Uncommon Ground

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.

From xkcd.com. The title there? "Frequentists vs. Bayesians".

You read that right. Even though there was serious debate about whether it was worth it to try and prevent California condors from going extinct, they're now a pest in Bear Valley Springs, California.

Flocks of California condors have descended upon Bear Valley Springs. Residents, who are allowed to do little to chase them away, say the huge birds peck off roof shingles, damage air conditioners and leave porches coated in droppings. And although the majestic birds, with a wingspan of nine feet, are widely admired, the gated community of about 5,200 about 80 miles north of Los Angeles has seen enough of them.

"A lot of people used to think seeing a condor was amazing," local realtor Beth Hall told FoxNews.com.  "After seeing the damage they have done, they have become less popular with people, myself included." (source)

If Google Maps is showing me the right Bear Valley Springs, there are two reasons why I'm really interested.


View Larger Map

First, I spent a lot of time in this area (when there were very few California condors alive). The only known localities of Clarkia tembloriensis subsp. calientensis are in the vicinity of Caliente, just a little north of Bear Springs. There were no California condors in the area when I was working there, but it's nice to imagine seeing one soaring overhead if I ever get back for a visit.

Second, when I was in graduate school there were so few California condors in existence that I remember serious debates among scientists and policy makers who cared deeply about preventing extinctions of endangered species about whether it was worth the time, effort, and money that was being spent to try to save them. It was a reasonable debate to have, and I have to confess that I leaned toward the "It's not worth it side", but it's nice to look back 30+ years later and think that even though the California condor is still endangered it's become a bit of a pest in one tiny piece of its former range.

Related articles

• California Condor conundrum in Bear Valley Springs (kget.com)
• With Condors on the Brink, California Considers a Lead-Bullet Ban for Hunters (science.kqed.org)
• 4 of 8 California condors died from lead poisoning ()
• Turbine Plans Affect California Condors (drudge.com)
• The biggest threat to endangered California condors: lead poisoning (oregonlive.com)
• Feds won't prosecute wind farm for condor deaths (utsandiego.com)

Earlier this year the National Science Foundation announced a competition for graduate students in science, technology, engineering, or math. Here's a bit of the original announcement:

The Division of Graduate Education at the National Science Foundation challenges STEM graduate students across the nation to submit innovative ideas to prepare them for tomorrow's opportunities and challenges. Entries are solicited for ideas with the potential to improve graduate education and professional development. Ideas can be directed toward, for example, students, faculty, departments, institutions, professional societies, and/or federal agencies. Make your voice heard on STEM graduate education! (source)

Entries were due on April 15, so why am I mentioning this now? Because NSF announced the winners on Thursday. You can see a list of the winners and read their winning proposal at http://www.nsf.gov/news/special_reports/gradchallenge/winners.html.

Since I'm Vice Provost for Graduate Education and Dean of the Graduate School, I'm going to be studying these proposals carefully to see what ideas we might be able to adopt here. All of the ideas are great, but some of them are national-scale efforts that I'd be happy to be part of (or lead) from the University of Connecticut. It's just that we can't do them alone.

Here are the ones that have caught my eye that we might be able to do something about:

• Retaining Women in STEM Careers: Graduate Students as the Building Blocks of Change
• Communicating Science to the Public: A New Graduate Course and Practicum
• Beyond the Academy: Enhancing STEM Education through External Graduate Assistantships
• Creating a Cooperative Environment for Graduate Studies and Career Preparation
• RELATE: Researchers Expanding Lay-Audience Teaching and Engagement

Obviously, we can't do all of these. But with NextGenerationCT coming on line, it's a perfect time for us to think expansively and creatively about graduate education, and you can bet I'll be doing it.¹

If you have ideas or suggestions about which of these projects would be most useful to UConn graduate students, please leave a comment -- especially if you're a UConn gradute student. I'd love to hear from you.

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.

I've argued before that impact factors are useless or worse and that altmetrics or, even better, textual analysis of articles is a much better way to judge the impact of a scientific work.

Impact factors provide one crude metric by which the "quality" of journals can be compared. When libraries are forced to make decisions about what journals they subscribe to, an impact factor is one way of judging how useful the content of a journal might be. Of course, if the library already subscribes to a journal, local usage statistics are vastly superior. So knowing a journal's impact factor is one datum a librarian might use in deciding whether to subscribe to a new journal. Of course, interest from library patrons is likely to be the overriding factor. So again, the usefulness of impact factors is limited. And they will become ever more limited as more and more of the scholarly literature becomes available under an open access license.

Related articles

• Just say no to impact factors (guardian.co.uk)
• Scientists join journal editors to fight Impact Factor abuse (blogs.nature.com)
• Journal impact factor 'distorts science' (abc.net.au)
• In 'Insurrection,' Scientists, Editors Call for Abandoning Journal Impact Factors (news.sciencemag.org)

Elementa is now accepting submissions. In case you don't remember, Elementa is a fully open access journal led by BioOne and Dartmouth in collaboration with the University of Colorado, the University of Michigan, the Georgia Institute of Technology, and the University of Washington.

Elementa publishes in six knowledge domains relevant to the science of the anthropocene: atmospheric science, ecology, sustainable engineering, earth and environmental science, ocean science, and sustainability transitions. If you work in one of those areas, I encourage you to become one of Elementa's first authors.

Head over to http://elementascience.org/submission/ and get started.