How to get the most out of your sabbatical

I’m just coming off sabbatical (ok, so I still have the summer, but it FEELS like it is almost over) and thought discussing how I made the most of sabbatical could be a good blog post. A little background first. I am at a small liberal arts school with high teaching and service loads. Traditionally we haven’t had much expectation for scholarship, but that is changing. I’ve had a modest research program mostly focusing on the same questions as my dissertation using the same techniques and managed to get a couple publications out since I’ve been here. My goal was to update my approach by learning next-generation sequencing and analysis of microbial communities and to get some more pubs out. I’m really pleased with what I’ve been able to accomplish thus far and I think there were some key decisions that made my sabbatical so successful.

  1. Get out of town, if at all possible.

It can be far too easy to get sucked into the campus milieu. For the most part, you’ve probably earned a sabbatical because your colleague respect you and want to know your opinion on things. If you’re there, they will find you and suddenly your time is frittering away into discussions of curriculum, the latest power struggles, and, let’s face it, gossip. I know, I’ve seen it happen to colleagues; heck, I’ve probably done it to colleagues. Sabbatical is not just about jazzing up your scholarship, but it is also about recharging and it’s hard to do that if you don’t remove yourself from the day-to-day. Where to go? For field biologists, that’s often easy—go to your field site. For me, I knew the techniques and questions I wanted to get up to speed on and made some connections. If you at least have money to support yourself, other researchers are often happy to host visiting scholars. You bring a new perspective to their lab and even if you are untrained in the area in which you’ll be directly working, you pick up things fast and don’t take much of their time. And heck, you’re cheap (free) labor! But I have kids, significant other, pets, etc., you say—how did you do this? I don’t have kids, but I did have to leave behind a spouse in another professional field. Luckily, my sabbatical campus was only 3 hours away and we usually saw each other 2-3 times a month. I was able to find an affordable, quiet, furnished apartment that even came with a cat! For housing, check with the provost/grad/research dean’s office. They often have short-term leases posted for incoming faculty and post-docs (often other faculty on sabbatical away from their campus).

  1. Set an automatic reply on your campus email and don’t reply before at least a week has gone by.

So you got out of town, but email can reach you anywhere you go. Be sure to set an autoreply on your email (at least to any domain associated with your home campus) that states when you are on sabbatical and that you are not checking your email regularly. Because I was the director for the biology program up through the term before my sabbatical leave started, I knew I would still be getting emails from students, faculty, and vendors that need contact with the director. I listed the current director and his email (sorry James) for time sensitive issues. I also tried to resist the urge to respond to advisees and colleagues as soon as I saw an email (because of course, I was checking it). By taking a week at the beginning of my sabbatical to respond, people bothered me less as the term went on. Also useful—see if you can unsubscribe from any campus-based listserves while on sabbatical.

  1. Learn something new.

Sabbatical only comes every 7 years (if you’re lucky), so make it count! Think of sabbatical as your own mini-Kuhnian paradigm shift. Having 100% of your time to focus on research means you can go outside of your comfort zones. Sabbatical also means that you have tenure, so you can take more risks. I have viewed sabbatical as the kick-starter for the next 7 years of my research program. Instead of struggling with the same issues, I’m reinvigorated about science in general. Learning something new also means working with new people and thinking about problems in a completely new way. This is another advantage to going to visit another lab on sabbatical.

  1. Make an exit strategy.

So you’ve learned lots of new things and now it is time to go back to your home campus. How do you keep the momentum going? I chose to spend the semester (4.5 months) at my host campus focusing primarily on lab work, my summer will be back at my home campus analyzing data and writing manuscripts. I’m also spending some of the summer figuring out how to physically and financially set up my lab here for my new research interests. One of the ways I’m going to get my new research program up and running is to incorporate it into one of my upper-level courses. This will allow me to generate preliminary data and because it is for a course, the college will cover the costs.

My sabbatical was (IS—it’s not over yet!) an amazing, rejuvenating experience. Make sure that you protect and take advantage of this precious time.

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Contagious Asexuality?

New research from Indiana University used genomic sequencing of Daphnia to determine that all asexual lineages share common alleles on 2 chromosomes.  More highlights:

  • asexual males spread elements that suppress meiosis throughout sexual populations
  • asexual strains are even younger than once thought (origin ~1250 years ago)
  • introduction of meiotic suppressors leads to localized extinction of populations due to accumulation of deleterious mutations
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How to read and understand a scientific paper: a guide for non-scientists

This looks like a great potential assignment for undergrads learning to read primary literature. Senior sem students: this is a little bit of overkill for you guys at this point, but it’s worth reviewing and using for denser/difficult articles.

Violent metaphors

Update (8/30/14): I’ve written a shorter version of this guide for teachers to hand out to their classes. If you’d like a PDF, shoot me an email: jenniferraff (at) utexas (dot) edu.

Last week’s post (The truth about vaccinations: Your physician knows more than the University of Google) sparked a very lively discussion, with comments from several people trying to persuade me (and the other readers) that their paper disproved everything that I’d been saying. While I encourage you to go read the comments and contribute your own, here I want to focus on the much larger issue that this debate raised: what constitutes scientific authority?

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Baby Got Horns

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A new paper in tomorrow’s issue of Nature finds a surprisingly simple explanation for the variation in horn size among Soay sheep on an uninhabited Scottish isle. Because males with the biggest horns tend to win more battles, get access to more females, and therefore have higher reproductive success, we would expect that given such strong directional sexual selection there would be little variation left in terms of horn size.  Instead, horn size varies from really big to downright petite (scurred, see photo above).  So how is this variation maintained in light of strong directional selection for large horns?  A few hypotheses have been forwarded, but some of the most favored include good genes and genetic trade-offs. In the good genes hypothesis, many genes determine condition in males, and those in the best condition have the most sexually desirable trait. Because so many genes are involved there is great potential for mutation thus, variation is maintained.  In the genetic trade-off hypothesis there is a trade-off between natural and sexual selection (imagine if your horns got too long you wouldn’t be able to lift your head). 

Johnson et al. offer a 3rd hypothesis, although it is connected to the genetic trade-off hypothesis: heterozygote advantage.  Heterozygote advantage is a case in which heterozygous individuals that possess two different alleles (version of a gene) have greater fitness (survivorship and reproduction) than individuals that have two of the same alleles (homozygotes).  Probably the most famous example of heterozygote advantage is the case of sickle cell anemia (but see this blog on relaxed heterozygote advantage). Two copies of a mutated allele results in sickle-cell anemia while two copies of the wild-type allele makes individuals more susceptible to malaria.  One copy of each allele is ‘just right;’ those individuals have higher fitness because they are less susceptible to malaria nor do they suffer the ill effects of sickle-cell anemia.  While heterozygote advantage has been shown in a few cases of natural selection, this is the first evidence I’ve seen for heterozygote advantage in sexual selection.

So why has heterozygote advantage rarely been documented (and never before in sexual selection as far as I know)?  First, traits are rarely determined by a single gene.  In a previous article, Johnson and colleagues found that horn size was almost completely controlled by a single gene locus and it has only two alleles.  As long as an individual possesses one normal allele (Ho+), they have big horns.  Possession of two mutated alleles (HoP) results in less than impressive horns (see Figure from Johnson et al. above).  After genotyping and tracking the fitness of 1750 sheep, Johnson et al. found that individuals homozygous for HoP had significantly lower reproductive success than heterozygotes or those homozygous for Ho+.  Homozygotes for Ho+, however, had significantly lower survivorship than the other two genotypes.  Heterozygotes, then, get the mating AND survivorship advantage and thus have the highest fitness.  With heterozygotes being favored, the HoP allele is maintained in the population and scurred horn males remain.

So why are two copies of the Ho+ gene detrimental to survivorship? The authors argue that with big horns males spend more time fighting and defending their females and thus spend less time on feeding and other survivorship necessities.  I don’t find this argument compelling because it doesn’t explain how heterozygotes maintain high survivorship.  Likely the authors will need to explore exactly how this gene affects horn growth.  In mice the gene is known to play a role in both bone formation and male sexual development.  I’m guessing we’ll be seeing more from this research group soon.

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Musings on monogamy or the challenges of senior seminar writing

OK, I waited way too long to get to this post.  On 2 August two papers on the origin of monogamy in mammals were published in PNAS and Science.  These papers got me excited because: 1) the evolution of monogamy is a very cool topic, 2) they are an illustration of how to hone in on a great topic for a senior seminar paper, and 3) they are a great illustration of the challenge of close reading of primary science texts.  I’d like to address each of these issues in turn, but I’ll probably spend more time on 2 and 3 as the blogosphere has already covered the content of these papers extensively (see links at the end of this post).

Unlike in birds, monogamy is relatively rare in mammals (~9%).  Three main hypotheses have been forwarded to explain those rare cases of monogamy: 1) male parental care increases survivorship of offspring, 2) non-overlapping ranges of females leads to males defending a single female, and 3) protection from infanticide.  Interestingly, these two papers came to different conclusions.  Opie et al. conclude that monogamy evolved as a defense against infanticide, while Lukas and Clutton-Brock conclude that low female density (and male guarding) is the cause of monogamy.  These kinds of conflicting results are exactly what make for a great senior seminar topic.  As with all writing, your senior seminar paper should be making an argument.  Arguments are much more interesting where competing hypotheses still exist and evidence has been generated both for and against these hypotheses.

Of course, these active areas of debate really require you to read the texts closely.  Do no ‘trust’ the analysis of someone in a review article.  Do not stop at the abstract.  Let me illustrate with how I approached reading these two papers with contradictory conclusions.  First, I had to spend a lot more time on the methods and really working through the figures than I would for something in my research field.  In fact, I actually had to delve into supplementary materials available on-line (more and more information is being moved out of the article and into supplementary material these days).  I spent a frustrating long time trying to understand how the figure in Opie et al. actually illustrated their results.  After my close reading, I tried to assess why these authors came to such different conclusions.  They both used a phylogenetic approach to address their questions although their statistical approaches were somewhat different.  Their datasets, however, were quite different.  Opie et al. focused solely on primates and examined 230 species, while Lukas and Clutton-Brock examined 2534 mammal species.  They also scored mating systems differently.  Opie et al. had only two states: monogamy or polygyny whereas Lukas and Clutton-Brock had three states: solitary, monogamous, or group living. In the end, I was more convinced by the Lukas and Clutton-Brock argument.  Perhaps it supported a stance I already had, but I also felt their classification of mating systems and their much larger data set allows for broader conclusions.  I had a hard time accepting that infanticide selects for monogamy when some of the highest rates of infanticide are actually in polygynous/polyandrogynous species.  This debate is clearly not over, and biologists in the field seem split in terms of whose evidence is most compelling.  Great fodder for a senior seminar topic!

Despite Two New Studies on Motives for Monogamy, the Debate Continues by Carl Zimmer

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Special Issue of Science on Climate Change

This week’s (2 August 2013) Science is a special issue focusing on climate change.  Check out this podcast interviewing four of the authors whose research is featured in the issue.

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Mitochondrial Eve and Chromosomal Adam may have existed at the same time

ImageHuman evolutionary geneticists  use DNA passed only through the female line, mitochondrial DNA (mtDNA), or male line, the Y chromosome, to make estimates about the last common ancestor for all living humans. Earlier work suggested that the most recent common male ancestor lived 35,000 to 190,000 years AFTER the most recent common female ancestor. Poznik et al. in this week’s Science report the results of sequencing 9.9 million base-pair length of the Y chromosome from 69 men from across the globe.  Their data suggests that the Y chromosomal Adam existed between 120 and 156 thousand years ago, much closer to the estimate for the mtEve betwen 99 and 148 thousand years ago.  Why did this study move Adam’s birthday back so much?  Well, there have been lots of technical difficulties in reconstructing the sequence of the Y-chromosome, but this research group was able to deal with some of those difficulties and use much more of the Y chromosome.  This deeper sequencing allowed the researchers to identify more variation among Y chromosomes.  Linking these differences to well-dated events in human migration (e.g. peopling the Americas), the researchers were able to make a better estimate of Y chromosome mutation rates.  As always, the researchers did have to make certain assumptions in their models of mutation rates (which I’m sure will be explored by other researchers), their approach seems robust.  Dating the most recent common male and female ancestors to essentially the same time period should reduce some of the mental gymnastics that paleoanthropologists having been doing to explain why the male ancestor lived relatively recently.  In addition to moving the most recent male ancestor further back in time, this approach to the Y chromosome has also unearthed a greater amount of diversity than was known among Y haplotypes.  Further work using this methodology should help human evolutionary geneticists male migration with more accuracy.

Y chromosome analysis moves Adam closer to Eve

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