Archive for The language of science

Excel invents genes

Mark Ziemann, Yotam Eren and Assam El-Osta, "Gene name errors are widespread in the scientific literature", Genome Biology 2016:

The spreadsheet software Microsoft Excel, when used with default settings, is known to convert gene names to dates and floating-point numbers. A programmatic scan of leading genomics journals reveals that approximately one-fifth of papers with supplementary Excel gene lists contain erroneous gene name conversions.

Read the rest of this entry »

Comments (17)

Language Log literally changes your brain

Emily Hopkins, Deena Weisberg, and Jordan Taylor, "The seductive allure is a reductive allure: People prefer scientific explanations that contain logically irrelevant reductive information", Cognition 2016:

Previous work has found that people feel significantly more satisfied with explanations of psychological phenomena when those explanations contain neuroscience information — even when this information is entirely irrelevant to the logic of the explanations. This seductive allure effect was first demonstrated by Weisberg, Keil, Goodstein, Rawson, and Gray (2008), and has since been replicated several times (Fernandez-Duque, Evans, Christian, & Hodges, 2015; Minahan & Siedlecki, 2016; Rhodes, Rodriguez, & Shah, 2014; Weisberg, Taylor, & Hopkins, 2015). However, these studies only examined psychological phenomena. The current study thus investigated the generality of this effect and found that it occurs across several scientific disciplines whenever the explanations include reductive information: reference to smaller components or more fundamental processes. These data suggest that people have a general preference for reductive information, even when it is irrelevant to the logic of an explanation.

Read the rest of this entry »

Comments (12)

Science

John Oliver on TV Science — featuring the TODD talks ("Trends, Observations, and Dangerous Drivel"):

Read the rest of this entry »

Comments off

It's about time

Biologists are figuring out what many other fields learned decades ago:

See Amy Harmon, "Handful of Biologists Went Rogue and Published Directly to Internet", NYT 3/15/2016. Also see "Reviewer Two must die".

Academic journals are on their way to playing the same role in the life of science and engineering that caps and gowns do: a quaint cultural relic that plays a role in celebratory rituals, but has nothing to do with the day-to-day process of exploration, discovery and communication.

Comments (9)

How to turn one out of five into three out of four

Towards the end of last year, there was a bit of a fuss in the UK about the role of alcohol in hospital costs. Thus Sarah Knapton, "Three in four people in A&E at weekend are there because of alcohol: 70 per cent of people are admitted to emergency units at the weekend as a result of drinking", The Telegraph 12/21/2015 — illustrated with the rather atypical picture on the right.

And there was plenty of other coverage, e.g. "Alcohol-related A&E cases rise to 70% of workload at weekends", Daily Mail 12/21/2015; Mike Doran, "Alcohol responsible for up to 70% of all A&E admissions as experts renew minimum unit price calls", The Mirror 12/21/2015; Annalee Newitz, "Drunk people account for 70% of weekend emergency room visits in UK city: Drinking binges are now a scientifically measurable phenomenon", Ars Technica 12/22/2015.

But there's just one little wrinkle: the actual rates that the study found (of alcohol involvement in weekend emergency-room visits) were more like 20%. So how did the journalists get from "one in five" to "three in four"? Well, basically in the same way that we're allowed to conclude that in 1986, the rate of space-shuttle explosions was one per week. After all, there was one week in that year (the last week of January) when there was an explosion. And in the cited study, there was one weekend hour (2:00-3:00 a.m.) when a bit over 70% of the patients were measured with a non-zero breath alcohol content.

Read the rest of this entry »

Comments (8)

Positivity?

Christiaan H Vinkers et al., "Use of positive and negative words in scientific PubMed abstracts between 1974 and 2014: retrospective analysis", BMJ 2015:

Design Retrospective analysis of all scientific abstracts in PubMed between 1974 and 2014.  

Methods The yearly frequencies of positive, negative, and neutral words (25 preselected words in each category), plus 100 randomly selected words were normalised for the total number of abstracts. […]

Results The absolute frequency of positive words increased from 2.0% (1974-80) to 17.5% (2014), a relative increase of 880% over four decades.

Read the rest of this entry »

Comments (12)

Nicholas Wade's DNA decoded

Today's xkcd:

Mouseover title:  "Researchers just found the gene responsible for mistakenly thinking we've found the gene for specific things. It's the region between the start and the end of every chromosome, plus a few segments in our mitochondria."

For background, see "The hunt for the Hat Gene", 11/15/2009.

Comments (7)

Replicability vs. reproducibility — or is it the other way around?

The term reproducible research, in its current sensewas coined about 1990 by the geophysicist Jon Claerbout.  Thus Jon Claerbout & Martin Karrenbach, "Electronic Documents Give Reproducible Research a New Meaning", Society of Exploration Geophysics 1992 [emphasis added, here and throughout]:

A revolution in education and technology transfer follows from the marriage of word processing and software command scripts. In this marriage an author attaches to every figure caption a pushbutton or a name tag usable to recalculate the figure from all its data, parameters, and programs. This provides a concrete definition of reproducibility in computationally oriented research. Experience at the Stanford Exploration Project shows that preparing such electronic documents is little effort beyond our customary report writing; mainly, we need to file everything in a systematic way. […]

The principal goal of scientific publications is to teach new concepts, show the resulting implications of those concepts in an illustration, and provide enough detail to make the work reproducible. In real life, reproducibility is haphazard and variable. Because of this, we rarely see a seismology PhD thesis being redone at a later date by another person. In an electronic document, readers, students, and customers can readily verify results and adapt them to new circumstances without laboriously recreating the author's environment.

Read the rest of this entry »

Comments (11)

Statistical cognition in the media

Bianca Nogrady, "Music preferences reveal your inner thoughts", ABC Science 7/23/2015:

There is a clear link between people's cognitive styles and the type and depth of emotion they prefer in music, say researchers.

Their work, published today in PLOS ONE, shows people who are more empathetic — have a greater ability to identify, predict and respond to the emotions of others — are drawn to more mellow, sad, poetic and sensual music, such as R&B, adult contemporary and soft rock.

However people with more analytical tendencies (called 'systemisers') go in the opposite direction, seeking punk, heavy metal, avant garde jazz and hard rock.

Read the rest of this entry »

Comments (16)

Wendiceratops

Sasha Harris-Lovett, "Meet Wendiceratops, a horned dinosaur unlike any other", LA Times 7/8/2015:

Move over Indominus Rex – scientists have discovered a previously unknown dinosaur in Canada that's cooler than any “Jurassic World” creation. And it’s real.

The creature, a member of the family of horned dinosaurs, was an older cousin of Triceratops that lived about 79 million years ago. Like Triceratops, it had horns emanating from its face and head, along with a bony beak that it used to shred plants before eating them. […]

The story begins with professional fossil hunter Wendy Sloboda, who spotted something that appeared to be a dinosaur bone sticking out of a steep hill in southern Alberta, Canada, in 2010.

Read the rest of this entry »

Comments (16)

The Insular Islands

The most recent xkcd has the mouseover title

I just learned about the Slide Mountain Ocean, which I like because it's three nouns that sound like they can't possibly all refer to the same thing.

But it gets better — the extended Slide Mountain Ocean story line, known as the Omineca Episode,  includes the Bridge River Ocean, the Intermontane Superterrane, and my personal favorite, the Insular Islands (which star in the next chapter, the Coast Range Episode).

Comments (5)

Brain wiring and science reporting

People have been asking Language Log (well, at least one somewhat off-topic commenter asked once) whether we have a view about the recent study alleging sex differences in brain wiring by Ragini Verma and colleagues. Language Log does not really regard this as a linguistic story, but keeps an eye on such neurophysiological topics for their occasional implications for language and the way it is implemented in the brain, and also on the language in which such science is reported. The study has been (of course) wildly overhyped, with newpaper stories around the world talking about men's and women's brains being wired completely differently (guys, you have tons of front-back wiring to aid you in spear-chucking and direction-finding; gals, you have oodles of left-right cross-connections to aid you in gossiping and domestic multi-tasking; that sort of thing). For a short, sharp, and well-informed critique of the way ideology (and philosophical error) warps the press interpretation of brain-scan results, take a look at the letter by Rae Langton and John Dupré in the Guardian, submitted by two excellent British philosophers with interests in both the biology and ideology of the relations between the sexes. They call the press coverage of this study a "deterministic fairy-tale" that is "bad for men and women, bad for science, bad for us all."

Update: A fuller version of the Langton/Dupré letter with discussion can be found on Brian Leiter's blog, and there is more here on Language Log here and here.

Comments off

Prestigious nonsense, tendentious frames

Kimmo Ericksson, "The nonsense math effect", Judgment and Decision Making 7(6) 2012:

In those disciplines where most researchers do not master mathematics, the use of mathematics may be held in too much awe. To demonstrate this I conducted an online experiment with 200 participants, all of which had experience of reading research reports and a postgraduate degree (in any subject). Participants were presented with the abstracts from two published papers (one in evolutionary anthropology and one in sociology). Based on these abstracts, participants were asked to judge the quality of the research. Either one or the other of the two abstracts was manipulated through the inclusion of an extra sentence taken from a completely unrelated paper and presenting an equation that made no sense in the context. The abstract that included the meaningless mathematics tended to be judged of higher quality.

Read the rest of this entry »

Comments (19)