Counting rats, part 1

No, this isn’t about pet rats, even though I just did a post on pet rats.

It’s about numbers — how we count things, and what we do with the numbers we get.

It’s about two otherwise unrelated recent articles that both dealt with counting city rat populations.  One was about Boston rats (by Heather Hopp-Bruce at the Boston Globe), which I will discuss here.  The other was about New York City rats (by James Barron at the New York Times), which I’ll cover in a subsequent post.

The Hopp-Bruce piece is a delightful riff on how data can be misinterpreted.  She starts with public data available on the City of Boston website, concerning the number of citizen complaints about rodents that occurred between April and September of this year.  She presents a simple graph of these data, showing that complaints shot up from a fairly stable average of about 9 complaints per month, recorded over the 10 months between June 2013 and April 2014, to an astronomical 95 complaints in September 2014 — a 9-fold increase in only 5 months!  But wait, there’s a problem here, she points out.  This was an increase in complaints.  It doesn’t necessarily follow that this reflects an actual increase in the number of rodents, or even the number of rats more specifically, although it could.  Complaints, at best, are an imperfect index of the rodent population.  After all, one rat can elicit multiple complaints.  We need to validate this relationship.

But whether or not complaints equal number of rats, how might one explain this uptick?   Well, one typically starts out by paying attention to comparable patterns in correlated events.  In this case, Hopp-Bruce notes two similar upward trend lines that occurred over the same period of time in Boston.  One involved significant developments in the activities of the state Gaming Commission that led, in September, to awarding a Boston-area license to Wynn Resorts.  The other involved substantial increases in complaints about open graffiti in the city, with a 13-month high reached in September.  Clearly, these two trend lines were chosen to be obviously silly; there is no face validity to a relationship of fluctuating complaints about rodent populations with either decisions about gambling or complaints about street art.  But the point is still made.  Focusing on one possible correlation to the exclusion of others is subjective at best, and horribly misleading at worst.  One needs to dig deeper, search more widely.

And that is what Hopp-Bruce did.  She contacted the city’s department of environmental services, which includes animal control, and learned of two correlated events that are much more likely to account for the increase in rodent complaints.  They have face validity because they involve policy changes at the department pertaining specifically to rodent complaints.  One is that the department is now actively soliciting complaints.  The other is that inspectors now apply a single sighting to all of the buildings on the block, meaning that one rodent can indeed lead to multiple complaints, but in this case as a matter of policy and record.  Both policy changes would be expected to result in an increase in recorded complaints.  And both policy changes were instituted this past May, at precisely the turning point in recorded complaints.  Mystery solved!

I am reminded by this story of documented increases in cases of autism that have been reported in recent years.  One might have concluded that the incidence of autism per se was increasing and spreading more widely in the populace.  But the uptick also happened to coincide with the merger of diagnostic criteria for autism and related disorders into a broader “spectrum” that resulted in more cases assigned to the same category.  Unfortunately, with parents looking for other, less valid explanations for the increased incidence of autism, such as the now invalidated association with MMR vaccines, the ensuing scare that caused many parents to avoid the vaccine had tragically unintended but perfectly predictable consequences, namely, an increase in the incidence of measles.

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Feeling guilty about “smushing” an ant, and other musings about our relationship to animals

I have been following the regular postings on a new Opinionator blog at the New York Times called Menagerie, about our relationships with other animals.  Some of the essays are a little sentimental for my taste, and one was even a fictional short story.  But there have been some that offer interesting insights into our scientific understanding of animal behavior, such as a piece last month by David Rothenberg on whale songs.

I first started paying attention in August, with Tim Kreider’s essay about his unnamed, but nearly conjugal live-in pet cat.  As a former keeper of cats, I could relate to dealing with the eccentricities of feline behavior, though not to the extent of having provoked, as he did, the jealousy of family and friends.   As far as I can determine, the series started in June, with a piece by Jon Mooallem about wildlife cams that allow us to eavesdrop on the lives of nestling eagles and other critters.  His essay importantly explores when and how it is appropriate for us as humans to intervene in the lives of the wild animals that we monitor.

The current post is another by Tim Kreider, this time confessing his conflicted relationship with wild animals, like ants, fruit flies, and neighborhood raccoons.  Yes, they are pests, but they are also living beings, he demurs, thumb hovering over the ant invader.   He goes on to explore the moral landscape for relating to mosquitos, mice, and others, and gives a link to a hilarious (and perhaps not so funny) Rueben Bolling cartoon in the “Tom the Dancing Bug” series, on “Human Morality Made Simple.”   “Menagerie” mostly lives up to the series subtitle that this discussion is “Just between us species,” despite the reference in the mission statement to how “Menagerie explores the strange and diverse ways the human and animal worlds intersect.”  I hope the intent is closer to the former than to the latter.  Certainly, that would be more appropriate biologically, as we are animals, too.

My favorite piece so far was posted in August by Julie Metz, on “My Daughter, Her Rat.” I have worked with a variety of rodents in my research, and kept some as pets, either at home or in the lab, so I know how sociable and interesting rats can be.  Julie tells a delightful story about a pet rat named Eden, rescued from a pet store as future python food, who becomes her daughter’s “wingman” and close companion as she finishes high school and moves to the opposite coast for college.  One can imagine a live-in version of Remy, the rat chef from Ratatouille, making her an after-school snack.  In focusing on the challenge of transporting Eden out to her daughter’s college, Julie brings to light the misconception that rats are dangerous and difficult to handle, more like snakes and spiders than their brethren hamsters and guinea pigs.  It turns out that hamsters and guinea pigs are preferred by the airlines over rats, even though rats are far more interesting as pets, especially when raised in your care from a young age.   Hamsters may seem more cuddly, but they are persistent escape artists, whether from a cage or your lap, whereas rats can be given the run of the house and still come back to you for a game of tag.  Interesting in particular is one airline’s preference for guinea pigs over rats.  Can you imagine a 6-hr flight with a wailing guinea pig on board??

 

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“I’m back” and then back again, still looking for the sweet spot

Back last May, I initiated a blog mechanism that I called “What We’re Reading Now”, which I hoped would give me a basis for more regular, if shorter posts.  That didn’t work the way that I had hoped, for two reasons.

I decided that I don’t like the bundling of individual posts, for one thing, once I had a chance to see the bundles in action.  Each post loses it’s identity in these bundles, especially the separate tags and categories that help people to find my posts on the web, and help them at least to search the blog for posts on specific topics.  That’s why I have gone back and dismantled the confinement of “What We’re Reading Now,” releasing the individual posts to stand on their own, jiggered to keep the same May posting dates (a wonderful feature of WordPress, I might add).

The other failure of this ruse is that it didn’t facilitate more regular posts.  As I shared in the “I’m back” post last May, I tend to approach my blog as a scholarly outlet, with the goal of being factually correct and at least reasonably thoughtful about the ideas I put forth.  They will be my ideas, for sure, but they will have been self-edited to at least be more than idle rants. That takes time, and my life as a full-time professor doesn’t leave much of it available.

Paul Raeburn at Knight Science Journalism Tracker had an inspiring essay over the summer about compulsiveness in blogging that touches on this very topic. The focus of the essay was a response to, and an analysis of, a post by Smithsonian Magazine blogger David Schultz, who endeavors to write his blog posts quickly, “in an hour,” in part by curating other people’s posts and in part by forgoing deep analysis in favor of turnaround.  Paul offered respect for the approach, especially when it involves thorough attribution to the work being curated, but also seemed to find speed-writing more challenging personally.  I posted a comment to Paul’s post, which I offer here:

The example you give of short posts from NOVA Next reminds me of what some non-science outlets like The Dish do, namely, a lot of curating.  As de Chant says, and not in a self-serving way, I think, there is honesty in citing, but then passing through, entire chunks of another writer’s ideas.  Certainly, in the case of The Dish, there is no missing Andrew Sullivan’s philosophy lurking behind every curation, so the pieces selected come to represent the blog as a whole, and sometimes even a common theme (e.g., the recent posts on neuroscience).  They each are small contributions, perhaps, but useful, nonetheless.  That said, I am grateful that “thinkers” like you and your colleagues at the Tracker take the necessary time to flesh out and more thoroughly consider the nuances of a story, no matter the length of the piece.

Thus, I share Paul’s conclusion that there is a place in the science blogosphere for curation, as well as his personal experience that this often goes against the grain of one’s own tendency to want to accomplish more.  As for my own writing, I am still searching for the sweet spot.

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Measles surge years after vaccine-autism scare: science denial comes home to roost

The AP reported this past week that the incidence of measles has surged in the UK since Andrew Wakefield and colleagues first made their report in 1998, now considered fraudulent, that cases of autism are linked to administration of the measles-mumps-rubella (MMR) vaccine to children.  Many parents in the UK and throughout the world thought that withholding the vaccine from their children would protect them from autism, when in fact it made them more susceptible to contracting measles, and in turn made it more likely that they could spread it to others.  Ironically, this spring is the 50th anniversary of the creation of the first mumps vaccine by American microbiologist Maurice Hilleman, as chronicled in a fascinating story by Richard Conniff at the New York Times.  Hilleman ultimately combined his mumps vaccine with measles and rubella vaccines developed by other scientists to create and refine the MMR vaccine that was the source of the trumped-up controversy.  Now, medical professionals are scrambling to convince hesitant parents to bring in their unvaccinated children, a challenge exacerbated by the lack of a legal requirement in the UK for MMR vaccination.

 

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What tooth chemistry says about Neanderthal behavior: a classical example of science sleuthing

It’s only one case.  One tooth from a Neanderthal infant.  One tooth that provides a suggestive piece of evidence for when that infant may have transitioned from mother’s milk to solid food some 100,000 years ago. But the foundation of science built around this one case, as explored in coverage by Adam Cole at NPR, John Noble Wilford at the New York Times, and others,  make it an impressive example of how scientists attempt to reconstruct biology and behavior in the distant past, and come away with some degree of confidence in their effort.  The research reported in Nature was not in fact focused on the Neanderthal tooth, but instead on documenting how weaning from breastmilk in modern human and macaque infants affects, and can be documented in, tooth development.  However, these studies served as critical positive controls for the Neanderthal analysis, essentially validations for using the same techniques in studying a fossil tooth.  To wit, the element barium is reliably transferred in breast milk from primate mothers to their infants, and can be detected with substantial precision in layers of tooth enamel, with an inherent time stamp, producing similar patterns detectable in the infant teeth of humans, macaques, and now a Neanderthal, which indicate when weaning off breast milk occurs in each case.  Sure, the news reports probably put too much emphasis on the Neanderthal part of the research.  One case certainly does not prove that Neanderthal infants stop breast feeding at about 14 months.  On the other hand, there is good reason to expect that this finding will be affirmed as additional cases are studied, with the interesting possibility that Neanderthals were not obviously different from their primate cousins.

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Angelina’s mastectomy story overshadows the Myriad gene patent case

As covered widely in numerous news outlets over the past several weeks (see links and critique by Paul Raeburn at KSJ Tracker), Angelina Jolie recently announced that she had a double mastectomy based on the positive outcome of genetic testing for the BRCA genes, predictive of certain kinds of breast cancer, using test kits developed and patented by Myriad Genetics.  There appears to be widespread admiration for the decision she made, facing significant certainty that she would eventually develop breast cancer.  However, as some have complained, the gene tests from Myriad are enormously expensive, and beyond the reach of some women, because of the monopoly they hold on any testing for the BRCA genes, derived from their patents.  Myriad defends their monopoly by arguing that the BRCA tests are provided free to those who can’t afford it, and are normally covered by insurance.  However, there is a more fundamental issue at stake, that is often overlooked in these stories:  should genes, any genes, be patentable?  Indeed, Myriad Genetics is defending the constitutionality of these patents in a case currently before the U.S. Supreme Court (Assoc. for Molecular Pathology v Myriad Genetics), with a ruling expected in the next few weeks.  SCOTUSblog is a huge resource on the arguments (see summary posts by Amy Howe and Lyle Denniston after the initial hearing in the case in April, plus the posts from a symposium on the case held in February).  Also worthy is a recent edition of the WGBH Radio program, Innovation Hub, hosted by Kara Miller, on “Your Genes: Patent Pending.”    

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Say it isn’t so, CJR

The Columbia Journalism Review may be cutting back or dropping The Observatory and its editor, Curtis Brainard, according to a post by Paul Raeburn at the Knight Science Journalism Tracker, based on an article by Joe Pompeo at Capital New York.  This would be a huge loss of an important, and critical voice in science journalism, especially concerning environmental science.  And, it comes on the heels of the January’s announcement by the New York Times that they, too, are cutting back on their commitment of staff and resources to coverage of environmental news.  This includes the recent cancellation of the Green blog that Brainard 1st reported.    As climate change and other environmental issues appear in the news with increasing frequency, this couldn’t be a worse time for critical voices to be silenced.

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The moral and scientific issues surrounding Plan B

I have struggled with the appropriate reading of the issues swirling around the implementation of Plan B as an approved and freely available emergency contraceptive. On the one hand, there is the clear scientific evidence that Plan B is a contraceptive, preventing ovulation, not an abortifacient drug like RU486.  However, assuming that there is little basis for concern about any possible negative health effects of Plan B on young girls, and that is not entirely clear, was it inappropriate for our executive branch of government to modify the recommendation from solid physiological and medical science to make a policy conform to a different social norm (i.e., concerning parental responsibility for minors)?  A recent piece by Joanna Weiss at the Boston Globe provides a compelling perspective on the debate that I hadn’t seen before.  She offers the view that making Plan B freely available to all ensures that those, generally poorer girls who lack significant parental guidance will still be able to avoid unwanted pregnancies.  Since half of all pregnancies are unplanned, and pregnancy is a significant challenge to a women’s health, there is a significant medical and scientific basis for seeking to reduce the incidence of unintended pregnancy.  If making Plan B freely available can help, even if it sidesteps a parent’s responsibility for a minor, but sexually active daughter, then that’s what we should do.  So, I’m rooting for Judge Korman on this one.

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I’m back

I am returning to active writing on this blog after a hiatus of nearly 9 months.  Not coincidentally, this is also the period of my academic year as a university professor that followed starting up the blog last summer 2012.  This is when my work as a classroom teacher, research mentor, and professional colleague all took precedence over my contributions to the blog.  This is regrettable, and unacceptable, as the purpose of a blog, I think, ought to be regular postings to stimulate continuing conversations, in this case, about public science.  But also it is unnecessary, as there is no reason why my work on Dissecting Public Science should have lower priority than other activities in my professional life.

After all, I consider my writing and research on public science to be a distinct part of my continuing scholarship as an academic scientist, along with my laboratory research on olfaction and my pedagogical research on classroom technology.  But perhaps that’s the rub.  In approaching my blog posts as scholarship, I usually am engaging in a time-consuming process of research, fact-checking, and editing that prohibits timeliness.  After all, “dissecting” requires careful attention to detail.  And I can be rather obsessive-compulsive about research and writing, as my colleagues, students and family know well.

Yet, public science is anchored in journalism, which is often fast paced and can’t wait for too much depth.  While I would prefer science journalism to be more scholarly at times, I recognize that events often move too quickly for that.  Daily deadlines and competition to be first proscribe depth, or at least interfere with work on anything else that day.  Comprehensiveness comes later, upon reflection and more extensive research.

So, what’s a scholarly blogger to do?  I’ve decided to follow the suggestion of my daughter Amy, who is editor of this blog, to institute regular “What We’re Reading” posts, every week or so, that will give short comments on a small set of recent articles that deserve more attention (including here, in subsequent, more elaborate essays on the blog).  At the very least, this will keep the blog reasonably current, and provide a hint of more expansive things to come.

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Overbye’s teaching moment about scientific discovery and uncertainty

In my humble opinion (alright:  IMHO), the best science writing combines reporting on current advances in science — the knowledge or content — with insights into the process of science — how the new knowledge was acquired, and with what certainty.

Thus, I was delighted to read a recent article by Dennis Overbye in the New York Times about the kerfuffle over the claimed discovery of a so-called Goldilocks planet — aka, Gliese 581g  Continue reading

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