Recently in Personal Category

figshare just announced that everything I upload there can be embedded in another web page (source). The screen shot above shows the five items I've uploaded so far.¹ (Click on the figure, and it will open a new window with a larger, easier-to-read version.) I've set up a series of posts to appear over the next several weeks. Each one of them will consist of the embedded version of one of the items above. I will also embed any new items I post.

All of my embedded figshare posts will be put in a "figshare" category under "Personal" just like this one, so if for some reason you want to find a figshare post in the future, it should be easy to do.

In yesterday's post I mentioned some of the physical challenges Nora and Jane overcame to collect all of the Protea punctata and P. venusta samples Nora needs for part of her dissertation research. To the left you see the Waboomsberg site, one of the places where I was actually able to help them. We sampled P. venusta starting at the top of the rocks just to the right of the saddle and collected our 20 samples between there and the bottom of the rocks just to the right of the cloud shadow. Other than the collecting we did later that day along the Swartberg Pass road, this was the easiest site from which Nora and Jane collected samples.¹

But that's not the incident I refer to. No, the incident I refer to happened before we even got to where we could start our sampling.

We rented a 4x4 through Drive South Africa. We picked up a sturdy Nissan Double Cab 4x4 from KEA Camper Rentals at Cape Town International at 8:00am on a Friday and left on the N2 for El Yolo One. We stopped at the Peregrine Farm Stall in Grabouw to pick up something for lunch along the way. We continued on the N2 to just past Swellendam, where we turned off on the R324. We stopped for lunch in Tradouw Pass a little after noon and continued on our way. We joined the R62 at Barrydale and headed toward Ladismith. Then it happened.

About 30km south of Ladismith we driving along at about 100kph when we heard a loud "bang" and the truck started to lurch left. My immediate thought was that we'd blown a tire. It didn't make sense, because we hadn't hit anything. But I hit the brakes and guided us to the shoulder.

That's when our wheel came bouncing by on the left, glanced off our left front fender, and knocked down a nearby highway sign, snapping the wooden supports as if they were toothpicks. We got out and went around to the front left side to see what had happened, since we were obviously leaning that way. The whole wheel was missing. We'd driven on the brake pad for the 100m or so that it took me to get us stopped.

Some motorcyclists who were passing by saw what had happened and stopped to ask if we were OK. I was still pretty dazed and trying to figure out what to do when one of them pointed out that we could use lug nuts from the spare on back to put a wheel back on. Well, it turns out that the lug nuts holding the spare on weren't the same size as those that held on the wheels. Although it probably would have been fine to put the original wheel back on, I decided to use the spare -- and steal lug nuts from the other wheel.

I couldn't get any off the right front wheel, so I took two (of six) from the right rear wheel and one from the left rear wheel. There were only three usable bolts on the right front wheel. One had been sheared off, and the threads on two more were damaged. Unfortunately, the three usable lugs were adjacent to one another, so the wheel wasn't evenly balanced in its connection to the brake pad.

So I turned on the emergency flashers, and drove slowly into Ladismith, about 30kph. Jane called ahead and found us a place to stay. KEA sent a replacement vehicle that night, and after that we had no problems at all. Jane and Nora seemed amazed at my skill in keeping the car under control, but honestly, all I did was to hit the brake and steer us to the left shoulder. I wasn't thinking about anything, just acting instinctively.

I left Capetown about 8:00pm last Thursday (2:00pm EDT), and I arrived back in Hartford just before 7:00pm EDT on Friday (1:00am Saturday in Capetown, 29 hours after I left). The flight was long, but uneventful.

My personal bag and, more importantly, the duffle with DNA samples arrived with me. The trip was a great success.

The focus of this trip was to collect samples in a hybrid zone between Protea punctata and Protea venusta at Blesberg and to collect additional samples of both species in areas of Swartberg Pass where they are not known to be hybridizing.

Nora will use the samples to unravel the dynamics of this hybrid zone. She left dataloggers in place at Blesberg to record temperature and humidity for the next year. She'll use the results from analysis of RAD SNPs (more on that in a moment) to develop a hybrid index, look at performance of individuals along the steep environmental gradient, and relate individual performance to traits. In addition, she collected seed for half-sib families which she'll use for paternity analysis to determine whether there are asymmetries in gene exchange and to identify the causes of any asymmetry she detects.

The hybrid zone is also of great interest for the Dimensions of Biodiversity project. Justin will use RAD sequencing to identify a large number of polymorphic SNPs. We'll use those SNPs as markers in a genome-wide association study to dissect the genetic basis of traits that distinguish these two very different species.

Nora and Jane did remarkable work in getting all of the samples. Notice I said "Nora and Jane did remarkable work." I bagged out on a lot of it. I made it down the slope at Blesberg on the first day of work there. That's a Protea venusta in the foreground about 2/3 of the way to the bottom. What the photograph doesn't show is that the only way to where we were when I took it was down the cliffs in the background. We were about 200m below the top when I took the photo. The other thing the photo doesn't show is that it had rained heavily the day before so that the rocks and restios were slick.

On the first day of work at Blesberg, I know that I slowed things down, because I'm not as sure on my feet as Nora and Jane. On the second day, I started down again and was making progress slowly. But as I was clambering down a particularly steep pitch about 150m from the top my legs started to give out. It wasn't just that I was moving slowly. I was afraid that if I descended any further, I wasn't going to make it back to the top. I asked Nora and Jane to go on without me. I climbed back to the top by myself -- slowly -- and waited for them to return.

For the next two days I didn't even try to make the descent and help. I collected some samples of Protea montana and looked for more than the single individual of Protea pruinosa -- without success. But Nora and Jane made the trip quicker every day, even though the conditions got worse.

At least it didn't snow while we -- they -- were working on Blesberg. A few days later we were working in Swartberg Pass. I made the (short) steep hike to Waboomsberg without a hitch. It was cold and windy, but the trail was dry. We quickly found the 20 individuals of Protea venusta we went for and returned to the pass. Then I even managed to remember where the Protea venusta population in the pass was better than Jane. I was pretty proud of myself about that.

The next day, we were planning a longer, 14km hike to Oliewensberg (7km each way), but we passed a policeman on our way up to the pass, and when we arrived at Teeberg, we decided to turn around. The road was covered with ice and snow. I'm sure our 4x4 would have made it, but we were 200m or so below the summit, and the hiking conditions would have been even worse.

We left Prince Albert the next morning making contingency plans, since we didn't think the snow would have melted and we didn't expect to be able to collect samples. To our surprise, the drive to the summit was pretty easy, so we started up the path. At first, the going wasn't bad, occasional patches of snow, but the trail was mostly bare, although it was a bit wet.

Once again it became clear that I was going to slow Nora and Jane down, but since we had plenty of time, and I was only slowing them down a little, we kept going. At about kilometer 3, though, things changed. The going got very steep, which would have been fine had the trail been clear. Unfortunately, it was covered in 10-15cm of heavy, wet snow. I was climbing through it -- very, very slowly. Nora and Jane waited for me at the top of an intermediate summit, and just before I got there, I looked at my watch. We'd come about 3.5km in an hour, and we had another 3.5km to go -- under worse conditions. This time I could have made it, but I was moving so slowly because of my unsteadiness, it would have taken us another couple of hours to get to where we needed to sample. And once I arrived, I wouldn't have been able to help. I told them to go on without me, and I went back to the summit and waited in the car.

In the end, Nora and Jane got a lot of really good samples. We even picked up several taxa for the trait-environment analysis in Dimensions that we hadn't sampled before. So it was a very successful trip. At the same time, I began to wonder about my future in South Africa during the flight home.

Nora needs someone dependable, i.e. someone other than me, to help her when she goes back next year. We've collected samples and trait data from all of the taxa it's reasonable to imagine we can get for our trait-environment analyses. Jane doesn't need me as a field assistant for her polymorphism work. I can't think of a good reason that anyone should spend good money to get me to South Africa next year.

I don't like thinking this, but I have to wonder whether 2013 may have been my swan song.

In April, I gave the banquet address at the Centennial Celebration of the California Botanical Society. Tomorrow I'll share a brief report on my time in South Africa. Until then you're welcome to watch this presentation -- if you have 40 minutes to waste.

We celebrated the 134th commencement at UConn over the weekend with ceremonies for every school and college¹In addition to reading the names of all doctoral degree recipients and shaking the hands of hundreds of masters candidates in the ceremony for The Graduate School, I had the honor of welcoming the Class of 2013 to the second ceremony of the College of Liberal Arts and Sciences.

Here's what I had to say:

A year and a half ago I was asked to serve as Interim Vice Provost for Graduate Education and Dean of the Graduate School. My term officially began on 13 January 2012. It ended on a week ago yesterday when "Interim" was removed from my title. I am now Vice Provost for Graduate Education and Dean of the Graduate School. Here's a copy of the announcement that went out in yesterday's Daily Digest.

• VP for Graduate Education & Dean, Graduate School

  This announcement is sent on behalf of Provost Mun Choi and Vice Provost Sally Reis:

  We are very pleased to announce that Dr. Kent Holsinger has been appointed as the Vice Provost for Graduate Education and Dean of the Graduate School, following an internal search. Kent is an outstanding teacher and scholar, and he has strongly lead the Graduate School while serving as interim dean, and he will continue to guide the School and University in pursuit of excellence in graduate education and research.

  Kent, a Board of Trustees Distinguished Professor of Ecology & Evolutionary Biology and Adjunct Professor of Statistics, is well known for his work in population genetics, plant evolutionary biology, and conservation biology. His most influential work involves the development and analysis of mathematical models that describe the evolution of plant mating systems and of statistical models used to analyze genetic variation within populations. His most recent work on mechanisms responsible for the extraordinary diversity of plants in southwestern South Africa has uncovered a complex interplay between adaptation to environmental gradients and the accumulation of random differences among geographically isolated population. He has regularly taught an undergraduate course in evolutionary biology, and he continues to teach graduate courses in population genetics and conservation biology. For many years he taught the introductory biology course for biology majors, and, for nearly fifteen years, he co-taught a course in philosophy of science. Kent was elected a Fellow of the American Association for the Advancement of Science in 2003 and of the Connecticut Academy of Science and Engineering in 2010. In 2006, he received the Centennial Award from the Botanical Society of America and the Distinguished Alumni Award from the College of Idaho in 2008. In 2012, he was named a Board of Trustees Distinguished Professor. As interim dean, Kent has made significant accomplishments in graduate student and post-doctoral scholar services, diversity, and the administrative structure of the Graduate School.

  We would like to express our deep appreciation to Dean Gregory Weidemann, Ms. Cynthia Bastek and the entire search committee for their thoughtful work throughout the search process.

  Please join us in congratulating Kent and the Graduate School!

   

  For more information, contact: Office of the Provost at provost@uconn.edu

Other stories from the Daily Digest for Monday, April 22, 2013 >>

If you're drowning in e-mail, here's something you can do: Adopt the e-mail charter, and encourage your friends and colleagues to do the same.

10 Rules to Reverse the Email Spiral

1. Respect Recipients' Time This is the fundamental rule. As the message sender, the onus is on YOU to minimize the time your email will take to process. Even if it means taking more time at your end before sending. 2. Short or Slow is not Rude Let's mutually agree to cut each other some slack. Given the email load we're all facing, it's OK if replies take a while coming and if they don't give detailed responses to all your questions. No one wants to come over as brusque, so please don't take it personally. We just want our lives back! 3. Celebrate Clarity Start with a subject line that clearly labels the topic, and maybe includes a status category [Info], [Action], [Time Sens] [Low Priority]. Use crisp, muddle-free sentences. If the email has to be longer than five sentences, make sure the first provides the basic reason for writing. Avoid strange fonts and colors. 4. Quash Open-Ended Questions It is asking a lot to send someone an email with four long paragraphs of turgid text followed by "Thoughts?". Even well-intended-but-open questions like "How can I help?" may not be that helpful. Email generosity requires simplifying, easy-to-answer questions. "Can I help best by a) calling b) visiting or c) staying right out of it?!" 5. Slash Surplus cc's cc's are like mating bunnies. For every recipient you add, you are dramatically multiplying total response time. Not to be done lightly! When there are multiple recipients, please don't default to 'Reply All'. Maybe you only need to cc a couple of people on the original thread. Or none.

6. Tighten the Thread Some emails depend for their meaning on context. Which means it's usually right to include the thread being responded to. But it's rare that a thread should extend to more than 3 emails. Before sending, cut what's not relevant. Or consider making a phone call instead. 7. Attack Attachments Don't use graphics files as logos or signatures that appear as attachments. Time is wasted trying to see if there's something to open. Even worse is sending text as an attachment when it could have been included in the body of the email. 8. Give these Gifts: EOM NNTR If your email message can be expressed in half a dozen words, just put it in the subject line, followed by EOM (= End of Message). This saves the recipient having to actually open the message. Ending a note with "No need to respond" or NNTR, is a wonderful act of generosity. Many acronyms confuse as much as help, but these two are golden and deserve wide adoption. 9. Cut Contentless Responses You don't need to reply to every email, especially not those that are themselves clear responses. An email saying "Thanks for your note. I'm in." does not need you to reply "Great." That just cost someone another 30 seconds. 10. Disconnect! If we all agreed to spend less time doing email, we'd all get less email! Consider calendaring half-days at work where you can't go online. Or a commitment to email-free weekends. Or an 'auto-response' that references this charter. And don't forget to smell the roses.

I avoid political comment on this blog, although I do share my thoughts on policies related to biodiversity and the environment. But I recently received an e-mail I found greatly disturbing. It shines a light on a part of American culture that I didn't want to believe existed. I don't recognize the e-mail address of the sender (not even the domain), and I won't repeat it here, but what you find below is the full text of an e-mail I received with the subject line "Obama's martial law plans exposed."

Some of you know that I've been putting lecture notes for my graduate course in population genetics on-line for many years. This year I finally took the small amount of additional time I needed to pull them together into a single PDF, complete with title page, table of contents, and index. It's formatted in such a way that it can be printed double-sided and bound. It's available on Figshare with a CC-BY license.