Showing posts from March, 2019


The end of a project is always an uphill climb. I marvel at how most people consider a task "finished" when it is 98% done - and then I am astounded at how long it takes to complete the last 2%! What was a gentle hike suddenly becomes a trek up Mt. Everest as the last bits and pieces are figured out. Maybe some of you know what I'm talking about. Friends, I must admit to you I just made the mistake I've described. I had finished a task 98% of the way and shuffled it out of my brain as "done." But I was wrong. Ok, so the DNA samples I was processing with Hanny were finally ready . We had extracted and diluted all of them. All that was left was to pack up the samples and ship them off for sequencing. Sounds simple, right? Not exactly. DNA degrades at room temperature, so the samples had to be shipped cold. Very cold. Dry ice cold.  Come to find out, dry ice is not the easiest material to work with. There is exactly one place to buy it through my in

Colonization in slow motion

Friends, I am proud to announce the publication of another of my scientific papers! This article, published in the journal Limnology and Oceanography , describes the results of a long-term colonization experiment in the Arctic deep sea. In 1999, my German collaborators at the Alfred Wegener Institute placed a metal frame on the seafloor with settlement plates made from plastic and brick. The frame was visited in 2003, then again in 2011 (I was on the ship that year), and finally recovered in 2017. I told you about recovering the frame when I was at sea in 2017 and described some of the most common species that were living on the panels. Then I recounted  my disappointment  when the 2003 panels could not be located in storage at the AWI. However, I was able to use ROV video footage, recorded observations, and my own counts of organisms on the 2017 panels to craft a great manuscript. Find the full paper here: The AW


It is early morning, and the building is quiet. Most people have yet to arrive, but I am already in the lab. After so many days in a row of genetic work, I am beginning to approach the lab bench the way some people approach a yoga mat. When I arrive in the space, I am reminded of all the past successes and failures that have unfolded there, and I sit quietly with each of my thoughts for a moment. I set an intention. I consciously slow my breathing. Then I clean the slate-black benchtop with water and ethanol, and I set to work. I am preparing samples of coral DNA from Palau for sequencing. My collaborator, Hanny , and I settled on an analysis technique called RAD sequencing, which requires very high-quality DNA. Moreover, it requires very high-quality DNA  at a known concentration,  and the concentration has to be similar among all samples. Hanny and I chose a range of DNA concentrations that would work for RAD. Some of our samples had concentrations below that range, so we wo

Tiger stripes

Alright, friends, so Hanny and I figured out the perfect recipe for making copies of the DNA in our samples . Our struggle resulted in beautiful and delicious metaphorical baked goods. What now? The specific region of DNA we were working with is called a microsatellite. It's a part of the DNA that doesn't code for proteins, and in fact, nobody really knows what microsatellites are for. Still, we can make use of them. Microsatellites have short sequences (something like ATA) repeated over and over again, and the number of repeats varies. In our case, the number of repeats varies between different species of corals in the genus Acropora , so we can use the microsatellites to tell us if we accidentally collected multiple species instead of just one. Check out the image below. This is an electrophoresis gel . I've shown you images of them before, but basically, you load a sub-sample of the DNA into a gel, run an electrical current through it, and then fragments of DNA with

The baker from Boston

I love baking muffins. Not just baking - specifically baking muffins. Cakes are ok; bread takes too long; cookies never turn out well, but muffins - I can bake muffins. Muffins are resilient. You can make all sorts of substitutions, vary the ratios, throw in something extra, and they still turn out well. In fact, in grad school, I would make muffins from a banana, crushed-up cereal, baking soda, fruit juice, and flour. They were fluffy and fruity and absolutely delicious. The polymerase chain reaction (PCR), used for making copies of DNA in the lab, is a lot like baking, but not like baking muffins. It's like baking cookies - you look at the batter the wrong way, and they come out dry and burnt and gross. I suck at baking cookies. And I suck at PCR. Well, I did. An electrophoresis gel showing the successful results of our PCR troubleshooting Over the past several weeks, I have struggled to get even a single PCR to work . My collaborator, Hanny , fielded my frustrate