but you have to worry when the people in charge of it all might be coming from a position of dismissing expert opinion, just becuase it is expert opinion. It's fair enough to always be somewhat ... wary of expert opinion, experts aren't always right (economists and financial crisis anyone). In science though you tend to get to be an expert because you've spent a along time studying the topic at hand. And if there are flaws in your reasoning, you'll have them pointed out by other scientists well before they reach the public sphere. There's something to be said for paying attention to experts even if you don't accept their word as gospel.

Wednesday, September 7, 2011

Conflicting themes. Sort of. Not quite though.

This, I thought was quite interesting. The first part, the rise in segments of the population attempting to intimidate scientists (or at least the appearance of such) is indeed a worrying phenomena. There's an observation made somewhere down in the middle that "Science works best when it exists in a bit of a bubble". This is not meant to imply that science should be inaccessible  to the general public - it shouldn't be, at the very least a significant amount of science is paid for by public purses around the world and the I think people generally should have the right to know what their money is being spent on.
It does mean that the process of science generally needs to be left alone from outside interference - not necessarily the direction (that's another argument) but the process. The problem being that science can often come up with results that conflict with parts of peoples world view. Which leaves you with a large problem, namely how to be both open with the general public while not letting them interfere with the process without being arrogant and at the same time dealing with a public, some parts of which just don't want to know. Possibly it's going to be a case of we're not going to be able to help everyone understand the world, but it's both sad (for the) and annoying (for scientists) if a decent chunk of a population is going to be willfully blind to reality.

Monday, September 5, 2011

Quietly quietly.

Just had my first day at work, so my attention span for things not work related is quite limited at the moment. There was a couple of days off for the purposes of going to Tiritiri Matangi (very, very cool btw) and then recovering. Then, of course the news that one of my favourite games of all time ever, Deus Ex has a new iteration, caught my attention. Not that ones computer is currently in any state to be able to play such a game. In general though, life looks like it will be quiet for the next few days, I'm got my nose stuck in papers about metabolic and gene regulatory networks in cells. I am contemplating putting together a post of the next few days with a passable explanation of what those are and why they're important to what I'm doing. We'll see how that goes though.

Thursday, September 1, 2011

More Reading.

I've added the NZ Energy Strategy report to my reading list for the near future along with at least trying to glance at the draft Auckland plan. Doesn't fill me with warm fuzzies and hope after a review like this one though.

The Price of Science.

There's a piece on wired at the moment, discussing the stupid amounts of money one has to pay to access to work both current and past. I seen it first hand, the past few months as my enrolment at Uni lapsed, I lost access to the online journals. $30 US a paper? There was no way I could afford to keep up to date other than asking friends at Uni to print out the odd paper for me. It's not even as if the journals are producing something original, they're taking scientists work and then charging them for access to it.
It's going to be something I'm going to have to consider shortly. I'm starting my PhD in a few days, I'm rather fond of the Open Science movement and I'd really rather like to have a decent chunk of what I'm doing coming through on the blog. The intellectual property angle might not be too tricky, the problem I'll be working on is rather urgent and thus the backers want all the information out to other researchers as quickly as possible. The having to hold back on what I'm saying before publication though, I'll probably have to do it, but that's going annoy me.

I seem to find the comments more interesting these days.

The latest of our election year polls came out yesterday. Labour doing unsurprisingly badly. Greens doing well, which is a good thing, given they're the ones acting all grown up like. Labour is unlikely to recover sufficiently at this point methinks to be able to win power in the coming election. That's a good thing btw, a somewhat ... boisterous breakdown of possibilities is provided by QoT.
Also of interest are the comments to the stuff article that is briefly going over the poll results. In particular, the comments that are attacking the Greens.
"I think that should be the new motto for the greens: "Are you pathetic or hard-of-thinking? "
"The greens are anti everything oh well I suppose thats about 10% of Kiwis"
"More beshevelled, hemp-wearing, civil-union, vegan liberalists out there than I thought!"
It's like we have a bunch of people quite willing to put forward their view without thinking at all about what they're saying. I can understand someone disagreeing with the Greens policies, but these commenters don't appear to be doing that. As best I can tell, they are using stereotypes of the greens from about 15 years ago, completely ignoring the current crop of Greens (some of which are worrying the vegan liberalists a bit much because they are connected to big business and are more focused on getting shit done rather than waiting for utopia). I must say, I do find it odd that people are willing to assume what they thought they knew 15 years ago is still true (in politics even) and continue of express said views without checking. Hrmm.