Posts filed under General (3156)

If you know who Aaron Swartz was, you’ve probably already heard that he died yesterday.

Swartz was a computer prodigy and internet activist, who was focused on providing access to information, especially information that was theoretically already public but not readily available.

As a high-school kid, he was one of the developers of the RSS standard for web newsfeeds, which make it easy to integrate updates from many web sites.  He played a major role in the RECAP database, which allows people who pay for (public-domain) US court transcripts to make them available to others.

More recently, he downloaded millions of old academic articles from the JSTOR database, presumably intending to make some of them available in some form, though he never did. The Herald says

In 2011, he was arrested in Boston and charged with stealing millions of scientific journals from a computer archive at the Massachusetts Institute of Technology.

but he was actually charged with the very flexible offences of wire fraud and computer misuse, not with anything to do with theft or copyright violation.

If you want to read more about his life and death, it seems appropriate to suggest searching the Internet. It’s all there.

According to the New York Times, researchers at the University of Connecticut are planning to sequence the genome of the Newtown school murderer.  They aren’t specifically saying why, though the obvious interpretation is that they are looking for genetic causes of violence (there could be more cynical interpretations, but let’s not go there).  This seems a bad idea.

Firstly, they won’t find anything.  If you have a difference between groups of people that is completely explained by a single genetic variant, you can find the variant with genotypes on only a few dozen people in each group (eg blond hair in Melanesians, intolerance of the HIV drug abacavir).  That’s still a lot more than the number of mass murderers they will have conveniently available any time soon.   If the phenomenon you’re trying to explain is not controlled by a single genetic variant, the necessary sample sizes shoot up by orders of magnitude.  The problem is that an individual has perhaps 2-3 million differences from the reference genome, tens of thousands of which will never have been seen before. These variants are spread through 20 000 genes, regulatory regions, poorly-understood bits of non-coding RNA, and genuine junk DNA.  There would be no way to tell which of these differences is the ‘real cause’ even if there were a ‘real cause’ to find.

Secondly, what would they do with it if they found it? We already know of a common single-gene genetic variant that, in US residents, increases the risk of becoming a mass gun murderer by a factor of about 60. People with this variant are actually more likely to be employed as armed guards, and are specifically targeted by gun industry advertising.  A genetic effect would have to be much larger than this to be actually useful, and that’s before you start to consider the ethical and legal implications of screening for propensity to possibly commit a crime in the future.

And finally, if you want to understand biological contributions to violence for public health reasons, it probably makes more sense to focus on the 99+% of murders that aren’t mass shootings.

(a similar list from Jeff Leek at Simply Statistics)

As you will soon get tired of hearing around here, it’s the International Year of Statistics.

The Wall Street Journal has a story on what sorts of changes in reporting we might like to see this year.  These will be familiar to StatsChat readers:  routine reporting of uncertainty, the need for denominators and other context, an understanding of regression to the mean, and a reduced in coincidences that are only superficially unlikely.

Oddstuff has a story on German research involving cloning good-looking Christmas trees.

The story shouldn’t really seem odd to Kiwis: we’ve got whole industries based on cloned trees, including vast plantations of cloned pine trees.  And even in the northern hemisphere, parts of the Christmas tree industry already use cloned trees because some popular plants are sterile hybrids that can only be propagated as clones.

I’ve occasionally thought it would be entertaining to stage a protest about cloned apples outside a supermarket, just to see how people react…

In the early 1980s there was a significant advance in research on Parkinson’s Disease, when a number of young drug users showed up with a sudden onset of the disease.  Investigations showed that a synthetic opioid ‘legal high’ called MPPP was responsible; the methods used to synthesize it produced a byproduct MPTP that was metabolised into a potent neurotoxin and selectively absorbed into cells that thought they were getting dopamine.   Of course, this is a one-off problem with that specific drug, and not something that’s ever likely to happen again.

This sort of thing is why both animal and human safety testing is required before medications are approved, and it’s why medical chemists get rather upset at people who market untested compounds. However, it isn’t the main point behind the current NZ plans for testing legal highs, since none of the cannabis analogues Mr Dunne has banned using the interim laws would have failed basic toxicity tests. In fact, the safety problem with the cannabis analogues seems to be precisely that they are psychoactive, and that they are much easier to overdose on than real cannabis (they are ‘full agonists’, THC is a ‘partial agonist’ at the same receptors).

The problem with the new laws is that they are trying to reconcile inconsistent views of the level of safety needed.  Before Kronic started large-scale marketing and distribution, the cannabis analogues were in the sort of slightly dodgy market where you wouldn’t expect a great deal of safety testing, users knew this, and we had a pretty good compromise. When the drugs started being advertised and sold in dairies (and not just ones on K Rd), the implied level of safety was a lot higher, there were more overdose in young users, and their parents got, quite reasonably, upset.  After Mr Dunne grants his nihil obstat on production and sale, the implied safety level will even higher, and probably not achievable.

That’s why I think the animal testing issue is largely a distraction. If the regulations are going to be consistent with Mr Dunne’s bans over the past year or so, anything that has a high enough chance of approval to make the tests commercially feasible is likely to be pretty much a placebo (or placebo plus caffeine for party pills).   Whether the net health effect is positive or negative depends a lot on what is substituted for the previously-legal highs.  If it’s healthy exercise or meditation, we might come out ahead. If it’s alcohol, the impact is going to be negative.  Unfortunately, although I’m betting on a negative effect, I don’t see any easy way of getting back to the pre-Kronic situation.

[PS to Eric Crampton: Yes, I am indeed ignoring the benefits people get from being high. I’m pretty sure Peter Dunne is, too]

It’s the season for lists from the year in review.  Buzzfeed has one entitled “27 Science Fictions That Became Science Facts In 2012”. Some of these are real, but some became science facts quite a while ago, others are still in the future, and some appear to be completely bogus.

Good:

• a quadriplegic has a robot arm controlled directly by her brain.
• Voyager I leaves the solar system

Badly headlined

• DNA photographed for the first time. No, DNA is easy to extract and has been photographed many times. Individual chromosomes under a microscope were photographed years ago, and Crick and Watson used X-ray photographs to work out the structure.  What’s new is an electron microscope photograph of DNA where you can actually see the helix.
• Genetically Modified Silk Is Stronger Than Steel. This is about genetically modified silkworms that produce something closer to spider silk. Spider silk is the strongest natural fibre, and has higher tensile strength than steel, weight for weight, but actually so does ordinary silkworm silk.

Still Science Fiction

• Stem Cells Could Extend Human Life by Over 100 Years. This is actually a story about stem cells extending the life of mutant rapidly-aging mice by 50 days.  Not quite the same thing.  Stem cells extending human life is definitely still science fiction.

Probably bogus

• Invisibility Cloak Technology Took a Huge Leap Forward. You have all seen the ‘invisibility cloak’ stories that turn out to be about bending microwaves around a small toy.  This one is different. It has a perfect camouflage cloak that even knows which things behind it you want to hide, and which ones you want to reveal. It’s almost as good as Photoshop. Um. yes. Never mind.

That still leaves 21 for you to check if you get bored over the holidays

This summer, we have a number of fantastic students who received a Department of Statistics scholarship to work on fascinating projects with our staff members. We’ll be profiling them here on Stats Chat and we’d love to hear your feedback on their projects!

Liza Bolton is working with Mark Holmes on an interactive simulation of interacting particle systems.

Of the scholarship, Liza says:

“I am delighted to have this opportunity over the summer, as I’m in love with mathematics and statistics (my two majors in a Bachelor of Science) and was keen to sink my teeth into learning Java. The opportunity to solve problems, sometimes completely abstract, and sometimes with very relevant practical importance, has always drawn me to these subjects. I’ve just completed the second year of my BSc and hope to go on to Honours after my undergrad, before working for a while, and then probably finding my way back to further study.”

Liza explains what the research project is about:

“Imagine you’re on a balcony, looking down on a crowded public square. Below you there’s a sort of multi-party political expo going on. The east wall has a line of Labour Party supporters against it. There are National Party supporters lined up against the west wall, and a line of Green Party supporters on the north wall.

“Do you have that picture in your head? Now, these people lining the walls of the square are never going to change their mind about who they want to vote for. But next, imagine that all the other people in the square (it’s absolutely packed, people are shoulder to shoulder) are far more malleable in their political views. In fact, each person might change their opinion based on the people around them. To stretch the allegory just a little, you can tell that all this is happening from your perch up on the balcony because people are wearing coloured hats to show their party choice, and change to a hat of their new party’s colour when they change their mind.

“Now, political opinion is more complicated than the scenario above, but I hope this might help you picture the actual process of what I’m getting up to this summer. I’m working on creating an interactive simulation of interacting particle systems with Dr Mark Holmes.

“Instead of people, in a square, with peculiar party-appropriate headwear, think instead of a grid with each square (or particle) in the grid a colour. In each time step, one of the squares in the grid is randomly selected to change colour, based on the colours of the squares with an edge adjacent to it. If a blue square is going to change in a particular time step, and has two red and two green squares next to it, it is with probability 0.5 that it will change to green, and likewise to red. And just as with the people you can choose to line the sides of the grid with squares that will not change colour.

The goal for this research is:

“To create a Java applet that people can interact with online that exhibits this idea and also communicates what is going on in a way that will be widely accessible. By the end people will be able to play with this applet, select the colour and position of invariant squares however they like, and watch the system progress through time. Hopefully, it will be a fun little way to create patterns and watch them form, and allow for a basic introduction to the complex and fascinating world of interacting particle systems.”

When Liza’s not going square-eyed staring at grids this summer …

“… I’ll be wearing the hat of Chief Operations Officer for P3 Foundation, a completely youth-lead non-governmental organisation working to empower Kiwi youth to eradicate extreme poverty in the Asia-Pacific. I’ll be doing a bit of work for Teach First NZ, an organisation working to tackle educational inequality in New Zealand, and the family holiday programme at the Voyager Maritime Museum, too. And of course, eating ice cream, reading good books, watching Vlogbrothers and hanging out with my lovely whānau.”

The United States National Oceanic and Atmospheric Administration (NOAA) released a usual monthly State of the Climate Global Analysis in October 2012 which was anything but usual. Buried in the report was this astounding factoid: “This is the 332nd consecutive month with an above-average temperature”. What that means is, if you’re 27 or younger, you’ve never experienced a colder-than-average month. I find that phenomenal, a trend which if it continues might allow many to become ‘old timers’ who can “recollect the ‘good old days’ when a monthly temperature could be below average” (i.e. prior to March 1985).

This statement is certainly headline-grabbing, although there is some devil in the detail. Specifically, what is the ‘average’ which the NOAA benchmark against? A bit of research reveals that the NOAA use a reasonably robust 3-decade (1981-2010) average for their graphics, but the phrasing of the paragraph in question suggests that in this case they are comparing to the 20^th century average. If it was the 3-decade dataset then the months Jan 1981 – Feb 1985 would have had to have been exceptionally cold to skew the average so low that it could be exceeded 332 times consecutively.

The field of time series and calculating moving averages (and variabilities) is fascinating, and no doubt with sufficient data-mining, as in any field (imagine sporting statistics), a number of other shocking statistics could be extracted. Nonetheless a 332 month run is still impressive (or incredibly concerning). Interpretation of climate change will more and more require punters to be comfortable with interpreting both running averages and changing variabilities. We can have extremely cold snaps in a month (variability) while still having an above average month for temperature.

From the Tow Center for Digital Journalism, at Columbia University, a new report: “Post Industrial Journalism: Adapting to the Present”

• Journalism matters.
• Good journalism has always been subsidized.
• The internet wrecks advertising subsidy.
• Restructuring is, therefore, a forced move.
• There are many opportunities for doing good work in new ways.

In another story bemoaning the affordability of housing outside Auckland, the Herald also tells us

The median sale price of a home in central Auckland is now $690,000 – slightly up on the previous quarter and 12.5 per cent on the 2007 boom.

That’s still down on the 2007 boom in real terms.  The story was followed the very next day by

Auckland real estate asking prices fell 2 per cent last month

The signal to noise ratio in real-estate industry press releases is not all that high.