Thursday, November 17, 2016

How to tell if your aphid is done reproducing.

If you want to know if a parthenogenetic pea aphid is all done reproducing, look at her abdomen. If there are eyespots, she still has embryos in her. If not, she's done. If she is post-reproductive, she's likely to move to the edge of the colony, where risk of predator attack is highest. Details are here, in a paper written with some very talented undergraduates at Bates College.

How not to respond to unhelpful peer reviewers

For as long as I've been a scientist, and longer, there has been extensive discussion on the many ways that peer review is broken. Peer review is how, in theory, science gets evaluated and hopefully improved, before publication, and therefore hard to dispense with, despite being widely seen as inefficient, biased, and corrupt. It goes like this: Author submits manuscript to journal, journal sends it out to independent experts for feedback, these experts (the scientific peers of the author) decide whether they are expert and independent enough to give appropriate feedback carefully read it, think about it, identify its flaws, make constructive detailed suggestions, and finally recommend to the journal whether it should be published as is, fixed and then reevaluated, or just rejected. That is, at least ideally, how is supposed to work.

There are a great many ways in which that ideal can fail. I draw a great deal of schadenfreude from reading Retraction Watch, which is effectively a blog about cases where peer review failed in one of many ways, something was published, and mistakes or misdeed were later found out. I, like most scientists, know a few people whose work may show up all over Retraction Watch some day.

Which brings me to the fact that I am currently figuring out how to respond to a review that has failed with regards to independence, expertise, detail, fact, specificity and constructiveness. I would have suggested to the journal that this person could not be an independent reviewer, except that it never occurred to me that anyone would consider him to know anything about the topic of the paper. Explaining the long history of this interaction to the journal, we have now been assured that our re-submission would be sent out to different reviewers. Even so, in resubmitting, I have to respond to all the reviewer's comments, even those that are wildly counterfactual, have nothing to do with the current manuscript, or are just complaints about the reviewer's own work not being cited more extensively. And it has to be done politely and factually. So one must never include responses like these:
  • This highlights a fundamental difference in approach to science. Reviewer's comment, and publications, suggest that scientific papers should be fishing expeditions in which everything that can be gotten out of a data set is analyzed and those results that test significant published breathlessly. We started with one, a priori original question, gathered all of the available data to address it, and got a clear result, which we state concisely. While some authors would stretch the results section out to numerous exploratory paragraphs, expounding upon questions that were tailored to fit the results of the numerous analyses, that would surely be a disservice to science.
  • It is not clear what this means. Perhaps the reviewer did not find our Methods section. It is in there between the Introduction and the Results.
  • It does not seem that the Reviewer has any idea what kind of data we are using, despite the six paragraphs on the topic.
  • Furthermore, a reading of the manuscript would have revealed that no matrix models are employed. Reviewer's comments would seem to be hastily copied and pasted from review of an unrelated paper.
  • The Reviewer's publications are not relevant or useful here. Perhaps they were relevant to the paper for which most of this review was written?
  • This is counterfactual and the Reviewer has excellent reason to know that.
  • These quotes of the journal's rules are from an entirely different journal that the Reviewer often reviews for.
  • Not only can we find no mention of this statistical rule anywhere, we note that Reviewer's own papers don't follow it. We asked an expert in these methods about this 'rule.' She called it, "hilariously made up." 
I need some empenadas.

Wednesday, November 16, 2016

Ghosts of papers that may some day be

The world is full of science that only half exists: Experiments done but not written up, manuscripts waiting for revision, results too unimpressive to prioritize for publication. Where fetuses are gestated for months but born in hours, data sets often take longer to put out into the world than they took to create. Until it is published, academic research is only a nascent fluffy squishy wispy gelatinous downy larval effervescent ephemeral eufloccinaucinihilipilificatable translucent apparition, neither seen nor heard nor here nor there. Once published, research gains visibility, permanence, and perhaps even value.

While most scientists have things they would like to get around to publishing,  I feel like I've accumulated a particularly long list of research projects I need to push out. This summer and fall I've actually had some time to dedicated to that. I've made a goodly dent, but the list is still long, and new tasks and projects emerge like mosquitoes from an abandoned hot tub.

I've published four good papers this year, another is ready to go as soon as my coauthor has time to look at it, and a sixth just needs a few final touches, and should be submitted in a week or two. Both of those 'full term' papers will, hopefully, come out next year. I think that's pretty good considering I spent most of the last year on intensive teaching, had a months-long battle with epidemic keratoconjunctivitis, have moved my family four times in the last year and a half, and have three children five and under. There are days I wonder why I am so tired, and then there are days I remember why I am so tired. And on those days, I don't feel the least bit bad about keeping all those manuscripts, and coauthors, waiting.

Monday, October 24, 2016

Why we cosleep with our infant and you (perhaps) should too

The feeling of a soft little one gradually melting into my arms is lovely, and I wouldn't soon give up rocking my baby to sleep. That said, shifting from foot to foot in the dark several hundred times night after night can get repetitive. So tonight, as I was rocking little Peregrine, I set myself an intellectual challenge. I was going to simultaneously count how many times I shifted from foot to foot and plan out this blog post. It turned out that after only 564 rocks he woke up and demanded to be nursed, but I will write what I planned anyway.

Peregrine is now almost two months old, and we've slept with him in our bed with us from the very beginning, as we did with both his older sisters. I can hear the million voices crying out in horror, but hold on and let me explain why. The benefits, I hope are obvious (snuggles, not needing to wake up to nurse the baby, baby sleeping better, family bonding, etc.) but most people (in the US anyway) don't sleep in the same bed as their baby, don't feel allowed to, because the public health advice is that it can cause the infant to strangle or suffocate.
Zero day old Peregrine cosleeping (don't tell the nurses)
Our three children were born in Germany, Denmark and Wisconsin, respectively, and we have learned to be quite skeptical of official advice and cultural mandates that vary wildly from place to place. Advice regarding infant suffocation risk certainly depends on where one lives. When we told our Japanese friends how strongly Americans are cautioned against cosleeping, they were surprised and amused. In Japan, apparently, the official advice and common practice is for the baby to sleep between the mother and father, like Lancelot's sword (misplaced cultural reference, I know.) Our German friend warned us strongly against letting our cat near our baby, as a smothering would surely ensue.
Tigerlily and Flopper, dressed for Halloween
As an American scientist with a professional interest in early mortality, and with kids, I of course looked up the science upon which the American advice is based. The most common reference regarding the risks of cosleeping is:
Blair et al. (1999). Babies sleeping with parents: case-control study of factors influencing the risk of the sudden infant death syndrome. British Medical Journal. 319, 1457-1462.
There are more recent papers on this conducted in several countries, and as far as I can see none of them have basically contradicted Blair et al.'s clearly stated "Key messsages" (sic):

Key messsages

  • Cosleeping with an infant on a sofa was associated with a particularly high risk of sudden infant death syndrome
  • Sharing a room with the parents was associated with a lower risk
  • There was no increased risk associated with bed sharing when the infant was placed back in his or her cot
  • Among parents who do not smoke or infants older than 14 weeks there was no association between infants being found in the parental bed and an increased risk of sudden infant death syndrome
  • The risk linked with bed sharing among younger infants seems to be associated with recent parental consumption of alcohol, overcrowded housing conditions, extreme parental tiredness, and the infant being under a duvet
Now, my wife and I do not smoke, do not drink, are not sleeping on a sofa, do not put the baby under a duvet, do not have overcrowded housing conditions and are merely very, rather than extremely, tired. As this 2016 study makes clear, cosleeping is often associated with overcrowding because people in poverty don't have the money for an extra room or an extra bed. Poverty increases the risk of almost all causes of death, especially infant deaths, and much of the risk from cosleeping may actually be risk from poverty. Our baby is under 14 weeks, but according to Blair et al.'s findings, without these other risk factors (particularly smoking), there is no increased risk associated with cosleeping, even for neonates.

Not child endangerment (with Tigerlily)
Other studies have added parental obesity and extreme youth as risk factors. I am certainly overweight by the standard definition, but not obese. We are not particularly young parents. But still, if there is any risk at all of rolling over onto the baby, wouldn't it be safer to have him in a crib in another room? Emphatically, disastrously, not. Blair et al. write, "There was an increased risk for ... infants who slept in a separate room from their parents." Their estimate, that having the baby sleep in another room increases risk by about ten times, has been revised by more recent research to increasing risk by about half. Long story short, having the baby in a separate room is dangerous, while having him in our bed with us presents no documented risk compared to a good modern crib.

This presents two obvious questions: How should parents who aren't trained in interpreting regression tables make this decision? And, why is the official US advice (which resembles that in several other countries) what it is?
My interpretation, based on Blair et al., and the studies that have followed from their work: Always sleep in the same room as the baby. (Shockingly, this has only now become the advice from the American Academy of Pediatrics)  Never sleep on the couch with the baby (they tend to roll into the cracks, and this is truly dangerous). Don't cosleep with a baby under 14 weeks old if you are a smoker, are under the influence, are obese, are overcrowded (which is associated with poverty and all its ills), or are otherwise difficult to wake. If those risk factors don't apply to you, there are hundreds of hours of baby snuggling available to you, and you can decide to take them or leave the baby in a proper crib in your room. Quitting smoking is astoundingly good for your children's survival, even if you don't smoke inside the home.

Now why is the official advice a simple, "Never cosleep," or starker versions thereof? Because official advice has to be short and simple to be effective. My paragraph of advice, above, is 150 words. "Never cosleep" is two. "Don't live in poverty," would be great, if people were given the opportunity of escaping. People are, on the whole, really bad at following complex advice, and really good at finding reasons why things don't apply to them. Have my wife and I really never used a duvet with a baby? Questionable. Am I really overweight rather than obese? I haven't weighed myself in over a year. How tired is "extremely?" Have I ever fallen asleep on the couch with a baby? Certainly. You see, it gets messy, and it is easier for officialdom to just say, "No."
Baby Kestrel sleeping on the couch with Big Sister. Closely supervised.
So my message to you, should you be in the position of choosing where to sleep your baby is to make an informed decision. Good slogans are rarely good advice, and extensive snuggles are one of the things babies need most.
This baby (Kestrel) is not asleep. A desk drawer is not a proper crib.

Sunday, October 02, 2016

Leucistic Chickadee

We've intentionally left some dead wood and tangled sticks in the cedars at the back of our yard. This morning during breakfast a very light colored bird caught my eye. It didn't strike me as any bird I know. I ran to find my binoculars and camera.

It helpfully had come to the railing of our deck. It moved like a chickadee, but the coloration was weird.

White bill, pink legs, white patches all over the feathers, especially on the head.

A leucistic chickadee, repeatedly visiting our backyard feeder in Madison, WI.
Leucistic birds (those lacking some or all of their pigment) are not particularly rare, but still fun to spot.

Wednesday, September 21, 2016

Not for the sake of the species

I frequently come across statements implying that a particular trait evolved because it increases the fitness of the species or that a behavior observed in some animal exists because it helps the species. I hear this from not only members of the general public, but also from biology students and even biologists whose work does not directly address evolutionary questions. Please be aware that this is almost entirely wrong.

In most circumstances, natural selection favors traits that increase the fitness of those individuals that have those traits. If a heritable traits is good for the species but bad for the fitness of those organisms that have it, then those that have it will tend to survive or reproduce less well than those that don't, such that in subsequent generations, the trait will be repeatedly rarer in the population. Even if it is good for the species but has no effect on the fitness of the individual, there is no strong reason to expect that it will increase in frequency.

In some special situations, selection can favor a trait that increases the frequency of a gene in the population, even if that gene causes the individuals that carry it to live less long or reproduce less well than individuals that don't have it. And there are indeed some cases where some biologists reasonably argue that selection occurs at the group level, with traits of the population or group determining which groups survive and which die out. But in almost any popular science context, if you imply that something is for the good of the species, you have gotten it wrong.

Note: this is something I started writing about a year ago, and never finished, until now. I had some particular example in mind, but don't know what it was.

Decleration of intent to start blogging again, I hope.

In some weird way things have settled down enough that I can consider blogging (briefly) again. I do miss it. So much to say, so little time. Much of my blogging will likely be done late in the evening while holding my tiny baby and listening to my sleeping girls. But I'll try.

Let's start with this: I don't have to move my family anywhere in the near future. We are in Madison, Wisconsin, and I have a great job here: Associate Scientist in the Department of Botany at UW-Madison. Being a scientist who doesn't have to currently think about moving to another country or continent is kind of lovely.

Okay, more soon, I hope, about science, I hope.