Archive for Language of science

When half of a quarter is all, or at least mostly

Steve Connor, "Nature rather than nurture governs intelligent behaviour in primates, scientists discover", The Independent 7/10/2014:

The vexed question of whether intelligence is inherited from birth or acquired through education seems to have been answered – for chimpanzees at least.

Scientists have found that being a smart primate is down to genes rather than upbringing, suggesting that nature rather than nurture governs intelligent behaviour in our closest living relatives.

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North, south, east, west

Bill Watkins, who teaches Chinese and science at a small independent high school near Baltimore, asks three semi-related questions about directional words.

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Nicholas Wade: Genes, culture, and history

Nicholas Wade never met a genetic just-so story that he didn't like. For a partial survey, see "The hunt for the Hat Gene", 11/15/2009, where I observed that he pivots smoothly from mere over-interpretation to complete fabrication:

Nicholas Wade is an inveterate gene-for-X enthusiast — he's got 68 stories in the NYT index with "gene" in the headline — and he's had two opportunities to celebrate this idea in the past few days: "Speech Gene Shows Its Bossy Nature", 11/12/2009, and "The Evolution of the God Gene", 11/14/2009. The first of these articles is merely a bit misleading, in the usual way. The second verges on the bizarre.

Now Mr. Wade has packaged a large-scale version of this move as a book, where a somewhat tendentious account of human genetic diversity transitions into a fictional narrative proposing genetic explanations for essentially every aspect of human cultural, social, and economic history: A Troublesome Inheritance: Genes, Race and Human History, 2014.

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Wallflower no more

Yesterday afternoon at an ICASSP-2014 session on music transcription. Just as in the session on Diarization that I wrote about yesterday, most of the papers reported results on published data, and several also offered links to their code. Thus Ken O'Hanlon and Mark D. Plumbley, "Polyphonic Piano Transcription using Non-negative matrix factorisation and group sparsity", which ends with this note:

6. REPRODUCIBLE RESEARCH
This research benefits from the efforts of other researchers to share their code [5] and dataset [21]. The open availability of these resources is commendable, allowing other researchers to easily and accurately compare methods. The code used in the experiments described in this paper is available at http://code.soundsoftware.ac.uk/projects/gs bnmf/.

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When 90% is 32%

I've occasionally complained that when it comes to comparing sampled distributions, modern western intellectuals are mostly just as clueless as the members of the Pirahã  tribe in the Amazon are said to be with respect to counting (see e.g.  "The Pirahã and us", 10/6/2007).  And it doesn't take high-falutin concepts like "variance" or "effect size" to engage this incapacity — simple percentages are often enough.

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(Mis-) Interpreting medical tests

Jon Hamilton, "Alzheimer's Blood Test Raises Ethical Questions", NPR Morning Edition 3/9/2014:

An experimental blood test can identify people in their 70s who are likely to develop Alzheimer's disease within two or three years. The test is accurate more than 90 percent of the time, scientists reported Sunday in Nature Medicine.

The finding could lead to a quick and easy way for seniors to assess their risk of Alzheimer's, says Dr. Howard Federoff, a professor of neurology at Georgetown University. And that would be a "game changer," he says, if researchers find a treatment that can slow down or stop the disease.  

But because there is still no way to halt Alzheimer's, Federoff says, people considering the test would have to decide whether they are prepared to get results that "could be life-altering." 

But  having a prediction with no prospect for a cure is not, in my opinion, the biggest problem with tests of this kind.

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The inclusion epidemic

Last week, a journalist asked me a question in connection with the recent flurry of stories on changes in childhood obesity percentages in the period from 2001 to 2012. When I looked into it, what struck me was that a category defined as "BMI at or above the 95th percentile" applied to about 15-17% of the population throughout the period discussed.

This sounds like a statistical approximation to Garrison Keillor's joke about his home town, where "all of the children are above average". But the normative percentiles are based on data from an earier time, and so it's perfectly logical that 17.1% of the age-2-19 sample in the 2003-2004 period should be at or above the 95th percentile for the 1963-1994 period. This is just a symptom, after all, of the famous "obesity epidemic".

Still, I remained curious about just when this large change really took place. (Most of) the raw data is available on line from the CDC, and I decided to spend an hour or so satisfying my curiosity about what is going on here: has there actually been a gradual climb over 50 years, which looks steep when a threshold derived from 1963-1994 is used for data from 2003 to the present? Or was there a steeper climb over a narrower stretch of time?

I found a clear answer to this question. But when I looked into it further, I found some additional information that made me wonder whether there has really been any change over time at all.

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(Not) trusting data

Pete Warden, "Why you should never trust a data scientist", 7/18/2013:

The wonderful thing about being a data scientist is that I get all of the credibility of genuine science, with none of the irritating peer review or reproducibility worries. [...]

I’ve never ceased to be disturbed at how the inclusion of numbers and the mention of large data sets numbs criticism. The articles live in a strange purgatory between journalism, which most readers have a healthy skepticism towards, and science, where we sub-contract verification to other scientists and so trust the public output far more. If a sociologist tells you that people in Utah only have friends in Utah, you can follow a web of references and peer review to understand if she’s believable. If I, or somebody at a large tech company, tells you the same, there’s no way to check. The source data is proprietary, and in a lot of cases may not even exist any more in the same exact form as databases turn over, and users delete or update their information. Even other data scientists outside the team won’t be able to verify the results. The data scientists I know are honest people, but there’s no external checks in the system to keep them that way.

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The Afterlife Ethnographic Survey

Franz Boas has a facebook page, whose contents suggest that his acumen is undimmed by death. A couple of weeks ago, one of his facebook friends asked this:

When Freud gave his famous "introductory lectures" at Clark University in 1909, Boas was a faculty member at the same university. I wonder if he attended the lectures? I have read some off-hand comments in Franz Boas's writing indicating that apparently he didn't think much of Freud. But does anyone know of any more in-depth historical accounts of this (missed?) encounter between papa Freud and papa Boas? Thank you hive mind!!!

Boas responded:

When I read Totems and Taboos I thought it was one of the most brilliant parodies ever written. You can imagine my surprise when I learned that Sigmund was serious about all that elders urinating on the fire nonsense. Such flights of fancy, imposing Victorianism on the human subconscious as a human universal. He has not fared well here in the afterlife, last time I saw him he was living in a van down by the river with L. Ron Hubbard.

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"Significance", in 1885 and today

There's an ongoing argument about the interpretation of Katherine Baicker et al., "The Oregon Experiment — Effects of Medicaid on Clinical Outcomes", NEJM 5/2/2013, and one aspect of this debate has focused on the technical meaning of the word significant. Thus Kevin Drum, "A Small Rant About the Meaning of Significant vs. 'Significant'", Mother Jones 5/13/2013:

Many of the results of the Oregon study failed to meet the 95 percent standard, and I think it's wrong to describe this as showing that "Medicaid coverage generated no significant improvements in measured physical health outcomes in the first 2 years."

To be clear: it's fine for the authors of the study to describe it that way. They're writing for fellow professionals in an academic journal. But when you're writing for a lay audience, it's seriously misleading. Most lay readers will interpret "significant" in its ordinary English sense, not as a term of art used by statisticians, and therefore conclude that the study positively demonstrated that there were no results large enough to care about.

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Importance of publishing data and code

J.W. writes:

In connection with some of your prior statements on the Log about the importance of publishing underlying data, you might be interested in Thomas Herndon, Michael Ash, and Robert Pollin, "Does High Public Debt Consistently Stifle Economic Growth? A Critique of Reinhart and Rogoff", PERI 4/15/2013 (explanation in lay language at "Shocking Paper Claims That Microsoft Excel Coding Error Is Behind The Reinhart-Rogoff Study On Debt", Business Insider 4/16/2013). In sum, a look at the data spreadsheet underlying a really influential 2010 economics paper reveals that its results were driven by selective data exclusions, idiosyncratic weighting, and an Excel coding error [!].

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More journalists with reading disabilities

Or maybe this is about press-release writers who don't express themselves clearly. According to "Chemical in Tap Water Linked to Food Allergies", Drugwatch 12/7/2012 (emphasis added, here and throughout):

A new study in the Annals of Allergy, Asthma and Immunology links high levels of dichlorophenols–chemicals used for chlorinating tap water–to a higher risk of food allergies. According to the study, people with higher levels of these chemicals in their urine have a greater risk of developing food allergies.

Out of the 2,211 people with high levels of dichlorophenols who participated in the study, 411 had food allergies and 1,016 had an environmental allergy, according to researchers.

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Psycho kids today

Kevin Dutton, "Psychopathy's Double Edge", Chronicle of Higher Education 10/22/2012:

[I]n a survey that has so far tested 14,000 volunteers, Sara Konrath and her team at the University of Michigan's Institute for Social Research has found that college students' self-reported empathy levels (as measured by the Interpersonal Reactivity Index, a standardized questionnaire containing such items as "I often have tender, concerned feelings for people less fortunate than me" and "I try to look at everybody's side of a disagreement before I make a decision") have been in steady decline over the past three decades—since the inauguration of the scale, in fact, back in 1979. A particularly pronounced slump has been observed over the past 10 years. "College kids today are about 40 percent lower in empathy than their counterparts of 20 or 30 years ago," Konrath reports.

As is all too often true for stories about results in social psychology — and especially stories about the Problems with Kids Today — this one is misleading in almost every particular.

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Dinosaurs, baboons, and science journalists

It is well known within organic chemistry circles that there is a very strong bias toward L rather than D homochirality in the structure of earth's organic compounds. A recent paper offered a speculation about a possible explanation of the bias:

If there was … right circularly polarized light with energy in the uv or higher irradiating the asteroid belt when the amino acids were present on a particle that later came to Earth, this could account for the small excesses of the L anantiomers seen in the α-methyl amino acids.

And what did the PR/media machine do to make news out of this finding? The headlines ultimately mutated as far as this:

Claim: Advanced dinosaurs may rule other planets

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From wraith to smoking duck

I previously described the evolution of the Higgs Boson from Leon Lederman's "wraithlike presence throughout the universe that is keeping us from understanding the true nature of matter", perhaps bowdlerized by his editors from "the goddamn particle" to "the God particle", and onwards to Dennis Overbye's "kind of cosmic molasses [...] that would impart mass to formerly massless particles trying to move through it like a celebrity trying to get to the bar".

Yesterday, the high-energy euphoria at CERN seems to have excited some really exotic metaphorical resonances, combining the elementary building-blocks of cultural cognition in ways not normally seen on earth.

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