Author Archives: Jeff

El Nino, SAM, and sea ice conditions at Palmer

Posted on August 6, 2015 by Jeff

In 2 and a half months, and unless there’s another government shutdown, I’m heading down to Palmer Station to collect a key set of samples for one of my projects.  The idea is to time this sampling effort with the … Continue reading →

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BMSIS Undergraduate Essay Contest

Posted on August 3, 2015 by Jeff

Reposted from www.bmsis.org, please share widely! Mars is on the horizon for future space explorers, with national space agencies as well as private corporations making plans to send humans to the red planet in the coming decades. Meanwhile, remote exploration … Continue reading →

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How do common research scales match up across ocean science disciplines?

Posted on July 17, 2015 by Jeff

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 →

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US science funding since 1963

Posted on July 10, 2015 by Jeff

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

Posted on June 18, 2015 by Jeff

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

Posted on June 14, 2015 by Jeff

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

Posted on June 2, 2015 by Jeff

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?

Posted on May 24, 2015 by Jeff

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

Posted on May 7, 2015 by Jeff

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

Posted on May 6, 2015 by Jeff

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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