Friday, September 28, 2012

Nerdnite - Chapter 2.

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

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

Tally ho.

Extractions

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

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

Tuesday, September 25, 2012

Open source science - equipment.

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

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

Monday, September 24, 2012

Surprisingly relevant

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

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

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

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

Thursday, September 20, 2012

When is a good time to talk?

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

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

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

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

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

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

Tuesday, September 18, 2012

Where's a good place to talk?

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

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

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

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

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

One little thing.

Via Twitter:

Working to keep NZ GE free

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

Friday, September 14, 2012

Some thoughts about crowd-funding

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

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

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

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

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

Thursday, September 13, 2012

A fine distinction maybe?

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

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

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

Tuesday, September 11, 2012

Cue spin ....

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

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

Friday, September 7, 2012

And a smile for Friday.

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

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

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



Thursday, September 6, 2012

Who stole the editors?

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

Wednesday, September 5, 2012

Fighting the forces of evil.

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

An example.

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

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

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

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

Tuesday, September 4, 2012

One size doesn't fit all.

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

Nerdnite - Chapter 2.

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

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