Insignificant figures

Before writing a paper I make lots of figures. Some will be improved upon and included in the paper. Others just help me understand what the data are telling me. Graphical data analysis.

Still others, like this one, end up being rather pointless exercises. This categorizes those barnacle larvae that died during our study, based on the stage during which they died, and whether they spent abnormally long in that stage and/or the previous stage before dying. The reason this is pointless, despite the nice colors and nested boxitude, is that all the same information can more compactly and clearly be displayed in a table. However, I now know how to use, and when not to use, the R package treemap.

Choosing peer reviewers

Several years back, I was unbearably excited to be, for the first time, submitting my own manuscript to a real scientific journal. I'd spent months polishing it, and was totally confident it should be published. Working through the various steps of submission (input author names and contact info, input title, input abstract, keywords, ect.) I was surprised to be asked to input names and contact info for three recommended reviewers. Defendants in courts don't get to recommend specific peers to serve on their juries, how could science be served by asking me to recommend peers to evaluate my work? Confused, I emailed one of my advisers, who happens to be an outspoken crank when it comes to all of officialdom, and came away with the impression that this was not to be taken too seriously. I hastily plugged my keywords into Google and chose three prominent names I had never heard of before, who went on to tell the journal my paper was technically sound but not of the greatest interest. I was extremely lucky in that the editors of the journal found it very interesting, and published it anyway. Failing to have learned my lesson, a few papers I submitted since then were sent to unfavorable reviewers that I had recommended.

Now, journal editors can decide to ignore these recommendations, and those invited to review can say no, but in a large portion of cases (I have no data, this is simply a strong impression), some or all of those recommended end up writing reviews. The reason journals ask for such recommendations is to help the journal editors quickly find people who are highly qualified to review. I already know who is very knowledgeable about my specific topic, while the journal editors may not. Many journals have editors who are not paid anything for their service, and all have editors whose time is limited. Asking for and using these recommendations saves time, and probably helps avoid unqualified reviewers.

Doing so, however, has some pretty clear corrupting influence. Those who are good at this game pay great attention to whom they recommend, not only carefully considering the knowledge, viewpoints and interests of those they will recommend, but crafting the paper to raise as few objections as possible from these individuals. Papers that defy much of what is well established in one field regularly are published based on the recommendations of reviewers whose knowledge comes from another branch, and this fact is not ignored in making these recommendations. If the paper is very likely to be sent to a particular reviewer, that person's terminology and definitions will be used and his or her papers referenced. At scientific meetings, people will say, "I like this idea, list me as a reviewer." At its worst, peer review is reduced to a popularity contest, with well established authors having their work (not only journal articles, but also grant applications) evaluated mostly by their friends and allies.

Mixing moral distaste, political naivity, and hurry, I have generally spent no more than a few minutes on the question of who my recommended reviewers will be. The latest iteration of this came with a paper on which two of my undergraduate students are lead authors. We submitted it to one journal with a recommended list of reviewers that was hastily thrown together, experts on the organism we were working on but not necessarily interested in our particular topic. They trashed it solely on the basis that no one cared. We submitted the same manuscript, with very few edits, to another journal, listing reviewers with some knowledge of the organism, but a strong interest in questions related to our own. We got back three extremely positive reviews, praising our highly original and relevant work, recommending several very minor changes and urging the editors to publish this paper. Yesterday morning we submitted these revisions, and yesterday evening this journal officially accepted our paper.

So I've not only learned my lesson, but decided to heed it. Whom I ask to review a paper is (depressingly) almost as important as the quality of the work. I see truly terrible papers come out in excellent journals, presumably approved by carefully chosen reviewers, and some very good papers get rejected by less selective journals, in part because of poorly considered recommendations. From now on, I will put my qualms aside and think carefully, early in the process, about whom I will recommend as reviewers. After all, everybody else is doing it.

Very pleasing

There is something peculiarly satisfying about publishing an experiment which has, for its central instrumentation, a small magnet suspended by a human hair.

Good practice

Always order paper reprints for your undergraduate coauthors to give to their parents.

Teaching mark-recapture with dor beetles

The key step in the planning of any good field course is to spend some time at the field site observing and asking questions. What is the habitat like, what lives there, what are the facilities, what are potential challenges or dangers to working there, etc? When I first went to do this at Svanninge Bjerge, the location of my zoology field course, I immediately started seeing big blue dung beetles all over the place. Bikuben Foundation, who operate the place, run cattle there. There is no lack of dung. These big plodding dor beetles (Geotrupidae) were all over the place, and it didn't take me long to decide I wanted to work them into the course. I wanted to introduce mark-recapture methods, and these seemed like perfect subjects. Mark-recapture methods involve catching animals, marking them in some way that would allow them to be recognized if re-sighted, letting them go, and then trying to recapture them. Such methods have a huge range of applications from tracking individual movements and estimating population sizes to monitoring growth and survival and studying behavior and sociality. To teach this in a field course, I wanted an invertebrate animal that wasn't too likely to leave the study area, that is easy to capture, mark and handle without damage, and that has enough charisma to capture students' attention. Dor beetles have all this. They are big and slow, and so easy to find and catch by hand. They don't bite or sting. They will collect in large numbers in pitfall traps baited with cow dung. They have big hard upper wings (elytra) that can be marked in any number or ways without harming them (we used this system with nail polish, but I've now got a battery-powered cautery). They are extremely numerous. They are shiny and blue. They can fly, but don't often do so.

Students mark a live beetle for release. Photo by Kim Lundgreen.

They make such an ideal intro to mark-recapture that I almost worry that I've given the student a false sense that this is easy, where in fact such studies are often very hard work. Still, if you want an efficient system for teaching mark-recapture methods and have beetles like this at your location, I strongly recommend them to you.

Why lightning talks work

Last week was the second annual meeting of the Evolutionary Demography Society. It was fabulous. Close to 100 people, over three days, at Stanford. Man there is a lot of good food around there. A friend and I were sitting outside, eating burritos when this dude from a farmers' market booth came over and started giving us samples of gluten-free baked goods. Delicious. Great weather, friendly people. Oh, yes, something else. What was it now? Ah! We talked about a lot of great science. Roughly 70 presentations. Post-reproductive lifespan, evolution of aging, all the topics I like best and every talk on a topic of at least some interest. Fabulous.

Many conferences (but not this one) have what are called concurrent sessions. In one room there might be a series of perhaps 15 minute long talks about matrix models, while in another they are talking about theoretical modelling, and in a third it could be all about field data on hunter gatherers. The benefits of this are allowing more people to give talks in a short period of time, and letting audience members pick and choose which topics they spend their time hearing about. At EvoDemoS, we address these same problems in a very different way. Most presenters give a lightning talk plus poster. The lightning talk is five minutes (plus five for questions), and then after each session there is a break for coffee and posters. But the posters are mostly from the same people who gave the lightning talks, on the same subject. So you get up, give a rapid intro to the work, answer a few questions, and then because there are no concurrent sessions, everyone at the conference knows who you are and what you are working on. If they are interested in it, they come talk to you at your poster. If you didn't bother to print your poster, they already know what you are working on and come talk to you anyway. If they aren't  interested, they don't have to sit through 15 minutes of you talking about it. The frequent and lengthy breaks (made possible by the shortness of the presentations) make it easier to stay alert through the talks, and let us achieve a much higher conversation-to-passive-listening ratio, and it is really the conversations that are the point of the conference for me.

Now the obvious downside is that many speakers are used to having more than five minutes. Some won't come because they can't have more time, use their connections and seniority to push for more time, or simply prepare the same talk they would for a much longer slot and largely ignore the warnings that their time is almost up. One speaker, to remain nameless, was on slide 4 of 26 when the one minute warning came and sped up only slightly. So the moderators need to be a bit firm in some cases. The more senior the speaker, the more likely an overage, in my experience. This is partly a matter of habit, but also that the more senior people often have more work to present. There were a few talks where the theoretical framing got almost completely cut to make time for more methods and results, and that was sometimes problematic. A is consistently greater than B, but what does that tell us? That said, the great majority of the five minute speakers were able to state the question clearly, say a word or two about methods, give a main result (or maybe two) and draw a conclusion or three before inviting us to see the poster. And almost everyone I talked to at the conference, both as speakers and audience, thought it worked well in this context.

For a conference with thousands of people, I'm not sure lightning talks would work. I'd be interested to hear from anyone who has tried it. But for anyone organizing a small conference like ours, I absolutely recommend it.

Asimov on Creativity

Isaac Asimov's essays have been favorites of mine since I was a teenager, and while I can't claim to have read them all (he was the most prolific writer in the history of the world, if one excludes 'writers' who have computers write for them) I have read a lot. So I was excited to hear that a previously unpublished essay of his, On Creativity. And like many of his essays, this is spot on.

To summarize his conclusions, intellectual creativity (creation of startlingly new scientific ideas in particular, but not only that) tends to occur when previously unconnected ideas are examined together by a person in a conducive situation. And, he argues, a key feature of that conducive environment is the freedom to be playful, to unabashedly look foolish, to pursue ideas that don't seem likely to go anywhere with people whose expertise has no obvious connection to one's own. He implies, and it is at least as true now as when he wrote it in 1959, that the structure and strictures of science-as-a-business (including in academia) tend to discourage this. Connecting previously unconnected ideas is less likely when everyone is a specialist in her own field, not only unaware of the big ideas in other areas of science, but obligated by the strictures of specialist journals, specialist department, etc. to not wander too far afield. In the world of reputation building and publish or perish,  things like playfulness, acceptance of foolishness, and exploration of uncertain goals is potentially fatal. Funding applications not only require that you know exactly where you will end up, but also that you already have a significant portion of the data needed to get there.

At previous jobs, and in previous stages of my life, I often felt (and was told) that my intellectual creativity was my greatest strength. As things now stand, I have surprisingly little space for creativity, and when I do come out with something really original, I get something along the lines of, "Huh. That's different. What about this other thing that we all know about?" So the question I must ask myself is, how (and where) can I find a place where my creativity is an asset, not only for me, but for science and the world?

Ear to Ear

Yesterday, two students came to my office. They asked me to help them organize a BioBlitz, a rapid assessment of what species are present, at Svanninge Bjerge, the site where I taught my field course this spring. One of these students was in that course, the other I have seen around but don't really know. I asked all the basic questions. What do you envisage? Where will you do it? When? How will it be funded? We had a good long conversation, and I offered what support I can, while making clear I may no longer be in Denmark when this all happens. They frowned. I asked, "Where did you get the idea to do this? Why do you want to?" They looked at each other. The one I don't know, smiled sheepishly. "Well, I couldn't take your course last year. And after the course, all the students who did take it made all of us who couldn't fell incredibly jealous. They talked about it endlessly, like it was everything they could ever want in a course. Like we would go to a bar and instead of whatever we were talking about, they would be all about pinning beetles. Rather than fight about it, we agreed to try to organize something similar for ourselves. And it would really be great if you could be involved." I needed a moment to focus on maintaining my composure.

Jeg kan aila dig!

My three year old has already learned that she can insult us in Danish with relative impunity.  Recently, when angry, she shouts "Jeg kan aila dig!" which means "I can aila you!" only we don't know what illa is, or what Danish word she is actually using there. She was calling us "superfalig" which means, "extremely dangerous" for months before we figured out what she was saying, at which point it lost its appeal.

Having our toddler speak the local language better than we do is a comic indignity, but my failure to learn Danish has more serious consequences. While three quarters of everyone we meet here speaks decent English, the culture, administration, government, commerce, etc. are mostly conducted in Danish, and my engagement in any of these is therefore quite limited. Iris's Danish is vastly better than mine, while still far from fluent. In a fairly open and engaging society we are bound by these linguistic barriers.

Why, you may justly ask, don't I just buckle down and learn Danish? A few reasons immediately come to mind. A more-than-full-time job and two young daughters don't give me a great deal of time for down-buckling. Danish is, even the Danes often say, an unusually difficult spoken language. The correspondence between what a work looks like and sounds like is even looser than in English. Many of the consonants are silent or nearly so, and I just can't detect any differences between some of the very many vowel sounds and stops that make up most of the spoken language.

Danish teacher: The first is Å and the second is Å.
Me: You just said the same sound twice, you said O and O.
Danish teacher: No, Ååååååå vs. Ååååååå. No, you are pronouncing too hard. Oooooo is a third sound, and has long and short forms.
Me: What do the long and short forms sound like?
Danish teacher: Oooooo vs. Ooooo.
Me: Maybe we should skip to grammar.

My students say that my attempts to pronounce Danish make me sound like a drunken Norwegian. I do understand a lot more spoken Norwegian than Danish, as Norwegian is a relatively phonetic sister of Danish and I can read simple Danish. If the Danes would agree to compromise on drunken Norwegian, I would learn it.

But when my department sends me scientific reports to grade (what they call censoring), I know my Danish is not nearly good enough to know if they make sense. My course descriptions all state prominently that the entire course will be taught in English. I Google Translate every email sent out to the department to find out if it is something I need to do something about. Google Translate is less good at Danish than it is at German, for example.

Another reason for my linguistic failing is the linguistic proficiency of the Danes. One look and they can tell that I am not Danish. They start speaking English before I even open my mouth. My daughter's three-year-old friends may not speak English, but their seven-year-old siblings do.

Finally, there is the broader motivation problem. Denmark is a wonderful country in which we do not want to spend the rest of our lives. We want to be closer to family, in a more familiar and diverse culture, in a place where we speak the language (and oh what I wouldn't give for a decent bagel, or a burrito with spicy black beans and nopales). Knowing that we don't want to stay makes it easy to not learn, which makes it easy to not want to stay.

This experience has reinforced my long-standing intolerance for the intolerance toward immigrants and linguistic minorities that is very much on display in many parts of the US and Europe. I could spend the rest of my life in Denmark, and actually apply myself to learning, and would never speak the language well. Those countries that have the harshest attitudes towards immigrants tend to be the ones that need immigrants the most urgently. And being an immigrant is hard enough, even in a relatively accepting culture like Denmark's.

Beware of Slippery Slope Arguments

Once you start making them, it is hard to stop.

Rejection

Getting a paper rejection from a journal is always frustrating. So much time, effort and care goes into a paper that to have anonymous strangers say its no good can't help but hurt. I've just had a paper rejected, and it still hurts even though they had nothing bad to say about the paper.

The starfish paper I wrote with my students documents something that hasn't been documented before, but is certainly not the world's most important paper. It doesn't fit neatly into any field or derive from the pressing questions in any literature. So we sent it to a journal that explicitly says they don't care if it is important, so long as it is original, technically sound research. The reviewers agree that is passes these hurdles, but question its importance to their field. On this basis alone, the academic editor rejected it. I can't say I'm entirely surprised, as PLOS ONE has become a relatively high-impact journal. That type of success naturally brings them to function like a more traditional print journal competing for the flashiest papers. I filled out their feedback form to suggest that they update their stated criteria for acceptance, but won't otherwise protest.

There are two upsides to all this. The reviewers found the paper convincing and novel, with no technical or language faults. So we just need reformat for another journal and submit it there. Perhaps more importantly, this gives my student co-authors a window into yet another aspect of the scientific process that most of their peers never see.

Unsolicited parenting advice

I have decided to share with you one of the big points of baby raising that Iris and I learned by hard experience.

We have a million books on baby care, Iris reads a bunch of "mommy blogs," and we know lot of people with babies; we felt quite confident in our baby skills before our first daughter was born. For the most part that confidence was justified, but there was one thing we just had no idea about. Once we figured it out, it transformed our parenting experience: helping a baby fart. One hears all about midnight feedings and how to deal with diaper rashes, but we had no idea it was necessary to help a baby fart. She would be crying inconsolably, and we would be going crazy trying everything we could think of to sooth her, and then at 3 or 4 or 5AM, she would finally fart, and immediately fall asleep. This happened repeatedly for weeks, maybe months, until we figured out that belly massage, light pressure on the belly, or alternatively pushing her knees up toward her belly would squeeze the fart out. With practice one can feel exactly where the gas bubble is and guide it up and around and down and out. We got good at this, and could make her fart almost immediately, bypassing the hours of gas pains and ear pains. 

P.S.  Another thing I found very useful, when woken up for the 14th time that night, was to have a posted list of things to try to help the baby. It seems like it would easy to remember to check the diaper, but when sleep deprived enough this can be quite hard. So here it is:

Belly Massage

Milk

Temperature

Wrap

Rock

Light

Sing/Hum

Diaper

Clean skin

Nose

In almost every case where she wasn't actually sick, one of those was it. Print it poster size and put it near a nightlight.

Picture show (in Danish)

This spring I taught a field course in terrestrial zoology at Svanninge Bjerge, a nature area owned and operated by the Bikuben Foundation. The foundation had Casper Tybjerg, a well known Danish photographer, join us and take photos. Bikubenfonden has featured the course on the Svanninge Bjerge website, including posting many of his photos (including the above). If you start here, and click to the right, most of the next several dozen photos are from our course, and all are beautiful. The accompany text is in Danish.

It makes me all happy and proud and sad-that-it-is-over to look through these and remember what amazing fun that course was.

Chocranut

Lightly-salted peanut wrapped in a sweetened dried cranberry, then covered in dark (>75%) chocolate.

Student scientists study sea stars, produce plaudable publication

A good university science education should give students the opportunity to engage in scientific research. This is widely agreed upon, and most of the biology position announcements I consider state that the successful applicant's research should present opportunities for student participation. The general model is that the professor has the research program, and a question that needs answering, and a plan for answering it, and the student gets to see how research happens by carrying out, or at best refining, that plan. I'm all in favor of this, but I'd like to take it a step further.

My first publication, way back in 2003, was with one of my professors at Bennington College, based on work that she planned, and I, as an undergraduate, helped carry out. I made alterations to the experimental protocols, did a lot of lab work with minimal supervision, and chose to work on this project rather than others that were available, but I can take no credit for any of the ideas in the publication. In retrospect the one thing I would add to my own undergraduate education, if I was to be my own professor, was working through the entire process of generating a primary paper, from initial observations and idea generation to publication.

Implausible you say? Impracticable? If generating publishable science is so easy, why doesn't every professional scientist publish a paper a week? Well, I've just finished doing it with two of my students, and I'll tell you about it.

'Finished' is vague. We've submitted the paper, and I think it good, but we have to wait to hear if the reviewers agree. I'm not going to give you too much detail on what we found because you'll have to read the paper (or a future post) when it comes out.

It happened like this: At SDU, where I currently work, all natural science students in their second semester have to complete a group project. A group of students (four in my case) are assigned a faculty mentor who gives them a question to answer and guides them in answering it. In my case, the question was, "Can we use PIT-tags (like a vet puts in your cat) to mark starfish for a long-term demographic study?" We brought some starfish into the lab, talked about animal care and experimental design, showed them how to inject the tags and pretty much let them do their own thing.

They did great, but the tags just kept coming out. After a few weeks, all the tags were out. They answered my question with confidence: No, PIT-tags cannot be used to mark starfish long term. But the thing is, they didn't stop there. With no pay, no additional course credit, no requests for recommendation letters or such, two of the four students just decided to keep going. We met occasionally and I offered encouragement and comments, but little more.

They presented their results to the Evolutionary Demography Society, and long after the course was over they kept doing more experiments to figure out how the starfish were ejecting the tags. Notice that this is their own question. I asked, "Do the tags stay?" and my students answered this then asked, "How do they get rid of the tags?" And when we had an open house at the laboratory, they presented what they had learned to the public. Just by chance, one of the visitors they talked to had access to an ultrasound machine. This let them repeatedly image exactly where within the starfish the foreign body was moving. A year after they started, they convinced me that they had discovered, and had the data to back up, a previously unknown mechanism by which starfish can eliminate foreign objects from within their body cavities. "Okay," I said, "write it up for publication, and tell me now by what date you will have a finished draft." They missed their self-assigned deadline. They needed more help with data analysis than they expected. They put in all the wrong references in all the wrong places, and the flow of the article was terrible. English is not their first language. But not so long after they said they would, they sent me a draft that had most everything I needed to make it good. With the co-authorship of a couple of marine biologists (did I mention that I know next to nothing about starfish and have no other starfish research ongoing?) and with the continued input of these two students, we made a respectable manuscript out of it.

What lessons do I draw from this? Motivated undergraduates, with just enough guidance, can basically have their own successful research programs. The paper we produced still took a bit of my time to write up, and isn't the most important paper in the world, but they discovered something completely new (answering a question that someone who knew the literature would never think to ask), and they learned. They learned a lot. Refining questions. Starfish anatomy and function. Experimental design and practice. Ultrasound imaging. Cox regression in R. Scientific English. Literature searching and use. Collaboration. Communicating science to peers and the public. Preparing and submitting a manuscript for publication. Now they will get to see how peer review really works, or doesn't. These students, just starting their third year as undergraduates, have a fuller experience of what goes into making a scientific publication than I did when I started my third year as a doctoral student. Chew on that for a minute.

It is important here to think about these students' motivation. Judging by their grades, they are not academic stars. Neither of them has described a lifelong fascination with starfish. They did this, so far as I can tell, because it was their first chance to truly be scientists rather than just science students.

I told them early on that:
A) That they would have a strong say in the direction of the research and
B) that if they produced something publishable, I would help them submit it for publication.

These are not promises to be made lightly. Publishing things, especially things outside one's own central line of research, is time consuming. Giving first year undergraduates even this limited version of academic freedom in their research is, understandably, not common practice. But it seems to me to be damn good educational practice, and I plan to continue offering this type of opportunity to students when possible. Students will do much better, and more, work when they are exercising agency and following their own curiosity. Even if they don't choose careers in science, they know how science happens from start to finish, and that is surely something science students should be given the chance to learn.

Toddler naturalist

It was only 45 minutes until dinner and my girl was antsy. We decided to head out into the woods and see what we could see. We got on a bike brought along an almond and raisin snack, a water bottle, a doll, and stuffed orangutan. Five minutes later we were standing in the woods outside of town looking at this piece of wood. "This is a perfect cover object," I told Tigerlily. It was flat or even slightly concave underneath, it was on the soil but not in the soil, it was broad, and it was in the sunlight. "I want to look under it," she said. We lifted it up and found this shiny black toad.

We talked about toad poison and washing hands before eating. She hadn't finished her raisin and almond snack so only I held the toad.

Next we went for a little walk in the woods. She said she wanted to find insects. Instead, we found blackberries.

Or rather, she stumbled into them and I recognized what they were. I tried one just to make sure they were good, and they were. I didn't use my hands. Toad poison.

She left only the underripe ones. On our way back to our bike, she said, "what's this? An insect?" It was a beautiful dragonfly that I had walked right past. I couldn't get a good picture of it but you can get a sense of how colorful it was. 

Now it was dinner time and we walked straight back to our bike. My girl was tired and hungry but learning about the woods and was ready to come home.

To-write-list

I keep a running list of papers to write on my whiteboard.

This list currently has 15 entries.

Two of these have been accepted for publication this year but not yet taken off my list because it is nice to see them there.

 

Another was submitted, rejected, and is waiting rewriting.

Two have nearly complete manuscripts written and have been sent to colleagues for comments.

Five more are actively being worked on by me or co-authors and will hopefully be finished by the end of the year.

Four others are collaborations that are currently not moving. One of those is a project died for some specific reasons (like the data couldn't answer the question) and I just haven't entirely decided what to do about it. The others are things that neither I nor my collaborators are currently prioritizing that I hope we will get back to.

Finally, I have one project on my list that I want to write, but I don't even know exactly what data I need or the approach I want to take. I just know it is an important paper to write.

There are roughly a million other ideas I could put on my list, but I'm having a moratorium. I have decided I am not allowed to start on anything else until my list gets a lot shorter. As I have mentioned, I am applying for jobs, and I'd like to have most of this backlog cleared up before I go.

Too consise?

I'm preparing a manuscript to submit to Nature. In addition to a low acceptance rate (8%), they have severe word limits. The 'main text' should be "about 1500 words" excluding introductory paragraph, references, methods, figure legends, etc. It is the intro, summary of results, and the discussion all in one. My main text, of which I now have a complete but not final draft, is 1138. It was not hard to make it this short. This is just how long I wrote it. This of course makes me think that there are all sorts of vital things that I should have said but left out. I will think about what these might be after my wife and daughter are asleep.

Nightly visitor

Hedgehog! We have a hedgehog picking up the seed under our feeder every night at 11. The feeder is just outside our bathroom window so when we hear it cracking seeds we creep over, open the window and watch. One night there were two of them, mating, being pretty loud about it. Europeans are mostly pretty blasé about hedgehogs, but to us they are cool and exotic (there are none, except pets, in the Americas).

So many reference to choose from, may as well alliterate

"Many different processes are commonly referred to as asexual reproduction and numerous authorities have set out systems of terminology dividing these up and labeling them (e.g., Schön et al. 2009; Schulz-Schaeffer 1980; Suomalainen 1950)."