BigSmoke

Smokes your problems, coughs fresh air.

Author: Rowan Rodrik (Page 6 of 27)

Rowan is mainly a writer. This blog here is a dumping ground for miscellaneous stuff that he just needs to get out of his head. He is way more passionate about the subjects he writes about on Sapiens Habitat: the connections between humans, each other, and to nature, including their human nature.

If you are dreaming of a holiday in the forests of Drenthe (the Netherlands), look no further than “De Schuilplaats”: a beautiful vacation home, around which Rowan maintains a magnificent ecological garden and a private heather field, brimming with biological diversity.

FlashMQ is a business that offers managed MQTT hosting and other services that Rowan co-founded with Jeroen and Wiebe.

Metabolism & Nutrition – Eatmeter

March 17, 2015 /

One of the tutorials for the RuG Metabolism & Nutrition course involves keeping a food log for at least 5 days. During the introductory lecture today, we were told to use the “My diary” (NL: Mijn dagboek) function offered by the Dutch Voedingscentrum.

The diary data can be exported for use in a spreadsheet, which I have to do to calculate my mean food intake over the five days. This data then has to be submitted to secr.menv@umcg.nl before 9:00 on March 26. [Which I just did this file, as per March 25.]

Metabolism & Nutrition – Lecture 1: Introduction

March 17, 2015 /

Janine Kruit, as the coordinator of the RuG Metabolism & Nutrition course, delivered the introductory lecture today, a day late, because she was too sick to teach yesterday. The altered course schedule is now available on the course’s Nestor environment [Blackboard].

The gist of the course is how nutrition, by affecting metabolism, can contribute to or substract from our health, i.e. nutrition → metabolism → health. The subject matter is broken down into the following topics/lectures:

  • energy metabolism [Lecture 2];
  • fat/carbohydrate/protein metabolism [Lecture 3/4/6]; and
  • metabolic regulation [Lecture 5].
  • Lecture 7 integrates the topics of the previous lectures.

After the lectures are finished on Thursday, the following tutorials are planned for group C (my group), with those that are obligatory for me in bold:

Tutorial schedule for Group C.

Date Time Room Subject Lecturer
Tutorial 1 Fri, March 20 13:00–15:00 3211.0125 Caloric restriction Kathrin Thedieck
Tutorial 2 Mon, March 23 10:00–12:00 3211.0125 Cardiovascular disease Uwe Tietge
Tutorial 3 Tue, March 24 10:00–12:00 3211.0125 Nutrition & epigenetics Torsten Plosch
Tutorial 4 Wed, March 25 09:00–11:00 3211.0125 Nutrition & microbiota Hermie Harmsen
Tutorial 5 Thu, March 26 11:00–13:00 3211.0125 Diet Maaike Oosterveer
Tutorial 6 Fri, March 27 11:00–13:00 3111.0017A Metabolic regulation Hans Jonkers
Tutorial 7 Tue, March 31 09:00–11:00 3111.0217 Eatmeter

Nutrients and nutrition

Besides some housekeeping details and a general overview of the course, in this introductory lecture, Janine also ran through some of the basics of nutrition and nutrient breakdown.

Nutrients are divided in

  • macronutrients, which include fats, proteins, and carbohydrates (incl. fibers); and
  • micronutrients: vitamins, minerals, dietary elements (sporenelementen), and bioactives (phytochemicals).

Nutrients are necessary to support energy metabolism, cell synthesis, optimalisation and cellulair repair.
Macronutrients can be classified based on whether they are essential as fuel and/or as substrate for cell synthesis.

Essential and non-essential macronutrients.

Nutrient Essential Not essential
Fats W3/w6 PUFA Energy source
Proteins Amino acids Amino acids
Energy source
Carbohydrates * Energy source

* [Janine leaves this empty, but, of course, carbohydrates are required as a glucose source, at least for the brain and red blood cells.]

Digestion

Most nutrient absorption takes place in the small intestine. Proteins, lipids, carbohydrates, vitamins and minerals can be absorbed with or without prior digestion by the enzymes and salts present in bile acid. Undigested food stuffs get passed to the large intestine, where fermentation take makes available even more nutrients.

Digestion enzymes

  • Carbohydrates are split into monosaccharides by amylase, maltase, sucrase, and lactase. [More in a later lecture on carbohydrate metabolism.]
  • Proteins are split into peptides and amino acids by endopeptidases and exopeptidases. [More in the protein metabolism lecture.]
  • Fats are split into free fatty acids and monoglycerides by lipases.

Bile salts

Digestion of fats in the small intestine is aided by bile acid, which contains bile salts (Dutch: galzouten). Bile salts are amphiphilic, meaning that they are simultaneously lipophilic and hydrophilic.

Metabolism & Nutrition – Editorial on metabolic regulation

March 17, 2015 /

For the 2015 RuG Metabolism & Nutrition course, 25% of the final grade is determined by an editorial I have to write with 3 other students. Scratch that; one of them is no longer enrolled. Good for me! The less, the merrier! The remaining two students in group C with the same subject—metabolic regulation—are: Jesse E. Kuindersma and Vera E. Otten. Based on the editorial, we also have to prepare a presentation.

Janine Kruit explained today that the editorial has to be in the style typical of scientific editorials that promote a scientific article. So, it might be a good idea to look at a few published editorials for inspiration. One important feature she mentioned is that the editorial has to be positive about the study. Of course, the results can be negative, such as in [my example]: “dieting does not lead to long term weight loss”. She did suggest putting a positive spin on results such as these; e.g.: “There’s no need to force yourself to stick to some diet; dieting doesn’t work anyway.” 😉

The editoral has to be 800–1000 words long and is meant to highlight the most important results from a study and place them in a broader context that is applicable to the audience. The audience are the co-enrolled students who will witness the presentation and who will be able to access the editorial through the course’s Nestor environment.

One schematic illustration (of some metabolic pathway) is expected to accompany the text of the editoral. I’m guessing the presentation may contain more figures.

The presenation should take ± 20 minutes. Before the presentation, a concept-editoral has to be handed in by our group. Our presenation will be on Friday, March 27, sometime between 11:00–13:00, during the tutorial [Tutorial 6] in room 3111.0017A.

Update March 31: We just handed in the finished editorial.

Programming is talking to the future

March 16, 2015 /

One day, some day long ago, I said to Jeroen Dekker, a photographer friend of mine, who was still learning to program at the time: “Programming is talking to the future.” He thought it was a good quote. Coming across it again now, so do I. It’s good because it’s true, which everybody who has ever debugged some old code—be it their own or someone else’s—can attest to.

Installed MathJax-LaTeX WordPress plugin for blog.bigsmoke.us

March 16, 2015 /

Soon, I wish to document some statistical issues I’ve been running into lately due to the lack of understanding maintained by my recipe-level statistics training. Also, I’d like to document some of the things I did learn over the years, and, hopefully, the things I find out while working myself out of the modelling mountain that I currently find so difficult to mount. For this I will need to use some mathematical language, which is why I just installed the MathJaX-LaTeX WordPress plugin. MathJax-LaTeX uses the MathJax JavaScript library to support LaTeX and MathML math equations in WordPress without requiring the browser to have MathML support.

As for testing it, my knowledge (\(K()\)) of MathML (\(M\)) is pretty much nonexistant, while I’m quite comfortable with LaTeX (\(L\)) math exations, which is why I’m typing the LaTeX code “K(M) \ll K(L)” to generate the following simple equation:

\(K(M) \ll K(L)\)

The insecurity of security questions

March 14, 2015 /

Another article link from my dusted-over ~jot directory: The Insecurity of Security Questions: Why I met my wife in CWmKryWzuxCSAnMDuIg. [So dusted-over is my ~/jot directory that Tom Moertel, the article’s author, has changed he link schema of his blog without providing redirects. (The slashes in the date turned to dashed.) Cool URLs don’t change, Tom, not according to the W3C and Jacob Nielsen. 😉 ]

Anyway, I am one of those people who randomly generates his (often overly long) passwords, which I store in a strongly encrypted file, but the article provided a great reminder that I should do the same for my answers to ‘security’ questions.

Dubai as an example for us all

March 14, 2015 /

Some Oct 2 2012 wisdom from SlashDot user fuzzyfuzzyfungus: “Dubai is an example of the glorious harmony between (middle) east and west! A city that wraps the middle east’s robust traditions of rule of law and enlightenment liberalism and the west’s values of sober financial honesty in the civic-planning expertise of Vegas developers on PCP… Truly, an example for us all.”

Learning to ‘hack’ with Security Override

March 14, 2015 /

In August 2011, probably while procrastinating learning for my university admission exams, with one mouldy foot still in my IT-past, I signed up for Security Override, an online game designed to turn network security n00bs such as myself into novices.

I’ve never dedicated the 20 hours to learn anything to the game, which I should have spent Josh Kaufman to ascent my n00b-state, but I nevertheless had some solid fun with it. 🙂

How to learn anything, according to Josh Kaufman

March 14, 2015 /

Judging by the following notes in my ~/jot directory, I was inspired two years ago (Oct 23, 2013) by a TEDx talk by Josh Kaufman on learning:

Josh’s advice boils down to 4 major points:

  1. Deconstruct the skill.
  2. Learn enough to self-correct (don’t procrastinate by reading text-books).
  3. Remove practice barriers (distractions).
  4. Practice for at least 20 hours. [This is the gist of his talk, but I guess it is a complitely arbitrary out-of-his-ass thing.]

Perhaps I could apply this approach to figuring out which statistical model(s) to use for the peat moss fluorescence data which I’ve been struggling with these past few weeks. Since I don’t have a statistics text-book, I can’t exercise my love of text-book-aided procrastination, a shortcoming which I’ve compensated by my old debugging procrastination strategy—just fiddling around until something useful happens. Sadly, it is becoming apparent to me that with statistics, nothing useful is learned if you don’t understand what you’re doing and why. :'(

The Architecture of Open Source Applications book

March 14, 2015 /

This link to The Architecture of Open Source Applications book was gathering dust somewhere in my ~/jot directory. In true free software spirit, it is released under a Creative Commons licence and the individual chapters are readable online. Each chapter about the architecture of a particular open source software project is written by the (co-)author of that respective project.

[…] In these two books, the authors of four dozen open source applications explain how their software is structured, and why. What are each program’s major components? How do they interact? And what did their builders learn during their development? In answering these questions, the contributors to these books provide unique insights into how they think.

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