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…
Philosophy Monday: Heat
From the ancient times of philosophical thought to the advent of the first chemical theories of Becher, heat had been a mysterious concept. It is almost a wonder that something as ubiquitous as heat could be debated, but often daily experience is a poor substitute for real understanding. Although a defining character in differentiating chemistry from…
Code Walkthrough: Inverse Modeling
In previous articles (here and earlier here) I covered in some cursory way my current research into the California Current and about the technique of Inverse Modeling, so today I wanted to delve into the actual tools and code that I’ve developed. To review, an inverse model is An inverse model seeks to solve a series…
Philosophy Monday: Lonergan Part 1
The following is a series of short essays based on an assignment I had with Dr Braman at Boston College. Since Lonergan’s philosophy has surely impacted me in ways that I know not of, and since so many people have trouble delving into his work, I thought it most responsible to share the following.
Quantifying Error
Being able to appropriately address uncertainty and error is fundamental to the pursuit of science. Without it, results and theory would never match up since theory usually involves a level of abstraction that permits simplification of the problem and observational results are never perfect and include all sorts of uncertainty. Recently I’ve been trying to…
Spurious diapycnal mixing in z coordinate models
Introduction Diapycnal mixing is a natural process whereby water parcels of different temperature and/or salinity get mixed. This process, as opposed to advection, is non-adiabatic (non-reversible) and is governed by diffusive mechanisms. The rate of diapycnal mixing is elevated in coastal waters relative to the open ocean and is responsible for the introduction of nutrients…
End of the Semester
Believe it or not, but it is already the end of the semester for me and my peers. Somehow nearly four months have disappeared once again into that historical accident that we call the past. Since each of my three classes have required a project to be done for the final, I figure that I may…
Remote Sensing Part 2
In a previous article I described a technique to determine the dye concentration from drone images, and I hope it sounded like a reasonable plan. Nevertheless, this plan did go ary when less than ideal conditions arose and the results got jumbled with the imperfections of the real world. So to make amends, I will…
Philosophy Monday: Einstein v Newton
The source for the tension between Newton’s view of the universe and of Einstein’s stems from each person’s respective choice of axioms. Newton choose to take the most concrete axioms for his mechanics: absolute nature of space and time. These intuitive assumptions mark and define the whole of Newtonian mechanics since all the other definitions…