Optical Instruments Two rosette-mounted optical instruments were used during the cruise: the underwater vision profiler (Hydroptic UVP5; sn009) and the laser in situ scatterometer and transmissometer (Sequoia LISST-200x; sn2167). Both instruments measure particle abundance and size spectra during the downcast. The UVP5 was used on almost all casts (n = 68) and assesses particles between […]
Category: Science
NGA LTER Spring Voyage: Biogeochemistry Section Report
During the cruise 6 deployments of the surface-tethered sediment trap arrays were completed with a target duration of 24h. Deployments were conducted across a representative set of pelagic stations (KOD5, KOD9, MID10, GAK4, GAK8, and GAK15) in order to measure gravitationally settling organic matter quantity and quality. Each array was outfitted with 2-3 cross-frames placed […]
Programming for the rest of us: Introducing a new R package to help solve problems
As a self trained, informal, fly by the seat of my pants programmer, I am hardly the “best” person to give advice about teaching other how to program. I have no formal background in computer science and have never had anyone teach me to program, it’s just been something that I’ve played around in by […]
Faster Gridding in R
So all oceanographers are familiar with the results of gridding, even if they are not so familiar with the process. Gridding is, in general, any method that will take observations and output interpolated (and sometimes extrapolated) data that is placed onto a regular, well-behaving grid. Below is a simple illustration of just such a process […]
Building Sediment Traps
Sediment traps are an oceanographic tool used to collect sinking material from the water column, much like how a rain gauge catches falling water droplets. Previously I’ve described some of the history of the sediment trap (link) as well as how they work (link), but now I’m going to share with you a brief overview […]
Linking conceptual models with laboratory experiments
A recent project is leading my adviser and I to design and build a large, acrylic tank which will be able to hold several hundred litres of seawater. Since a tank like this will take both time and money to build, it is logical to develop multiple experiments to run in it. These experiments will […]
Daily Dose: Correlations in a Warmer Ocean
A recent project, which is still in the very early stages, is looking for changes in patterns in the surface ocean due to el Nino. El Nino is a decadal mode of variability in the atmospheric forcings on the Pacific Ocean leading to anomalously warmer ocean temperatures throughout the eastern Pacific. This water, like a […]
Daily Dose: Unity in Science
Although all around us, there are few things as universally spectacular as natural phenomena. Whether it is a volcano, the changing of the leaves or, most recently, a solar eclipse; people love spectacles and nature sure can be spectacular at times. So why is this called “Unity in Science” and not “Unity in Nature”? Well, […]
Time is money: The value of opportunistic sampling
NOTE: This article is a reposting on one originally posted on the UNOLS Chief Scientist Workshop website (here) with slight modifications. Aboard the R/V Sikuliaq we often run around-the-clock operations and do our best to collect every last bit of data. Not only is our time limited, but ship time is valuable—really valuable. Even if […]
Learning to Drive the Boat: the Start of Chief Sci Training
For those of you who are unfamiliar with the terminology used for scientific, research cruises; a chief scientists is the de facto boss of the science party and coordinates the research plan with the captain and crew of the ship. This role often incorporates traits from other positions such as diplomate (between crew and science party), […]
The benefits of interdisciplinarity: residence time
The so-called residence time of a system is both an immensely useful and highly intuitive conception which provides a relevant timescale for processes. For example, the residence time of nutrients flowing into a pond would be the average ‘lifetime’ of the nutrients before being taking up by the pond creatures. If it is a small […]
Modern Data Organization for the Modern Scientist
Scientists handle a lot of data, I mean a lot of data. The type and format of the data varies, but the predominate format used in oceanography is definitely the humble spreadsheet. Without firsthand knowledge of the practices common in other disciplines I cannot comment on the universality of spreadsheets, but I imagine that the situation […]
Call me Ishmael: Seahab
Living on a ship for three weeks means that you pick up a few tidbits of knowledge such as the difference between tieing a bend and a hitch, but a term that is rather unique to sailing on National Science Foundation (NSF) vessels is Seahab. All research vessels control the supply of alcohol on board, […]
Call me Ishmael: Professional Insomnia
All professionals accept that there will be occasions when work gets in the way of sleep and that odd hours me be required to get the job done. Generally this interruption in sleep is temporary and isolated to project deadlines or mission critical tasks, but for scientists aboard research vessels this may be a de […]
Daily Dose: Radiation Trouble
Update: See update section following the article for the latest. I recently described in general terms a new method that I’m developing which uses Yttrium to estimate the carbon export from the ocean’s photic zone, so today I saw it fitting to rant about an issue I’m currently facing. Assuming that you have either read […]
Method Development: Yttrium
An ongoing topic of research in Oceanography involves the cycling and sequestration of carbon within the world’s oceans. While it should be no surprise that such a topic is the focus of many labs, including my own, it may be hard to believe that scientists are still grappling with how to best measure the exchange […]
Interpolating Bathymetry to Unstructured Mesh
A few weeks (perhaps months) ago I introduced the side project that I am involved with (here) whereby our aim is to develop a hydrographic model for Apalachicola Bay, Fl. Today I wanted to provide an update for that project while also sharing some interesting problems that we’ve had to work around. To see the […]
Marine Geochemistry: a particle flux model
While on a run yesterday in my new Xero brand running sandals[1], I found myself thinking about the proposal I have to write for marine geochemistry. Since I have read a fairly comprehensive assortment of water column particle flux papers, I figure it might be a good fit for this proposal. Vertical carbon flux, which […]
Sediment Traps: Historical Trends and the Promise of Inovation
[NB: The first entry in this series was published here, Introduction to Sediment Traps, which covers the motivation, use and issues of sediment traps.] Although validation of the data was lacking, sediment traps (or sedimentation traps as they were once called) were being used by the 1970s in the study of lakes (Davison et al., 1982; […]
Introduction to Sediment Traps
[NB: The second entry in this series was published here, Sediment Traps: Historical Trends and the Promise of Innovation, which covers some of the history and development of sediment traps as well as my own hopes for the field moving forward.] The biological carbon pump (BCP) is the mechanism whereby marine, biological systems sequester atmospheric carbon into […]
Common Image Formats Explained
After a recent conversation with a friend about photography and digital images, there seems to be many unanswered questions out there regarding the wide variety of image formats which have become commonplace in our lives. A few months ago I wrote a short article on HDR Photography (link) since so many people were asking questions […]
Independent Exploration: Picking a Model
At the onset of the semester, myself along with Taylor, Xu and Erick committed to setting up and running a 3d hydrographic model of Apalachicola Bay. Since the primary goal of these weekly meetings was to learn how to take a modelling project from start to finish, we needed to be deliberate about our choice […]
Quick introduction to EOF/PCA analysis
In the field of oceanography, statistical analysis of complex data is a fundamental skill that often calls for mathematics beyond the training of the student. Here I would like to walk through some simple linear algebra and connect it to a well-used yet poorly understood statistical analysis technique. Eigenpairs Given a linear transformation (e.g. ), […]
Philosophy Monday: On the Origin, Propagation and Cause of Variations
Darwin’s On the Origins of Species provided a vivid and practical mechanism to explain how variations within a species can be selected for. This mechanism became known as natural selection or, perhaps less accurately, survival of the fittest. Although Darwin’s natural selection mechanism was not novel—Malthus described a similar mechanism as actively limiting a population’s […]
Analyzing YSI data through clustering
Update 10/13/15 – Minor improvements to code and an update to the latest findings. CTD data (conductivity, temperature and depth) from a YSI provides a quick and methodologically simple way to estimate the current water column state by, literally, dropping an instrument off the side of a boat. During each deployment the YSI records the […]
The Future of R
On a day to day basis, I use the R programing language more than any other language (e.g Python, Java, Fortran, Matlab…), and there is a good reason for it: R excels at the sort of work I do. It has been extremely well suited to my modeling work, especially when going to analyze the […]
Grassroots Learning: Independent Explorations
Taylor and myself have traditionally spent a fair bit of time outside of lectures and meetings going over material that we find interesting, confusing or useful. Often these topics would push one of us into delving more deeply into the literature or logic of the problem and then sharing the insight and answer with the […]
Markov Chain Monte Carlo: A Practical Introduction
Markov Chain Monte Carlo simulation sounds, admittedly, like a method better left to professional practitioners and the like; but please don’t let the esoteric name fool you. MCMC, as we like to call is, is a powerful yet deceptively simple technique that can be useful in problems ranging throughout science and engineering. Since this promises […]
Finalizing my research, the CCELIM model, in R
For the past 6 months I’ve been working on an inverse modeling project as a ‘starter’ graduate project, and today I am announcing that I can see the light at the end of the tunnel. While there is certainly more work ahead, especially with regards to the manuscript, the model and the code are just […]
Statistical Analysis for my Inverse Modeling
For the past week I’ve been working on a small but important facet of my inverse modeling research: a sensitivity analysis. Since some of the constraints placed on the model are estimated from measured quantities and not really nailed down, we need to be confident that a small change in the measurement wouldn’t make a […]