ideas, writings, and musings
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…
So as many of you know, most of my work to date has been on the California Current ecosystem and, in particular, on modeling the ecosystem there. In just a few short days I’ll be heading out from the Scripps pier for a 22 day cruise. The goal for the cruise is to measure the…
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…
I’m pretty sure I have never written anything that would be classified as self help; and while that section of the bookstore always repels me, the ideas and promises suggested are always quite appealing. For example, who wouldn’t want a “4 Hour Work Week” (link) or to know the “7 Habits of Highly Effective People” (Amazon)? It…
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…
Since starting on my kitchen remodel project last month, I’ve been uncertain about what to do with the floors. Currently the floors are simple, glued-down vinyl, which has worked great and makes a lot of sense over a slab foundation, but my kitchen deserves something a bit better. Initially I figured tile would be the…
While it scarcely seems possible, it was just a year ago that I moved into my first house and started my graduate school career. If the passage of life, and the measure of that life, is to be defined by the events within it, then for the past year I have done a lot of…
[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;…
[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…
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…
Here are photos from my latest project. It is still a work in progress; new article will be posted when completed.
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…
Ever since setting up my workshop last month, I’ve been working on making the space as versatile and organized as possible–a bit of a trial and error process. One step in the right direction was setting up a ventilation system so that the fumes and dust created by the various projects would be taken care…
This essay is taken nearly verbatim from notes on the subject taken during a seminar at Boston College and later compiled into essay form. All information was presented by Dr. Fukuyama with additional content and context provided by me. Fukuyama is perhaps best known for his influential textbook, The End of History and the Last…
Over the past two weeks I’ve been running around town either before or after work in the hope of negotiating a fair price for some granite countertops in my latest kitchen remodel. Since I’ve found the experience frustrating and painstaking, I wanted to share my experience with the local businesses in case anyone finds themselves…
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. ),…
As the title hints, this will be a post about a recipe I created over this past weekend. On Saturday I was hosting a BBQ to celebrate the end of the fall semester and because I wanted to show friends around my place. While I may be able to get by on a charcoal grill,…
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…
Over the years I have certainly been the recipient of plenty of concern regarding the sometimes dangerous recreation I pursue, yet I’m always confident because I have a plan. Now there is always risk–a tree could fall and kill me or a poisonous snake could catch me at a bad time–but risk is only dangerous is…
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…
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…
I’m not sure about you, but I have always struggled with keeping all of my digital files organized and readily available. Often times it feels as if sorting and organizing physical copies would be much easier, but alas! that’s not a realistic option. Instead I always end up resorting these files into a bunch of…
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 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…
Over the last couple days I’ve been working pretty hard trying to get a home workshop together, and I wanted to share the progress I’ve made. My house has an attached 1 car garage which also houses both the laundry area and the trash bins, so space is a bit tight. Let’s jump right in…
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…
The novel 1984 by George Orwell is a classic all its own. Sure there’s WE, Brave New World and countless other dystopian novels from the early to mid 20th century[1]; yet none of these novels are quite so prescient or relevant decades after their release. While literary critics and poor graduate students will certainly continue…
Today makes the beginning of a slow transition over to a new domain name: TKelly.org. Over the course of the past couple years, I’ve grown fond of the .me domain[1] and it has served my needs well. But as fate would have it, it’s time for a change. My hosting service, the company that manages the…
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…
Go up to any student of a modern literature course as ask what their reading. Perhaps you’ll hear about Shelly’s Frankenstein or Dostoevsky’s Crime and Punishment or perhaps Orwell’s 1984. Regardless of which works make their reading list, if you ask this student if what they’re reading is ‘True’ with a capital T you’ll likely…