Author Archives: Jeff
How do common research scales match up across ocean science disciplines?
Apparently not very well. A couple weeks ago I came across a really cool paper by some current and former students at the University of Washington School of Oceanography and the UW School of Aquatic and Fisheries Science. The authors … Continue reading
US science funding since 1963
One way to get some great data on US science funding is to sign up for the National Science Foundation’s email notifications. In addition to announcements on funding opportunities you get notifications on the publication of a wide range of … Continue reading
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Making friends in the DOC pool
I’m going to keep draining the pool analogy until it’s dry… I’m going to miss the biological oceanography journal club at LDEO tomorrow in order to attend the Sequencing the Urban Genome symposium at the NY Academy of Sciences. It’s … Continue reading
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Science (de)funding
Note: I had intended this post to be a quick discussion of how science funding supports jobs, and why we need more science funding at the federal level. As you can see below, I never quite got there, but I … Continue reading
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Predicting metabolic pathways in a metagenome
For an ongoing project I needed to predict the metabolic pathways that are present in a metagenome. This is actually something that I’ve been interested in trying to do for a while, as metabolic pathways can tell us much more … Continue reading
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Trick question: Is the oligotrophic ocean net autotrophic or heterotrophic?
Answer: Both! For this week’s LDEO biological oceanography journal club we discussed a very interesting paper recently published in Nature Communications by Pablo Serret et al., titled Both respiration and photosynthesis determine the scaling of plankon metabolism in the oligotrophic … Continue reading
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Adult swim – Old carbon in the DOC pool
We’re starting a summer biological oceanography journal club at LDEO and the inaugural paper is by Lechtenfield et al. (2015), published just a couple of months ago in Nature Communications. Titled Marine sequestration of carbon in bacterial metabolites, the paper … Continue reading
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Protein flexibility calculation with Python
In a couple chapters of my dissertation I made use of protein flexibility values calculated with the ProtParam module in Biopython (Bio.SeqUtils.ProtParam). The flexibility function makes use of amino acid β-factors as reported by Vihinen et al. (1994). We were … Continue reading
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Sea ice biogeochemistry postdoc position
There’s a great sea ice biogeochemistry/microbiology postdoc position open in Jaqueline Stefels group at the University of Groningen in the Netherlands. Jaqueline is one of the leading experts on the marine sulfur cycle and the project focuses on the DMS/DMSP … Continue reading
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A tale of two studies: Big Data and a cautionary analogy
One of the chapters of my dissertation was just rejected for publication a second time. I haven’t decided what to do with it yet, but in the meantime it makes an interesting case study in rejection. In brief, what we … Continue reading
