Stats Chat

From the Herald, based on this paper

Dietary advice issued to tens of millions had warned that fat consumption should be strictly limited to cut the risk of heart disease and death.

But experts say the recommendations, which have been followed for the past 30 years, were not backed up by scientific evidence and should not have been issued.

Firstly, the “not  backed up by scientific evidence” actually means “not backed up by randomised trials”. When there’s a shortage of randomised trials on a topic it doesn’t mean there is no evidence. Randomised trials are ideal, but they are very hard to do usefully for effects of diet.  The same issue of the scientific journal has a useful commentary piece talking about the evidence and policy questions.

Second,  it’s true that there were real gaps in knowledge on the difference between types of fat back then. All fat isn’t the same, and neither is all saturated fat, or all polyunsaturated fat. Since I wasn’t in epidemiology back then, I don’t know how much this was a known unknown that should have led to more caution versus an unknown unknown.

Third, in the US at least, people didn’t really reduce their fat consumption as a result of the guidelines. For example, in a paper in the American Journal of Clinical Nutrition

In a comparison of NHANES 2005–2006 with NHANES I, men had a decreased absolute daily fat intake (by 20 ± 23 kcal, from 909 to 889 kcal), whereas women had an increased absolute daily fat intake (by 27 ± 14 kcal, from 577 to 605 kcal).

Fat intake as a proportion of calories decreased quite a lot, because calories went up, but absolute fat intake stayed fairly stable. Saying the recommendations ‘have been followed for the past 30 years’ is misleading.

Fourth, as this shows we don’t know a lot about how to make recommendations that translate to the right sort of behaviour changes. This is another area where there’s shortage of randomised trials. And of scientific evidence generally.

And finally, there was a good story by Martin Johnston in the Herald in December that gives more background on the issue. There’s genuine disagreement, but the establishment view isn’t what the caricatures suggest:

Professor Jackson reckons the Japanese and traditional Mediterranean diets offer insights. He says the balance of carbs and fats is probably unimportant as long as most fat is not saturated and most carb is the complex variety, not sugar and white flour-based refined carbs.

If a brain imaging study finds greater activation in the asymmetric diplodocus region or increased thinning in the posterior homiletic, what does that mean?

There are two main possibilities. Some studies look at groups who are different and try to understand why. Other studies try to use brain imaging as an alternative to measuring actual behaviour. The story in the Herald (from the Washington Post), “Benefit of kids’ music lessons revealed – study” is the second type.

The researchers looked at 334 MRI brain images from 232 young people (so mostly one each, some with two or three), and compared the age differences in young people who did or didn’t play a musical instrument.  A set of changes that happens as you grow up happened faster for those who played a musical instrument.

“What we found was the more a child trained on an instrument,” said James Hudziak, a professor of psychiatry at the University of Vermont and director of the Vermont Center for Children, Youth and Families, “it accelerated cortical organisation in attention skill, anxiety management and emotional control.

An obvious possibility is that kids who play a musical instrument have different environments in other ways, too.  The researchers point this out in the research paper, if not in the story.  There’s a more subtle issue, though. If you want to measure attention skill, anxiety management, or emotional control, why wouldn’t you measure them directly instead of measuring brain changes that are thought to correlate with them?

Finally, the effect (if it is an effect) on emotional and behavioural maturation (if it is on emotional and behavioural maturation) is very small. Here’s a graph from the paper

The green dots are the people who played a musical instrument; the blue dots are those who didn’t.  There isn’t any dramatic separation or anything — and to the extent that the summary lines show a difference it looks more as if the musicians started off behind and caught up.

• Ways of visualising uncertainty in statistics, from Visualising Data
• Football competes with internet porn for audience: analysis from Pornhub
  
  The zero line is ‘average day and time’: a better comparison would have been a typical winter Sunday.
• The New Yorker, on the problems with so-called precision medicine: The pace of genetics research, the variability of test methods and results, and the aura of infallibility with which the tests are marketed, she told me, make this advance a more complicated one than the EKG.  But, as the demand for DNA testing increases, she says, “it will probably be a bit worse before it gets better.”
• A panel of the Institute of Medicine has come out with a definition, diagnostic criteria, and a new name for ‘chronic fatigue syndrome’.  The question wasn’t whether people were sick — that’s pretty obvious. The question was which set of people have the same thing wrong with them, and how to tell.  It’s a statistical issue because a definition leads to counting people who satisfy it.
• It sees you when you’re sleeping; it knows when you’re awake: smart power meters on the front page of the Dominion Post.  (It also sends you lots of email whenever you alter your habits, eg, by travelling).
• “There’s no plague on the New York subway. No platypuses either”.  Ed Yong on false positives in DNA testing. His team swabbed tomato plants in a field in Virginia, analysed the DNA in those samples, and found matches to the duck-billed platypus—an Australian animal, not known to live in Virginia. They then analysed over 19,000 publicly available microbiome samples from around the world; around a third threw up matches for platypus DNA. Either the platypus secretly rules the world or, more likely, this was a hilarious case of false positives gone mad.
• NHS Choices makes StatsChat look tactful and friendly: they are going after the newspapers on Twitter
  
• “But these headlines are without serious foundation, and through no fault of the journalists.”  David Spiegelhalter on UK coverage of a study of health associations with low-level alcohol consumption.
• How to release data in a spreadsheet: clean-sheet.org.  Send this to everyone who know who releases data, or just put it on your blog in a passive-aggressive way. The key point is that data release is different from data presentation.

From the UK press, rather than NZ, but by Twitter request

• Independent Drinking red wine could help overweight people burn fat better, scientists claim
• DailyMail How a glass of red wine can be slimming
• Telegraph: Drinking wine or red grape juice ‘can help burn fat’

From the Oregon State University press release:

“We didn’t find, and we didn’t expect to, that these compounds would improve body weight,”

So, the headlines are misleading at best.

Previous research, about a year ago, showed that feeding grape extracts to mice reduced fat accumalation in the liver. The new research looked at human cells grown in a lab: cells from fat and liver cells, and showed that these extracts made them synthesise less fat, providing some support for the idea that this might work in people as well. The doses are not insane — about a cup and a half of grapes per day.

There are some important reservations (aren’t there always?)

First, the research looked at extracts from muscadine grapes, not ordinary wine or table grapes. The chemical being studied, ellagic acid, isn’t found at any significant level in the type of grapes grown in NZ (or, probably , the UK). There is some ellagic acid in ordinary wine, but only from oak aging and cork corks, so not that much in NZ wines.  There’s nothing in the research about whether you could get relevant amounts of ellagic acid from wine.

Second, while ellagic acid may reduce fat accumulation in the liver, alcohol tends to increase it. The mice and cell cultures got lots of ellagic acid and no alcohol; lots of alcohol and moderate amounts of ellagic acid might not be any good.

Finally, and more technically, the press release speculates about the biochemical mechanism

Shay hypothesizes that the ellagic acid and other chemicals bind to these PPAR-alpha and PPAR-gamma nuclear hormone receptors, causing them to switch on the genes that trigger the metabolism of dietary fat and glucose. Commonly prescribed drugs for lowering blood sugar and triglycerides act in this way, Shay said.

“Commonly prescribed” is pushing it. The best-known PPAR-gamma ligand drug was rosiglitazone (Avandia), famous for having been recalled from market.  There are still drugs that target PPAR-alpha and PPAR-gamma, but they aren’t that widely used. If this is how ellagic acid works, I’d want to see careful human trials before trusting it — it could have nasty side effects.

Thousand words edition:

• From the Sydney Morning Herald (I’m in the West Island at the moment), new recommendations for amounts of sleep now have extra ‘may be appropriate’ uncertainty fringes around the central band, representing our lack of real knowledge about sleep.  If you are an adult and get 5 or less hours sleep a night, you aren’t getting enough. On the other hand, you probably have a small child and know you aren’t getting enough, or are Margaret Thatcher.
  

• A graph for showing inequality. This has potential, but it would be more convincing if the examples involved real data. School decile data would be one possibility
  
• Orange and blue: A circular histogram of the colour profiles in film trailers (from, via)
  

Q: Did you see the headline in Stuff that eggs actually make you kinder?

A: Yes.

Q: A bit ironic, isn’t it?

A: You mean because of how eggs are usually produced?

Q: Yes. Did they use free-range eggs, or battery farmed?

A: No eggs were harmed in the research.

Q: But it says “eggs” in the headline

A: Yes, it does.

Q: Was it another mouse lab study?

A: No, this was real people (university students) in a randomized experiment. The story says that, and even links to the paper.

Q: So it’s real?

A: I wouldn’t go that far.

Q: But experiment. And causal. And Science. Yes?

A: Very small experiment with marginally-significant results that could easily be due to chance.

Q: You’ve got a thing about psychologists, like Andrew Gelman does, haven’t you?

A: No, I’ve got a thing about over-promoted, under-powered research, like Andrew Gelman does.

Q: Ok, let’s calm down and get back to the study. What did they use instead of eggs?

A:  800 mg of tryptophan powder (or placebo) in orange juice.

Q: Is that a lot?

A: They say it’s the equivalent of three eggs.

Q: Why do you sound dubious?

A: Because other websites think there’s less than that. I haven’t found any definitive primary source, but there’s about 6g of protein in a 50g egg, and from Table 2 in this 1973 paper you can compute that egg protein is about 1.8% tryptophan, which works out as 108mg.  Or in a 70g egg (‘Jumbo’ in NZ, ‘Large’ in Europe) about 150mg. It looks like you’d need more than five 70g eggs to get 800mg of tryptophan.

Q: How about other foods? Are eggs especially high in tryptophan?

A: Not especially. Chicken, or cheese, or oats, or chickpeas, for example, have more tryptophan per 100g.

Q: So if they didn’t use eggs in the experiment, and eggs aren’t particularly high in tryptophan, why are the headlines about eggs? Were they sponsored by the Egg Foundation?

A: No, nothing like that. And the university news post just talks about “the amino acid tryptophan, found in fish, soya, eggs and spinach.” It’s probably because the dose in the study was described in terms of eggs.

As I’ve often said on StatsChat, if you’re eating dark chocolate or drinking red wine primarily for the health benefits, you’re doing it wrong. Now the problem is spreading to beer. Stuff has a headline “Could beer help fend off Alzheimer’s and Parkinson’s?” As you’d expect, the answer is “Not really.” 

The story is unusually light on information, not giving the journal name, the names of any of the researchers, or the names of any of their institutions.  Through Google, I found a story in the Telegraph, where the headline is even worse — “Beer could help ‘protect brain against Parkinson’s and Alzheimer’s'” — but at least they link to a press release.

The press release headline “Beer compound could help fend off Alzheimer’s and Parkinson’s diseases”  looks less extreme than the newspaper ones, but the lead is

The health-promoting perks of wine have attracted the spotlight recently, leaving beer in the shadows. But scientists are discovering new ways in which the latter could be a more healthful beverage than once thought.

They, finally, do link to the research paper, in the Journal of Agricultural and Food Chemistry. If you think that sounds a slightly strange place to publish research about the health effects of beer, well, it would be if that was what the research was about.  The abstract says

As an active component in beers, [xanthohumol]’s presence has been suggested to be linked to the epidemiological observation of the beneficial effect of regular beer drinking.

That is, the research assumes a beneficial effect of beer and is trying to work out what the mechanism might be. The research wasn’t in people, or even in mice, or even in mouse brain cells. It was in a standard lab cell line of nerve-like cells originally from a cancer of the adrenal gland in a rat.

You might also ask if there’s any research closer to live people. Last year, scientists at Oregon State University studied high doses of xanthohumol in mice.  They found it improved cognitive function in young mice, but not in old mice, and also pointed out

 the levels of xanthohumol used in this study were only possible with supplements. As a fairly rare micronutrient, the only normal dietary source of it would be through the hops used in making beer, and “a human would have to drink 2000 liters of beer a day to reach the xanthohumol levels we used in this research.”

That’s not really compatible with the new drink-driving limits.

Every year, the Department of Statistics offers summer scholarships to a number of students so they can work with staff on real-world projects. Christopher, right, is working on the OpenAPI project with Associate Professor Paul Murrell. Chris explains:

“Government data is becoming increasingly available. However, this does not mean it is readable – few individuals possess the knowledge and skills to make use of these data by themselves.

“In an ideal world, the code used by fellow statisticians would be available to everyone. It would be even more ideal if it were transferable. Sites like Wiki New Zealand  are doing a remarkable job of displaying some of New Zealand’s trends, but with no source code it can sometimes be impossible to recreate.

“The OpenAPI project is developing a flow-based framework that is primarily aimed at lowering the barriers to use of open data by the general public. My project is about creating an architecture for programmers and statisticians of all levels. Our goal is for anyone interested to have the ability to perform analyses on open government data. The idea is that there are publicly available snippets of code from fellow statisticians that can be easily linked in a meaningful way. The less expertise required by the end user, the better.

“My job is to come up with questions I am interested in answering, then figuring out how a potential lay observer would solve them. So far it has yielded some interesting results.

“I’m a third-year student at the University of Auckland, studying a Bachelor of Laws/Bachelor of Science conjoint. My skills lie in statistics and computer science, but I need the literal side to keep a balanced life.

“I got hooked on statistics when I discovered the Poisson distribution. There’s something about statistics that never seems to get old, and I’m discovering new things every day. It’s nice knowing I can actually attempt an answer to the curiosities in my head.”

Here’s a graph from the Economist showing the impact of the measles vaccine:

The number of measles cases fell from over half a million per year to about 100 per year when the vaccine was introduced. That’s a 99.98% reduction, in a disease that (in a healthy population) kills about two people in a thousand.

Here’s a graph from the Centers for Disease Control showing that little blip in 1990 on an expanded scale:

They say

The most important cause of the measles resurgence of 1989–1991 was low vaccination coverage. Measles vaccine coverage was low in many cities, including some that experienced large outbreaks among preschool-aged children throughout the early to mid-1980s. Surveys in areas experiencing outbreaks among preschool-aged children indicated that as few as 50% of children had been vaccinated against measles by their second birthday, and that black and Hispanic children were less likely to be age-appropriately vaccinated than were white children.

Vaccine coverage isn’t as bad as that now, but the profile of unvaccinated kids is different. Black and Hispanic children are just as likely as white children to have had at least one doses of the measles vaccine, and children in poverty have a rate only 1.5 percentage points lower. Now, a substantial chunk of the problem is parents who are anti-vaccine.

Kieran Healy has an interesting post on the ‘personal belief exemption’ data for kindergarten children in California.  They are only 3.36% of children, but they cluster.  That’s important because US is just on the edge of having high enough vaccine coverage to stop an epidemic from spreading, at least if the unvaccinated were evenly spread through the population. They aren’t:

the number of kindergarteners with PBEs, even in Berkeley, is not huge—about 67 kids out of 850 in the city. But 20 of those 67 are in the same school, and probably the same room.

Anti-vaccine hysteria is more prominent in the US than New Zealand: partly because our mainstream media don’t go in for it, and partly because everything is more prominent in the US. Similarly, reaction to the risks posed by unvaccinated children has been more prominent in the US. However,  New Zealand has a similar rate of measles vaccination. Our schools or early childhood services cannot refuse enrollment based on vaccination (no special paperwork is required as in California), and (like California) can only temporarily exclude unvaccinated children if they are known to have been exposed.

Last year, New Zealand had 283 cases of measles. Scaled for population, last year in NZ was about half as bad as the US in 1990, and about thirty times bigger than the current US outbreak (so far).

Every year, the Department of Statistics offers summer scholarships to a number of students so they can work with staff on real-world projects. Daniel, right, is working on a project called Working with data from conservation monitoring schemes with Associate Professor Rachel Fewster. Daniel explains:

“The university is involved in a project called CatchIT, an online system that aims to help community conservation schemes by proving users with a place where they can input and store their data for reference. The project also produces maps and graphics so that users can assess the effectiveness of their conservation schemes and identify areas where changes can be made.

“My role in the project is to help analyse the data that users put into the project. This involves correctly formatting and cleaning the data so that it is usable. I assist users in the technical aspects relating to their data and help them communicate their data in a meaningful way.

“It’s important to maintain and preserve the wildlife and plant species we have in New Zealand so that future generations have the opportunity to experience them as we have. Our environments are a defining factor of our culture and lifestyles as New Zealanders and we have a large amount of native species in New Zealand. It would be a shame to see them eradicated.

“I am currently studying a BCom/BA conjoint, majoring in Statistics, Economics and Finance. I’m hoping to do Honours in statistics and I am looking at a career in banking.

“Over summer, I hope to enjoy the nice weather, whether out on the boat fishing, at the beach or going for a run.”