Friday, August 04, 2017

Meiosis kills! (Now in print, and video)


Scientists are rarely dispassionate about their research. Why spend years trying to figure out the fine details of something you have no interest in? Before my wife and I lost two pregnancies, I had thought abstractly about the question of why developmental failure is so common across plants and animals, but it wasn't personal. I was interested in the fact that dying before reproductive age means an individual does not get to pass on whatever traits caused it to die. In other words, natural selection should quickly remove any heritable trait that commonly causes developmental failure. At the same time, pretty much any organism loses some of its offspring, implying some broad based mechanism WAS commonly causing developmental failure. I even went so far as to publish a review article focusing on what this mechanism might be.

But once developmental failure became personal, I wasn't just interested, I needed to know.  

The result of that impulse was just published by Proceedings B, one of my favorite scientific journals. 



In addition, I worked with Sarah Friedrich, the extremely talented Graphics Specialist in my department, to make this video explaining the science in public-friendly ways:

Wednesday, July 26, 2017

I, lichen.

This fungal individual makes lots of complex structures, on which microbes live. So do you.
A lichen is an ecosystem. It consists of a multicellular fungus that provides the gross structure of the lichen, and a community of microbes that live in and on that structure, including photosynthesizers.

A human is an ecosystem. It consists of a multicellular animal that that provides the gross structure of the human, and a community of microbes that live in and on that structure. A human, unlike a lichen, generally cannot photosynthesize. 

We usually see humans as individuals, but lichens as ecosystems. In the last few years some scientists have advocating deep thought about humans as ecosystems. There has been very little deep thought about lichens as individuals.

Friday, May 19, 2017

Me as a peer reviwer

I find it painful to read a very critical peer review, even if it clearly intended to be constructive. This is somehow especially true when I am the reviewer. That I've just written a rejection-worthy critical review, and seem to do so fairly often (always accompanied by specific suggestions for improvements) is part of my job, but not one I relish.

Friday, March 24, 2017

My brother and the failure of TrumpCare


Why, please ask yourself, do the Republicans, after years of wishing to replace the Affordable Care Act, have no replacement even they can support? One clear answer is illustrated by my brother, Jason Levitis, an unsung American hero. I've mostly kept quiet about this, because he has, but the cat is out of the bag, Jason is out of government, and the time has come. In his recent article in Vox, his byline reads, "Jason A. Levitis is a senior fellow at the Solomon Center for Health Law and Policy at Yale Law School. He led ACA implementation at the Treasury Department during the Obama administration." That's all true, but Jason was on this long before the ACA was law. He was the single most frequent visitor to the White House throughout the entire Obama administration, and he wasn't there for the tour. I feel safe in saying that no one in the world knows the Affordable Care Act better than my brother, or has thought more deeply about why each part of it functions as it does. When President Trump said, "Nobody knew health care could be so complicated," my response was, "actually, my brother knows exactly how complicated."

I can clearly remember Jason telling me that he was going to reform the U.S. healthcare system in the year 2000. He and I were both recovering from injuries, limping through the newly reopened Hayden Planetarium at the American Museum of Natural History. Both of us, as patients, had been screwed by the healthcare system. Our parents, both physicians, had recently retired early because they just couldn't stand being part of that system anymore. As we crept along, two very similar looking young men on canes, to an evening planetarium show, he explained matter-of-factly that he had decide that the most important thing he could do was fix American Healthcare. This, he explained, would require years of work to understand the system, probably a law degree, the building of connections in the policy world, and an activist White House brave enough to succeed where "HillaryCare" had failed. His younger brother, I had to admit he was talented enough to carry out each step, and still found it improbable.  As we watched billions of years of galactic evolution whiz around us, I wondered how long my always swirling brother could focus on this very long-term plan.

Seventeen years later, he is still following his plan. He built his detailed understanding of the system as a Senior Analyst in the health economics department at the Greater New York Hospital Association. Then he got his law degree at Yale. Then he built connections and expertise in health law at Connecticut Voices for Children. He moved from there to being a Senior Analyst and Counsel at the Center on Budget and Policy Priorities, a DC think tank that is just as wonkish and unflashy as its name implies. He testified before various state legislatures about earned income tax credits and other stuff that I only understand because he explains it well, and I thought his singular focus on health policy had melted. I was wrong. He had become a respected part of DC health policy wonkdom, and with his co-wonks was working up a national policy resembling Massachusetts’s health reforms, aka RomneyCare. By 2008, when Obama ran for president, their framework was far better developed than the final TrumpCare bill that failed today.

President Obama appointed Jason as Senior Advisor to the Assistant Secretary for Tax Policy, Department of the Treasury. In practice, Jason worked day and night, often over 100 hours a week, writing the text of the bill that would come to be known as the Affordable Care Act. He would come to an important family event and would pull out two Blackberries, communicating on both simultaneously with the half dozen other people writing the bill with him. He would go into the bathroom and be arguing with somebody about the wording and punctuation of some sentence that was likely to be challenged in court.  He fought for fine policy details that his training in both law and economics told him would actually help the American people, not just make good TV. He sat next to Obama's people as they testified before Congress, feeding them the details they needed to give full answers. He undertook endless last-minute rewrites to try to meet the demands of that one last wavering Democratic Senator. Once the bill became law, he spent years writing the regulations needed to implement it. He, with a few close colleagues, is the policy brain of the Affordable Care Act.

I tell you all of this not only to praise my brother, although he clearly deserves it. The Affordable Care Act has brought health coverage to millions of Americans, slowed the increase in healthcare costs, spurred needed innovation and raised standards across the American healthcare system, and in the process saved countless lives. My purpose here is not to litigate the merits of the law, but to point out the intellectual rigor at the heart of the Affordable Care Act, and contrast it with the mushy sloganeering and flailing demagoguery that is the Republican approach to health legislation. The entire Republican machine spent years scheming to replace the ACA, made that their mantra, and have utterly failed to find any solution that isn't demonstrably, disastrously worse. There is no Republican reflection of my brother, no Nosaj Sitivel, because one can't take the details and ramifications as seriously as Jason does without rejecting conservative "principles." There is no health policy wonk taken seriously by Republican leaders who saw these problems  two decades ago and resolved, without ideological baggage, to learn how to increase healthcare access and quality. There is no one in the Republican establishment willing to fight for effective policy that is hard to explain and harder to sell. So as many years as they spent railing against Obamacare's imagined failings, and promising to replace it with bottled heaven, they remain incapable of offering any substance. TrumpCare failed because nobody involved in writing it actually cares.

You want to know how to improve on the ACA? Ask my brother. He, of course, has detailed, well researched, carefully considered lists of fixes. Will our current all facade, no building, leaders implement any of that? Of course not, they want the ACA to fail so they can blame Democrats. But with the defeat of the American Health Care Act of 2017, it seems much more likely that government with an honest interest in good policy will be back. Facts matter, logic matters, policy matters, even in politics. And that is reason for hope.

Thursday, February 02, 2017

Friendly Advice for Your First NSF Pre-proposal

It is going to be okay. Very okay.

Let's start with the important information that until last month I, like anyone who needs to read this post, had never applied for, let alone received, US National Science Foundation research funding. Having been out of the US for most of my time since earning my Ph.D., and other extenuating circumstances, kept me from applying to this extremely important source of funds. As with my posts on applying for NIH and ERC funding (which I didn't get), I'm writing this not as an expert, but because most people who write advice on applying for NSF funding are to varying degrees experts, and have been doing it for so long that they have no idea what us newbies might not know. I've never been on an NSF panel, I've never been to NSF, and all my attempts to talk to NSF employees have been unsuccessful. I am, like you, an outsider. So I learned a lot along the way, much of it later than I should have, and I'd like to share some key points. Before we begin, let's take a moment to contemplate this bodacious caterpillar I found in the University of Wisconsin Arboretum last summer:

Wow!

Alright, now that you remember that you love science, and brim with important and exciting questions about the world, let's delve.

1. NSF, we can agree, does not have the funds to support more than a small fraction of the grant applications they receive. Other huge governmental funders of science, like NIH, are in a similar situation. (I am assuming here, perhaps in vain, that the US government under El Presidentisimo continues to invest in funding basic research at some meaningful level.) This is a problem not only in terms of almost-everybody-doesn't-get-funded, but in terms of the phenomenal amount of time that scientists squander writing unsuccessful grant applications. In many cases, months of each year are spent applying for funding that is not available. On the flip side, NSF has to harness huge amounts of scientists' time to serve on committees, wading through the reams of applications finding reasons to reject as many of them as possible.

NSF has attempted a partial solution to this problem: the preliminary application. Basically, one starts by writing a short (four pages of text, plus many ancillary documents, including a one page Project Summary) version that has to be approved by a committee before one is invited to submit a full application. Most applicants (about 75%, in the program I'm applying to) only have to write the short version before being rejected, and the committees mostly have to read piles of short applications, with relatively few longer ones coming after that.

2. Writing the preliminary application was honestly not that bad. Several reasons: No budget is required, and many of the ancillary documents that NSF needs before they can fund anyone don't get submitted until your preliminary proposal is approved. More importantly, I have good collaborators, who are in practice writing these things. There is a huge amount to know about NSF specific 'grantsmanship.' When the committee gets to our application, after having already scanned scores of others, they will be both eager to find something really interesting that keeps them awake, and eager to find some reason that the thing can be rejected, so that they can get it over with. They will be looking for key phrases that everyone should have, and possible pitfalls indicated by things only people who have served on these committees (or maybe only that particular committee) know about. In short, it would be tremendously surprising if someone who just had phenomenal scientific ideas but no insider guidance as to the evaluation process ever got funding. I am lucky to have had that guidance; while it means I did a lot of rewriting to try to conform to a culture I've never encountered, it also, hopefully, means we have some chance of being invited to submit a full proposal. If so, that's what I'll be doing this summer, again with about a 20-25% chance of success.

3. As with any funding application, reading past successful applications to the same program is important. Notice not only the language used, the level of methodological detail given, and the structure of the proposal, but also the scope and scale of the proposed science.

4. Write, and revise, the one page Project Summary, and make sure everyone in the project agrees on it, before bothering with the longer Project Description. I made the mistake of drafting the Project Summary, receiving only minimal feedback on it from one of my collaborators, then writing the rest of the grant. By the time I got more extensive feedback from this collaborator, I had only a few days to reconsider the scope of the work being proposed and extensively rewrite. The proposal ended up much better for it, but I could have gotten a lot more sleep if I'd pushed for more feedback after writing just the summary.

5. The whole thing really isn't that much writing. Given that one knows what one is doing, and has good communication with collaborators, a good draft can be banged out in a couple of solid days.

6. In most cases, the one page Summary has to be uploaded as unformatted text, and it takes up more space the way NSF automatically formats it than it would if you or I formatted it according to their rules. I, and a few people I've talked to, ended up hacking down the one page summary very shortly before the deadline when we figured this out.

7. In order to apply, you need an "NSF ID." Looking on the NSF web page, you will find lots of information on retrieving your NSF ID, what to do if you have two NSF IDs, whether NSF ID is the same thing as various other identifiers NSF has used in the past, and so on. You will not find any information about how to get an NSF ID if you don't already have one. If you call NSF to ask how to get one, they will be so confused by you that they won't be able to help you, as if you had called to ask how to breath in before speaking. You just do it, and you must already know how. So I will tell you the secret: somewhere in your university or other approved research organization, there is some individual with the official power to communicate with NSF to get you your very own NSF ID. You will have to find out who that person is and request the NSF ID several days before the application deadline. My collaborator at another university didn't get a reply to his request until a few hours before we submitted, and we were actively discussing what would happen if we had to leave him off the PI list. Don't let that happen to you.

8. Which reminds me of another important point. I was advised to contact the NSF Program Officer for my application when I had a nearly final Project Summary worked up. As mentioned above, that didn't happen until less than a week before the grant deadline, at which point the Project Officers were all swamped by others trying to meet the same deadline. I emailed the Program Officer, and got back a very short email, but never got to talk with her. Finishing your Project Summary early will allow you to get input from your Project Officer.

9. Be smart, work very hard, and have extremely good luck.

Thursday, January 19, 2017

Large Alligators, explained.




I've now seen several reactions to this video shouting questions like, "Why aren't they all dead?!", "Why aren't they running for their lives!?"

Well, sit yerself down my friend, I'm going to be brief.

1. Telephoto lens makes that ol' gator look bigger and closer than it is.
2. Gators rarely attack people unless fed by people, or defending nests. Average is less than one fatal attack a year in the US.
3. Gators are aquatic ambush predators. They don't run down large prey on land.
4.  Florida has well over a million gators. Spend time there, you learn not to worry about them.
5. I stepped on a live, submerged gator while working in the Everglades. It moved away. So did I.
6. Florida,  outside Miami Beach, is the deep South. Somebody, possibly everybody, in that crowd is armed.
7. If they had all run away there would be no video of it.

 "Video: Large Gator Spotted in Florida" isn't quite fake news, but it certainly isn't news.

Friday, January 13, 2017

Adventitious knowledge

Joseph Grinnell, eminent ecologist and zoologist of the early 20th century, and founding Director of the Museum of Vertebrate Zoology, where I was a graduate student, wrote some hilarious stuff. Google Scholar lists 376 publications in his name, most of which are actually by him, including foundational papers in niche ecology, bio-geography, museum science, and so forth. He took so many thousands of pages of detailed, elegant, highly legible, informative, rigorous, lyrical, systematic field notes that if I told you how many, I'd have to look it up again, and it is getting late here. And he is rightly revered as a founder and role model in the MVZ. But perhaps my favorite thing of all about Joseph Grinnell is his nearly forgotten, mildly disturbing, profoundly droll paper, "A Striking Case of Adventitious Coloration." I have no memory of how I first encountered this paper, other than that it was in my former life as an ornithologist at the MVZ. I have never come across another paper that cited it, and Google Scholar lists none. It is, at core, a mystery.

The whole story is available here. The first two sentences:
On February 8, 1920, I spent the afternoon with my family at a point in Moraga Valley, Contra Costa County, California, some five miles, airline, northeast of Berkeley. My son Willard undertook to exercise the shotgun for the purpose of securing some specimens of local birds such as happened to be needed at the Museum.
So ornately informal, so precisely vague, so informatively not-to-the-point, I am in love with this opening. No reputable journal would publish it these days, and that is a shame. He's storytelling, and quite well. The story strides on: Willard blasts a mated pair of Oak Titmice, both of whom have bright yellow breasts. Why bright yellow? Oak Titmice are grey, never yellow.  Grinnell rushes the five airline miles back to Berkeley, marches into the botany department with his dead birds, and tells them to figure out what kind of yellow pollen these birds have got on them. Not pollen, say the botanists. Grinnell marches into a mycology lab and tells them to figure out what kind of yellow spores his birds have on their breasts. Maybe slime molds, hard to tell, say the mycologists. Grinnell concludes that possibly bird feathers could be an important means of dispersal in slime molds! He finishes by pointedly mentioning that if anyone is interested, these two birds "and their loads of spores, constitute Nos. 40,391 and 40,392 in the bird collection of the Museum of Vertebrate Zoology." He publishes the whole thing in The Auk, and that is the end of that, for almost a century. A century, by the way, is how long Grinnell said some of the MVZ's specimens might have to wait before they would be put to some as yet un-imagined use. It has been 97 years.

Which brings me to that wonderful word in Grinnell's title, "adventitious." It means something on the order of "acquired by chance" which is how those titmice presumably got their yellow, and how I came to the knowledge that in a drawer in Berkeley two spore laden titmice waited.  What did I intend to do with this knowledge? Keep it in a drawer, until, perhaps after one hundred years, it proved valuable.

Now, I unexpectedly find myself with colleagues interested in spore dispersal ecology, and somebody mentioned spore dispersal via bird feathers. Which started me rummaging around in my dusty rusty musty gusty fusty drawers of ornithology, hunting for memory of birds with spores on them. All I remembered clearly was Willard undertaking to exercise the shotgun, but eventually (this morning) I found first memory, then paper, and shared both. And by afternoon my new mycology colleagues had requested access to Nos. 40,391 and 40,392 from my old ornithology colleagues at the MVZ, so that we can collect some of the long faded yellow dust. A little bit of molecular genetics wizardry (our lab is set up for sequencing DNA from dried fungal museum specimens) and we may finally be able to discover what made Grinnell's birds so yellow. If it is a new species of anything, we must surely name it after Willard.

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.

Friday, June 12, 2015

Back to posting: Seastar Video

It has been a long time. Here, to get things rolling again, is an awesome little video (with English subtitles) that SDU made about the discovery my students made (unexpectedly) and my friends and I helped them publish. The part at the end where the starfish squeezes out the tag through its skin in slow motion is pretty damn cool.

Olsen, T. B., Christensen, F. E. G., Lundgreen, K., Dunn, P. H., & Levitis, D. A. (2015). Coelomic Transport and Clearance of Durable Foreign Bodies by Starfish (Asterias rubens). The Biological Bulletin, 228(2), 156-162.

If you want to hear more about this process and how awesome my students are, see this post and this post and this post.  Oh, and especially this post here.

Friday, March 27, 2015

Old pea aphids


You are a post-reproductive pea aphid. You have spent a long and happy life sucking the juices out of a pea plant. As the plant has grown, so has your large and clonal family, who you love as you love yourself, because genetically they are self. You were born with all your daughters already developing in your ovaries, and now the last one is out, and already reproducing, and what are you going to do with yourself? You may be only halfway thorough your lifespan. What to do with the remaining weeks? Pompano Beach is out, too many insecticides.

The obvious answer if you are a natural selection minded aphid is you'd like to help all the clones of yourself you've created to grow fast, live long and reproduce a lot. But how? Reproductive adults contribute more to the growth of the colony than do the young'uns, so throughout your reproductive lifespan, you've tried hard to stay at the center of the colony, where there is a touch of protection from predators. So maybe now you should move to the edge? If a hungry predator comes along, you can martyr yourself for the good of the clone. You don't have any chemical defenses or strong sharp pokey bits, and your kick is frankly rather unimpressive, but maybe if the predator eats you, it will allow time for your great-great-grandkids to escape, or at least make the predator full enough that it eats fewer of them. And maybe, just maybe, when that predator comes, you will be brave enough to just stay put and get eaten for the team.

Or perhaps rather than just sitting around waiting to get eaten, you can help to feed the family? Aphids suck sap, so if you could either put some chemical into the plant, or create enough suction, you could stimulates flow to that part of the plant where your family resides. Your young might grow faster or start reproducing sooner.

I mean, I don't really know. No post-reproductive aphid has ever sought my advice before. I'll do some experiments and get back to you.