Beth’s Data Viz Fan Club

Want to read more from me? Check out my latest mini-project, updated a couple times a week: Beth’s Data Visualization Fan Club, a tumblr of stunning and playful data analysis.

Concussion testing in roller derby

My latest print article is out. Read about concussion testing in roller derby (part 1 of 2) in Issue 10 of Fiveonfive Magazine. For this piece I talked to several people in our league’s safety committee, our main EMT, and two concussion experts based at UPMC.

Earlier this year I knew next-to-nothing about concussions and had never heard of concussion testing. Bottom line: a concussion is a nearly invisible brain injury that can cause trouble down the line if you get another one before the first is fully healed.

Coaches and players in many sports, famously including the NFL, are beginning to take concussion recovery seriously. Tests can help tell if an injured athlete’s brain function is truly back to normal so they can safely return to play. My league, Steel City, is possibly the first roller derby league to formally address this issue.

Twitter transcript of #sciwri10 stats talk

 (Posting this here so I can link to it from a post I’m going to make on the official ScienceWriters2010 blog)

BethSkw:        Next up: Get the Numbers Right: a workshop on reporting statistics http://bit.ly/bXrIH9 #sciwri10 #stats

DanielleVenton:        Are you in the right? Get the Numbers Right session about to start. #sciwri10

BethSkw:        Some stuff from this session will be posted on www.stephenornes.com #sciwri10 #stats

BethSkw:        SO on fact checking: marks up article, makes a report. Pet peeve: even good writers have hard time w odds ratios #sciwri10 #stats

BethSkw:        SO: OR=odds ratio 2.38 does NOT mean 138% inc risk. Instead: 2.38x the odds. Rel risk intuitive, this not. #sciwri10 #stats

BethSkw:        More on odds ratio vs. relative risk (my googling) http://bit.ly/aVA6V2 #sciwri10 #stats

BethSkw:       rel btw OR and a % risk not straightforward to calculate - ask a researcher (& hope they know what they’re doing) - Gelman #sciwri10 #stats

BethSkw:        SO www.stats.org “are you a journalist?” link - ask stats questions #sciwri10 #stats

daviddespain:        Are you a sci jorno who wants to ask a question of a statistician? http://www.stats.org/ #sciwri10

BethSkw:        Here’s the direct link for stats help for journalists: http://stats.org/journalist.htm #sciwri10 #stats

DanielleVenton:        Odds ratios don’t translate into percents. See stats.org to get help from a stats expert #sciwri10 #stats

BethSkw:        SO: almost impossible to find absolute risk. Rel risk compares eg smokers to nonsmokers but does not tell ACTUAL risk. #sciwri10 #stats

BethSkw:        SO: when RR=1, no difference. RR=2 means 100% increase in one group vs. the other #sciwri10 #stats

BethSkw:        SO: Comparing events with 80% and 67% prob - odds ratio is 2 but 80% is not twice the risk of 67%! #sciwri10 #stats

BethSkw:        SO: When in doubt, ask the investigator AND THEN ask an independent statistician, or stats.org. #sciwri10 #stats

BethSkw:        SO: Befriend a statistician. When you talk to one, ask if you can come back with Qs later, many will say yes. #sciwri10 #stats

DanielleVenton:        Relative risk is more accurate, double check your stats! #sciwri10 make friends with a statistician

BethSkw:        Andrew Gelman: statisticians are not alike, hate when reporters ask one about sth outside their field. Ask their bg. #sciwri10 #stats

BethSkw:        2000 Bush v. Gore case used stats expert who was smart guy, not qualified in the area, confident enough to show up anyway #sciwri10 #stats

BethSkw:        AG: Statisticians often like to be helpful, we want to see our names in the paper! #sciwri10 #stats

jamesian:        Beware trusting experts in stats who lack specific credibility - Gelman of Columbia #sciwri10

BethSkw:        AG: Silly studies like that influence how ppl think about sex stereotypes, meaning theyre important to discuss #sciwri10 #stats

DanielleVenton:        AG: look at studies in context, not isolation, what did you expect to see? #sciwri10 #stats

BethSkw:        AG: 51% of babies are boys, more boy babies die, at age 20 the numbers are 50/50 #sciwri10 #stats

BethSkw:       AG: extr poverty/famine: sex ratio effects as high as 3%. Smaller effects (race, age, season) < 1%. ergo expect beauty <1% #sciwri10 #stats

BethSkw:        AG: some studies “more vampirical than empirical - unable to be killed by mere evidence” - Freese 2007 http://bit.ly/9g4zVM #sciwri10 #stats

DanielleVenton:        AG: sex ratio studies can be more ‘vampirical’ than ‘empirical’ unable to be killed by mere evidence #sciwri10 #stats

BethSkw:        AG compares results to People’s Most Beautiful lists. Can’t find small effects with this sample size #sciwri10 #stats

Deb_acle:        RT @BethSkw: More on odds ratio vs. relative risk (my googling) http://bit.ly/aVA6V2 #sciwri10 #stats

jamesian:        Scientific method is “machine for exaggeration” says Gelman #sciwri10

DanielleVenton:        AG: be suspicious when something is 10 - 100x larger than expected effects. #sciwri10 #stats

rachelsklar:        Pls blog it!!! RT @arikia: This stats session is amaaazing. @fivethirtyeight you’ve turned me into a total stats head… #sciwri10

BethSkw:        AG: in peer reviewed lit, there is a bias toward overestimating effects. Need to know topic bg to spot red flags #sciwri10 #stats

DanielleVenton:        AG: most effects reported in peer-reviewed lit are overestimated. #sciwri10 #stats

BethSkw:        AG: many “politically incorrect” studies essentially random results b/c no statistical power #sciwri10 #stats

BethSkw:        Next speaker: Tom Siegfried of Science News (prev article of his here: http://bit.ly/d5CjYw) #sciwri10 #stats

davemosher:       Andrew Gelman, statistician at Columbia: Journal system = little black box of overestimation (in regards to reporting sig results) #sciwri10

BethSkw:        TS: stat significant means 95% prob effect isn’t chance? NO! doesn’t even mean that it’s “significant”. #sciwri10 #stats

arikia:       The woman sitting next to me in the stats talk just yelped when Tom Siegfried called the commonly accepted def of stat sig wrong #sciwri10

arikia:        ”Evidence that you’ve seen something unlikely is not evidence that the opposite is true.” #sciwri10

davemosher:        ”Evidence that I don’t own the house is not evidence that the house owns me.” -Tim Siegfried #sciwri10

BethSkw:        TS: Stat significant = less than 5% chance of seeing effect of this magnitude if there really is no effect. #sciwri10 #stats

arikia:        This session is obviously ruffling some feathers but this is stats 101 stuff. Excellently delivered, I might add. #sciwri10

BethSkw:        Wish I could tell the Tom Siegfried’s swimming-in-winter example in 140 chars. Explained the idea nicely! #sciwri10 #stats

BethSkw:        RT @arikia: This session is obviously ruffling some feathers but this is stats 101 stuff. Excellently delivered, I might add. #sciwri10

BethSkw:        TS: If result isn’t statistically significant, can say “did not establish a link” or “…but could have been due to chance” #sciwri10 #stats

BethSkw:        TS: huge confidence interval means result is uncertain. Ex phrasing: “in the range of about 10 to 40%” #sciwri10 #stats

DanielleVenton:        TS: reporting elevated risk? State the comparison point. #sciwri10 #stats

BethSkw:        TS: When reporting Relative Risk, say relative to WHAT. #sciwri10 #stats

BethSkw:        TS: Reader may not know how to interpret simple math like “50% increase” so think carefully when describing numbers #sciwri10 #stats

BethSkw:        TS: Red flags for wrong results: 1st report, hot field, contrary to prev belief (why say prev belief wrong?) #sciwri10 #stats

daviddespain:        Recipe for wrong science news: 1 first report of something 2 advance in hot research field 3 contrary to previous belief #sciwri10

BethSkw:        TS: recipe for wrong science == recipe for hot news. So have to be careful. #sciwri10 #stats

bohemianone:        RT @BethSkw: TS: Reader may not know how to interpret simple math like “50% increase” so think carefully when describing numbers #sciwri10 #stats

arikia:        The recipe for bad science is the same recipe as what’s often sought after for science news. #sciwri10

BethSkw:        Gelman: Maybe drop idea of effect vs. no effect - effect is rarely zero, Q is how much. #sciwri10 #stats

arikia:        There are situations where single events are newsworthy, eg: if you find a talking dog… #sciwri10

BethSkw:        Q: single case study newsworthy? TS: Can be. Stats are just to sort out complicated situations. #sciwri10 #stats

daviddespain:        Forgotten frequently (or conveniently) by reporters RT @BethSkw: TS: When reporting Relative Risk, say relative to WHAT. #sciwri10 #stats

BethSkw:        Andrew Gelman’s blog: http://www.stat.columbia.edu/~gelman/blog/ #sciwri10 #stats

TomLevenson:        3 flags for bad science/science news-first report of something/in a hot field/contrary to prior belief. Amen and amen. #sciwri10

marynmck:        RT @arikia: The recipe for bad science is the same recipe as what’s often sought after for science news. #sciwri10

BethSkw:        AG: psychologists have research on how to communicate risk/probability. TS: “risk communication” field #sciwri10 #stats

BethSkw:        A few risk communication links: http://bit.ly/ak4som http://bit.ly/bFjqh4 http://bit.ly/bNsm02 #sciwri10 #stats

DanielleVenton:        Get comfortable with the numbers in the study before you trust them. No snap judgments. #sciwri10 #stats

arikia:        Untapped resource on finding statistical flaws in research: ppl who don’t like the people who published it. #sciwri10

DanielleVenton:        Stats resource: other researchers who don’t like the author, good for explaining study flaws. #sciwri10 #stats

TomLevenson:        @caribbeanscot: three reasons to question new science (news): it’s a first report in a hot field contradicting prior belief. #sciwri10

maggiekb1:        RT @arikia: “Evidence that you’ve seen something unlikely is not evidence that the opposite is true.” #sciwri10

BethSkw:        SO: OR=odds ratio 2.38 does NOT mean 138% inc risk. Instead: 2.38x the odds. Rel risk intuitive, this not. #sciwri10 #stats

Why I’m writing a novel this month

For the third straight year, I’m writing a novel in November. It’s a national (really, worldwide) challenge: 30 days, 50,000 words in a single work of fiction. Did I mention that I’m really not into fiction? And that I’ve never written a word of the stuff in my adult life, outside of NaNoWriMo (as it’s called)?

When I tell people, they usually have questions like “What is your novel about?” - which surprises me, because their question really should be “Why?!?”

NaNo really takes over November. Thanksgiving puts a wrench in the works but I try to be far enough along by then that I’m not worried about my word count. I spend between 1 and 2 hours per day on it, not counting the time I spend planning in October. Yes, I do this on top of my regular job, child care duties, roller derby practices, and so on.

I do it because it’s an amazing productivity exercise: sit down, pound out the words, and be done for the day. I track my words to date, words per hour, how far ahead I am, my projected total by the end of the month, and so on.

When my “real job” is made of writing that matters and has to be done carefully, it’s easy to procrastinate, to work slowly, to pretend to myself that I’m already working at top speed and it’s just that the work is so tough. I might struggle all week in my day job to squeeze out the number of words I get in two hours of noveling. It’s a real productivity wake-up call.

I also do it so I can surprise myself with my creativity. The thing that got me to try my first NaNo was Chris Baty’s description (in the book “No Plot, No Problem”) of how his characters, once half-written, took on lives of their own and turned the jumble of words into a story:

That’s the beauty of novel writing. A panoply of strange characters, spread out over cities or continents, will somehow end up banding together midbook to construct your plot. You probably won’t see how this will happen early in the writing process, and you shouldn’t worry about it yet. Your role as a writer in Week One is just to continue to wave all of these players down onto the field, and then write like hell to keep up with them.

There’s another benefit: Every year when I plan my novel in late October, I read up on characters and plot and pacing and conflicts and foreshadowing and climaxes and set pieces. Ever since that first cold November night I sat down with a story being born, I’ve noticed these things in the media I consume, and even what I write. Any sort of writing has traits in common with storytelling, and when a page-turning couple of pages produces itself out of my mountain of first-draft drivel (which happens surprisingly often in November!), I say Aha! This is how you make something worth reading!

Also, I have a thing for crazy projects. Like joining a roller derby team, winning a gold medal in the Knitting Olympics, taking trapeze lessons (only did it once but wish I could go again), training to swim a mile while 5 months pregnant (only missed the race because a family funeral was the same day), you get the idea. It’s great to have a project to devote yourself to, then walk away from with a sense of accomplishment. “I’ll never do anything like that again,” you say. “Until next year.”

November 2008: wrote my first novel
November 2009: wrote my second novel while caring for a newborn babe
November 2010: writing my third novel on a typewriter (while caring for a 1-year-old). Not sure how I’m gonna top that for 2011, but I’ll try.

Is genetic privacy overrated?

Why keep secrets? The 12 bloggers at Genomes Unzipped (an interesting genetics blog I didn’t know about till just now) are releasing their genetic data, mainly 23andme results, to the world. Daniel MacArthur writes that the need to keep genetic data private makes valuable data-sharing difficult, so he and his friends are making a gift to science: The raw data is here. They also plan to release any software they create.

I liked his point that genetic privacy is overrated anyway, when you shed hair and skin everywhere you go.

A similar, more ambitious effort is the Personal Genome Project, which aims to build a repository of 100,000 individuals who have decided to share their data. (They’re up to 10 so far. [Update: now it’s 1,000]) That project’s privacy statement includes the reverse idea: that if someone has your genetic data, it’s not so hard for them to know who you are.

We question the long-held belief that research endeavors involving human genome sequencing can guarantee, in perpetuity, the confidentiality or anonymity of the information revealed from a personal genome sequence. For example, it is becoming easier to glean personally indentifiable knowledge from DNA sequences, including hair and eye color, height, and facial features. Protecting the identity of indviduals is particularly difficult while the number of personal genome sequences existing in the world is small.

Anyhow, I’m reading this as I sit at home watching the twitter feed (#bgt2010) for Beyond the Genome, a conference in Boston about “the true gene count, human evolution, and disease genomics.” Sounds like fun!

Are you math phobic?

I spent the evening at a workshop learning how to tutor GED students (in a handful of high school subjects) and came home to a lively twitter discussion called #mathchat. The topic of the night was math phobia. Where does it come from and what can math teachers do about it?

At the workshop, even the person teaching us how to teach math made a few math-phobic comments - not about the things we’d teach, but more about the things we don’t have to, like thank god there’s no trigonometry, or graphing calculators.

I used to be math-phobic too. That changed, not when I learned more math (I didn’t) but as I saw other people being math-phobic and realized it was a little out of proportion. Is math really that bad? Really?

Some of the comments from #mathchat really brought back memories, mainly the idea of being “bad at math”. I always thought I was bad at math, but I got decent grades and was in the high level classes. And in what other subject do we - especially once we’re out of school - say things like “oh, I can’t do that at all, I’m bad at social studies.” Or “OMG, I can’t deal with anything that mentions the French Revolution”.

I’ve given a lot of thought to why I disliked math classes so much. Partly I felt like I was bad at math because even though I could do the problems, I didn’t understand how the concepts connected to each other. Almost every math class I took was taught the same (boring, disconnected) way. I loved geometry, though! It was visual and full of puzzles.

I also liked science classes that used math, so long as the math was a tool to answer an interesting question. Not so much when the experiment was a transparent set-up for a boring math problem.

These and other ideas cropped up in the chat, which will be archived here. These are some of the relevant tweets:

@familyonbikes I so wish we could remove that idea that being bad at math is OK. Where did that come from anyway?

@lovedrummin I believe [w]hen teachers stop teaching by rote and math begins to encourage ingenuity students become engaged. http://bit.ly/cXOM7l

@maggiekb1 It took years before I learned there was difference between “can’t do math” and “can’t do enough math problems in 3 minutes.”

@NicolRHoward #mathphobia may be a fear of not being able to use rote memorization forever

One tweeter mentioned CGI Math, a strategy in which teachers ask students to come up with ways of solving a problem, then the class discusses and compares the methods they came up with. Another said that a great way to teach number places (the ones place, the tens place, and so on) is to bring in a ton of beans and give the class all day to count them. Soon they’ll be grouping the beans, and grouping the groups, and discover the idea on their own. The CGI Math page says: “students who learn the standard addition algorithm often learn little more than a procedure to find the correct answer. Students who develop their own strategies to solve addition problems are likely to intuitively use the commutative and associative properties of addition in their strategies.”

I loved the recommendations to use discussions, bookless lessons, puzzles, applications the students are interested in such as video games, and pervasive everyday math, like choosing a cell phone plan, or catching a thrown object (hello parabola!). Dan Meyer’s blog has examples of a fun approach: show a picture or some other piece of information, then ask the students what questions they have about it, and let them figure out how to answer them.

What do you think? Are you math phobic?

Postcards to the fetus

I mentioned last week that a new book by Annie Paul likens a fetus’s experience in the womb to getting “biological postcards” from the world outside. Babble followed up their review of the book with a couple of excerpts.

One is on food, and I love that Paul doesn’t just parrot warnings about sushi but observes that setting up food as dangerous to a fetus, and the mother as responsible for that danger, has as much to do with our culture’s screwed-up attitudes about eating and motherhood as it does with biology. Taking the postcard view, a mom is sharing flavors (not to mention nutrients) with her little parasite.

The other one, on stress, is likewise fascinating. I’d love to hear the story of how stress went from “not on the list” of risk factors for pre-term birth to being considered a number-one cause of it. Meanwhile, the placenta breaks down some of the stress hormone, cortisol, but mild stress may be necessary for later cognition.

I just came across a study today showing that people who were in utero during a WWII famine in the Netherlands may have trouble with selective attention tasks as they get older. The authors think this means their cognition is declining faster than average, because people typically do worse on this test as they age. Previous studies on the “Dutch Famine Birth Cohort,” as this group is called, showed that they are more prone to heart disease and diabetes.

I have to wonder, in light of the “postcards from outside” hypothesis, whether being worse at selective attention means being better at something else. Could a supposedly poor score on the test reflect something like multitasking ability? And could that ability be adaptive in the face of periodic famines?

Quick links: reproductive & digestive tract edition

So much good stuff this week! A lot of these warrant their own posts but it’s a busy week for me so all I’ve got is the links. Better short than never:

Researchers turn off severe food allergies in mice by feeding them a modified form of the food they’re allergic to. This binds to a special receptor on immune cells in the digestive tract, apparently re-training the immune system.

Sneaky comb jellies suck prey into their mouths without the prey noticing. Neat!

Breaking news: somebody is finally looking at how (monkey) dads’ bodies and brains change when they have a kid. Plenty of this research has been done on moms in the past, of course.

Review of Origins: How the Nine Months Before Birth Shape the Rest of Our Lives. It seems a mom’s body sends signals to the baby to prepare him for life on the outside. If food is scarce, for example, his metabolism will be prepared for that. The author likens the phenomenon to “biological postcards from the world outside.”

Gene found for age-related macular degeneration. That’s a major cause of blindness in old folks. The gene, when working normally, protects the cells of the macula with signposts that tell the immune system not to destroy them.

Pictures of a python digesting a rat. No comment, except this is awesome.

Underwire bras make you poop less: What bewilders me is that every outlet that reported this story used pictures of women in bras, but none used pictures of poop.

An oxytocin nose spray may help people with autism or other disorders connect with others socially. I know that when I had to take methergine, an oxytocic drug, it made me super happy and talkative. This comment on the article makes some good points (with pubmed references!) about the effects of oxytocin, a link to autism, and the ethics of this kind of therapy.

Antibiotics play hell with gut flora - you probably could have guessed, but the germs living in your intestines are important to your health and digestion - and killing them off with antibiotics is wiping out a whole ecosystem. You might not get some of those species back, afterwards. Tying that into our other theme for today: I wonder how routine antibiotics during birth (given as a “better safe than sorry” sort of measure) affect the gut flora of the newborn. More about gut flora & babies here. This is an area I’d love to dig into more.

Quick links: Ancient antibiotics to Yo-yo dieting

Ancient Nubians may have purposely brewed antibiotic-rich beer and fed it to sick people.

Scientists discover the properties of the perfect sports bra, but no bra on the market fits the description.

Study claims to disprove that “diets don’t work” by finding that it’s eating more post-diet that makes dieters fatter in the long run. Their results say the opposite to me: if the binge is typically triggered by dieting, doesn’t that make dieting the culprit?

To avoid overheating during exercise, you should drink more water, right? Probably not, say the guys at Science of Sport. Drinking a little extra doesn’t affect your body temperature much.

Some universities experiment with opening the online portion of classes to everybody - different than OpenCourseWare projects since the students can interact with each other.

It’s off-topic, but this guy is traveling the world with no baggage of any kind, just a vest with pockets. (The trip is sponsored by the maker of the vest). Yes, he keeps a change of underwear in his vest. Like the idea? Check out One Bag for tips on traveling with just a carry-on, no matter how far or how long you’re gone.

How safe is the HPV vaccine? A nice visualization of the risks of dying from the vaccine, vs. dying from the cancer it prevents, vs. dying from other causes including “ignition of nightwear.”

Take a look at this skull. Look again.

Take a look at this skull. Look again - it’s a pair of children. Now back to the skull. Now back to the children. Scientists may have found the part of the brain that switches between two interpretations of an image. People who switch faster between two options (in the experiment, a sphere that seems to be rotating one way or another) show differences in their superior parietal lobes. Possibly the switching occurs because our brain re-evaluates what we see, to be sure it doesn’t get stuck on a wrong interpretation.

Want to see some more neat optical illusions? Sure you do. Here are some.