Analysis: Do the shoes matter in marathon running?

Kevin Quealy and Josh Katz for The Upshot analyzed shoe and running data to see if Nike’s Vaporfly running shoes really helped marathoners achieve faster times. Accounting for a number of confounding factors, the results appear to point to yes.

We found that the difference was not explained by faster runners choosing to wear the shoes, by runners choosing to wear them in easier races or by runners switching to Vaporflys after running more training miles. Instead, the analysis suggests that, in a race between two marathoners of the same ability, a runner wearing Vaporflys would have a real advantage over a competitor not wearing them.

Very statistics-y, even for The Upshot. I like it.

It takes me back to my fourth grade science fair project where I asked: Do Nike’s really make you jump higher? Our results pointed to yes too. Although our sample size of five with no control or statistical rigor might not stand up to more technical standards. My Excel charts were dope though.

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Bacterial Doubling Times in the Wild

How fast do bacteria grow outside the laboratory? This simple question is very difficult to address directly, because it is near-impossible to track a lineage of bacterial cells, ancestor-to-decendant, inside an infected patient or through a river. Now in new work published in Proceedings B, Beth Gibson, Ed Feil, Adam Eyre-Walker and I exploit genome sequencing to try to get a handle on the problem indirectly.

We have done it by comparing two known quantities and taking the ratio: the rate at which DNA mutates in bacteria per year, and the rate it mutates per replication. This tells us in theory how many replications there are per year.

The mutation rate per replication has long been studied in the laboratory, and is around once per billion letters. Meanwhile, the recent avalanche of genomic data has allowed microbiologists to quantify the rate at which bacteria evolve over short time scales such as a year, including during outbreaks and even within individual infected patients. Most bugs mutate about once per million letters per year, with ten-fold variation above and below this not uncommon among different species.

For five species both these quantities exist. The fastest bug we looked at causes cholera and we estimate it doubles once every hour on average (give or take 30 minutes). The slowest was Salmonella, which we estimate doubles once a day on average (give or take 8 hours). In between were Staph. aureus and Pseudomonas at about two hours each, and E. coli at 15 hours. These are average over the very diverse and often hostile conditions that a bacterial cell may find itself in during the course of its natural lifecycle. To find out more about the work, please check out the paper.

Data-centric view of birth control

Birth control is one of those topics often saved for private conversations, so people’s views are often anecdotal. Someone knows what their friend, family member, etc used, but not much else. Amber Thomas for The Pudding provides a wider view of birth control using data from the CDC’s ongoing National Survey of Family Growth.

You see what other people use, how the method changes with age, and side effects. There’s a Clippy-like character for added information on the different methods. So there’s a good amount of information there to make the choice that’s right for you.

Sidenote on the NSFG data: I looked at the data a few times. It’s a good, messy dataset to explore if you want some practice.

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A university is revoking a student’s PhD — but not because of misconduct

Earlier this month, Tokushima University in Japan announced it was revoking a student’s PhD degree — but for a somewhat unusual reason. The student didn’t appear to commit misconduct. Rather, the authors discovered a series of errors that invalidated the paper’s central conclusion. The case has us wondering about how universities should respond when they … Continue reading A university is revoking a student’s PhD — but not because of misconduct

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July 25 NCBI Minute: Five Teaching Examples Using NCBI BLAST

Next Wednesday, July 25, 2018, NCBI staff will show you a set of simple teaching examples that use BLAST and related alignment tools at NCBI to explore modern biology concepts and techniques including evolution, taxonomy, homology, multiple sequence alignment, phylogenetic … Continue reading

The new BLAST widget seamlessly integrates your results into NCBI’s Genome Data Viewer (GDV)

Want to analyze your BLAST results in the context of a genome browser? Want to compare those results against other genome assembly annotations? The BLAST widget, a new browser feature, lets you do that. It provides direct access within GDV … Continue reading

The Rollercoaster of Exploding Pollen

  When I think about reading peer-reviewed natural history papers — including contemporary articles in a ‘Natural History Miscellany Note’ or ‘The Scientific Naturalist’ section — I imagine them mostly as a classic throwback: just

Interactive to see street orientation everywhere

After seeing polar charts of street orientation in major cities, Vladimir Agafonkin, an engineer at Mapbox, implemented an interactive version that lets you see directions for everywhere:

Extracting and processing the road data for every place of interest to generate a polar chart seemed like too much work. Could I do it on an interactive map? It turns out that this is a perfect use case for Mapbox vector maps — since the map data is there on the client, we can analyze and visualize it instantly for any place in the world.

Fun.

So someone’s going to take the next step to rank and rate griddyness around the world, right?

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Study claiming “abortion reversal” is safe and effective temporarily withdrawn for ethical issues

A journal has temporarily removed a study by a researcher who has long championed a highly controversial “abortion reversal” method over concerns about its ethical approval. The study, “A Case Series Detailing the Successful Reversal of the Effects of Mifepristone Using Progesterone,” appeared in Issues In Law And Medicine in April. Its first author, George … Continue reading Study claiming “abortion reversal” is safe and effective temporarily withdrawn for ethical issues