Posts from January 2016 (28)

Every summer, the Department of Statistics offers scholarships to a number of students so they can work with staff on real-world projects. Xiangjie, right, is working on vector generalized linear and additive models (VGAM) for R with Dr Thomas Lee. Xiangjie explains:

“I am trying to help Dr Yee to improve the functionality of the VGAM package. This includes writing some functions from scratch, improving the efficiency of the existing functions and testing functions. To do this, I will need to learn the underlying structure of R and write or translate some functions from other computing languages to C or R.

“I came to the University of Auckland to do my undergraduate Applied Mathematics and Operations Research in 2012.

“After I finished, I received offers to do both Applied Mathematics and Statistics. When I was trying to decide the topic of my Honours project, I realised that Statistics covers a very broad range of topics and that they are very closely related to each other – I could learn data analysis, computing or probability theory and stochastic processes. All of these topics are really useful in our daily lives. I was really fascinated by this, so I decided to study Statistics instead of Applied Mathematics. I am thinking about pursuing a masters degree or a PhD in Statistics this year.

“This summer, I am hoping to travel more in New Zealand. In fact I went camping recently with my high-school friends in Whangarei and the Bay of Islands region and I had a great time. Besides travelling, I’d like to spend some time relaxing at home, watching my favourite shows.”

• New progress in awful graphs, via Andrew Gelman

• Scientific American‘s predictions for the future, from 2005

• “Claims that forensic experts can match a bullet or shell casing found at a crime scene to a specific weapon lack a scientific basis and should be barred from criminal trials as misleading, a D.C. Court of Appeals judge wrote this week.”  The judge objected to claims that the evidence proved a ‘unique’ match. And quite right, too.

• You can prove that a treatment works without knowing how it works, but it’s much harder to find treatments that way. Lithium for bipolar and other mood disorders is an excellent example

• You might have heard of CRISPR in the news and wondered what exactly it was.  It’s a technique for cutting DNA at very easily customised locations, for example, to allow for new sequences to be inserted. Good references
  • Wired
  • Gizmodo (more comparison with other gene editing techniques)
  • New York Times (more on implications)
  • Wikipedia (more technical)

“The ‘kudzu’ could cure your hangover”, says the Herald (from the Daily Mail)

We’ve had stories based on unpublished research before. This one is a bit special, because the ‘unpublished research’ is a BBC television programme that won’t be shown for a few days (or, at all, in NZ). And because it didn’t study hangovers or people with hangovers.

The BBC programme is apparently going to report a placebo-controlled crossover trial of how much free booze people drank when they had taken kudzu root extract or a dummy pill — they say they saw a 20% difference. The design is a good one, and given the general theme of the show there probably isn’t much risk of publication bias. Having a reasonably good design fits with seeing a benefit that’s only about half of what was seen in earlier US research.

The big problems with the BBC study are that it’s probably small (the stories don’t say) and doesn’t (so far)give any idea of the uncertainty in the 20% reduction, and that open-bar drinking in a television science experiment may be importantly different from the sort of drinking they’d like to decrease.

As science, the BBC study might actually be ok. But reducing alcohol consumption by 20%, if it does, is unlikely to have a big impact in preventing hangovers. And there is not the slightest suggestion in the research that kudzu root would work as a hangover cure.

Every summer, the Department of Statistics offers scholarships to a number of students so they can work with staff on real-world projects. Eva, right, is working on a sociolinguistic study with Dr Steffen Klaere. Eva, right,  explains:

“How often do you recognise the dialect of a neighbour and start classifying them into a certain category? Sociolinguistics studies patterns and structures in spoken language to identify some of the traits that enable us to do this kind of classification.

“Linguists have known for a long time that this involves recognising relevant signals in speech, and using those signals to differentiate some speakers and group others. Specific theories of language predict that some signals will cluster together, but there are remarkably few studies that seriously explore the patterns that might emerge across a number of signals.

“The study I am working on was carried out on Bequia Island in the Eastern Caribbean. The residents of three villages, Mount Pleasant, Paget Farm and Hamilton, say that they can identify which village people come from by their spoken language. The aim of this study was to detect signals in speech that tied the speaker to a location.

“One major result from this project was that the data are sometimes insufficient to answer the researchers’ questions satisfactorily. So we are tapping into the theory of experimental design to develop sampling protocols for sociolinguistic studies that permit researchers to answer their questions satisfactorily.

“I am 22 and come from Xanten in Germany. I studied Biomathematics at the Ernst-Moritz-Arndt-University in Greifswald, and have just finished my bachelor degree.

“What I like most about statistics is its connection with mathematical theory and its application to many different areas. You can work with people who aren’t necessarily statisticians.

“This is my first time in New Zealand, so with my time off I am looking forward to travelling around the country. During my holidays I will explore Northland and the Bay of Islands. After I have finished my project, I want to travel from Auckland to the far south and back again.”

I saw on Twitter this morning the claim “90% of the worlds data was created in the last 12 months”, raising the twin questions “Says who?” and “What does that even mean?”.

The tweet linked to a story at the Huffington Post, which attributed the claim to Constellation Research, but with no further information on how they found it out or when, or what they meant by it. Further Google searches find that most occurrences of the claim are either completely unsourced, attributed to the guy who wrote the HuffPo story, or also just say “Constellation Research”.

IBM has claimed “Everyday, we create 2.5 quintillion bytes of data–so much that 90% of the data in the world today has been created in the last two years alone.” But that’s two years, not 12 months. And they’ve been saying it for some time:

In 2012, the skeptics site at stackexchange.com discussed the IBM claim and found it plausible then — assuming that ‘data has been created’ meant that ‘data has been stored in some permanent medium of the sort IBM sells’. It’s not just business data, as some of the citations imply — it will include cat videos on mobile phones, data from the Large Hadron Collider, the NSA’s archive of your email, and lots and lots of porn.

It still could be that Constellation Research has a new estimate, not the recycled one from the days before Siri. However, a 2015 Oracle presentation (PDF, slide 7) says “90% of the world’s data has been created in the last two years“, and cites “ Constellation Research: “Businesses Must Answer the Call for Cloud Based Integration”“. So I’m guessing maybe not.

Q: Did you see that laughing can burn as many calories as a brisk walk?

A: In the Herald? Yes.

Q: Can it?

A: A very short brisk walk, yes.

Q: What do you mean?

A: They say “flat out, uncontrollable, roll on the floor howling – was found to burn 120 calories an hour, similar to the amount burnt by walking at a moderate pace.”

Q: So you just need to do that for an hour, nonstop?

A: That’s right.

Q: This was a British scientist, right?

A: ….yes?

Q: The BBC has pretty good comedies

A: Not that good

Q: Do they have any real estimates of how much exercise you could get?

A: Not in the Herald, but another newspaper says their estimated maximum for the funniest show they looked at was 32 ­calories of laughter over 45 minutes.

Q: So like a quarter of an hour of brisk walking?

A: Pretty much

Q: Which show?

A: Taskmaster

Q: ?

A: I think you had to be there.

Q: And how about humour producing wry smiles and the occasional snigger?

A: That burns about as much energy as reading blogs.

Q: It doesn’t sound like a serious suggestion. Is it possible that the papers which printed this story just didn’t get the joke?

A: Could easily be.

The FDA collects data on adverse events in people taking any prescription drugs. This information is, as it should be, available for other uses. I’ve been involved in research using it.

The data are also available for less helpful purposes. As Scott Alexander found,  if you ask Google whether basically anything could cause basically anything, there are companies that make sure Google will return some pages reporting that precise association.  And, as he explains, this is serious.

For example, I tried “Adderall” and “plantar fasciitis” as an implausible combination and got 4 hits based on FDA data. And “Accutane” and “plantar fasciitis”, and “Advair” and “plantar fasciitis”, and “acyclovir” and “plantar fasciitis”. Then I got bored.

It’s presumably true that there are people who have been taking Adderall and at the same time have had plantar fasciitis. But given enough patients to work with, that will be true for any combination of drug and side effect. And, in fact, the websites will happily put up a page saying there are no reported cases, but still saying “you are not alone” and suggesting you join their support group.

These websites are bullshit in the sense of philosopher Harry Frankfurt: it is irrelevant to their purpose whether Adderall really causes plantar fasciitis or not. They make their money from the question, not from the answer.

(via Keith Ng)

Every summer, the Department of Statistics offers scholarships to a number of students so they can work with staff on real-world projects. David, right, is working on the New Zealand General Social Survey 2014 with Professor Thomas Lumley and Associate Professor Brian McArdle of Statistics, and  Senior Research Fellow Roy Lay-Yee and Professor Peter Davis from COMPASS, the Centre of Methods and Policy Application in the Social Sciences. David explains:

“My project involves exploring the social network data collected by the New Zealand General Social Survey 2014, which measures well-being and is the country’s biggest social survey outside the five-yearly census. I am essentially profiling each respondent’s social network, and then I’ll investigate the relationships between a person’s social network and their well-being.

“Measurements of well-being include socio-economic status, emotional and physical health, and overall life satisfaction. I intend to explore whether there is a link between social networks and well-being. I’ll then identify what kinds of people make a social network successful and how they influence a respondent’s well-being.

“I have just completed a conjoint Bachelor of Music and Bachelor of Science, majoring in composition and statistics respectively.  When I started my conjoint, I wasn’t too sure why statistics appealed to me. But I know now – statistics appeals to me because of its analytical nature to solving both theoretical and real-life problems.

“This summer, I’m planning to hang out with my friends and family. I’m planning to work on a small music project as well.”

OneNews had a strange-looking story about multiple sclerosis tonight, with lots of footage of one British guy who’d got much better after treatment, and some mentions of an ongoing trial. With the trial still going on, it wasn’t clear why there was publicity now, or why it mostly involved just one patient.

I Google these things so you don’t have to.

So. It turns out there was a new research paper behind the publicity. There is an international trial of immune stem cell transplant for multiple sclerosis, which plans to follow patients for five years after treatment. The research paper describes what happened for the first three years.

As the OneNews story says, there has been a theory for a long time that if you wipe out someone’s immune system and start over again, the new version wouldn’t attack the nervous system and the disease would be cured. The problem was two-fold. First, wiping out someone’s immune system is an extraordinarily drastic treatment — you give a lethal dose of chemotherapy, and then rescue the patient with a transplanted immune system. Second, it didn’t work reliably.

The researcher behind the current trial believes that the treatment would work reliably if it was done earlier — during one of the characteristic remissions in disease progress, rather than after all else fails. This trial involves 25 patients, and so far the results are reasonably positive, but three years is really to soon to tell whether the benefits are worth the treatment. Even with full follow-up of this uncontrolled study it probably won’t be clear exactly who the treatment is worthwhile for.

Why the one British guy? Well,

The BBC’s Panorama programme was given exclusive access to several patients who have undergone the stem cell transplant.

The news story is clipped from a more in-depth current-affairs programme. That BBC link also shows a slightly worrying paranoid attitude from the lead researcher

He said: “There has been resistance to this in the pharma and academic world. This is not a technology you can patent and we have achieved this without industry backing.”

That might explain pharma, but there’s no real reason for the lack of patents to be a problem for academics. It’s more likely that doctors are reluctant to recommend ultra-high-dose chemotherapy without more concrete evidence. After all, it was supposed to work for breast cancer and didn’t, and it was theorised to work for HIV and doesn’t seem to. And at least in the past it didn’t work reliably for multiple sclerosis.

All in all, I think the OneNews story was too one-sided given the interim nature of the data and lack of availability of the treatment.  It could also have said a bit more about how nasty the treatment is.  I can see it being fine as part of a story in a current affairs programme such as Panorama, but as TV news I think it went too far.

The Herald has a Daily Mail story about vitamin D for making you generally feel better. It’s not so long ago that the NZ media had a lot of less supportive coverage on vitamin D — Ian Reid, Mark Bolland, and Andrew Grey won the Prime Minister’s Science Prize last year for their work showing that calcium and vitamin D aren’t all they’re cracked up to be.

The story does have some new evidence.

In the study, by a medical team in Edinburgh, volunteers were asked to cycle for 20 minutes. They were then given either a placebo or vitamin D and, two weeks later, were asked to cycle for 20 minutes again.