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.

Tuesday, March 17, 2015

Who has an adaptive post-reproductive life-stage?

To establish a case for an adaptive post-reproductive life-stage, one needs to show (at least) the following things:

(1) Prevalence: Across environments, but especially in a wild or non-protected environment, the population experiences more post-reproductive lifespan than is expected due solely to demographic stochasticity.

(2) Utility: Post-reproductive individuals do something selectively advantageous, such as helping younger kin to survive or reproduce.

In many cases, one would like to also address

(3) Advantage: Those individuals who become post-reproductive have a selective advantage over same-age individuals who simply continuing reproducing indefinitely.

However, this third is more complicated, because in many cases there are no individuals who fail to stop reproducing to compare to. For example, 55 year old women giving birth are rare and not easily compared to those who stopped at a more usual time. So testing (3) requires extrapolation and counter-factuals. This assumes that if continuing to reproduce past the current age of cessation were selectively advantageous, that the species' reproductive physiology would allow for it. In many cases, theoretically advantageous traits simply don't exist in the population, and therefore cannot be selected for. If the choice is not between ceasing reproducing or continuing, but rather between ceasing and being useful or ceasing and not being useful, useful wins.

So we are left with basically two fairly simple tests to make decent case an adaptive post-reproductive life-stage. And after some decades of interest in the evolution of post-reproductive lifespan, for how many species has this case been convincingly made? By my count, three. Humans, orcas and a gall-forming social aphid, Quadrartus yoshinomiyai. There are several other likely candidates. Short-finned pilot whales, and possibly other social cetaceans. African and Asian elephants. But I've become very interested in a much more accessible and experimentally tractable species. It lives in multi-generational groups of (very) closely related individuals.  Individuals play subtly different roles in the group throughout their lives. Older individuals stop reproducing and can (assuming no one comes along and kills them) live for extended periods post-reproductively (on the time scale these things live). You may have it in your garden.

Any guesses? Later this week I'll give you the answer.

Monday, March 16, 2015


For years, I've been worrying about about my chronic backlog of papers I should have written a long time ago and just haven't had time for. I'm very happy to report that my to-write list is getting a lot shorter. Three of the papers on that list will come out in the first half of this year. Number four is currently out for review, 5&6 need to be revised and resubmitted, a seventh is written and currently with colleagues awaiting their comments. The eighth has figures made and large chunks of text in their second or third drafts. If all goes well, all eight should be at least submitted by the end of the year, and I'm guessing that six will have come out. Of course there are several more that I need to get to, and new projects being planned, but it feels good to be clearing the backlog a bit. Especially nice is that after spending too long on methods papers, incidental discoveries and other tangents, the manuscripts I am working on now actually address the central points that motivated the research in the first place.

1. Levitis DA. (2015) Evolutionary Demography: a synthesis of two population sciences. In: International Encyclopedia of Social and Behavioral Sciences, 2nd Edition. ed.: J.D. Wright. (Coming out in May)
I am an evolutionary demographer, and while encyclopedia articles are not my bread and butter, this is very much on topic.

2. Olsen TB, Christensen FEG, Lundgreen K, Dunn PH, Levitis DA. (2015) Coelomic transport and clearance of foreign bodies by sea stars (Asterias rubens). Biological Bulletin. (Coming out in April)
This started as a student project to develop methods for studying the evolutionary demography of starfish, but when it became clear the animals wouldn't stay tagged, my students decided to investigate why. Their result was cool enough that we're publishing it.

3. Oravecz Z, Levitis DA, Faust K, Batchelder WH. (2015) Studying the existence and attributes of consensus on psychological concepts by a cognitive psychological model. American Journal of Psychology 128: 61-75.
My most cited paper (on the biological meaning of the word behavior) is one I started as a graduate student, even before it became clear I would be an evolutionary demographer. It got a nice write-up in the New York Times. Many of those citing it are in philosophy or psychology. A couple of years ago I was contacted by some psychologists who wanted to work with me to reanalyze those data. I never expected to publish in a psychology journal.

4. Zimmerman K, Levitis D, Addicott E, Pringle A. (2014) Maximizing the mean nearest neighbor distance of a trait to choose among potential crosses and design a fully crossed mating experiment.
This methods paper, currently out for review but with an earlier version already archived online and therefore available (journals are increasingly okay with this) grew out of a collaboration that is part of my ontogenescence project. In trying to answer my evolutionary question, my collaborator invented a new method for designing mating experiments, and we wrote it up. 

5. On raven populations in the Eastern US. One reviewer loved it just as it was, the other made numerous (and useful) comments on how to improve the analysis. Being worked on by my colleagues who are primarily responsible for the analysis.

6. Part of the same ontogenescence collaboration as #4, this was just rejected by a high impact journal on the basis that they rejected it (no reason or feedback given, as is common with such journals) and will be submitted to another in April.

7. Another ontogenescence paper, this time in a marine ecology context. Our plan is to submit in May. Between now and then the main order of business is to get feedback from colleagues and use it to improve the text.

8. Same project as #s 4 and 6.

9. On post-reproductive lifespan, building on the papers and methods that came out of my dissertation. We have cool results proving an interesting point, but it still needs a fair bit of work.

They probably won't be submitted in exactly this order, as a lot of it depends on factors beyond my control, but this is more or less the order I'm prioritizing them in. Beyond that it is hard to predict. Some older things I still do really need to write up, some fruitful student projects on post-reproductive lifespan that are looking good, some vague ideas. 

One thing I've decide is that at least for the moment, no papers that are outside the main foci of my research program (evolution of pre-reproductive mortality and post-reproductive survival) are going to make the list. Numbers 1-3 & 5 above don't directly address either of these topics, and 4 is tangential. That is a bad habit, and one I'm going to break.

Thursday, January 29, 2015

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.

Saturday, January 24, 2015

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.

Friday, January 23, 2015

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.

Wednesday, January 21, 2015

Good practice

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